1
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Dagher MC, Ersayin A, Seyve L, Castellan M, Moreau C, Choisnard L, Thielens N, Marlu R, Polack B, Thomas A. Toward non-factor therapy in hemophilia: an antithrombin insensitive Gla-domainless factor Xa as tissue factor pathway inhibitor bait. Res Pract Thromb Haemost 2023; 7:102175. [PMID: 37841511 PMCID: PMC10568284 DOI: 10.1016/j.rpth.2023.102175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 07/24/2023] [Accepted: 08/06/2023] [Indexed: 10/17/2023] Open
Abstract
Background Gla-domainless factor (F) Xa (GD-FXa) was proposed as a trap to endogenous anticoagulant tissue factor pathway inhibitor (TFPI) to restore thrombin generation in hemophilia. Using computational chemistry and experimental approaches, we previously showed that S195A GD-FXa also binds TFPI and restores ex vivo coagulation in plasma obtained from person(s) with hemophilia. Methods To design a GD-FXa variant with improved anti-TFPI affinity, we performed molecular dynamics simulations and identified suitable sites for mutagenesis. The calculations identified residues R150FXa and K96Fxa as cold-spots of interaction between GD-FXa and the K2 domain of TFPI. In the three-dimensional model, both residues face toward TFPI hydrophobic residues and are thus potential candidates for mutagenesis into hydrophobic residues to favor an improved protein-protein interaction. Results Catalytically inactive GD-FXa variants containing the S195A mutation and the additional mutations K96Y, R150I, R150G, R150F, and K96YR150F, were produced to experimentally confirm these computational hypotheses. Among these mutants, the R150FFXa and the K96YR150FFXa were slightly more effective than S195A GD-FXa in restoring coagulation in FVIII deficient plasmas. However, in surface plasmon resonance experiments, they showed TFPI binding affinities in the same range and acted similarly as S195A GD-FXa in FXa/TFPI competition assays. In contrast, the R150 mutants completely lost their interactions with antithrombin as observed in the surface plasmon resonance experiments. Conclusions We therefore conclude that their antithrombin resistance is responsible for their improved thrombin generation, through an extension of their half-lives.
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Affiliation(s)
- Marie-Claire Dagher
- Univ. Grenoble Alpes, UMR5525, CNRS, TIMC, Grenoble, France
- Univ. Grenoble Alpes, UMR5075, CEA, CNRS, IBS, Grenoble, France
| | - Atanur Ersayin
- Univ. Grenoble Alpes, UMR5525, CNRS, TIMC, Grenoble, France
| | - Landry Seyve
- Haemostasis Unit, Hematology Laboratory, University Grenoble Hospital, Grenoble Alpes University, Grenoble, France
| | | | - Cyril Moreau
- Univ. Grenoble Alpes, UMR5525, CNRS, TIMC, Grenoble, France
| | - Luc Choisnard
- Univ. Grenoble Alpes, UMR5063, ICMG FR 2607, CNRS, Département de Pharmacochimie Moléculaire, Grenoble, France
| | - Nicole Thielens
- Univ. Grenoble Alpes, UMR5075, CEA, CNRS, IBS, Grenoble, France
| | - Raphaël Marlu
- Univ. Grenoble Alpes, UMR5525, CNRS, TIMC, Grenoble, France
- Haemostasis Unit, Hematology Laboratory, University Grenoble Hospital, Grenoble Alpes University, Grenoble, France
| | - Benoît Polack
- Univ. Grenoble Alpes, UMR5525, CNRS, TIMC, Grenoble, France
| | - Aline Thomas
- Univ. Grenoble Alpes, UMR5063, ICMG FR 2607, CNRS, Département de Pharmacochimie Moléculaire, Grenoble, France
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2
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Zálešák F, Kováč O, Lachetová E, Št'astná N, Pospíšil J. Unified Approach to Benzo[ d]thiazol-2-yl-Sulfonamides. J Org Chem 2021; 86:11291-11309. [PMID: 34479409 DOI: 10.1021/acs.joc.1c00317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this paper, we report a unified approach to N-substituted and N,N-disubstituted benzothiazole (BT) sulfonamides. Our approach to BT-sulfonamides starts from simple commercially available building blocks (benzo[d]thiazole-2-thiol and primary and secondary amines) that are connected via (a) a S oxidation/S-N coupling approach, (b) a S-N coupling/S-oxidation sequence, or via (c) a S-oxidation/S-F bond formation/SuFEx approach. The labile N-H bond in N-monoalkylated BT-sulfonamides (pKa (BTSO2N(H)Bn) = 3.34 ± 0.05) further allowed us to develop a simple weak base-promoted N-alkylation method and a stereoselective microwave-promoted Fukuyama-Mitsunobu reaction. N-Alkyl-N-aryl BT-sulfonamides were accessed with the help of the Chan-Lam coupling reaction. Developed methods were further used in stereo and chemoselective transformations of podophyllotoxin and several amino alcohols.
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Affiliation(s)
- František Zálešák
- Department of Organic Chemistry, Faculty of Science, Palacky University, tř. 17. listopadu 1192/12, CZ-771 46 Olomouc, Czech Republic
| | - Ondřej Kováč
- Department of Organic Chemistry, Faculty of Science, Palacky University, tř. 17. listopadu 1192/12, CZ-771 46 Olomouc, Czech Republic
| | - Eliška Lachetová
- Department of Organic Chemistry, Faculty of Science, Palacky University, tř. 17. listopadu 1192/12, CZ-771 46 Olomouc, Czech Republic
| | - Nikola Št'astná
- Department of Organic Chemistry, Faculty of Science, Palacky University, tř. 17. listopadu 1192/12, CZ-771 46 Olomouc, Czech Republic
| | - Jiří Pospíšil
- Department of Organic Chemistry, Faculty of Science, Palacky University, tř. 17. listopadu 1192/12, CZ-771 46 Olomouc, Czech Republic.,Laboratory of Growth Regulators, Palacky University & Institute of Experimental Botany AS CR, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic
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3
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Suruzhon M, Bodnarchuk MS, Ciancetta A, Viner R, Wall ID, Essex JW. Sensitivity of Binding Free Energy Calculations to Initial Protein Crystal Structure. J Chem Theory Comput 2021; 17:1806-1821. [PMID: 33534995 DOI: 10.1021/acs.jctc.0c00972] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Binding free energy calculations using alchemical free energy (AFE) methods are widely considered to be the most rigorous tool in the computational drug discovery arsenal. Despite this, the calculations suffer from accuracy, precision, and reproducibility issues. In this publication, we perform a high-throughput study of more than a thousand AFE calculations, utilizing over 220 μs of total sampling time, on three different protein systems to investigate the impact of the initial crystal structure on the resulting binding free energy values. We also consider the influence of equilibration time and discover that the initial crystal structure can have a significant effect on free energy values obtained at short timescales that can manifest itself as a free energy difference of more than 1 kcal/mol. At longer timescales, these differences are largely overtaken by important rare events, such as torsional ligand motions, typically resulting in a much higher uncertainty in the obtained values. This work emphasizes the importance of rare event sampling and long-timescale dynamics in free energy calculations even for routinely performed alchemical perturbations. We conclude that an optimal protocol should not only concentrate computational resources on achieving convergence in the alchemical coupling parameter (λ) space but also on longer simulations and multiple repeats.
