51
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Min QQ, Yin Z, Feng Z, Guo WH, Zhang X. Highly selective gem-difluoroallylation of organoborons with bromodifluoromethylated alkenes catalyzed by palladium. J Am Chem Soc 2014; 136:1230-3. [PMID: 24417183 DOI: 10.1021/ja4114825] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A first example of Pd-catalyzed gem-difluoroallylation of organoborons using 3-bromo-3,3-difluoropropene (BDFP) in high efficiency with high α/γ-substitution regioselectivity has been developed. The reaction can also be extended to substituted BDFPs and has advantages of low catalyst loading (0.8 to 0.01 mol %), broad substrate scope, and excellent functional group compatibility, thus providing a facile route for practical application in drug discovery and development.
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Affiliation(s)
- Qiao-Qiao Min
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences , 345 Lingling Road, Shanghai 200032, China
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52
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Mehta AY, Jin Y, Desai UR. An update on recent patents on thrombin inhibitors (2010 – 2013). Expert Opin Ther Pat 2013; 24:47-67. [DOI: 10.1517/13543776.2014.845169] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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53
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Stepan AF, Mascitti V, Beaumont K, Kalgutkar AS. Metabolism-guided drug design. MEDCHEMCOMM 2013. [DOI: 10.1039/c2md20317k] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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54
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Fluorescence polarization assay for inhibitors of the kinase domain of receptor interacting protein 1. Anal Biochem 2012; 427:164-74. [PMID: 22658960 DOI: 10.1016/j.ab.2012.05.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 04/18/2012] [Accepted: 05/21/2012] [Indexed: 01/07/2023]
Abstract
Necrotic cell death is prevalent in many different pathological disease states and in traumatic injury. Necroptosis is a form of necrosis that stems from specific signaling pathways, with the key regulator being receptor interacting protein 1 (RIP1), a serine/threonine kinase. Specific inhibitors of RIP1, termed necrostatins, are potent inhibitors of necroptosis. Necrostatins are structurally distinct from one another yet still possess the ability to inhibit RIP1 kinase activity. To further understand the differences in the binding of the various necrostatins to RIP1 and to develop a robust high-throughput screening (HTS) assay, which can be used to identify new classes of RIP1 inhibitors, we synthesized fluorescein derivatives of Necrostatin-1 (Nec-1) and Nec-3. These compounds were used to establish a fluorescence polarization (FP) assay to directly measure the binding of necrostatins to RIP1 kinase. The fluorescein-labeled compounds are well suited for HTS because the assays have a dimethyl sulfoxide (DMSO) tolerance up to 5% and Z' scores of 0.62 (fluorescein-Nec-1) and 0.57 (fluorescein-Nec-3). In addition, results obtained from the FP assays and ligand docking studies provide insights into the putative binding sites of Nec-1, Nec-3, and Nec-4.
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55
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On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities. Proc Natl Acad Sci U S A 2012; 109:1937-42. [PMID: 22308365 DOI: 10.1073/pnas.1114017109] [Citation(s) in RCA: 188] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We apply a free energy perturbation simulation method, free energy perturbation/replica exchange with solute tempering, to two modifications of protein-ligand complexes that lead to significant conformational changes, the first in the protein and the second in the ligand. The approach is shown to facilitate sampling in these challenging cases where high free energy barriers separate the initial and final conformations and leads to superior convergence of the free energy as demonstrated both by consistency of the results (independence from the starting conformation) and agreement with experimental binding affinity data. The second case, consisting of two neutral thrombin ligands that are taken from a recent medicinal chemistry program for this interesting pharmaceutical target, is of particular significance in that it demonstrates that good results can be obtained for large, complex ligands, as opposed to relatively simple model systems. To achieve quantitative agreement with experiment in the thrombin case, a next generation force field, Optimized Potentials for Liquid Simulations 2.0, is required, which provides superior charges and torsional parameters as compared to earlier alternatives.
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56
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Lill MA, Thompson JJ. Solvent interaction energy calculations on molecular dynamics trajectories: increasing the efficiency using systematic frame selection. J Chem Inf Model 2011; 51:2680-9. [PMID: 21870864 DOI: 10.1021/ci200191m] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
End-point methods such as linear interaction energy (LIE) analysis, molecular mechanics generalized Born solvent-accessible surface (MM/GBSA), and solvent interaction energy (SIE) analysis have become popular techniques to calculate the free energy associated with protein-ligand binding. Such methods typically use molecular dynamics (MD) simulations to generate an ensemble of protein structures that encompasses the bound and unbound states. The energy evaluation method (LIE, MM/GBSA, or SIE) is subsequently used to calculate the energy of each member of the ensemble, thus providing an estimate of the average free energy difference between the bound and unbound states. The workflow requiring both MD simulation and energy calculation for each frame and each trajectory proves to be computationally expensive. In an attempt to reduce the high computational cost associated with end-point methods, we study several methods by which frames may be intelligently selected from the MD simulation including clustering and address the question of how the number of selected frames influences the accuracy of the SIE calculations.
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Affiliation(s)
- Markus A Lill
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States.
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57
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Integrating structure-based and ligand-based approaches for computational drug design. Future Med Chem 2011; 3:735-50. [PMID: 21554079 DOI: 10.4155/fmc.11.18] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Methods utilized in computer-aided drug design can be classified into two major categories: structure based and ligand based, using information on the structure of the protein or on the biological and physicochemical properties of bound ligands, respectively. In recent years there has been a trend towards integrating these two methods in order to enhance the reliability and efficiency of computer-aided drug-design approaches by combining information from both the ligand and the protein. This trend resulted in a variety of methods that include: pseudoreceptor methods, pharmacophore methods, fingerprint methods and approaches integrating docking with similarity-based methods. In this article, we will describe the concepts behind each method and selected applications.
