Value through Innovation21 April 2014

Scientific Publications

Boehringer Ingelheim offers an overview of scientific publications on the following pages. This overview represents all publications of the last three years (YTD) where employees of Boehringer Ingelheim worldwide were involved.

262 publications regarding Chemistry
  • Author:
    Desrosiers J-N; Kelly CB; Fandrick DR; Nummy L; Campbell SJ; Wei X; Sarvestani M; Lee H; Sienkiewicz A; Sanyal S; Zeng X; Grinberg N; Ma S; Song JJ; Senanayake CH
    Title:
    A scalable and regioselective synthesis of 2-difluoromethyl pyridines from commodity chemicals
    Source:
    Org Lett 16 (6), 1724-1727 (2014)
    Abstract:
    A scalable de novo synthesis of difluoromethyl pyridines from inexpensive materials is reported. The pyridyl subunit is built around the difluoromethyl group rather than a late stage introduction of this moiety. This user-friendly approach allows access to a diverse range of substitution patterns on all positions on the ring system and on the difluoromethyl group. © 2014 American Chemical Society.
  • Author:
    Harcken C; Riether D; Kuzmich D; Liu P; Betageri R; Ralph M; Emmanuel M; Reeves JT; Berry A; Souza D; Nelson RM; Kukulka A; Fadra TN; Zuvela-Jelaska L; Dinallo R; Bentzien J; Nabozny GH; Thomson DS
    Title:
    Identification of highly efficacious glucocorticoid receptor agonists with a potential for reduced clinical bone side effects
    Source:
    J Med Chem 57 (4), 1583-1598 (2014)
    Abstract:
    Synthesis and structure-activity relationship (SAR) of a series of nonsteroidal glucocorticoid receptor (GR) agonists are described. These compounds contain "diazaindole" moieties and display different transcriptional regulatory profiles in vitro and are considered "dissociated" between gene transrepression and transactivation. The lead optimization effort described in this article focused in particular on limiting the transactivation of genes which result in bone side effects and these were assessed in vitro in MG-63 osteosarcoma cells, leading to the identification of (R)-18 and (R)-21. These compounds maintained anti-inflammatory activity in vivo in collagen induced arthritis studies in mouse but had reduced effects on bone relevant parameters compared to the widely used synthetic glucocorticoid prednisolone 2 in vivo. To our knowledge, we are the first to report on selective glucocorticoid ligands with reduced bone loss in a preclinical in vivo model. © 2014 American Chemical Society.
  • Author:
    Eggersgluess JK; Richter M; Dieterle M; Strube J
    Title:
    Multi-stage aqueous two-phase extraction for the purification of monoclonal antibodies
    Source:
    Chem Eng Technol 37 (4), 675-682 (2014)
    Abstract:
    Using monoclonal antibodies in a cell culture harvest as an example for complex biomolecules, a mini-plant-scale aqueous two-phase purification process was studied. The results of this study indicate that antibodies can be concentrated and purified in a single extraction step employing a small phase ratio. Following the extraction step, a multi-stage wash-extraction for further purification was investigated. Starting at a test tube-scale cross-current wash, the process was advanced towards a continuous counter-current mixer-settler and column wash process. It was shown that a test tube cross-current extraction operation can predict the multi-stage purity reasonably well. The hydrodynamic process performance for the multi-stage wash column was evaluated and related to the separation performance. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
  • Author:
    Brächer A; Hoch S; Albert K; Kost HJ; Werner B; Von Harbou E; Hasse H
    Title:
    Thermostatted micro-reactor NMR probe head for monitoring fast reactions
    Source:
    J Magn Reson 242, 155-161 (2014)
    Abstract:
    A novel nuclear magnetic resonance (NMR) probe head for monitoring fast chemical reactions is described. It combines micro-reaction technology with capillary flow NMR spectroscopy. Two reactants are fed separately into the probe head where they are effectively mixed in a micro-mixer. The mixed reactants then pass through a capillary NMR flow cell that is equipped with a solenoidal radiofrequency coil where the NMR signal is acquired. The whole flow path of the reactants is thermostatted using the liquid FC-43 (perfluorotributylamine) so that exothermic and endothermic reactions can be studied under almost isothermal conditions. The set-up enables kinetic investigation of reactions with time constants of only a few seconds. Non-reactive mixing experiments carried out with the new probe head demonstrate that it facilitates the acquisition of constant highly resolved NMR signals suitable for quantification of different species in technical mixtures. Reaction kinetic measurements on a test system are presented that prove the applicability of the novel NMR probe head for monitoring fast reactions. © 2014 Elsevier Inc. All rights reserved
  • Author:
    El Kerdawy A; Tautermann CS; Clark T; Fox T
    Title:
    Economical and accurate protocol for calculating hydrogen-bond-acceptor strengths
    Source:
    J Chem Inform Modeling 53 (12), 3262-3272 (2014)
    Abstract:
    A series of density functional/basis set combinations and second-order Møller-Plesset calculations have been used to test their ability to reproduce the trends observed experimentally for the strengths of hydrogen-bond acceptors in order to identify computationally efficient techniques for routine use in the computational drug-design process. The effects of functionals, basis sets, counterpoise corrections, and constraints on the optimized geometries were tested and analyzed, and recommendations (M06-2X/cc-pVDZ and X3LYP/cc-pVDZ with single-point counterpoise corrections or X3LYP/aug-cc-pVDZ without counterpoise) were made for suitable moderately high-throughput techniques. © 2013 American Chemical Society.
  • Author:
    Busacca CA; Eriksson MC; Haddad N; Han ZS; Lorenz JC; Qu B Zeng X; Senanayake CH
    Title:
    Practical synthesis of di-tert-butyl-phosphinoferrocene
    Source:
    Org Synth 90, 316-326 (2013)
    Abstract:
    no Abstract available
  • Author:
    Oeckl P; Scheffold A; Lechel A; Rudolph KL; Ferger B
    Title:
    Substantial telomere shortening in the substantia nigra of telomerase-deficient mice does not increase susceptibility to MPTP-induced dopamine depletion
    Source:
    NeuroReport 25 (5), 335-339 (2014)
    Abstract:
    The most important risk factor for developing Parkinson's disease (PD) is age. Aging is ascribed to different mechanisms, including telomere shortening. Telomeres consist of repetitive DNA sequences and stabilize chromosome integrity. Currently, however, the data reported on telomere shortening in PD patients are inconsistent. We investigated the effect of telomere shortening in the MPTP mouse model of PD using late-generation telomerase-deficient mice (G3 Terc mice). G3 Terc mice showed a reduction in telomere length in nigral tyrosine hydroxylase-positive neurons by 40%, as indicated by quantitative fluorescence in-situ hybridization. There was no difference in the total motor activity and striatal tissue concentrations of dopamine, DOPAC (3,4-dihydroxyphenylacetic acid), HVA (4-hydroxy-3-methoxyphenylacetic acid), and 3-MT (3-methoxytyramine) concentrations or dopamine turnover in G3 Terc mice in comparison with controls without MPTP treatment. Low-dose MPTP treatment (four injections, 2 h intervals, 2×5 and 2×7.5 mg/kg) led to a significant decrease in striatal dopamine concentrations that did not differ in G3 Terc mice compared with control mice (19.15±0.44 to 12.81±1.26 ng/mg in control mice in comparison with 19.51±0.59 to 13.56±1.10 ng/mg in G3 Terc mice). In conclusion, telomere shortening does not increase susceptibility to MPTP-induced dopamine depletion in mice. These data indicate that other age-related mechanisms in the brain may play a more important role in enhancing MPTP-induced dopamine depletion. © 2014 Wolters Kluwer Health - Lippincott Williams & Wilkins.
  • Author:
    LaPlante SR; Nar H; Lemke CT; Jakalian A; Aubry N; Kawai SH
    Title:
    Ligand bioactive conformation plays a critical role in the design of drugs that target the hepatitis C virus NS3 protease
    Source:
    J Med Chem 57 (5), 1777-1789 (2014)
    Abstract:
    A ligand-focused strategy employed NMR, X-ray, modeling, and medicinal chemistry to expose the critical role that bioactive conformation played in the design of a variety of drugs that target the HCV protease. The bioactive conformation (bound states) were determined for key inhibitors identified along our drug discovery pathway from the hit to clinical compounds. All adopt similar bioactive conformations for the common core derived from the hit peptide DDIVPC. A carefully designed SAR analysis, based on the advanced inhibitor 1 in which the P1 to P3 side chains and the N-terminal Boc were sequentially truncated, revealed a correlation between affinity and the relative predominance of the bioactive conformation in the free state. Interestingly, synergistic conformation effects on potency were also noted. Comparisons with clinical and recently marketed drugs from the pharmaceutical industry showed that all have the same core and similar bioactive conformations. This suggested that the variety of appendages discovered for these compounds also properly satisfy the bioactive conformation requirements and allowed for a large variety of HCV protease drug candidates to be designed. © 2013 American Chemical Society.
  • Author:
    Moreau B; O'Meara JA; Bordeleau J; Garneau M; Godbout C; Gorys V; Leblanc M; Villemure E; White PW; Llinàs-Brunet M
    Title:
    Discovery of hepatitis C Virus NS3-4A protease inhibitors with improved barrier to resistance and favorable liver distribution
    Source:
    J Med Chem 57 (5), 1770-1776 (2014)
    Abstract:
    Given the emergence of resistance observed for the current clinical-stage hepatitis C virus (HCV) NS3 protease inhibitors, there is a need for new inhibitors with a higher barrier to resistance. We recently reported our rational approach to the discovery of macrocyclic acylsulfonamides as HCV protease inhibitors addressing potency against clinically relevant resistant variants. Using X-ray crystallography of HCV protease variant/inhibitor complexes, we shed light on the complex structural mechanisms by which the D168V and R155K residue mutations confer resistance to NS3 protease inhibitors. Here, we disclose SAR investigation and ADME/PK optimization leading to the identification of inhibitors with significantly improved potency against the key resistant variants and with increased liver partitioning. © 2013 American Chemical Society.
  • Author:
    Hucke O; Coulombe R; Bonneau P; Bertrand-Laperle M; Brochu C; Gillard J; Joly M-A; Landry S; Lepage O; Llinàs-Brunet M; Pesant M; Poirier M P; oirier M; McKercher G; Marquis M; Kukolj G; Beaulieu PL; Stammers TA
    Title:
    Molecular dynamics simulations and structure-based rational design lead to allosteric HCV NS5B polymerase thumb pocket 2 inhibitor with picomolar cellular replicon potency
    Source:
    J Med Chem 57 (5), 1932-1943 (2014)
    Abstract:
    The design and preliminary SAR of a new series of 1H-quinazolin-4-one (QAZ) allosteric HCV NS5B thumb pocket 2 (TP-2) inhibitors was recently reported. To support optimization efforts, a molecular dynamics (MD) based modeling workflow was implemented, providing information on QAZ binding interactions with NS5B. This approach predicted a small but critical ligand-binding induced movement of a protein backbone region which increases the pocket size and improves access to the backbone carbonyl groups of Val 494 and Pro 495. This localized backbone shift was consistent with key SAR results and was subsequently confirmed by X-ray crystallography. The MD protocol guided the design of inhibitors, exploiting novel H-bond interactions with the two backbone carbonyl groups, leading to the first thumb pocket 2 NS5B inhibitor with picomolar antiviral potency in genotype (gt) 1a and 1b replicons (EC50 = 120 and 110 pM, respectively) and with EC50 . 80 nM against gt 2-6. © 2013 American Chemical Society.
  • Author:
    LaPlante SR; Forgione P; Boucher C; Coulombe R; Gillard J; Hucke O; Jakalian A; Joly M-A; Kukolj G; Lemke C; McCollum R; Titolo S; Beaulieu PL; Stammers T
    Title:
    Enantiomeric atropisomers inhibit HCV polymerase and/or HIV matrix: Characterizing hindered bond rotations and target selectivity
    Source:
    J Med Chem 57 (5), 1944-1951 (2014)
    Abstract:
    An anthranilic acid series of allosteric thumb pocket 2 HCV NS5B polymerase inhibitors exhibited hindered rotation along a covalent bond axis, and the existence of atropisomer chirality was confirmed by NMR, HPLC analysis on chiral supports, and computational studies. A thorough understanding of the concerted rotational properties and the influence exerted by substituents involved in this steric phenomenon was attained through biophysical studies on a series of truncated analogues. The racemization half-life of a compound within this series was determined to be 69 min, which was consistent with a class 2 atropisomer (intermediate conformational exchange). It was further found by X-ray crystallography that one enantiomer of a compound bound to the intended HCV NS5B polymerase target whereas the mirror image atropisomer was able to bind to an unrelated HIV matrix target. Analogues were then identified that selectively inhibited the former. These studies highlight that atropisomer chirality can lead to distinct entities with specific properties, and the phenomenon of atropisomerism in drug discovery should be evaluated and appropriately managed. © 2013 American Chemical Society.
  • Author:
    Guccione J; Pesce A; Pascale M; Tommasini N; Garofalo F; Di Loria A; Cortese L; Salzano C; Ciaramella P
    Title:
    Short communication: Effects of systemic treatment with penethamate hydriodide on udder health and milk yields in dry primiparous Mediterranean buffaloes (Bubalus bubalis)
    Source:
    J Dairy Sci 97 (4), 2219-2225 (2014)
    Abstract:
    The effects of penethamate hydriodide (Mamyzin, Boehringer Ingelheim, Ingelheim, Germany) on udder health and milk yields were evaluated in primiparous Mediterranean buffaloes (Bubalus bubalis). An intramuscular administration of 10 million international units was performed in 20 buffaloes at 7 d precalving (treatment group; TG), and 20 animals were enrolled as the control group (CG). Evening milk samplings were performed at 10, 30, and 60 d in milk (DIM). Somatic cell count (SCC) values were evaluated on composite milk samples, whereas bacteriological culture and California Mastitis Test were performed on quarter milk. Daily milk yields were recorded after all milkings. After 60 DIM, composite milk samples from each animal were collected for monthly SCC and bacteriological culture until drying off. Statistically significant differences were found between the prevalence of mastitic quarters in the 2 groups at 10 and 30 DIM, and between the incidence of mastitic animals during the examined period (TG: 4/20, 20% vs. CG: 10/20, 50%). Even though lower and higher values of SCC and milk yields were found in TG during each sampling, statistically significant differences were only found at 30 (SCC) and 60 DIM (milk yields). In our study, the antibiotic administration precalving showed good bactericidal activity against the most common udder-specific pathogens that cause mastitis in primiparous Mediterranean buffaloes, and greater efficacy was observed at 10 and 30 DIM compared with 60 DIM. Given the significant decrease in SCC and increase in yields achieved, use of this antibiotic could be economically beneficial in buffalo breeding. © 2014 American Dairy Science Association.
  • Author:
    Yokoyama WM; Christensen M; Santos GD; Miller D; Ho J; Wu T; Dziegelewski M; Neethling FA
    Title:
    Production of monoclonal antibodies
    Source:
    Curr Protocols Immunol (Suppl 102) art no 2.5 (2013)
    Abstract:
    This unit describes the production of monoclonal antibodies beginning with immunization, cell fusion, and selection. Support protocols are provided for screening primary hybridoma supernatants for antibodies of desired specificity, establishment of stable hybridoma lines, cloning of theseBcell lines by limiting dilution to obtain monoclonal lines, and preparation of cloning/expansion medium. An alternate protocol describes cell fusion and one-step selection and cloning of hybridomas utilizing a semi-solid methylcellulosebased medium (ClonaCell-HY from StemCell Technologies). © 2013 by John Wiley & Sons, Inc.
  • Author:
    Kredel S; Wolff M; Gierschik P; Heilker R
    Title:
    Phenotypic analysis of chemokine-driven actin reorganization in primary human neutrophils
    Source:
    Assay Drug Dev Technol 12 (2), 120-128 (2014)
    Abstract:
    The chemokine-driven activation of CXC-type chemokine receptors 1/2 (CXCR1/2) and the subsequent reorganization of the neutrophilic actin are early key events in the induction of neutrophil migration toward centers of inflammation. In this study, an image analysis algorithm was developed to detect subtle chemokine-induced changes in the actin cytoskeleton of primary human neutrophils. By this means, a discrete early step of neutrophil activation was dissected that could be initiated by concentrations of growth-related oncogen . (Gro-.) or interleukin-8 (IL-8) just above their resting-state plasma levels. The associated half-maximal effective concentration (EC50) values for Gro-. and IL-8 of 8 and 22 pM, respectively, are between two and three orders of magnitude below the so-far reported EC50 values of these chemokines for the induction of neutrophilic calcium release, integrin expression, degranulation, and receptor internalization. Sch527123, a known inhibitor of CXCR2 (KD=49 pM) and with a lower potency/affinity also of CXCR1 (KD=3.9 nM), antagonized actin remodeling with half-maximal inhibitory concentration (IC50) values of 400 pM for the CXCR2-specific agonist Gro-. and of 36 nM for the CXCR1/2-promiscuous agonist IL-8. This observation indicates that the here-described early step of chemokine-driven actin reorganization is modulated by both CXCR1 and CXCR2. Thus, the imaging-based assay format, as developed in this work, may be employed in a phenotypic screening campaign to identify inhibitors of an early step in CXCR1/2-induced neutrophilic chemotaxis. © Copyright 2014, Mary Ann Liebert, Inc. 2014.
  • Author:
    Grottke O; van Ryn J; Rossaint R
    Title:
    In a trauma experimental pig model prothrombin complex concentrates and a specific antidote (idarucizumab) are effective to reverse the anticoagulant effects of dabigatran
    Source:
    Internation Symposium on Intensive Care and Emergency Medicine (ISICEM), Brussels, Belgium, March 18-21, 2014
  • Author:
    Seeliger D; Karow A; Spitz J; Schulz P; Hörer S; Studts J; Garidel P
    Title:
    Rational Antibody Sequence Optimization to Improve CMC Properties
    Source:
    Gordon Conference on Antibody Therapy and Engineering, 2014
  • Author:
    Schnapp G; Klein T; Hoevels Y; Schreiner P; Mark M; Bakker R A; Nar H
    Title:
    Analysis of binding kinetics and thermodynamics of DPPIV Inhibitors and its relationship to structure
    Source:
    Abstract for presentation at the Workshop: The aspect of time in drug design, Rauischholzhausen, Germany, Mar 24-27, 2014
  • Author:
    Tautermann C
    Title:
    CPCR structures in drug design: a case study on the residence time of antimuscarinc drugs
    Source:
    Vortrag am 28th Molecular Modeling Workshop, Erlangen, Germany, Mar 17-18, 2014
  • Author:
    Traub S
    Title:
    Modulation of neurogenesis and neuronal connectivity by experimental tool compounds and Pharmaceuticals
    Source:
    PhD Programme, Evaluation seminar, Homberg, Germany, Feb 24-26, 2014
  • Author:
    Beilmann Dr M
    Title:
    Research Prospectus: Stern cell derived (SCD)systems in toxicity assessment
    Source:
    European Commission, stakeholders in industry and funding bodies
  • Author:
    Zeeb Dr M
    Title:
    Application of Microscale Thermophoresis in Hit Identification and Validation
    Source:
    Microscale Thermophoresis Drug Discovery Forum, Munich, Germany Feb 10-11, 2014
  • Author:
    Reeves JT; Han ZS; Goyal N; Lee H; Busacca CA; Senanayake CH
    Title:
    Cationic triazinium heterocycles by intramolecular N{single bond}N bond formation
    Source:
    Tetrahedron Lett Article in Press (2014)
    Abstract:
    Tricyclic heterocycles with a cationic triazinium core were prepared by an intramolecular N{single bond}N bond forming reaction of an azine oxime precursor. The azine oxime substrates were prepared by SNAr N-arylation of 2-formylpyrroles followed by oxime formation of the formyl moiety. The synthesis was demonstrated with five different azines and several functional groups. © 2014 Elsevier Ltd. All rights reserved.
  • Author:
    Razavi H; Riether D; Harcken C; Bentzien J; Dinallo RM; Souza D; Nelson RM; Kukulka A; Fadra-Khan TN; Pack Jr EJ; Zuvela-Jelaska L; Pelletier J; Panzenbeck M; Torcellini CA; Proudfoot JR; Nabozny GH; Thomson DS
    Title:
    Discovery of a potent and dissociated non-steroidal glucocorticoid receptor agonist containing an alkyl carbinol pharmacophore
    Source:
    Bioorg Med Chem Lett Article in Press (2014)
    Abstract:
    Synthesis and structure-activity relationship (SAR) of a series of alkyl and cycloalkyl containing non-steroidal dissociated glucocorticoid receptor (GR) agonists is reported. This series of compounds was identified as part of an effort to replace the CF3 group in a scaffold represented by 1a. The study culminated in the identification of compound 14, a t-butyl containing derivative, which has shown potent activity for GR, selectivity against the progesterone receptor (PR) and the mineralocorticoid receptor (MR), in vitro anti-inflammatory activity in an IL-6 transrepression assay, and dissociation in a MMTV transactivation counter-screen. In a collagen-induced arthritis mouse model, 14 displayed prednisolone-like efficacy, and lower impact on body fat and free fatty acids than prednisolone at an equivalent anti-inflammatory dose. © 2014 Elsevier Ltd. All rights reserved
  • Author:
    Dollinger H; Jung B
    Title:
    Anti-inflammatory approaches for the treatment of respiratory diseases
    Source:
    Presentation for Frontiers in Medicinal Chemistry, Tübingen Mar 16-19, 2014
  • Author:
    Sampson C; Fox T; Tautermann C S; Woods C; Skylaris C-K
    Title:
    Free Energy Calculations from Large-Scale DFT Total Energies
    Source:
    Young Modellers Forum,London, UK, 29 Nov 2013
  • Author:
    Reeves JT; Camara K; Han ZS; Xu Y; Lee H; Busacca CA; Senanayake CH
    Title:
    The reaction of grignard reagents with bunte salts: A thiol-free synthesis of sulfides
    Source:
    Org Lett 16 (4), 1196-1199 (2014)
    Abstract:
    no Abstract available
  • Author:
    Eggersgluess JK; Richter M; Dieterle M; Strube J
    Title:
    Multi-stage aqueous two-phase extraction for the purification of monoclonal antibodies
    Source:
    Chem Eng Technol Article in Press (2014)
    Abstract:
    no Abstract available
  • Author:
    Llombart V; Dominguez C; Bustamante A; Rodriguez-Sureda V; Martín-Gallán P; Vilches A; García-Berrocoso T; Penalba A; Hernández-Guillamon M; Rubiera M; Ribó M; Eschenfelder C; Giralt D; Molina CA; Alvarez-Sabín J; Rosell A; Montaner J
    Title:
    Fluorescent molecular peroxidation products a prognostic biomarker of early neurologic deterioration after thrombolysis
    Source:
    Stroke 45 (2), 432-437 (2014)
    Abstract:
    Background and Purpose - Fluorescent molecular peroxidation products (FMPPs) are considered potential markers of molecular oxidative damage and may provoke increased permeability and disruption of the blood-brain barrier. This study aimed to determine the value of FMPPs as a biomarker to predict neurological worsening related to early hemorrhagic transformation. Methods - Baseline FMPP levels were measured in 186 consecutive acute ischemic stroke patients before tissue plasminogen activator treatment was administered. A serial FMPP profile (baseline before tissue plasminogen activator treatment, and 1, 2, 12, and 24 hours from treatment) was determined in a subset of 100 patients. Computed tomographic scans were performed at admission and repeated at 24 to 48 hours or after neurological worsening occurred. Symptomatic intracranial hemorrhage was defined as blood at any site in the brain associated with neurological deterioration. Results - Patients who worsened had higher median FMPP levels compared with those who did not (59.68 [48.63-85.73] versus 44.87 [36.37-58.90] Uf/mL; P=0.035) at baseline. After logistic regression multivariate analysis, FMPP >48.2 Uf/ mL together with age, hypertension, and systolic blood pressure remained baseline predictors of worsening at 48 hours. Moreover, baseline FMPP determination helped to distinguish between patients who worsened and those who did not (Integrated Discrimination Improvement index, 5.7%; P=0.0004). Finally, within patients who had worsened at 48 hours, those with symptomatic intracranial hemorrhage had higher FMPP levels (P=0.038). Conclusions - FMPPs might be a valuable biomarker of poor early neurological outcome and be related to the appearance of symptomatic intracranial hemorrhage in tissue plasminogen activator-treated patients, one of the most feared neurological complications after thrombolytic treatment of acute ischemic stroke. © 2013 American Heart Association, Inc.
  • Author:
    Qu B; Samankumara LP; Savoie J; Fandrick DR; Haddad N; Wei X; Ma S; Lee H; Rodriguez S; Busacca CA; Yee NK; Song JJ; Senanayake CH
    Title:
    Synthesis of pyridyl-dihydrobenzooxaphosphole ligands and their application in asymmetric hydrogenation of unfunctionalized alkenes
    Source:
    J Org Chem 79 (3), 993-1000 (2014)
    Abstract:
    Synthesis of the electron-rich 2-substituted-6-(phenylsulfonyl)pyridines is presented. A series of air-stable, tunable, P-chiral pyridyl- dihydrobenzooxaphosphole ligands were designed and synthesized by a diastereoselective SNAr substitution of the corresponding sulfonyl pyridines. The ligands were successfully applied in the Ir-catalyzed asymmetric hydrogenation of unfunctionalized alkenes with good enantioselectivities. © 2014 American Chemical Society.
  • Author:
    Latli B; Hrapchak M; Gorys V; Llinàs-Brunet M; Campbell SS; Song J; Senanayake CH
    Title:
    Hepatitis C virus serine protease: Synthesis of radioactive and stable isotope-labeled potent inhibitors
    Source:
    J Label Compd Radiopharm Article in Press (2014)
    Abstract:
    Drug candidates labeled with radioactive and stable isotopes are required for absorption, distribution, metabolism, and excretion (ADME) studies, pharmacokinetics, autoradiography, bioanalytical, and other research activities. The findings from these studies are crucial in the development of a drug candidate and its approval for human use. Herein, we report the synthesis of potent and selective hepatitis C virus serine protease inhibitors related to BILN 2061 and BI 201335 labeled with radioactive and stable isotopes. Synthetic efforts were focused on the common substituted thiazole moiety, which is easily accessible via a Hantzsch's reaction of alpha-bromoketones and mono-substituted thioureas. In the radioactive synthesis, commercially available carbon-14 thiourea was utilized to prepare mono-substituted thioureas, which upon condensation with alpha-bromoketones in isopropanol followed by ester hydrolysis gave the desired carbon-14-labeled protease inhibitors. The same strategy was used to prepare these inhibitors labeled with stable isotopes. Mono-substituted thioureas were obtained from commercially available deuterium-labeled intermediates and then condensed with alpha-bromoketones followed by ester hydrolysis to give the deuterium-labeled inhibitors. © 2014 John Wiley & Sons, Ltd.
  • Author:
    Poulsen MH; Lucas S; Strømgaard K; Kristensen AS
    Title:
    Inhibition of AMPA Receptors by Polyamine Toxins is Regulated by Agonist Efficacy and Stargazin
    Source:
    Neurochem Res, 1-8 Article in Press (2014)
    Abstract:
    The .-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptors (AMPARs) are glutamate-gated cation channels mediating the majority of fast excitatory synaptic transmission in the central nervous system (CNS). Polyamine toxins derived from spiders and wasps are use- and voltage-dependent channel blockers of Ca2+-permeable AMPARs. Recent studies have suggested that AMPAR block by polyamine toxins is modulated by auxiliary subunits from the class of transmembrane AMPAR regulatory proteins (TARPs), which may have implications for their use as tool compounds in native systems. We have explored the effect of the TARP .-2 (also known as stargazin) on the inhibitory potency of three structurally different polyamine toxins at Ca2+-permeable homomeric GluA1 AMPARs expressed in oocytes. We find that polyamine toxin IC50 is differentially affected by presence of stargazin depending on the efficacy of the agonists used to activate GluA1. Co-assembly of GluA1 receptors with stargazin increases the potency of the polyamine toxins when activated by the weak partial agonist kainate, but has no effect in presence of full-agonist l-glutamate (Glu) and partial agonist (RS)-willardiine. © 2014 Springer Science+Business Media New York.
  • Author:
    Maier A
    Title:
    Protein expresion and purification
    Source:
    Universität Ulm, Vortrag der Praktika in der Seminarwoche im Rahmen des Master Moleculare Medizin
  • Author:
    Schildknecht S; Weber A; Gerding HR; Pape R; Robotta M; Drescher M; Marquardt A; Daiber A; Ferger B; Leist M
    Title:
    The NOX1/4 inhibitor GKT136901 as selective and direct scavenger of peroxynitrite
    Source:
    Curr Med Chem 21 (3), 365-376 (2014)
    Abstract:
    NADPH oxidases (NOX), catalyzing the reduction of molecular oxygen to form the superoxide radical anion (.O2 -) and hydrogen peroxide (H2O2), are involved in several pathological conditions, such as stroke, diabetes, atherosclerosis, but also in chronic neurodegenerative diseases such as Parkinson's disease, Alzheimer's disease, or multiple sclerosis. GKT136901 is a novel NOX-1/4 inhibitor with potential application in the areas of diabetic nephropathy, stroke, or neurodegeneration. In the present study, we investigated additional pharmacological activities of the compound with respect to direct free radical scavenging. GKT136901 did not interact with nitric oxide (.NO), .O2 -, or hydroxyl radicals ( .OH), but it acted as selective scavenger of peroxynitrite (PON) already in the submicromolar concentration range. Alpha synuclein (ASYN) is a protein involved in the pathogenesis of Parkinson's disease and a known target for PON-dependent tyrosine nitration. Submicromolar concentrations of GKT136901 prevented tyrosine nitration and di-tyrosine-dependent dimer formation of ASYN by PON as indicated by Western blot and mass spectrometric analysis. GKT136901 itself was degraded when exposed to PON. In a human neuronal cell model, GKT136901 prevented both the depletion of reduced intracellular glutathione, and the degeneration of neurites when present during PON treatment of the cells. When GKT136901 was applied after PON treatment, no protective effect was observed, thus excluding an impact of GKT136901 on cellular death/survival pathways. In summary, selective scavenging of PON is an additional pharmacological property of the NOX-1/4 inhibitor GKT136901, and this may add to the efficiency of the drug in several disease models. © 2014 Bentham Science Publishers.
