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Gallego RA, Edwards MP, Montgomery TP. An update on lipophilic efficiency as an important metric in drug design. Expert Opin Drug Discov 2024; 19:917-931. [PMID: 38919130 DOI: 10.1080/17460441.2024.2368744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 06/12/2024] [Indexed: 06/27/2024]
Abstract
INTRODUCTION Lipophilic efficiency (LipE) and lipophilic metabolic efficiency (LipMetE) are valuable tools that can be utilized as part of a multiparameter optimization process to advance a hit to a clinical quality compound. AREAS COVERED This review covers recent, effective use cases of LipE and LipMetE that have been published in the literature over the past 5 years. These use cases resulted in the delivery of high-quality molecules that were brought forward to in vivo work and/or to clinical studies. The authors discuss best-practices for using LipE and LipMetE analysis, combined with lipophilicity-focused compound design strategies, to increase the speed and effectiveness of the hit to clinical quality compound optimization process. EXPERT OPINION It has become well established that increasing LipE and LipMetE within a series of analogs facilitates the improvement of broad selectivity, clearance, solubility, and permeability and, through this optimization, also facilitates the achievement of desired pharmacokinetic properties, efficacy, and tolerability. Within this article, we discuss lipophilic efficiency-focused optimization as a tool to yield high-quality potential clinical candidates. It is suggested that LipE/LipMetE-focused optimization can facilitate and accelerate the drug-discovery process.
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2
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Xia F, Zhang H, Yang H, Zheng M, Min W, Sun C, Yuan K, Yang P. Targeting polyketide synthase 13 for the treatment of tuberculosis. Eur J Med Chem 2023; 259:115702. [PMID: 37544185 DOI: 10.1016/j.ejmech.2023.115702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/15/2023] [Accepted: 07/29/2023] [Indexed: 08/08/2023]
Abstract
Tuberculosis (TB) is one of the most threatening diseases for humans, however, the drug treatment strategy for TB has been stagnant and inadequate, which could not meet current treatment needs. TB is caused by Mycobacterial tuberculosis, which has a unique cell wall that plays a crucial role in its growth, virulence, and drug resistance. Polyketide synthase 13 (Pks13) is an essential enzyme that catalyzes the biosynthesis of the cell wall and its critical role is only found in Mycobacteria. Therefore, Pks13 is a promising target for developing novel anti-TB drugs. In this review, we first introduced the mechanism of targeting Pks13 for TB treatment. Subsequently, we focused on summarizing the recent advance of Pks13 inhibitors, including the challenges encountered during their discovery and the rational design strategies employed to overcome these obstacles, which could be helpful for the development of novel Pks13 inhibitors in the future.
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Affiliation(s)
- Fei Xia
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Haoling Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Huanaoyu Yang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Mingming Zheng
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Wenjian Min
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Chengliang Sun
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
| | - Kai Yuan
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
| | - Peng Yang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China; Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing, 211198, China.
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3
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Garnsey MR, Smith AC, Polivkova J, Arons AL, Bai G, Blakemore C, Boehm M, Buzon LM, Campion SN, Cerny M, Chang SC, Coffman K, Farley KA, Fonseca KR, Ford KK, Garren J, Kong JX, Koos MRM, Kung DW, Lian Y, Li MM, Li Q, Martinez-Alsina LA, O'Connor R, Ogilvie K, Omoto K, Raymer B, Reese MR, Ryder T, Samp L, Stevens KA, Widlicka DW, Yang Q, Zhu K, Fortin JP, Sammons MF. Discovery of the Potent and Selective MC4R Antagonist PF-07258669 for the Potential Treatment of Appetite Loss. J Med Chem 2023; 66:3195-3211. [PMID: 36802610 DOI: 10.1021/acs.jmedchem.2c02012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
The melanocortin-4 receptor (MC4R) is a centrally expressed, class A GPCR that plays a key role in the regulation of appetite and food intake. Deficiencies in MC4R signaling result in hyperphagia and increased body mass in humans. Antagonism of MC4R signaling has the potential to mitigate decreased appetite and body weight loss in the setting of anorexia or cachexia due to underlying disease. Herein, we report on the identification of a series of orally bioavailable, small-molecule MC4R antagonists using a focused hit identification effort and the optimization of these antagonists to provide clinical candidate 23. Introduction of a spirocyclic conformational constraint allowed for simultaneous optimization of MC4R potency and ADME attributes while avoiding the production of hERG active metabolites observed in early series leads. Compound 23 is a potent and selective MC4R antagonist with robust efficacy in an aged rat model of cachexia and has progressed into clinical trials.
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Affiliation(s)
| | - Aaron C Smith
- Pfizer, Incorporated, Groton, Connecticut 06340, United States
| | - Jana Polivkova
- Pfizer, Incorporated, Groton, Connecticut 06340, United States
| | - Autumn L Arons
- Pfizer, Incorporated, Cambridge, Massachusetts 02139, United States
| | - Guoyun Bai
- Pfizer, Incorporated, Groton, Connecticut 06340, United States
| | | | - Markus Boehm
- Pfizer, Incorporated, Cambridge, Massachusetts 02139, United States
| | - Leanne M Buzon
- Pfizer, Incorporated, Groton, Connecticut 06340, United States
| | - Sarah N Campion
- Pfizer, Incorporated, Groton, Connecticut 06340, United States
| | - Matthew Cerny
- Pfizer, Incorporated, Groton, Connecticut 06340, United States
| | - Shiao-Chi Chang
- Pfizer, Incorporated, Cambridge, Massachusetts 02139, United States
| | - Karen Coffman
- Pfizer, Incorporated, Groton, Connecticut 06340, United States
| | | | - Kari R Fonseca
- Pfizer, Incorporated, Cambridge, Massachusetts 02139, United States
| | - Kristen K Ford
- Pfizer, Incorporated, Groton, Connecticut 06340, United States
| | - Jeonifer Garren
- Pfizer, Incorporated, Cambridge, Massachusetts 02139, United States
| | - Jimmy X Kong
- Pfizer, Incorporated, Cambridge, Massachusetts 02139, United States
| | - Martin R M Koos
- Pfizer, Incorporated, Groton, Connecticut 06340, United States
| | - Daniel W Kung
- Pfizer, Incorporated, Groton, Connecticut 06340, United States
| | - Yajing Lian
- Pfizer, Incorporated, Groton, Connecticut 06340, United States
| | - Monica M Li
- Pfizer, Incorporated, Cambridge, Massachusetts 02139, United States
| | - Qifang Li
- Pfizer, Incorporated, Groton, Connecticut 06340, United States
| | | | | | - Kevin Ogilvie
- Pfizer, Incorporated, Groton, Connecticut 06340, United States
| | - Kiyoyuki Omoto
- Pfizer, Incorporated, Cambridge, Massachusetts 02139, United States
| | - Brian Raymer
- Pfizer, Incorporated, Cambridge, Massachusetts 02139, United States
| | - Matthew R Reese
- Pfizer, Incorporated, Groton, Connecticut 06340, United States
| | - Tim Ryder
- Pfizer, Incorporated, Groton, Connecticut 06340, United States
| | - Lacey Samp
- Pfizer, Incorporated, Groton, Connecticut 06340, United States
| | | | | | - Qingyi Yang
- Pfizer, Incorporated, Cambridge, Massachusetts 02139, United States
| | - Kaicheng Zhu
- Pfizer, Incorporated, Groton, Connecticut 06340, United States
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4
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Wang H, Pan X, Zhang Y, Wang X, Xiao X, Ji C. MolHyb: A Web Server for Structure-Based Drug Design by Molecular Hybridization. J Chem Inf Model 2022; 62:2916-2922. [PMID: 35695435 DOI: 10.1021/acs.jcim.2c00443] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular hybridization is a widely used ligand design method in drug discovery. In this study, we present MolHyb, a web server for structure-based ligand design by molecular hybridization. The input of MolHyb is a protein file and a seed compound file. MolHyb tries to generate novel ligands through hybridizing the seed compound with helper compounds that bind to the same protein target or similar proteins. To facilitate the job of getting helper compounds, we compiled a modeled protein-ligand structure database as an extension to crystal structures in the PDB database by placing the bioactive compounds in ChEMBL into their corresponding 3D protein binding pocket properly. MolHyb works by searching for helper compounds from the protein-ligand structure database and migrating chemical moieties from helper compounds to the seed compound efficiently. Hybridization is performed at both cyclic and acyclic bonds. The users can also input their own helper compounds to MolHyb. We hope that MolHyb will be a useful tool for rational drug design. MolHyb is freely available at http://molhyb.xundrug.cn/.