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58
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Vulpetti A, Schiering N, Dalvit C. Combined use of computational chemistry, NMR screening, and X-ray crystallography for identification and characterization of fluorophilic protein environments. Proteins 2011; 78:3281-91. [PMID: 20886466 DOI: 10.1002/prot.22836] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
(19)F NMR screening of fluorinated fragments with different Local Environment of Fluorine, a.k.a. LEF library, is an experimental methodology which, beyond providing useful starting fragments for fragment-based drug discovery projects, offers, in combination with crystal and computational analysis, an approach for the identification of fluorophilic hot-spots in the proteins of interest. The application of this approach in the identification of fluorinated fragments binding to the serine protease trypsin, and the X-ray structures of the complexes are presented. The specific nature of the observed fluorine-protein interactions is discussed and compared with the interactions detected for other fluorinated ligands reported in the protein data bank. The presence of similar 3D arrangements of protein atoms at the fluorine sub-sites is identified with a newly developed tool. In this approach, protein sub-sites are extracted around each fluorine contained in the protein data bank and compared with the query of interest by using a pharmacophoric description.
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Affiliation(s)
- Anna Vulpetti
- Global Chemistry Discovery, Novartis Institutes for Biomedical Research, CH-4002 Basel, Switzerland.
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59
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Chen Z, Zhu J, Xie H, Li S, Wu Y, Gong Y. A cascade process for the synthesis of gem-difluoromethylene compounds. Org Biomol Chem 2011; 9:3878-85. [DOI: 10.1039/c1ob00027f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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60
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Herrebout WA, Nagels N, Verbeeck S, van der Veken BJ, Maes BUW. A DFT Study of Site-Selectivity in Oxidative Addition Reactions with Pd0 Complexes: The Effect of an Azine Nitrogen and the Use of Different Types of Halogen Atoms in the Substrate. European J Org Chem 2010. [DOI: 10.1002/ejoc.200900808] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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61
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Synthesis of a versatile 2 (1H)-pyrazinone core for the preparation of Tissue Factor-Factor VIIa inhibitors. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.02.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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62
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Zhuo X, Hartz RA, Bronson JJ, Wong H, Ahuja VT, Vrudhula VM, Leet JE, Huang S, Macor JE, Shu YZ. Comparative biotransformation of pyrazinone-containing corticotropin-releasing factor receptor-1 antagonists: minimizing the reactive metabolite formation. Drug Metab Dispos 2010; 38:5-15. [PMID: 19833844 DOI: 10.1124/dmd.109.028910] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
(S)-5-Chloro-1-(1-cyclopropylethyl)-3-(2,6-dichloro-4-(trifluoromethyl)phenylamino)pyrazin-2(1H)-one (BMS-665053), a pyrazinone-containing compound, is a potent and selective antagonist of corticotropin-releasing factor receptor-1 (CRF-R1) that showed efficacy in the defensive withdrawal model for anxiety in rats, suggesting its use as a potential treatment for anxiety and depression. In vitro metabolism studies of BMS-665053 in rat and human liver microsomes revealed cytochrome P450-mediated oxidation of the pyrazinone moiety, followed by ring opening, as the primary metabolic pathway. Detection of a series of GSH adducts in trapping experiments suggested the formation of a reactive intermediate, probably as a result of epoxidation of the pyrazinone moiety. In addition, BMS-665053 (20 mg/kg i.v.) underwent extensive metabolism in bile duct-cannulated (BDC) rats. The major drug-related materials in rat plasma were the pyrazinone oxidation products. In rat bile and urine (0-7 h), only a trace amount of the parent drug was recovered, whereas significant levels of the pyrazinone epoxide-derived metabolites and GSH-related conjugates were detected. Further evidence suggested that GSH-related conjugates also formed at the dichloroarylamine moiety possibly via an epoxide or a quinone imine intermediate. Other major metabolites in BDC rat bile and urine included glucuronide conjugates. To reduce potential liability due to metabolic activation of BMS-665053, a number of pyrazinone analogs with different substituents were synthesized and investigated for reactive metabolite formation, leading to the discovery of a CRF-R1 antagonist with diminished in vitro metabolic activation.
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Affiliation(s)
- Xiaoliang Zhuo
- Departments of Biotransformation, Bristol-Myers Squibb Company, 5 Research Parkway, Wallingford, CT 06492, USA.
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63
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Sokolov VB, Aksinenko AY. Reactions of methyl 3,3,3-trifluoro-2-(pyridin-2-ylimino)-propanoates with mono- and difunctional nucleophiles. RUSS J GEN CHEM+ 2010. [DOI: 10.1134/s1070363210010147] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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64
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Lu T, Markotan T, Ballentine SK, Giardino EC, Spurlino J, Brown K, Maryanoff BE, Tomczuk BE, Damiano BP, Shukla U, End D, Andrade-Gordon P, Bone RF, Player MR. Discovery and Clinical Evaluation of 1-{N-[2-(Amidinoaminooxy)ethyl]amino}carbonylmethyl-6-methyl-3-[2,2-difluoro-2-phenylethylamino]pyrazinone (RWJ-671818), a Thrombin Inhibitor with an Oxyguanidine P1 Motif. J Med Chem 2010; 53:1843-56. [DOI: 10.1021/jm901802n] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tianbao Lu
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Thomas Markotan
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Shelley K. Ballentine
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Edward C. Giardino
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - John Spurlino
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Kathryn Brown
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Bruce E. Maryanoff
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Bruce E. Tomczuk
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Bruce P. Damiano
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Umesh Shukla
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - David End
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Patricia Andrade-Gordon
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Roger F. Bone
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Mark R. Player
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
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65
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Halgren TA. Identifying and Characterizing Binding Sites and Assessing Druggability. J Chem Inf Model 2009; 49:377-89. [DOI: 10.1021/ci800324m] [Citation(s) in RCA: 968] [Impact Index Per Article: 64.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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66
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Krishnasamy C, Raghuraman A, Kier L, Desai U. Application of Molecular Connectivity and Electro-Topological Indices in Quantitative Structure-Activity Analysis of Pyrazole Derivatives as Inhibitors of Factor Xa and Thrombin. Chem Biodivers 2008; 5:2609-20. [DOI: 10.1002/cbdv.200890216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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67
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Wu E, Han K, Zhang J. Selectivity of Neutral/Weakly Basic P1 Group Inhibitors of Thrombin and Trypsin by a Molecular Dynamics Study. Chemistry 2008; 14:8704-14. [DOI: 10.1002/chem.200800277] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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68
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(d)-2-tert-Butoxycarbonylamino-5,5-difluoro-5-phenyl-pentanoic acid: Synthesis and incorporation into the growth hormone secretagogues. Bioorg Med Chem Lett 2008; 18:4072-4. [DOI: 10.1016/j.bmcl.2008.05.100] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2008] [Revised: 05/22/2008] [Accepted: 05/27/2008] [Indexed: 11/18/2022]
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69
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Teng X, Keys H, Yuan J, Degterev A, Cuny GD. Structure-activity relationship and liver microsome stability studies of pyrrole necroptosis inhibitors. Bioorg Med Chem Lett 2008; 18:3219-23. [PMID: 18467094 PMCID: PMC2519155 DOI: 10.1016/j.bmcl.2008.04.048] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2008] [Accepted: 04/22/2008] [Indexed: 01/18/2023]
Abstract
Necroptosis is a regulated caspase-independent cell death pathway resulting in morphology reminiscent of passive non-regulated necrosis. Several diverse structure classes of necroptosis inhibitors have been reported to date, including a series of [1,2,3]thiadiazole benzylamide derivatives. However, initial evaluation of mouse liver microsome stability indicated that this series of compounds was rapidly degraded. A structure-activity relationship (SAR) study of the [1,2,3]thiadiazole benzylamide series revealed that increased mouse liver microsome stability and increased necroptosis inhibitory activity could be accomplished by replacement of the 4-cyclopropyl-[1,2,3]thiadiazole with a 5-cyano-1-methylpyrrole. In addition, the SAR and the cellular activity profiles, utilizing different cell types and necroptosis-inducing stimuli, of representative [1,2,3]thiadiazole and pyrrole derivatives were very similar suggesting that the two compound series inhibit necroptosis in the same manner.