  • Author:
    Christ CD; Fox T
    Title:
    Accuracy assessment and automation of free energy calculations for drug design
    Source:
    J Chem Inform Modeling 54 (1), 108-120 (2014)
    Abstract:
    As the free energy of binding of a ligand to its target is one of the crucial optimization parameters in drug design, its accurate prediction is highly desirable. In the present study we have assessed the average accuracy of free energy calculations for a total of 92 ligands binding to five different targets. To make this study and future larger scale applications possible we automated the setup procedure. Starting from user defined binding modes, the procedure decides which ligands to connect via a perturbation based on maximum common substructure criteria and produces all necessary parameter files for free energy calculations in AMBER 11. For the systems investigated, errors due to insufficient sampling were found to be substantial in some cases whereas differences in estimators (thermodynamic integration (TI) versus multistate Bennett acceptance ratio (MBAR)) were found to be negligible. Analytical uncertainty estimates calculated from a single free energy calculation were found to be much smaller than the sample standard deviation obtained from two independent free energy calculations. Agreement with experiment was found to be system dependent ranging from excellent to mediocre (RMSE = [0.9, 8.2, 4.7, 5.7, 8.7] kJ/mol). When restricting analyses to free energy calculations with sample standard deviations below 1 kJ/mol agreement with experiment improved (RMSE = [0.8, 6.9, 1.8, 3.9, 5.6] kJ/mol). © 2013 American Chemical Society.
  • Author:
    Rodríguez S; Qu B; Fandrick KR; Buono F; Haddad N; Xu Y; Herbage MA; Zeng X; Ma S; Grinberg N; Lee H; Han ZS; Yee NK; Senanayake CH
    Title:
    Amine-Tunable Ruthenium Catalysts for Asymmetric Reduction of Ketones
    Source:
    Adv Synth Catal 342 (8) Article in Press (2014)
    Abstract:
    A series of efficient ruthenium catalysts has been developed for the asymmetric hydrogenation and transfer hydrogenation of ketones with high reactivities and selectivities. The new chiral bisdihydrobenzooxaphosphole (BIBOP)/diamine-ruthenium complexes catalyzed the enantioselective hydrogenation of substrates such as aryl and heteroaryl cyclic and alkyl ketones with substrate/catalyst (S/C) ratios of up to 100,000. The opposite sense of enantioselectivity can be obtained by proper selection of a diamine with a given chirality of the phosphine. The usefulness of the new system has been demonstrated in the asymmetric hydrogenation of a complex synthetic intermediate towards cholesteryl ester transfer protein (CETP) inhibitors at S/C 20,000 on large-scale operation. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
  • Author:
    Xu G; Fu W; Liu G; Senanayake CH; Tang W
    Title:
    Efficient syntheses of korupensamines A, B and michellamine B by asymmetric Suzuki-Miyaura coupling reactions
    Source:
    J Am Chem Soc 136 (2), 570-573 (2014)
    Abstract:
    Efficient asymmetric Suzuki-Miyaura coupling reactions are employed for the first time in total syntheses of chiral biaryl natural products korupensamine A and B in combination with an effective diastereoselective hydrogenation, allowing ultimately a concise and stereoselective synthesis of michellamine B. Chiral monophosphorus ligands L1-3 are effective for the syntheses of a series of functionalized chiral biaryls by asymmetric Suzuki-Miyaura coupling reactions in excellent yields and enantioselectivities (up to 99% ee). The presence of a polar-. interaction between the highly polarized BOP group and the extended . system of arylboronic acid coupling partner is believed to be important for the high enantioselectivity. © 2013 American Chemical Society.
  • Author:
    Elsayed SM; Heller R; Thoenes M; Zaki MS; Swan D; Elsobky E; Zühlke C; Ebermann I; Nürnberg G; Nürnberg P; Bolz HJ
    Title:
    Autosomal dominant SCA5 and autosomal recessive infantile SCA are allelic conditions resulting from SPTBN2 mutations
    Source:
    Eur J Hum Genet 22 (2), 286-288 (2014)
    Abstract:
    Although many genes have been identified for the autosomal recessive cerebellar ataxias (ARCAs), several patients are unlinked to the respective loci, suggesting further genetic heterogeneity. We combined homozygosity mapping and exome sequencing in a consanguineous Egyptian family with congenital ARCA, mental retardation and pyramidal signs. A homozygous 5-bp deletion in SPTBN2, the gene whose in-frame mutations cause autosomal dominant spinocerebellar ataxia type 5, was shown to segregate with ataxia in the family. Our findings are compatible with the concept of truncating SPTBN2 mutations acting recessively, which is supported by disease expression in homozygous, but not heterozygous, knockout mice, ataxia in Beagle dogs with a homozygous frameshift mutation and, very recently, a homozygous SPTBN2 nonsense mutation underlying infantile ataxia and psychomotor delay in a human family. As there was no evidence for mutations in 23 additional consanguineous families, SPTBN2-related ARCA is probably rare. © 2014 Macmillan Publishers Limited All rights reserved.
  • Author:
    Zheng J-C; Liu H; Lee N-K; Lee D
    Title:
    Dimerization behavior of substituted bicyclo[3.1.0]hex-1-ene derivatives
    Source:
    Eur J Org Chem 2014 (3), 506-510 (2014)
    Abstract:
    The different reaction profiles of lithium trimethylsilyldiazomethane with various 4-alkenyl ketones are described. It was found that the individual steps along the reaction pathway including a Brook rearrangement, elimination of lithium trimethylsilanolate to form alkylidene carbenes, and their addition to an alkene to form strained bicyclo[3.1.0]hex-1-ene derivatives were significantly affected by the substituents near or on the alkene moiety. Especially, the dimerization of bicyclo[3.1.0]hex-1-enes depends critically on the substituent pattern of the alkene, which controls the reaction to proceed in a concerted or a stepwise manner. On the basis of X-ray diffraction analysis, the dimers, which are of unprecedented structural complexity, were unambiguously elucidated. The reactivity of various intermediates derived from 4-alkenyl ketones and lithium trimethylsilyldiazomethane is controlled by the substituent pattern on the ketone substrate. In particular, the formation of bicyclo[3.1.0]hex-1-enes and their dimerization through either a concerted mechanism or a trimethylenemethane diyl intermediate are dictated by the substituents. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
  • Author:
    Konstan MW; Döring G; Heltshe SL; Lands LC; Hilliard KA; Koker P; Bhattacharya S; Staab A; Hamilton A
    Title:
    A randomized double blind, placebo controlled phase 2 trial of BIIL 284 BS (an LTB4 receptor antagonist) for the treatment of lung disease in children and adults with cystic fibrosis
    Source:
    J Cystic Fibros Article in press (2014)
    Abstract:
    Background: Airway inflammation, mediated in part by LTB4, contributes to lung destruction in patients with cystic fibrosis (CF). LTB4-receptor inhibition may reduce airway inflammation. We report the results of a randomized, double-blind, placebo-controlled study of the efficacy and safety of the leukotriene B4 (LTB4)-receptor antagonist BIIL 284 BS in CF patients. Methods: CF patients aged . 6 years with mild to moderate lung disease were randomized to oral BIIL 284 BS or placebo once daily for 24 weeks. Co-primary endpoints were change in FEV1 and incidence of pulmonary exacerbation. Results: After 420 (155 children, 265 adults) of the planned 600 patients were randomized, the trial was terminated after a planned interim analysis revealed a significant increase in pulmonary related serious adverse events (SAEs) in adults receiving BIIL 284 BS. Final analysis revealed SAEs in 36.1% of adults receiving BIIL 284 BS vs. 21.2% receiving placebo (p = 0.007), and in 29.6% of children receiving BIIL 284 BS vs. 22.9% receiving placebo (p = 0.348). In adults, the incidence of protocol-defined pulmonary exacerbation was greater in those receiving BIIL 284 BS than in those receiving placebo (33.1% vs. 18.2% respectively; p = 0.005). In children, the incidence of protocol-defined pulmonary exacerbation was 19.8% in the BIIL 284 BS arm, and 25.7% in the placebo arm (p = 0.38). Conclusions: While the cause of increased SAEs and exacerbations due to BIIL 284 BS is unknown, the outcome of this trial provides a cautionary tale for the administration of potent anti-inflammatory compounds to individuals with chronic infections, as the potential to significantly suppress the inflammatory response may increase the risk of infection-related adverse events. © 2014 European Cystic Fibrosis Society.
  • Author:
    Finco D; Grimaldi C; Fort M; Walker M; Kiessling A; Wolf B; Salcedo T; Faggioni R; Schneider A; Ibraghimov A; Scesney S; Serna D; Prell R; Stebbings R; Narayanan PK
    Title:
    Cytokine release assays: Current practices and future directions
    Source:
    Cytokine Article in press (2014)
    Abstract:
    As a result of the CD28 superagonist biotherapeutic monoclonal antibody (TGN 1412) "cytokine storm" incident, cytokine release assays (CRA) have become hazard identification and prospective risk assessment tools for screening novel biotherapeutics directed against targets having a potential risk for eliciting adverse pro-inflammatory clinical infusion reactions. Different laboratories may have different strategies, assay formats, and approaches to the reporting, interpretation, and use of data for either decision making or risk assessment. Additionally, many independent contract research organizations (CROs), academic and government laboratories are involved in some aspect of CRA work. As a result, while some pharmaceutical companies are providing CRA data as part of the regulatory submissions when necessary, technical and regulatory practices are still evolving to provide data predictive of cytokine release in humans and that are relevant to safety. This manuscript provides an overview of different approaches employed by the pharmaceutical industry and CROs, for the use and application of CRA based upon a survey and post survey follow up conducted by ILSI-Health and Environmental Sciences Institute (HESI) Immunotoxicology Committee CRA Working Group. Also discussed is ongoing research in the academic sector, the regulatory environment, current limitations of the assays, and future directions and recommendations for cytokine release assays. © 2013 Elsevier Ltd.
  • Author:
    Gadekar PK; Hoermann M; Corbo F; Sharma R; Sarveswari S; Roychowdhury A
    Title:
    Reductive removal of methoxyacetyl protective group using sodium borohydride
    Source:
    Tetrahedron Lett 55 (2), 503-506 (2014)
    Abstract:
    Herein, we have developed a mild and selective reductive deprotection method for the MAc protected alcohols using sodium borohydride. The new deprotection conditions provide a complete orthogonality between O-MAc and other protecting groups such as tert-butyl ester, N-Boc, Fmoc, Cbz, O-TBDMS, N-benzyl, O-benzyl, O-acetyl, N-acetyl, N-MAc, etc. In addition to O-MAc deprotection, this method is also applicable for S-MAc deprotection. © 2013 Elsevier Ltd. All rights reserved.
  • Author:
    Fritzsche R; Karra D; Bennett KL; Ang F; Heraud-Farlow JE; Tolino M; Doyle M; Bauer KE; Thomas S; Planyavsky M; Arn E; Bakosova A; Jungwirth K; Hörmann A; Palfi Z; Sandholzer J; Schwarz M; Macchi P; Colinge J; Superti-Furga G; Kiebler MA
    Title:
    Interactome of two diverse RNA granules links mRNA localization to translational repression in neurons
    Source:
    Cell Rep 5 (6), 1749-1762 (2013)
    Abstract:
    Transport of RNAs to dendrites occurs in neuronal RNA granules, which allows local synthesis of specific proteins at active synapses on demand, thereby contributing to learning and memory. To gain insight into the machinery controlling dendritic mRNA localization and translation, we established a stringent protocol to biochemically purify RNA granules from rat brain. Here, we identified a specific set of interactors for two RNA-binding proteins that are known components of neuronal RNA granules, Barentsz and Staufen2. First, neuronal RNA granules are much more heterogeneous than previously anticipated, sharing only a third of the identified proteins. Second, dendritically localized mRNAs, e.g., Arc and CaMKII., associate selectively with distinct RNA granules. Third, our work identifies a series of factors with known roles in RNA localization, translational control, and RNA quality control that are likely to keep localized transcripts in a translationally repressed state, often in distinct types of RNPs. © 2013 The Authors.
  • Author:
    Mathur A; Tweedie DJ; Maw HH-H; Li Y
    Title:
    Unexpected interaction between CYP3A4 and BI 11634: Is BI 11634 interacting with CYP3A4 similar to nifedipine?
    Source:
    Drug Metab Drug Interact 28 (4), 239-246 (2013)
    Abstract:
    Background: Interactions between cytochrome P450 3A4 (CYP3A4) and its substrates are complex with multiple binding sites within the active site. BI 11634 is a factor Xa inhibitor in drug development and its interaction with CYP3A4 was evaluated. Methods: Reaction phenotyping studies were conducted to determine human isoform(s) of cytochrome P450 responsible for BI 11634 metabolism using recombinant CYPs and specific chemical inhibitors. Metabolite identification and quantitation were performed for incubations of [14C]BI 11634 with human liver microsomes (HLMs) or recombinant CYP3A4 (rCYP3A4) using a highperformance liquid chromatography-mass spectrometry-radiomatic detector. Inhibition of the CYP3A4-mediated metabolism of BI 11634 by quinidine was further evaluated. Results: From the reaction phenotyping studies, it was shown that the metabolism of BI 11634 in HLM was inhibited by ketoconazole and quinidine, well-accepted specific inhibitors of CYP3A4 and CYP2D6, respectively. In contrast, BI 11634 metabolism was exclusively mediated by rCYP3A4. Additional studies confirmed that BI 11634 was metabolized by CYP3A4 to form one major metabolite and this reaction was inhibited by quinidine with a Ki of 7 .M. Conclusions: These data indicated that BI 11634 may interact with CYP3A4 similar to nifedipine. CYP3A4 substrates have been categorized into three subgroups, including a stand-alone subgroup for dihydropyridine calcium channel blockers such as nifedipine and felodipine. In addition, this study emphasizes the importance of using rCYP in conjunction with approaches relying on inhibition when conducting CYP450 reaction phenotyping studies, as one single method may generate misleading results. The specificity of quinidine as a CYP2D6 inhibitor is questionable as it can also significantly inhibit CYP3A4-mediated metabolism of some compounds
  • Author:
    Kelley M; Beaver C; Stevenson LF; Bamford R; Gegwich P; Katsuhiko Y; Li D; Little S; Muruganandam A; Stoellner D; Trivedi RK
    Title:
    Large Molecule Run Acceptance: Recommendation for Best Practices and Harmonization from the Global Bioanalysis Consortium Harmonization Team
    Source:
    BMC Biol, 1-5 Article in press (2014)
    Abstract:
    The L1 Global Harmonization Team provides recommendations specifically for run acceptance of ligand binding methods used in bioanalysis of macromolecules in support of pharmacokinetics. The team focused on standard curve calibrators and quality controls for use in both pre-study validation and in-study sample analysis, including their preparation and acceptance criteria. The team also considered standard curve editing and the concept of total error. © 2014 American Association of Pharmaceutical Scientists.
  • Author:
    Zheng JC; Liu H; Lee NK; Lee D
    Title:
    Dimerization Behavior of Substituted Bicyclo[3.1.0]hex-1-ene Derivatives
    Source:
    Eur J Org Chem Article in press (2013)
    Abstract:
    The different reaction profiles of lithium trimethylsilyldiazomethane with various 4-alkenyl ketones are described. It was found that the individual steps along the reaction pathway including a Brook rearrangement, elimination of lithium trimethylsilanolate to form alkylidene carbenes, and their addition to an alkene to form strained bicyclo[3.1.0]hex-1-ene derivatives were significantly affected by the substituents near or on the alkene moiety. Especially, the dimerization of bicyclo[3.1.0]hex-1-enes depends critically on the substituent pattern of the alkene, which controls the reaction to proceed in a concerted or a stepwise manner. On the basis of X-ray diffraction analysis, the dimers, which are of unprecedented structural complexity, were unambiguously elucidated. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
  • Author:
    Mirnik J; Gro.elj U; Novak A; Dahmann G; Golobic A; Kasunic M; Stanovnik B; Svete J
    Title:
    A novel synthesis of tetrahydropyrazolo[1,5-c]pyrimidine-2,7(1 H,3 H)-diones
    Source:
    Synthesis 45 (24), 3404-3412 (2013)
    Abstract:
    A novel simple five-step synthesis of 1,6-disubstituted tetrahydropyrazolo[1,5-c]pyrimidine-2,7(1H,3H)-diones has been developed. The synthetic protocol starts with 'ring switching' transformation of commercially available 5,6-dihydro-2H-pyran-2-one into the 5-(2-hydroxyethyl)pyrazolidin-3- one, followed by addition of the latter to isocyanates, Appel bromination, cyclization, and N(1)-alkylation with alkyl halides to give the title compounds. In comparison to a 12-step synthesis reported recently, the present method is clearly superior with respect to the number of synthetic steps and versatility of substituents at position 6.© Georg Thieme Verlag KG Stuttgart
  • Author:
    Cai Z; Liu G; Jiao G; Senanayake CH; Tang W
    Title:
    Practical syntheses of N-acetyl (E)-.-arylenamides
    Source:
    Synthesis 45 (24), 3355-3360 (2013)
    Abstract:
    A facile and practical method for the preparation of (E)-.- arylenamides [(E)-N-(1-arylprop-1-en-2-yl]acetamides] has been developed by reductive acetylation of the corresponding oximes with iron(II) acetate as the reducing reagent. Employment of hexamethylphosphoramide as the solvent was found to be critical for the high E/Z selectivity. The methodology has been applied in efficient syntheses of a key chiral intermediate of tamsulosin by asymmetric hydrogenation. © Georg Thieme Verlag Stuttgart . New York.
  • Author:
    Kunz Dr U
    Title:
    Case studies of non-parallelism in various ELISAs
    Source:
    EBF Open Symposium in Barcelona (European Bioanalytical Forum Nov 2013
  • Author:
    Gadekar PK; Hoermann M; Corbo F; Sharma R; Sarveswari S; Roychowdhury A
    Title:
    Reductive removal of methoxyacetyl protective group using sodium borohydride
    Source:
    Tetrahedron Lett Article in press (2013)
    Abstract:
    Herein, we have developed a mild and selective reductive deprotection method for the MAc protected alcohols using sodium borohydride. The new deprotection conditions provide a complete orthogonality between O-MAc and other protecting groups such as tert-butyl ester, N-Boc, Fmoc, Cbz, O-TBDMS, N-benzyl, O-benzyl, O-acetyl, N-acetyl, N-MAc, etc. In addition to O-MAc deprotection, this method is also applicable for S-MAc deprotection. © 2013 Elsevier Ltd. All rights reserved.
  • Author:
    Kuzmich D; Bentzien J; Betageri R; Disalvo D; Fadra-Khan T; Harcken C; Kukulka A; Nabozny G; Nelson R; Pack E; Souza D; Thomson D
    Title:
    Function-regulating pharmacophores in a sulfonamide class of glucocorticoid receptor agonists
    Source:
    Bioorg Med Chem Lett 23 (24), 6640-6644 (2013)
    Abstract:
    A class of .-methyltryptamine sulfonamide glucocorticoid receptor (GR) modulators was optimized for agonist activity. The design of ligands was aided by molecular modeling, and key function-regulating pharmacophoric points were identified that are critical in achieving the desired agonist effect in cell based assays. Compound 27 was profiled in vitro and in vivo in models of inflammation. Analogs could be rapidly prepared in a parallel approach from aziridine building blocks. © 2013 Elsevier Ltd. All rights reserved.
  • Author:
    Disalvo D; Kuzmich D; Bentzien J; Regan J; Kukulka A; Fadra-Khan T; Nelson R; Harcken C; Thomson D; Nabozny G
    Title:
    Substituted phenyl as a steroid A-ring mimetic: Providing agonist activity to a class of arylsulfonamide nonsteroidal glucocorticoid ligands
    Source:
    Bioorg Med Chem Lett 23 (24), 6645-6648 (2013)
    Abstract:
    A class of arylsulfonamide glucocorticoid receptor agonists that contains a substituted phenyl group as a steroid A-ring mimetic is reported. The structural design and SAR that provide the functional switching of a GR antagonist to an agonist is described. A combination of specific hydrogen bonding and lipophilic elements on the A-ring moiety is required to achieve potent GR agonist activity. This study culminated in the identification of compound 23 as a potent GR agonist with selectivity over the PR and MR nuclear hormone receptors. © 2013 Elsevier Ltd. All rights reserved.
  • Author:
    Shun He; Carolyn Cheney; Susan Whitman; Jianhua Yu; Sumithra Vasu; William Blum; Karl-Heinz Heider; Guido Marcucci N; atarajan Muthusamy
    Title:
    Decitabine or 5-Azacytidine pre-treatment does not compromise the novel Fc-engineered Antibody mAb 33.1 mediated ADCC against primary AML blasts -A rationale for combination therapy
    Source:
    551 ASH Annual Meeting, New Orleans, USA, Dec 7, 2013
  • Author:
    Ding Dr S
    Title:
    New Legislation impacting IMP QPs
    Source:
    IMP Pre-Conference Workshop, QP Forum 2013, Lisbon, Portugal, 27 November 2013
  • Author:
    Carrero-González L; Kaulisch T; Stiller D
    Title:
    In vivo diffusion-weighted MRI using perfluorinated gases: ADC comparison between healthy and elastase-treated rat lungs
    Source:
    Magn Reson Med 70 (6), 1761-1764 (2013)
    Abstract:
    Purpose MRI with perfluorinated gases has been shown as an alternative to hyperpolarized gases to image both microstructure and gas diffusivity in the lung. The aim of this study was to measure diffusion restriction of C 2F6 in rat lungs and to compare the different levels of restriction between healthy and emphysematous tissue. Methods For this purpose, two groups of rats - healthy and mono-lobar elastase-induced animals - were measured. While being ventilated with a mixture of C2F6 and oxygen four diffusion weighted 19F-images where acquired for each animal and corresponding ADC-maps were calculated. Results No significant apparent diffusion coefficient (ADC) differences were found between healthy lungs; however, the elastase treated lungs showed a significant increase in ADC. Conclusion These results demonstrate that ADC measurements with C 2F6 are sensitive to the microstructure of rat lungs showing that the diffusion of this gas is limited to different levels in healthy and in emphysematous tissue. Magn Reson Med 70:1761-1764, 2013. © 2013 Wiley Periodicals, Inc. Copyright © 2012 Wiley Periodicals, Inc.
  • Author:
    Schiele F; Park J; Redemann N; Luippold G; Nar H
    Title:
    An Antibody against the C-Terminal Domain of PCSK9 Lowers LDL Cholesterol Levels In Vivo
    Source:
    J Mol Biol Article in press (2013)
    Abstract:
    Proprotein convertase subtilisin/kexin type 9 (PCSK9) is associated with autosomal dominant hypercholesterolemia, a state of elevated levels of LDL (low-density lipoprotein) cholesterol. Autosomal dominant hypercholesterolemia can result in severe implications such as stroke and coronary heart disease. The inhibition of PCSK9 function by therapeutic antibodies that block interaction of PCSK9 with the epidermal growth factor-like repeat A domain of LDL receptor (LDLR) was shown to successfully lower LDL cholesterol levels in clinical studies. Here we present data on the identification, structural and biophysical characterization and in vitro and in vivo pharmacology of a PCSK9 antibody (mAb1). The X-ray structure shows that mAb1 binds the module 1 of the C-terminal domain (CTD) of PCSK9. It blocks access to an area bearing several naturally occurring gain-of-function and loss-of-function mutations. Although the antibody does not inhibit binding of PCSK9 to epidermal growth factor-like repeat A, it partially reverses PCSK9-induced reduction of the LDLR and LDL cholesterol uptake in a cellular assay. mAb1 is also effective in lowering serum levels of LDL cholesterol in cynomolgus monkeys in vivo. Complete loss of PCSK9 is associated with insufficient liver regeneration and increased risk of hepatitis C infections. Blocking of the CTD is sufficient to partially inhibit PCSK9 function. Antibodies binding the CTD of PCSK9 may thus be advantageous in patients that do not tolerate complete inhibition of PCSK9. © 2013 Elsevier Ltd. All rights reserved.
  • Author:
    Egert T
    Title:
    Fit-for-Purpose Analytical Concepts Adequately Monitoring Targets while Capturing Non- Targets
  • Author:
    Seeliger D
    Title:
    Development of Scoring Functions for Antibody Sequence Assessment and Optimization
    Source:
    PLoS ONE 8 (10) art.no.e76909 (2013)
    Abstract:
    Antibody development is still associated with substantial risks and difficulties as single mutations can radically change molecule properties like thermodynamic stability, solubility or viscosity. Since antibody generation methodologies cannot select and optimize for molecule properties which are important for biotechnological applications, careful sequence analysis and optimization is necessary to develop antibodies that fulfil the ambitious requirements of future drugs. While efforts to grab the physical principles of undesired molecule properties from the very bottom are becoming increasingly powerful, the wealth of publically available antibody sequences provides an alternative way to develop early assessment strategies for antibodies using a statistical approach which is the objective of this paper. Here, publically available sequences were used to develop heuristic potentials for the framework regions of heavy and light chains of antibodies of human and murine origin. The potentials take into account position dependent probabilities of individual amino acids but also conditional probabilities which are inevitable for sequence assessment and optimization. It is shown that the potentials derived from human sequences clearly distinguish between human sequences and sequences from mice and, hence, can be used as a measure of humaness which compares a given sequence with the phenotypic pool of human sequences instead of comparing sequence identities to germline genes. Following this line, it is demonstrated that, using the developed potentials, humanization of an antibody can be described as a simple mathematical optimization problem and that the in-silico generated framework variants closely resemble native sequences in terms of predicted immunogenicity. © 2013 Daniel Seeliger.
  • Author:
    Haebel P; Nar H; Zentgraf M
    Title:
    High concentration Fragment Screening
    Source:
    EMBL-EBI-Wellcome Trust Course: Resources for Computational Drug Discovery
  • Author:
    Busacca CA; Fandrick DR; Song JJ; Senanayake CH
    Title:
    Transition Metal Catalysis in the Pharmaceutical Industry
    Source:
    Appl of Transit Met Catalysis in Drug Discov and Dev
    Source:
    Appl of Transit Met Catalysis in Drug Discov and Dev, 1-24 ( 2012)
    Abstract:
    no abstract available
  • Author:
    Buono FG; Gonzalez MA; Müslehiddinoglu J
    Title:
    Flow Reactors
    Source:
    Green Tech for Organic Synth and Medicinal Chem, 523-549 (2012)
  • Author:
    Yee N; Wei X; Senanayake C
    Title:
    Challenge and Opportunity in Scaling-Up Metathesis Reaction: Synthesis of Ciluprevir (BILN 2061)
    Abstract:
    no abstract available
  • Author:
    Stammers TA; Coulombe R; Duplessis M; Fazal G; Gagnon A; Garneau M; Goulet S; Jakalian A; LaPlante S; Rancourt J; Thavonekham B; Wernic D; Kukolj G; Beaulieu PL
    Title:
    Anthranilic acid-based Thumb Pocket 2 HCV NS5B polymerase inhibitors with sub-micromolar potency in the cell-based replicon assay
    Source:
    Bioorg Med Chem Lett Article in press (2013)
    Abstract:
    Optimization efforts on the anthranilic acid-based Thumb Pocket 2 HCV NS5B polymerase inhibitors 1 and 2 resulted in the identification of multiple structural elements that contributed to improved cell culture potency. The additive effect of these elements resulted in compound 46, an inhibitor with enzymatic (IC50) and cell culture (EC50) potencies of less than 100 nanomolar. © 2013 Elsevier Ltd. All rights reserved.
  • Author:
    Li QC; Qiu F; McWilliams W; Pape C; Song JJ; Swanek F; Wang X-j; Cohen K; O'Connor D
    Title:
    Best Practices for Drug Substance Stress and Stability Studies During Early Stage Development. Part III-How to Make Science- and Risk-based Stability Testing Decisions for Drug Substance Batches Produced after Manufacturing Process Changes
    Source:
    J Pharm Innov, 1-11 Article in press (2013)
    Abstract:
    During phase 1 and phase 2 drug development (early stage drug development), it is normal to continuously improve a manufacturing process, with changes made to the synthetic pathway, reagents, reaction conditions, crystallization parameters, drying conditions, or manufacturing equipment or scale or site. These manufacturing process changes ("process changes" used thereafter) may or may not affect quality attributes such as impurities, and quality attribute changes may or may not affect drug substance (DS) stability. But a common misconception is that almost all process changes and/or quality attribute changes affect DS stability, and a new (or repeat) stability study is conducted for the DS batch produced after process changes. This misconception is clearly refuted by our many years of DS stability experience. To understand how process changes might affect DS stability, we compiled and analyzed manufacturing processes, quality test results, and stability data for 48 batches from seven drug substances in recent development. Of these 48 batches, the seven first DS clinical batches were used as references against which the other respective 41 batches, which were produced after process changes, were compared for changes in manufacturing processes, quality test results, and stability data. This comparison showed that the chemical and physical stability of 36 (of the 41) batches was not affected by process changes, and the chemical or physical stability of the other 5 batches was affected by residual inorganic impurities, significant amounts of water or residual solvents, or significant changes in DS particle size distribution or surface area. These quality attributes that affect stability are called stability-related quality attributes (SRQAs). A new (or repeat) stability study is warranted only if process changes significantly affect SRQAs. We have established a procedure to systematically assess changes in manufacturing process and quality attributes (particularly impurity profiles), to identify SRQAs (risk assessment), and to make science- and risk-based stability testing decisions on whether and how stability testing for new DS batches should be conducted (risk management). © 2013 Springer Science+Business Media New York.
  • Author:
    Ahmetaj S; Velikanje N; Gro.elj U; .terbal I; Prek B; Golobic A; Kocar D; Dahmann G; Stanovnik B; Svete J
    Title:
    Parallel synthesis of 7-heteroaryl-pyrazolo[1,5-a]pyrimidine-3-carboxamides
    Source:
    Mol Divers 17 (4), 731-743 (2013)
    Abstract:
    A simple and practical four-step protocol for the parallel synthesis of 7-heteroaryl-pyrazolo[1,5-a ]pyrimidine-3-carboxamides was developed. The synthesis starts with transformation of commercially available 2-acetylpyridine and acetylpyrazine with N, N -dimethylformamide dimethylacetal into the corresponding (E) -3-(dimethylamino)-1-(heteroaryl)prop-2-en-1-ones followed by cyclisation with methyl 5-amino-1 H -pyrazole-4-carboxylate to give methyl 7-heteroarylpyrazolo[1,5-a ]pyrimidine-3-carboxylates. Hydrolysis of the ester group and subsequent amidation of the so formed carboxylic acids with 12 primary and secondary aliphatic amines furnished a library of 24 title compounds in good overall yields and purity. © 2013 Springer Science+Business Media Dordrecht.
  • Author:
    Reinert Dirk
    Title:
    "Quite some throughput" crystallography at Boehringer-Ingelheim or: How much automation do we need?