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Affiliation(s)
- Hao Wang
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Xiaolin Pan
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Yueqing Zhang
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Xingyu Wang
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Xudong Xiao
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Changge Ji
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
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5
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Wilson C, Ray P, Zuccotto F, Hernandez J, Aggarwal A, Mackenzie C, Caldwell N, Taylor M, Huggett M, Mathieson M, Murugesan D, Smith A, Davis S, Cocco M, Parai MK, Acharya A, Tamaki F, Scullion P, Epemolu O, Riley J, Stojanovski L, Lopez-Román EM, Torres-Gómez PA, Toledo AM, Guijarro-Lopez L, Camino I, Engelhart CA, Schnappinger D, Massoudi LM, Lenaerts A, Robertson GT, Walpole C, Matthews D, Floyd D, Sacchettini JC, Read KD, Encinas L, Bates RH, Green SR, Wyatt PG. Optimization of TAM16, a Benzofuran That Inhibits the Thioesterase Activity of Pks13; Evaluation toward a Preclinical Candidate for a Novel Antituberculosis Clinical Target. J Med Chem 2022; 65:409-423. [PMID: 34910486 PMCID: PMC8762665 DOI: 10.1021/acs.jmedchem.1c01586] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Indexed: 11/28/2022]
Abstract
With increasing drug resistance in tuberculosis (TB) patient populations, there is an urgent need for new drugs. Ideally, new agents should work through novel targets so that they are unencumbered by preexisting clinical resistance to current treatments. Benzofuran 1 was identified as a potential lead for TB inhibiting a novel target, the thioesterase domain of Pks13. Although, having promising activity against Mycobacterium tuberculosis, its main liability was inhibition of the hERG cardiac ion channel. This article describes the optimization of the series toward a preclinical candidate. Despite improvements in the hERG liability in vitro, when new compounds were assessed in ex vivo cardiotoxicity models, they still induced cardiac irregularities. Further series development was stopped because of concerns around an insufficient safety window. However, the demonstration of in vivo activity for multiple series members further validates Pks13 as an attractive novel target for antitubercular drugs and supports development of alternative chemotypes.
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Affiliation(s)
- Caroline Wilson
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Peter Ray
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Fabio Zuccotto
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Jorge Hernandez
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Anup Aggarwal
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Claire Mackenzie
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Nicola Caldwell
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Malcolm Taylor
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Margaret Huggett
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Michael Mathieson
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Dinakaran Murugesan
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Alasdair Smith
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Susan Davis
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Mattia Cocco
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Maloy K. Parai
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Arjun Acharya
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Fabio Tamaki
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Paul Scullion
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Ola Epemolu
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Jennifer Riley
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Laste Stojanovski
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Eva Maria Lopez-Román
- Global
Health Pharma R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | | | - Ana Maria Toledo
- Global
Health Pharma R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Laura Guijarro-Lopez
- Global
Health Pharma R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Isabel Camino
- Global
Health Pharma R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Curtis A. Engelhart
- Department
of Microbiology and Immunology, Weill Cornell
Medical College, New York, New York 10065, United States
| | - Dirk Schnappinger
- Department
of Microbiology and Immunology, Weill Cornell
Medical College, New York, New York 10065, United States
| | - Lisa M. Massoudi
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology, and
Pathology, Colorado State University, 200 W. Lake Street, Fort Collins, Colorado 80523-1682, United States
| | - Anne Lenaerts
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology, and
Pathology, Colorado State University, 200 W. Lake Street, Fort Collins, Colorado 80523-1682, United States
| | - Gregory T. Robertson
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology, and
Pathology, Colorado State University, 200 W. Lake Street, Fort Collins, Colorado 80523-1682, United States
| | - Chris Walpole
- Structural
Genomics Consortium, Research Institute
of the McGill University Health Centre, 1001 Boulevard Décarie, Site Glen Block
E, ES1.1614, Montréal, Québec H4A 3J1, Canada
| | - David Matthews
- Structural
Genomics Consortium, Research Institute
of the McGill University Health Centre, 1001 Boulevard Décarie, Site Glen Block
E, ES1.1614, Montréal, Québec H4A 3J1, Canada
| | - David Floyd
- Structural
Genomics Consortium, Research Institute
of the McGill University Health Centre, 1001 Boulevard Décarie, Site Glen Block
E, ES1.1614, Montréal, Québec H4A 3J1, Canada
| | - James C. Sacchettini
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Kevin D. Read
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Lourdes Encinas
- Global
Health Pharma R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Robert H. Bates
- Global
Health Pharma R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Simon R. Green
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Paul G. Wyatt
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
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6
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Cherney RJ, Anjanappa P, Selvakumar K, Batt DG, Brown GD, Rose AV, Vuppugalla R, Chen J, Pang J, Xu S, Yarde M, Tebben AJ, Paidi VR, Cvijic ME, Mathur A, Barrish JC, Mandlekar S, Zhao Q, Carter PH. BMS-813160: A Potent CCR2 and CCR5 Dual Antagonist Selected as a Clinical Candidate. ACS Med Chem Lett 2021; 12:1753-1758. [PMID: 34795864 DOI: 10.1021/acsmedchemlett.1c00373] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/06/2021] [Indexed: 11/29/2022] Open
Abstract
BMS-813160 (compound 3) was identified as a potent and selective CCR2/5 dual antagonist. Compound 3 displayed good permeability at pH = 7.4 in PAMPA experiments and demonstrated excellent human liver microsome stability. Pharmacokinetic studies established that 3 had excellent oral bioavailability and exhibited low clearance in dog and cyno. Compound 3 was also studied in the mouse thioglycollate-induced peritonitis model, which confirmed its ability to inhibit the migration of inflammatory monocytes and macrophages. As a result of this profile, compound 3 was selected as a clinical candidate.
