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Zhang X, Jiang W, Richter JM, Bates JA, Reznik SK, Stachura S, Rampulla R, Doddalingappa D, Ulaganathan S, Hua J, Bostwick JS, Sum C, Posy S, Malmstrom S, Dickey J, Harden D, Lawrence RM, Guarino VR, Schumacher WA, Wong P, Yang J, Gordon DA, Wexler RR, Priestley ES. Discovery of Potent and Selective Quinoxaline-Based Protease-Activated Receptor 4 (PAR4) Antagonists for the Prevention of Arterial Thrombosis. J Med Chem 2024; 67:3571-3589. [PMID: 38385264 DOI: 10.1021/acs.jmedchem.3c01986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
PAR4 is a promising antithrombotic target with potential for separation of efficacy from bleeding risk relative to current antiplatelet therapies. In an effort to discover a novel PAR4 antagonist chemotype, a quinoxaline-based HTS hit 3 with low μM potency was identified. Optimization of the HTS hit through the use of positional SAR scanning and the design of conformationally constrained cores led to the discovery of a quinoxaline-benzothiazole series as potent and selective PAR4 antagonists. The lead compound 48, possessing a 2 nM IC50 against PAR4 activation by γ-thrombin in platelet-rich plasma (PRP) and greater than 2500-fold selectivity versus PAR1, demonstrated robust antithrombotic efficacy and minimal bleeding in the cynomolgus monkey models.
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Affiliation(s)
- Xiaojun Zhang
- Research & Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Wen Jiang
- Research & Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Jeremy M Richter
- Research & Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - J Alex Bates
- Research & Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Samuel K Reznik
- Research & Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Sylwia Stachura
- Research & Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Richard Rampulla
- Research & Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Dyamanna Doddalingappa
- Department of Discovery Synthesis, Biocon Bristol Myers Squibb R&D Centre, Syngene International Ltd., Biocon Park, Plot No. 2 & 3, Bommasandra-Jigani Road, Bangalore 560099, India
| | - Sankar Ulaganathan
- Department of Discovery Synthesis, Biocon Bristol Myers Squibb R&D Centre, Syngene International Ltd., Biocon Park, Plot No. 2 & 3, Bommasandra-Jigani Road, Bangalore 560099, India
| | - Ji Hua
- Research & Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Jeffrey S Bostwick
- Research & Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Chi Sum
- Research & Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Shana Posy
- Research & Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Sarah Malmstrom
- Research & Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Joyce Dickey
- Research & Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - David Harden
- Research & Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - R Michael Lawrence
- Research & Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Victor R Guarino
- Research & Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - William A Schumacher
- Research & Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Pancras Wong
- Research & Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Jing Yang
- Research & Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - David A Gordon
- Research & Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Ruth R Wexler
- Research & Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - E Scott Priestley
- Research & Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
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Klei HE, Moriarty NW, Echols N, Terwilliger TC, Baldwin ET, Pokross M, Posy S, Adams PD. Ligand placement based on prior structures: the guided ligand-replacement method. Acta Crystallogr D Biol Crystallogr 2014; 70:134-43. [PMID: 24419386 PMCID: PMC3919265 DOI: 10.1107/s1399004713030071] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 11/02/2013] [Indexed: 11/10/2022]
Abstract
The process of iterative structure-based drug design involves the X-ray crystal structure determination of upwards of 100 ligands with the same general scaffold (i.e. chemotype) complexed with very similar, if not identical, protein targets. In conjunction with insights from computational models and assays, this collection of crystal structures is analyzed to improve potency, to achieve better selectivity and to reduce liabilities such as absorption, distribution, metabolism, excretion and toxicology. Current methods for modeling ligands into electron-density maps typically do not utilize information on how similar ligands bound in related structures. Even if the electron density is of sufficient quality and resolution to allow de novo placement, the process can take considerable time as the size, complexity and torsional degrees of freedom of the ligands increase. A new module, Guided Ligand Replacement (GLR), was developed in Phenix to increase the ease and success rate of ligand placement when prior protein-ligand complexes are available. At the heart of GLR is an algorithm based on graph theory that associates atoms in the target ligand with analogous atoms in the reference ligand. Based on this correspondence, a set of coordinates is generated for the target ligand. GLR is especially useful in two situations: (i) modeling a series of large, flexible, complicated or macrocyclic ligands in successive structures and (ii) modeling ligands as part of a refinement pipeline that can automatically select a reference structure. Even in those cases for which no reference structure is available, if there are multiple copies of the bound ligand per asymmetric unit GLR offers an efficient way to complete the model after the first ligand has been placed. In all of these applications, GLR leverages prior knowledge from earlier structures to facilitate ligand placement in the current structure.
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Affiliation(s)
- Herbert E. Klei
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Research and Development, Bristol-Myers Squibb, Princeton, NJ 08543-4000, USA
| | - Nigel W. Moriarty
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Nathaniel Echols
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Eric T. Baldwin
- Research and Development, Bristol-Myers Squibb, Princeton, NJ 08543-4000, USA
- Natural Discovery LLC, Princeton, NJ 08542-0096, USA
| | - Matt Pokross
- Research and Development, Bristol-Myers Squibb, Princeton, NJ 08543-4000, USA
| | - Shana Posy
- Research and Development, Bristol-Myers Squibb, Princeton, NJ 08543-4000, USA
| | - Paul D. Adams
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California at Berkeley, Berkeley, CA 94720-1762, USA
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