    Source:
    Talk at PSDI 2013 Protein Structure Determination in Industry Nov 4-5, 2013
  • Author:
    Mirnik J; Gro.elj U; Novak A; Dahmann G; Golobi A; Kasuni M; Stanovnik B; Svete J
    Title:
    A Novel Synthesis of Tetrahydropyrazolo[1,5-c]pyrimidine-2,7(1H,3H)-diones
    Source:
    Synthesis 45 Article in press (2013)
    Abstract:
    A novel simple five-step synthesis of 1,6-disubstituted tetrahydropyrazolo[1,5-c]pyrimidine-2,7(1H,3H)-diones has been developed. The synthetic protocol starts with 'ring switching' transformation of commercially available 5,6-dihydro-2H-pyran-2-one into the 5-(2-hydroxyethyl)pyrazolidin-3-one, followed by addition of the latter to isocyanates, Appel bromination, cyclization, and N(1)-alkylation with alkyl halides to give the title compounds. In comparison to a 12-step synthesis reported recently, the present method is clearly superior with respect to the number of synthetic steps and versatility of substituents at position 6. © Georg Thieme Verlag.
  • Author:
    Cai Z; Liu G; Jiao G; Senanayake CH; Tang W
    Title:
    Practical Syntheses of N-Acetyl (E)-.-Arylenamides
    Source:
    Synthesis Article in press (2013)
    Abstract:
    A facile and practical method for the preparation of (E)-.-arylenamides [(E)-N-(1-arylprop-1-en-2-yl]acetamides] has been developed by reductive acetylation of the corresponding oximes with iron(II) acetate as the reducing reagent. Employment of hexamethylphosphoramide as the solvent was found to be critical for the high E/Z selectivity. The methodology has been applied in efficient syntheses of a key chiral intermediate of tamsulosin by asymmetric hydrogenation. © Georg Thieme Verlag.
  • Author:
    Wellenzohn B; Lessel U; Weskamp N
    Title:
    (Combinatorial) Library Design with KNIME
    Source:
    Industrietreffen Molecular Modelling (IMM), Sanofi-Aventis, Frankfurt, Germany, Oct 16-17, 2013
  • Author:
    Wu H S; Lunter A K; Spillner E; Schmitz N; Heider K H; Zeis M
    Title:
    A Novel Anti-CD37 Antibody shows superior Antibody dependent cellular Cytotoxic activity (ADCC) compared to Rituximab against Patient-Derived Lymphoma cells
    Source:
    DGHO Jahrestagung, Wien, Austria, Oct 18-22, 2013
  • Author:
    Voehringer P; Fuertig R; Ferger B
    Title:
    A novel liquid chromatography/tandem mass spectrometry method for the quantification of glycine as biomarker in brain microdialysis and cerebrospinal fluid samples within 5min
    Source:
    J Chromatogr (B) 939, 92-97 (2013)
    Abstract:
    Glycine is an important amino acid neurotransmitter in the central nervous system (CNS) and a useful biomarker to indicate biological activity of drugs such as glycine reuptake inhibitors (GRI) in the brain. Here, we report how a liquid chromatography/tandem mass spectrometry (LC-MS/MS) method for the fast and reliable analysis of glycine in brain microdialysates and cerebrospinal fluid (CSF) samples has been established. Additionally, we compare this method with the conventional approach of high performance liquid chromatography (HPLC) coupled to fluorescence detection (FD). The present LC-MS/MS method did not require any derivatisation step. Fifteen microliters of sample were injected for analysis. Glycine was detected by a triple quadrupole mass spectrometer in the positive electrospray ionisation (ESI) mode. The total running time was 5. min. The limit of quantitation (LOQ) was determined as 100. nM, while linearity was given in the range from 100. nM to 100. .M. In order to demonstrate the feasibility of the LC-MS/MS method, we measured glycine levels in striatal in vivo microdialysates and CSF of rats after administration of the commercially available glycine transporter 1 (GlyT1) inhibitor LY 2365109 (10. mg/kg, p.o.). LY 2365109 produced 2-fold and 3-fold elevated glycine concentrations from 1.52. .M to 3.6. .M in striatal microdialysates and from 10.38. .M to 36. .M in CSF, respectively. In conclusion, we established a fast and reliable LC-MS/MS method, which can be used for the quantification of glycine in brain microdialysis and CSF samples in biomarker studies. © 2013 Elsevier B.V.
  • Author:
    Pautsch A
    Title:
    Structural Research in Pharma
    Source:
    KoRS-CB Course; Determination of Macromolecular Structures, Konstanz, Germany, 2013
  • Author:
    Lessard I A D
    Title:
    VanX d-,d-Dipeptidase
    Source:
    Handb of Proteolytic Enzymes 1, 1385-1401 (2013)
    Abstract:
    no abstract available
  • Author:
    Gorell M D; Park J E
    Title:
    Fibroblast Activation Protein .
    Source:
    Handb of Proteolytic Enzymes 3, 3395-3401 (2013)
    Abstract:
    no abstract available
  • Author:
    Eisen T; Shparyk Y; Macleod N; Jones R; Wallenstein G; Temple G; Khder Y; Dallinger C; Studeny M; Loembe A-B; Bondarenko I
    Title:
    Effect of small angiokinase inhibitor nintedanib (BIBF 1120) on QT interval in patients with previously untreated, advanced renal cell cancer in an open-label, phase II study
    Source:
    Invest. New Drugs 31 (5), 1283-1293 (2013)
    Abstract:
    Purpose Some targeted anticancer agents are associated with serious ventricular tachyarrhythmias, which may be predicted by electrocardiographic evaluation of drug-related QT prolongation. We studied the effects of nintedanib (BIBF 1120; an oral, triple angiokinase inhibitor targeting vascular endothelial growth factor, fibroblast growth factor, and platelet-derived growth factor receptors) on the QT interval in patients with renal cell carcinoma (RCC) participating in an open-label phase II trial. Methods Treatment-naïve, adult patients with unresectable/metastatic, clear cell RCC received nintedanib 200 mg twice daily. QT intervals were evaluated at baseline (day -1), on day 1 (after the first dose), and on day 15 (steady state) by 12-lead electrocardiograms (ECGs) performed in triplicate. Pharmacokinetic sampling was also undertaken. Results Among 64 evaluable patients, the upper limits of the 2-sided 90 % confidence intervals for the adjusted mean time-matched changes in QTcF interval (corrected for heart rate by Fridericia's method) from baseline to day 1 and 15 (primary ECG endpoint) were well below the regulatory threshold of 10 ms at all times. No relationship between nintedanib exposure and change from baseline in QTcF was seen. Nintedanib was generally well tolerated with no drug-related cardiovascular adverse events. Conclusion Nintedanib administered at 200 mg twice daily was not associated with clinically relevant QT prolongation. © 2013 Springer Science+Business Media New York.
  • Author:
    Bühler Dr S
    Title:
    SFCMS in early Drug Research
    Source:
    MS Technology Day, Stuttgart 2013
  • Author:
    Lamorte L; Titolo S; Lemke CT; Goudreau N; Mercier J-F; Wardrop E; Shah VB; Von Schwedler UK; Langelier C; Banik SSR; Aiken C; Sundquist WI; Mason SW
    Title:
    Discovery of novel small-molecule HIV-1 replication inhibitors that stabilize capsid complexes
    Source:
    Antimicrob Agents Chemother 57 (10), 4622-4631 (2013)
    Abstract:
    The identification of novel antiretroviral agents is required to provide alternative treatment options for HIV-1-infected patients. The screening of a phenotypic cell-based viral replication assay led to the identification of a novel class of 4,5-dihydro-1Hpyrrolo[ 3,4-c]pyrazol-6-one (pyrrolopyrazolone) HIV-1 inhibitors, exemplified by two compounds: BI-1 and BI-2. These compounds inhibited early postentry stages of viral replication at a step(s) following reverse transcription but prior to 2 long terminal repeat (2-LTR) circle formation, suggesting that they may block nuclear targeting of the preintegration complex. Selection of viruses resistant to BI-2 revealed that substitutions at residues A105 and T107 within the capsid (CA) amino-terminal domain (CANTD) conferred high-level resistance to both compounds, implicating CA as the antiviral target. Direct binding of BI-1 and/or BI-2 to CANTD was demonstrated using isothermal titration calorimetry and nuclear magnetic resonance (NMR) chemical shift titration analyses. A high-resolution crystal structure of the BI-1:CANTD complex revealed that the inhibitor bound within a recently identified inhibitor binding pocket (CANTD site 2) between CA helices 4, 5, and 7, on the surface of the CANTD, that also corresponds to the binding site for the host factor CPSF-6. The functional consequences of BI-1 and BI-2 binding differ from previously characterized inhibitors that bind the same site since the BI compounds did not inhibit reverse transcription but stabilized preassembled CA complexes. Hence, this new class of antiviral compounds binds CA and may inhibit viral replication by stabilizing the viral capsid. Copyright © 2013, American Society for Microbiology. All Rights Reserved
  • Author:
    Buckle DR; Erhardt PW; Ganellin CR; Kobayashi T; Perun TJ; Proudfoot J; Senn-Bilfinger J
    Title:
    Glossary of terms used in medicinal chemistry Part II (IUPAC recommendations 2013)
    Source:
    Annu Rep Med Chem 48, 386-418 (2013)
    Abstract:
    The evolution that has taken place in Medicinal Chemistry practice as a result of major advances in genomics and molecular biology arising from the Human Genome Project has carried with it an extensive additional working vocabulary that has become both integrated and essential terminology for the medicinal chemist. Some of this augmented terminology has been adopted from the many related and interlocked scientific disciplines with which the modern medicinal chemist must be conversant, but many other terms have been introduced to define new concepts and ideas as they have arisen. In this supplementary Glossary, we have attempted to collate and define many of the additional terms that are now considered to be essential components of the medicinal chemist's expanded repertoire. © 2013 Elsevier Inc.
  • Author:
    Velazquez-Carrasco L
    Title:
    Expression and purification of CCR3 for structural and biophysical studies
    Source:
    University of Manchester Project report for placement year at BI
  • Author:
    Ciossek T
    Title:
    Increased alpha-Synuclein aggregation in mutant MnSOD (+/-) mice
    Source:
    MEFOPA & Neurasync Joint Final Meeting, Rome, Italy, Sep 19-20, 2013
  • Author:
    Maier Dr U
    Title:
    Talk: Targeting Ubiquitin Signaling Mediated Disease Pathology of LDL Receptors
    Source:
    11th annual Discovery on Target Congress, Boston, USA, Sep 24-26, 2013
  • Author:
    Trieselmann Dr T
    Title:
    Hexahydrofuroquinoline Derivatives as Cholesteryl Ester Transfer Protein (CETP) Inhibitors
    Source:
    Hochschule trifft Industrie, Sep 18-20, 2013
  • Author:
    Priepke H
    Title:
    BICLAIM: A new Option for Virtual Screening BI Comprehensive Library of Accessible Innovative Molecules
    Source:
    Hochschule trifft Industrie, Beuggen, Sep 18-20, 2013
  • Author:
    Gnamm Dr C
    Title:
    What to do with a PhD . Medicinal Chemist at Boehringer Ingelheim
    Source:
    ACS on campus, Aachen, Germany Sep 26, 2013
  • Author:
    Pautsch A
    Title:
    Structural Research in Pharma
    Source:
    27th Rhine-Knee Regiomeeting on Biocrystallography, Schluchsee, Germany, 2013
  • Author:
    Lessel U
    Title:
    Detection of specific gaps in screening collections and strategies to fill those via combinatorial library design: e.g.search for potential PPI inhibitors
    Source:
    Vortrag bei der Tagung "9th Intelliget Comound Libraries", Berlin, Germany, Oct 28-29,2013
  • Author:
    Bergner A
    Title:
    Exploration of chemical space using multiple similarity methods
    Source:
    7th Summer School on Drug Design, Vienna, Austria, Sep 19, 2013
  • Author:
    Adeniji AK; Belle SH; Wahed AS
    Title:
    Incorporating diagnostic accuracy into the estimation of discrete survival function
    Source:
    J Appl Stat Article in press (2013)
    Abstract:
    Empirical distribution function (EDF) is a commonly used estimator of population cumulative distribution function. Survival function is estimated as the complement of EDF. However, clinical diagnosis of an event is often subjected to misclassification, by which the outcome is given with some uncertainty. In the presence of such errors, the true distribution of the time to first event is unknown. We develop a method to estimate the true survival distribution by incorporating negative predictive values and positive predictive values of the prediction process into a product-limit style construction. This will allow us to quantify the bias of the EDF estimates due to the presence of misclassified events in the observed data. We present an unbiased estimator of the true survival rates and its variance. Asymptotic properties of the proposed estimators are provided and these properties are examined through simulations. We evaluate our methods using data from the VIRAHEP-C study. © 2013 Taylor & Francis.
  • Author:
    Sutter A; Amberg A; Boyer S; Brigo A; Contrera JF; Custer LL; Dobo KL; Gervais V; Glowienke S; Gompel JV; Greene N; Muster W; Nicolette J; Reddy MV; Thybaud V; Vock E; White AT; Müller L
    Title:
    Use of in silico systems and expert knowledge for structure-based assessment of potentially mutagenic impurities
    Source:
    Regul Toxicol Pharmacol 67 (1), 39-52 (2013)
    Abstract:
    Genotoxicity hazard identification is part of the impurity qualification process for drug substances and products, the first step of which being the prediction of their potential DNA reactivity using in silico (quantitative) structure-activity relationship (Q)SAR models/systems. This white paper provides information relevant to the development of the draft harmonized tripartite guideline ICH M7 on potentially DNA-reactive/mutagenic impurities in pharmaceuticals and their application in practice. It explains relevant (Q)SAR methodologies as well as the added value of expert knowledge. Moreover, the predictive value of the different methodologies analyzed in two surveys conveyed in the US and European pharmaceutical industry is compared: most pharmaceutical companies used a rule-based expert system as their primary methodology, yielding negative predictivity values of .78% in all participating companies. A further increase (>90%) was often achieved by an additional expert review and/or a second QSAR methodology. Also in the latter case, an expert review was mandatory, especially when conflicting results were obtained. Based on the available data, we concluded that a rule-based expert system complemented by either expert knowledge or a second (Q)SAR model is appropriate. A maximal transparency of the assessment process (e.g. methods, results, arguments of weight-of-evidence approach) achieved by e.g. data sharing initiatives and the use of standards for reporting will enable regulators to fully understand the results of the analysis. Overall, the procedures presented here for structure-based assessment are considered appropriate for regulatory submissions in the scope of ICH M7. © 2013 Elsevier Inc.
  • Author:
    Cerny M A
    Title:
    Progress towards clinically useful aldosterone synthase inhibitors
    Source:
    Curr Top Med Chem 13 (12), 1385-1401 (2013)
    Abstract:
    Owing to the high degree of similarity between aldosterone synthase (CYP11B2) and cortisol synthase (CYP11B1), the design of selective inhibitors of one or the other of these two enzymes was, at one time, thought to be impossible. Through development of novel enzyme screening assays and significant medicinal chemistry efforts, highly potent inhibitors of CYP11B2 have been identified with selectivities approaching 1000-fold between the two enzymes. Many of these molecules also possess selectivity against other steroidogenic cytochromes P450 (e.g. CYP17A1 and CYP19A1) as well as hepatic drug metabolizing P450s. Though not as well developed or explored, inhibitors of CYP11B1, with selectivities approaching 50-fold, have also been identified. The therapeutic benefits of affecting the renin-angiotensin-aldosterone system have been well established with the therapeutically useful angiotensin-converting enzymes inhibitors, angiotensin receptor blockers, and mineralocorticoid receptor antagonists. Data regarding the additional benefits of an aldosterone synthase inhibitor (ASi) are beginning to emerge from animal models and human clinical trials. Despite great promise and much progress, additional challenges still exist in the path towards development of a therapeutically useful ASi. © 2013 Bentham Science Publishers.
  • Author:
    Rioux N; Bellavance E; Bourg S; Garneau M; Ribadeneira MD; Duan J
    Title:
    Assessment of CYP3A-mediated drug-drug interaction potential for victim drugs using an in vivo rat model
    Source:
    Biopharm Drug Dispos Article in Press (2013)
    Abstract:
    Owing to the high degree of similarity between aldosterone synthase (CYP11B2) and cortisol synthase (CYP11B1), the design of selective inhibitors of one or the other of these two enzymes was, at one time, thought to be impossible. Through development of novel enzyme screening assays and significant medicinal chemistry efforts, highly potent inhibitors of CYP11B2 have been identified with selectivities approaching 1000-fold between the two enzymes. Many of these molecules also possess selectivity against other steroidogenic cytochromes P450 (e.g. CYP17A1 and CYP19A1) as well as hepatic drug metabolizing P450s. Though not as well developed or explored, inhibitors of CYP11B1, with selectivities approaching 50-fold, have also been identified. The therapeutic benefits of affecting the renin-angiotensin-aldosterone system have been well established with the therapeutically useful angiotensin-converting enzymes inhibitors, angiotensin receptor blockers, and mineralocorticoid receptor antagonists. Data regarding the additional benefits of an aldosterone synthase inhibitor (ASi) are beginning to emerge from animal models and human clinical trials. Despite great promise and much progress, additional challenges still exist in the path towards development of a therapeutically useful ASi. © 2013 Bentham Science Publishers.
  • Author:
    Nagao S
    Title:
    Acceleration factor for propagation of a stationary wave in its wave medium: Movement of energy in the 3-D space
    Source:
    J Phys Conf Ser 442 (1) art no 012067 (2013)
    Abstract:
    According to the formerly reported 4-D spherical model of the time and universe, any energy in the 3-dimensional space is a vibration of the intrinsic space energy. There is a special frame stationary to the space energy and the principle of relativity is no longer valid. Accordingly, abandonment of the Special Relativity and then introduction of a factor of acceleration for energy in the 3-D space are proposed. © Published under licence by IOP Publishing Ltd.
  • Author:
    Latli B; Haddad N; Hrapchak M; Wei X; Tang W; Song JJ; Senanayake CH
    Title:
    Sodium-proton exchanger isoform-1: Synthesis of a potent inhibitor labeled with deuterium and carbon-14
    Source:
    Curr Radiopharm 6 (1), 7-11 (2013)
    Abstract:
    Sodium-proton exchangers, NHEs are plasma membrane proteins that are essential in the regulation of intracellular pH of the myocardium. There are nine known variously expressed isoforms of NHEs with NHE-1 being the predominant isoform in the heart. N-[4-(1-acetyl-piperidin-4-yl)-3-trifluoromethyl-benzoyl]-guanidine (1) is a potent NHE 1inhibitor with good pharmacokinetics. It was prepared labeled with deuterium and carbon-14 to aid in drug metabolism, pharmacokinetics, and other studies. The combination of Comins' reaction and reduction under deuterium gas was used to access deuterium labeled (1) starting from deuterium labeled pyridine. Carbon-14 labeled zinc cyanide was used to prepare [14C]-(1) in three steps, with a specific activity of 55.6 mCi/mmol. © 2013 Bentham Science Publishers.
  • Author:
    Ghosh P; Vahedipour K; Lin M Vogel; JH Haynes C; von Lieres E
    Title:
    Computational fluid dynamic simulation of axial and radial flow membrane chromatography: Mechanisms of non-ideality and validation of the zonal rate model
    Source:
    J Chromatogr A 1305, 114-122 (2013)
    Abstract:
    Membrane chromatography (MC) is increasingly being used as a purification platform for large biomolecules due to higher operational flow rates. The zonal rate model (ZRM) has previously been applied to accurately characterize the hydrodynamic behavior in commercial MC capsules at different configurations and scales. Explorations of capsule size, geometry and operating conditions using the model and experiment were used to identify possible causes of inhomogeneous flow and their contributions to band broadening. In the present study, the hydrodynamics within membrane chromatography capsules are more rigorously investigated by computational fluid dynamics (CFD). The CFD models are defined according to precisely measured capsule geometries in order to avoid the estimation of geometry related model parameters. In addition to validating the assumptions and hypotheses regarding non-ideal flow mechanisms encoded in the ZRM, we show that CFD simulations can be used to mechanistically understand and predict non-binding breakthrough curves without need for estimation of any parameters. When applied to a small-scale axial flow MC capsules, CFD simulations identify non-ideal flows in the distribution (hold-up) volumes upstream and downstream of the membrane stack as the major source of band broadening. For the large-scale radial flow capsule, the CFD model quantitatively predicts breakthrough data using binding parameters independently determined using the small-scale axial flow capsule, identifying structural irregularities within the membrane pleats as an important source of band broadening. The modeling and parameter determination scheme described here therefore facilitates a holistic mechanistic-based method for model based scale-up, obviating the need of performing expensive large-scale experiments under binding conditions. As the CFD model described provides a rich mechanistic analysis of membrane chromatography systems and the ability to explore operational space, but requires detailed knowledge of internal capsule geometries and has much greater computational requirements, it is complementary to the previously described strengths and uses of the ZRM for process analysis and design. © 2013 Elsevier B.V.
  • Author:
    Sakamoto A; Matsumaru T; Yamamura N; Uchida Y; Tachikawa M; Ohtsuki S; Terasaki T
    Title:
    Quantitative expression of human drug transporter proteins in lung tissues: Analysis of regional, gender, and interindividual differences by liquid chromatography-tandem mass spectrometry
    Source:
    J Pharm Sci 102 (9), 3395-3406 (2013)
    Abstract:
    The purpose of the present study was to clarify the expression levels of transporter proteins in human lung tissue and to analyze regional and interindividual differences in primary cultured epithelial cells. Organic cation/carnitine tranporter 1 (OCTN1) protein expression was highest (2.08 ± 1.19 fmol/.g protein) in human lung tissue, followed by multidrug resistance-associated protein 1 (MRP1) and breast cancer resistance protein expression (1.41 ± 0.41, 1.30 ± 1.29 fmol/.g protein, respectively). Interestingly, the same expression levels of OATP2B1 protein were demonstrated among the epithelial cells derived from all pulmonary regions for the first time. These results suggest that OCTN1 may be the best target transporter protein for pulmonary disease drug design, and OATP2B1 may be an alternative target. MRP1 protein expression was also high and mainly localized in bronchial and alveolar regions. Regarding interindividual differences, the MRP1 protein showed a significant 18-fold maximal difference in the bronchial region among five donors. Sixteen of the 18 transporters showed higher expression in female lungs than in male lungs, especially MRP8 showed a 7.32-fold maximal difference. In conclusion, the protein expression profiles of pulmonary drug transporters and regional, gender, and interindividual differences were clarified. These findings may provide significant insights for pulmonary disease drug design and indicate that administration by inhalation may be viable. © 2013 Wiley Periodicals, Inc.
  • Author:
    Nijmeijer S; Engelhardt H; Schultes S; Van De Stolpe AC; Lusink V; De Graaf C; Wijtmans M; Haaksma EEJ; De Esch IJP; Stachurski K; Vischer HF; Leurs R
    Title:
    Design and pharmacological characterization of VUF14480, a covalent partial agonist that interacts with cysteine 983.36 of the human histamine H4 receptor
    Source:
    Br J Pharmacol 170 (1), 89-100 (2013)
    Abstract:
    Background and Purpose The recently proposed binding mode of 2-aminopyrimidines to the human (h) histamine H4 receptor suggests that the 2-amino group of these ligands interacts with glutamic acid residue E1825.46 in the transmembrane (TM) helix 5 of this receptor. Interestingly, substituents at the 2-position of this pyrimidine are also in close proximity to the cysteine residue C983.36 in TM3. We hypothesized that an ethenyl group at this position will form a covalent bond with C983.36 by functioning as a Michael acceptor. A covalent pyrimidine analogue will not only prove this proposed binding mode, but will also provide a valuable tool for H4 receptor research. Experimental Approach We designed and synthesized VUF14480, and pharmacologically characterized this compound in hH4 receptor radioligand binding, G protein activation and .-arrestin2 recruitment experiments. The ability of VUF14480 to act as a covalent binder was assessed both chemically and pharmacologically. Key Results VUF14480 was shown to be a partial agonist of hH4 receptor-mediated G protein signalling and .-arrestin2 recruitment. VUF14480 bound covalently to the hH4 receptor with submicromolar affinity. Serine substitution of C983.36 prevented this covalent interaction. Conclusion and Implications VUF14480 is thought to bind covalently to the hH4 receptor-C983.36 residue and partially induce hH4 receptor-mediated G protein activation and .-arrestin2 recruitment. Moreover, these observations confirm our previously proposed binding mode of 2-aminopyrimidines. VUF14480 will be a useful tool to stabilize the receptor into an active confirmation and further investigate the structure of the active hH4 receptor. Linked Articles This article is part of a themed issue on Histamine Pharmacology Update. To view the other articles in this issue visit http://dx.doi.org/10.1111/bph.2013. 170.issue-1 © 2013 The Authors. British Journal of Pharmacology © 2013 The British Pharmacological Society.
  • Author:
    Nolte Dr T; Rogerson Dr P; Mukaratirwa Dr S; Deschl Prof Dr U
    Title:
    Beta 2-adrenergic agonists
    Source:
    Veröffentlichung auf der CD "Classical Examples in toxicologic Pathology", 5th edition
  • Author:
    Reeves JT; Tan Z; Marsini MA; Han ZS; Xu Y; Reeves DC; Lee H; Lu BZ; Senanayake CH
    Title:
    A practical procedure for reduction of primary, secondary and tertiary amidesto amines
    Source:
    Adv Synth Catal 355 (1), 47-52 (2013)
    Abstract:
    A mild and general procedure for reduction of primary, secondary, and tertiary amides using catalytic triruthenium dodecacarbonyl and 1,1,3,3-tetramethyldisiloxane as reductant is described. The reaction is tolerant of numerous functional groups, and the amine products can offen be isolated by direct crystallization as hydrochloride salts. The catalyst and silane are commercially available, air stable, and inexpensive, making the procedure accessible for both laboratory and large-scale applications. Copyright© 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
  • Author:
    Busacca CA; Lorenz JC; Saha AK; Cheekoori S; Haddad N; Reeves D; Lee H; Li Z; Rodriguez S; Senanayake CH
    Title:
    Development ofthe BIPIIigands for asymmetric hydrogenation
    Source:
    Catalysis 2 (10), 2083-2089 (2012)
    Abstract:
    The detailed development of unique BIPI ligands suitable for asymmetric hydrogenation is described, and the process research leading to their kilogram-scale manufacture is discussed. Full optimization of each Iigand region is shown, and the complete design features for these ligands are explained. Application of the best members of this Iigand class to asymmetric hydrogenations of ureaesters, BOC- and CBZ-enecarbamates, and a variety of enamides are described. A novel resolution of P-chiralligand precursors via their zinc complexes is described, and the research leading to the discovery of catalysts capable of carrying out asymmetric hydrogenations in >99% ee at multi-kilogram scale are presented. © 2012 The Royal Society of Chemistry.
  • Author:
    Buckle DR; Erhardt PW; Ganellin CR; Kobayashi T; Perun TJ; Proudfoot J; Senn-Bilfinger J
    Title:
    Glossary of terms used in medicinal chemistry. Part II (IUPAC recommendations 2013)
    Source:
    Pure Appl Chem 85 (8), 1725-1758 (2013)
    Abstract:
    The evolution that has taken place in medicinal chemistry practice as a result of major advances in genomics and molecular biology arising from the Human Genome Project has carried with it an extensive additional working vocabulary that has become both integrated and essential terminology for the medicinal chemist. Some of this augmented terminology has been adopted from the many related and interlocked scientific disciplines with which the modern medicinal chemist must be conversant, but many other terms have been introduced to define new concepts and ideas as they have arisen. In this supplementary Glossary, we have attempted to collate and define many of the additional terms that are now considered to be essential components of the medicinal chemist's expanded repertoire. © 2013 IUPAC.
  • Author:
    Wüster T; Kaczybura N; Brückner R; Keller M
    Title:
    Synthesis of enantiomerically pure model compounds of the glucose-6-phosphate-T1-translocase inhibitors kodaistatins A-D. Inferences with regard to the stereostructure of the natural products
    Source:
    Tetrahedron 69 (36), 7785-7809 (2013)
    Abstract:
    The kodaistatins A and C (5a,b) inhibit a step in glucose-metabolism at .100 nM concentrations. This makes them potential 'leads' in the therapy of diabetes. We elucidated the (S)-configuration of the side-chain stereocenter of kodaistatin A by ozonolysis/reduction. The 13C NMR shifts of kodaistatin A model cis-11 suggest that the diol moiety in the dihydroxycyclopentanone core of kodaistatin is trans-configured. This model was prepared from the Feringa lactone (21) and (S)-2-methylbutanal (27) in 23 steps (14 steps in the longest linear sequence). We employed the same strategy for the simplified kodaistatin A model iso-cis-12, which resulted from the same substrates in 11 steps (6 steps in the longest linear sequence). The cyclopentenone cores of both targets stemmed from a C4+C1 approach. The C4 components were masked 'tartaric ketones' (16a,b) and a masked 'tartaric aldehyde' (18), respectively. The C1 components were the lithium-derivatives of the side-chain bearing phosphonates 19 and 22, respectively. The desired acylation/deprotonation/Horner-Wadsworth- Emmons tandem reaction succeeded in a single operation with the 'tartaric aldehyde' 18 but required partly or exclusively additional operations when we incorporated the 'tartaric ketones' 16a or 16b, respectively. The 'tartaric ketones' 16a,b contained an .-siloxyethyl substituent. It is noteworthy that it had to be introduced by adding the benzyltrimethylammonium enolate of lactone 18 to acetaldehyde because the lithium enolate of this lactone fragmented by an acetone-releasing .-elimination. © 2013 Elsevier Ltd. All rights reserved.
  • Author:
    Tautermann C S
    Title:
    Target based virtual screening by docking into automatically generated GPCR models.
    Source:
    Methods Mol Biol 914, 255-270 (2012)
    Abstract:
    Target based virtual screening (VS) combined with high-throughput measurements is an extremely useful tool to identify small molecule hits for proteins and in particular for G-protein coupled receptors (GPCRs). However, this is a quite difficult process for GPCRs due to the paucity of 3D structural information on these receptors. Therefore, the only possibility for target based VS is to build a structural model of the GPCR to be used for docking. However, GPCR model building is a very time consuming process, if the model should be able to explain allexperimental findings and this investment is not always justified, if the model is only used for VS. Thus, a fully automated workflow is presented here, where a large number of GPCR models is built, and the best model is identified to be used for docking. The workflow Ieads to moderate enrichments with a very low effort. The inputs required are the sequence of the targeted GPCR, a reference Iigand with experimental information and a database of small molecules to be used for docking. Manual intervention is recommended at various points, but it is strictly speaking not necessary.
