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Darsaraee M, Kaveh S, Mani-Varnosfaderani A, Neiband MS. General structure-activity/selectivity relationship patterns for the inhibitors of the chemokine receptors (CCR1/CCR2/CCR4/CCR5) with application for virtual screening of PubChem database. J Biomol Struct Dyn 2023:1-19. [PMID: 37599469 DOI: 10.1080/07391102.2023.2248255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 08/08/2023] [Indexed: 08/22/2023]
Abstract
CC chemokine receptors (CCRs) form a crucial subfamily of G protein-linked receptors that play a distinct role in the onset and progression of various life-threatening diseases. The main aim of this research is to derive general structure-activity relationship (SAR) patterns to describe the selectivity and activity of CCR inhibitors. To this end, a total of 7332 molecules related to the inhibition of CCR1, CCR2, CCR4, and CCR5 were collected from the Binding Database and analyzed using machine learning techniques. A diverse set of 450 molecular descriptors was calculated for each molecule, and the molecules were classified based on their therapeutic targets and activities. The variable importance in the projection (VIP) approach was used to select discriminatory molecular features, and classification models were developed using supervised Kohonen networks (SKN) and counter-propagation artificial neural networks (CPANN). The reliability and predictability of the models were estimated using 10-fold cross-validation, an external validation set, and an applicability domain approach. We were able to identify different sets of molecular descriptors for discriminating between active and inactive molecules and model the selectivity of inhibitors towards different CCRs. The sensitivities of the predictions for the external test set for the SKN models ranged from 0.827-0.873. Finally, the developed classification models were used to screen approximately 2 million random molecules from the PubChem database, with average values for areas under the receiver operating characteristic curves ranging from 0.78-0.96 for SKN models and 0.75-0.89 for CPANN models.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- M Darsaraee
- Chemometrics and Cheminformatics Laboratory, Department of Analytical Chemistry, Tarbiat Modares University, Tehran, Iran
| | - S Kaveh
- Chemometrics and Cheminformatics Laboratory, Department of Analytical Chemistry, Tarbiat Modares University, Tehran, Iran
| | - A Mani-Varnosfaderani
- Chemometrics and Cheminformatics Laboratory, Department of Analytical Chemistry, Tarbiat Modares University, Tehran, Iran
| | - M S Neiband
- Department of Chemistry, Payame Noor University (PNU), Tehran, Iran
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2
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Barhate CL, Donnell AF, Davies M, Li L, Zhang Y, Yang F, Black R, Zipp G, Zhang Y, Cavallaro CL, Priestley ES, Weller HN. Microscale purification in support of high-throughput medicinal chemistry. Chem Commun (Camb) 2021; 57:11037-11040. [PMID: 34608906 DOI: 10.1039/d1cc03791a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In recent years, successful assay miniaturization has enabled the exploration of synthesis scale reduction in pharmaceutical discovery. Miniaturization of pharmaceutical synthesis and purification allows a reduction in material consumption and shortens timelines, which ultimately reduces the cost per experiment without compromising data quality. Isolating and purifying the compounds of interest is a key step in the library synthesis process. In this manuscript we describe a high-throughput purification workflow in support of microscale (1-5 μmol or 0.5-2 mg) library synthesis. The optimized microscale purification system can routinely purify 384-well reaction plates with an analysis time of 4 min per sample. Instrument optimization, critical parameters such as column loading, delay time calibration, ultrafast pre- and post-purification analysis and library purification examples are provided.
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Affiliation(s)
- Chandan L Barhate
- Separation and Analysis Technology Team, Bristol Myers Squibb, Lawrenceville, NJ, USA.
| | - Andrew F Donnell
- Chemotype Discovery and Optimization, Bristol Myers Squibb, Lawrenceville, NJ, USA
| | - Merrill Davies
- Separation and Analysis Technology Team, Bristol Myers Squibb, Lawrenceville, NJ, USA.
| | - Ling Li
- Chemotype Discovery and Optimization, Bristol Myers Squibb, Lawrenceville, NJ, USA
| | - Yong Zhang
- Novel Drug Modalities, Bristol Myers Squibb, Lawrenceville, NJ, USA
| | - Fukang Yang
- Novel Drug Modalities, Bristol Myers Squibb, Lawrenceville, NJ, USA
| | - Regina Black
- Agilent Technologies, Incorporated, Wilmington, Delaware 19808, USA
| | - Greg Zipp
- Separation and Analysis Technology Team, Bristol Myers Squibb, Lawrenceville, NJ, USA.
| | - Yingru Zhang
- Separation and Analysis Technology Team, Bristol Myers Squibb, Lawrenceville, NJ, USA.
| | - Cullen L Cavallaro
- Chemotype Discovery and Optimization, Bristol Myers Squibb, Lawrenceville, NJ, USA
| | - E Scott Priestley
- Chemotype Discovery and Optimization, Bristol Myers Squibb, Lawrenceville, NJ, USA
| | - Harold N Weller
- Separation and Analysis Technology Team, Bristol Myers Squibb, Lawrenceville, NJ, USA.