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Affiliation(s)
- Xin Teng
- Laboratory for Drug Discovery in Neurodegeneration, Harvard NeuroDiscovery Center, Brigham & Women’s Hospital and Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA
| | - Heather Keys
- Department of Biochemistry, Tufts University Medical School, 136 Harrison Avenue, Stearns 703, Boston, MA 02111, USA
| | - Junying Yuan
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Alexei Degterev
- Department of Biochemistry, Tufts University Medical School, 136 Harrison Avenue, Stearns 703, Boston, MA 02111, USA
| | - Gregory D. Cuny
- Laboratory for Drug Discovery in Neurodegeneration, Harvard NeuroDiscovery Center, Brigham & Women’s Hospital and Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA
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70
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Orally efficacious thrombin inhibitors with cyanofluorophenylacetamide as the P2 motif. Bioorg Med Chem Lett 2008; 18:2865-70. [DOI: 10.1016/j.bmcl.2008.03.087] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2008] [Accepted: 03/31/2008] [Indexed: 11/19/2022]
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71
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Hernandez Prada JA, Madden SL, Ostrov DA, Hernandez MA. Molecular modeling optimization of anticoagulant pyridine derivatives. J Mol Graph Model 2008; 26:1365-9. [PMID: 18372200 DOI: 10.1016/j.jmgm.2008.01.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2007] [Revised: 01/25/2008] [Accepted: 01/26/2008] [Indexed: 12/01/2022]
Abstract
Intravascular clotting remains a major health problem in the United States, the most prominent being deep vein thrombosis, pulmonary embolism and thromboembolic stroke. Previous reports on the use of pyridine derivatives in cardiovascular drug development encourage us to pursue new types of compounds based on a pyridine scaffold. Eleven pyridine derivatives (oximes, semicarbazones, N-oxides) previously synthesized in our laboratories were tested as anticoagulants on pooled normal plasma using the prothrombin time (PT) protocol. The best anticoagulant within the oxime series was compound AF4, within the oxime N-oxide series was compound AF4-N-oxide, and within the semicarbazone series, compound MD1-30Y. We also used a molecular modeling approach to guide our efforts, and found that there was good correlation between coagulation data and computational energy scores. Molecular docking was performed to target the active site of thrombin with the DOCK v5.2 package. The results of molecular modeling indicate that improvement in anticoagulant activities can be expected by functionalization at the three-position of the pyridine ring and by N-oxide formation. Results reported here prove the suitability of DOCK in the lead optimization process.
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Affiliation(s)
- Jose A Hernandez Prada
- University of Florida, Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, Gainesville, FL, USA
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72
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Stürzebecher A, Dönnecke D, Schweinitz A, Schuster O, Steinmetzer P, Stürzebecher U, Kotthaus J, Clement B, Stürzebecher J, Steinmetzer T. Highly Potent and Selective Substrate Analogue Factor Xa Inhibitors ContainingD-Homophenylalanine Analogues as P3 Residue: Part 2. ChemMedChem 2007; 2:1043-53. [PMID: 17541992 DOI: 10.1002/cmdc.200700031] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A series of highly potent substrate-analogue factor Xa inhibitors containing D-homophenylalanine analogues as the P3 residue has been identified by systematic optimization of a previously described inhibitor structure. An initial lead, benzylsulfonyl-D-hPhe-Gly-4-amidinobenzylamide (3), inhibits fXa with an inhibition constant of 6.0 nM. Most modifications of the P2 amino acid and P4 benzylsulfonyl group did not improve the affinity and selectivity of the compounds as fXa inhibitors. In contrast, further variation at the P3 position led to inhibitors with significantly enhanced potency and selectivity. Inhibitor 27, benzylsulfonyl-D-homo-2-pyridylalanyl(N-oxide)-Gly-4-amidinobenzylamide, inhibits fXa with a K(i) value of 0.32 nM. The inhibitor has strong anticoagulant activity in plasma and doubles the activated partial thromboplastin time and prothrombin time at concentrations of 280 nM and 170 nM, respectively. Compound 27 inhibits the prothrombinase complex with an IC(50) value of 5 nM and is approximately 50 times more potent than the reference inhibitor DX-9065a in this assay.