  • Author:
    Beaulieu PL; Coulombe R; Gillard J; Brochu C; Duan J; Garneau M; Jolicoeur E; Kuhn P; Poupart M-A; Rancourt J; Stammers TA; Thavonekham B; Kukolj
    Title:
    Allosteric N-acetamide-indole-6-carboxylic acid thumb pocket 1 inhibitors of hepatitis C virus NS5B polymerase­ Acylsulfonamides and acylsulfamides as carboxylic acid replacements
    Source:
    Can J Chem 91 (1), 66-81 (2013)
    Abstract:
    Acylsulfonamide and acylsulfamide as surrogates for the carboxylic acid function of N-acetamide-indole-6-carboxylic acids were evaluated as allosteric inhibitors of hepatitis C virus (HCV) NS5B polymerase. Several analogs displayed excellent antiviral potency against both 1a and 1b HCV genotypes in cell-based subgenomic replicon assays. Structure-activity relationships (SAR) are discussed in the context of the crystal structure of an inhibitor-NS5B polymerase complex. Absorption, distribution, metabolism, and excretion pharmacokinetic (ADME-PK) properties of this class of inhibitors are also described. © 2012 Published by NRC Research Press.
  • Author:
    Gorham L; Just S; Kramer G; Corradini L; Doods H
    Title:
    Molecular mechanisms contributing to the analgesia of SSTR4 agonists.
    Source:
    Deutscher Schmerzkongress 2013
  • Author:
    Pochert A; Bergman L; Stiller D; Rasche V; Linden M
    Title:
    Hollew mesoparaus silica spheres as 19F-MRI imaging agents
    Source:
    World Molecular lmaging Congress 2013, Savannah, USA,Sep 2013
  • Author:
    Carrero-Gonzalez L; Tibiletti M; Kirchherr A; Gehrke N; Kaulisch T; Briel A; Rasche V; Stiller D
    Title:
    (Dynamic) Contrast-enhanced MRI of pulmonary perfusion
    Source:
    World Molecular lmaging Congress 2013,Savannah, USA, Sep 2013
  • Author:
    Kirchherr A; Kaulisch T; Stiller D; Briel A
    Title:
    Novel MRI Blood Pool Agents with different Chemical Structures: An in vivo Comparison
    Source:
    World Molecular Imaging Congress 2013,Savannah, USA, Sep 2013
    Abstract:
    -
  • Author:
    Stiller D
    Title:
    µJCT in animal models of lung diseases
    Source:
    International workshop on Jung targeting and imaging, Bordeaux, France, Sep 30- Oct 2, 2013
    Abstract:
    -
  • Author:
    Hoffmann L; Nubbemeyer U
    Title:
    A Novel Approach towards Equisetin Analog Syntheses
    Source:
    Poster for Dechema-Naturstofftagung 1st European Conference on Natural Products,Frankfurt, Germany, Sep 22-25,2013
    Abstract:
    -
  • Author:
    Kerdawy A E; Tautermann C S; Clark T; Fox T
    Title:
    An Economical and Aceurate Protocol for Calculating Hydrogen-Bond Acceptor Strengths
    Source:
    Gordon Research Conference "Computer-Aided Drug Design" Mt. Snow Resort, West Dover, VT, USA, Jul 21-25, 2013
    Abstract:
    -
  • Author:
    Kerdawy A E; Tautermann C S; Clark T; Fox T
    Title:
    An Economical and Aceurate Protocol for Calculating Hydrogen-Bond Acceptor Strengths
    Source:
    49th Symposium on Theoretical Chemistry - Bridging Scales in Theoretical Chemistry, Erlangen, Germany, Sep 22-26, 2013
    Abstract:
    -
  • Author:
    Phadke M; Haarberg H E; Sini P; Smalley K SM
    Title:
    BI847325 (BI5) reverses aquired BRAF inhibitor resistance throuh dual inhibition of MEK and CDK6
    Source:
    Society for Melanoma Research 2013 Congress, Philadelphia, Pennsylvania, USA, Nov 17-20, 2013
  • Author:
    Krämer O
    Title:
    Selection of Compound Subsets for Hit Identification in Cancer Drug Discovery
    Source:
    Frontiers in Medicinal Chemistry, San Francisco, USA, Jun 23-26, 2013
  • Author:
    Ishiguro N; Kishimoto W; Volz A; Ludwig-Schwellinger E; Ebner T; Schaefer O
    Title:
    Impact of Endogenous Esterase Activity on In Vitro P-gp profiling of Dabigatran Etexilate in Caco-2-monolayers
    Source:
    JSSX, Oct 2013
  • Author:
    Earnshaw WC; Allshire RC; Black BE; Bloom K; Brinkley BR; Brown W; Cheeseman IM; Choo KHA; Copenhaver GP; Deluca JG; Desai A; Diekmann S; Erhardt S; Fitzgerald-Hayes M; Foltz D; Fukagawa T; Gassmann R; Gerlich DW; Glover DM; Gorbsky GJ; Harrison SC; Heun P; Hirota T; Jansen LET; Karpen G; Kops GJPL; Lampson MA; Lens SM; Losada A; Luger K; Maiato H; Maddox PS; Margolis RL; Masumoto H; McAinsh AD; Mellone BG; Meraldi P; Musacchio A; Oegema K; O'Neill RJ; Salmon ED; Scott KC; Straight AF; Stukenberg PT; Sullivan BA; Sullivan KF; Sunkel CE; Swedlow JR; Walczak CE; Warburton PE; Westermann S; Willard HF; Wordeman L; Yanagida M; Yen TJ; Yoda K; Cleveland DW
    Title:
    Esperanto for histones: CENP-A, not CenH3, is the centromeric histone H3 variant
    Source:
    Chromosome Res 21 (2), 101-106 (2013)
    Abstract:
    The first centromeric protein identified in any species was CENP-A, a divergent member of the histone H3 family that was recognised by autoantibodies from patients with scleroderma-spectrum disease. It has recently been suggested to rename this protein CenH3. Here, we argue that the original name should be maintained both because it is the basis of a long established nomenclature for centromere proteins and because it avoids confusion due to the presence of canonical histone H3 at centromeres. © 2013 The Author(s).
  • Author:
    Mair B; Popow J; Mechtler K; Weitzer S; Martinez J
    Title:
    Intron excision from precursor tRNA molecules in mammalian cells requires ATP hydrolysis and phosphorylation of tRNA-splicing endonuclease components
    Source:
    Biochem Soc Trans 41 (4), 831-837 (2013)
    Abstract:
    The process of tRNA splicing entails removal of an intron by TSEN (tRNA-splicing endonuclease) and ligation of the resulting exon halves to generate functional tRNAs. In mammalian cells, the RNA kinase CLP1 (cleavage and polyadenylation factor I subunit) associates with TSEN and phosphorylates the 3; exon at the 5' end in vitro, suggesting a role for CLP1 in tRNA splicing. Interestingly, recent data suggest that the ATP-binding and/or hydrolysis capacity of CLP1 is required to enhance pre-tRNA cleavage. In vivo, the lack of CLP1 kinase activity leads to progressive motor neuron loss and accumulation of novel 5' leader-5' exon tRNA fragments. We have extended the investigation of the biochemical requirements in pre-tRNA splicing and found that .- . -hydrolysable ATP is crucial for the productive generation of exon halves. In addition, we provide evidence that phosphorylation of the TSEN complex components supports efficient pre-tRNA cleavage. Taken together, our data improve the mechanistic understanding of mammalian pre-tRNA processing and its regulation. © 2013 Biochemical Society.
  • Author:
    Laplante SR; Bilodeau F; Aubry N; Gillard JR; O'Meara J; Coulombe R
    Title:
    N- versus O-alkylation: Utilizing NMR methods to establish reliable primary structure determinations for drug discovery
    Source:
    Bioorg Med Chem Lett 23 (16), 4663-4668 (2013)
    Abstract:
    A classic synthetic issue that remains unresolved is the reaction that involves the control of N- versus O-alkylation of ambident anions. This common chemical transformation is important for medicinal chemists, who require predictable and reliable protocols for the rapid synthesis of inhibitors. The uncertainty of whether the product(s) are N- and/or O-alkylated is common and can be costly if undetermined. Herein, we report an NMR-based strategy that focuses on distinguishing inhibitors and intermediates that are N- or O-alkylated. The NMR strategy involves three independent and complementary methods. However, any combination of two of the methods can be reliable if the third were compromised due to resonance overlap or other issues. The timely nature of these methods (HSQC/HMQC, HMBC. ROESY, and 13C shift predictions) allows for contemporaneous determination of regioselective alkylation as needed during the optimization of synthetic routes. © 2013 Elsevier Ltd. All rights reserved.
  • Author:
    Lu Bruce Z; Li Guisheng; Rodriguez Sonia; LiuJianxu; Eriksson Magnus C; Tan Zhulin; Song Jinhua J; Yee Nathank; Senanayake Chris H
    Title:
    Development of a practical synthesis of 4-[6-(morpholinomethyl)-pyridin-3- yl]naphthalen-1-amine, a key intermediate for the synthesis of birb 1017,a potent p38 map kinase inhibitor.
    Source:
    Synlett 24 (3), 317-322 (2013)
    Abstract:
    The development of synthetic routes to 4-[6-(morpholinomethyl)pyridin-3-yl] naphthalen-1-amine, the key intermediate of p38 MAP kinase inhibitor BIRB 1017, via (1) trialkylmagnesium ate complex mediated metalation and borylation followed by Suzuki coupling reactions and (2) pyridine-ring formation from a vinamidinium salt, is described. .COPYRGT. Georg Thieme Verlag Stuttgart
  • Author:
    Liu JR; Jensen-Kondering UR; Zhou JJ; Sun F; Feng XY; Shen XL; Deuschl G; Jansen O; Herdegen T; Meyne J; Zhao Y; Eschenfelder C
    Title:
    Transient filament occlusion of the middle cerebral artery in rats: does the reperfusion method matter 24 hours after perfusion?
    Source:
    BMC Neurosci 13 (2012)
    Abstract:
    BACKGROUND: There are two widely used transient middle cerebral artery occlusion (MCAO) methods, which differ in the use of unilateral or bilateral carotid artery reperfusion (UNICAR and BICAR). Of the two methods, UNICAR is easier to perform. This study was designed to comprehensively compare the two reperfusion methods to determine if there are any differences in outcomes. RESULTS: The UNICAR and BICAR groups each included 9 rats. At baseline, the average pO(2) was 20.54 ± 9.35 and 26.43 ± 7.39, for the UNICAR and BICAR groups, respectively (P = 0.519). Changes in pO(2), as well as other physiological parameters measured within the ischemic lesion, were similar between the UNICAR and BICAR groups during 90 min of MCAO and the first 30 min of reperfusion (all P > 0.05). Furthermore, both the Bederson score and Garcia score, which are used for neurological assessment, were also similar (both P > 0.05). There were also no significant differences in T2WI lesion volume, DWI lesion volume, PWI lesion volume, or TTC staining infarct volume between the two groups (all P > 0.05). CONCLUSION: UNICAR and BICAR have similar capability for inducing acute brain ischemic injury and can be considered interchangeable up to 24 hours after reperfusion.
  • Author:
    Hwang Soo Seok; Kim Young Uk; Lee Sumin; Jang Sung Woong; Kim Min Kyung; Koh Byung Hee; Lee Wonyong; Lee Gap Ryol
    Title:
    Transcription factor YY1 is essential for regulation of the Th2 cytokine locus and for Th2 cell differentiation
    Source:
    Proc Natl Acad Sci USA 110 (1), 276-281 (2013)
    Abstract:
    The Th2 locus control region (LCR) has been shown to be important in efficient and coordinated cytokine gene regulation during Th2 cell differentiation. However, the molecular mechanism for this is poorly understood. To study the molecular mechanism of the Th2 LCR, we searched for proteins binding to it. We discovered that transcription factor YY1 bound to the LCR and the entire Th2 cytokine locus in a Th2-specific manner. Retroviral overexpression of YY1 induced Th2 cytokine expression. CD4-specific knockdown of YY1 in mice caused marked reduction in Th2 cytokine expression, repressed chromatin remodeling, decreased intrachromosomal interactions, and resistance in an animal model of asthma. YY1 physically associated with GATA-binding protein-3 (GATA3) and is required for GATA3 binding to the locus. YY1 bound to the regulatory elements in the locus before GATA3 binding. Thus, YY1 cooperates with GATA3 and is required for regulation of the Th2 cytokine locus and Th2 cell differentiation.
  • Author:
    Lampert Fabienne; Mieck Christine; Alushin Gregory M; Nogales Eva; Westermann Stefan
    Title:
    Molecular requirements for the formation of a kinetochore-microtubule interface by Dam1 and Ndc80 complexes.
    Source:
    J Cell Biol 200 (1), 21-30 (2013)
    Abstract:
    Kinetochores are large protein complexes that link sister chromatids to the spindle and transduce microtubule dynamics into chromosome movement. In budding yeast, the kinetochore-microtubule interface is formed by the plus end-associated Dam1 complex and the kinetochore-resident Ndc80 complex, but how they work in combination and whether a physical association between them is critical for chromosome segregation is poorly understood. Here, we define structural elements required for the Ndc80-Dam1 interaction and probe their function in vivo. A novel ndc80 allele, selectively impaired in Dam1 binding, displayed growth and chromosome segregation defects. Its combination with an N-terminal truncation resulted in lethality, demonstrating essential but partially redundant roles for the Ndc80 N-tail and Ndc80-Dam1 interface. In contrast, mutations in the calponin homology domain of Ndc80 abrogated kinetochore function and were not compensated by the presence of Dam1. Our experiments shed light on how microtubule couplers cooperate and impose important constraints on structural models for outer kinetochore assembly.
  • Author:
    van Wieringen Jan-Peter; Booij Jan; Shalgunov Vladimir; Elsinga; Philip Michel; Martin C
    Title:
    Agonist high- and low-affinity states of dopamine D-2 receptors: methods of detection and clinical implications.
    Source:
    Naunyn Schmiedebergs Arch Pharmacol 386 (2), 135-154 (2013)
    Abstract:
    Dopamine D(2) receptors, similar to other G-protein-coupled receptors, exist in a high- and low-affinity state for agonists. Based upon a review of the methods for detecting D(2) receptor agonist high-affinity states, we discuss alterations of such states in animal models of disease and the implications of such alterations for their labelling with positron emission tomography (PET) and single-photon emission computed tomography (SPECT) tracers. The classic approach of detecting agonist high-affinity states compares agonist competition for antagonist radioligands, in most cases using [(3)H]-spiperone as the radioligand; alternative approaches and radioligands have been proposed, but their claimed advantages have not been substantiated by other investigators. In view of the advantages and disadvantages of various techniques, we critically have reviewed reported findings on the detection of D(2) receptor agonist high-affinity states in a variety of animal models. These data are compared to the less numerous findings from human in vivo studies based on PET and SPECT tracers; they are interpreted in light of the finding that D(2) receptor agonist high-affinity states under control conditions may differ between rodent and human brain. The potential advantages of agonist ligands in studies of pathophysiology and as diagnostics are being discussed.
  • Author:
    Lewis Nuruddeen D; Haxhinasto Sokol A; Anderson Shawn M; Stefanopoulos Dimitria E; Fogal Steven E; Adusumalli Prathima; Desai Sudha N; Patnaude Lori A; Lukas Susan M; Ryan Kelli R; Slavin Anthony J; Brown Maryanne L; Modis Louise K
    Title:
    Circulating Monocytes Are Reduced by Sphingosine-1-Phosphate Receptor Modulators Independently of S1P3.
    Source:
    J Immunol 190 (7), 3533-3540 (2013)
    Abstract:
    Sphingosine-1-phosphate (S1P) receptors are critical for lymphocyte egress from secondary lymphoid organs, and S1P receptor modulators suppress lymphocyte circulation. However, the role of S1P receptors on monocytes is less clear. To elucidate this, we systematically evaluated monocytes in rats and mice, both in naive and inflammatory conditions, with S1P receptor modulators FTY720 and BAF312. We demonstrate that S1P receptor modulators reduce circulating monocytes in a similar time course as lymphocytes. Furthermore, total monocyte numbers were increased in the spleen and bone marrow, suggesting that S1P receptor modulation restricts egress from hematopoietic organs. Monocytes treated ex vivo with FTY720 had reduced CD40 expression and TNF-. production, suggesting a direct effect on monocyte activation. Similar reductions in protein expression and cytokine production were also found in vivo. Suppression of experimental autoimmune encephalomyelitis in mice and rats by FTY720 correlated with reduced numbers of lymphocytes and monocytes. These effects on monocytes were independent of S1P3, as treatment with BAF312, a S1P1,4,5 modulator, led to similar results. These data reveal a novel role for S1P receptors on monocytes and offer additional insights on the mechanism of action of S1P receptor modulators in disease.
  • Author:
    Zhao Q; Li C; Senanayake CH; Tang W
    Title:
    An Efficient Method for Sterically Demanding Suzuki-Miyaura Coupling Reactions
    Source:
    Chemistry (Weinheim) 19 (7), 2261-2265 (2013)
    Abstract:
    An efficient method for sterically demanding Suzuki-Miyaura coupling reactions has been developed with two catalysts, Pd/BI-DIME (see scheme) and Pd/phenanthrene-based ligand. The Pd/BI-DIME catalyst facilitates the syntheses of extremely hindered biaryls bearing ortho-isopropyl substituents. The other catalyst is efficient for the synthesis of functionalized tetra-ortho-substituted biaryls at low catalyst loadings.
  • Author:
    Haug K G; Lehr T; Staab A
    Title:
    Development and validation of a semi-physiological model of amyloid-.beta. biosynthesis and degradation in human cerebrospinal fluid including the impact of the .gamma.-secretase inhibitor semagacestat.
    Source:
    Clin Pharmacol Ther 93 (1), S75 (2013)
    Abstract:
    BACKGROUND: Accumulation of amyloid-.beta. (A.beta.) in the central nervous system is believed to play a crucial role in Alzheimer's disease (AD). Stable isotope labeling kinetics (SILK) was successfully applied to quantify endogenous A.beta. synthesis and clearance in human cerebrospinal fluid (CSF) [1]. A mathematical model implementing key physiological processes to describe A.beta. biosynthesis and degradation in human CSF should be developed and validated, including the impact of the .gamma.-secretase inhibitor (GSI) semagacestat on A.beta. production. METHODS: Mean CSF semagacestat and A.beta.1-x concentrationtime profiles following a SILK study were digitized from published data [2]. Model building was performed stepwise utilizing NONMEM VI. The final model was validated by predicting three individual A.beta. profiles available from literature [1]. RESULTS: The average A.beta. profile was best described by a semi-physiological model. Following labeled leucine infusion, A.beta. biosynthesis was adequately characterized by six transit compartments. At each transition step, a first-order degradation process was implemented. Clearance of A.beta. from CSF followed a first-order process with an estimated half-life of 8.3-9 h. A two-compartment model with first-order elimination best described CSF semagacestat concentration- time profiles. In the final combined model, the impact of the GSI was incorporated by linking semagacestat concentrations to the last transition during A.beta. production by means of an inhibitory Emax model. Three individual A.beta. profiles were successfully predicted utilizing the final model. CONCLUSION: Based on limited literature data, a mathematical model to quantify the physiological processes of A.beta. synthesis and clearance in human CSF was developed and validated. The final model may serve as a valuable tool for the investigation of AD pathophysiology as well as for the future design of clinical studies applying the SILK methodolog
  • Author:
    Gazda L; Pokrzywa W; Hellerschmied D; Löwe T Forné I; Mueller-Planitz F; Hoppe T; Clausen T
    Title:
    The myosin chaperone UNC-45 is organized in tandem modules to support myofilament formation in C. elegans.
    Source:
    Cell 152 (1-2), 183-195 (2013)
    Abstract:
    The UCS (UNC-45/CRO1/She4) chaperones play an evolutionarily conserved role in promoting myosin-dependent processes, including cytokinesis, endocytosis, RNA transport, and muscle development. To investigate the protein machinery orchestrating myosin folding and assembly, we performed a comprehensive analysis of Caenorhabditis elegans UNC-45. Our structural and biochemical data demonstrate that UNC-45 forms linear protein chains that offer multiple binding sites for cooperating chaperones and client proteins. Accordingly, Hsp70 and Hsp90, which bind to the TPR domain of UNC-45, could act in concert and with defined periodicity on captured myosin molecules. In vivo analyses reveal the elongated canyon of the UCS domain as a myosin-binding site and show that multimeric UNC-45 chains support organization of sarcomeric repeats. In fact, expression of transgenes blocking UNC-45 chain formation induces dominant-negative defects in the sarcomere structure and function of wild-type worms. Together, these findings uncover a filament assembly factor that directly couples myosin folding with myofilament formation.
  • Author:
    Wellenzohn B; Lessel U; Beller A; Isambert T; Hoenke C; Nosse B
    Title:
    Identification of New Potent GPR119 Agonists by Combining Virtual Screening and Combinatorial Chemistry
    Source:
    J Med Chem 55 (24), 11031-11041 (2012)
    Abstract:
    Virtual screening in a huge collection of virtual combinatorial libraries has led to the identification of two new structural classes of GPR119 agonists with submicromolar in vitro potencies. Herein, we describe the virtual screening process involving feature trees fragment space searches followed by a 3D postprocessing step. The in silico findings were then filtered and prioritized, and finally, combinatorial libraries of target molecules were synthesized. Furthermore the so-called "activity-anchor principle" is introduced as an element to increase the chance to generate true hits. An activity anchor is a structural element expected to provide key contributions to a certain biological activity. Application of this technique has led to the discovery of two new GPR119-agonist hit series, one of which was further optimized to progress as a novel lead class.
  • Author:
    Reeves Jonathan T; Tan Zhulin; Marsini Maurice A; Han Zhengxu S; Xu Yibo; Reeves Diana C; Lee Heewon; Lu Bruce Z; Senanayakea Chris H
    Title:
    A Practical Procedure for Reduction of Primary, Secondary and Tertiary Amides to Amines
    Source:
    Adv Synth Catal 355 (1), 47-52 (2013)
    Abstract:
    A mild and general procedure for reduction of primary, secondary, and tertiary amides using catalytic triruthenium dodecacarbonyl and 1,1,3,3-tetramethyldisiloxane as reductant is described. The reaction is tolerant of numerous functional groups, and the amine products can often be isolated by direct crystallization as hydrochloride salts. The catalyst and silane are commercially available, air stable, and inexpensive, making the procedure accessible for both laboratory and large-scale applications.
  • Author:
    Tremblay S; Pelletier A; Ribadeneira M; SturinoC; Mason S; Lamorte L; Bethell R; Rajotte D
    Title:
    Discovery of a Novel HIV-1 Nucleotide Competing RT Inhibitor Series.
    Source:
    Intersci Conf Antimicrob Agents Chemother Program Abstr 52 H556a (2012)
    Abstract:
    -
  • Author:
    Okle O; Stemmer K; Deschl U; Dietrich DR
    Title:
    (L)-BMAA Induced ER Stress and Enhanced Caspase 12 Cleavage in Human Neuroblastoma SH-SY5Y Cells at Low Nonexcitotoxic Concentrations
    Source:
    Toxicol Sci 131 (1), 217-224 (2013)
    Abstract:
    The cyanobacterial .-N-methylamino-L-alanine (L-BMAA) is described as a low-potency excitotoxin, possibly a factor in the increased incidence of amyotrophic lateral sclerosis (ALS) and Parkinsonism-dementia complex (PDC) in Guam. The latter association is intensively disputed, as L-BMAA concentrations required for toxic effects exceed those assumed to occur via food. The question thus was raised whether L-BMAA leads to neurodegeneration at nonexcitotoxic conditions. Using human SH-SY5Y neuroblastoma cells, L-BMAA-transport, incorporation into proteins, and subsequent impairment of cellular protein homeostasis were investigated. Binding of L-BMAA to intracellular proteins, but no clear protein incorporation was detected in response to (14)C-L-BMAA exposures. Nevertheless, low L-BMAA concentrations (. 0.1mM, 48 h) increased protein ubiquitination, 20S proteasomal and caspase 12 activity, expression of the endoplasmic reticulum (ER) stress marker CHOP, and enhanced phosphorylation of elf2. in SH-SY5Y cells. In contrast, high L-BMAA concentrations (. 1mM, 48 h) increased reactive oxygen species and protein oxidization, which were partially ameliorated by coincubation with vitamin E. L-BMAA-mediated cytotoxicity was observable 48 h following . 2mM L-BMAA treatment. Consequently, the data presented here suggest that low L-BMAA concentrations result in a dysregulation of the cellular protein homeostasis with ensuing ER stress that is independent from high-concentration effects such as excitotoxicity and oxidative stress. Thus, the latter could be a contributing factor in the onset and slow progression of ALS/PDC in Guam.
  • Author:
    Whelan G; Kreidl E; Peters JM; Eichele G
    Title:
    The non-redundant function of cohesin acetyltransferase Esco2 Some answers and new questions
    Source:
    Nucleus-Austin 3 (4), 330-334 (2012)
    Abstract:
    Cohesin and cohesin regulatory proteins function in an essential pathway enabling proper cohesion and segregation of sister chromatids. Additionally, these proteins are involved in double-strand break (DSB) repair and transcriptional regulation. Mutations in Establishment of cohesion 1 homolog 2 (Esco2), an evolutionary conserved cohesin acetyltransferase, are the cause of Roberts syndrome (RBS), a human congenital disorder. To explore the mechanism by which the deficiency in Esco2 affects cohesin's functions, we generated a mouse harboring a conditional Esco2 allele. To our surprise and in marked contrast to RBS, mouse Esco2 turns out to be a cell viability factor, the absence of which results in severe chromosome segregation defects and apoptosis. We found that the acetylation of the cohesin subunit Smc3 is significantly reduced in Esco2-deficient cells resulting in a marked reduction of Sororin recruitment to several, but not all cohesin bound loci. Here, we provide evidence that Esco2 is also required for DSB repair, which is consistent with previous studies in RBS cells.
  • Author:
    Schultes S; Engelhardt H; Roumen L; Zuiderveld OP; Haaksma EE; de Esch IJ; Leurs R; de Graaf C
    Title:
    Combining Quantum Mechanical Ligand Conformation Analysis and Protein Modeling to Elucidate GPCR-Ligand Binding Modes
    Source:
    ChemMedChem 8 (1), 49-53 (2013)
    Abstract:
    SAR beyond protein-ligand interactions: By combining structure-affinity relationships, protein-ligand modeling studies, and quantum mechanical calculations, we show that ligand conformational energies and basicity play critical roles in ligand binding to the histamine H4 receptor, a GPCR that plays a key role in inflammation. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
  • Author:
    Groselj Uros; Podlogar Anja; Novak Ana; Golobic Amalija; Stanovnik Branko; Svete Jurij
    Title:
    Synthesis of Tetrahydropyrazolo[1,5-c]pyrimidine-2,7(1H,3H)-diones
    Source:
    Synthesis 45 (5), 639-650 (2013)
  • Author:
    Moreau Benoit; O'Meara Jeff A; Bordeleau Josee; Garneau Michel; Godbout Cedrickx; Gorys Vida; Leblanc Melissa; Villemure Elisia; White Peter W; Llinas-Brunet Montse
    Title:
    Discovery of Hepatitis C Virus NS3-4A Protease Inhibitors with Improved Barrier to Resistance and Favorable Liver Distribution
    Source:
    J Med Chem (2013)
    Abstract:
    Given the emergence of resistance observed for the current clinical-stage hepatitis C virus (HCV) NS3 protease inhibitors, there is a need for new inhibitors with a higher barrier to resistance. We recently reported our rational approach to the discovery of macrocyclic acylsulfonamides as HCV protease inhibitors addressing potency against clinically relevant resistant variants. Using X-ray crystallography of HCV protease variant/inhibitor complexes, we shed light on the complex structural mechanisms by which the D168V and R155K residue mutations confer resistance to NS3 protease inhibitors. Here, we disclose SAR investigation and ADME/PK optimization leading to the identification of inhibitors with significantly improved potency against the key resistant variants and with increased liver partitioning.
  • Author:
    Zhang Yongda; Li Ning; Qu Bo Ma; Shengli; Lee Heewon; Gonnella Nina C; Gao Joe; Li Wenjie; Tan Zhulin; Reeves Jonathan T; Wang Jun; Lorenz Jon C; Li Guisheng; Reeves Diana C; Premasiri Ajith; Grinberg Nelu; Haddad Nizar; Lu Bruce Z; Song Jinhua J; Senanayake Chris H
    Title:
    Asymmetric Methallylation of Ketones Catalyzed by a Highly Active Organocatalyst 3,3'-F2-BINOL
    Source:
    Org Lett 15 (7), 1710-1713 (2013)
    Abstract:
    (S)-3,3'-F2-BINOL has been synthesized for the first time and demonstrated as a highly active organocatalyst for asymmetric methallylation of ketones.Up to 98:2 enantioselectivity and 99% yield were obtained with 5 mol % catalyst loading. The catalyst (S)-3,3'-F2-BINOL could be easily recovered and reused.
  • Author:
    Goudreau Nathalie; Lemke Christopher T; Faucher Anne-Marie; Grand-Maitre Chantal; Goulet Sylvie; Lacoste Jean-Eric; Rancourt Jean; Malenfant Eric; Mercier Jean-Francois; Titolo Steve; Mason Stephen W
    Title:
    Novel Inhibitor Binding Site Discovery on HIV-1 Capsid N-Terminal Domain by NMR and X-ray Crystallography.
    Source:
    ACS Chem Biol (2013)
    Abstract:
    The HIV-1 capsid (CA) protein, a domain of Gag, which participates in formation of both the mature and immature capsid, represents a potential target for anti-viral drug development. Characterization of hits obtained via high-throughput screening of an in vitro capsid asse mbly assay led to multiple compounds having this potential. We previo usly presented the characterization of two inhibitor series that bind the N-terminal domain of the capsid (CANTD), at a site located at the bottom of its helical bundle, often referred to as the CAP-1 binding s ite. In this work we characterize a novel series of benzimidazole hit s. Initial optimization of this series led to compounds with improved in vitro assembly and anti-viral activity. Using NMR spectroscopy we found that this series binds to a unique site on CANTD, located at the apex of the helical bundle, well removed from previously characterized binding sites for CA inhibitors. 2D (1)H-(15)N HSQC and (19)F NMR sho wed that binding of the benzimidazoles to this distinct site does not affect the binding of either cyclophilin A (CypA) to the CypA-binding loop or a benzodiazepine-based CA assembly inhibitor to the CAP-1 site Unfortunately, while compounds of this series achieved promising in vitro assembly and anti-viral effects, they also were found to be qui te sensitive to a number of naturally occurring CANTD polymorphisms ob served among clinical isolates. Despite the negative impact of this f inding for drug development, the discovery of multiple inhibitor binding si tes on CANTD shows that capsid assembly is much more complex than prev iously realized.
