1
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A M Subbaiah M, Mandal U, Patankar V, Bhaskaran S, Nutakki R, Rami B, Shah DP, Mahammad S, Murphy BJ, Huang C, Robl JA, Washburn WN. Exploring monocyclic core: Discovery of pyrrol-2-one derivatives as a new series of potent MCHR1 antagonists with in vivo efficacy. Eur J Med Chem 2024; 276:116686. [PMID: 39053192 DOI: 10.1016/j.ejmech.2024.116686] [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: 04/27/2024] [Revised: 07/13/2024] [Accepted: 07/15/2024] [Indexed: 07/27/2024]
Abstract
With an objective to improve the profiles of the 1st generation non-basic MCHR1 antagonists, a lean design approach of replacing the bicyclic thienopyrimidine core with a monocyclic pyrrol-2-one chemotype was examined in the context of reducing aromatic ring count, while also contemplating enhanced flexibility as a means of decreasing flat character. The new compounds exhibited potent antagonism up to the sub-nanomolar range, thereby implying that the monocyclic ring could effectively serve as an effective bioisostere of the bicyclic system. The prototype compound 2m offered benefits like improved potency, reduced half-life, and enhanced solubility, while also demonstrating >5% reduction in weight gain in rats, thereby providing proof-of-concept for this new class of compounds as anti-obesity agents.
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Affiliation(s)
- Murugaiah A M Subbaiah
- Department of Medicinal Chemistry, Biocon-Bristol Myers Squibb Research and Development Centre, Biocon Park, Bommasandra IV Phase, Jigani Link Road, Bangalore, PIN 560099, Karnataka, India.
| | - Umasankar Mandal
- Department of Medicinal Chemistry, Biocon-Bristol Myers Squibb Research and Development Centre, Biocon Park, Bommasandra IV Phase, Jigani Link Road, Bangalore, PIN 560099, Karnataka, India
| | - Vidya Patankar
- Department of Medicinal Chemistry, Biocon-Bristol Myers Squibb Research and Development Centre, Biocon Park, Bommasandra IV Phase, Jigani Link Road, Bangalore, PIN 560099, Karnataka, India
| | - Selvakumar Bhaskaran
- Department of Medicinal Chemistry, Biocon-Bristol Myers Squibb Research and Development Centre, Biocon Park, Bommasandra IV Phase, Jigani Link Road, Bangalore, PIN 560099, Karnataka, India
| | - Ravikumar Nutakki
- Department of Biology, Biocon-Bristol Myers Squibb Research and Development Centre, Biocon Park, Bommasandra IV Phase, Jigani Link Road, Bangalore, PIN 560099, Karnataka, India
| | - Bhadresh Rami
- Department of Biology, Biocon-Bristol Myers Squibb Research and Development Centre, Biocon Park, Bommasandra IV Phase, Jigani Link Road, Bangalore, PIN 560099, Karnataka, India
| | - Devang Praful Shah
- Department of Pharmaceutical Candidate Optimization, Biocon-Bristol Myers Squibb Research and Development Centre, Biocon Park, Bommasandra IV Phase, Jigani Link Road, Bangalore, PIN 560099, Karnataka, India
| | - Shahe Mahammad
- Department of Biopharmaceutics, Biocon-Bristol Myers Squibb Research and Development Centre, Biocon Park, Bommasandra IV Phase, Jigani Link Road, Bangalore, PIN 560099, Karnataka, India
| | - Brian J Murphy
- Department of Metabolic Diseases Biology, Bristol Myers Squibb Research and Early Development, PO Box 4000, Princeton, NJ, 08543-4000, USA
| | - Christine Huang
- Department of Pharmaceutical Candidate Optimization, Bristol Myers Squibb Research and Early Development, PO Box 4000, Princeton, NJ, 08543-4000, USA
| | - Jeffrey A Robl
- Department of Metabolic Diseases Chemistry, Bristol Myers Squibb Research and Early Development, PO Box 4000, Princeton, NJ, 08543-4000, USA
| | - William N Washburn
- Department of Metabolic Diseases Chemistry, Bristol Myers Squibb Research and Early Development, PO Box 4000, Princeton, NJ, 08543-4000, USA
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2
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Soroushmanesh M, Dinari M, Farrokhpour H. Comprehensive Computational Investigation of the Porphyrin-Based COF as a Nanocarrier for Delivering Anti-Cancer Drugs: A Combined MD Simulation and DFT Calculation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:19073-19085. [PMID: 39189806 DOI: 10.1021/acs.langmuir.4c02154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
As nanomaterials have gained prominence in drug delivery technology, exploring their feasibility through computational methods is beneficial before practical tests. In this study, we aim to evaluate the capability of the porphyrin-based covalent organic framework COF-366 as a nanocarrier for two anticancer drugs, irinotecan (IRI) and doxorubicin (DOX). The optimal binding conformation of the drug molecules on the COF surface was predicted by using molecular docking. Subsequently, molecular dynamic simulation (MD) was performed to assess the adsorption mechanism of drug molecules on the COF in the aqueous environment. The free energy of adsorption for DOX and IRI was estimated to be -20.07 and -23.89 kcal/mol, respectively. The adsorption of both drugs on the COF surface is mainly influenced by the π-π interaction. Furthermore, density functional theory (DFT) calculation, natural bond orbital (NBO), and quantum theory of atoms in molecules (QTAIM) analyses were employed to investigate the structural stability of Drug@COF complexes and gain a detailed understanding of the interaction between them at the molecular level. Based on DFT results, it was found that in addition to π-π interaction, the bis-piperidine-phenylene interaction affects the adsorption of IRI on the COF surface. Moreover, the diffusion behavior of the drug molecule inside the COF pore was simulated using a ten-layer COF. Based on the mean square displacement analysis, the diffusion coefficients of DOX and IRI within the COF pore were calculated to be 108 and 97 um2/s, respectively. This computational study sheds light on how different types of interactions between the drug molecule and COF affect the adsorption and diffusion process. Our findings validated that the porphyrin-based COF-366 can serve as a nanobased platform for delivering DOX and IRI.