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73
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Kamoune L, De Borggraeve WM, Gielens C, Voet A, Robeyns K, De Maeyer M, Van Meervelt L, Compernolle F, Hoornaert G. Design, Synthesis and Evaluation of Serine Protease Inhibitor Analogues. European J Org Chem 2007. [DOI: 10.1002/ejoc.200700180] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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74
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Erve JC. Chemical toxicology: reactive intermediates and their role in pharmacology and toxicology. Expert Opin Drug Metab Toxicol 2007; 2:923-46. [PMID: 17125409 DOI: 10.1517/17425255.2.6.923] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Reactive intermediates formed during the metabolism of drugs have been investigated extensively over the past decades. Today, interest in reactive intermediates in drug discovery is focused on minimising bioactivation in hopes of reducing the risk of causing so-called idiosyncratic toxicity. These efforts are justified based on the 'hapten hypothesis', namely, that on binding to protein, reactive intermediates may elicit an immune response to the modified protein, leading to a cascade of events that ultimately manifests as a toxic outcome. However, the pharmacological action of certain drugs depends on reactive intermediates that modify critical amino acid residues of proteins, typically enzymes, thereby altering their activity. Thus, the notion that reactive intermediates are inherently dangerous is unjustified. When a reactive intermediate is necessary for the desired pharmacological effect of a drug, the selectivity it displays towards the target protein is crucial, as off-target binding may produce unwanted toxicities. On the other hand, reactive intermediates may play no role in toxicity. This review provides a balanced perspective, primarily focusing on the proposed role of reactive intermediates in drug toxicity, while also highlighting examples in which they are involved in causing the desired pharmacology. It is hoped that this knowledge can help scientists involved in drug discovery and development in their challenging task of producing safe and effective drugs.
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Affiliation(s)
- John Cl Erve
- Wyeth Research, Drug Safety and Metabolism, Collegeville, PA 19426, USA.
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75
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Hanessian S, Therrien E, van Otterlo WAL, Bayrakdarian M, Nilsson I, Fjellström O, Xue Y. Phenolic P2/P3 core motif as thrombin inhibitors—Design, synthesis, and X-ray co-crystal structure. Bioorg Med Chem Lett 2006; 16:1032-6. [PMID: 16290930 DOI: 10.1016/j.bmcl.2005.10.082] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2005] [Revised: 10/14/2005] [Accepted: 10/24/2005] [Indexed: 10/25/2022]
Abstract
Prototypical thrombin inhibitors were synthesized based on a trisubstituted phenol as a core motif. A naphthylsulfonamide analogue showed excellent antithrombin activity. An X-ray co-crystal structure showed the expected interactions.
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Affiliation(s)
- Stephen Hanessian
- Department of Chemistry, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, PQ, Canada H3C 3J7.
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Deng JZ, McMasters DR, Rabbat PMA, Williams PD, Coburn CA, Yan Y, Kuo LC, Lewis SD, Lucas BJ, Krueger JA, Strulovici B, Vacca JP, Lyle TA, Burgey CS. Development of an oxazolopyridine series of dual thrombin/factor Xa inhibitors via structure-guided lead optimization. Bioorg Med Chem Lett 2005; 15:4411-6. [PMID: 16137886 DOI: 10.1016/j.bmcl.2005.07.022] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2005] [Revised: 07/19/2005] [Accepted: 07/20/2005] [Indexed: 11/29/2022]
Abstract
Thrombin-inhibitor X-ray crystal structures, in combination with the installation of binding elements optimized within the pyrazinone series of thrombin inhibitors, were utilized to transform a weak triazolopyrimidine lead into a series of potent oxazolopyridines. A modification intended to attenuate plasma protein binding (i.e., conversion of the P3 pyridine to a piperidine) conferred significant factor Xa activity to this series. Ultimately, these dual thrombin/factor Xa inhibitors demonstrated excellent in vitro and in vivo anticoagulant efficacy.
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Affiliation(s)
- James Z Deng
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, USA
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Lin CC, Wong BK, Burgey CS, Gibson CR, Singh R. In vitro metabolism of a thrombin inhibitor and quantitation of metabolically generated cyanide. J Pharm Biomed Anal 2005; 39:1014-20. [PMID: 16023819 DOI: 10.1016/j.jpba.2005.05.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2005] [Revised: 05/27/2005] [Accepted: 05/27/2005] [Indexed: 10/25/2022]
Abstract
During the metabolic characterization of compound I, 2-{6-cyano-3-[(2,2-difluoro-2-pyridin-2-ylethyl)amino]-2-oxopyrazin-1(2H)-yl]-N-[(3-fluoropyridin-2-yl)methyl]acetamide, evidence was obtained for extensive oxidative bioactivation of the pyrazinone ring system and some of the resulting metabolites were apparently devoid of the cyano moiety. Two assays, a spectrophotometric and a high-pressure liquid chromatography (HPLC) pre-column derivatization method, were evaluated for their ability to detect and quantify cyanide that is metabolically generated from liver microsomal incubations. When I was incubated (45 microM) in the presence of NADPH-fortified human liver microsomes for 2h, 7.5 microM of cyanide was detected using the spectrophotometric assay and 8.9 microM was measured using the HPLC methodology. Overall, the results from the two assays appeared to agree reasonably well with each other. However, the HPLC assay was the preferred method for the evaluation of cyanide formation in vitro due to its sensitivity, reliability, and ease of use.
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Affiliation(s)
- C Charles Lin
- Department of Drug Metabolism, Merck Research Laboratories, Merck and Co. Inc., Merck Research Labs, BLA-33, P.O. Box 4, PA 19486, USA
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78
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Kranjc A, Masic LP, Reven S, Mikic K, Prezelj A, Stegnar M, Kikelj D. Novel pyrazinone and pyridinone thrombin inhibitors incorporating weakly basic heterobicyclic P1-arginine mimetics. Eur J Med Chem 2005; 40:782-91. [PMID: 15890436 DOI: 10.1016/j.ejmech.2005.03.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2004] [Revised: 03/07/2005] [Accepted: 03/07/2005] [Indexed: 11/30/2022]
Abstract
The design, synthesis and biological activity of new thrombin inhibitors with a pyridinone or pyrazinone core and different heterobicyclic P(1) arginine side-chain mimetics are described. The arginine side-chain mimetics used in this study are (+/-)-4,5,6,7-tetrahydro-2H-indazol-5-ylmethanamine and both enantiomers thereof, (+/-)-4,5,6,7-tetrahydro-1,3-benzothiazole-2,6-diamine and the corresponding R enantiomer. Compound 25, the most potent in the series of pyrazinone inhibitors, exhibited a K(i) of 41 nM in vitro and high selectivity against trypsin and factor Xa.