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Chen J, Ribeiro B, Li H, Myer L, Chase P, Surti N, Lippy J, Zhang L, Cvijic ME. Leveraging the IncuCyte Technology for Higher-Throughput and Automated Chemotaxis Assays for Target Validation and Compound Characterization. SLAS DISCOVERY 2017; 23:122-131. [PMID: 28957636 DOI: 10.1177/2472555217733437] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Chemotaxis is the directional movement of cells in response to a chemical stimulus and is vital for many physiological processes, including immune responses, tumor metastasis, wound healing, and blood vessel formation. Therefore, modulation of chemotaxis is likely to be of therapeutic benefit. Hence, a high-throughput means to conduct chemotaxis assays is advantageous for lead evaluation and optimization in drug discovery. In this study, we have validated a novel approach for a higher-throughput, label-free, image-based IncuCyte chemotaxis assay encompassing various cell types, including T cells, B cells, mouse Th17, immature and mature dendritic cells, monocyte THP-1, CCRF-CEM, monocytes, neutrophils, macrophages, and MDA-MB-231. These assays enable us to visualize chemotactic cell migration in real time and perform kinetic cell motility studies on an automated platform, thereby allowing us to incorporate the quantitative studies of cell migration behavior into a routine drug discovery screening cascade.
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Affiliation(s)
- Jing Chen
- 1 Leads Discovery & Optimization, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Bert Ribeiro
- 1 Leads Discovery & Optimization, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Han Li
- 1 Leads Discovery & Optimization, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Larnie Myer
- 1 Leads Discovery & Optimization, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Peter Chase
- 1 Leads Discovery & Optimization, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Neha Surti
- 1 Leads Discovery & Optimization, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Jonathan Lippy
- 1 Leads Discovery & Optimization, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Litao Zhang
- 1 Leads Discovery & Optimization, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Mary Ellen Cvijic
- 1 Leads Discovery & Optimization, Bristol-Myers Squibb Company, Princeton, NJ, USA
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Khan JA, Camac DM, Low S, Tebben AJ, Wensel DL, Wright MC, Su J, Jenny V, Gupta RD, Ruzanov M, Russo KA, Bell A, An Y, Bryson JW, Gao M, Gambhire P, Baldwin ET, Gardner D, Cavallaro CL, Duncia JV, Hynes J. Developing Adnectins that target SRC co-activator binding to PXR: a structural approach toward understanding promiscuity of PXR. J Mol Biol 2015; 427:924-942. [PMID: 25579995 DOI: 10.1016/j.jmb.2014.12.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 12/19/2014] [Accepted: 12/29/2014] [Indexed: 02/08/2023]
Abstract
The human pregnane X receptor (PXR) is a promiscuous nuclear receptor that functions as a sensor to a wide variety of xenobiotics and regulates expression of several drug metabolizing enzymes and transporters. We have generated "Adnectins", derived from 10th fibronectin type III domain ((10)Fn3), that target the PXR ligand binding domain (LBD) interactions with the steroid receptor co-activator-1 (SRC-1) peptide, displacing SRC-1 binding. Adnectins are structurally homologous to the immunoglobulin superfamily. Three different co-crystal structures of PXR LBD with Adnectin-1 and CCR1 (CC chemokine receptor-1) antagonist Compound-1 were determined. This structural information was used to modulate PXR affinity for a related CCR1 antagonist compound that entered into clinical trials for rheumatoid arthritis. The structures of PXR with Adnectin-1 reveal specificity of Adnectin-1 in not only targeting the interface of the SRC-1 interactions but also engaging the same set of residues that are involved in binding of SRC-1 to PXR. Substituting SRC-1 with Adnectin-1 does not alter the binding conformation of Compound-1 in the ligand binding pocket. The structure also reveals the possibility of using Adnectins as crystallization chaperones to generate structures of PXR with compounds of interest.