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Affiliation(s)
- Mohsen Soroushmanesh
- Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111, Islamic Republic of Iran
| | - Mohammad Dinari
- Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111, Islamic Republic of Iran
| | - Hossein Farrokhpour
- Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111, Islamic Republic of Iran
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3
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Tsien J, Hu C, Merchant RR, Qin T. Three-dimensional saturated C(sp 3)-rich bioisosteres for benzene. Nat Rev Chem 2024; 8:605-627. [PMID: 38982260 DOI: 10.1038/s41570-024-00623-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2024] [Indexed: 07/11/2024]
Abstract
Benzenes, the most ubiquitous structural moiety in marketed small-molecule drugs, are frequently associated with poor 'drug-like' properties, including metabolic instability, and poor aqueous solubility. In an effort to overcome these limitations, recent developments in medicinal chemistry have demonstrated the improved physicochemical profiles of C(sp3)-rich bioisosteric scaffolds relative to arenes. In the past two decades, we have witnessed an exponential increase in synthetic methods for accessing saturated bioisosteres of monosubstituted and para-substituted benzenes. However, until recent discoveries, analogous three-dimensional ortho-substituted and meta-substituted biososteres have remained underexplored, owing to their ring strain and increased s-character hybridization. This Review summarizes the emerging synthetic methodologies to access such saturated motifs and their impact on the application of bioisosteres for ortho-substituted, meta-substituted and multi-substituted benzene rings. It concludes with a perspective on the development of next-generation bioisosteres, including those within novel chemical space.
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Affiliation(s)
- Jet Tsien
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chao Hu
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Rohan R Merchant
- Department of Discovery Chemistry, Merck & Co., Inc., South San Francisco, CA, USA
| | - Tian Qin
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, USA.
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4
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Zou Y, Wang X, Chen P, Zheng Z, Li X, Chen Z, Guo M, Zhou Y, Sun C, Wang R, Zhu W, Zheng P, Cho WJ, Cho YC, Liang G, Tang Q. Fragment-Based Anti-inflammatory Agent Design and Target Identification: Discovery of AF-45 as an IRAK4 Inhibitor to Treat Ulcerative Colitis and Acute Lung Injury. J Med Chem 2024; 67:10687-10709. [PMID: 38913701 DOI: 10.1021/acs.jmedchem.4c00202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
UC and ALI are inflammatory diseases with limited treatment in the clinic. Herein, fragment-based anti-inflammatory agent designs were carried out deriving from cyclohexylamine/cyclobutylamine and several fragments from anti-inflammatory agents in our lab. AF-45 (IC50 = 0.53/0.60 μM on IL-6/TNF-α in THP-1 macrophages) was identified as the optimal molecule using ELISA and MTT assays from the 33 synthesized compounds. Through mechanistic studies and a systematic target search process, AF-45 was found to block the NF-κB/MAPK pathway and target IRAK4, a promising target for inflammation and autoimmune diseases. The selectivity of AF-45 targeting IRAK4 was validated by comparing its effects on other kinase/nonkinase proteins. In vivo, AF-45 exhibited a good therapeutic effect on UC and ALI, and favorable PK proprieties. Since there are currently no clinical or preclinical trials for IRAK4 inhibitors to treat UC and ALI, AF-45 provides a new lead compound or candidate targeting IRAK4 for the treatment of these diseases.
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Affiliation(s)
- Yu Zou
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325024, China
| | - Xiemin Wang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325024, China
| | - Pan Chen
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325024, China
- Department of Cardiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325035, China
| | - Zhiwei Zheng
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325024, China
- College of Pharmacy, Chonnam National University, Gwangju 61186, Korea
| | - Xiaobo Li
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325024, China
| | - Zhichao Chen
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325024, China
| | - Mi Guo
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325024, China
| | - Ying Zhou
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325024, China
| | - Chenhui Sun
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325024, China
| | - Ran Wang
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Wufu Zhu
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Pengwu Zheng
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Won-Jea Cho
- College of Pharmacy, Chonnam National University, Gwangju 61186, Korea
| | - Young-Chang Cho
- College of Pharmacy, Chonnam National University, Gwangju 61186, Korea
| | - Guang Liang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
- School of Pharmacy, Hangzhou Medical College, Hangzhou 311399, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325024, China
- Department of Cardiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325035, China
| | - Qidong Tang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325024, China
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5
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Meanwell NA. Applications of Bioisosteres in the Design of Biologically Active Compounds. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:18087-18122. [PMID: 36961953 DOI: 10.1021/acs.jafc.3c00765] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The design of bioisosteres represents a creative and productive approach to improve a molecule, including by enhancing potency, addressing pharmacokinetic challenges, reducing off-target liabilities, and productively modulating physicochemical properties. Bioisosterism is a principle exploited in the design of bioactive compounds of interest to both medicinal and agricultural chemists, and in this review, we provide a synopsis of applications where this kind of molecular editing has proved to be advantageous in molecule optimization. The examples selected for discussion focus on bioisosteres of carboxylic acids, applications of fluorine and fluorinated motifs in compound design, some applications of the sulfoximine functionality, the design of bioisosteres of drug-H2O complexes, and the design of bioisosteres of the phenyl ring.