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Affiliation(s)
- Robert J. Cherney
- Bristol Myers Squibb Company, Research and Early Development, Princeton, New Jersey 08540-4000, United States
| | - Prakash Anjanappa
- Biocon Bristol Myers Squibb Research and Development Center, Bangalore 560099, India
| | - Kumaravel Selvakumar
- Biocon Bristol Myers Squibb Research and Development Center, Bangalore 560099, India
| | - Douglas G. Batt
- Bristol Myers Squibb Company, Research and Early Development, Princeton, New Jersey 08540-4000, United States
| | - Gregory D. Brown
- Bristol Myers Squibb Company, Research and Early Development, Princeton, New Jersey 08540-4000, United States
| | - Anne V. Rose
- Bristol Myers Squibb Company, Research and Early Development, Princeton, New Jersey 08540-4000, United States
| | - Ragini Vuppugalla
- Bristol Myers Squibb Company, Research and Early Development, Princeton, New Jersey 08540-4000, United States
| | - Jing Chen
- Bristol Myers Squibb Company, Research and Early Development, Princeton, New Jersey 08540-4000, United States
| | - Jian Pang
- Bristol Myers Squibb Company, Research and Early Development, Princeton, New Jersey 08540-4000, United States
| | - Songmei Xu
- Bristol Myers Squibb Company, Research and Early Development, Princeton, New Jersey 08540-4000, United States
| | - Melissa Yarde
- Bristol Myers Squibb Company, Research and Early Development, Princeton, New Jersey 08540-4000, United States
| | - Andrew J. Tebben
- Bristol Myers Squibb Company, Research and Early Development, Princeton, New Jersey 08540-4000, United States
| | - Venkatram Reddy Paidi
- Biocon Bristol Myers Squibb Research and Development Center, Bangalore 560099, India
| | - Mary Ellen Cvijic
- Bristol Myers Squibb Company, Research and Early Development, Princeton, New Jersey 08540-4000, United States
| | - Arvind Mathur
- Bristol Myers Squibb Company, Research and Early Development, Princeton, New Jersey 08540-4000, United States
| | - Joel C. Barrish
- Bristol Myers Squibb Company, Research and Early Development, Princeton, New Jersey 08540-4000, United States
| | - Sandhya Mandlekar
- Bristol Myers Squibb Company, Research and Early Development, Princeton, New Jersey 08540-4000, United States
| | - Qihong Zhao
- Bristol Myers Squibb Company, Research and Early Development, Princeton, New Jersey 08540-4000, United States
| | - Percy H. Carter
- Bristol Myers Squibb Company, Research and Early Development, Princeton, New Jersey 08540-4000, United States
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7
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Truong J, George A, Holien JK. Analysis of physicochemical properties of protein-protein interaction modulators suggests stronger alignment with the "rule of five". RSC Med Chem 2021; 12:1731-1749. [PMID: 34778774 DOI: 10.1039/d1md00213a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 07/27/2021] [Indexed: 11/21/2022] Open
Abstract
Despite the important roles played by protein-protein interactions (PPIs) in disease, they have been long considered as 'undruggable'. However, recent advances have suggested that PPIs are druggable but may not follow conventional rules of 'drug ability'. Here we explore which physicochemical parameters are essential for a PPI modulator to be a clinical drug by analysing the physicochemical properties of small-molecule PPI modulators in the market, in clinical trials, and published. Our analysis reveals that those compounds currently on the market have a larger range of values for most of the physicochemical parameters, whereas those in clinical trials fit much more stringently to standard drug-like parameters. This observation was particularly true for molecular weight, clog P and topological polar surface area, where aside from a few outliers, most of the compounds in clinical trials fit within standard drug-like parameters. This implies that the newer PPI modulators are more drug-like than those currently on the market, suggesting that designing new PPI-specific screening libraries should remain within standard drug-like parameters in order to obtain a clinical candidate. Taken together, our analysis has important implications for designing future drug discovery campaigns aimed at targeting PPIs.
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Affiliation(s)
- Jia Truong
- STEM College, RMIT University Vic Australia
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8
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Wang Z, Zalloum WA, Wang W, Jiang X, De Clercq E, Pannecouque C, Kang D, Zhan P, Liu X. Discovery of Novel Dihydrothiopyrano[4,3- d]pyrimidine Derivatives as Potent HIV-1 NNRTIs with Significantly Reduced hERG Inhibitory Activity and Improved Resistance Profiles. J Med Chem 2021; 64:13658-13675. [PMID: 34432448 DOI: 10.1021/acs.jmedchem.1c01015] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enlightened by the available structural biology information, a novel series of dihydrothiopyrano[4,3-d]pyrimidine derivatives were rationally designed via scaffold hopping and molecular hybridization strategies. Notably, compound 20a yielded exceptionally potent antiviral activities (EC50 = 4.44-54.5 nM) against various HIV-1 strains and improved resistance profiles (RF = 0.5-5.6) compared to etravirine and rilpivirine. Meanwhile, 20a exhibited reduced cytotoxicity (CC50 = 284 μM) and higher SI values (SI = 5210-63992). Molecular dynamics simulations were performed to rationalize the distinct resistance profiles. Besides, 20a displayed better solubility (sol. = 12.8 μg/mL) and no significant inhibition of the main CYP enzymes. Furthermore, 20a was characterized for prominent metabolic stability and in vivo safety properties. Most importantly, the hERG inhibition profile of 20a (IC50 = 19.84 μM) was a remarkable improvement. Overall, 20a possesses huge potential to serve as a promising drug candidate due to its excellent potency, low toxicity, and favorable drug-like properties.
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Affiliation(s)
- Zhao Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, Shandong 250012, PR China
| | - Waleed A Zalloum
- Department of Pharmacy, Faculty of Health Science, American University of Madaba, P.O. Box 2882, Amman 11821, Jordan
| | - Wenbo Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, Shandong 250012, PR China
| | - Xiangyi Jiang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, Shandong 250012, PR China
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K. U. Leuven, Herestraat 49 Postbus 1043 (09.A097), Leuven B-3000, Belgium
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K. U. Leuven, Herestraat 49 Postbus 1043 (09.A097), Leuven B-3000, Belgium
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, Shandong 250012, PR China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, Jinan, Shandong 250012, PR China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, Shandong 250012, PR China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, Jinan, Shandong 250012, PR China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, Shandong 250012, PR China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, Jinan, Shandong 250012, PR China
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9
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Richardson P. Applications of fluorine to the construction of bioisosteric elements for the purposes of novel drug discovery. Expert Opin Drug Discov 2021; 16:1261-1286. [PMID: 34074189 DOI: 10.1080/17460441.2021.1933427] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Introduction There continues to be an exponential rise in the number of small molecule drugs that contain either a fluorine atom or a fluorinated fragment. While the unique properties of fluorine enable the precise modulation of a molecule's physicochemical properties, strategic bioisosteric replacement of fragments with fluorinated moieties represents an area of significant growth.Areas covered This review discusses the strategic employment of fluorine substitution in the design and development of bioisosteres in medicinal chemistry. In addition, the classic exploitation of trifluoroethylamine group as an amide bioisostere is discussed. In each of the case studies presented, emphasis is placed on the context-dependent influence of the fluorinated fragment on the overall properties/binding of the compound of interest.Expert opinion Whereas utilization of bioisosteric replacements to modify molecular structures is commonplace within drug discovery, the overarching lesson to be learned is that the chances of success with this strategy significantly increase as the knowledge of the structure/environment of the biological target grows. Coupled to this, breakthroughs and learnings achieved using bioisosteres within a specific program are context-based, and though may be helpful in guiding future intuition, will not necessarily be directly translated to future programs. Another important point is to bear in mind what implications a structural change based on a bioisosteric replacement will have on the candidate molecule. Finally, the development of new methods and reagents for the controlled regioselective introduction of fluorine and fluorinated moieties into biologically relevant compounds particularly in drug discovery remains a contemporary challenge in organic chemistry.