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Affiliation(s)
- Javed A Khan
- Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA.
| | - Daniel M Camac
- Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA
| | - Simon Low
- Adnexus, 100 Beaver Street, Waltham, MA 02453, USA
| | - Andrew J Tebben
- Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA
| | | | | | - Julie Su
- Adnexus, 100 Beaver Street, Waltham, MA 02453, USA
| | | | | | - Max Ruzanov
- Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA
| | | | - Aneka Bell
- Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA
| | - Yongmi An
- Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA
| | - James W Bryson
- Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA
| | - Mian Gao
- Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA
| | | | - Eric T Baldwin
- Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA
| | - Daniel Gardner
- Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA
| | - Cullen L Cavallaro
- Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA
| | - John V Duncia
- Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA
| | - John Hynes
- Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA
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5
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Santella JB, Gardner DS, Duncia JV, Wu H, Dhar M, Cavallaro C, Tebben AJ, Carter PH, Barrish JC, Yarde M, Briceno SW, Cvijic ME, Grafstrom RR, Liu R, Patel SR, Watson AJ, Yang G, Rose AV, Vickery RD, Caceres-Cortes J, Caporuscio C, Camac DM, Khan JA, An Y, Foster WR, Davies P, Hynes J. Discovery of the CCR1 Antagonist, BMS-817399, for the Treatment of Rheumatoid Arthritis. J Med Chem 2014; 57:7550-64. [DOI: 10.1021/jm5003167] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joseph B. Santella
- Bristol Myers Squibb Company, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Daniel S. Gardner
- Bristol Myers Squibb Company, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - John V. Duncia
- Bristol Myers Squibb Company, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Hong Wu
- Bristol Myers Squibb Company, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Murali Dhar
- Bristol Myers Squibb Company, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Cullen Cavallaro
- Bristol Myers Squibb Company, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Andrew J. Tebben
- Bristol Myers Squibb Company, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Percy H. Carter
- Bristol Myers Squibb Company, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Joel C. Barrish
- Bristol Myers Squibb Company, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Melissa Yarde
- Bristol Myers Squibb Company, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Stephanie W. Briceno
- Bristol Myers Squibb Company, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Mary Ellen Cvijic
- Bristol Myers Squibb Company, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - R. Robert Grafstrom
- Bristol Myers Squibb Company, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Richard Liu
- Bristol Myers Squibb Company, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Sima R. Patel
- Bristol Myers Squibb Company, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Andrew J. Watson
- Bristol Myers Squibb Company, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Guchen Yang
- Bristol Myers Squibb Company, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Anne V. Rose
- Bristol Myers Squibb Company, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Rodney D. Vickery
- Bristol Myers Squibb Company, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Janet Caceres-Cortes
- Bristol Myers Squibb Company, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Christian Caporuscio
- Bristol Myers Squibb Company, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Daniel M. Camac
- Bristol Myers Squibb Company, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Javed A. Khan
- Bristol Myers Squibb Company, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Yongmi An
- Bristol Myers Squibb Company, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - William R. Foster
- Bristol Myers Squibb Company, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Paul Davies
- Bristol Myers Squibb Company, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - John Hynes
- Bristol Myers Squibb Company, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
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6
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Gardner DS, Santella JB, Duncia JV, Carter PH, Dhar T, Wu H, Guo W, Cavallaro C, Van Kirk K, Yarde M, Briceno SW, Robert Grafstrom R, Liu R, Patel SR, Tebben AJ, Camac D, Khan J, Watson A, Yang G, Rose A, Foster WR, Cvijic ME, Davies P, Hynes J. The discovery of BMS-457, a potent and selective CCR1 antagonist. Bioorg Med Chem Lett 2013; 23:3833-40. [DOI: 10.1016/j.bmcl.2013.04.079] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 04/24/2013] [Accepted: 04/29/2013] [Indexed: 02/07/2023]
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7
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Pennell AMK, Aggen JB, Sen S, Chen W, Xu Y, Sullivan E, Li L, Greenman K, Charvat T, Hansen D, Dairaghi DJ, Wright JJK, Zhang P. 1-(4-Phenylpiperazin-1-yl)-2-(1H-pyrazol-1-yl)ethanones as novel CCR1 antagonists. Bioorg Med Chem Lett 2013; 23:1228-31. [PMID: 23374868 DOI: 10.1016/j.bmcl.2013.01.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 12/31/2012] [Accepted: 01/02/2013] [Indexed: 11/16/2022]
Abstract
A novel series of CCR1 antagonists based on the 1-(4-phenylpiperazin-1-yl)-2-(1H-pyrazol-1-yl)ethanone scaffold was identified by screening a compound library utilizing CCR1-expressing human THP-1 cells. SAR studies led to the discovery of the highly potent and selective CCR1 antagonist 14 (CCR1 binding IC(50)=4 nM using [(125)I]-CCL3 as the chemokine ligand). Compound 14 displayed promising pharmacokinetic and toxicological profiles in preclinical species.
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