  • Author:
    Mulder JA; Frutos RP; Patel ND; Qu B Sun X; Tampone TG; Gao J; Sarvestani M; Eriksson MC; Haddad N; Shen S; Song JJ; Senanayake CH
    Title:
    Development of a safe and economical synthesis of methyl 6-chloro-5-(trifluoromethyl)nicotinate: Trifluoromethylation on kilogram scale
    Source:
    Org Process Res Dev 17 (6), 940-945 (2013)
    Abstract:
    Reported herein is a safe and economical synthesis of methyl 6-chloro-5-(trifluoromethyl)nicotinate, an intermediate in the synthesis of novel anti-infective agents. The key to this process is the trifluoromethylation of an aryl iodide using an inexpensive methyl chlorodifluoroacetate (MCDFA)/KF/CuI system, with an emphasis on the development work which led to this effective process. © 2013 American Chemical Society.
  • Author:
    Han ZS; Herbage MA; Mangunuru HPR; Xu Y; Zhang L; Reeves JT; Sieber JD; Li Z; Decroos P; Zhang Y; Li G; Li N; Ma S; Grinberg N; Wang X; Goyal N; Krishnamurthy D; Lu B; Song JJ; Wang G; Senanayake CH
    Title:
    Design and synthesis of chiral oxathiozinone scaffolds: Efficient synthesis of hindered enantiopure sulfinamides and sulfinyl ketimines
    Source:
    Angew Chem Int Ed 52 (26), 6713-6717 (2013)
    Abstract:
    Is that S-O? The title scaffolds have a highly active and properly differentiated S-O bond for the efficient synthesis of enantiopure sulfinamides. The method is practical, green, and has the potential to provide an economical commercial process for the synthesis of bulky sulfinamides. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
  • Author:
    Bonderoff SA; Grant TN; West FG; Tremblay M
    Title:
    Nazarov reactions of vinyl cyclopropylamines: An approach to the imino-nazarov problem
    Source:
    Org Lett 15 (11), 2888-2891 (2013)
    Abstract:
    Dichlorocyclopropanation of 2-amino-1,3-dienes affords 1-alkenyl-1-amino-2, 2-dichlorocyclopropanes which undergo silver-assisted 2-. electrocyclic opening to furnish 3-aminopentadienyl cations. Nazarov-type cyclization of these intermediates leads to cyclopentenone iminium salts, which provide allylic amines upon reduction. This process, the imino version of the traditional Nazarov reaction, can also be combined with an interrupted Nazarov domino process to give polycyclic amines. © 2013 American Chemical Society
  • Author:
    Zhang Y; Li N; Goyal N; Li G; Lee H; Lu BZ; Senanayake CH
    Title:
    Solvent-free methallylboration of ketones accelerated by tert-alcohols
    Source:
    J Org Chem 78 (11), 5775-5781 (2013)
    Abstract:
    A solvent- and metal-free process has been developed for the direct methallylboration of ketones employing the stable B-methallylborinane 1, which was accelerated by tertiary alcohols. In the presence of 2.0 equiv of readily available tertiary alcohols such as tert-amyl alcohol, the methallylation products were prepared at room temperature in excellent yields. The salient features of the described process include simple operation, high efficiency, and mild reaction conditions. © 2013 American Chemical Society.
  • Author:
    Frutos RP; Wei X; Patel ND; Tampone TG; Mulder JA; Busacca CA; Senanayake CH
    Title:
    One-pot synthesis of 2,5-disubstituted pyrimidines from nitriles
    Source:
    J Org Chem 78 (11), 5775-5781 (2013)
    Abstract:
    A practical, one-step process for the synthesis of 2,5-disubstituted pyrimidines is presented. The protocol proved to be general for the synthesis of a variety of pyrimidine-containing compounds bearing an assortment of functional groups. © 2013 American Chemical Society.
  • Author:
    LaPlante SR; Bilodeau F; Aubry N; Gillard JR; O'Meara J; Coulombe R
    Title:
    Compound aggregation in drug discovery: Implementing a practical NMR assay for medicinal chemists
    Source:
    Bioorg Med Chem Lett article in press (2013)
    Abstract:
    A classic synthetic issue that remains unresolved is the reaction that involves the control of N- versus O-alkylation of ambident anions. This common chemical transformation is important for medicinal chemists, who require predictable and reliable protocols for the rapid synthesis of inhibitors. The uncertainty of whether the product(s) are N- and/or O-alkylated is common and can be costly if undetermined. Herein, we report an NMR-based strategy that focuses on distinguishing inhibitors and intermediates that are N- or O-alkylated. The NMR strategy involves three independent and complementary methods. However, any combination of two of the methods can be reliable if the third were compromised due to resonance overlap or other issues. The timely nature of these methods (HSQC/HMQC, HMBC. ROESY, and 13C shift predictions) allows for contemporaneous determination of regioselective alkylation as needed during the optimization of synthetic routes. © 2013 Elsevier Ltd. All rights reserved.
  • Author:
    Beaulieu PL; Coulombe R; Duan J; Fazal G; Godbout C; Hucke O; Jakalian A; Joly M-A; Lepage O; Llinàs-Brunet M; Naud J; Poirier M; Rioux N; Thavonekham B; Kukolj G; Stammers TA
    Title:
    Structure-based design of novel HCV NS5B thumb pocket 2 allosteric inhibitors with submicromolar gt1 replicon potency: Discovery of a quinazolinone chemotype
    Source:
    Bioorg Med Chem Lett 23 (14), 4132-4140 (2013)
    Abstract:
    We describe the structure-based design of a novel lead chemotype that binds to thumb pocket 2 of HCV NS5B polymerase and inhibits cell-based gt1 subgenomic reporter replicons at sub-micromolar concentrations (EC50 <200 nM). This new class of potent thumb pocket 2 inhibitors features a 1H-quinazolin-4-one scaffold derived from hybridization of a previously reported, low affinity thiazolone chemotype with our recently described anthranilic acid series. Guided by X-ray structural information, a key NS5B-ligand interaction involving the carboxylate group of anthranilic acid based inhibitors was replaced by a neutral two-point hydrogen bonding interaction between the quinazolinone scaffold and the protein backbone. The in vitro ADME and in vivo rat PK profile of representative analogs are also presented and provide areas for future optimization of this new class of HCV polymerase inhibitors. © 2013 Elsevier Ltd. All rights reserved.
  • Author:
    Bailey MD; Bordeleau J; Garneau M; Leblanc M; Lemke CT; O'Meara J; White PW; Llinàs-Brunet M
    Title:
    Peptide backbone replacement of hepatitis C virus NS3 serine protease C-terminal cleavage product analogs: Discovery of potent succinamide inhibitors
    Source:
    Bioorg Med Chem Lett 23 (15), 4447-4452 (2013)
    Abstract:
    A number of potent peptidic inhibitors of the NS3 protease have been described in the literature based on a substrate-based approach. In an on-going effort to reduce the peptidic character of this class of inhibitors, two novel series of analogs have been prepared in which the usual P3 amino acid residue is replaced by a succinamide fragment. This new backbone modification not only reduces the peptidic nature of traditional inhibitors but also provides new SAR opportunities for the capping group. Optimization of each of these two series resulted in inhibitors with sub-nanomolar potencies. © 2013 Elsevier Ltd. All rights reserved.
  • Author:
    Steven P; Vickers Sharon C; Cheetham Katie; R Headland; Keith Dickinson; Rolf Grempler; Eric Mayoux; Michael Mark; Thomas Klein
    Title:
    Combination of the SGLT2 inhibitor, empagliflozin, with orlistat or sibutramine further improves the body weight reduction and glucose homeostasis of obese rats fed a cafeteria diet.
  • Author:
    Taylor SJ; Padyana AK; Abeywardane A; Liang S; Hao M-H; De Lombaert S; Proudfoot J; Farmer BS; Li X; Collins B; Martin L; Albaugh DR; Hill-Drzewi M; Pullen SS; Takahashi H
    Title:
    Discovery of potent, selective chymase inhibitors via fragment linking strategies
    Source:
    J Med Chem 56 (11), 4465-4481 (2013)
    Abstract:
    Chymase plays an important and diverse role in the homeostasis of a number of cardiovascular processes. Herein, we describe the identification of potent, selective chymase inhibitors, developed using fragment-based, structure-guided linking and optimization techniques. High-concentration biophysical screening methods followed by high-throughput crystallography identified an oxindole fragment bound to the S1 pocket of the protein exhibiting a novel interaction pattern hitherto not observed in chymase inhibitors. X-ray crystallographic structures were used to guide the elaboration/linking of the fragment, ultimately leading to a potent inhibitor that was >100-fold selective over cathepsin G and that mitigated a number of liabilities associated with poor physicochemical properties of the series it was derived from. © 2013 American Chemical Society.
  • Author:
    Engelhardt H; Schultes S; De Graaf C; Nijmeijer S; Vischer HF; Zuiderveld OP; Dobler J; Stachurski K; Mayer M; Arnhof H; Scharn D; Haaksma EEJ; De Esch IJP; Leurs R
    Title:
    Bispyrimidines as potent histamine H4 receptor ligands: Delineation of structure-activity relationships and detailed H4 receptor binding mode
    Source:
    J Med Chem 56 (11), 4264-4276 (2013)
    Abstract:
    The basic methylpiperazine moiety is considered a necessary substructure for high histamine H4 receptor (H4R) affinity. This moiety is however also the metabolic hot spot for various classes of H4R ligands (e.g., indolcarboxamides and pyrimidines). We set out to investigate whether mildly basic 2-aminopyrimidines in combination with the appropriate linker can serve as a replacement for the methylpiperazine moiety. In the series of 2-aminopyrimidines, the introduction of an additional 2-aminopyrimidine moiety in combination with the appropriate linker lead to bispyrimidines displaying pKi values for binding the human H4R up to 8.2. Furthermore, the methylpiperazine replacement results in compounds with improved metabolic properties. The attempt to transfer the knowledge generated in the class of bispyrimidines to the indolecarboxamides failed. Combining the derived structure-activity relationships with homology modeling leads to new detailed insights in the molecular aspects of ligand-H4R binding in general and the binding mode of the described bispyrimidines in specific. © 2013 American Chemical Society.
  • Author:
    Zhang Yongda; Li Ning; Qu Bo; Ma Shengli; Lee Heewon; Gonnella Nina C; Gao Joe; Li Wenjie; Tan Zhulin; Reeves Jonathan T; Wang Jun; Lorenz Jon C; Li Guisheng Reeves; Diana C Premasiri; Ajith Grinberg; Nelu Haddad; Nizar Lu; Bruce Z; SongJinhua J; Senanayake Chris H
    Title:
    Asymmetric Methallylation of Ketones Catalyzed by a Highly Active Organocatalyst 3,3 '-F-2-BINOL.
    Source:
    Org Lett 15 (7), 1523-7052 (2013)
    Abstract:
    (S)-3,3'-F-2-BINOL has been synthesized for the first time and demonstrated as a highly active organocatalyst for asymmetric methallylation of ketones. Up to 98:2 enantioselectivity and 99% yield were obtained with 5 mol % catalyst loading. The catalyst (S)-3,3'-F-2-BINOL could be easily recovered and reused.
  • Author:
    Rioux N; Batonga J; Colombo F; Massé J; Zouki C; Ribadeneira MD; Duan J; Bethell RC
    Title:
    A simplified approach to predict CYP3A-mediated drug-drug interactions at early drug discovery: Validation with clinical data
    Source:
    Xenobiotica 43 (7), 592-597 (2013)
    Abstract:
    1. The present study evaluates which factors should be incorporated into a simplified approach to reasonably predict CYP3A-mediated drug-drug interaction (DDI) at an early drug discovery stage. 2. CYP3A IC50 values were obtained using human liver microsomes (HLM) and hepatocytes. Plasma and microsomal protein binding and in vitro hepatocyte partition coefficient (Kp) were also determined for 10 drugs. Therapeutic human maximum plasma concentrations (Cmax) were retrieved from the literature. DDI predictions were performed using an equation incorporating the fraction of the substrate metabolized by CYP3A with the total or free plasma Cmax, with or without correction for hepatocyte Kp. 3. Based on the Ki data from HLM, the use of total Cmax provided a prediction of DDI within 2-fold of the observed clinical values for 9 out of 10 drugs. 4. In comparison, free drug corrections for both Cmax and Ki values from HLM led to an underprediction of DDI (>3-fold error for five drugs). 5. Data from hepatocytes showed, in general, lower prediction accuracy than data from HLM. 6. CYP3A-mediated DDIs can be predicted with a high level of accuracy based on Ki estimates from HLM data and the total therapeutic plasma Cmax of the inhibitors. This approach should be widely applicable to the assessment of clinically significant DDIs risk in early drug discovery programs © 2013 Informa UK Ltd. All rights reserved.
  • Author:
    Beaulieu PL; Coulombe R; Duan J; Fazal G; Godbout C; Hucke O; Jakalian A; Joly M-A; Lepage O; Llinàs-Brunet M; Naud J; Poirier M; Rioux N; Thavonekham B; Kukolj G; Stammers TA
    Title:
    Structure-based design of novel HCV NS5B thumb pocket 2 allosteric inhibitors with submicromolar gt1 replicon potency: Discovery of a quinazolinone chemotype
    Source:
    Bioorg Med Chem Lett Article in press (2013)
    Abstract:
    We describe the structure-based design of a novel lead chemotype that binds to thumb pocket 2 of HCV NS5B polymerase and inhibits cell-based gt1 subgenomic reporter replicons at sub-micromolar concentrations (EC50 <200 nM). This new class of potent thumb pocket 2 inhibitors features a 1H-quinazolin-4-one scaffold derived from hybridization of a previously reported, low affinity thiazolone chemotype with our recently described anthranilic acid series. Guided by X-ray structural information, a key NS5B-ligand interaction involving the carboxylate group of anthranilic acid based inhibitors was replaced by a neutral two-point hydrogen bonding interaction between the quinazolinone scaffold and the protein backbone. The in vitro ADME and in vivo rat PK profile of representative analogs are also presented and provide areas for future optimization of this new class of HCV polymerase inhibitors. © 2013 Elsevier Ltd. All rights reserved.
  • Author:
    Bailey MD; Bordeleau J; Garneau M; Leblanc M; Lemke CT; O'Meara J; White PW; Llinàs-Brunet M
    Title:
    Peptide backbone replacement of hepatitis C virus NS3 serine protease C-terminal cleavage product analogs: Discovery of potent succinamide inhibitors
    Source:
    Bioorg Med Chem Lett Article in press (2013)
    Abstract:
    A number of potent peptidic inhibitors of the NS3 protease have been described in the literature based on a substrate-based approach. In an on-going effort to reduce the peptidic character of this class of inhibitors, two novel series of analogs have been prepared in which the usual P3 amino acid residue is replaced by a succinamide fragment. This new backbone modification not only reduces the peptidic nature of traditional inhibitors but also provides new SAR opportunities for the capping group. Optimization of each of these two series resulted in inhibitors with sub-nanomolar potencies. © 2013 Elsevier Ltd. All rights reserved.
  • Author:
    Sturino CF; Bousquet Y; James CA; Deroy P; Duplessis M; Edwards PJ; Halmos T; Minville J; Morency L; Morin S; Thavonekham B; Tremblay M; Duan J; Ribadeneira M; Garneau M; Pelletier A; Tremblay S; Lamorte L; Bethell R; Cordingley MG; Rajotte D; Simoneau B
    Title:
    Identification of potent and orally bioavailable nucleotide competing reverse transcriptase inhibitors: In vitro and in vivo optimization of a series of benzofurano[3,2-d]pyrimidin-2-one derived inhibitors
    Source:
    Bioorg Med Chem Lett 23 (13), 3967-3975 (2013)
    Abstract:
    Recently, a new class of HIV reverse transcriptase (HIV-RT) inhibitors has been reported. The novel mechanism of inhibition by this class involves competitive binding to the active site of the RT enzyme and has been termed Nucleotide-Competing Reverse Transcriptase Inhibitors (NcRTIs). In this publication we describe the optimization of a novel benzofurano[3,2-d]pyrimidin- 2-one series of NcRTIs. The starting point for the current study was inhibitor 2, which had high biochemical and antiviral potency but only moderate permeability in a Caco-2 assay and high B-to-A efflux, resulting in moderate rat bioavailability and low Cmax. We present herein the results and strategies we employed to optimize both the potency as well as the permeability, metabolic stability and pharmacokinetic profile of this series. One of the key observations of the present study was the importance of shielding polar functionality, at least in the context of the current chemotype, to enhance permeability. These studies led to the identification of inhibitors 39 and 45, which display sub-nanomolar antiviral potency in a p24 ELISA assay with significantly reduced efflux ratios (ratios <1.5). These inhibitors also display excellent rat pharmacokinetic profiles with high bioavailabilities and low clearance. © 2013 Elsevier Ltd. All rights reserved.
  • Author:
    Mayoux,Eric
    Title:
    SGLT2 inhibitor empagliflozin attenuates hyperglycemia, kidney growth, and albuminuria and prevents glomerular hyperfiltration in diabetic Akita mice.
  • Author:
    Mayoux E
    Title:
    SGLT2 inhibition only excretes 50-60% of filtered glucose in euglycemic mice because of compensation by SGLT1.
  • Author:
    Beck B
    Title:
    BioProfile - Extract knowledge about compound cross reactivities from corporate databases
    Source:
    Abstract 6th Joint Sheffield Conference an Chemoinformatics 22nd-24th July, 2013
    Abstract:
    In the last two decades, many new technologies and approaches have been implemented in research in the pharmaceutical industry. These include high-throughput screening and combinatorial chemistry, which result in a rapidly growing number of biological assay and structural data in the corporate databases. Efficient use of the data from this growing data mountain is a key success factor. Here we describe an approach, initiated several years ago, to obtain as much information as possible from historical assay data stored in the corporate database. Both primary-screen and dose-response data are used. lt will be shown how important a careful preprocessing of the data is for enhancing its information content. The preconditioned data is used to analyze the relation between assays, cross reactivities of compounds in a given hit set, or for frequent hitter analysis. The preprocessing workflow and some sample applications are described.
  • Author:
    Löhle A; Stadler N; Pautsch A; Schnapp G
    Title:
    Expression, purification and crystallisation Glucokinase regulatory protein (GKRP)
    Source:
    Protein production workshop, Oxford, Jul 1-3, 2013, Organized by the Structural Genomics Consortium Oxford
  • Author:
    Reeves J T; Tan Z; Senanayake C H
    Title:
    Copper-catalyzed annulation of 2-formylazoles with aminoiodopyrazoles: Synthesis of new heterocyclic ring systems
    Source:
    J Heterocyclic Chem 50 (3), 680-683 (2013)
    Abstract:
    Various 2-formylazoles underwent CuI/sparteine-catalyzed annulation with 1-substituted-4-iodo-5-aminopyrazoles to produce four new heterocyclic ring systems. The reaction was demonstrated for 2-formylpyrroles, 2-formylindoles, 2-formylimidazole, and 3-methyl-5-formylpyrazole. 3-Substitution of the iodopyrazole was tolerated. © 2013 HeteroCorporation.
  • Author:
    Lemke C T; Titolo S; Goudreau N; Faucher A M; Mason S W; Bonneau P
    Title:
    A novel inhibitor-binding site on the HIV-1 capsid N-terminal domain leads to improved crystallization via compound-mediated dimerization
    Source:
    Crystallogr Sect D Biol Crystallogr 69 (6), 1115-1123 (2013)
    Abstract:
    Nck links phosphotyrosine-based signaling to Arp2/3-dependent actin polymerization during many different cellular processes as well as actin-based motility of enteropathogenic Escherichia coli (EPEC) [1, 2], vaccinia [3, 4], and other vertebrate poxviruses [5] by interacting with N-WASP/WASP [6, 7]. Nck also binds WASP-interacting protein (WIP) [8], which inhibits the ability of N-WASP to activate the Arp2/3 complex until it receives an appropriate signaling input [9, 10]. Using mouse embryonic fibroblasts (MEFs) lacking Nck, WIP, or N-WASP [3, 11, 12], we have investigated whether an interaction of Nck with both WIP and N-WASP is required for their recruitment to vaccinia during Arp2/3-dependent actin assembly. We find that WIP or its homolog WIRE is required for N-WASP recruitment and actin-based motility of the virus. WIP contains two Nck-binding sites and is recruited to the virus, bound to N-WASP, by interacting with the second SH3 domain of Nck. N-WASP also contains two Nck-binding sites, but its recruitment is dependent on its interaction with WIP rather than Nck. The first and third SH3 domains of Nck are not required to recruit the WIP:N-WASP complex but are essential to stimulate actin assembly. We have established that WIP acts as an essential link between Nck and N-WASP. Our observations provide important insights into the hierarchy and connections in one of the major cellular signaling networks stimulating Arp2/3 complex-dependent actin polymerization. © 2013 Elsevier Ltd.
  • Author:
    Kimura T; Ohta H; Wada K; Jinno K; Ueta I; Saito Y
    Title:
    Molecular Shape Selectivity for Polycyclic Aromatic Compounds on a Core-Shell Octadecylsilica Stationary Phase at Subambient Column Temperatures
    Source:
    Chromatographia, 1-7 Article in Press (2013)
    Abstract:
    Molecular shape selectivity for polycyclic aromatic compounds on a core-shell-type octadecylsilica (ODS) phase at subambient column temperatures was studied in reversed-phase liquid chromatography. The plate height on the core-shell ODS column was relatively stable at subambient column temperatures when compared with that of a conventional ODS column. In order to compare the sample diffusivities in the conventional and core-shell ODS columns, van Deemter plots were prepared. The plate height of the core-shell column was significantly lower than that of conventional column, suggesting an advantageous feature of the core-shell-type stationary phase especially at a high flowrate of the mobile phase. An enhanced molecular shape recognition capability of the core-shell ODS phase was also confirmed at subambient column temperature. The result could be consistent with an improved shape selectivity as normally observed on conventional ODS phases at low temperatures, however, the enhanced molecular shape recognition capability of the core-shell phase enables a good separation between benz[a]anthracene and chrysene at subambient column temperatures. Similar improved shape selectivities for terphenyl isomers were also confirmed on the core-shell phase. © 2013 Springer-Verlag Berlin Heidelberg.
  • Author:
    Hörer S; Reinert D; Ostmann K; Hoevels Y; Nar H
    Title:
    Crystal-contact engineering to obtain a crystal form of the Kelch domain of human Keap1 suitable for ligand-soaking experiments
    Source:
    Acta Crystallogr Sect F Struct Biol Cryst Commun 69 (6), 592- 596 (2013)
    Abstract:
    Keap1 is a substrate adaptor protein for a Cul3-dependent ubiquitin ligase complex and plays an important role in the cellular response to oxidative stress. It binds Nrf2 with its Kelch domain and thus triggers the ubiquitinylation and degradation of Nrf2. Oxidative stress prevents the degradation of Nrf2 and leads to the activation of cytoprotective genes. Therefore, Keap1 is an attractive drug target in inflammatory diseases. The support of a medicinal chemistry effort by structural research requires a robust crystallization system in which the crystals are preferably suited for performing soaking experiments. This facilitates the generation of protein-ligand complexes in a routine and high-throughput manner. The structure of human Keap1 has been described previously. In this crystal form, however, the binding site for Nrf2 was blocked by a crystal contact. This interaction was analysed and mutations were introduced to disrupt this crystal contact. One double mutation (E540A/E542A) crystallized in a new crystal form in which the binding site for Nrf2 was not blocked and was accessible to small-molecule ligands. The crystal structures of the apo form of the mutated Keap1 Kelch domain (1.98 Å resolution) and of the complex with an Nrf2-derived peptide obtained by soaking (2.20 Å resolution) are reported. © 2013 International Union of Crystallography. All rights reserved.
  • Author:
    Tautermann C; Christ C; Bodnachuk M
    Title:
    Grand Canonical Monte Carlo Calculations on PTK2
    Source:
    To bes sent to academic collaborator as feedback on his calculations
  • Author:
    Wagner K G; Frank K J
    Title:
    Dataset of 10 terminated compounds, consiting of physicochemical data, formulation data preclinical and clinical data, as well as informations about the methods and media.
    Source:
    Database of the IMI-project: OrBiTo (oral biopharmaceutics tools). A description of the project and the setup of the database is provided in the attachments.
  • Author:
    Friedl Dr T; Frank Dr K
    Title:
    Combining biopharmaceutical information from preclinical models for further project advancement into 7 IN man trials
    Source:
    Oral presentation at the "5th World conference an drug absorption, transport and delivery (WCDATD): Responding to challenging situations"
  • Author:
    Ma S; Grinberg N; Haddad N; Rodriguez S; Busacca CA; Fandrick K; Lee H; Song JJ; Yee N; Krishnamurthy D; Senanayake CH; Wang J; Trenck J; Mendonsa S; Claise PR; Gilman RJ; Evers TH
    Title:
    Heart-cutting two-dimensional ultrahigh-pressure liquid chromatography for process development: Asymmetric reaction monitoring
    Source:
    Org Process Res Dev 17 (5), 806-810 (2013)
    Abstract:
    This contribution presents the first application of two-dimensional, ultrahigh-pressure liquid chromatography (2D-UHPLC) for monitoring asymmetric reactions in process development. Several asymmetric transformations were studied to illustrate the operation of the instrument and evaluate the performance of 2D-UHPLC. Two-dimensional UHPLC is particularly advantageous because it allows a simultaneous analysis of the reaction conversion and its enantiomeric excess. By employing UHPLC the analysis time can be reduced significantly, and the achiral-chiral 2D coupling approach allows for direct injection of the reaction mixture. This study demonstrates the utility of 2D-UHPLC in asymmetric transformations for drug development. © 2013 American Chemical Society.
  • Author:
    Busacca CA; Qu B; Gret N; Fandrick KR; Saha AK; Marsini M; Reeves D; Haddad N; Eriksson M; Wu J-P; Grinberg N; Lee H; Li Z; Lu B; Chen D; Hong Y; Ma S; Senanayake CH
    Title:
    Tuning the peri effect for enantioselectivity: Asymmetric hydrogenation of unfunctionalized olefins with the BIPI ligands
    Source:
    Adv Synth Catal 355 (8), 1455-1463 (2013)
    Abstract:
    The modular nature of the BIPI ligands allows for systematic optimization of each ligand region. The development of ligands optimized for asymmetric hydrogenation of the challenging unfunctionalized olefin substrate class is described. The naphthyl peri position, C-8, has been identified as a critical stereocontrol element in the design of these ligands. Highly enantioselective ligands suitable for hydrogenation of tri- and tetrasubstituted olefins are detailed. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
  • Author:
    Proudfoot J R
    Title:
    Reaction schemes visualized in network form: The syntheses of strychnine as an example
    Source:
    J Chem Inform Modeling 53 (5), 1035-1042 (2013)
    Abstract:
    Representation of synthesis sequences in a network form provides an effective method for the comparison of multiple reaction schemes and an opportunity to emphasize features such as reaction scale that are often relegated to experimental sections. An example of data formatting that allows construction of network maps in Cytoscape is presented, along with maps that illustrate the comparison of multiple reaction sequences, comparison of scaffold changes within sequences, and consolidation to highlight common key intermediates used across sequences. The 17 different synthetic routes reported for strychnine are used as an example basis set. The reaction maps presented required a significant data extraction and curation, and a standardized tabular format for reporting reaction information, if applied in a consistent way, could allow the automated combination of reaction information across different sources. © 2013 American Chemical Society.
  • Author:
    Décor A; Grand-Maître C; Hucke O; O'Meara J; Kuhn C Forget LC; Brochu C; Malenfant E; Bertrand-Laperle M; Bordeleau J; Ghiro E; Pesant M; Fazal G; Gorys V; Little M; Boucher C; Bordeleau S; Turcotte P; Guo T; Garneau M; Spickler C; Gauthier A
    Title:
    Design, synthesis and biological evaluation of novel aminothiazoles as antiviral compounds acting against human rhinovirus
    Source:
    Bioorg Med Chem Lett Article in Press (2013)
    Abstract:
    We describe here the design, synthesis and biological evaluation of antiviral compounds acting against human rhinovirus (HRV). A series of aminothiazoles demonstrated pan-activity against the HRV genotypes screened and productive structure-activity relationships. A comprehensive investigational library was designed and performed allowing the identification of potent compounds with lower molecular weight and improved ADME profile. 31d-1, 31d-2, 31f showed good exposures in CD-1 mice. The mechanism of action was discovered to be a host target: the lipid kinase phosphatidylinositol 4-kinase III beta (PI4KIIIß). The identification of the pan-HRV active compound 31f combined with a structurally distinct literature compound T-00127-HEV1 allowed the assessment of target related tolerability of inhibiting this kinase for a short period of time in order to prevent HRV replication. © 2013 Elsevier Ltd. All rights reserved.
  • Author:
    Belval R; Alamir A; Corte C; DiValentino J; Fernandes J; Frerking S; Jenkins D; Rogers G; Sanville-Ross M; Sledziona C; Taylor P
    Title:
    Conception through build of an automated liquids processing system for compound management in a low-humidity environment.
    Source:
    J Lab Automat 17 (6), 458-468 (2012)
    Abstract:
    Boehringer Ingelheim's Automated Liquids Processing System (ALPS) in Ridgefield, Connecticut, was built to accommodate all compound solution-based operations following dissolution in neat DMSO. Process analysis resulted in the design of two nearly identical conveyor-based subsystems, each capable of executing 1400 × 384-well plate or punch tube replicates per batch. Two parallel-positioned subsystems are capable of independent execution or alternatively executed as a unified system for more complex or higher throughput processes. Primary ALPS functions include creation of high-throughput screening plates, concentration-response plates, and reformatted master stock plates (e.g., 384-well plates from 96-well plates). Integrated operations included centrifugation, unsealing/piercing, broadcast diluent addition, barcode print/application, compound transfer/mix via disposable pipette tips, and plate sealing. ALPS key features included instrument pooling for increased capacity or fail-over situations, programming constructs to associate one source plate to an array of replicate plates, and stacked collation of completed plates. Due to the hygroscopic nature of DMSO, ALPS was designed to operate within a 10% relativity humidity environment. The activities described are the collaborative efforts that contributed to the specification, build, delivery, and acceptance testing between Boehringer Ingelheim Pharmaceuticals, Inc. and the automation integration vendor, Thermo Scientific Laboratory Automation (Burlington, ON, Canada).