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Affiliation(s)
- Andreja Kranjc
- Faculty of Pharmacy, University of Ljubljana, Askerceva 7, 1000 Ljubljana, Slovenia
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79
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Ahlström MM, Ridderström M, Luthman K, Zamora I. Virtual Screening and Scaffold Hopping Based on GRID Molecular Interaction Fields. J Chem Inf Model 2005; 45:1313-23. [PMID: 16180908 DOI: 10.1021/ci049626p] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, a set of strategies for structure-based design using GRID molecular interaction fields (MIFs) to derive a pharmacophoric representation of a protein is reported. Thrombin, one of the key enzymes involved in the blood coagulation cascade, was chosen as the model system since abundant published experimental data are available related to both crystal structures and structurally diverse sets of inhibitors. First, a virtual screening methodology was developed either using a pharmacophore representation of the protein based on GRID MIFs or using GRID MIFs from the 3D structure of a set of chosen thrombin inhibitors. The search was done in a 3D multiconformation version of the Available Chemical Directory (ACD) database, which had been spiked with 262 known thrombin inhibitors (multiple conformers available per compound). The model managed to find 80% of the known thrombin inhibitors among the 74,291 conformers in the ACD by only searching 5% of the database; hence, a 15-fold enrichment of the library was achieved. Second, a scaffold hopping methodology was developed using GRID MIFs, giving the scaffold interaction pattern and the shape of the scaffold, together with the distance between the anchor points. The scaffolds reported by Dolle in the Journal of Combinatorial Chemistry summaries (2000 and 2001) and scaffolds built or derived from ligands cocomplexed with the thrombin enzyme were parameterized using a new set of descriptors and saved into a searchable database. The scaffold representation from the database was then compared to a template scaffold (from a thrombin crystal structure), and the thrombin-derived scaffolds included in the database were found among the top solutions. To validate the usefulness of the methodology to replace the template scaffold, the entire molecule was built (scaffold and side chains) and the resulting compounds were docked into the active site of thrombin. The docking solutions showed the same binding pattern as the cocomplexed compound, hence, showing that this method can be a valuable tool for medicinal chemists to select interchangeable core structures (scaffolds) in an easy manner and retaining the binding properties from the original ligand.
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Affiliation(s)
- Marie M Ahlström
- DMPK & BAC Department, AstraZeneca R&D Mölndal, SE-431 81 Mölndal, Sweden.
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80
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Nantermet PG, Burgey CS, Robinson KA, Pellicore JM, Newton CL, Deng JZ, Selnick HG, Lewis SD, Lucas BJ, Krueger JA, Miller-Stein C, White RB, Wong B, McMasters DR, Wallace AA, Lynch JJ, Yan Y, Chen Z, Kuo L, Gardell SJ, Shafer JA, Vacca JP, Lyle TA. P2 pyridine N-oxide thrombin inhibitors: a novel peptidomimetic scaffold. Bioorg Med Chem Lett 2005; 15:2771-5. [PMID: 15911253 DOI: 10.1016/j.bmcl.2005.03.110] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2005] [Revised: 03/28/2005] [Accepted: 03/29/2005] [Indexed: 11/17/2022]
Abstract
In this study, we have demonstrated that the critical hydrogen bonding motif of the established 3-aminopyrazinone thrombin inhibitors can be effectively mimicked by a 2-aminopyridine N-oxide. As this peptidomimetic core is more resistant toward oxidative metabolism, it also overcomes the metabolic liability associated with the pyrazinones. An optimization study of the P(1) benzylamide delivered the potent thrombin inhibitor 21 (K(i) = 3.2 nM, 2xaPTT = 360 nM), which exhibited good plasma levels and half-life after oral dosing in the dog (C(max) = 2.6 microM, t(1/2) = 4.5 h).
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Affiliation(s)
- Philippe G Nantermet
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, USA.
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81
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A comparison between two polarizability parameters in chemical–biological interactions. Bioorg Med Chem 2005; 13:2355-72. [DOI: 10.1016/j.bmc.2005.01.051] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2004] [Revised: 01/25/2005] [Accepted: 01/26/2005] [Indexed: 10/25/2022]
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82
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Scarborough RM, Pandey A, Zhang X. Small Molecule Anticoagulant/Antithrombotic Agents. ANNUAL REPORTS IN MEDICINAL CHEMISTRY VOLUME 40 2005. [DOI: 10.1016/s0065-7743(05)40006-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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83
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Hopkins C, Neuenschwander K, Scotese A, Jackson S, Nieduzak T, Pauls H, Liang G, Sides K, Cramer D, Cairns J, Maignan S, Mathieu M. Novel pyrazinone inhibitors of mast cell tryptase: synthesis and SAR evaluation. Bioorg Med Chem Lett 2004; 14:4819-23. [PMID: 15341931 DOI: 10.1016/j.bmcl.2004.07.051] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2004] [Revised: 07/22/2004] [Accepted: 07/23/2004] [Indexed: 10/26/2022]
Abstract
In this manuscript, the synthesis and SAR evaluation of a novel pyrazinone class of tryptase inhibitors is described. Chemical optimization of the P1 and P4 groups led to the identification of 7p (K(i)=93 nM) as a potent inhibitor of mast cell tryptase.
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Affiliation(s)
- Corey Hopkins
- Department of Medicinal Chemistry, Drug Innovation and Approval, Aventis Pharmaceuticals, Route 202-206, Bridgewater, NJ 08807, USA.
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84
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Kranjc A, Peterlin-Masic L, Ilas J, Prezelj A, Stegnar M, Kikelj D. Novel thrombin inhibitors incorporating weakly basic heterobicyclic P1-arginine mimetics: optimization via modification of P1 and P3 moieties. Bioorg Med Chem Lett 2004; 14:3251-6. [PMID: 15149685 DOI: 10.1016/j.bmcl.2004.03.085] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2004] [Revised: 03/16/2004] [Accepted: 03/29/2004] [Indexed: 10/26/2022]
Abstract
Optimization of lead compounds 1 and 2 resulted in novel, selective, and potent thrombin inhibitors incorporating weakly basic heterobicyclic P(1)-arginine mimetics. The design, synthesis, and biological activity of racemic thrombin inhibitors 17-29 and enantiomerically pure thrombin inhibitors 30-33 are described. The arginine side-chain mimetics used in this study are 4,5,6,7-tetrahydro-1,3-benzothiazol-2-amine, 4,5,6,7-tetrahydro-2H-indazole, and 2-imino-4,5,6,7-tetrahydro-1,3-benzothiazol-3(2H)-ylamine.