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Affiliation(s)
- Nicholas A Meanwell
- The Baruch S. Blumberg Institute, 3805 Old Easton Rd, Doylestown, Pennsylvania 18902, United States
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6
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Gordhan HM, Miller ST, Clancy DC, Ina M, McDougal AV, Cutno DK, Brown RV, Lichorowic CL, Sturdivant JM, Vick KA, Williams SS, deLong MA, White JC, Kopczynski CC, Ellis DA. Eyes on Topical Ocular Disposition: The Considered Design of a Lead Janus Kinase (JAK) Inhibitor That Utilizes a Unique Azetidin-3-Amino Bridging Scaffold to Attenuate Off-Target Kinase Activity, While Driving Potency and Aqueous Solubility. J Med Chem 2023. [PMID: 37314941 DOI: 10.1021/acs.jmedchem.3c00519] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
An unmet medical need remains for patients suffering from dry eye disease (DED). A fast-acting, better-tolerated noncorticosteroid anti-inflammatory eye drop could improve patient outcomes and quality of life. Herein, we describe a small-molecule drug discovery effort to identify novel, potent, and water-soluble JAK inhibitors as immunomodulating agents for topical ocular disposition. A focused library of known 3-(4-(2-(arylamino)pyrimidin-4-yl)-1H-pyrazol-1-yl)propanenitriles was evaluated as a molecular starting point. Structure-activity relationships (SARs) revealed a ligand-efficient (LE) JAK inhibitor series, amenable to aqueous solubility. Subsequent in vitro analysis indicated the potential for off-target toxicity. A KINOMEscan selectivity profile of 5 substantiated the likelihood of widespread series affinity across the human kinome. An sp2-to-sp3 drug design strategy was undertaken to attenuate off-target kinase activity while driving JAK-STAT potency and aqueous solubility. Tactics to reduce aromatic character, increase fraction sp3 (Fsp3), and bolster molecular complexity led to the azetidin-3-amino bridging scaffold in 31.
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Affiliation(s)
- Heeren M Gordhan
- Alcon Research, LLC, Durham, North Carolina 27703, United States
| | - Steven T Miller
- Alcon Research, LLC, Durham, North Carolina 27703, United States
| | - Daphne C Clancy
- Alcon Research, LLC, Durham, North Carolina 27703, United States
| | - Maria Ina
- Alcon Research, LLC, Durham, North Carolina 27703, United States
| | - Alan V McDougal
- Alcon Research, LLC, Durham, North Carolina 27703, United States
| | - D'Quan K Cutno
- Alcon Research, LLC, Durham, North Carolina 27703, United States
| | - Robert V Brown
- Alcon Research, LLC, Durham, North Carolina 27703, United States
| | | | | | - Kyle A Vick
- ID Business Solutions, Ltd., Boston, Massachusetts 02210, United States
| | | | | | - Jeffrey C White
- Baxter Healthcare Corp., Deerfield, Illinois 60015, United States
| | | | - David A Ellis
- Alcon Research, LLC, Durham, North Carolina 27703, United States
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7
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Brown GD, Batalla D, Cavallaro CL, Perez HL, Wrobleski ST, Sherwood TC. A compact, practical photoreactor for multi-reaction arrays. REACT CHEM ENG 2022. [DOI: 10.1039/d2re00062h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report here the BMS-PR460: a photoreactor designed for multi-reaction arrays at various scales and temperatures with irradiation at 460 nm. Transformations of interest to pharmaceutical research have been performed to demonstrate reactor utility.
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Affiliation(s)
- Gregory D. Brown
- Research and Development, Bristol Myers Squibb Company, Route 206 and Province Line Road, Princeton, NJ 08543-4000, USA
| | - Daniel Batalla
- Research and Development, Bristol Myers Squibb Company, Route 206 and Province Line Road, Princeton, NJ 08543-4000, USA
| | - Cullen L. Cavallaro
- Research and Development, Bristol Myers Squibb Company, Route 206 and Province Line Road, Princeton, NJ 08543-4000, USA
| | - Heidi L. Perez
- Research and Development, Bristol Myers Squibb Company, Route 206 and Province Line Road, Princeton, NJ 08543-4000, USA
| | - Stephen T. Wrobleski
- Research and Development, Bristol Myers Squibb Company, Route 206 and Province Line Road, Princeton, NJ 08543-4000, USA
| | - Trevor C. Sherwood
- Research and Development, Bristol Myers Squibb Company, Route 206 and Province Line Road, Princeton, NJ 08543-4000, USA
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8
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Subbaiah MAM, Meanwell NA. Bioisosteres of the Phenyl Ring: Recent Strategic Applications in Lead Optimization and Drug Design. J Med Chem 2021; 64:14046-14128. [PMID: 34591488 DOI: 10.1021/acs.jmedchem.1c01215] [Citation(s) in RCA: 168] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The benzene moiety is the most prevalent ring system in marketed drugs, underscoring its historic popularity in drug design either as a pharmacophore or as a scaffold that projects pharmacophoric elements. However, introspective analyses of medicinal chemistry practices at the beginning of the 21st century highlighted the indiscriminate deployment of phenyl rings as an important contributor to the poor physicochemical properties of advanced molecules, which limited their prospects of being developed into effective drugs. This Perspective deliberates on the design and applications of bioisosteric replacements for a phenyl ring that have provided practical solutions to a range of developability problems frequently encountered in lead optimization campaigns. While the effect of phenyl ring replacements on compound properties is contextual in nature, bioisosteric substitution can lead to enhanced potency, solubility, and metabolic stability while reducing lipophilicity, plasma protein binding, phospholipidosis potential, and inhibition of cytochrome P450 enzymes and the hERG channel.