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10
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Kang D, Sun Y, Murugan NA, Feng D, Wei F, Li J, Jiang X, De Clercq E, Pannecouque C, Zhan P, Liu X. Structure-Activity Relationship Exploration of NNIBP Tolerant Region I Leads to Potent HIV-1 NNRTIs. ACS Infect Dis 2020; 6:2225-2234. [PMID: 32619096 DOI: 10.1021/acsinfecdis.0c00327] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Previous efforts in our lab have led to the development of human immunodeficiency virus type 1 (HIV-1) non-nucleoside reverse transcriptase inhibitor (NNRTI) thiophene[3,2-d]pyrimidine compound 1 (K-5a2) with promising activity against wild-type and mutant HIV-1 strains. In this work, a series of novel diarylpyrimidines derivatives carrying a structurally diverse motif at the right wing of the lead K-5a2 was designed and synthesized as potential anti-HIV-1 agents. The results demonstrated that 8a yielded exceptionally potent activity against HIV-1 wild-type (50% effective concentration (EC50) = 3.30 nM) and mutant strain RES056 (EC50 = 22.6 nM) in MT-4 cells; in the reverse transcriptase inhibitory assay, 8a (half maximal inhibitory concentration (IC50) = 0.028 μM) was remarkably superior to that of K-5a2 (IC50 = 0.300 μM) and comparable to that of etravirine (ETR; IC50 = 0.011 μM). Notably, 8a exhibited better druggability than that of K-5a2, including significantly reduced CYP enzymatic inhibitory activity (IC50 > 50 μM), lower human ether-à-go-go related gene (hERG) inhibition (IC50 > 30 μM), and improved metabolic stability (short half-life, T1/2 = 77.5 min) in vitro.
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Affiliation(s)
- Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
- Suzhou Research Institute, Shandong University, Room 522, Building H of NUSP, No. 388 Ruoshui Road, SIP, 215123 Suzhou, Jiangsu, P.R. China
| | - Yanying Sun
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - N. Arul Murugan
- Department of Theoretical Chemistry and Biology, School of Chemistry, Biotechnology and Health,, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden
| | - Da Feng
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Fenju Wei
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Jing Li
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Xiangyi Jiang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, PR China
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11
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Kang D, Feng D, Sun Y, Fang Z, Wei F, De Clercq E, Pannecouque C, Liu X, Zhan P. Structure-Based Bioisosterism Yields HIV-1 NNRTIs with Improved Drug-Resistance Profiles and Favorable Pharmacokinetic Properties. J Med Chem 2020; 63:4837-4848. [PMID: 32293182 DOI: 10.1021/acs.jmedchem.0c00117] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
- China−Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Da Feng
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Yanying Sun
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Zengjun Fang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
- The Second Hospital of Shandong University, No. 247 Beiyuan Avenue, 250033 Jinan, Shandong, P.R. China
| | - Fenju Wei
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
- China−Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
- China−Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, PR China
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12
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Kang D, Ruiz FX, Feng D, Pilch A, Zhao T, Wei F, Wang Z, Sun Y, Fang Z, De Clercq E, Pannecouque C, Arnold E, Zhan P, Liu X. Discovery and Characterization of Fluorine-Substituted Diarylpyrimidine Derivatives as Novel HIV-1 NNRTIs with Highly Improved Resistance Profiles and Low Activity for the hERG Ion Channel. J Med Chem 2020; 63:1298-1312. [PMID: 31935327 PMCID: PMC9677951 DOI: 10.1021/acs.jmedchem.9b01769] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Our previous efforts have led to the development of two potent NNRTIs, K-5a2 and 25a, exhibiting effective anti-HIV-1 potency and resistance profiles compared with etravirine. However, both inhibitors suffered from potent hERG inhibition and short half-life. In this article, with K-5a2 and etravirine as leads, series of novel fluorine-substituted diarylpyrimidine derivatives were designed via molecular hybridization and bioisosterism strategies. The results indicated 24b was the most active inhibitor, exhibiting broad-spectrum activity (EC50 = 3.60-21.5 nM) against resistant strains, significantly lower cytotoxicity (CC50= 155 μM), and reduced hERG inhibition (IC50 > 30 μM). Crystallographic studies confirmed the binding of 24b and the role of the fluorine atom, as well as optimal contacts of a nitrile group with the main-chain carbonyl group of H235. Furthermore, 24b showed longer half-life and favorable safety properties. All the results demonstrated that 24b has significant promise in circumventing drug resistance as an anti-HIV-1 candidate.
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Affiliation(s)
- Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
- Suzhou Research Institute, Shandong University, Room522, Building H of NUSP, NO.388 Ruoshui Road, SIP, Suzhou, 215123 Jiangsu, P.R. China
| | - F. Xavier Ruiz
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, 08854, United States
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854, United States
| | - Da Feng
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Alyssa Pilch
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, 08854, United States
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854, United States
| | - Tong Zhao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Fenju Wei
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Zhao Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Yanying Sun
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Zengjun Fang
- The Second Hospital, Shandong University, No. 247 Beiyuan Avenue, Jinan 250033, China
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, 08854, United States
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854, United States
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
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13
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Brown DG, Smith GF, Wobst HJ. Promiscuity of in Vitro Secondary Pharmacology Assays and Implications for Lead Optimization Strategies. J Med Chem 2019; 63:6251-6275. [PMID: 31714773 DOI: 10.1021/acs.jmedchem.9b01625] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We conducted an analysis on screening data generated from 1445 compounds against a panel of 130 enzymes, ion channels, and receptors to assess secondary pharmacological risks. Hit rates of these targets as well as physicochemical properties for those hits were evaluated. A majority of targets yielded hits with higher clogP, molecular weight, and more basic character than inactive compounds. Although most targets favored lipophilic hits, the average clogP of hits at a given target did not correlate with its hit rate. Furthermore, a matched pair analysis was completed to determine structural changes that impacted off-target activities. A correlation of binding assays used in this analysis illustrated that some pharmacologically related binding assays are highly correlative and may be substituted for a smaller set of surrogate assays.
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Affiliation(s)
- Dean G Brown
- Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
| | - Graham F Smith
- Data Science and Artificial Intelligence, Clinical Pharmacology & Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Heike J Wobst
- Neuroscience, BioPharmaceuticals R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
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14
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Bresciani A, Ontoria JM, Biancofiore I, Cellucci A, Ciammaichella A, Di Marco A, Ferrigno F, Francone A, Malancona S, Monteagudo E, Nizi E, Pace P, Ponzi S, Rossetti I, Veneziano M, Summa V, Harper S. Improved Selective Class I HDAC and Novel Selective HDAC3 Inhibitors: Beyond Hydroxamic Acids and Benzamides. ACS Med Chem Lett 2019; 10:481-486. [PMID: 30996783 DOI: 10.1021/acsmedchemlett.8b00517] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 11/27/2018] [Indexed: 12/11/2022] Open
Abstract
The application of class I HDAC inhibitors as cancer therapies is well established, but more recently their development for nononcological indications has increased. We report here on the generation of improved class I selective human HDAC inhibitors based on an ethylketone zinc binding group (ZBG) in place of the hydroxamic acid that features the majority of HDAC inhibitors. We also describe a novel set of HDAC3 isoform selective inhibitors that show stronger potency and selectivity than the most commonly used HDAC3 selective tool compound RGFP966. These compounds are again based on an alternative ZBG with respect to the ortho-anilide that is featured in HDAC3 selective compounds reported to date.