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Affiliation(s)
- Andreja Kranjc
- Faculty of Pharmacy, University of Ljubljana, Askerceva 7, 1000 Ljubljana, Slovenia
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85
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Young MB, Barrow JC, Glass KL, Lundell GF, Newton CL, Pellicore JM, Rittle KE, Selnick HG, Stauffer KJ, Vacca JP, Williams PD, Bohn D, Clayton FC, Cook JJ, Krueger JA, Kuo LC, Lewis SD, Lucas BJ, McMasters DR, Miller-Stein C, Pietrak BL, Wallace AA, White RB, Wong B, Yan Y, Nantermet PG. Discovery and Evaluation of Potent P1 Aryl Heterocycle-Based Thrombin Inhibitors. J Med Chem 2004; 47:2995-3008. [PMID: 15163182 DOI: 10.1021/jm030303e] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In an effort to discover potent, clinically useful thrombin inhibitors, a rapid analogue synthetic approach was used to explore the P(1) region. Various benzylamines were coupled to a pyridine/pyrazinone P(2)-P(3) template. One compound with an o-thiadiazole benzylic substitution was found to have a thrombin K(i) of 0.84 nM. A study of ortho-substituted five-membered-ring heterocycles was undertaken and subsequently demonstrated that the o-triazole and tetrazole rings were optimal. Combination of these potent P(1) aryl heterocycles with a variety of P(2)-P(3) groups produced a compound with an extraordinary thrombin inhibitory activity of 1.4 pM. It is hoped that this potency enhancement in P(1) will allow for more diversification in the P(2)-P(3) region to ultimately address additional pharmacological concerns.
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Affiliation(s)
- Mary Beth Young
- Medicinal Chemistry, Merck Research Laboratories, Merck and Co., Inc., WP14-3, Post Office Box 4, Sumneytown Pike, West Point, PA 19486, USA.
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86
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Euler D, Frech P, Karki S, Cowden C, Pearce G, Mehta P, Lindemann C, Byway P, Wang M, Gibson T, Cheng Y, Kwei G, Rose J. Influence of physicochemical properties and intestinal region on the absorption of 3-fluoro-2-pyrimidylmethyl 3-(2,2-difluoro-2-(2-pyridyl)ethylamino)-6-chloropyrazin-2-one-1-acetamide, a water insoluble thrombin inhibitor, in dogs. Int J Pharm 2004; 275:19-27. [PMID: 15081135 DOI: 10.1016/j.ijpharm.2003.12.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2003] [Revised: 12/16/2003] [Accepted: 12/22/2003] [Indexed: 11/17/2022]
Abstract
In this paper, we describe the physicochemical and biopharmaceutical properties of 3-fluoro-2-pyrimidylmethyl 3-(2,2-difluoro-2-(2-pyridyl)ethylamino)-6-chloropyrazin-2-one-1-acetamide, a direct thrombin inhibitor (1, Fig. 1). Three crystalline forms were characterized and studies were planned to investigate the absorption characteristics of the three selected crystalline forms. Due to the short half-life observed in preclinical species, regional absorption studies were also conducted to support potential controlled release formulation development. Results showed that the absorption of 1 was dependent on the surface area of the particles administered as suspensions and was independent of the crystal forms. From Caco-2 cell transport studies, it was determined that the permeability of 1 was high. Based on the low aqueous solubility it would be classified as a class 2 compound in the Biopharmaceutics Classification System. Regional absorption results suggested that the compound was absorbed along the gastrointestinal tract in Beagle dogs, however colonic absorption appeared to be reduced by slower dissolution.
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Affiliation(s)
- Danielle Euler
- Department of Pharmaceutical Research and Development, Merck & Co., Inc., West Point, PA 19486, USA
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87
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Ashwood MS, Alabaster RJ, Cottrell IF, Cowden CJ, Davies AJ, Dolling UH, Emerson KM, Gibb AD, Hands D, Wallace DJ, Wilson RD. Development of a Scaleable Synthesis of a 3-Aminopyrazinone Acetamide Thrombin Inhibitor. Org Process Res Dev 2004. [DOI: 10.1021/op0341420] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michael S. Ashwood
- Department of Process Research, Merck Sharp and Dohme Research Laboratories, Hertford Road, Hoddesdon, Hertfordshire EN11 9BU, UK, and Department of Process Research, Merck Research Laboratories, Rahway, New Jersey 07065, U.S.A
| | - Ramon J. Alabaster
- Department of Process Research, Merck Sharp and Dohme Research Laboratories, Hertford Road, Hoddesdon, Hertfordshire EN11 9BU, UK, and Department of Process Research, Merck Research Laboratories, Rahway, New Jersey 07065, U.S.A
| | - Ian F. Cottrell
- Department of Process Research, Merck Sharp and Dohme Research Laboratories, Hertford Road, Hoddesdon, Hertfordshire EN11 9BU, UK, and Department of Process Research, Merck Research Laboratories, Rahway, New Jersey 07065, U.S.A
| | - Cameron J. Cowden
- Department of Process Research, Merck Sharp and Dohme Research Laboratories, Hertford Road, Hoddesdon, Hertfordshire EN11 9BU, UK, and Department of Process Research, Merck Research Laboratories, Rahway, New Jersey 07065, U.S.A
| | - Antony J. Davies
- Department of Process Research, Merck Sharp and Dohme Research Laboratories, Hertford Road, Hoddesdon, Hertfordshire EN11 9BU, UK, and Department of Process Research, Merck Research Laboratories, Rahway, New Jersey 07065, U.S.A
| | - Ulf H. Dolling
- Department of Process Research, Merck Sharp and Dohme Research Laboratories, Hertford Road, Hoddesdon, Hertfordshire EN11 9BU, UK, and Department of Process Research, Merck Research Laboratories, Rahway, New Jersey 07065, U.S.A
| | - Khateeta M. Emerson
- Department of Process Research, Merck Sharp and Dohme Research Laboratories, Hertford Road, Hoddesdon, Hertfordshire EN11 9BU, UK, and Department of Process Research, Merck Research Laboratories, Rahway, New Jersey 07065, U.S.A
| | - Andrew D. Gibb
- Department of Process Research, Merck Sharp and Dohme Research Laboratories, Hertford Road, Hoddesdon, Hertfordshire EN11 9BU, UK, and Department of Process Research, Merck Research Laboratories, Rahway, New Jersey 07065, U.S.A