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Affiliation(s)
- Murugaiah A M Subbaiah
- Department of Medicinal Chemistry, Biocon-Bristol Myers Squibb Research and Development Centre, Biocon Park, Bommasandra IV Phase, Jigani Link Road, Bangalore, Karnataka 560099, India
| | - Nicholas A Meanwell
- Department of Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
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9
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Swidorski JJ, Jenkins S, Hanumegowda U, Parker DD, Beno BR, Protack T, Ng A, Gupta A, Shanmugam Y, Dicker IB, Krystal M, Meanwell NA, Regueiro-Ren A. Design and exploration of C-3 benzoic acid bioisosteres and alkyl replacements in the context of GSK3532795 (BMS-955176) that exhibit broad spectrum HIV-1 maturation inhibition. Bioorg Med Chem Lett 2021; 36:127823. [PMID: 33508465 DOI: 10.1016/j.bmcl.2021.127823] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 01/11/2021] [Accepted: 01/18/2021] [Indexed: 11/30/2022]
Abstract
GSK3532795 (formerly BMS-955176) is a second-generation HIV-1 maturation inhibitor that has shown broad spectrum antiviral activity and preclinical PK predictive of once-daily dosing in humans. Although efficacy was confirmed in clinical trials, the observation of gastrointestinal intolerability and the emergence of drug resistant virus in a Phase 2b clinical study led to the discontinuation of GSK3532795. As part of the effort to further map the maturation inhibitor pharmacophore and provide additional structural options, the evaluation of alternates to the C-3 phenyl substituent in this chemotype was pursued. A cyclohexene carboxylic acid provided exceptional inhibition of wild-type, V370A and ΔV370 mutant viruses in addition to a suitable PK profile following oral dosing to rats. In addition, a novel spiro[3.3]hept-5-ene was designed to extend the carboxylic acid further from the triterpenoid core while reducing side chain flexibility compared to the other alkyl substituents. This modification was shown to closely emulate the C-3 benzoic acid moiety of GSK3532795 from both a potency and PK perspective, providing a non-traditional, sp3-rich bioisostere of benzene. Herein, we detail additional modifications to the C-3 position of the triterpenoid core that offer effective replacements for the benzoic acid of GSK3532795 and capture the interplay between these new C-3 elements and C-17 modifications that contribute to enhanced polymorph coverage.
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Affiliation(s)
- Jacob J Swidorski
- Department of Discovery Chemistry, Bristol Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA.
| | - Susan Jenkins
- Department of Pharmaceutical Candidate Optimization, Bristol Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Umesh Hanumegowda
- Department of Pharmaceutical Candidate Optimization, Bristol Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Dawn D Parker
- Department of Pharmaceutical Candidate Optimization, Bristol Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Brett R Beno
- Department of Computer-Assisted Drug Design, Bristol Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Tricia Protack
- Department of Virology, Bristol Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Alicia Ng
- Department of Discovery Chemistry, Bristol Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Anuradha Gupta
- Biocon Bristol Myers Squibb Research & Development Center, Bangalore, India
| | - Yoganand Shanmugam
- Biocon Bristol Myers Squibb Research & Development Center, Bangalore, India
| | - Ira B Dicker
- Department of Virology, Bristol Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Mark Krystal
- Department of Virology, Bristol Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Nicholas A Meanwell
- Department of Discovery Chemistry, Bristol Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Alicia Regueiro-Ren
- Department of Discovery Chemistry, Bristol Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
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10
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Ding L, Zhuang C, Chen F. Druggability modification strategies of the diarylpyrimidine-type non-nucleoside reverse transcriptase inhibitors. Med Res Rev 2021; 41:1255-1290. [PMID: 33497504 DOI: 10.1002/med.21760] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/04/2020] [Accepted: 11/18/2020] [Indexed: 12/20/2022]
Abstract
Drug discovery of human immunodeficiency virus (HIV) is a hot field in medicinal chemistry community for many years. The diarylpyrimidines (DAPYs) are the second-generation non-nucleoside reverse transcriptase inhibitors (NNRTIs) targeting reverse transcriptase, playing a great irreplaceable role in HIV transcriptional therapy. However, fast-growing drug-resistant mutations as nonnegligible challenge are still unpredictably appeared in the clinical practice, leading to deactivate or reduce the existing drugs. In the last 20 years, more and more novel DAPY derivatives have developed with the purpose to counter the mutants. Nevertheless, most of them have dissatisfactory pharmacokinetics (PK) or poor antiviral activity toward resistant mutant strains. In this article, we will analyze the NNRTI derivatives with promising druggability, and summarize a series of druggability modification strategies to improve the antiviral activity, reduce toxicity and improve the PK properties in recent years. The prospects of DAPYs and the directions for future efforts will be discussed.