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Affiliation(s)
- Miroslav Suruzhon
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K
| | | | | | - Russell Viner
- Syngenta, Jealott's Hill International Research Centre, Bracknell RG42 6EY, U.K
| | - Ian D Wall
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Jonathan W Essex
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K
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4
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Mei H, Han J, White S, Graham DJ, Izawa K, Sato T, Fustero S, Meanwell NA, Soloshonok VA. Tailor-Made Amino Acids and Fluorinated Motifs as Prominent Traits in Modern Pharmaceuticals. Chemistry 2020; 26:11349-11390. [PMID: 32359086 DOI: 10.1002/chem.202000617] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/23/2020] [Indexed: 12/11/2022]
Abstract
Structural analysis of modern pharmaceutical practices allows for the identification of two rapidly growing trends: the introduction of tailor-made amino acids and the exploitation of fluorinated motifs. Curiously, the former represents one of the most ubiquitous classes of naturally occurring compounds, whereas the latter is the most xenobiotic and comprised virtually entirely of man-made derivatives. Herein, 39 selected compounds, featuring both of these traits in the same molecule, are profiled. The total synthesis, source of the corresponding amino acids and fluorinated residues, and medicinal chemistry aspects and biological properties of the molecules are discussed.
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Affiliation(s)
- Haibo Mei
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, P.R. China
| | - Jianlin Han
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, P.R. China
| | - Sarah White
- Oakwood Chemical, Inc., 730 Columbia Hwy. N, Estill, SC, 29918, USA
| | - Daniel J Graham
- Oakwood Chemical, Inc., 730 Columbia Hwy. N, Estill, SC, 29918, USA
| | - Kunisuke Izawa
- Hamari Chemicals Ltd., 1-4-29 Kunijima, Higashi-Yodogawa-ku, Osaka, 533-0024, Japan
| | - Tatsunori Sato
- Hamari Chemicals Ltd., 1-4-29 Kunijima, Higashi-Yodogawa-ku, Osaka, 533-0024, Japan
| | - Santos Fustero
- Departamento de Química Orgánica, Universidad de Valencia, 46100, Burjassot, Valencia, Spain
| | - Nicholas A Meanwell
- Department of Small Molecule Drug Discovery, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, NJ, 08543-4000, USA
| | - Vadim A Soloshonok
- Department of Organic Chemistry I, Faculty of Chemistry, University of the Basque Country UPV/EHU, Paseo Manuel Lardizábal 3, 20018, San Sebastián, Spain.,IKERBASQUE, Basque Foundation for Science, María Díaz de Haro 3, Plaza Bizkaia, 48013, Bilbao, Spain
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5
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Hao X, Zuo X, Kang D, Zhang J, Song Y, Liu X, Zhan P. Contemporary medicinal-chemistry strategies for discovery of blood coagulation factor Xa inhibitors. Expert Opin Drug Discov 2019; 14:915-931. [DOI: 10.1080/17460441.2019.1626821] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Xia Hao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
| | - Xiaofang Zuo
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
| | - Jian Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
| | - Yuning Song
- Department of Clinical Pharmacy, Qilu Hospital of Shandong University, Jinan, China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
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6
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Roos K, Wu C, Damm W, Reboul M, Stevenson JM, Lu C, Dahlgren MK, Mondal S, Chen W, Wang L, Abel R, Friesner RA, Harder ED. OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules. J Chem Theory Comput 2019; 15:1863-1874. [PMID: 30768902 DOI: 10.1021/acs.jctc.8b01026] [Citation(s) in RCA: 633] [Impact Index Per Article: 126.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Katarina Roos
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, United States
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24 Uppsala, Sweden
| | - Chuanjie Wu
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Wolfgang Damm
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Mark Reboul
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - James M. Stevenson
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Chao Lu
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Markus K. Dahlgren
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Sayan Mondal
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Wei Chen
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Lingle Wang
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Robert Abel
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Richard A. Friesner
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, United States
| | - Edward D. Harder
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
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7
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Young RJ, Leeson PD. Mapping the Efficiency and Physicochemical Trajectories of Successful Optimizations. J Med Chem 2018; 61:6421-6467. [DOI: 10.1021/acs.jmedchem.8b00180] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Robert J. Young
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Paul D. Leeson
- Paul Leeson Consulting Ltd., The Malt House, Main Street, Congerstone, Nuneaton, Warwickshire CV13 6LZ, U.K
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8
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Xia S, Li J, Zu M, Li J, Liu J, Bai X, Chang Y, Chen K, Gu W, Zeng L, Zhao L, Xing G, Xing G. Small size fullerenol nanoparticles inhibit thrombosis and blood coagulation through inhibiting activities of thrombin and FXa. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2018; 14:929-939. [DOI: 10.1016/j.nano.2017.12.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 12/16/2017] [Accepted: 12/16/2017] [Indexed: 12/13/2022]
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9
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The selectivity and bioavailability improvement of novel oral anticoagulants: An overview. Eur J Med Chem 2018; 146:299-317. [PMID: 29407959 DOI: 10.1016/j.ejmech.2018.01.067] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/18/2018] [Accepted: 01/19/2018] [Indexed: 01/23/2023]
Abstract
Anticoagulants have exhibited a critical role in the prevention and/or treatment of thrombotic diseases. Up to now, kinds of novel oral anticoagulants, inhibiting plasma serine proteases in the coagulation cascade, have been developed to overcome the clinical limitations of classical anticoagulants (like warfarin and heparins). Some of them, such as Apixaban, Rivaroxaban, Edoxaban, and Dabigatran, have been approved by FDA in recent years. This review summarizes the discovery and optimization of representative novel oral anticoagulants with the aim to improve selectivity and bioavailability of compounds. The impact of different targets in the cascade on bleeding risk also is discussed. We hope some more effective, selective, and safer anticoagulants can be developed in the future on the basis of these design experiences.