  • Author:
    Reeves J T; Tan Z; Lu B Z; Senanayake C H
    Title:
    Copper-catalyzed annulation of 2-formylazoles with aminoiodopyrazoles: Synthesis of new heterocyclic ring systems
    Source:
    J Heterocyclic Chem Article in Press (2013)
    Abstract:
    Various 2-formylazoles underwent CuI/sparteine-catalyzed annulation with 1-substituted-4-iodo-5-aminopyrazoles to produce four new heterocyclic ring systems. The reaction was demonstrated for 2-formylpyrroles, 2-formylindoles, 2-formylimidazole, and 3-methyl-5-formylpyrazole. 3-Substitution of the iodopyrazole was tolerated. © 2013 HeteroCorporation.
  • Author:
    Rajotte D; Tremblay S; Pelletier A; Salois P; Bourgon L; Coulombe R; Mason S; Lamorte L; Sturino C F; Bethell R
    Title:
    Identification and characterization of a novel HIV-1 nucleotide-competing reverse transcriptase inhibitor series
    Source:
    Antimicrob Agents Chemother 57 (6), 2712-2718 (2013)
    Abstract:
    Several groups have recently reported on the identification of nucleotide-competing reverse transcriptase inhibitors (NcRTIs), a new class of RT inhibitors. NcRTIs reversibly inhibit binding of the incoming nucleotide to the RT active site but do not act as chain terminators, unlike the nucleos(t)ide reverse transcriptase inhibitor (NRTI) class. We identified a novel benzo[4,5]furo[3,2,d]pyrimidin-2-one NcRTI chemical series. Structure-activity relationship evaluation of this series with both RT and viral replication assays led to the identification of compound A, a new NcRTI. Compound A inhibited HIV-1 RT in a primer extension assay (50% inhibitory concentration, 2.6 nM) but had no measurable activity against human DNA polymerase ± at 10 ?M. It potently inhibited HIV-1 replication in vitro (50% effective concentration, 1.5 nM). The antiviral potency of compound A was unaffected by the presence of nonnucleotide RT inhibitor (NNRTI) mutations tested (L100I, K103N/Y181C, V106A, or Y188L). Notably, viruses encoding K65R were hypersusceptible to inhibition by compound A. Compound A also retained full activity against viruses encoding M184V. In vitro selection for resistant virus to compound A led to the selection of a single substitution within RT: W153L. A recombinant virus encoding the RT W153L was highly resistant to compound A (fold change, 160). W153 is a highly conserved residue in HIV RT and has not been previously associated with drug resistance. In summary, a novel NcRTI series with optimized antiviral activity, minimal cross-resistance to existing RT inhibitor classes, and a distinct resistance profile has been discovered. These results further establish NcRTIs as an emerging class of antiretroviral agents. Copyright © 2013, American Society for Microbiology. All Rights Reserved.
  • Author:
    Thai K; Langdon S M; Bilodeau F; Gravel M
    Title:
    Highly chemo- and enantioselective cross-benzoin reaction of aliphatic aldehydes and ?-ketoesters
    Source:
    Org Lett 15 (9), 2214-2217 (2013)
    Abstract:
    An electron-deficient, valine-derived triazolium salt is shown to catalyze a highly chemo- and enantioselective cross-benzoin reaction between aliphatic aldehydes and ?-ketoesters. This methodology represents the first high yielding and highly enantioselective intermolecular cross-benzoin reaction using an organocatalyst (up to 94% ee). Further diastereoselective reduction of the products gives access to densely oxygenated compounds with high chemo- and diastereoselectivity. © 2013 American Chemical Society.
  • Author:
    Lu B Z; Wei H X; Zhang W; Dufour M; Li G; Farina V; Senanayake C H
    Title:
    One-pot and regiospecific synthesis of 2,3-disubstituted indoles from 2-bromoanilides via consecutive palladium-catalyzed sonogashira coupling, amidopalladation, and reductive elimination
    Source:
    J Org Chem 78 (9), 4558-4562 (2013)
    Abstract:
    A practical one-pot and regiospecific three-component process for the synthesis of 2,3-disubstituted indoles from 2-bromoanilides was developed via consecutive palladium-catalyzed Sonogashira coupling, amidopalladation, and reductive elimination. © 2013 American Chemical Society.
  • Author:
    Firestone, R A
    Title:
    The low energy of concert in many symmetry-allowed cycloadditions supports a stepwise-diradical mechanism
    Source:
    Int J Chem Kinet 45 (7), 415-428 (2013)
    Abstract:
    The thesis of this paper is that orbital symmetry allowedness does not guarantee concert. The activation energy (Ea) for concerted Diels-Alder and 1,3-dipolar cycloadditions must be substantially lower than that for a stepwise-diradical pathway because the diradical has two fewer bonding electrons than anything on the concerted reaction coordinate, including the transition state. Two bonding electrons provide tens of kcal/mol of stabilization. The difference between the experimental Ea and that for diradicals is called the energy of concert (Econ). If experiment represents concert, Econ must be large, and if it represents diradicals Econ will be very small. In this paper, 42 examples are adduced in which firm experimental data show that Econ = 0. These cycloadditions cannot be concerted. While concert remains possible for all cycioadditions not proven stepwise, there is none with compelling evidence for concert. © 2013 Wiley Periodicals, Inc.
  • Author:
    Reeves J T; Fandrick D R; Tan Z; Song J J; Rodriguez S; Qu B; Kim S; Niemeier O; Li Z; Byrne D; Campbell S; Chitroda A; Decroos P; Fachinger T; Fuchs V; Connella N C; Grinberg N; Haddad N; Jäger B; Lee H; Lorenz J C; Ma S; Narayanan B A Nummy L J; Premasiri A; Roschangar F; Sarvestani M; Shen S; Spinelli E; Sun X; Varsolona R J; Yee N; Brenner M; Senanayake CH
    Title:
    Development of a large scale asymmetric synthesis of the glucocorticoid agonist BI 653048 BS H3PO4
    Source:
    J Org Chem 78 (8), 3616-2635 (2013)
    Abstract:
    The development of a large scale synthesis of the glucocorticoid agonist BI 653048 BS H3PO4 (1·H3PO4) is presented. A key trifluoromethyl ketone intermediate 22 containing an N-(4-methoxyphenyl)ethyl amide was prepared by an enolization/bromine-magnesium exchange/electrophile trapping reaction. A nonselective propargylation of trifluoromethyl ketone 22 gave the desired diastereomer in 32% yield and with dr = 98:2 from a 1:1 diastereomeric mixture after crystallization. Subsequently, an asymmetric propargylation was developed which provided the desired diastereomer in 4:1 diastereoselectivity and 75% yield with dr = 99:1 after crystallization. The azaindole moiety was efficiently installed by a one-pot cross coupling/indolization reaction. An efficient deprotection of the 4-methoxyphenethyl group was developed using H3PO4/anisole to produce the anisole solvate of the API in high yield and purity. The final form, a phosphoric acid cocrystal, was produced in high yield and purity and with consistent control of particle size. © 2013 American Chemical Society.
  • Author:
    Fandrick D R; Reeves J T; Bakonyi J M; Nyalpatla P R; Tan Z; Niemeier O; Akalay D; Fandrick K R; Wohlleben W; Ollenberger S; Song J J; Sun X; Qu B; Haddad N; Sanyal S; Shen S; Ma S; Byme D; Chitroda A; Fuchs V; Narayanan B A; Grinberg N; Lee N; Vrenner M; Senanayake C H
    Title:
    Zinc catalyzed and mediated asymmetric propargylation of trifluoromethyl ketones with a propargyl boronate
    Source:
    J Org Chem 78 (8), 3592-3615 (2013)
    Abstract:
    The development of zinc-mediated and -catalyzed asymmetric propargylations of trifluoromethyl ketones with a propargyl borolane and the N-isopropyl-l-proline ligand is presented. The methodology provided moderate to high stereoselectivity and was successfully applied on a multikilogram scale for the synthesis of the Glucocorticoid agonist BI 653048. A mechanism for the boron-zinc exchange with a propargyl borolane is proposed and supported by modeling at the density functional level of theory. A water acceleration effect on the zinc-catalyzed propargylation was discovered, which enabled a catalytic process to be achieved. Reaction progress analysis supports a predominately rate limiting exchange for the zinc-catalyzed propargylation. A catalytic amount of water is proposed to generate an intermediate that catalyzes the exchange, thereby facilitating the reaction with trifluoromethyl ketones. © 2013 American Chemical Society.
  • Author:
    Riniker S; Barandun L J; Diederich F; Krämer O; Steffen A; Van Gusteren W F
    Title:
    Free enthalpies of replacing water molecules in protein binding pockets
    Source:
    J Comput Aided Mol Des 26 (12), 1293-1309 (2012)
    Abstract:
    Water molecules in the binding pocket of a protein and their role in ligand binding have increasingly raised interest in recent years. Displacement of such water molecules by ligand atoms can be either favourable or unfavourable for ligand binding depending on the change in free enthalpy. In this study, we investigate the displacement of water molecules by an apolar probe in the binding pocket of two proteins, cyclin-dependent kinase 2 and tRNA-guanine transglycosylase, using the method of enveloping distribution sampling (EDS) to obtain free enthalpy differences. In both cases, a ligand core is placed inside the respective pocket and the remaining water molecules are converted to apolar probes, both individually and in pairs. The free enthalpy difference between a water molecule and a CH3 group at the same location in the pocket in comparison to their presence in bulk solution calculated from EDS molecular dynamics simulations corresponds to the binding free enthalpy of CH3 at this location. From the free enthalpy difference and the enthalpy difference, the entropic contribution of the displacement can be obtained too. The overlay of the resulting occupancy volumes of the water molecules with crystal structures of analogous ligands shows qualitative correlation between experimentally measured inhibition constants and the calculated free enthalpy differences. Thus, such an EDS analysis of the water molecules in the binding pocket may give valuable insight for potency optimization in drug design. © 2012 Springer Science+Business Media Dordrecht.
  • Author:
    Reeves J T; Tan Z; Herbage M A; Han Z S; Marsini M A; Li Z; Li G; Xu Y; Fandrick K R; Gonella N C; Campbell S; Ma S; Grinberg N; Lee H; Lu B Z; Senanayake C H
    Title:
    Carbamoyl anion addition to N -sulfinyl imines: Highly diastereoselective synthesis of ?-amino amides
    Source:
    J Am Chem Soc 135 (15), 5565-5568 (2013)
    Abstract:
    Carbamoyl anions, generated from N,N-disubstituted formamides and lithium diisopropylamide, add with high diastereoselectivity to chiral N-sulfinyl aldimines and ketimines to provide alpha -amino amides. The methodology enables the direct introduction of a carbonyl group without the requirement of unmasking steps as with other nucleophiles. The products may be converted to alpa-amino esters or 1,2-diamines. Iterative application of the reaction enabled the stereoselective synthesis of a dipeptide. Spectroscopic and computational studies support an anion structure with ?2 coordination of lithium by the carbonyl group. © 2013 American Chemical Society.
  • Author:
    Fandrick K R; Ogikubo J; Fandrick D R; Patel N D; Saha J; Lee H; Ma S; Grinberg N; Busacca C A; Senanayake C H
    Title:
    Copper-catalyst-controlled site-selective allenylation of ketones and aldehydes with propargyl boronates
    Source:
    Org Lett 15 (6), 1214-1217 (2013)
    Abstract:
    A practical and highly site-selective copper-PhBPE-catalyst-controlled allenylation with propargyl boronates has been developed. The methodology has shown to be tolerant of diverse ketones and aldehydes providing the allenyl adducts in high selectivity. The BPE ligand and boronate substituents were shown to direct the site selectivity for which either propargyl or allenyl adducts can be acquired in high selectivity. A model is proposed that explains the origin of the site selectivity. © 2013 American Chemical Society.
  • Author:
    Taylor S J; Soleymanzadeh F; Muegge I; Akiba I; Taki N; Ueda S; Mainolfi E; Eldrup A B
    Title:
    Deconstruction of sulfonamide inhibitors of the urotensin receptor (UT) and design and synthesis of benzylamine and benzylsulfone antagonists
    Source:
    Bioorg Med Chem Lett 23 (7), 2177-2180 (2013)
    Abstract:
    Potent small molecule antagonists of the urotensin receptor are described. These inhibitors were derived via systematically deconstructing a literature inhibitor to understand the basic pharmacophore and key molecular features required to inhibit the protein receptor. The series of benzylamine and benzylsulfone antagonists herein reported display a combination of nanomolar molecular and cellular potency as well as acceptable in vitro permeability and metabolic stability. © 2013 Elsevier Ltd. All rights reserved.
  • Author:
    James C A; DeRoy P; Duplessis M; Edwards P J; Halmos T; Minville J; Morency L; Morin S Simoneau B; Tremblay M; Bethell R; Cordingley M; Duan J; Lamorte L; Pelletier A; Rajotte D; Salois P; Tremblay S; Sturino C F
    Title:
    Nucleotide competing reverse transcriptase inhibitors: Discovery of a series of non-basic benzofurano[3,2-d]pyrimidin-2-one derived inhibitors
    Source:
    Bioorg Med Chem Lett Article in Press (2013)
    Abstract:
    A HTS screen led to the identification of a benzofurano[3,2-d]pyrimidin-2-one core structure which upon further optimization resulted in 1 as a potent HIV-1 nucleotide competing reverse transcriptase inhibitor (NcRTI). Investigation of the SAR at N-1 allowed significant improvements in potency and when combined with the incorporation of heterocycles at C-8 resulted in potent analogues not requiring a basic amine to achieve antiviral activity. Additional modifications at N-1 resulted in 33 which demonstrated excellent antiviral potency and improved physicochemical properties. © 2013.
  • Author:
    Tremblay M; Bethell R C; Cordingley M G; DeRoy P; Duan J; Duplessis M; Edwards P J; Faucher A M; Halmos T; James C A; Kuhn C; Lacoste J E; Lamorte L; LaPlante S R; Malenfant E; Minville J; Moremcy L; Morin S; Rajotte D; Salois P; Simoneau B; Tremblay S; Sturino C F
    Title:
    Identification of benzofurano[3,2-d]pyrimidin-2-ones, a new series of HIV-1 nucleotide-competing reverse transcriptase inhibitors
    Source:
    Bioorg Med Chem Lett Article in Press (2013)
    Abstract:
    Screening of our sample collection led to the identification of a set of benzofurano[3,2-d]pyrimidine-2-one hits acting as nucleotide-competing HIV-1 reverse transcriptase inhibitiors (NcRTI). Significant improvement in antiviral potency was achieved when substituents were introduced at positions N1, C4, C7 and C8 on the benzofuranopyrimidone scaffold. The series was optimized from low micromolar enzymatic activity against HIV-1 RT and no antiviral activity to low nanomolar antiviral potency. Further profiling of inhibitor 30 showed promising overall in vitro properties and also demonstrated that its potency was maintained against viruses resistant to the other major classes of HIV-1 RT inhibitors. © 2013 Elsevier Ltd. All rights reserved.
  • Author:
    Duplessis M; Morency L; James C; Minville J; Deroy P; Morin S; Thavonekham B; Tremblay M; Halmos T; Simoneau B; Bousquet Y; Sturino C
    Title:
    Multi-gram synthesis of a nucleotide-competing reverse transcriptase inhibitor
    Source:
    Tetrahedron Lett Article in Press (2013)
    Abstract:
    An efficient multi-gram synthesis of a nucleotide-competing reverse transcriptase inhibitor is reported. The synthesis features a chiral auxiliary-assisted alcohol resolution, a Mitsunobu reaction involving a carbamate, followed by a lithium-iodide exchange/Weinreb ketone synthesis tandem. These chemical transformations were optimized in order to increase the yield of the synthesis. The route is concluded by a late-stage palladium-catalyzed cyanation followed by a pyrimidine-2-one ring formation. © 2013.
  • Author:
    Blaschka T; Hassa H
    Title:
    Second osmotic virial coefficients and aggregation of monoclonal antibodies by static laser light scattering
    Source:
    Z Phys Chem 227 (2-3), 333-343 (2013)
    Abstract:
    The second osmotic virial coefficient and the apparent molar mass of two human and one mouse monoclonal antibodies were measured in different aequeous buffer solutions which also contained sodium chloride or ammonium sulfate, respectively, by static laser light scattering in batch mode. The apparent molar mass indicates aggregation. At a constant pH value of 6.5 the sodium chloride concentration was varied from 0 to 2 M and the ammonium sulfate concentration from 0 to 0.8 M, respectively. A 20 mM sodium-phosphate buffer was used for all experiments. Furthermore the pH value was varied without adding additional salt from 4.5 to 10. The results of the salt dependency are in line with the Hofmeister-series. The results of the pH dependency correspond to the net charge of the molecules. © by Oldenbourg Wissenschaftsverlag, München.
  • Author:
    Mahut M; Gargano A; Schuchnigg H; Lindner W; Lämmernhofer M
    Title:
    Chemoaffinity material for plasmid DNA analysis by high-performance liquid chromatography with condition-dependent switching between isoform and topoisomer selectivity
    Source:
    Anal Chem 85 (5), 2913-2920 (2013)
    Abstract:
    Plasmid DNA may exist in three isoforms, the linear, open-circular (oc, "nicked"), and covalently closed circular (ccc, " supercoiled") form. We have recently reported on the chromatographic separation of supercoiled plasmid topoisomers on cinchona-alkaloid modified silica-based stationary phases. Herein, we present a selectivity switching mechanism to achieve separation of isoforms and/or supercoiled topoisomers using the very same chromatographic column and system. While salt gradient elution facilitates topoisomer separation, the supercoiled species are eluting as a single peak upon elution by a mixed pH and organic modifier gradient, still well separated from the other isoforms. We have found that a mobile phase pH value near the pI of the zwitterionic adsorbent surface leads to full recovery of all plasmid DNA isoforms, which is a major issue when using anion exchange-based resins. Furthermore, the observed elution pattern, oc < linear < ccc, is constant upon changes of mobile phase composition, gradient slope, and plasmid size. The remarkable isoform selectivity found on quinine-based selectors is explained by van't Hoff plots, revealing a different binding mechanism between the supercoiled plasmid on one hand and the oc and linear isoforms on the other hand. © 2013 American Chemical Society.
  • Author:
    Busacca C A; Qu B; Farber E; Haddad N; Gret N; Saha A K; Eriksson M C; Wu J P; Fandrick K R; Han S; Grinberg N; Ma S; Lee H; Li Z; Spinelli M; Gold A; Wang Z; Wang G; Wipf P; Senanayaka C H
    Title:
    [2,3]-Sigmatropic rearrangements of 2-phosphineborane 2-propen-1-ols: Rapid access to enantioenriched diphosphine monoxide derivatives
    Source:
    Org Lett 15 (5), 1136-1139 (2013)
    Abstract:
    Hydrophosphination of secondary propargylic alcohols generates phosphine-containing allylic alcohols that undergo facile [2,3]-sigmatropic rearrangements with chlorophosphines, furnishing highly enantioenriched, crystalline diphosphine monoxides. The configuration at the newly formed stereocenter is opposite to that expected based on prior studies, and an ab initio computational evaluation of the possible transition states was performed to help explain the stereochemical course of the reaction. © 2013 American Chemical Society.
  • Author:
    Wei X; Shu C; Haddad N; Zeng X; Patel N D; Tan Z; Liu J; Lee H; Shen S; Campbell S; Varsolona R J; Busacca C A; Hossain A; Yee N K; Senanayake C H
    Title:
    A highly convergent and efficient synthesis of a macrocyclic hepatitis C virus protease inhibitor BI 201302
    Source:
    Org Lett 15 (5), 1016-1019 (2013)
    Abstract:
    A highly convergent large scale synthesis of a 15-membered macrocyclic hepatitis C virus (HCV) protease inhibitor BI 201302 was achieved, in which the key features are the practical macrocyclization by Ru-catalyzed ring-closing metathesis (0.1 mol % Grela catalyst, 0.1-0.2 M concentration) and the efficient sulfone-mediated SNAr reaction. © 2013 American Chemical Society.
  • Author:
    Busacca C A; Qu B; Farber E; Haddad N; Gret n; Saha A K; Eriksson M C; Wu J P; Fandrick K R; Han S; Grinberg N; Ma S; Lee H; Li Z; Spinelli M; Gold A; Wang G; Wipf P; Senanayake C H
    Title:
    Hydrophosphination of propargylic alcohols and amines with phosphine boranes
    Source:
    Org Lett 15 (5), 1132-1135 (2013)
    Abstract:
    The first uncatalyzed hydrophosphinations of propargylic amines and alcohols with phosphine- borane complexes are described. The reactions proceed at ambient temperature or below without the use of protecting groups or the need to handle pyrophoric secondary phosphines, furnishing air-stable phosphineborane-amines and alcohols in good yields. Utilization of chiral propargylic substrates and unsymmetrical secondary phosphineboranes leads to diastereomeric P-chiral products that can be separated by fractional crystallization or chromatography. Initial applications of these new P-X species to asymmetric catalysis are detailed. © 2013 American Chemical Society.
  • Author:
    Frese C K; Zhou H; Taus T; Altelaar A F M; Mechtler K; Heck A J R; Mohammed S
    Title:
    Unambiguous phosphosite localization using electron-transfer/higher-energy collision dissociation (EThcD)
    Source:
    J Proteome Res 12 (3), 1520-1525 (2013)
    Abstract:
    We recently introduced a novel scheme combining electron-transfer and higher-energy collision dissociation (termed EThcD), for improved peptide ion fragmentation and identification. We reasoned that phosphosite localization, one of the major hurdles in high-throughput phosphoproteomics, could also highly benefit from the generation of such EThcD spectra. Here, we systematically assessed the impact on phosphosite localization utilizing EThcD in comparison to methods employing either ETD or HCD, respectively, using a defined synthetic phosphopeptide mixture and also using a larger data set of Ti4+-IMAC enriched phosphopeptides from a tryptic human cell line digest. In combination with a modified version of phosphoRS, we observed that in the majority of cases EThcD generated richer and more confidently identified spectra, resulting in superior phosphosite localization scores. Our data demonstrates the distinctive potential of EThcD for PTM localization, also beyond protein phosphorylation. © 2013 American Chemical Society.
  • Author:
    Manosroi J; Lohcharoenkal W; Götz F; Werner R G; Manosroi W; Manosroi A
    Title:
    Transdermal absorption and stability enhancement of salmon calcitonin by Tat peptide
    Source:
    Drug Dev Ind Pharm 39 (4), 520-525 (2013)
    Abstract:
    Abstract Context: Highly organized structure of stratum corneum (SC) is the major barrier of the delivery of macromolecules such as proteins and peptides across the skin. Recently, cell penetrating peptides (CPPs) such as HIV1-trans-activating transcriptional (Tat) have been used to enhance the topical delivery of proteins and peptides. Objective: This study aimed to enhance the transdermal absorption and chemical stability of salmon calcitonin (sCT) by co-incubation with Tat. Materials and methods: Tat-sCT mixture at 1:1 molar ratio was prepared. Transdermal absorption and chemical stability of the mixture was evaluated in comparing with free sCT. Results: Tat-sCT mixture gave higher cumulative amounts and fluxes of sCT than free sCT. The maximum percentage of sCT of 58.36 ± 12.33% permeated into the receiving chamber was found in Tat-sCT mixture at 6 h which was 3.50 folds of free sCT. Tat-sCT mixture demonstrated better sCT stability than sCT solution after 1 month storage at 4°C, 25°C and 45°C. Discussion: The positively-charged arginine groups in Tat might be responsible for the binding of peptide complexes to negatively charged cell surfaces by electrostatic interactions and also the translocation of sCT through the excised skin. Conclusion: This study demonstrated the enhancements of transdermal absorption and stability of sCT by Tat peptide with potential for further application in transdermal delivery of other therapeutic peptides. © 2013 Informa Healthcare USA, Inc.
  • Author:
    Groselj U; Podiogar A; Novak A; Dahmann G; Golobic A; Stanovnik B; Svete J
    Title:
    Synthesis of tetrahydropyrazolo[1,5- C ]pyrimidine-2,7(1 H,3 H)-diones
    Source:
    Synthesis 45 (5), 639-650 SS-2012-Z0909-OP (2013)
    Abstract:
    A series of tetrahydropyrazolo[1,5-c]pyrimidine-2,7(1H,3H)-diones 3a-h as the first representatives of the so far unexplored saturated heterocyclic system have been synthesized, formally in 12 steps from methyl acrylate (4). The synthesis comprises a four-step preparation of methyl N-Cbz-5-alkylamino-3- oxopentanoates 9a-c, their three-step transformation into 5-{2-[(alkyl) (benzyloxycarbonyl)amino]ethyl}pyrazolidin-3-ones 12a-c, three-step selective alkylation of the amidic N-2 to give 2-alkyl-5-{2-[(alkyl)(benzyloxycarbonyl) amino]ethyl}pyrazolidin-3-ones 16b-h, followed by hydrogenolytic Cbz-deprotection and subsequent cyclization of the intermediate 1,4-diamine with CDI to furnish the title compounds 3. Most of the synthetic steps were performed as a one-pot transformation. © Georg Thieme Verlag Stuttgart New York.
  • Author:
    Trost B M; Lam T M; Herbage M A
    Title:
    Regio-and enantioselective synthesis of pyrrolidines bearing a quaternary center by palladium-catalyzed asymmetric [3 + 2] cycloaddition of trimethylenemethanes
    Source:
    J Am Chem Soc 135 (7), 2459-2461 (2013)
    Abstract:
    Herein we describe the first use of disubstituted donors in the palladium-catalyzed trimethylenemethane (TMM) cycloaddition resulting in an enantioselective synthesis of highly substituted pyrrolidines. These cyanoalkyl donors 1 form all-carbon quaternary centers in a catalytic, asymmetric, and intermolecular manner uniquely using diamidophosphite ligands L2 and L3, generating synthetically important chiral building blocks in good yields and selectivities. © 2013 American Chemical Society.
  • Author:
    Han Z S; Goyal N; Herbage M A; Sieber J D; Qu B; Xu Y; Li Z; Reeves J T; Desrosiers J N; Ma S; Grinberg N; Lee H; Mangunuru H P R; Zhang Y; Krishnamurthy D; Lu B Z; Song J J; Wang G; Senanayake C H
    Title:
    Efficient asymmetric synthesis of P -chiral phosphine oxides via properly designed and activated benzoxazaphosphinine-2-oxide agents
    Source:
    J Am Chem Soc 135 (7), 2474-2477 (2013)
    Abstract:
    A general, efficient, and highly diastereoselective method for the synthesis of structurally and sterically diverse P-chiral phosphine oxides was developed. The method relies on sequential nucleophilic substitution on the versatile chiral phosphinyl transfer agent 1,3,2-benzoxazaphosphinine-2-oxide, which features enhanced and differentiated P-N and P-O bond reactivity toward nucleophiles. The reactivities of both bonds are fine-tuned to allow cleavage to occur even with sterically hindered nucleophiles under mild conditions. © 2013 American Chemical Society.
  • Author:
    Chambers D; Guo G; Kleintop B; Rasmussen H; Deegan S; Nowak S; Patterson K; Spicuzza J; Szulc M; Tombaugh K; Trone M D; Yuabova Z
    Title:
    Gmps for method validation in early development
    Source:
    Pharm Technol North Am 36 (7), 76-84 (2012)
    Abstract:
    no Abstract available
  • Author:
    Zhao Q; Li C; Senanayake C H; Tang W
    Title:
    Genetic and Pharmacological Modifications of Thrombin Formation in Apolipoprotein E-deficient Mice Determine Atherosclerosis Severity and Atherothrombosis Onset in a Neutrophil-Dependent Manner
    Source:
    Chemistry (Weinheim) 19 (7), 2261-2265 (2013)
    Abstract:
    Background: Variations in the blood coagulation activity, determined genetically or by medication, may alter atherosclerotic plaque progression, by influencing pleiotropic effects of coagulation proteases. Published experimental studies have yielded contradictory findings on the role of hypercoagulability in atherogenesis. We therefore sought to address this matter by extensively investigating the in vivo significance of genetic alterations and pharmacologic inhibition of thrombin formation for the onset and progression of atherosclerosis, and plaque phenotype determination. Methodology/Principal Findings: We generated transgenic atherosclerosis-prone mice with diminished coagulant or hypercoagulable phenotype and employed two distinct models of atherosclerosis. Gene-targeted 50% reduction in prothrombin (FII-/WT:ApoE-/-) was remarkably effective in limiting disease compared to control ApoE-/- mice, associated with significant qualitative benefits, including diminished leukocyte infiltration, altered collagen and vascular smooth muscle cell content. Genetically-imposed hypercoagulability in TMPro/Pro:ApoE-/- mice resulted in severe atherosclerosis, plaque vulnerability and spontaneous atherothrombosis. Hypercoagulability was associated with a pronounced neutrophilia, neutrophil hyper-reactivity, markedly increased oxidative stress, neutrophil intraplaque infiltration and apoptosis. Administration of either the synthetic specific thrombin inhibitor Dabigatran etexilate, or recombinant activated protein C (APC), counteracted the pro-inflammatory and pro-atherogenic phenotype of pro-thrombotic TMPro/Pro:ApoE-/- mice. Conclusions/Significance: We provide new evidence highlighting the importance of neutrophils in the coagulation-inflammation interplay during atherogenesis. Our findings reveal that thrombin-mediated proteolysis is an unexpectedly powerful determinant of atherosclerosis in multiple distinct settings. These studies suggest that selective anticoagulants employed to prevent thrombotic events may also be remarkably effective in clinically impeding the onset and progression of cardiovascular disease. © 2013 Borissoff et al.