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Affiliation(s)
- Li Ding
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, Shanghai, China.,Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, China
| | - Chunlin Zhuang
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, Shanghai, China.,Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, China
| | - Fener Chen
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, Shanghai, China.,Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, China.,Institute of Pharmaceutical Science and Technology, Zhejiang University of Technology, Hangzhou, China
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11
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Patel M, Cianci C, Allard CW, Parker DD, Simmermacher J, Jenkins S, Mcauliffe B, Minassian B, Discotto L, Krystal M, Meanwell NA, Naidu BN. Design, synthesis and SAR study of novel C2-pyrazolopyrimidine amides and amide isosteres as allosteric integrase inhibitors. Bioorg Med Chem Lett 2020; 30:127516. [PMID: 32860982 DOI: 10.1016/j.bmcl.2020.127516] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/18/2020] [Accepted: 08/20/2020] [Indexed: 10/23/2022]
Abstract
The design, synthesis and structure-activity relationships associated with a series of C2-substituted pyrazolopyrimidines as potent allosteric inhibitors of HIV-1 integrase (ALLINIs) are described. Structural modifications to these molecules were made in order to examine the effect on potency and, for select compounds, pharmacokinetic properties. We examined a variety of C2-substituted pyrazolopyrimidines and found that the C2-amide derivatives demonstrated the most potent antiviral activity of this class against HIV-1 infection in cell culture.
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Affiliation(s)
- Manoj Patel
- Departments of Discovery Chemistry and Molecular Technologies, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA; ViiV Healthcare, 36 East Industrial Parkway, Branford, CT 06405, USA.
| | - Christopher Cianci
- Virology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Christopher W Allard
- Departments of Discovery Chemistry and Molecular Technologies, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Dawn D Parker
- Departments of Discovery Chemistry and Molecular Technologies, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA; ViiV Healthcare, 36 East Industrial Parkway, Branford, CT 06405, USA
| | - Jean Simmermacher
- Departments of Discovery Chemistry and Molecular Technologies, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA; ViiV Healthcare, 36 East Industrial Parkway, Branford, CT 06405, USA
| | - Susan Jenkins
- Departments of Discovery Chemistry and Molecular Technologies, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA; ViiV Healthcare, 36 East Industrial Parkway, Branford, CT 06405, USA
| | - Brian Mcauliffe
- Virology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA; ViiV Healthcare, 36 East Industrial Parkway, Branford, CT 06405, USA
| | - Beatrice Minassian
- Virology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Linda Discotto
- Virology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Mark Krystal
- Virology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA; ViiV Healthcare, 36 East Industrial Parkway, Branford, CT 06405, USA
| | - Nicholas A Meanwell
- Departments of Discovery Chemistry and Molecular Technologies, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - B Narasimhulu Naidu
- Departments of Discovery Chemistry and Molecular Technologies, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA; ViiV Healthcare, 36 East Industrial Parkway, Branford, CT 06405, USA
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12
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Wei W, Cherukupalli S, Jing L, Liu X, Zhan P. Fsp 3: A new parameter for drug-likeness. Drug Discov Today 2020; 25:1839-1845. [PMID: 32712310 DOI: 10.1016/j.drudis.2020.07.017] [Citation(s) in RCA: 154] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/26/2020] [Accepted: 07/16/2020] [Indexed: 12/19/2022]
Abstract
The drug-likeness of a compound is a key factor during the initial phases of drug discovery. It can be defined as the similarity between compounds and drugs. Here, we collate research related to the fraction of sp3 carbon atoms (Fsp3), including related high-throughput screening (HTS) cases, structural modifications based on Fsp3, and strategies to improve it. We also introduce new synthetic methods for spirocyclic scaffolds. It is likely that the reasonable rigidity of spirocyclic scaffolds will provide a new generation of drug candidates.
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Affiliation(s)
- Wenxiu 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
| | - Srinivasulu Cherukupalli
- 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
| | - Lanlan Jing
- 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.
| | - 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.
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13
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Blagojević Filipović JP, Hall MB, Zarić SD. Stacking interactions of resonance-assisted hydrogen-bridged rings and C 6-aromatic rings. Phys Chem Chem Phys 2020; 22:13721-13728. [PMID: 32529195 DOI: 10.1039/d0cp01624a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Stacking interactions between six-membered resonance-assisted hydrogen-bridged (RAHB) rings and C6-aromatic rings were systematically studied by analyzing crystal structures in the Cambridge Structural Database (CSD). The interaction energies were calculated by quantum-chemical methods. Although the interactions are stronger than benzene/benzene stacking interactions (-2.7 kcal mol-1), the strongest calculated RAHB/benzene stacking interaction (-3.7 kcal mol-1) is significantly weaker than the strongest calculated RAHB/RAHB stacking interaction (-4.7 kcal mol-1), but for a particular composition of RAHB rings, RAHB/benzene stacking interactions can be weaker or stronger than the corresponding RAHB/RAHB stacking interactions. They are also weaker than the strongest calculated stacking interaction between five-membered saturated hydrogen-bridged rings and benzene (-4.4 kcal mol-1) and between two five-membered saturated hydrogen-bridged rings (-4.9 kcal mol-1). SAPT energy decomposition analyses show that the strongest attractive term in RAHB/benzene stacking interactions is dispersion, however, it is mostly canceled by a repulsive exchange term; hence the geometries of the most stable structures are determined by an electrostatic term.