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10
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Pinheiro PDSM, Rodrigues DA, Alves MA, Tinoco LW, Ferreira GB, de Sant’Anna CMR, Fraga CAM. Theoretical and experimental characterization of 1,4-N⋯S σ-hole intramolecular interactions in bioactive N-acylhydrazone derivatives. NEW J CHEM 2018. [DOI: 10.1039/c7nj03543h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Sigma-hole (σ-hole) bonds are interactions that are gaining special attention in medicinal chemistry.
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Affiliation(s)
- Pedro de Sena Murteira Pinheiro
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio)
- Instituto de Ciências Biomédicas
- Universidade Federal do Rio de Janeiro
- PO Box 68023
- Rio de Janeiro
| | - Daniel Alencar Rodrigues
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio)
- Instituto de Ciências Biomédicas
- Universidade Federal do Rio de Janeiro
- PO Box 68023
- Rio de Janeiro
| | - Marina Amaral Alves
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio)
- Instituto de Ciências Biomédicas
- Universidade Federal do Rio de Janeiro
- PO Box 68023
- Rio de Janeiro
| | - Luzineide Wanderley Tinoco
- Programa de Pós-Graduação em Farmacologia e Química Medicinal
- Instituto de Ciências Biomédicas
- Universidade Federal do Rio de Janeiro
- 21941-902
- Rio de Janeiro
| | - Glaucio Braga Ferreira
- Programa de Pós-Graduação em Química
- Instituto de Química
- Universidade Federal Fluminense
- Niterói
- Rio de Janeiro
| | - Carlos Mauricio Rabello de Sant’Anna
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio)
- Instituto de Ciências Biomédicas
- Universidade Federal do Rio de Janeiro
- PO Box 68023
- Rio de Janeiro
| | - Carlos Alberto Manssour Fraga
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio)
- Instituto de Ciências Biomédicas
- Universidade Federal do Rio de Janeiro
- PO Box 68023
- Rio de Janeiro
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11
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Parrish RM, Sitkoff DF, Cheney DL, Sherrill CD. The Surprising Importance of Peptide Bond Contacts in Drug–Protein Interactions. Chemistry 2017; 23:7887-7890. [DOI: 10.1002/chem.201701031] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Indexed: 01/08/2023]
Affiliation(s)
- Robert M. Parrish
- Center for Computational Molecular Science and Technology School of Chemistry and Biochemistry School of Computational Science and Engineering Georgia Institute of Technology Atlanta GA 30332-0400 USA
| | - Doree F. Sitkoff
- Molecular Structure and Design Bristol-Myers Squibb Company 311 Pennington-Rocky Hill Road Pennington NJ 08534 USA
| | - Daniel L. Cheney
- Molecular Structure and Design Bristol-Myers Squibb Company 311 Pennington-Rocky Hill Road Pennington NJ 08534 USA
| | - C. David Sherrill
- Center for Computational Molecular Science and Technology School of Chemistry and Biochemistry School of Computational Science and Engineering Georgia Institute of Technology Atlanta GA 30332-0400 USA
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12
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Carlson HA, Smith RD, Damm-Ganamet KL, Stuckey JA, Ahmed A, Convery MA, Somers DO, Kranz M, Elkins PA, Cui G, Peishoff CE, Lambert MH, Dunbar JB. CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma. J Chem Inf Model 2016; 56:1063-77. [PMID: 27149958 DOI: 10.1021/acs.jcim.5b00523] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The 2014 CSAR Benchmark Exercise was the last community-wide exercise that was conducted by the group at the University of Michigan, Ann Arbor. For this event, GlaxoSmithKline (GSK) donated unpublished crystal structures and affinity data from in-house projects. Three targets were used: tRNA (m1G37) methyltransferase (TrmD), Spleen Tyrosine Kinase (SYK), and Factor Xa (FXa). A particularly strong feature of the GSK data is its large size, which lends greater statistical significance to comparisons between different methods. In Phase 1 of the CSAR 2014 Exercise, participants were given several protein-ligand complexes and asked to identify the one near-native pose from among 200 decoys provided by CSAR. Though decoys were requested by the community, we found that they complicated our analysis. We could not discern whether poor predictions were failures of the chosen method or an incompatibility between the participant's method and the setup protocol we used. This problem is inherent to decoys, and we strongly advise against their use. In Phase 2, participants had to dock and rank/score a set of small molecules given only the SMILES strings of the ligands and a protein structure with a different ligand bound. Overall, docking was a success for most participants, much better in Phase 2 than in Phase 1. However, scoring was a greater challenge. No particular approach to docking and scoring had an edge, and successful methods included empirical, knowledge-based, machine-learning, shape-fitting, and even those with solvation and entropy terms. Several groups were successful in ranking TrmD and/or SYK, but ranking FXa ligands was intractable for all participants. Methods that were able to dock well across all submitted systems include MDock,1 Glide-XP,2 PLANTS,3 Wilma,4 Gold,5 SMINA,6 Glide-XP2/PELE,7 FlexX,8 and MedusaDock.9 In fact, the submission based on Glide-XP2/PELE7 cross-docked all ligands to many crystal structures, and it was particularly impressive to see success across an ensemble of protein structures for multiple targets. For scoring/ranking, submissions that showed statistically significant achievement include MDock1 using ITScore1,10 with a flexible-ligand term,11 SMINA6 using Autodock-Vina,12,13 FlexX8 using HYDE,14 and Glide-XP2 using XP DockScore2 with and without ROCS15 shape similarity.16 Of course, these results are for only three protein targets, and many more systems need to be investigated to truly identify which approaches are more successful than others. Furthermore, our exercise is not a competition.