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Affiliation(s)
- Alberto Bresciani
- IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Jesus M. Ontoria
- IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | | | | | | | - Annalise Di Marco
- IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Federica Ferrigno
- IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | | | - Savina Malancona
- IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Edith Monteagudo
- IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Emanuela Nizi
- IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Paola Pace
- IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Simona Ponzi
- IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Ilaria Rossetti
- IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Maria Veneziano
- IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Vincenzo Summa
- IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Steven Harper
- IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
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15
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Munawar S, Windley MJ, Tse EG, Todd MH, Hill AP, Vandenberg JI, Jabeen I. Experimentally Validated Pharmacoinformatics Approach to Predict hERG Inhibition Potential of New Chemical Entities. Front Pharmacol 2018; 9:1035. [PMID: 30333745 PMCID: PMC6176658 DOI: 10.3389/fphar.2018.01035] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 08/27/2018] [Indexed: 12/17/2022] Open
Abstract
The hERG (human ether-a-go-go-related gene) encoded potassium ion (K+) channel plays a major role in cardiac repolarization. Drug-induced blockade of hERG has been a major cause of potentially lethal ventricular tachycardia termed Torsades de Pointes (TdPs). Therefore, we presented a pharmacoinformatics strategy using combined ligand and structure based models for the prediction of hERG inhibition potential (IC50) of new chemical entities (NCEs) during early stages of drug design and development. Integrated GRid-INdependent Descriptor (GRIND) models, and lipophilic efficiency (LipE), ligand efficiency (LE) guided template selection for the structure based pharmacophore models have been used for virtual screening and subsequent hERG activity (pIC50) prediction of identified hits. Finally selected two hits were experimentally evaluated for hERG inhibition potential (pIC50) using whole cell patch clamp assay. Overall, our results demonstrate a difference of less than ±1.6 log unit between experimentally determined and predicted hERG inhibition potential (IC50) of the selected hits. This revealed predictive ability and robustness of our models and could help in correctly rank the potency order (lower μM to higher nM range) against hERG.
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Affiliation(s)
- Saba Munawar
- Research Center for Modeling and Simulation, National University of Science and Technology, Islamabad, Pakistan.,Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
| | | | - Edwin G Tse
- School of Chemistry, The University of Sydney, Sydney, NSW, Australia
| | - Matthew H Todd
- School of Chemistry, The University of Sydney, Sydney, NSW, Australia
| | - Adam P Hill
- Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
| | | | - Ishrat Jabeen
- Research Center for Modeling and Simulation, National University of Science and Technology, Islamabad, Pakistan
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16
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Parthasarathy S, Henry K, Pei H, Clayton J, Rempala M, Johns D, De Frutos O, Garcia P, Mateos C, Pleite S, Wang Y, Stout S, Condon B, Ashok S, Lu Z, Ehlhardt W, Raub T, Lai M, Geeganage S, Burkholder TP. Discovery of chiral dihydropyridopyrimidinones as potent, selective and orally bioavailable inhibitors of AKT. Bioorg Med Chem Lett 2018; 28:1887-1891. [PMID: 29655979 DOI: 10.1016/j.bmcl.2018.03.092] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 03/30/2018] [Accepted: 03/31/2018] [Indexed: 12/17/2022]
Abstract
During the course of our research efforts to develop potent and selective AKT inhibitors, we discovered enatiomerically pure substituted dihydropyridopyrimidinones (DHP) as potent inhibitors of protein kinase B/AKT with excellent selectivity against ROCK2. A key challenge in this program was the poor physicochemical properties of the initial lead compound 5. Integration of structure-based drug design and physical properties-based design resulted in replacement of a highly hydrophobic poly fluorinated aryl ring by a simple trifluoromethyl that led to identification of compound 6 with much improved physicochemical properties. Subsequent SAR studies led to the synthesis of new pyran analog 7 with improved cell potency. Further optimization of pharmacokintetics properties by increasing permeability with appropriate fluorinated alkyl led to compound 8 as a potent, selective AKT inhibitors that blocks the phosphorylation of GSK3β in vivo and had robust, dose and concentration dependent efficacy in the U87MG tumor xenograft model.
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Affiliation(s)
- Saravanan Parthasarathy
- Lilly Research Laboratories, Lilly Corporate Center, Eli Lilly and Company, Indianapolis, IN 46285-0150, United States.
| | - Kenneth Henry
- Lilly Research Laboratories, Lilly Corporate Center, Eli Lilly and Company, Indianapolis, IN 46285-0150, United States
| | - Huaxing Pei
- Lilly Research Laboratories, Lilly Corporate Center, Eli Lilly and Company, Indianapolis, IN 46285-0150, United States
| | - Josh Clayton
- Lilly Research Laboratories, Lilly Corporate Center, Eli Lilly and Company, Indianapolis, IN 46285-0150, United States
| | - Mark Rempala
- Lilly Research Laboratories, Lilly Corporate Center, Eli Lilly and Company, Indianapolis, IN 46285-0150, United States
| | - Deidre Johns
- Lilly Research Laboratories, Lilly Corporate Center, Eli Lilly and Company, Indianapolis, IN 46285-0150, United States
| | - Oscar De Frutos
- Lilly S.A., Avda.de la Industria 30, 28108 Alcobendas, Madrid, Spain
| | - Pablo Garcia
- Lilly S.A., Avda.de la Industria 30, 28108 Alcobendas, Madrid, Spain
| | - Carlos Mateos
- Lilly S.A., Avda.de la Industria 30, 28108 Alcobendas, Madrid, Spain
| | - Sehila Pleite
- Lilly S.A., Avda.de la Industria 30, 28108 Alcobendas, Madrid, Spain
| | - Yong Wang
- Lilly Research Laboratories, Lilly Corporate Center, Eli Lilly and Company, Indianapolis, IN 46285-0150, United States
| | - Stephanie Stout
- Lilly Research Laboratories, Lilly Corporate Center, Eli Lilly and Company, Indianapolis, IN 46285-0150, United States
| | - Bradley Condon
- Lilly Research Laboratories, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA 92121, United States
| | - Sheela Ashok
- Lilly Research Laboratories, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA 92121, United States
| | - Zhohai Lu
- Lilly Research Laboratories, Lilly Corporate Center, Eli Lilly and Company, Indianapolis, IN 46285-0150, United States
| | - William Ehlhardt
- Lilly Research Laboratories, Lilly Corporate Center, Eli Lilly and Company, Indianapolis, IN 46285-0150, United States
| | - Tom Raub
- Lilly Research Laboratories, Lilly Corporate Center, Eli Lilly and Company, Indianapolis, IN 46285-0150, United States
| | - Mei Lai
- Lilly Research Laboratories, Lilly Corporate Center, Eli Lilly and Company, Indianapolis, IN 46285-0150, United States
| | - Sandaruwan Geeganage
- Lilly Research Laboratories, Lilly Corporate Center, Eli Lilly and Company, Indianapolis, IN 46285-0150, United States
| | - Timothy P Burkholder
- Lilly Research Laboratories, Lilly Corporate Center, Eli Lilly and Company, Indianapolis, IN 46285-0150, United States
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17
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Lipophilicity Studies on Thiosemicarbazide Derivatives. Molecules 2017; 22:molecules22060952. [PMID: 28594381 PMCID: PMC6152747 DOI: 10.3390/molecules22060952] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 06/01/2017] [Indexed: 12/21/2022] Open
Abstract
The lipophilicity of two series of thiosemicarbazide derivatives was assessed by the RP-HPLC method with the RP-18 chromatographic column and the methanol–water mixture as the mobile phase. Distribution coefficients logPHPLC were compared to calculated values generated by commonly used AClogP software and quantum chemical calculations. The reliability of the predictions was evaluated using the correlation matrix and PCA. For 4-benzoylthiosemicarbazides, a high correlation between theoretical and experimental logP parameters was obtained using the XlogP3 algorithm, while for 4-aryl/(cyclohexyl)thiosemicarbazides, the XlogP2 parameter was strongly correlated with the experimentally obtained logP.