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Affiliation(s)
| | - Michael B Hall
- Department of Chemistry, Texas A&M University, College Station, TX 77843-3255, USA
| | - Snežana D Zarić
- Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade, Serbia.
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14
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Liu B, Trout REL, Chu GH, McGarry D, Jackson RW, Hamrick JC, Daigle DM, Cusick SM, Pozzi C, De Luca F, Benvenuti M, Mangani S, Docquier JD, Weiss WJ, Pevear DC, Xerri L, Burns CJ. Discovery of Taniborbactam (VNRX-5133): A Broad-Spectrum Serine- and Metallo-β-lactamase Inhibitor for Carbapenem-Resistant Bacterial Infections. J Med Chem 2019; 63:2789-2801. [PMID: 31765155 PMCID: PMC7104248 DOI: 10.1021/acs.jmedchem.9b01518] [Citation(s) in RCA: 174] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
A major resistance mechanism in Gram-negative bacteria
is the production
of β-lactamase enzymes. Originally recognized for their ability
to hydrolyze penicillins, emergent β-lactamases can now confer
resistance to other β-lactam drugs, including both cephalosporins
and carbapenems. The emergence and global spread of β-lactamase-producing
multi-drug-resistant “superbugs” has caused increased
alarm within the medical community due to the high mortality rate
associated with these difficult-to-treat bacterial infections. To
address this unmet medical need, we initiated an iterative program
combining medicinal chemistry, structural biology, biochemical testing,
and microbiological profiling to identify broad-spectrum inhibitors
of both serine- and metallo-β-lactamase enzymes. Lead optimization,
beginning with narrower-spectrum, weakly active compounds, provided 20 (VNRX-5133, taniborbactam), a boronic-acid-containing pan-spectrum
β-lactamase inhibitor. In vitro and in vivo studies demonstrated
that 20 restored the activity of β-lactam antibiotics
against carbapenem-resistant Pseudomonas aeruginosa and carbapenem-resistant Enterobacteriaceae. Taniborbactam is the
first pan-spectrum β-lactamase inhibitor to enter clinical development.
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Affiliation(s)
- Bin Liu
- Venatorx Pharmaceuticals, Inc., 30 Spring Mill Drive, Malvern, Pennsylvania 19355, United States
| | - Robert E Lee Trout
- Venatorx Pharmaceuticals, Inc., 30 Spring Mill Drive, Malvern, Pennsylvania 19355, United States
| | - Guo-Hua Chu
- Venatorx Pharmaceuticals, Inc., 30 Spring Mill Drive, Malvern, Pennsylvania 19355, United States
| | - Daniel McGarry
- Venatorx Pharmaceuticals, Inc., 30 Spring Mill Drive, Malvern, Pennsylvania 19355, United States
| | - Randy W Jackson
- Venatorx Pharmaceuticals, Inc., 30 Spring Mill Drive, Malvern, Pennsylvania 19355, United States
| | - Jodie C Hamrick
- Venatorx Pharmaceuticals, Inc., 30 Spring Mill Drive, Malvern, Pennsylvania 19355, United States
| | - Denis M Daigle
- Venatorx Pharmaceuticals, Inc., 30 Spring Mill Drive, Malvern, Pennsylvania 19355, United States
| | - Susan M Cusick
- Venatorx Pharmaceuticals, Inc., 30 Spring Mill Drive, Malvern, Pennsylvania 19355, United States
| | - Cecilia Pozzi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy
| | - Filomena De Luca
- Department of Medical Biotechnology, University of Siena, I-53100 Siena, Italy
| | - Manuela Benvenuti
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy
| | - Stefano Mangani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy
| | - Jean-Denis Docquier
- Department of Medical Biotechnology, University of Siena, I-53100 Siena, Italy
| | - William J Weiss
- UNT System College of Pharmacy, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, Texas 76107-2699, United States
| | - Daniel C Pevear
- Venatorx Pharmaceuticals, Inc., 30 Spring Mill Drive, Malvern, Pennsylvania 19355, United States
| | - Luigi Xerri
- Venatorx Pharmaceuticals, Inc., 30 Spring Mill Drive, Malvern, Pennsylvania 19355, United States
| | - Christopher J Burns
- Venatorx Pharmaceuticals, Inc., 30 Spring Mill Drive, Malvern, Pennsylvania 19355, United States
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15
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Sherwood TC, Xiao HY, Bhaskar RG, Simmons EM, Zaretsky S, Rauch MP, Knowles RR, Dhar TGM. Decarboxylative Intramolecular Arene Alkylation Using N-(Acyloxy)phthalimides, an Organic Photocatalyst, and Visible Light. J Org Chem 2019; 84:8360-8379. [DOI: 10.1021/acs.joc.9b00432] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Trevor C. Sherwood
- Research and Development, Bristol-Myers Squibb Company, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Hai-Yun Xiao
- Research and Development, Bristol-Myers Squibb Company, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Roshan G. Bhaskar
- Research and Development, Bristol-Myers Squibb Company, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Eric M. Simmons
- Chemical and Synthetic Development, Bristol-Myers Squibb, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Serge Zaretsky
- Chemical and Synthetic Development, Bristol-Myers Squibb, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Martin P. Rauch
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Robert R. Knowles
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - T. G. Murali Dhar
- Research and Development, Bristol-Myers Squibb Company, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
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16