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Affiliation(s)
- Heather A Carlson
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church St., Ann Arbor, Michigan 48109-1065, United States
| | - Richard D Smith
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church St., Ann Arbor, Michigan 48109-1065, United States
| | - Kelly L Damm-Ganamet
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church St., Ann Arbor, Michigan 48109-1065, United States
| | - Jeanne A Stuckey
- Center for Structural Biology, University of Michigan , 3358E Life Sciences Institute, 210 Washtenaw Ave., Ann Arbor, Michigan 48109-2216, United States
| | - Aqeel Ahmed
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church St., Ann Arbor, Michigan 48109-1065, United States
| | - Maire A Convery
- Computational and Structural Sciences, Medicines Research Centre, GlaxoSmithKline Research & Development , Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Donald O Somers
- Computational and Structural Sciences, Medicines Research Centre, GlaxoSmithKline Research & Development , Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Michael Kranz
- Computational and Structural Sciences, Medicines Research Centre, GlaxoSmithKline Research & Development , Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Patricia A Elkins
- Computational and Structural Sciences, GlaxoSmithKline Research & Development , 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Guanglei Cui
- Computational and Structural Sciences, GlaxoSmithKline Research & Development , 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Catherine E Peishoff
- Computational and Structural Sciences, GlaxoSmithKline Research & Development , 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Millard H Lambert
- Computational and Structural Sciences, GlaxoSmithKline Research & Development , 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - James B Dunbar
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church St., Ann Arbor, Michigan 48109-1065, United States
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13
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Harder E, Damm W, Maple J, Wu C, Reboul M, Xiang JY, Wang L, Lupyan D, Dahlgren MK, Knight JL, Kaus JW, Cerutti DS, Krilov G, Jorgensen WL, Abel R, Friesner RA. OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins. J Chem Theory Comput 2015; 12:281-96. [PMID: 26584231 DOI: 10.1021/acs.jctc.5b00864] [Citation(s) in RCA: 2047] [Impact Index Per Article: 227.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The parametrization and validation of the OPLS3 force field for small molecules and proteins are reported. Enhancements with respect to the previous version (OPLS2.1) include the addition of off-atom charge sites to represent halogen bonding and aryl nitrogen lone pairs as well as a complete refit of peptide dihedral parameters to better model the native structure of proteins. To adequately cover medicinal chemical space, OPLS3 employs over an order of magnitude more reference data and associated parameter types relative to other commonly used small molecule force fields (e.g., MMFF and OPLS_2005). As a consequence, OPLS3 achieves a high level of accuracy across performance benchmarks that assess small molecule conformational propensities and solvation. The newly fitted peptide dihedrals lead to significant improvements in the representation of secondary structure elements in simulated peptides and native structure stability over a number of proteins. Together, the improvements made to both the small molecule and protein force field lead to a high level of accuracy in predicting protein-ligand binding measured over a wide range of targets and ligands (less than 1 kcal/mol RMS error) representing a 30% improvement over earlier variants of the OPLS force field.
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Affiliation(s)
- Edward Harder
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Wolfgang Damm
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Jon Maple
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Chuanjie Wu
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Mark Reboul
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Jin Yu Xiang
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Lingle Wang
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Dmitry Lupyan
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Markus K Dahlgren
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Jennifer L Knight
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Joseph W Kaus
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - David S Cerutti
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Goran Krilov
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - William L Jorgensen
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States
| | - Robert Abel
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Richard A Friesner
- Department of Chemistry, Columbia University , 3000 Broadway, New York, New York 10027, United States
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14
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Prathipati P, Mizuguchi K. Integration of Ligand and Structure Based Approaches for CSAR-2014. J Chem Inf Model 2015; 56:974-87. [PMID: 26492437 DOI: 10.1021/acs.jcim.5b00477] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The prediction of binding poses and affinities is an area of active interest in computer-aided drug design (CADD). Given the documented limitations with either ligand or structure based approaches, we employed an integrated approach and developed a rapid protocol for binding mode and affinity predictions. This workflow was applied to the three protein targets of Community Structure-Activity Resource-2014 (CSAR-2014) exercise: Factor Xa (FXa), Spleen Tyrosine Kinase (SYK), and tRNA (guanine-N(1))-methyltransferase (TrmD). Our docking and scoring workflow incorporates compound clustering and ligand and protein structure based pharmacophore modeling, followed by local docking, minimization, and scoring. While the former part of the protocol ensures high-quality ligand alignments and mapping, the subsequent minimization and scoring provides the predicted binding modes and affinities. We made blind predictions of docking pose for 1, 5, and 14 ligands docked into 1, 2, and 12 crystal structures of FXa, SYK, and TrmD, respectively. The resulting 174 poses were compared with cocrystallized structures (1, 5, and 14 complexes) made available at the end of CSAR. Our predicted poses were related to the experimentally determined structures with a mean root-mean-square deviation value of 3.4 Å. Further, we were able to classify high and low affinity ligands with the area under the curve values of 0.47, 0.60, and 0.69 for FXa, SYK, and TrmD, respectively, indicating the validity of our approach in at least two of the three systems. Detailed critical analysis of the results and CSAR methodology ranking procedures suggested that a straightforward application of our workflow has limitations, as some of the performance measures do not reflect the actual utility of pose and affinity predictions in the biological context of individual systems.