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18
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Tschammer N, Kokornaczyk AK, Strunz AK, Wünsch B. Selective and Dual Targeting of CCR2 and CCR5 Receptors: A Current Overview. CHEMOKINES 2014; 14. [PMCID: PMC7123309 DOI: 10.1007/7355_2014_40] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The chemokine receptor 2 (CCR2) and chemokine receptor 5 (CCR5) are important mediators of leukocyte trafficking in inflammatory processes. The emerging evidence for a role of CCR2 and CCR5 receptors in human inflammatory diseases led to a growing interest in CCR2- and CCR5-selective antagonists. In this review, we focus on the recent development of selective CCR2/CCR5 receptor ligands and dual antagonists. Several compounds targeting CCR2, e.g., INCB8761 and MK0812, were developed as promising candidates for clinical trials, but failed to show clinical efficacy as presumed from preclinical models. The role of CCR5 receptors as the second co-receptor for the HIV-host cell fusion led to the development of various CCR5-selective ligands. Maraviroc is the first CCR5-targeting drug for the treatment of HIV-1 infections on the market. The role of CCR5 receptors in the progression of inflammatory processes fueled the use of CCR5 antagonists for the treatment of rheumatoid arthritis. Unfortunately, the use of maraviroc for the treatment of rheumatoid arthritis failed due to its inefficacy. Some of the ligands, e.g., TAK-779 and TAK-652, were also found to be dual antagonists of CCR2 and CCR5 receptors. The fact that CCR2 and CCR5 receptor antagonists contribute to the treatment of inflammatory diseases renders the development of dual antagonists as promising novel therapeutic strategy.
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Affiliation(s)
- Nuska Tschammer
- Dept. of Chemistry and Pharmacy, Friedrich Alexander University, Erlangen, Germany
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Alkylsulfone-containing trisubstituted cyclohexanes as potent and bioavailable chemokine receptor 2 (CCR2) antagonists. Bioorg Med Chem Lett 2014; 24:1843-5. [PMID: 24613378 DOI: 10.1016/j.bmcl.2014.02.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 01/31/2014] [Accepted: 02/04/2014] [Indexed: 12/24/2022]
Abstract
We describe novel alkylsulfones as potent CCR2 antagonists with reduced hERG channel activity and improved pharmacokinetics over our previously described antagonists. Several of these new alkylsulfones have a profile that includes functional antagonism of CCR2, in vitro microsomal stability, and oral bioavailability. With this improved profile, we demonstrate that two of these antagonists, 2 and 12, are orally efficacious in an animal model of inflammatory recruitment.
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20
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Ekins S. Progress in computational toxicology. J Pharmacol Toxicol Methods 2013; 69:115-40. [PMID: 24361690 DOI: 10.1016/j.vascn.2013.12.003] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 12/08/2013] [Indexed: 01/02/2023]
Abstract
INTRODUCTION Computational methods have been widely applied to toxicology across pharmaceutical, consumer product and environmental fields over the past decade. Progress in computational toxicology is now reviewed. METHODS A literature review was performed on computational models for hepatotoxicity (e.g. for drug-induced liver injury (DILI)), cardiotoxicity, renal toxicity and genotoxicity. In addition various publications have been highlighted that use machine learning methods. Several computational toxicology model datasets from past publications were used to compare Bayesian and Support Vector Machine (SVM) learning methods. RESULTS The increasing amounts of data for defined toxicology endpoints have enabled machine learning models that have been increasingly used for predictions. It is shown that across many different models Bayesian and SVM perform similarly based on cross validation data. DISCUSSION Considerable progress has been made in computational toxicology in a decade in both model development and availability of larger scale or 'big data' models. The future efforts in toxicology data generation will likely provide us with hundreds of thousands of compounds that are readily accessible for machine learning models. These models will cover relevant chemistry space for pharmaceutical, consumer product and environmental applications.
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Affiliation(s)
- Sean Ekins
- Collaborations in Chemistry, 5616 Hilltop Needmore Road, Fuquay Varina, NC 27526, USA; Department of Pharmaceutical Sciences, University of Maryland, 20 Penn Street, Baltimore, MD 21201, USA; Department of Pharmacology, Rutgers University-Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, NJ 08854, USA; Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, NC 27599-7355, USA.
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Žukauskaitė A, Mangelinckx S, Callebaut G, Wybon C, Šačkus A, De Kimpe N. Synthesis of 1,5-diazaspiro[2.3]hexanes, a novel diazaspirocyclic system. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.02.065] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Cumming JG, Tucker H, Oldfield J, Fielding C, Highton A, Faull A, Wild M, Brown D, Wells S, Shaw J. Balancing hERG affinity and absorption in the discovery of AZD5672, an orally active CCR5 antagonist for the treatment of rheumatoid arthritis. Bioorg Med Chem Lett 2012; 22:1655-9. [DOI: 10.1016/j.bmcl.2011.12.117] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 12/23/2011] [Accepted: 12/24/2011] [Indexed: 10/14/2022]
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Johnstone C. Medicinal chemistry matters - a call for discipline in our discipline. Drug Discov Today 2012; 17:538-43. [PMID: 22301070 DOI: 10.1016/j.drudis.2012.01.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Revised: 12/14/2011] [Accepted: 01/17/2012] [Indexed: 11/17/2022]
Abstract
Medicinal chemistry makes a vital contribution to small molecule drug discovery, and the quality of it contributes directly to research effectiveness as well as to downstream costs, speed and survival in development. In recent years, the discipline of medicinal chemistry has evolved and witnessed many noteworthy contributions that propose and offer potential improvements to medicinal chemistry practice; however, the impact of these ideas is limited by their acceptance and deployment into every-day activity and, as a result, the quality of medicinal chemistry remains variable. For the good of the industry and the medicinal chemistry discipline, there is a need to move from retrospective learning to prospective control of medicinal chemistry practice to improve cost effectiveness, probability of success and survival rates.
