1
|
Dawson JRD, Wadman GM, Zhang P, Tebben A, Carter PH, Gu S, Shroka T, Borrega-Roman L, Salanga CL, Handel TM, Kufareva I. Molecular determinants of antagonist interactions with chemokine receptors CCR2 and CCR5. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.15.567150. [PMID: 38014122 PMCID: PMC10680698 DOI: 10.1101/2023.11.15.567150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
By driving monocyte chemotaxis, the chemokine receptor CCR2 shapes inflammatory responses and the formation of tumor microenvironments. This makes it a promising target in inflammation and immuno-oncology; however, despite extensive efforts, there are no FDA-approved CCR2-targeting therapeutics. Cited challenges include the redundancy of the chemokine system, suboptimal properties of compound candidates, and species differences that confound the translation of results from animals to humans. Structure-based drug design can rationalize and accelerate the discovery and optimization of CCR2 antagonists to address these challenges. The prerequisites for such efforts include an atomic-level understanding of the molecular determinants of action of existing antagonists. In this study, using molecular docking and artificial-intelligence-powered compound library screening, we uncover the structural principles of small molecule antagonism and selectivity towards CCR2 and its sister receptor CCR5. CCR2 orthosteric inhibitors are shown to universally occupy an inactive-state-specific tunnel between receptor helices 1 and 7; we also discover an unexpected role for an extra-helical groove accessible through this tunnel, suggesting its potential as a new targetable interface for CCR2 and CCR5 modulation. By contrast, only shape complementarity and limited helix 8 hydrogen bonding govern the binding of various chemotypes of allosteric antagonists. CCR2 residues S1012.63 and V2446.36 are implicated as determinants of CCR2/CCR5 and human/mouse orthosteric and allosteric antagonist selectivity, respectively, and the role of S1012.63 is corroborated through experimental gain-of-function mutagenesis. We establish a critical role of induced fit in antagonist recognition, reveal strong chemotype selectivity of existing structures, and demonstrate the high predictive potential of a new deep-learning-based compound scoring function. Finally, this study expands the available CCR2 structural landscape with computationally generated chemotype-specific models well-suited for structure-based antagonist design.
Collapse
Affiliation(s)
- John R D Dawson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Grant M Wadman
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | | | | | - Percy H Carter
- Bristol Myers Squibb Company, Princeton, NJ, USA
- (current affiliation) Blueprint Medicines, Cambridge, MA, USA
| | - Siyi Gu
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- (current affiliation) Lycia Therapeutics, South San Francisco, CA
| | - Thomas Shroka
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- (current affiliation) Avidity Biosciences Inc., San Diego, CA
| | - Leire Borrega-Roman
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Catherina L Salanga
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Tracy M Handel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Irina Kufareva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| |
Collapse
|
2
|
Yang MG, Xiao Z, Zhao R, Tebben AJ, Wang B, Cherney RJ, Batt DG, Brown GD, Cvijic ME, Duncia JV, Gallela MA, Gardner DS, Khandelwal P, Malley MF, Pang J, Rose AV, Santella JB, Sarjeant AA, Xu S, Mathur A, Mandlekar S, Vuppugalla R, Zhao Q, Carter PH. Discovery of BMS-753426: A Potent Orally Bioavailable Antagonist of CC Chemokine Receptor 2. ACS Med Chem Lett 2021; 12:969-975. [PMID: 34141082 DOI: 10.1021/acsmedchemlett.1c00082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/20/2021] [Indexed: 12/18/2022] Open
Abstract
To improve the metabolic stability profile of BMS-741672 (1a), we undertook a structure-activity relationship study in our trisubstituted cyclohexylamine series. This ultimately led to the identification of 2d (BMS-753426) as a potent and orally bioavailable antagonist of CCR2. Compared to previous clinical candidate 1a, the tert-butyl amine 2d showed significant improvements in pharmacokinetic properties, with lower clearance and higher oral bioavailability. Furthermore, compound 2d exhibited improved affinity for CCR5 and good activity in models of both monocyte migration and multiple sclerosis in the hCCR2 knock-in mouse. The synthesis of 2d was facilitated by the development of a simplified approach to key intermediate (4R)-9b that deployed a stereoselective reductive amination which may prove to be of general interest.