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Sofia MJ. The Discovery and Early Clinical Evaluation of the HCV NS3/4A Protease Inhibitor Asunaprevir (BMS-650032). TOPICS IN MEDICINAL CHEMISTRY 2019. [PMCID: PMC7123690 DOI: 10.1007/7355_2018_58] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The discovery of asunaprevir (1) began with the concept of engaging the small and well-defined S1’ pocket of the hepatitis C virus (HCV) NS3/4A protease that was explored in the context of tripeptide carboxylic acid-based inhibitors. A cyclopropyl-acyl sulfonamide moiety was found to be the optimal element at the P1-P1’ interface enhancing the potency of carboxylic acid-based prototypes by 10- to >100-fold, dependent upon the specific background. Optimization for oral bioavailability identified a 1-substituted isoquinoline-based P2* element that conferred a significant exposure advantage in rats compared to the matched 4-substituted quinoline isomer. BMS-605339 (30) was the first cyclopropyl-acyl sulfonamide derivative advanced into clinical trials that demonstrated dose-related reductions in plasma viral RNA in HCV-infected patients. However, 30 was associated with cardiac events observed in a normal healthy volunteer (NHV) and an HCV-infected patient that led to the suspension of the development program. Using a Langendorff rabbit heart model, a limited structure-cardiac liability relationship was quickly established that led to the discovery of 1. This compound, which differs from 30 only by changes in the substitution pattern of the P2* isoquinoline heterocycle and the addition of a single chlorine atom to the molecular formula, gave a dose-dependent reduction in plasma viral RNA following oral administration to HCV-infected patients without the burden of the cardiac events that had been observed with 30. A small clinical trial of the combination of 1 with the HCV NS5A inhibitor daclatasvir (2) established for the first time that a chronic genotype 1 (GT-1) HCV infection could be cured by therapy with two direct-acting antiviral agents in the absence of exogenous immune-stimulating agents. Development of the combination of 1 and 2 was initially focused on Japan where the patient population is predominantly infected with GT-1b virus, culminating in marketing approval which was granted on July 4, 2014. In order to broaden therapy to include GT-1a infections, a fixed dose triple combination of 1, 2, and the allosteric NS5B inhibitor beclabuvir (3) was developed, approved by the Japanese health authorities for the treatment of HCV GT-1 infection on December 20, 2016 and marketed as Ximency®.
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17
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Sun AC, McClain EJ, Beatty JW, Stephenson CR. Visible Light-Mediated Decarboxylative Alkylation of Pharmaceutically Relevant Heterocycles. Org Lett 2018; 20:3487-3490. [PMID: 29856641 PMCID: PMC6014829 DOI: 10.1021/acs.orglett.8b01250] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A net redox-neutral method for the decarboxylative alkylation of heteroarenes using photoredox catalysis is reported. Additionally, this method features the use of simple, commercially available carboxylic acid derivatives as alkylating agents, enabling the facile alkylation of a variety of biologically relevant heterocyclic scaffolds under mild conditions.
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Affiliation(s)
- Alexandra C. Sun
- Willard Henry Dow Laboratory, Department of Chemistry, University of Michigan, 930 North University Ave., Ann Arbor, MI 48109, United States
| | - Edward J. McClain
- Willard Henry Dow Laboratory, Department of Chemistry, University of Michigan, 930 North University Ave., Ann Arbor, MI 48109, United States
| | - Joel W. Beatty
- Willard Henry Dow Laboratory, Department of Chemistry, University of Michigan, 930 North University Ave., Ann Arbor, MI 48109, United States
| | - Corey R.J. Stephenson
- Willard Henry Dow Laboratory, Department of Chemistry, University of Michigan, 930 North University Ave., Ann Arbor, MI 48109, United States
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18
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Lu X, Yang J, Kang D, Gao P, Daelemans D, De Clercq E, Pannecouque C, Zhan P, Liu X. The discovery of novel diarylpyri(mi)dine derivatives with high level activity against a wide variety of HIV-1 strains as well as against HIV-2. Bioorg Med Chem 2018; 26:2051-2060. [DOI: 10.1016/j.bmc.2018.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 02/27/2018] [Accepted: 03/02/2018] [Indexed: 11/29/2022]
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19
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Estimation of kinetic and thermodynamic ligand-binding parameters using computational strategies. Future Med Chem 2017; 9:507-523. [DOI: 10.4155/fmc-2016-0224] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Kinetic and thermodynamic ligand–protein binding parameters are gaining growing importance as key information to consider in drug discovery. The determination of the molecular structures, using particularly x-ray and NMR techniques, is crucial for understanding how a ligand recognizes its target in the final binding complex. However, for a better understanding of the recognition processes, experimental studies of ligand–protein interactions are needed. Even though several techniques can be used to investigate both thermodynamic and kinetic profiles for a ligand–protein complex, these procedures are very often laborious, time consuming and expensive. In the last 10 years, computational approaches have enormous potential in providing insights into each of the above effects and in parsing their contributions to the changes in both kinetic and thermodynamic binding parameters. The main purpose of this review is to summarize the state of the art of computational strategies for estimating the kinetic and thermodynamic parameters of a ligand–protein binding.