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Kruger FA, Overington JP. Global analysis of small molecule binding to related protein targets. PLoS Comput Biol 2012; 8:e1002333. [PMID: 22253582 PMCID: PMC3257267 DOI: 10.1371/journal.pcbi.1002333] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 11/16/2011] [Indexed: 11/29/2022] Open
Abstract
We report on the integration of pharmacological data and homology information for a large scale analysis of small molecule binding to related targets. Differences in small molecule binding have been assessed for curated pairs of human to rat orthologs and also for recently diverged human paralogs. Our analysis shows that in general, small molecule binding is conserved for pairs of human to rat orthologs. Using statistical tests, we identified a small number of cases where small molecule binding is different between human and rat, some of which had previously been reported in the literature. Knowledge of species specific pharmacology can be advantageous for drug discovery, where rats are frequently used as a model system. For human paralogs, we demonstrate a global correlation between sequence identity and the binding of small molecules with equivalent affinity. Our findings provide an initial general model relating small molecule binding and sequence divergence, containing the foundations for a general model to anticipate and predict within-target-family selectivity. Many drugs are small molecules that specifically bind to proteins involved in disease related processes. In this way, drugs modulate the function of a targeted protein and ultimately the process causing the disease. The development of drugs crucially relies on assays that measure the potency of the effect a small molecule exerts on its protein target. We compared the potencies of small molecules measured for human proteins and the corresponding (orthologous) protein in rat. Our results suggest that, after subtraction of statistical noise, most human proteins are equally susceptible to small molecule binding as their orthologs in rats. However, we identified a small number of exceptions to this rule, for example the histamine H3 receptor, a protein of the central nervous system. We also compared the potency of small molecules measured against a human protein and another member of the same protein family. In drug development it is often desired to target a protein selectively over other related proteins. The observed differences were generally greater than the statistical noise, indicating that most of the small molecules in our study have some degree of selectivity within protein families.
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Wang Y, Ai J, Yue J, Peng X, Ji Y, Zhao A, Gao X, Wang Y, Chen Y, Liu G, Gao Z, Geng M, Zhang A. Further SAR studies on 3,5-diamino-7-trifluoromethylquinolines as highly potent tyrosine kinase c-Met inhibitors: efforts to correct hERG inhibition. MEDCHEMCOMM 2012. [DOI: 10.1039/c2md20192e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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The influence of the 'organizational factor' on compound quality in drug discovery. Nat Rev Drug Discov 2011; 10:749-65. [DOI: 10.1038/nrd3552] [Citation(s) in RCA: 134] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Kazmierski WM, Anderson DL, Aquino C, Chauder BA, Duan M, Ferris R, Kenakin T, Koble CS, Lang DG, McIntyre MS, Peckham J, Watson C, Wheelan P, Spaltenstein A, Wire MB, Svolto A, Youngman M. Novel 4,4-disubstituted piperidine-based C-C chemokine receptor-5 inhibitors with high potency against human immunodeficiency virus-1 and an improved human ether-a-go-go related gene (hERG) profile. J Med Chem 2011; 54:3756-67. [PMID: 21539377 DOI: 10.1021/jm200279v] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We recently described ( J. Med. Chem. 2008 , 51 , 6538 - 6546 ) a novel class of CCR5 antagonists with strong anti-HIV potency. Herein, we detail SAR converting leads 1 and 2 to druglike molecules. The pivotal structural motif enabling this transition was the secondary sulfonamide substituent. Further fine-tuning of the substituent pattern in the sulfonamide paved the way to enhancing potency and bioavailability and minimizing hERG inhibition, resulting in discovery of clinical compound 122 (GSK163929).
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Yamashita T, Yamamoto E, Kushida I. Frozen water phase method for logD measurement using a 96-well plate. Talanta 2011; 84:809-13. [DOI: 10.1016/j.talanta.2011.02.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Revised: 02/08/2011] [Accepted: 02/09/2011] [Indexed: 11/15/2022]
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Abstract
The directed migration of cells in response to chemical cues is known as chemoattraction, and plays a key role in the temporal and spatial positioning of cells in lower- and higher-order life forms. Key molecules in this process are the chemotactic cytokines, or chemokines, which, in humans, constitute a family of approx. 40 molecules. Chemokines exert their effects by binding to specific GPCRs (G-protein-coupled receptors) which are present on a wide variety of mature cells and their progenitors, notably leucocytes. The inappropriate or excessive generation of chemokines is a key component of the inflammatory response observed in several clinically important diseases, notably allergic diseases such as asthma. Consequently, much time and effort has been directed towards understanding which chemokine receptors and ligands are important in the allergic response with a view to therapeutic intervention. Such strategies can take several forms, although, as the superfamily of GPCRs has historically proved amenable to blockade by small molecules, the development of specific antagonists has been has been a major focus of several groups. In the present review, I detail the roles of chemokines and their receptors in allergic disease and also highlight current progress in the development of relevant chemokine receptor antagonists.
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Sinha N, Sen S. Predicting hERG activities of compounds from their 3D structures: Development and evaluation of a global descriptors based QSAR model. Eur J Med Chem 2011; 46:618-30. [DOI: 10.1016/j.ejmech.2010.11.042] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Revised: 10/27/2010] [Accepted: 11/27/2010] [Indexed: 11/16/2022]
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Warner DJ, Griffen EJ, St-Gallay SA. WizePairZ: A Novel Algorithm to Identify, Encode, and Exploit Matched Molecular Pairs with Unspecified Cores in Medicinal Chemistry. J Chem Inf Model 2010; 50:1350-7. [DOI: 10.1021/ci100084s] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniel J. Warner
- Department of Chemistry, AstraZeneca R&D Charnwood, Bakewell Road, Loughborough, Leicestershire LE11 5RH, United Kingdom, and Cancer and Infection Research, AstraZeneca R&D Alderley, Alderley Park, Macclesfield, Cheshire. SK10 4TG, United Kingdom
| | - Edward J. Griffen
- Department of Chemistry, AstraZeneca R&D Charnwood, Bakewell Road, Loughborough, Leicestershire LE11 5RH, United Kingdom, and Cancer and Infection Research, AstraZeneca R&D Alderley, Alderley Park, Macclesfield, Cheshire. SK10 4TG, United Kingdom
| | - Stephen A. St-Gallay
- Department of Chemistry, AstraZeneca R&D Charnwood, Bakewell Road, Loughborough, Leicestershire LE11 5RH, United Kingdom, and Cancer and Infection Research, AstraZeneca R&D Alderley, Alderley Park, Macclesfield, Cheshire. SK10 4TG, United Kingdom