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Affiliation(s)
- Philip Prathipati
- National Institutes of Biomedical Innovation, Health and Nutrition , 7-6-8 Saito-Asagi, Ibaraki City, Osaka 567-0085, Japan
| | - Kenji Mizuguchi
- National Institutes of Biomedical Innovation, Health and Nutrition , 7-6-8 Saito-Asagi, Ibaraki City, Osaka 567-0085, Japan
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15
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Zhang X, Gong Z, Li J, Lu T. Intermolecular Sulfur···Oxygen Interactions: Theoretical and Statistical Investigations. J Chem Inf Model 2015; 55:2138-53. [DOI: 10.1021/acs.jcim.5b00177] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xuejin Zhang
- School
of Basic Science, China Pharmaceutical University, No. 24 Tongjiaxiang, Nanjing 210009, P. R. China
| | - Zhen Gong
- State
Key Laboratory of Lead Compound Research, WuXi AppTec, 288 Fute
Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Jian Li
- State
Key Laboratory of Lead Compound Research, WuXi AppTec, 288 Fute
Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Tao Lu
- School
of Basic Science, China Pharmaceutical University, No. 24 Tongjiaxiang, Nanjing 210009, P. R. China
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16
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Beno BR, Yeung KS, Bartberger MD, Pennington LD, Meanwell NA. A Survey of the Role of Noncovalent Sulfur Interactions in Drug Design. J Med Chem 2015; 58:4383-438. [DOI: 10.1021/jm501853m] [Citation(s) in RCA: 468] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Brett R. Beno
- Department of Computer-Assisted Drug Design, Bristol-Myers Squibb Research and Development, 5 Research Parkway Wallingford Connecticut 06492, United States
| | - Kap-Sun Yeung
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway Wallingford Connecticut 06492, United States
| | - Michael D. Bartberger
- Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Drive Thousand Oaks California 91320, United States
| | - Lewis D. Pennington
- Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Drive Thousand Oaks California 91320, United States
| | - Nicholas A. Meanwell
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway Wallingford Connecticut 06492, United States
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17
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Hammami M, Rühmann E, Maurer E, Heine A, Gütschow M, Klebe G, Steinmetzer T. New 3-amidinophenylalanine-derived inhibitors of matriptase. MEDCHEMCOMM 2012. [DOI: 10.1039/c2md20074k] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Hirayama F, Koshio H, Ishihara T, Hachiya S, Sugasawa K, Koga Y, Seki N, Shiraki R, Shigenaga T, Iwatsuki Y, Moritani Y, Mori K, Kadokura T, Kawasaki T, Matsumoto Y, Sakamoto S, Tsukamoto SI. Discovery of N-[2-Hydroxy-6-(4-methoxybenzamido)phenyl]-4- (4-methyl-1,4-diazepan-1-yl)benzamide (Darexaban, YM150) as a Potent and Orally Available Factor Xa Inhibitor. J Med Chem 2011; 54:8051-65. [DOI: 10.1021/jm200868m] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Fukushi Hirayama
- Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi,
Ibaraki 305-8585, Japan
| | - Hiroyuki Koshio
- Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi,
Ibaraki 305-8585, Japan
| | - Tsukasa Ishihara
- Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi,
Ibaraki 305-8585, Japan
| | - Shunichiro Hachiya
- Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi,
Ibaraki 305-8585, Japan
| | - Keizo Sugasawa
- Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi,
Ibaraki 305-8585, Japan
| | - Yuji Koga
- Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi,
Ibaraki 305-8585, Japan
| | - Norio Seki
- Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi,
Ibaraki 305-8585, Japan
| | - Ryouta Shiraki
- Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi,
Ibaraki 305-8585, Japan
| | - Takeshi Shigenaga
- Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi,
Ibaraki 305-8585, Japan
| | - Yoshiyuki Iwatsuki
- Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi,
Ibaraki 305-8585, Japan
| | - Yumiko Moritani
- Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi,
Ibaraki 305-8585, Japan
| | - Kenichi Mori
- Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi,
Ibaraki 305-8585, Japan
| | - Takeshi Kadokura
- Development, Astellas Pharma Inc., 17-1, Hasune 3-chome, Itabashi-ku, Tokyo
174-8612, Japan
| | - Tomihisa Kawasaki
- Development, Astellas Pharma Inc., 17-1, Hasune 3-chome, Itabashi-ku, Tokyo
174-8612, Japan
| | - Yuzo Matsumoto
- Drug Discovery
Research, Astellas Pharma Inc., 2-3-11,
Nihonbashi-Honcho, Chuo-ku,
Tokyo 103-8411, Japan
| | - Shuichi Sakamoto
- Technology Supply Chain & Manufacturing, Astellas Pharma Europe B.V., Elisabethhof 19, 2350 AC Leiderdorp, The Netherlands
| | - Shin-ichi Tsukamoto
- Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi,
Ibaraki 305-8585, Japan
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19
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Young RJ. The successful quest for oral factor Xa inhibitors; learnings for all of medicinal chemistry? Bioorg Med Chem Lett 2011; 21:6228-35. [DOI: 10.1016/j.bmcl.2011.08.119] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 08/26/2011] [Accepted: 08/27/2011] [Indexed: 11/29/2022]
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20
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Arylsulfonamidopiperidone derivatives as a novel class of factor Xa inhibitors. Bioorg Med Chem Lett 2011; 21:7516-21. [PMID: 22041058 DOI: 10.1016/j.bmcl.2011.06.098] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 06/22/2011] [Indexed: 11/23/2022]
Abstract
The design, synthesis and SAR of a novel class of valerolactam-based arylsulfonamides as potent and selective FXa inhibitors is reported. The arylsulfonamide-valerolactam scaffold was derived based on the proposed bioisosterism to the arylcyanoguanidine-caprolactam core in known FXa inhibitors. The SAR study led to compound 46 as the most potent FXa inhibitor in this series, with an IC(50) of 7 nM and EC(2×PT) of 1.7 μM. The X-ray structure of compound 40 bound to FXa shows that the sulfonamide-valerolactam scaffold anchors the aryl group in the S1 and the novel acylcytisine pharmacophore in the S4 pockets.
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21
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Watson NS, Adams C, Belton D, Brown D, Burns-Kurtis CL, Chaudry L, Chan C, Convery MA, Davies DE, Exall AM, Harling JD, Irvine S, Irving WR, Kleanthous S, McLay IM, Pateman AJ, Patikis AN, Roethke TJ, Senger S, Stelman GJ, Toomey JR, West RI, Whittaker C, Zhou P, Young RJ. The discovery of potent and long-acting oral factor Xa inhibitors with tetrahydroisoquinoline and benzazepine P4 motifs. Bioorg Med Chem Lett 2011; 21:1588-92. [DOI: 10.1016/j.bmcl.2011.01.129] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 01/26/2011] [Accepted: 01/27/2011] [Indexed: 10/18/2022]
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22
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Lee YK, Player MR. Developments in factor Xa inhibitors for the treatment of thromboembolic disorders. Med Res Rev 2011; 31:202-83. [DOI: 10.1002/med.20183] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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23
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Young RJ, Adams C, Blows M, Brown D, Burns-Kurtis CL, Chan C, Chaudry L, Convery MA, Davies DE, Exall AM, Foster G, Harling JD, Hortense E, Irvine S, Irving WR, Jackson S, Kleanthous S, Pateman AJ, Patikis AN, Roethka TJ, Senger S, Stelman GJ, Toomey JR, West RI, Whittaker C, Zhou P, Watson NS. Structure and property based design of factor Xa inhibitors: pyrrolidin-2-ones with aminoindane and phenylpyrrolidine P4 motifs. Bioorg Med Chem Lett 2011; 21:1582-7. [PMID: 21349710 DOI: 10.1016/j.bmcl.2011.01.131] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 01/26/2011] [Accepted: 01/27/2011] [Indexed: 11/30/2022]
Abstract
The rational design, syntheses and evaluation of potent sulfonamidopyrrolidin-2-one-based factor Xa inhibitors incorporating aminoindane and phenylpyrrolidine P4 motifs are described. These series delivered highly potent anticoagulant compounds with excellent oral pharmacokinetic profiles; however, significant time dependant P450 inhibition was an issue for the aminoindane series, but this was not observed with the phenylpyrrolidine motif, which produced candidate quality molecules with potential for once-daily oral dosing in humans.