Collapse
Affiliation(s)
- Michael G. Yang
- Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Zili Xiao
- Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Rulin Zhao
- Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Andrew J. Tebben
- Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Bei Wang
- Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Robert J. Cherney
- Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Douglas G. Batt
- Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Gregory D. Brown
- Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Mary Ellen Cvijic
- Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - John V. Duncia
- Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Michael A. Gallela
- Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Daniel S. Gardner
- Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Purnima Khandelwal
- Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Mary F. Malley
- Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Jian Pang
- Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Anne V. Rose
- Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Joseph B. Santella
- Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Amy A. Sarjeant
- Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Songmei Xu
- Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Arvind Mathur
- Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Sandhya Mandlekar
- Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Ragini Vuppugalla
- Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Qihong Zhao
- Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Percy H. Carter
- Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| |
Collapse
|
3
|
Yang MG, Xiao Z, Cherney RJ, Tebben AJ, Batt DG, Brown GD, Chen J, Cvijic ME, Dabros M, Duncia JV, Galella M, Gardner DS, Khandelwal P, Ko SS, Malley MF, Mo R, Pang J, Rose AV, Santella JB, Shi H, Srivastava A, Traeger SC, Wang B, Xu S, Zhao R, Barrish JC, Mandlekar S, Zhao Q, Carter PH. Use of a Conformational-Switching Mechanism to Modulate Exposed Polarity: Discovery of CCR2 Antagonist BMS-741672. ACS Med Chem Lett 2019; 10:300-305. [PMID: 30891130 DOI: 10.1021/acsmedchemlett.8b00439] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 01/16/2019] [Indexed: 12/21/2022] Open
Abstract
We encountered a dilemma in the course of studying a series of antagonists of the G-protein coupled receptor CC chemokine receptor-2 (CCR2): compounds with polar C3 side chains exhibited good ion channel selectivity but poor oral bioavailability, whereas compounds with lipophilic C3 side chains exhibited good oral bioavailability in preclinical species but poor ion channel selectivity. Attempts to solve this through the direct modulation of physicochemical properties failed. However, the installation of a protonation-dependent conformational switching mechanism resolved the problem because it enabled a highly selective and relatively polar molecule to access a small population of a conformer with lower polar surface area and higher membrane permeability. Optimization of the overall properties in this series yielded the CCR2 antagonist BMS-741672 (7), which embodied properties suitable for study in human clinical trials.
Collapse
Affiliation(s)
- Michael G. Yang
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Zili Xiao
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Robert J. Cherney
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Andrew J. Tebben
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Douglas G. Batt
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Gregory D. Brown
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Jing Chen
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Mary Ellen Cvijic
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Marta Dabros
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - John V. Duncia
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Michael Galella
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Daniel S. Gardner
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Purnima Khandelwal
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Soo S. Ko
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Mary F. Malley
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Ruowei Mo
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Jian Pang
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Anne V. Rose
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Joseph B. Santella
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Hong Shi
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Anurag Srivastava
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Sarah C. Traeger
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Bei Wang
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Songmei Xu
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Rulin Zhao
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Joel C. Barrish
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Sandhya Mandlekar
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Qihong Zhao
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Percy H. Carter
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| |
Collapse
|
4
|
Carter PH, Brown GD, Cherney RJ, Batt DG, Chen J, Clark CM, Cvijic ME, Duncia JV, Ko SS, Mandlekar S, Mo R, Nelson DJ, Pang J, Rose AV, Santella JB, Tebben AJ, Traeger SC, Xu S, Zhao Q, Barrish JC. Discovery of a Potent and Orally Bioavailable Dual Antagonist of CC Chemokine Receptors 2 and 5. ACS Med Chem Lett 2015; 6:439-44. [PMID: 25893046 DOI: 10.1021/ml500505q] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Accepted: 03/04/2015] [Indexed: 12/15/2022] Open
Abstract
We describe the hybridization of our previously reported acyclic and cyclic CC chemokine receptor 2 (CCR2) antagonists to lead to a new series of dual antagonists of CCR2 and CCR5. Installation of a γ-lactam as the spacer group and a quinazoline as a benzamide mimetic improved oral bioavailability markedly. These efforts led to the identification of 13d, a potent and orally bioavailable dual antagonist suitable for use in both murine and monkey models of inflammation.