  • Author:
    Bibee K P; Augustin R; Gazit V; Moley K H
    Title:
    The apical sorting signal for human GLUT9b resides in the N-terminus
    Source:
    Mol Cell Biochem, 1-11 Article in Press (2013)
    Abstract:
    The two splice variants of human glucose transporter 9 (hGLUT9) are targeted to different polarized membranes. hGLUT9a traffics to the basolateral membrane, whereas hGLUT9b traffics to the apical region. This study examines the sorting mechanism of these variants, which differ only in their N-terminal domain. Mutating a di-leucine motif unique to GLUT9a did not affect targeting. Chimeric proteins were made using GLUT1, a basolaterally targeted transporter, and GLUT3, an apically targeted protein whose signal lies in the C-terminus. Overexpression of the chimeric proteins in polarized cells demonstrates that the N-terminus of hGLUT9b contains a signal capable of redirecting GLUT1 to the apical membrane. The N-terminus of hGLUT9a, however, does not contain a basolateral signal sufficient enough to redirect GLUT3. Portions of the GLUT9a N-terminus were substituted with corresponding portions of the GLUT9b N-terminus to determine the motif responsible for apical targeting. The first 16 amino acids were not found to be a sufficient apical signal. The last ten amino acids of the N-termini differ only in amino-acid class at one location. In the B-form, leucine, a hydrophobic residue, is substituted for lysine, a basic residue, found in the A-form. However, mutation of the leucine in hGLUT9b to a lysine resulted in retention of the apical signal. We therefore believe the apical signal exists as an interplay between the final ten amino acids of the N-terminus and another motif within the protein such as the intracellular loop or other motifs within the N-terminus. © 2013 Springer Science+Business Media New York.
  • Author:
    Poulsen M H; Lucas S; Bach T B; Barslund A F; Wenzler C; Jensen C B; Kistensen A S; Stromgaard K
    Title:
    Structure-activity relationship studies of argiotoxins: Selective and potent inhibitors of ionotropic glutamate receptors
    Source:
    J Med Chem 56 (3), 1171-1181 (2013)
    Abstract:
    Argiotoxin-636 (ArgTX-636), a natural product from the spider Argiope lobata, is a potent but nonselective open-channel blocker of ionotropic glutamate (iGlu) receptors. Here, three series of analogues were designed to exploit selectivity among iGlu receptors, taking advantage of a recently developed solid-phase synthetic methodology for the synthesis of ArgTX-636 and analogues. Initially, the importance of secondary amino groups in the polyamine chain was studied by the synthesis of systematically modified ArgTX-636 analogues, which were evaluated for pharmacological activity at NMDA and AMPA receptors. This led to the identification of two compounds with preference for NMDA and AMPA receptors, respectively. These were further elaborated by systematically changing the aromatic headgroup and linker amino acid leading to compounds with increased potency and selectivity for NMDA and AMPA receptors, respectively. Thus, the first structure-activity relationship study of ArgTX-636 has been carried out and has provided lead compounds for probing the ion channel region of iGlu receptors. © 2013 American Chemical Society.
  • Author:
    MacDonald M J; Hesp C R; Schipper D J; Pesant M; Beauchemin A M
    Title:
    Highly enantioselective intermolecular hydroamination of allylic amines with chiral aldehydes as tethering catalysts
    Source:
    Chemistry (Weinheim) 19 (8), 2597-2601 (2013)
    Abstract:
    Chirally LinkedIn: Chiral aldehydes are effective tethering catalysts for enantioselective intermolecular hydroamination, which provides access to vicinal diamine motifs in good yields and excellent enantioselectivities (see scheme). This work highlights simple chiral ?-oxygenated aldehydes as effective organocatalysts capable of efficiently inducing asymmetry through transient intramolecularity. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
  • Author:
    Dziedzic, J; Fox, S. J.; Fox, T.; Tautermann, C.S.; Skylaris, C.-K.
    Title:
    Large-scale DFT calculations in implicit solvent - A case study on the T4 lysozyme L99A/M102Q protein
    Source:
    Int J Quantum Chem 113 (6), 771-785 (2013)
    Abstract:
    Recently, variants of implicit solvation models for first principles electronic structure calculations based on a direct solution of the nonhomogeneous Poisson equation in real space have been developed. These implicit solvation models are very elegant from a physical point of view as the solute cavity is defined directly via isosurfaces of the electronic density, and the molecular charge is polarized self-consistently by the reaction field of the dielectric continuum which surrounds the solute. Nevertheless, the implementation of these models is technically complex and requires great care. A certain level of care is required from users of such models as a number of numerical parameters need to be given appropriate values to obtain the most accurate and physically relevant results. Here, we describe in what parts of the solvent model each of these numerical parameters is involved and present a detailed study of how they can affect the calculation, using the solvation model which has been implemented in the ONETEP program for linear-scaling density functional theory (DFT) calculations. As ONETEP is capable of DFT calculations with thousands of atoms, we focus our investigation of the numerical parameters with a case study on protein-ligand complexes of the entire 2602-atom T4 Lysozyme L99/M102Q protein. We examine effects on solvation energies and binding energies, which are critical quantities for computational drug optimization and other types of biomolecular simulations. We propose optimal choices of these parameters suitable for routine "production" calculations. © 2012 Wiley Periodicals, Inc.
  • Author:
    Schultes S; Nijmeijer S; Engelhardt H; Kooistra AJ; Vischer HF; de Esch IJP; Haaksma EEJ; Leurs R; De Graaf C
    Title:
    Mapping histamine H4 receptor ligand binding modes.
    Source:
    MedChemComm 4 (1), 193-204 (2013)
  • Author:
    Grinberg N; Albu F; Fandrick K; Iorgulescu E; Medvedovici A
    Title:
    Assay at low ppm level of dimethyl sulfate in starting materials for API synthesis using derivatization in ionic liquid media and LC-MS.
    Source:
    J Pharm Biomed Anal 75, 1-6 (2013)
    Abstract:
    Dimethyl sulfate (DMS) is frequently used in pharmaceutical manufacturing processes as an alkylating agent. Trace levels of DMS in drug substances should be carefully monitored since the compound can become an impurity which is genotoxic in nature. Derivatization of DMS with dibenzazepine leads to formation of the N-methyl derivative, which can be retained on a reversed phase column and subsequently separated from other potential impurities. Such derivatization occurs relatively slowly. However, it can be substantially speed up if ionic liquids are used as reaction media. In this paper we report the use of 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide (IL1) and 1-butyl-4-methylpyridinium tetrafluoroborate (IL2) as reaction media for the derivatization of DMS with dibenzazepine. It was determined that the stoichiometry between the substrate and DMS may be 1:1 or 2:1, in relation with the nature of the reaction media. An (+)ESI-MS/MS approach was used for quantitation of the derivatized product. Alternatively, DMS derivatization may be carried out with pyridine in acetonitrile (ACN). The N-methylpyridinium derivative was separated by hydrophilic interaction liquid chromatography (HILIC) and detected through (+)ESI-MS (in the SIM mode). In both cases, a limit of quantitation (LOQ) of 0.05 µg/ml DMS was achievable, with a linearity range up to 10 µg/ml. Both analytical alternatives were applied to assay DMS in 4-(2-methoxyethyl)phenol, which is used as a starting material in the synthesis of metoprolol. © 2012 Elsevier B.V.
  • Author:
    Wellenzohn B; Lessel U; Beller A; Isambert T; Hoenke C; Nosse B
    Title:
    Identification of new potent GFR119 agonists by combining virtual screening and combinatorial chemistry
    Source:
    J Med Chem 55 (24), 11031-11041 (2012)
    Abstract:
    Virtual screening in a huge collection of virtual combinatorial libraries has led to the identification of two new structural classes of GPR119 agonists with submicromolar in vitro potencies. Herein, we describe the virtual screening process involving feature trees fragment space searches followed by a 3D postprocessing step. The in silico findings were then filtered and prioritized, and finally, combinatorial libraries of target molecules were synthesized. Furthermore the so-called "activity-anchor principle" is introduced as an element to increase the chance to generate true hits. An activity anchor is a structural element expected to provide key contributions to a certain biological activity. Application of this technique has led to the discovery of two new GPR119-agonist hit series, one of which was further optimized to progress as a novel lead class. © 2012 American Chemical Society.
  • Author:
    Schultes S; Engelhardt H; Roumen L; Zuiderveld OP; Haaksma EEJ; deEsch IJP; Leurs R; deGraaf C
    Title:
    Combining quantum mechanical ligand conformation analysis and protein modeling to elucidate GPCR-ligand binding modes.
    Source:
    ChemMedChem 8 (1), 49-53 (2013)
    Abstract:
    no abstract available
  • Author:
    Rinker S; Barandun LJ; Diederich F; Kraemer O; Steffen A; van Gunsteren WF
    Title:
    Free enthalpies of replacing water modules in protein binding pockets.
    Source:
    J Comput Aided Mol Des 26 (12), 1293-309 (2012)
  • Author:
    Sedykh A; Fourches D; Duan J; Hucke O; Garneau M; Zhu H; Bonneau P; Tropsha A
    Title:
    Human intestinal transporter database: QSAR modeling and virtual profiling of drug uptake. Efflux and interactions.
    Source:
    Pharm Res, 1-12 (2012)
  • Author:
    Dach R; Song JJ; Roschangar F; Samstag W; Senanayake CH
    Title:
    The eight criteria defining a good chemical manufacturing process.
    Source:
    Org Process Res Dev 16 (11), 1697-1706 (2012)
  • Author:
    Bieler M; Koeppen H
    Title:
    The role of chemogenomics in the pharmaceutical industry.
    Source:
    Drug Dev Res 73 (7), 357-364 (2012)
    Abstract:
    Preclinical Research The goal of chemogenomics is the exploration of all possible interactions between compounds from the chemical space and targets from the biological space. This huge interaction matrix is only sparsely filled with experimental data but can be complemented by predicted values for selected ligand-target pairs. The prediction by computational chemogenomics uses the similarity principle that states that similar compounds have similar properties and that targets with similar binding sites bind similar ligands. Chemogenomics has a number of interesting applications, e.g. the prediction of the bioprofile of drugs including an assessment of possible adverse drug effects or the support of phenotypic screening by target fishing. This review focuses on applications of computational chemogenomics in pharmaceutical research and on the role that it plays in an industrial environment. © 2012 Wiley Periodicals, Inc.
  • Author:
    Chambers D; Guo G; Kleintop B; Rasmussen H; Deegan S; Nowak S; Patterson K; Spicuzza J; Szulc M; Tombaugh K; Trone MD; Yuabova Z
    Title:
    Gmps for methods validation in early development.
    Source:
    Pharm Technol North Am 36 (7), 76-84 (2012)
  • Author:
    Coutant M; Ge Z; McElvain JS; Miller SA; O'Connor D; Swanek F; Szulk M; Trone MD; Wong-Moon K; Yazdanian M; Yehl P; Zhang S
    Title:
    Early development gmps for small-molecule specifications.
    Source:
    Pharm Technol North Am 36 (10), 86-94 (2012)
    Abstract:
    a Analytical Research and Development, Pfizer Inc, Groton, CT, United States b Analytical Chemistry, Merck and Co. Inc, Rahway, NJ, United States Analytical and QC, Kythera Biopharmaceuticals, Calabasas, CA, United States d Analytical and Bioanalytical Development, Bristol-Myers Squibb Company, New Brunswick, NJ, United States e Analytical Development, Boehringer Ingelheim Pharmaceuticals Inc, Ridgefield, CT, United States Analytical Development, Biogen Idec, Cambridge, MA, United States g Analytical Development-Small Molecule, Millennium Pharmaceuticals, Inc, Cambridge, MA, United States h Analytical Research and Development, Amgen Inc, Thousand Oaks, CA, United States 1Pharnnaceutical Development, Teva Global Branded Products R and D, West Chester, PA, United States j Small Molecule Analytical Chemistry and Quality Control at Genentech, South San Francisco, CA, United States Global Pharmaceutical R and D, Abbott Laboratories, North Chicago, IL, United States
  • Author:
    Wagner M; Reiche K; Blume A; Garidel P
    Title:
    The electrokinetic potential of therapeutic proteins and its modulation: Impact on protein stability.
    Source:
    Colloids Surf (A) 415, 421-430 (2012)
    Abstract:
    Colloidal protein stability in solution is governed by protein-protein interactions as well as by interactions with surrounding molecules (e.g. excipients, buffer and satt components, solvent molecules) and environmental conditions such as temperature. Also, the thermodynamic stability of a protein has an impact on the overall colloidal stability of protein in an aqueous environment. Electrostatic interactions between proteins have been described to be of high relevance for colloidal stability, for example the formation of protein particles. One parameter for the evaluation of such interactions in solution is the electrophoretic mobility from which the electrokinetic potential (EP) (also known as the zeta potential, ZP) is obtained. The electrokinetic potential, respective EP, refers to the potential at the shear surface where the protein molecules with their associated sheath of counter-ions and excipients slip through the solution, which is under the influence of an applied external electrical field. The current study investigated the electrokinetic potential of therapeutic proteins and how and to what extent the electrokinetic potential can be influenced by variations of solution conditions (e.g. pH, salts and buffer components, amino acids, carbohydrates or detergents). The interactions of proteins, such as monoclonal antibodies, with different excipients are discussed in terms of the DLVO theory and colloidal stability, respectively.Furthermore, the electrokinetic potential is used for the determination of the isoelectric point of several proteins and compared to theoretical values derived from the total net charge based on the primary amino acid sequence.ln addition, we investigated to what extent the electrokinetic potential of proteins can be modulated by solution conditions and whether the electrokinetic potential of various proteins in different solution conditions correlate with experimental derived colloidal and thermal stability. © 2012 Elsevier B.V.
  • Author:
    Moss N; Xiong Z; Burke M; Cogan D; Gao DA; Haverty K; Heim-Riether A; Hickey ER; Nagaraja R; Netherton M; O'Shea K; Ramsden P; Schwartz R; Shih D-T; Ward Y; Young E; Zhang Q
    Title:
    Exploration of cathepsin S inhibitors characterized by a triazole P1-P2 amide replacement.
    Source:
    Bioorg Med Chem Lett 22 (23), 7189-7193 (2012)
  • Author:
    Luner PE; Zhang Y; Abramov YA; Carvajal MT
    Title:
    Evaluation of milling method on the surface energetics of molecular crystals using inverse gas chromatography.
    Source:
    Crystal Growth Des 12 (11), 5271-5282 (2012)
  • Author:
    Davy JA; Mason JW; Moreau B; Wulff JE
    Title:
    Xanthates as synthetic equivalents of oxyacyl radicals: Access to lactones under tin-free conditions.
    Source:
    J Org Chem 77 (14), 6332-6339 (2012)
    Abstract:
    In addition to their utility in Barton-McCombie deoxygenations, xanthates can engage in 5-exo-trig radical cyclizations to afford lactones after oxidative workup. In this paper, we describe a tin-free protocol that provides direct access to lactones via hydrolysis of labile thioketal intermediates. Analysis of several systems of varying complexity reveals that the reaction is most applicable for constrained systems in which the reacting center is prepositioned near the radical-accepting alkene
  • Author:
    Tremblay M; Bonneau P; Bousquet Y; DeRoy P; Duan J; Duplessis M; Gagnon A; Garneau M; goudeau N; Guse I; Hucke O; Kawai S H; Lemke C T; Mason S W; Simoneau B; Surprenant S; Titolo S; Yoakim C
    Title:
    Inhibition of HIV-1 capsid assembly: Optimization of the antiviral potency by site selective modifications at N1, C2 and C16 of a 5-(5-furan-2-yl-pyrazol-1-yl)-1H-benzimidazole scaffold
    Source:
    Bioorg Med Chem Lett 22 (24), 7512-7517 (2012)
    Abstract:
    A uHTS campaign led to the discovery of a 5-(5-furan-2-ylpyrazol-1-yl)-1H-benzimidazole series that inhibits assembly of HIV-1 capsid. Synthetic manipulations at N1, C2 and C16 positions improved the antiviral potency by a . The X-ray structure of 33 complexed with the capsid N-terminal domain allowed identification of major interactions between the inhibitor and the protein. © 2012 Elsevier Ltd. All rights reserved.
  • Author:
    Beckers T; Mahboobi S; Sellmer A; Winkler M; Eichhorn E; Pongratz H; Maier T; Ciossek T; Baer T; Kelter G; Fiebig H-H; Schmidt M
    Title:
    Chimerically designed HDAC- and tyrosine kinase inhibitors. A series of erlotinib hybrids as dual-selective inhibitors of EGFR, HER2 and histone deacetylases.
    Source:
    MedChemComm 3 (7), 829-835 (2012)
    Abstract:
    The regulation of chromatin structure and, therefore, transcriptional activity of histone proteins by reversible lysine acetylation is an important posttranslational modification. Inhibitors of histone deacetylase (HDAC) are considered as promising new anti-neoplastic drugs. The hydroxamic acid SAHA e.g. is currently used in the treatment of advanced primary cutaneous T-cell lymphoma. The EGFR protein tyrosine kinase inhibitor erlotinib is a prominent drug in cancer chemotherapy and currently approved for treatment of non-small cell lung cancer. In this report, we present a novel strategy for cancer drug development by a combination of EGFR/HER2 kinase and HDAC inhibitory activity in one molecule. By combining two distinct pharmacological properties in one molecule, we expect a broader activity spectrum and less likelihood of drug resistance in cancer patients. The combination led to substances with both HDAC inhibitory properties and EGFR as well as HER2 kinase inhibitory activities. © The Royal Society of Chemistry 2012.
  • Author:
    Bonderoff SA; West FG; Tremblay M
    Title:
    Superacid-catalyzed friedel-crafts cyclization of unactivated alkenes.
    Source:
    Tetrahedron Lett 53 (34), 4600-4603 (2012)
    Abstract:
    Trifluoromethanesulfonimide is an effective catalyst for Friedel-Crafts cyclizations of simple, nonpolarized alkenes with a variety of pendant arenes. A catalyst loading of 0.5 - 1.0 mol % effects clean cyclization to form 5- to 7-membered carbocycles with generally short reaction times and good to excellent yields under reflux or microwave heating. © 2012 Elsevier Ltd. All rights reserved.
  • Author:
    Gapsys V; Seeliger D; De Groot BL
    Title:
    New soft-core potential function for molecular dynamics based alchemical free energie calculations.
    Source:
    J Chem Theor Comput 8 (7), 2373-2382 (2012)
    Abstract:
    The fields of rational drug design and protein engineering benefit from accurate free energy calculations based on molecular dynamics simulations. A thermodynamic integration scheme is often used to calculate changes in the free energy of a system by integrating the change of the systems Hamiltonian with respect to a coupling parameter. These methods exploit nonphysical pathways over thermodynamic cycles involving particle introduction and annihilation. Such alchemical transitions require the modification of the classical nonbonded potential energy terms by applying soft-core potential functions to avoid singularity points. In this work, we propose a novel formulation for a soft-core potential to be applied in nonequilibrium free energy calculations that alleviates singularities, numerical instabilities, and additional minima in the potential energy for all combinations of nonbonded interactions at all intermediate alchemical states. The method was validated by application to (a) the free energy calculations of a closed thermodynamic cycle, (b) the mutation influence on protein thermostability, (c) calculations of small ligand solvation free energies, and (d) the estimation of binding free energies of trypsin inhibitors. The results show that the novel soft-core function provides a robust and accurate general purpose solution to alchemical free energy calculations. © 2012 American Chemical Society.
  • Author:
    Fandrick DR; Roschangar F; Kim C; Hahm BJ; Cha MH; Kim HY; Yoo G; Kim T; Reeves JT; Song JJ; Tan Z; Qu B; Haddad N; Shen S; Grinberg N; Lee H; Yee N; Senanayake CH
    Title:
    Preparative synthesis via continuous flow of 4,4,5,5-tetramethyl-2-(3- trimethylsilyl-2-propynyl)-1,3,2-dioxaborolane: A general propagylation reagent.
    Source:
    Org Process Res Dev 16 (5), 1131-1140 (2012)
    Abstract:
    A scalable process for the preparation of 4,4,5,5-tetramethyl-2-(3- trimethylsilyl-2-propynyl)-1,3,2-dioxaborolane from trimethylsilylpropyne, isopropyl pinacol borate, and n-butyllithium is described. Problems associated with implementing a typical aqueous workup and batch process into production due to borolane "ate" equilibration and protonolysis are presented. To address these issues, a continuous-flow and distillation process was developed which efficiently produced 297 kg of the key propargylation reagent
  • Author:
    Li W; Gao JJ; Lorenz JC; Xu J; Johnson J; Ma S; Lee H; Grinberg N; Busacca CA; Lu B; Senanayake CH
    Title:
    Process development and pilot-plant synthesis of (S)-tert-butyl 1-oxo-1-(1-(pyridin-2-yl)cyclopropylamino)propan-2-ylcarbamate: Studies on the scale-up of Kulinkovich-Szymoniak cyclopropanation.
    Source:
    Org Process Res Dev 16 (5), 336-339 (2012)
    Abstract:
    A practical and scalable synthesis of (S)-tert-butyl 1-oxo-1-(1-(pyridin-2- yl)cyclopropylamino)propan-2-ylcarbamate, an intermediate in the manufacture of a lymphocyte function-associated antigen 1 inhibitor, is described. The titled compound is prepared via an efficient one-pot, two-step telescoped sequence starting from readily available materials. A modified Kulinkovich-Szymoniak cyclopropanation of a nitrile followed by in situ amide formation with an activated carboxylic acid derivative afforded the target product in about 50% overall isolated yield and >97% purity.
  • Author:
    Li Y; Xu J; Lai WG; Whitcher-Johnstone A; Tweedie DJ
    Title:
    Metabolic switching of BILR 355 in the presence of ritonavir. II. Uncovering novel contributions by gut bacteria and aldehyde oxidase
    Source:
    Drug Metab Dispos 40 (6), 1130-1137 (2012)
    Abstract:
    Ritonavir (RTV) was used as a boosting agent to increase the clinical exposure of 11-ethyl-5,11-dihydro-5-methyl-8-[2-[(1-oxido-4-quinolinyl) oxy]ethyl]-6H-dipyrido[3,2-b:2',3'-e][1,4]diazepin-6-one (BILR 355), an inhibitor of the human immunodeficiency virus, by inhibiting the CYP3A-mediated metabolism of BILR 355. However, although the levels of BILR 355 increased upon concomitant administration of RTV, a metabolite of BILR 355, BILR 516, which was not detected previously in humans dosed with BILR 355 alone, became a disproportionate human metabolite with levels exceeding the parent levels at steady state. This was an unusual finding based on the in vitro and in vivo metabolic profiles of BILR 355 available at that time. Our studies reveal that BILR 355 is reduced to an intermediate, BILR 402, by gut bacteria and the reduced metabolite (BILR 402) is then oxidized by aldehyde oxidase to form BILR 516, the disproportionate human metabolite. The role of aldehyde oxidase helped to explain the somewhat unique formation of BILR 516 in humans compared with preclinical animal species. This article underlines the increasing importance of two individually atypical enzymes in drug development, gut bacterial biotransformation and aldehyde oxidase, which in combination provided a unique metabolic pathway. In addition, this article clearly elucidates an example of novel metabolic switching and, it is hoped, raises awareness of the potential for metabolic switching in combination drug therapies
  • Author:
    Li Y; Lai WG; Whitcher-Johnstone A; Busacca CA C; Eriksson MC; Lorenz JC; Tweedie DJ
    Title:
    Metabolic switching of BILR 355 in the presence of ritonavir. I. Identifying an unexpected disproportionate human metabolite.
    Source:
    Drug Metab Dispos 40 (6), 1122-1129 (2012)
    Abstract:
    11-Ethyl-5,11-dihydro-5-methyl-8-[2-[(1-oxido-4-quinolinyl)oxy] ethyl]-6H-dipyrido[3,2-b:2',3'-e][1,4]diazepin-6-one (BILR 355) is an inhibitor of the human immunodeficiency virus-1. BILR 355 exhibited a nonlinear pharmacokinetic profile and low exposure after oral administration to humans. This article describes the in vitro metabolism of BILR 355, which is correlated with the in vivo nonlinearity findings. Our in vitro studies had demonstrated that BILR 355 was extensively metabolized by cytochrome P450 3A. Thus, BILR 355 was concomitantly administered with ritonavir (RTV) in an attempt to boost systemic exposure, which did occur in humans. In addition, the expectation was that the overall metabolism of BILR 355 would be decreased with concomitant administration of RTV. Subsequent metabolite profiling was performed using human plasma samples obtained from clinical phase Ib studies with concomitant administration of BILR 355 and RTV. A total of 18 metabolites was observed. Their structures were proposed on the basis of high-performance liquid chromatography-tandem mass spectrometry technologies, and 10 metabolites were confirmed by comparison with synthetic standards. We were surprised to find that a disproportionate human metabolite, BILR 516, was uncovered during this metabolite profiling study and pharmacokinetic analysis of BILR 516 showed that it had a longer half-life and higher exposure than the parent compound at steady state. Of interest, BILR 516 was not detected in human plasma when BILR 355 was administered alone. Therefore, whereas RTV boosted the exposure of BILR 355, it resulted in a significant metabolic switching of BILR 355. Overall, this article demonstrates an unusual example of metabolic switching and raises concern about the consequence of metabolic switching during drug development. Copyright © 2012 by The American Society for Pharmacology and Experimental Therapeutics. Reaxys Database Information
  • Author:
    Girard T; El-Far M; Gaucher D; Acuto O; Beaule G; Michel F; Mourad W; Sekaly R-P
    Title:
    A conserved polylysine motif in CD86 cytoplasmic tail is necessary for cytoskeletal association and efective costimulation.
    Source:
    Biochem Biophys Res Commun 423 (2), 301-307 (2012)
    Abstract:
    T cell activation requires both antigen specific and co-stimulatory signals that include the interaction of CD28 with its ligands CD80 and CD86. These signals are delivered by antigen presenting cells (APC) in the context of the immunological synapse (IS). Reorganization of the cytoskeleton is required for the formation and maintenance of the IS. Our results show that a highly conserved polylysine motif in CD86 cytoplasmic tail, herein referred to as the K4 motif, is responsible for the constitutive association of CD86 to the cytoskeleton in primary human APC as well as in a murine APC model. This motif is not involved in initial APC:T cell conjugate formation but mutation of the K4 motif affects CD86 reorientation at the IS. Importantly, APCs expressing CD86 with mutated K4 motif are severely compromised in their capacity to trigger complete T cell activation upon peptide presentation as measured by IL-2 secretion. Altogether, our results reveal the critical importance of the cytoskeleton-dependent CD86 polarization to the IS and more specifically the K4 motif for effective co-signaling. © 2012 Elsevier Inc. Reaxys Database Information
  • Author:
    Engelhardt H; de Esch IJP; Kuhn D; Smits RA; Zuiderveld OP; Dobler J; Mayer M; Lips S; Arnhof H; Scham D; Haaksma EEJ; Leurs R
    Title:
    Detailed structure-activity relationship of indolecarboxamides as H 4 receptors ligands.
    Source:
    Eur J Med Chem Article in Press (2012)
  • Author:
    Wang X-J; Zhang L; Sun X; Lee H; Krishnamurthy D; O'Meara JA; Landry S; Yoakim C; Simoneau B; Yee NK; Senanayake CH
    Title:
    Practical synthesis of a benzophenone-based NNRT inhibitor of HIV-1.
    Source:
    Org Process Res Dev 16 (4), 561-566 (2012)
    Abstract:
    A convergent synthesis of NNRTI 1 is described. The key step involves a direct coupling of acid chloride 4 with Grignard reagent 11 in the presence of bis[2-(N,N-dimethylamino)ethyl] ether that moderates the reactivity of the Grignard reagent to give benzophenone 7. An efficient 2-step process for the preparation of 2-fluoro-3-methyl-4-aminobenzoic acid (3) is also described. © 2012 American Chemical Society.
  • Author:
    Davy JA; Moreau B; Wulff JE
    Title:
    Tandem dihydroxylation, hemiketalization and conjugate addition leading to a singly anomeric spiroketal.
    Source:
    Synthesis 44 (12), 1854-1862 (2012)
    Abstract:
    A novel, highly stereoselective tandem dihydroxylation, hemiketalization and conjugate addition reaction is reported that transforms a linear meso-functionalized bis-enone into a substituted singly anomeric spiroketal, effectively controlling six stereocenters in a single operation. As part of an effort to explore the thermodynamic consequences of establishing the singly anomeric spiroketal in this system, the assembly of a related fully anomeric spiroketal possessing an unusual ketal-spiroketal-ketal framework is demonstrated. © 2012 Elsevier B.V. All rights reserved. Reaxys Database Information
  • Author:
    Baškovc J; Dahmann G; Golobic A; Grošelj U; Kocar D; Stanovnik B; Svete J
    Title:
    Diversity-oriented synthesis of 1-substituted 4-aryl-6-oxo-1,6- dihydropyridine-3-carboxamides. Diversity-oriented synthesis of 1-substituted 4-aryl-6-oxo-1,6- dihydropyridine-3-carboxamides.
    Source:
    QSAR Comb Sci 14 (9), 513-519 (2012)
    Abstract:
    A simple five-step diversity-oriented synthesis of 1-substituted 4-aryl-6-oxo-1,6-dihydropyridine-3-carboxamides was developed. Treatment of dimethyl 2-((dimethylamino)methylidene)-3-oxopentanedioate with twenty primary amines gave 1-substituted methyl 4-hydroxy-6-oxo-1,6-dihydropyridine-3- carboxylates. Transformation into the corresponding 4-tosyloxy and 4-chloro derivatives, followed by Suzuki-Miyaura arylations gave a series of eleven N-substituted methyl 4-aryl-6-oxo-1,6-dihydropyridine-3-carboxylates. Combinatorial screening was employed to establish suitable reaction conditions for Suzuki-Miyaura arylation of N-alkylpyridones. Hydrolysis of the esters followed by parallel solution-phase amidation of the corresponding carboxylic acids with primary and secondary amines furnished a library of seventeen final products. © 2012 American Chemical Society.
  • Author:
    Hill D W; Baveghems C L; Albaugh D R; Kormos T M; Lai S; Ng H K; Grant D F
    Title:
    Correlation of Ecom 50 values between mass spectrometers: Effect of collision cell radiofrequency voltage on calculated survival yield
    Source:
    Rapid Commun Mass Spectrom 25 (19), 2303-2310 (2012)
    Abstract:
    Ratione: The determination of the center-of-mass energy at which 50% of a precursor ion decomposes (Ecom 50) during collision-induced dissociation (CID) is dependent on the chemical structure of the ion as well as the physical and electrical characteristics of the collision cell. The current study was designed to identify variables influencing Ecom 50 values measured on four different mass spectrometers. Methods: Fifteen test compounds were protonated using + ve electrospray ionization and the resulting ions were fragmented across a range of collision energies by CID. Survival yield versus collision energy curves were then used to calculate Ecom 50 values for each of these [M+H] + ions on four different mass spectrometers. In addition, the relative recovery of the [M+H] + ions of eight compounds ranging in molecular weight from 46 to 854 Da were determined at collision cell radiofrequency (RF) voltages ranging from 0 to 600 V. RESULTS: Ecom 50 values determined on the four instruments were highly correlated (r 2 values ranged from 0.953 to 0.992). Although these overall correlations were high, we found different maximum ion recoveries depending on collision cell RF voltage. High-mass ions had greater recovery at higher collision cell RF voltages, whereas low-mass ions had greater recovery at lower collision cell RF voltages as well as a broader range of ion recoveries. CONCLUSIONS: Ecom 50 values measured on four different instruments correlated surprisingly well given the differences in electrical and physical characteristics of the collision cells. However, our results suggest caution when comparing Ecom 50 values or CID spectra between instruments without correcting for the effects of RF voltage on ion transfer efficiency. Copyright © 2012 John Wiley &amp; Sons, Ltd.