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Affiliation(s)
- Robert J Young
- GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire, United Kingdom.
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24
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Fujimoto T, Imaeda Y, Konishi N, Hiroe K, Kawamura M, Textor GP, Aertgeerts K, Kubo K. Discovery of a tetrahydropyrimidin-2(1H)-one derivative (TAK-442) as a potent, selective, and orally active factor Xa inhibitor. J Med Chem 2010; 53:3517-31. [PMID: 20355714 DOI: 10.1021/jm901699j] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Coagulation enzyme factor Xa (FXa) is a particularly promising target for the development of new anticoagulant agents. We previously reported the imidazo[1,5-c]imidazol-3-one derivative 1 as a potent and orally active FXa inhibitor. However, it was found that 1 predominantly undergoes hydrolysis upon incubation with human liver microsomes, and the human specific metabolic pathway made it difficult to predict the human pharmacokinetics. To address this issue, our synthetic efforts were focused on modification of the imidazo[1,5-c]imidazol-3-one moiety of the active metabolite 3a, derived from 1, which resulted in the discovery of the tetrahydropyrimidin-2(1H)-one derivative 5k as a highly potent and selective FXa inhibitor. Compound 5k showed no detectable amide bond cleavage in human liver microsomes, exhibited a good pharmacokinetic profile in monkeys, and had a potent antithrombotic efficacy in a rabbit model without prolongation of bleeding time. Compound 5k is currently under clinical development with the code name TAK-442.
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Affiliation(s)
- Takuya Fujimoto
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd., 2-17-85, Jusohomachi, Yodogawa-ku, Osaka 532-8686, Japan
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25
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Pinto DJP, Smallheer JM, Cheney DL, Knabb RM, Wexler RR. Factor Xa Inhibitors: Next-Generation Antithrombotic Agents. J Med Chem 2010; 53:6243-74. [PMID: 20503967 DOI: 10.1021/jm100146h] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Donald J. P. Pinto
- Research and Development, Bristol-Myers Squibb Company, P.O. Box 5400, Princeton, New Jersey, 08543
| | - Joanne M. Smallheer
- Research and Development, Bristol-Myers Squibb Company, P.O. Box 5400, Princeton, New Jersey, 08543
| | - Daniel L. Cheney
- Research and Development, Bristol-Myers Squibb Company, P.O. Box 5400, Princeton, New Jersey, 08543
| | - Robert M. Knabb
- Research and Development, Bristol-Myers Squibb Company, P.O. Box 5400, Princeton, New Jersey, 08543
| | - Ruth R. Wexler
- Research and Development, Bristol-Myers Squibb Company, P.O. Box 5400, Princeton, New Jersey, 08543
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26
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de Candia M, Lopopolo G, Altomare C. Novel factor Xa inhibitors: a patent review. Expert Opin Ther Pat 2010; 19:1535-80. [PMID: 19743898 DOI: 10.1517/13543770903270532] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
IMPORTANCE OF THE FIELD New oral anticoagulants with favorable safety profiles and fixed doses are required for the management of thromboembolism and stroke prevention in patients with atrial fibrillation. Among them, fXa inhibitors (the so-called xabans) are attractive options that can overcome limitations (e.g., bleeding) of the current oral antithrombotic therapy. The rational design of small-molecule direct fXa inhibitors, whose importance is testified by the growing number of publications and patents recently registered, has been fully supported by the X-ray crystallography of enzyme-ligand complexes. AREAS COVERED IN THIS REVIEW Pubmed, SciFinder Scholar, ISI web of knowledge(SM), http://ep.espacenet.com/ and Google websites were used as the main sources for literature retrieving, and > 100 patents filed between 2006 and April 2009, reviewed and discussed herein, highlight the variety among the P1 and P4 moieties on suitable scaffolds. WHAT THE READER WILL GAIN The replacement of the benzamidine P1 moiety, which characterizes the first generation, with less basic bioisosteric or nonpolar neutral P1 groups led to the disclosure of numerous fXa inhibitors with high potency, selectivity and oral bioavailability. Novel selective fXa inhibitors with stable pharmacokinetics, better therapeutic windows and ease-of-use than the existing anticoagulants are currently under advanced stage clinical trials. TAKE-HOME MESSAGE Available data from Phase II and Phase III studies reflect the drive towards fXa inhibitors as potentially more effective and safer antithrombotic drugs. Their development is expected to address two major needs for anticoagulation, namely safety and ease-of-use, and to significantly affect the anticoagulant market.
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Affiliation(s)
- Modesto de Candia
- University of Bari, Dipartimento Farmaco-Chimico, Via E. Orabona 4, I-70125 Bari, Italy
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27
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Wallnoefer HG, Fox T, Liedl KR, Tautermann CS. Dispersion dominated halogen–π interactions: energies and locations of minima. Phys Chem Chem Phys 2010; 12:14941-9. [DOI: 10.1039/c0cp00607f] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Fujimoto T, Tobisu M, Konishi N, Kawamura M, Tada N, Takagi T, Kubo K. Synthesis and biological evaluation of the metabolites of 2-(1-{3-[(6-chloronaphthalen-2-yl)sulfonyl]propanoyl}piperidin-4-yl)-5-methyl-1,2-dihydro-3H-imidazo[1,5-c]imidazol-3-one. Bioorg Med Chem 2009; 17:7993-8002. [DOI: 10.1016/j.bmc.2009.10.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Revised: 10/05/2009] [Accepted: 10/06/2009] [Indexed: 02/02/2023]
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29
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Kleanthous S, Borthwick AD, Brown D, Burns-Kurtis CL, Campbell M, Chaudry L, Chan C, Clarte MO, Convery MA, Harling JD, Hortense E, Irving WR, Irvine S, Pateman AJ, Patikis AN, Pinto IL, Pollard DR, Roethka TJ, Senger S, Shah GP, Stelman GJ, Toomey JR, Watson NS, West RI, Whittaker C, Zhou P, Young RJ. Structure and property based design of factor Xa inhibitors: pyrrolidin-2-ones with monoaryl P4 motifs. Bioorg Med Chem Lett 2009; 20:618-22. [PMID: 20006499 DOI: 10.1016/j.bmcl.2009.11.077] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Revised: 11/16/2009] [Accepted: 11/17/2009] [Indexed: 10/20/2022]
Abstract
Structure and property based drug design was exploited in the synthesis of sulfonamidopyrrolidin-2-one-based factor Xa inhibitors, incorporating neutral and basic monoaryl P4 groups, ultimately producing potent inhibitors with effective levels of anticoagulant activity and extended oral pharmacokinetic profiles. However, time dependant inhibition of Cytochrome P450 3A4 was a particular issue with this series.