| | - David Hands
- Department of Process Research, Merck Sharp and Dohme Research Laboratories, Hertford Road, Hoddesdon, Hertfordshire EN11 9BU, UK, and Department of Process Research, Merck Research Laboratories, Rahway, New Jersey 07065, U.S.A
| | - Debra J. Wallace
- Department of Process Research, Merck Sharp and Dohme Research Laboratories, Hertford Road, Hoddesdon, Hertfordshire EN11 9BU, UK, and Department of Process Research, Merck Research Laboratories, Rahway, New Jersey 07065, U.S.A
| | - Robert D. Wilson
- Department of Process Research, Merck Sharp and Dohme Research Laboratories, Hertford Road, Hoddesdon, Hertfordshire EN11 9BU, UK, and Department of Process Research, Merck Research Laboratories, Rahway, New Jersey 07065, U.S.A
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88
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Subramanian R, Lin CC, Ho JZ, Pitzenberger SM, Silva-Elipe MV, Gibson CR, Braun MP, Yu X, Yergey JL, Singh R. BIOACTIVATION OF THE 3-AMINO-6-CHLOROPYRAZINONE RING IN A THROMBIN INHIBITOR LEADS TO NOVEL DIHYDRO-IMIDAZOLE AND IMIDAZOLIDINE DERIVATIVES: STRUCTURES AND MECHANISM USING 13C-LABELS, MASS SPECTROMETRY, AND NMR. Drug Metab Dispos 2003; 31:1437-47. [PMID: 14570777 DOI: 10.1124/dmd.31.11.1437] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Thrombin is a serine protease that plays a key role in the blood coagulation cascade. Compound I [2-[6-chloro-3-[(2,2-difluoro-2-pyridin-2-ylethyl)amino]-2-oxopyrazin-1(2H)-yl]-N-[(3-fluoropyridin-2-yl)methyl]acetamide] is a potent, selective, and orally bioavailable thrombin inhibitor that is being studied as a possible anticoagulant. Biotransformation studies in rats revealed that 84% of an i.v. dose of I was excreted in the form of two metabolites. Both metabolites were formed by metabolic activation of the pyrazinone ring in I and subsequent rearrangement leading to two novel dihydro-imidazole and imidazolidine derivatives. The structures of these metabolites and their mechanism of formation were elucidated by additional use of two 13C single labels in the pyrazinone ring of I in combination with mass spectrometry and NMR techniques. The metabolite structures described here illustrate the rich metabolic chemistry of the amino-pyrazinone heterocycle.
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Affiliation(s)
- Raju Subramanian
- Department of Drug Metabolism, WP75-100, Merck Research Laboratories, West Point, PA 19486, USA.
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89
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Chung JYL, Cvetovich RJ, Tsay FR, Dormer PG, DiMichele L, Mathre DJ, Chilenski JR, Mao B, Wenslow R. Synthesis of 3-Aminopyrazinone Mediated by 2-Pyridylthioimidate−ZnCl2 Complexes. Development of an Efficient Route to a Thrombin Inhibitor. J Org Chem 2003; 68:8838-46. [PMID: 14604352 DOI: 10.1021/jo034835e] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A six-step preparation of thrombin inhibitor drug candidate 1 from pyrazinone 7 in 47% overall yield is described. The problem of low reactivity between weak amine nucleophile 4 and poor electrophile 3-bromopyrazinone 17 was overcome with the use of pyridinylthioimidate 27 in the presence of ZnCl(2) to afford adduct 3 in high yield. Several zinc complexes were characterized by solution and solid-state NMR and X-ray crystallographic analyses, and provided insight into the reaction mechanism. Preparation of pyridine N-oxide amine 4 was accomplished via a selective oxidation of the corresponding pyridinylamine 6. Pyridinylthioimidate 27 was prepared from pyrazinone 7 via a two-step one-pot process in near quantitative yield. Chlorination of the pyrazinone ring in 3 followed by hydrolysis and amide coupling completed the synthesis of 1. This chromatography-free synthesis was used successfully to prepare multikilogram quantities of the drug with reproducibility and high purity.
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Affiliation(s)
- John Y L Chung
- Department of Process Research, Merck Research Laboratories, P.O. Box 2000, Rahway, New Jersey 07065, USA.
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90
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Parlow JJ, Case BL, Dice TA, Fenton RL, Hayes MJ, Jones DE, Neumann WL, Wood RS, Lachance RM, Girard TJ, Nicholson NS, Clare M, Stegeman RA, Stevens AM, Stallings WC, Kurumbail RG, South MS. Design, parallel synthesis, and crystal structures of pyrazinone antithrombotics as selective inhibitors of the tissue factor VIIa complex. J Med Chem 2003; 46:4050-62. [PMID: 12954058 DOI: 10.1021/jm030131l] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structure-based drug design (SBDD) and polymer-assisted solution-phase (PASP) library synthesis were used to develop a series of pyrazinone inhibitors of the Tissue Factor/Factor VIIa (TF/VIIa) complex. The crystal structure of a tripeptide-alpha-ketothiazole complexed with TF/VIIa was utilized in a docking experiment to identify the pyrazinone core as a starting scaffold. The pyrazinone core could orient the substituents in the correct spatial arrangement to probe the S1, S2, and S3 pockets of the enzyme. A multistep PASP library synthesis was designed to prepare the substituted pyrazinones varying the P1, P2, and P3 moieties. Hundreds of pyrazinone TF/VIIa inhibitors were prepared and tested in several serine protease enzyme assays involved in the coagulation cascade. The inhibitors exhibited modest activity on TF/VIIa with excellent selectivity over thrombin (IIa) and Factor Xa. The structure-activity relationship of the pyrazinone inhibitors will be discussed and X-ray crystal structures of selected compounds complexed with the TF/VIIa enzyme will be described. This study ultimately led to the synthesis of compound 34, which exhibited 16 nM (IC50) activity on TF/VIIa with >6250 x selectivity vs Factor Xa and thrombin. This potent and highly selective inhibitor of TF/VIIa was chosen for preclinical, intravenous proof-of-concept studies to demonstrate the separation between antithrombotic efficacy and bleeding side effects in a nonhuman primate model of electrolytic-induced arterial thrombosis.