  • Author:
    Tang W; Patel ND; Xu G; Xu X; Savoie J; Ma S; Hao M-H; Keshipeddy S; Capacci AG; Wei X; Zhang Y; Gao JJ; Li W; Rodriguez S; Lu BZ; Yee NK; Senanayake CH
    Title:
    Efficient chiral monophosphorus ligands for asymmetric Suzuki-Miyaura coupling reactions
    Source:
    Org Lett 14 (9), 2258-2261 (2012)
    Abstract:
    A series of novel P-chiral monophosphorus ligands exhibit efficiency in asymmetric Suzuki-Miyaura coupling reactions, enabling the construction of an array of chiral biaryl products in high yields and excellent enantioselectivities (up to 96% ee) under mild conditions. The carbonyl-benzooxazolidinone moiety in these chiral biaryl products allows facile derivatization for further synthetic applications. A computational study has revealed that a pi-pi interaction between the two coupling partners can enhance the enantioselectivity of the coupling reaction. © 2012 American Chemical Society.
  • Author:
    Zimniak T; Fitz V; Zhou H; Lampert F; Opravil S; Mechtler K; Stolt-Bergner P; Westermann S
    Title:
    Spatiotemporal regulation of the lpl1/aurora activity by direct Cdk1 phosphorylation.
    Source:
    Curr Biol 22 (9), 787-793 (2012)
  • Author:
    Beck B
    Title:
    BioProfile - Extract knowledge from corporate databases to assess cross-reactivities of compounds.
    Source:
    Bioorg Med Chem 20 (18), 5428-5435 (2012)
    Abstract:
    In the last 10-15 years, many new technologies and approaches have been implemented in research in the pharmaceutical industry; these include high-throughput screening or combinatorial chemistry, which result in a rapidly growing amount of biological assay and structural data in the corporate databases. Efficient use of the data from this growing data mountain is a key success factor; 'provide as much knowledge as possible as early as possible and therefore enable research teams to make the best possible decision whenever this decision can be supported by stored data'. Here, an approach which started several years ago to obtain as much information as possible out of historical assay data stored in the corporate database is described. It will be shown how important a careful preprocessing of the stored data is to enhance its information. Different possibilities for accessing and to analyzing the preconditioned data are in place. Some of will be described in the examples. © 2011 Elsevier Ltd. All rights reserved.
  • Author:
    Gnamm C; Jeanguenat A; Datton A C; Grimm C; Kloer D P; Crossthwaite A J
    Title:
    Novel diamide insecticides: Sulfoximines, sulfonimidamides and other new sulfonimidoyl derivatives.
    Source:
    Bioorg Med Chem Lett 22 (11), 3800-3806 (2012)
    Abstract:
    Novel insecticidal anthranilamides with elaborated sulfur-containing groups are described. The synthesis of compounds with functional groups such as sulfoximines and scarcely reported groups such as sulfonimidoyl hydrazides and hydroxylamides, their in vitro and in vivo biological activity as well as their physical properties are reported. © 2012 Elsevier Ltd. All rights reserved.
  • Author:
    Crcek B; Baskovc J; Groselj U; Kocar D; Dahmann G; Stanovnik B; Svete J
    Title:
    Parallel synthesis of 2-substituted 6-(5-Oxo-1-phenylpyrrolidin-3yl) pyrimidine-5-carboxamides.
    Source:
    Molecules 17 (5), 5363-5384 (2012)
    Abstract:
    A library of 24 6-(5-oxo-1-phenylpyrrolidin-3-yl)pyrimidine-5-carboxamides 10{1,2; 1-12} was prepared by a parallel solution-phase approach. The synthesiscomprises a five-step transformation of itaconic acid (11) into 1-methyl and 1-phenyl substituted 6-(5-oxo-1-phenylpyrrolidin-3-yl)pyrimidine-5-carboxylic acids 17{1,2} followed by parallel amidation of 17{1,2} with a series of 12 aliphatic amines 18{1-12} to afford the corresponding carboxamides 10 in good overall yields and in 80-100% purity. © 2012 by the Authors. -------------------------------------------------------------------------- ------ Reaxys Database Information |
  • Author:
    Cozma A; Vlase L; Ignat A; Zaharia V; Gocan S; Grinberg N
    Title:
    Prediction of the lipophilicity of eight new p-toluenesulfonyl-hydrazinothiazole and hydrazine-bis-thiazole derivates: A comparison between RP-HPTLC and RP-HPLC.
    Source:
    J Liq Chromatogr Relat Technol 35 (4), 590-601 (2012)
  • Author:
    Frischmuth A; Unsinn A; Groll K; Stadtmüller H; Knochel P
    Title:
    Preparations and reactions of SF 5-substituted aryl and heteroaryl derivatives via Mg and Zn organometallics
    Source:
    Chemistry (Weinheim) 18 (33), 10234-10238 (2012)
    Abstract:
    Polyfunctional SF 5-substituted cycles: Several organometallic sequences using zinc, copper, and magnesium intermediates were developed to prepare a broad range of SF 5-substituted aromatic and heterocyclic compounds of potential interest for pharmaceutical applications. Copyright © 2012 WILEY-VCH Verlag GmbH &amp; Co. KGaA, Weinheim.
  • Author:
    Hampel T; Neubauer T; Van Leeuwen T; Bach T
    Title:
    Stereoselective preparation of (E)-configured 1,2-disubstituted propenes from two aldehydes by a two-carbon stitching strategy: Convergent synthesis of 18,21-diisopropyl-geldanamycin hydroquinone and its C7 epimer
    Source:
    chemistry (Weinheim) 18 (33), 10382-10392 (2012)
    Abstract:
    The title compounds were synthesized in a longest sequence of 27 linear steps and with an overall yield of 2.9 and 3.9 %. In the course of the synthesis, two aldehydes representing carbon fragments C1-C7 (Eastern fragment) and C9-C21 (Western fragment) were prepared from D-mannitol, each of which incorporated a key stereogenic center at the respective secondary methyl ether group (C6, C12) from the chiral pool material. The assembly of the two aldehydes was achieved employing ?-chloroethyl magnesium chloride as a two-carbon building block. The carbenoid reagent was generated from ?-chloroethyl para-tolylsulfoxide by sulfoxide-magnesium exchange and it added smoothly to the highly sensitive aldehyde of the Eastern fragment (C1-C7). Upon oxidation, an ?-chloroethyl ketone was generated, which underwent a clean and high-yielding reductive SmI 2-promoted addition to the other aldehyde fragment. Dehydration delivered the key double bond between C8 and C9 in an overall yield of 72 % over four steps. The method was shown to be generally applicable to the racemization-free conversion of several aldehydes into the respective ?-chloroethyl ketone (11 examples, 64-95 %) and to the coupling protocol (5 examples, 66-90 %). The further course of the geldanamycin hydroquinone synthesis included a diastereoselective reduction at C7 and the implementation of the amino group at C20. Since deprotection of the two isopropyl protecting groups could not be achieved in significant yields, the structure of 18,21-diisopropyl-geldanamycin hydroquinone was proven by its independent synthesis from the natural product. Convergency in the synthesis of the geldanamycin skeleton has been achieved by employing a magnesium carbenoid as a two-carbon building block, connecting two aldehyde fragments in an efficient and high yielding manner. The preparation of ?-chloroethyl ketones from aldehydes has been investigated (11 examples, 64-95 % yield) and the title compounds have been prepared from advanced precursor 1. Copyright © 2012 WILEY-VCH Verlag GmbH &amp; Co. KGaA, Weinheim.
  • Author:
    Jacob S; Mendonsa SD
    Title:
    Strategies for the analysis of pharmaceutical cocrystals using HPLC with charged aerosol detection.
    Source:
    Chromatographia 75 (7-8), 321-328 (2012)
    Abstract:
    Several active pharmaceutical ingredients are currently being developed as pharmaceutical cocrystals as these systems often have superior properties compared to traditional pharmaceutical forms. Pharmaceutical cocrystal formers typically used are polar, small molecule acids or bases which often lack a UV chromophore. Their polar nature results in almost no reversed phase retention and their detection typically cannot be done with UV. Here we discuss approaches for the analysis of pharmaceutical cocrystals using HPLCcolumns designed for polar retention, ion pairing chromatography (IPC), and hydrophilic interaction chromatography (HILIC) using model cocrystal formers. Corona charged aerosol detection (CAD) was used to monitor the cocrystal formers. L-alanine was used as a model basic cocrystal former, and succinic acid and glutaric acid were used as model acidic cocrystal formers. The acidic cocrystal formers were adequately retained on a C18 column. Heptafluorobutyric acid was used as the ionpairing reagent for L-alanine as it was unretained without the ion-pairing reagent. HILIC, a newer approach for polar compound retention, was also investigated. Using the HILIC mode, all three model cocrystal formers were retained adequately. Of all the approaches studied for the analysis of the cocrystal formers, HILIC appears to be the best choice as the same column can be used for both acidic and basic cocrystal formers. With IPC, the ion-pairing reagent permanently alters the column chemistry and dedicated columns are required for each ion-pairing reagent used. CAD detection provided a linear response in the 80-100% test concentration range for the analytes studied here. © 2012 Springer-Verlag.
  • Author:
    Engelhardt H; De Esch I J P; Kuhn D; Smits R A; Zuiderveld O P; Dobler J; Mayer M; Lips S; Amhof H; Scham D; Haaksma E E J; Leurs R
    Title:
    Detailed structure-activity relationship of indolecarboxamides as H 4 receptor ligands
    Source:
    Eur J Med Chem 54, 660-668 (2012)
    Abstract:
    A series of 76 derivatives of the indolecarboxamide 1 were synthesized, which allows a detailed SAR investigation of this well known scaffold. The data enable the definition of a predictive QSAR model which identifies several compounds with an activity comparable to 1. A selection of these new H 4R antagonists was synthesized and a comparison of predicted and measured values demonstrates the robustness of the model (47-55). In addition to the H 4-receptor activity general CMC and DMPK properties were investigated. Some of the new analogs are not only excellently soluble, but display a significantly increased half-life in mouse liver microsomes as well. These properties qualify these compounds as a possible new standard for future in vivo studies (e.g 51, 52 and 55). Moreover, the current studies also provide valuable information on the potential receptor ligand interactions between the indolcarboxamides and the H 4R protein. © 2012 Elsevier Masson SAS. All rights reserved.
  • Author:
    Neumann S; Bidon T; Branschädel M; Krippner Heidenreich A; Scheurich P; Doszczak M
    Title:
    The transmembrane domains of TNF-related apoptosis-inducing ligand (TRAIL) receptors 1 and 2 co-regulate apoptotic signaling capacity
    Source:
    PloS ONE 7 (8) e42526 (2012)
    Abstract:
    TNF-related apoptosis-inducing ligand (TRAIL) is a member of the tumor necrosis factor (TNF) ligand family that exerts its apoptotic activity in human cells by binding to two transmembrane receptors, TRAILR1 and TRAILR2. In cells co-expressing both receptors the particular contribution of either protein to the overall cellular response is not well defined. Here we have investigated whether differences in the signaling capacities of TRAILR1 and TRAILR2 can be attributed to certain functional molecular subdomains. We generated and characterized various chimeric receptors comprising TRAIL receptor domains fused with parts from other members of the TNF death receptor family. This allowed us to compare the contribution of particular domains of the two TRAIL receptors to the overall apoptotic response and to identify elements that regulate apoptotic signaling. Our results show that the TRAIL receptor death domains are weak apoptosis inducers compared to those of CD95/Fas, because TRAILR-derived constructs containing the CD95/Fas death domain possessed strongly enhanced apoptotic capabilities. Importantly, major differences in the signaling strengths of the two TRAIL receptors were linked to their transmembrane domains in combination with the adjacent extracellular stalk regions. This was evident from receptor chimeras comprising the extracellular part of TNFR1 and the intracellular signaling part of CD95/Fas. Both receptor chimeras showed comparable ligand binding affinities and internalization kinetics. However, the respective TRAILR2-derived molecule more efficiently induced apoptosis. It also activated caspase-8 and caspase-3 more strongly and more quickly, albeit being expressed at lower levels. These results suggest that the transmembrane domains together with their adjacent stalk regions can play a major role in control of death receptor activation thereby contributing to cell type specific differences in TRAILR1 and TRAILR2 signaling. © 2012 Neumann et al.
  • Author:
    Lessel U; Wellenzohn B; Fischer JR; Rarey M
    Title:
    Design of combinatoral libaries for the exploration of virtual hils from fragment space searches with LoFT.
    Source:
    J Chem Inform Modeling 52 (2), 373-379 (2012)
  • Author:
    Wassermann A M; Haebel P; Weskamp N; Bajorath J
    Title:
    SAR matrices: Automated extraction of information-rich SAR tables from large compound data sets
    Source:
    J Chem Inform Modeling 52 (7), 1769-1776 (2012)
    Abstract:
    We introduce the SAR matrix data structure that is designed to elucidate SAR patterns produced by groups of structurally related active compounds, which are extracted from large data sets. SAR matrices are systematically generated and sorted on the basis of SAR information content. Matrix generation is computationally efficient and enables processing of large compound sets. The matrix format is reminiscent of SAR tables, and SAR patterns revealed by different categories of matrices are easily interpretable. The structural organization underlying matrix formation is more flexible than standard R-group decomposition schemes. Hence, the resulting matrices capture SAR information in a comprehensive manner. © 2012 American Chemical Society.
  • Author:
    Christ C D; Zentgraf M; Kriegl J M
    Title:
    Mining electronic laboratory notebooks: Analysis, retrosynthesis, and reaction based enumeration
    Source:
    J Chem Inform Modeling 52 (7), 1745-1756 (2012)
    Abstract:
    An approach to automatically analyze and use the knowledge contained in electronic laboratory notebooks (ELNs) has been developed. Reactions were reduced to their reactive center and converted to a string representation (SMIRKS) which formed the basis for reaction classification and in silico (retro-)synthesis. Of the SMIRKS that occurred at least five times, 98% successfully regenerated the original product. The extracted reaction rules (SMIRKS) and corresponding reactants span a virtual chemical space which showed a strong dependence on the size of the reactive center. Whereas relatively few robust reaction types were sufficient to describe a large part of all reactions, considerably more reaction rules were necessary to cover all reactions in the ELN. Furthermore, reaction sequences were extracted to identify frequent combinations and diversifying reaction steps. Based on the extracted knowledge a (retro-)synthesis tool was built allowing for de novo design of compounds which have a high chance of being synthetically accessible. In an example application of the de novo design tool, various feasible retrosynthetic routes to the query molecule were obtained. Reaction based enumeration along the top ranked route yielded a library of 29 920 compounds with diverse properties, 99.9% of which are novel in the sense that they are unknown to the public domain. © 2012 American Chemical Society.
  • Author:
    Elsayad K; Urich A; Nemethova M; Small JV; Unterrainer K; Heinze KG
    Title:
    Fluorescence enhancements and spectral modifications near the cut-off frequency of plasmonic structure.
  • Author:
    Lessel U; Wellenzohn B; Fischer J R; Rarey M
    Title:
    Design of Combinatorial Libraries for the Exploration of Virtual Hits from Fragment Space Searches with LoFT.
    Source:
    J Chem Inform Modeling 52 (2), 373-379 (2012)
    Abstract:
    A case study is presented illustrating the design of a focused CDK2 library. The scaffold of the library was detected by a feature trees search in a fragment space based on reactions from combinatorial chemistry. For the design the software LoFT (Library optimizer using Feature Trees) was used. The special feature called FTMatch was applied to restrict the parts of the queries where the reagents are permitted to match. This way a 3D scoring function could be simulated. Results were compared with alternative designs by GOLD docking and ROC S 3D alignments.
  • Author:
    Haberstock S; Roos C; Hoevels Y; Doetsch V; Schnapp G; Pautsch A; Bernhard F
    Title:
    A systematic approach to increase the efficiency of membrane protein production in cell-free exression systems.
    Source:
    Protein Express Purif 82 (2), 308-316 (2012)
  • Author:
    Roy A; Chanana G
    Title:
    Analytical and formulation attributes: In developing generic sterile injectable liquid and lyophilized drugs (part 1)
    Source:
    Chim Oggi 30 (1), 78-80 (2012)
  • Author:
    Andrews MJI; Andrew Clase J; Bar G; Tricarico G; Edwards PJ; Brys R; Chambers M; Schmidt W; MacLeod A; Hirst K; Allen V; Birault V; Le J; Harris J; Self A; Nash K; Dixon G
    Title:
    Discovery of a series of imidazopyrazine small molecule inhibitors of the kinase MAPKAPK5, that show actifity using in vitro and in vivo models of rheumatoid arthritis.
    Source:
    Bioorg Med Chem Lett 22 (6), 2266-2270 (2012)
  • Author:
    Qu B; Haddad N; Rodriguez S; Lee H; Ma S; Zeng X; Reeves DC; Sidhu KPS; Lorenz JC; Grinberg N; Busacca CA; Krishnamurthy D; Senanayake CH
    Title:
    Chelation controlled reductive amination of cyclic ketones to trans-4-methoxycyclohexylamines: 9-BBN reduction mediated with FeCl3.
    Source:
    Tetrahedron Lett 53 (15), 1982-1986 (2012)
    Abstract:
    A novel trans-diastereoselective reductive amination of 4-substituted cyclohexanones is described using 9-BBN as reducing agent in the presence of FeCl 3. The method permits efficient synthesis of structurally diverse 4-trans-alkoxycyclohexylamines. © 2011 Elsevier Inc. All rights reserved.
  • Author:
    Larson ET; Ojo KK; Murphy RC; Johnson SM; Zhang Z; Kim JE; Leibly DJ; Fox AMW; Reid MC; Dale EJ; Perera BGK; Kim J; Hewitt SN; Hol WGJ; Verlinde CLMJ; Fan E; van Voorhis WC; Maly DJ; Merrit EA
    Title:
    Multiple determinants for selective inhibition of apicomplexan calcium-dependent protein kinase CDPK1.
    Source:
    J Med Chem 55 (6), 2803-2810 (2012)
    Abstract:
    Diseases caused by the apicomplexan protozoans Toxoplasma gondii and Cryptosporidium parvum are a major health concern. The life cycle of these parasites is regulated by a family of calcium-dependent protein kinases (CDPKs) that have no direct homologues in the human host. Fortuitously, CDPK1 from both parasites contains a rare glycine gatekeeper residue adjacent to the ATP-binding pocket. This has allowed creation of a series of C3-substituted pyrazolopyrimidine compounds that are potent inhibitors selective for CDPK1 over a panel of human kinases. Here we demonstrate that selectivity is further enhanced by modification of the scaffold at the C1 position. The explanation for this unexpected result is provided by crystal structures of the inhibitors bound to CDPK1 and the human kinase c-SRC. Furthermore, the insight gained from these studies was applied to transform an alternative ATP-competitive scaffold lacking potency and selectivity for CDPK1 into a low nanomolar inhibitor of this enzyme with no activity against SRC. © 2012 American Chemical Society.
  • Author:
    Timmerman P; Lausecker B; Barosso B; Van Amsterdam P; Luedtke S; Dijeksman J
    Title:
    Conference report:'Large meets small'. Connecting the bioanalytical community around peptide and protein bioanalysis with LC-MS/MS.
    Source:
    Bioanalysis 4 (6), 627-631 (2012)
  • Author:
    Dijksman J; Timmerman P; Abbott R; Barroso B; Kloeppel MB; Companjen A; Golob M; Gordon B; Herling C; Knutsson M; Luedtke S; Rasmussen BB; Stoellner D; Vieser E; Young G; Van Amsterdam P
    Title:
    Conference report: 'Less is More'. Defining modern bioanalysis.
    Source:
    Bioanalysis 4 (6), 633-642 (2012)
  • Author:
    Dziedzic J; Fox SJ; Fox T; Tautermann CS; Skylaris C-K
    Title:
    Large-scale DFT calculations in implicit solvent-A case study on the T4 lysozyme L99A/M102Q protein.
    Source:
    Int J Quantum Chem Article in Press (2012)
  • Author:
    Zhang L; Li Z; Wang X-J; Yee N; Senanayake C-H
    Title:
    Regioselective synthesis of polysubstituted N 2-alkylanyl-1,2,3-triazoles via 4-bromo-5-iodo-1,2,3-triazole.
    Source:
    Synlett 23 (7), 1052-1056 (2012)
  • Author:
    Feil SC; Hamilton S; Krippner GY; Lin B; Luttick A; McConnell DB; Nearn R; Parker MW; Ryan J; Stanislawski PC; Tucker SP; Watson KG; Morton CJ
    Title:
    An orally available 5-ethoxybenzisoxazole capsid binder with clinical activity against human rhinovirus.
    Source:
    ACS Med Chem Lett 3 (4), 303-307 (2012)
  • Author:
    Bantscheff M; Hobson S; Kuster B
    Title:
    Affinity purification of proteins binding to kinase inhibitors immobilized on self-assembling monolayers.
    Source:
    Methods Mol Biol 795, 149-160 (2012)
  • Author:
    Cozma A; Vlase L; Ignast A; Zaharia V; Gocan S; Grinberg N
    Title:
    Prediction of the lipophilicity of eight new p-toluenesulfonyl-hydrazinothiazole and hydrazine-bis-thiazole derivatives: A comparison between RP-HPTLC and RP-HPLC.
    Source:
    J Liq Chromatogr Relat Technol 35 (4), 590-601 (2012)
    Abstract:
    Using RP-HPTLC and RP-HPLC and a methanol-water mixture as the mobile phase, eight new p-toluenesulfonyl-hydrazinothiazole and hydrazine-bis-thiazole derivatives were studied. The linear correlation between R Mw, k W and methanol/water ratios showed high values, for the correlation coefficient R 2. The chromatographic hydrophobic index ? 0 was determined by using intercept and slope, the obtained values ranging between 60 and 98. A good linear correlation was obtained between R Mw, logk w, and slope. The log P values were calculated using database (Toronto, Canada). The matrices were formed with R Mw, logk w and logP and were subjected to principal component analysis (PCA). The best way to extract information from PCA was graphically, by plotting the obtained matrices. By analyzing the scores, the compounds can be grouped in two: the first group contains three compounds that have a phenyl moiety while the second group comprises other five compounds that contain: methyl, chlor-methyl, acetyl, and ethylic ester.
  • Author:
    Seeliger D; Soeroes S; Klingberg R; Schwarzer D; Grubmueller H; Fischle W
    Title:
    Quantitative assessment of protein interaction with methyl-lysine analogues by hybrid computational and experimental approaches.
    Source:
    ACS Chem Biol 7 (1), 150-154 (2012)
    Abstract:
    In cases where binding ligands of proteins are not easily available, structural analogues are often used. For example, in the analysis of proteins recognizing different methyl-lysine residues in histones, methyl-lysine analogues based on methyl-amino-alkylated cysteine residues have been introduced. Whether these are close enough to justify quantitative interpretation of binding experiments is however questionable. To systematically address this issue, we developed, applied, and assessed a hybrid computational/experimental approach that extracts the binding free energy difference between the native ligand (methyl-lysine) and the analogue (methyl-amino-alkylated cysteine) from a thermodynamic cycle. Our results indicate that measured and calculated binding differences are in very good agreement and therefore allow the correction of measured affinities of the analogues. We suggest that quantitative binding parameters for defined ligands in general can be derived by this method with remarkable accuracy.
  • Author:
    Reeves JT; Tan Z; Han ZS; Li G; Zhang Y; Xu Y; Reeves DC; Gonnella NC; Ma S; Lee H; Lu BZ; Senanayake C
    Title:
    Direct titanium-mediated conversion of ketones into enamides with ammonia and acetic anhydride.
    Source:
    Angew Chem Int Ed 51 (6), 1400-1404 (2012)
    Abstract:
    A one-step conversion of ketones into N-acetyl enamides was developed. The process employs safe and inexpensive reagents, proceeds under mild conditions, and tolerates diverse functional groups. The addition of edte (N,N,N ,N -tetrakis(2-hydroxyethyl)ethylenediamine) prior to workup enables water solubilization of Ti alkoxides and allows a simple extractive workup.
  • Author:
    Groselj U; Kralj D; Wagger J; Dahmann G; Stanovnik B; Svete J
    Title:
    Synthesis of 3-(2-aminoethyl)-5-hydroxy-1H-pyrazole derivates.
    Source:
    Arkivoc 2012 (3), 49-65 (2012)
  • Author:
    Whelan G; Eichele G; Kreidl E; Wutz G; Peters J-M; Egner A
    Title:
    Cohesin acetyltransferase Esco2 is a cell viability factor and is required for cohesion in pericenteric heterochromatin.
    Source:
    EMBO J 31 (1), 71-82 (2012)
  • Author:
    Zhang Y; Chitale S; Goyal N; Li G; Lu BZ; Han ZS; Shen S; Ma S; Grinberg N; Lee H; Senanayake CH
    Title:
    Asymmetric synthesis of sulfinamides using (-)-quinine as chiral auxiliary.
    Source:
    J Org Chem 77 (1), 690-695 (2012)
    Abstract:
    A process has been designed and demonstrated for the asymmetric synthesis of sulfinamides using quinine as auxiliary. A variety of chiral sulfinamides including N-alkyl sulfinamides with diverse structure were prepared in good yields and excellent enantioselectivity starting from easily available and inexpensive reagents. The auxiliary quinine could be recovered and recycled.
  • Author:
    Bantscheff M; Hobson S; Kuster B
    Title:
    Affinity purification of proteins binding to kinase inhibitors immobilized on self-assembling monolayers.
    Source:
    Methods Mol Biol 795, 149-160 (2012)
    Abstract:
    Kinase inhibitors represent a relatively new class of drugs that offer novel therapies targeting specific-malfunctioning kinase-mediated signaling pathways in oncology and potentially inflammation. As the ATP binding sites of the â^500 human kinases are structurally conserved and because most current drugs target the ATP binding site, there is a need to profile all the kinases that a drug may bind and/or inhibit. We have developed a chemical proteomics method that affinity purifies kinases from cell or tissue lysates using kinase inhibitors immobilized on self-assembling monolayers. The method can be applied to assess the selectivity of a given kinase inhibitor and thus to guide its preclinical or clinical development.
  • Author:
    Lagace I; White PW; Bousquet C; Dansereau N; Doe F; Linas-Brunet M; Marquis M; Massariol M-J; Maurice R; Spickler C; Thibeault D; Triki I; Zhao S; Kukolj G
    Title:
    In vitro resistance profile of the hepatitis C virus NS3 protease inhibitor BI 201335.
    Source:
    Antimicrob Agents Chemother 56 (1), 569-572 (2012)
    Abstract:
    The in vitro resistance profile of BI 201335 was evaluated through selection and characterization of variants in genotype 1a (GT 1a) and genotype 1b (GT 1b) replicons. NS3 R155K and D168V were the most frequently observed resistant variants. Phenotypic characterization of the mutants revealed shifts in sensitivity specific to BI 201335 that did not alter susceptibility to alpha interferon. In contrast to macrocyclic and covalent protease inhibitors, changes at V36, T54, F43, and Q80 did not confer resistance to BI 201335.
  • Author:
    Yashio K; Katayama Y; Takashima T; Ishiguro N; Doi H; Suzuki M; Wada Y; Tamai I; Watanabe Y
    Title:
    Synthesis of [11C]uric acid, using [11C]phosgene, as a possible biomarker in PET imaging for diagnosis of gout.
    Source:
    Bioorg Med Chem Lett 22 (1), 11-119 (2012)
    Abstract:
    The synthesis and in vivo evaluation of 11C -labeled uric acid ([11C]1), a potential imaging agent for the diagnosis of urate-related life-style diseases, was performed using positron emission tomography (PET) image analysis. First, the synthesis of [11C]1 was achieved by reacting 5,6-diaminouracil (2) with 11C-labeled phosgene ([11C]COCl2). The radiochemical yield of [11C]1 was 37 ± 7% (decay-corrected based on [11C]COCl2) with specific radioactivities of 96-152 GBq/?mol at the end of synthesis (n = 6). The average time of radiosynthesis from the end of bombardment, including formulation, was about 30 min with &gt;98% radiochemical purity. Second, the synthetic approach to [11C]1 was optimized using 5,6-diaminouracil sulfate (3) with [11C]COCl2 in the presence of 1,8-bis(dimethylamino)naphthalene. [11C]1 was synthesized in 36 ± 6% radiochemical yield, 89-142 GBq/?mol of specific radioactivities, and 98% radiochemical purity by this method (n = 5). This allowed the synthesis of [11C]1 to be carried out repeatedly and the radiochemical yield, specific radioactivities, average time of synthesis, and radiochemical purity of [11C]1 were similar to those obtained using 2. PET studies in rats showed large differences in the accumulation of radioligand in the limbs under normal and hyperuricemic conditions. Thus, an efficient and convenient automated synthesis of [11C]1 has been developed, and preliminary PET evaluation of [11C]1 confirmed the increased accumulation of radioactivity in the limbs of a rat model of hyperuricemia.
  • Author:
    Schultes S; de Graaf Ch; Berger H; Mayer M; Steffen A; Haaksma EEJ; de Esch IJP; Leurs R; Kraemer O
    Title:
    A medicinal chemistry perspective on melting point: Matched molecular pair analysis of the effects of simple descriptors on the melting points of drug like compounds.
    Source:
    13th Figon Dutch Medicine Days, Breukelen (Netherlands), Oct 3-5, 2011.MedChemComm 3 (5), 584-591 (2012)
    Abstract:
    The influence of simple molecular descriptors on the melting point temperature (T m) has been investigated using a matched molecular pair (MMP) analysis. This method has been used to identify small structural differences between pairs of molecules which are related to changes in T m. Our analysis shows that the number of hydrogen bond donors, hydrogen bond acceptors and rotatable bonds has a significant effect on the T m of a molecule. Hydrogen bond donors have the most pronounced effect. Furthermore, the studies reveal that not ClogP but rather the number of bromine and iodine atoms has a marked effect on the T m. The results of our MMP analysis are discussed within the context of drug solubility optimization.