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Affiliation(s)
- Savvas Kleanthous
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
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30
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Baum B, Mohamed M, Zayed M, Gerlach C, Heine A, Hangauer D, Klebe G. More than a simple lipophilic contact: a detailed thermodynamic analysis of nonbasic residues in the s1 pocket of thrombin. J Mol Biol 2009; 390:56-69. [PMID: 19409395 DOI: 10.1016/j.jmb.2009.04.051] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Revised: 04/23/2009] [Accepted: 04/23/2009] [Indexed: 11/26/2022]
Abstract
The field of medicinal chemistry aims to design and optimize small molecule leads into drug candidates that may positively interfere with pathological disease situations in humans or combat the growth of infective pathogens. From the plethora of crystal structures of protein-inhibitor complexes we have learned how molecules recognize each other geometrically, but we still have rather superficial understanding of why they bind to each other. This contribution surveys a series of 26 thrombin inhibitors with small systematic structural differences to elucidate the rationale for their widely deviating binding affinity from 185 microM to 4 nM as recorded by enzyme kinetic measurements. Five well-resolved (resolution 2.30 - 1.47 A) crystal structures of thrombin-inhibitor complexes and an apo-structure of the uncomplexed enzyme (1.50 A) are correlated with thermodynamic data recorded by isothermal titration calorimetry with 12 selected inhibitors from the series. Taking solubility data into account, the variation in physicochemical properties allows conclusions to be reached about the relative importance of the enthalpic binding features as well as to estimate the importance of the parameters more difficult to capture, such as residual ligand entropy and desolvation properties. The collected data reveal a comprehensive picture of the thermodynamic signature that explains the so far poorly understood attractive force experienced by m-chloro-benzylamides to thrombin.
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Affiliation(s)
- Bernhard Baum
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Germany
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31
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Shi Y, Sitkoff D, Zhang J, Klei HE, Kish K, Liu ECK, Hartl KS, Seiler SM, Chang M, Huang C, Youssef S, Steinbacher TE, Schumacher WA, Grazier N, Pudzianowski A, Apedo A, Discenza L, Yanchunas J, Stein PD, Atwal KS. Design, structure-activity relationships, X-ray crystal structure, and energetic contributions of a critical P1 pharmacophore: 3-chloroindole-7-yl-based factor Xa inhibitors. J Med Chem 2009; 51:7541-51. [PMID: 18998662 DOI: 10.1021/jm800855x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An indole-based P1 moiety was incorporated into a previously established factor Xa inhibitor series. The indole group was designed to hydrogen-bond with the carbonyl of Gly218, while its 3-methyl or 3-chloro substituent was intended to interact with Tyr228. These interactions were subsequently observed in the X-ray crystal structure of compound 18. SAR studies led to the identification of compound 20 as the most potent FXa inhibitor in this series (IC(50) = 2.4 nM, EC(2xPT) = 1.2 microM). An in-depth energetic analysis suggests that the increased binding energy of 3-chloroindole-versus 3-methylindole-containing compounds in this series is due primarily to (a) the more hydrophobic nature of chloro- versus methyl-containing compounds and (b) an increased interaction of 3-chloroindole versus 3-methylindole with Gly218 backbone. The stronger hydrophobicity of chloro- versus methyl-substituted aromatics may partly explain the general preference for chloro- versus methyl-substituted P1 groups in FXa, which extends beyond the current series.
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Affiliation(s)
- Yan Shi
- Bristol-Myers Squibb Research & Development, P.O. Box 5400, Princeton, New Jersey 08543-5400, USA.
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32
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Van Huis CA, Casimiro-Garcia A, Bigge CF, Cody WL, Dudley DA, Filipski KJ, Heemstra RJ, Kohrt JT, Leadley RJ, Narasimhan LS, McClanahan T, Mochalkin I, Pamment M, Thomas Peterson J, Sahasrabudhe V, Schaum RP, Edmunds JJ. Exploration of 4,4-disubstituted pyrrolidine-1,2-dicarboxamides as potent, orally active Factor Xa inhibitors with extended duration of action. Bioorg Med Chem 2009; 17:2501-11. [PMID: 19231206 DOI: 10.1016/j.bmc.2009.01.063] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2008] [Revised: 01/22/2009] [Accepted: 01/26/2009] [Indexed: 11/27/2022]
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33
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Nagata T, Yoshino T, Haginoya N, Yoshikawa K, Nagamochi M, Kobayashi S, Komoriya S, Yokomizo A, Muto R, Yamaguchi M, Osanai K, Suzuki M, Kanno H. Discovery of N-[(1R,2S,5S)-2-{[(5-chloroindol-2-yl)carbonyl]amino}-5-(dimethylcarbamoyl)cyclohexyl]-5-methyl-4,5,6,7-tetrahydrothiazolo[5,4-c]pyridine-2-carboxamide hydrochloride: A novel, potent and orally active direct inhibitor of factor Xa. Bioorg Med Chem 2009; 17:1193-206. [DOI: 10.1016/j.bmc.2008.12.037] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2008] [Revised: 12/10/2008] [Accepted: 12/12/2008] [Indexed: 10/21/2022]
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Antithrombotic potential of GW813893: a novel, orally active, active-site directed factor Xa inhibitor. J Cardiovasc Pharmacol 2008; 52:66-71. [PMID: 18645410 DOI: 10.1097/fjc.0b013e31817e9b9e] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Factor Xa (FXa) has been a target of considerable interest for drug development efforts aimed at suppressing thrombosis. In this report, a new orally active, small molecule, active-site directed FXa inhibitor, GW813893, has been profiled in a succession of in vitro and in vivo assays involved in its preclinical characterization as a potential antithrombotic therapeutic. METHODS In vitro profiling of GW813893 consisted of assessing its inhibitory potential against FXa and a broad panel of related and unrelated enzymes and receptors. Additionally, the FXa inhibition potential of GW813893 was assessed in prothrombinase and plasma-based clotting assays. In vivo characterization of GW813893 consisted of thrombosis studies in a rat inferior vena cava model, a rat carotid artery thrombosis model, and a rabbit jugular thrombosis model. Bleeding studies were conducted in a rat tail transection model. Ex vivo determinations of compound effects on FX and clotting activity were also undertaken. RESULTS GW813893 was more than 90-fold selective over all enzymes tested, and it inhibited FXa and prothrombinase activity with a Ki of 4.0 nM and 9.7 nM, respectively. In vivo, GW813893 concentration-dependently suppressed thrombotic activity in all models tested. The antithrombotic activity correlated with the suppression of plasma-based clotting activity and the inhibition of plasma FX activity (P < 0.02). Over the antithrombotic dose-range, an increased bleeding diathesis was not observed. CONCLUSION These experiments demonstrate that GW813893 is a potent, selective, orally active inhibitor of FXa. The data suggest that GW813893 has robust antithrombotic potential at doses that have no detectable hemostasis liability. Collectively, the profile suggests that GW813893 has the preclinical pharmacology underpinnings of an oral antithrombotic therapeutic.