Collapse
Affiliation(s)
- Percy H. Carter
- Departments of Discovery Chemistry, ‡Lead Discovery & Optimization, §Preclinical Candidate Optimization, ∥Molecular Discovery Technologies, and ⊥Disease Sciences & Biology, Research and Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Gregory D. Brown
- Departments of Discovery Chemistry, ‡Lead Discovery & Optimization, §Preclinical Candidate Optimization, ∥Molecular Discovery Technologies, and ⊥Disease Sciences & Biology, Research and Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Robert J. Cherney
- Departments of Discovery Chemistry, ‡Lead Discovery & Optimization, §Preclinical Candidate Optimization, ∥Molecular Discovery Technologies, and ⊥Disease Sciences & Biology, Research and Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Douglas G. Batt
- Departments of Discovery Chemistry, ‡Lead Discovery & Optimization, §Preclinical Candidate Optimization, ∥Molecular Discovery Technologies, and ⊥Disease Sciences & Biology, Research and Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Jing Chen
- Departments of Discovery Chemistry, ‡Lead Discovery & Optimization, §Preclinical Candidate Optimization, ∥Molecular Discovery Technologies, and ⊥Disease Sciences & Biology, Research and Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Cheryl M. Clark
- Departments of Discovery Chemistry, ‡Lead Discovery & Optimization, §Preclinical Candidate Optimization, ∥Molecular Discovery Technologies, and ⊥Disease Sciences & Biology, Research and Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Mary Ellen Cvijic
- Departments of Discovery Chemistry, ‡Lead Discovery & Optimization, §Preclinical Candidate Optimization, ∥Molecular Discovery Technologies, and ⊥Disease Sciences & Biology, Research and Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - John V. Duncia
- Departments of Discovery Chemistry, ‡Lead Discovery & Optimization, §Preclinical Candidate Optimization, ∥Molecular Discovery Technologies, and ⊥Disease Sciences & Biology, Research and Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Soo S. Ko
- Departments of Discovery Chemistry, ‡Lead Discovery & Optimization, §Preclinical Candidate Optimization, ∥Molecular Discovery Technologies, and ⊥Disease Sciences & Biology, Research and Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Sandhya Mandlekar
- Departments of Discovery Chemistry, ‡Lead Discovery & Optimization, §Preclinical Candidate Optimization, ∥Molecular Discovery Technologies, and ⊥Disease Sciences & Biology, Research and Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Ruowei Mo
- Departments of Discovery Chemistry, ‡Lead Discovery & Optimization, §Preclinical Candidate Optimization, ∥Molecular Discovery Technologies, and ⊥Disease Sciences & Biology, Research and Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - David J. Nelson
- Departments of Discovery Chemistry, ‡Lead Discovery & Optimization, §Preclinical Candidate Optimization, ∥Molecular Discovery Technologies, and ⊥Disease Sciences & Biology, Research and Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Jian Pang
- Departments of Discovery Chemistry, ‡Lead Discovery & Optimization, §Preclinical Candidate Optimization, ∥Molecular Discovery Technologies, and ⊥Disease Sciences & Biology, Research and Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Anne V. Rose
- Departments of Discovery Chemistry, ‡Lead Discovery & Optimization, §Preclinical Candidate Optimization, ∥Molecular Discovery Technologies, and ⊥Disease Sciences & Biology, Research and Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Joseph B. Santella
- Departments of Discovery Chemistry, ‡Lead Discovery & Optimization, §Preclinical Candidate Optimization, ∥Molecular Discovery Technologies, and ⊥Disease Sciences & Biology, Research and Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Andrew J. Tebben
- Departments of Discovery Chemistry, ‡Lead Discovery & Optimization, §Preclinical Candidate Optimization, ∥Molecular Discovery Technologies, and ⊥Disease Sciences & Biology, Research and Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Sarah C. Traeger
- Departments of Discovery Chemistry, ‡Lead Discovery & Optimization, §Preclinical Candidate Optimization, ∥Molecular Discovery Technologies, and ⊥Disease Sciences & Biology, Research and Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Songmei Xu
- Departments of Discovery Chemistry, ‡Lead Discovery & Optimization, §Preclinical Candidate Optimization, ∥Molecular Discovery Technologies, and ⊥Disease Sciences & Biology, Research and Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Qihong Zhao
- Departments of Discovery Chemistry, ‡Lead Discovery & Optimization, §Preclinical Candidate Optimization, ∥Molecular Discovery Technologies, and ⊥Disease Sciences & Biology, Research and Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Joel C. Barrish
- Departments of Discovery Chemistry, ‡Lead Discovery & Optimization, §Preclinical Candidate Optimization, ∥Molecular Discovery Technologies, and ⊥Disease Sciences & Biology, Research and Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543, United States
| |
Collapse
|