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Bromidge SM, Arban R, Bertani B, Bison S, Borriello M, Cavanni P, Dal Forno G, Di-Fabio R, Donati D, Fontana S, Gianotti M, Gordon LJ, Granci E, Leslie CP, Moccia L, Pasquarello A, Sartori I, Sava A, Watson JM, Worby A, Zonzini L, Zucchelli V. Design and Synthesis of Novel Tricyclic Benzoxazines as Potent 5-HT1A/B/D Receptor Antagonists Leading to the Discovery of 6-{2-[4-(2-methyl-5-quinolinyl)-1-piperazinyl]ethyl}-4H-imidazo[5,1-c][1,4]benzoxazine-3-carboxamide (GSK588045). J Med Chem 2010; 53:5827-43. [DOI: 10.1021/jm100482n] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Steven M. Bromidge
- Neurosciences CEDD, GlaxoSmithKline, New Frontiers Science Park, Third Avenue, Harlow, Essex CM19 5AW, U.K
| | - Roberto Arban
- Medicines Research Centre, Via A. Fleming 4, Verona 37135, Italy
| | - Barbara Bertani
- Medicines Research Centre, Via A. Fleming 4, Verona 37135, Italy
| | - Silvia Bison
- Medicines Research Centre, Via A. Fleming 4, Verona 37135, Italy
| | | | - Paolo Cavanni
- Medicines Research Centre, Via A. Fleming 4, Verona 37135, Italy
| | | | - Romano Di-Fabio
- Medicines Research Centre, Via A. Fleming 4, Verona 37135, Italy
| | - Daniele Donati
- Medicines Research Centre, Via A. Fleming 4, Verona 37135, Italy
| | - Stefano Fontana
- Medicines Research Centre, Via A. Fleming 4, Verona 37135, Italy
| | - Massimo Gianotti
- Medicines Research Centre, Via A. Fleming 4, Verona 37135, Italy
| | - Laurie J. Gordon
- Neurosciences CEDD, GlaxoSmithKline, New Frontiers Science Park, Third Avenue, Harlow, Essex CM19 5AW, U.K
| | - Enrica Granci
- Medicines Research Centre, Via A. Fleming 4, Verona 37135, Italy
| | - Colin P. Leslie
- Medicines Research Centre, Via A. Fleming 4, Verona 37135, Italy
| | - Luca Moccia
- Medicines Research Centre, Via A. Fleming 4, Verona 37135, Italy
| | | | - Ilaria Sartori
- Medicines Research Centre, Via A. Fleming 4, Verona 37135, Italy
| | - Anna Sava
- Medicines Research Centre, Via A. Fleming 4, Verona 37135, Italy
| | - Jeannette M. Watson
- Neurosciences CEDD, GlaxoSmithKline, New Frontiers Science Park, Third Avenue, Harlow, Essex CM19 5AW, U.K
| | - Angela Worby
- Neurosciences CEDD, GlaxoSmithKline, New Frontiers Science Park, Third Avenue, Harlow, Essex CM19 5AW, U.K
| | - Laura Zonzini
- Medicines Research Centre, Via A. Fleming 4, Verona 37135, Italy
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Tollefson MB, Acker BA, Jacobsen E, Hughes RO, Walker JK, Fox DN, Palmer MJ, Freeman SK, Yu Y, Bond BR. 1-(2-Ethoxyethyl)-1H-pyrazolo[4,3-d]pyrimidines as potent phosphodiesterase 5 (PDE5) inhibitors. Bioorg Med Chem Lett 2010; 20:3120-4. [DOI: 10.1016/j.bmcl.2010.03.111] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Tollefson MB, Acker BA, Jacobsen E, Hughes RO, Walker JK, Fox DN, Palmer MJ, Freeman SK, Yu Y, Bond BR. 1-(2-(2,2,2-Trifluoroethoxy)ethyl-1H-pyrazolo[4,3-d]pyrimidines as potent phosphodiesterase 5 (PDE5) inhibitors. Bioorg Med Chem Lett 2010; 20:3125-8. [DOI: 10.1016/j.bmcl.2010.03.106] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Revised: 03/25/2010] [Accepted: 03/26/2010] [Indexed: 11/30/2022]
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Mikhailov D, Traebert M, Lu Q, Whitebread S, Egan W. Should Cardiosafety be Ruled by hERG Inhibition? Early Testing Scenarios and Integrated Risk Assessment. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/9783527627448.ch16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Alelyunas YW, Pelosi-Kilby L, Turcotte P, Kary MB, Spreen RC. A high throughput dried DMSO LogD lipophilicity measurement based on 96-well shake-flask and atmospheric pressure photoionization mass spectrometry detection. J Chromatogr A 2010; 1217:1950-5. [DOI: 10.1016/j.chroma.2010.01.071] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Revised: 01/19/2010] [Accepted: 01/22/2010] [Indexed: 10/19/2022]
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Shamovsky I, de Graaf C, Alderin L, Bengtsson M, Bladh H, Börjesson L, Connolly S, Dyke HJ, van den Heuvel M, Johansson H, Josefsson BG, Kristoffersson A, Linnanen T, Lisius A, Männikkö R, Nordén B, Price S, Ripa L, Rognan D, Rosendahl A, Skrinjar M, Urbahns K. Increasing selectivity of CC chemokine receptor 8 antagonists by engineering nondesolvation related interactions with the intended and off-target binding sites. J Med Chem 2009; 52:7706-23. [PMID: 19954248 DOI: 10.1021/jm900713y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The metabolic stability and selectivity of a series of CCR8 antagonists against binding to the hERG ion channel and cytochrome Cyp2D6 are studied by principal component analysis. It is demonstrated that an efficient way of increasing metabolic stability and selectivity of this series is to decrease compound lipophilicity by engineering nondesolvation related attractive interactions with CCR8, as rationalized by three-dimensional receptor models. Although such polar interactions led to increased compound selectivity, such a strategy could also jeopardize the DMPK profile of compounds. However, once increased potency is found, the lipophilicity can be readjusted by engineering hydrophobic substituents that fit to CCR8 but do not fit to hERG. Several such lipophilic fragments are identified by two-dimensional fragment-based QSAR analysis. Electrophysiological measurements and site-directed mutagenesis studies indicated that the repulsive interactions of these fragments with hERG are caused by steric hindrances with residue F656.
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Affiliation(s)
- Igor Shamovsky
- Department of Medicinal Chemistry, AstraZeneca R&D Lund, S-22187 Lund, Sweden.
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Guo D, Klaasse E, de Vries H, Brussee J, Nalos L, Rook MB, Vos MA, van der Heyden MAG, Ijzerman AP. Exploring chemical substructures essential for HERG k(+) channel blockade by synthesis and biological evaluation of dofetilide analogues. ChemMedChem 2009; 4:1722-32. [PMID: 19725081 DOI: 10.1002/cmdc.200900203] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In this study we followed a new approach to analyze molecular substructures required for hERG channel blockade. We designed and synthesized 40 analogues of dofetilide (1), a potent hERG potassium channel blocker, and established structure-activity relationships (SAR) for their interaction with this important cardiotoxicity-related off-target. Structural modifications to dofetilide were made by diversifying the substituents on the phenyl rings and the protonated nitrogen and by varying the carbon chain length. The analogues were evaluated in a radioligand binding assay and SAR data were derived with the aim to specify structural features that give rise to hERG toxicity.
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Affiliation(s)
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- Division of Medicinal Chemistry, Leiden/Amsterdam Center for Drug Research, Leiden University, P.O. Box 9502, 2300 RA Leiden (The Netherlands)
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Stocks M, Wilden G, Pairaudeau G, Perry M, Steele J, Stonehouse J. A Practical Method for Targeted Library Design Balancing Lead-like Properties with Diversity. ChemMedChem 2009; 4:800-8. [DOI: 10.1002/cmdc.200900050] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Bromidge SM, Bertani B, Borriello M, Bozzoli A, Faedo S, Gianotti M, Gordon LJ, Hill M, Zucchelli V, Watson JM, Zonzini L. 8-[2-(4-Aryl-1-piperazinyl)ethyl]-2H-1,4-benzoxazin-3(4H)-ones: Dual-acting 5-HT1 receptor antagonists and serotonin reuptake inhibitors—Part II. Bioorg Med Chem Lett 2009; 19:2338-42. [DOI: 10.1016/j.bmcl.2009.02.056] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2008] [Revised: 02/12/2009] [Accepted: 02/13/2009] [Indexed: 11/25/2022]
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