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Imaeda Y, Kuroita T, Sakamoto H, Kawamoto T, Tobisu M, Konishi N, Hiroe K, Kawamura M, Tanaka T, Kubo K. Discovery of imidazo[1,5-c]imidazol-3-ones: weakly basic, orally active factor Xa inhibitors. J Med Chem 2008; 51:3422-36. [PMID: 18507371 DOI: 10.1021/jm701548u] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The coagulation enzyme factor Xa (FXa) has been recognized as a promising target for the development of new antithrombotic agents. We previously found compound 1 to be an orally bioavailable FXa inhibitor in fasted monkeys; however, 1 showed poor bioavailability in rats and fed monkeys. To work out the pharmacokinetic problems, we focused our synthetic efforts on the chemical conversion of the 4-(imidazo[1,2- a]pyridin-5-yl)piperazine moiety of 1 to imidazolylpiperidine derivatives (fused and nonfused), which resulted in the discovery of the weakly basic imidazo[1,5- c]imidazol-3-one 3q as a potent and selective FXa inhibitor. Compound 3q showed favorable oral bioavailability in rats and monkeys under both fasted and fed conditions and antithrombotic efficacy in a rat model of venous thrombosis after oral administration, without a significant increase in bleeding time (unlike warfarin). On the basis of these promising properties, compound 3q was selected for further evaluation.
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Affiliation(s)
- Yasuhiro Imaeda
- Pharmaceutical Research Division, Takeda Pharmaceutical Co., Ltd., 2-17-85, Jusohonmachi, Yodogawa-ku, Osaka 532-8686, Japan.
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Imaeda Y, Miyawaki T, Sakamoto H, Itoh F, Konishi N, Hiroe K, Kawamura M, Tanaka T, Kubo K. Discovery of sulfonylalkylamides: A new class of orally active factor Xa inhibitors. Bioorg Med Chem 2008; 16:2243-60. [DOI: 10.1016/j.bmc.2007.11.073] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2007] [Revised: 11/22/2007] [Accepted: 11/27/2007] [Indexed: 10/22/2022]
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Young RJ, Borthwick AD, Brown D, Burns-Kurtis CL, Campbell M, Chan C, Charbaut M, Convery MA, Diallo H, Hortense E, Irving WR, Kelly HA, King NP, Kleanthous S, Mason AM, Pateman AJ, Patikis AN, Pinto IL, Pollard DR, Senger S, Shah GP, Toomey JR, Watson NS, Weston HE, Zhou P. Structure and property based design of factor Xa inhibitors: Biaryl pyrrolidin-2-ones incorporating basic heterocyclic motifs. Bioorg Med Chem Lett 2008; 18:28-33. [DOI: 10.1016/j.bmcl.2007.11.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2007] [Revised: 11/06/2007] [Accepted: 11/08/2007] [Indexed: 11/28/2022]
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Mochizuki A, Nakamoto Y, Naito H, Uoto K, Ohta T. Design, synthesis, and biological activity of piperidine diamine derivatives as factor Xa inhibitor. Bioorg Med Chem Lett 2008; 18:782-7. [DOI: 10.1016/j.bmcl.2007.11.037] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2007] [Revised: 10/22/2007] [Accepted: 11/12/2007] [Indexed: 11/25/2022]
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Young RJ, Borthwick AD, Brown D, Burns-Kurtis CL, Campbell M, Chan C, Charbaut M, Chung CW, Convery MA, Kelly HA, Paul King N, Kleanthous S, Mason AM, Pateman AJ, Patikis AN, Pinto IL, Pollard DR, Senger S, Shah GP, Toomey JR, Watson NS, Weston HE. Structure and property based design of factor Xa inhibitors: Pyrrolidin-2-ones with biaryl P4 motifs. Bioorg Med Chem Lett 2008; 18:23-7. [DOI: 10.1016/j.bmcl.2007.11.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2007] [Revised: 11/06/2007] [Accepted: 11/08/2007] [Indexed: 11/29/2022]
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Young RJ, Brown D, Burns-Kurtis CL, Chan C, Convery MA, Hubbard JA, Kelly HA, Pateman AJ, Patikis A, Senger S, Shah GP, Toomey JR, Watson NS, Zhou P. Selective and dual action orally active inhibitors of thrombin and factor Xa. Bioorg Med Chem Lett 2007; 17:2927-30. [PMID: 17420122 DOI: 10.1016/j.bmcl.2007.03.080] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2007] [Revised: 03/23/2007] [Accepted: 03/24/2007] [Indexed: 11/15/2022]
Abstract
The synthetic entry to new classes of dual fXa/thrombin and selective thrombin inhibitors with significant oral bioavailability is described. This was achieved through minor modifications to the sulfonamide group in our potent and selective fXa inhibitor (E)-2-(5-chlorothien-2-yl)-N-{(3S)-1-[(1S)-1-methyl-2-(morpholin-4-yl)-2-oxoethyl]-2-oxopyrrolidin-3-yl}ethenesulfonamide and these observed activity changes have been rationalised using structural studies.
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Affiliation(s)
- Robert J Young
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK.
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N. Maiti S, Kasani A, Subedi R, Stier M, D. Holsworth D. Cardiovascular Agents: Renin Inhibitors and Factor Xa Inhibitors. HETEROCYCLES 2007. [DOI: 10.3987/rev-07-sr(u)1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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