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Affiliation(s)
- John J Parlow
- Department of Medicinal and Combinatorial Chemistry, Pharmacia Corporation, 800 North Lindbergh Boulevard, St. Louis, Missouri 63167, USA.
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91
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Abbiati G, Arcadi A, Bianchi G, Di Giuseppe S, Marinelli F, Rossi E. Sequential amination/annulation/aromatization reaction of carbonyl compounds and propargylamine: a new one-pot approach to functionalized pyridines. J Org Chem 2003; 68:6959-66. [PMID: 12946136 DOI: 10.1021/jo0347260] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A general one-pot synthesis of pyridines 4a-t from the reaction of dialkyl acyclic/cyclic ketones 1a-i, methyl, aryl/heteroaryl ketones 1m-r, and aldehydes bearing alpha-hydrogens 1s,t with propargylamine 2 is described. Gold and copper salts are efficient catalysts for the reaction of ketones with 2. The formation of the pyridines 4 is suggested to proceed through the sequential amination of carbonyl compounds followed by regioselective 6-endo-dig cyclization of the N-propargylenamine (N-propargyldienamine) intermediate 3(5) and aromatization reaction. Whereas the preparation of linear polycyclic pyridine 4i can be carried out by reacting cholestan-3-one 1i with 2, the angular polycyclic pyridine 4j has been obtained starting from cholest-5-en-3-one 1j. Selectivity of the reaction of polycyclic dicarbonyls 1k,l with 2 has also been investigated.
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Affiliation(s)
- Giorgio Abbiati
- Istituto di Chimica Organica Alessandro Marchesini, Facoltà di Farmacia, Università degli Studi di Milano, Via Venezian, 21, 20133 Milano, Italy
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92
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Nantermet PG, Barrow JC, Newton CL, Pellicore JM, Young M, Lewis SD, Lucas BJ, Krueger JA, McMasters DR, Yan Y, Kuo LC, Vacca JP, Selnick HG. Design and synthesis of potent and selective macrocyclic thrombin inhibitors. Bioorg Med Chem Lett 2003; 13:2781-4. [PMID: 12873514 DOI: 10.1016/s0960-894x(03)00506-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A series of potent and selective proline- and pyrazinone-based macrocyclic thrombin inhibitors is described. Detailed SAR studies led to the incorporation of specific functional groups in the tether that enhanced functional activity against thrombin and provided exquisite selectivity against trypsin and tPA. X-ray crystallography and molecular modeling studies revealed the inhibitor-enzyme interactions responsible for this selectivity.
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Affiliation(s)
- Philippe G Nantermet
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, USA.
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93
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South MS, Case BL, Wood RS, Jones DE, Hayes MJ, Girard TJ, Lachance RM, Nicholson NS, Clare M, Stevens AM, Stegeman RA, Stallings WC, Kurumbail RG, Parlow JJ. Structure-based drug design of pyrazinone antithrombotics as selective inhibitors of the tissue factor VIIa complex. Bioorg Med Chem Lett 2003; 13:2319-25. [PMID: 12824026 DOI: 10.1016/s0960-894x(03)00410-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Structure-based drug design coupled with polymer-assisted solution-phase library synthesis was utilized to develop a series of pyrazinone inhibitors of the tissue factor/Factor VIIa complex. The crystal structure of a tri-peptide ketothiazole complexed with TF/VIIa was utilized in a docking experiment that identified a benzyl-substituted pyrazinone as a P(2) surrogate for the tri-peptide. A 5-step PASP library synthesis of these aryl-substituted pyrazinones was developed. The sequence allows for attachment of a variety of P(1) and P(3) moieties, which led to synthesis pyrazinone 23. Compound 23 exhibited 16 nM IC(50) against TF/VIIa with >6250x selectivity versus Factor Xa and thrombin. This potent and highly selective inhibitor of TF/VIIa was chosen for pre-clinical intravenous proof-of-concept studies to demonstrate the separation between antithrombotic efficacy and bleeding side effects in a primate model of thrombosis.
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Affiliation(s)
- Michael S South
- Department of Medicinal and Combinatorial Chemistry, Pharmacia Corporation, 63167, St. Louis, MO, USA.
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94
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Burgey CS, Robinson KA, Lyle TA, Nantermet PG, Selnick HG, Isaacs RCA, Lewis SD, Lucas BJ, Krueger JA, Singh R, Miller-Stein C, White RB, Wong B, Lyle EA, Stranieri MT, Cook JJ, McMasters DR, Pellicore JM, Pal S, Wallace AA, Clayton FC, Bohn D, Welsh DC, Lynch JJ, Yan Y, Chen Z, Kuo L, Gardell SJ, Shafer JA, Vacca JP. Pharmacokinetic optimization of 3-amino-6-chloropyrazinone acetamide thrombin inhibitors. Implementation of P3 pyridine N-oxides to deliver an orally bioavailable series containing P1 N-benzylamides. Bioorg Med Chem Lett 2003; 13:1353-7. [PMID: 12657281 DOI: 10.1016/s0960-894x(03)00099-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In this manuscript we demonstrate that a modification principally directed toward the improvement of the aqueous solubility (i.e., introduction a P3 pyridine N-oxide) of the previous lead compound afforded a new series of potent orally bioavailable P1 N-benzylamide thrombin inhibitors. An expedited investigation of the P1 SAR with respect to oral bioavailability, plasma half-life, and human liver microsome stability revealed 5 as the best candidate for advanced evaluation.
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Affiliation(s)
- Christopher S Burgey
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, USA.
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95
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Nantermet PG, Selnick HG. Potent thrombin inhibitors via a 20-membered ring olefin metathesis macrocyclization. Tetrahedron Lett 2003. [DOI: 10.1016/s0040-4039(03)00216-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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