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20
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Chang G, Huard K, Kauffman GW, Stepan AF, Keefer CE. A multi-endpoint matched molecular pair (MMP) analysis of 6-membered heterocycles. Bioorg Med Chem 2017; 25:381-388. [DOI: 10.1016/j.bmc.2016.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/28/2016] [Accepted: 11/01/2016] [Indexed: 11/28/2022]
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21
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Kang D, Fang Z, Li Z, Huang B, Zhang H, Lu X, Xu H, Zhou Z, Ding X, Daelemans D, De Clercq E, Pannecouque C, Zhan P, Liu X. Design, Synthesis, and Evaluation of Thiophene[3,2-d]pyrimidine Derivatives as HIV-1 Non-nucleoside Reverse Transcriptase Inhibitors with Significantly Improved Drug Resistance Profiles. J Med Chem 2016; 59:7991-8007. [PMID: 27541578 DOI: 10.1021/acs.jmedchem.6b00738] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We designed and synthesized a series of human immunodeficiency virus type 1 (HIV-1) non-nucleoside reverse transcriptase inhibitors (NNRTIs) with a piperidine-substituted thiophene[3,2-d]pyrimidine scaffold, employing a strategy of structure-based molecular hybridization and substituent decorating. Most of the synthesized compounds exhibited broad-spectrum activity with low (single-digit) nanomolar EC50 values toward a panel of wild-type (WT), single-mutant, and double-mutant HIV-1 strains. Compound 27 was the most potent; compared with ETV, its antiviral efficacy was 3-fold greater against WT, 5-7-fold greater against Y181C, Y188L, E138K, and F227L+V106A, and nearly equipotent against L100I and K103N, though somewhat weaker against K103N+Y181C. Importantly, 27 has lower cytotoxicity (CC50 > 227 μM) and a huge selectivity index (SI) value (ratio of CC50/EC50) of >159101. 27 also showed favorable, drug-like pharmacokinetic and safety properties in rats in vivo. Molecular docking studies and the structure-activity relationships provide important clues for further molecular elaboration.
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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, Jinan 250012, 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, Jinan 250012, Shandong P.R. China.,The Second Hospital, Shandong University , No. 247 Beiyuan Avenue, Jinan 250033, China
| | - Zhenyu Li
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , 44 West Culture Road, Jinan 250012, Shandong P.R. China
| | - Boshi Huang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , 44 West Culture Road, Jinan 250012, Shandong P.R. China
| | - Heng Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , 44 West Culture Road, Jinan 250012, Shandong P.R. China
| | - Xueyi Lu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , 44 West Culture Road, Jinan 250012, Shandong P.R. China
| | - Haoran Xu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , 44 West Culture Road, Jinan 250012, Shandong P.R. China
| | - Zhongxia Zhou
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , 44 West Culture Road, Jinan 250012, Shandong P.R. China
| | - Xiao Ding
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , 44 West Culture Road, Jinan 250012, Shandong P.R. China
| | - Dirk Daelemans
- Rega Institute for Medical Research, KU Leuven , Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Erik De Clercq
- Rega Institute for Medical Research, KU Leuven , Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Christophe Pannecouque
- Rega Institute for Medical Research, KU Leuven , Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , 44 West Culture Road, Jinan 250012, Shandong P.R. 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, Jinan 250012, Shandong P.R. China
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22
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Meanwell NA. 2015 Philip S. Portoghese Medicinal Chemistry Lectureship. Curing Hepatitis C Virus Infection with Direct-Acting Antiviral Agents: The Arc of a Medicinal Chemistry Triumph. J Med Chem 2016; 59:7311-51. [PMID: 27501244 DOI: 10.1021/acs.jmedchem.6b00915] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The development of direct-acting antiviral agents that can cure a chronic hepatitis C virus (HCV) infection after 8-12 weeks of daily, well-tolerated therapy has revolutionized the treatment of this insidious disease. In this article, three of Bristol-Myers Squibb's HCV programs are summarized, each of which produced a clinical candidate: the NS3 protease inhibitor asunaprevir (64), marketed as Sunvepra, the NS5A replication complex inhibitor daclatasvir (117), marketed as Daklinza, and the allosteric NS5B polymerase inhibitor beclabuvir (142), which is in late stage clinical studies. A clinical study with 64 and 117 established for the first time that a chronic HCV infection could be cured by treatment with direct-acting antiviral agents alone in the absence of interferon. The development of small molecule HCV therapeutics, designed by medicinal chemists, has been hailed as "the arc of a medical triumph" but may equally well be described as "the arc of a medicinal chemistry triumph".
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Affiliation(s)
- Nicholas A Meanwell
- Department of Discovery Chemistry, Bristol-Myers Squibb Research & Development , Wallingford, Connecticut 06492, United States
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