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Research progress on the structure and biological diversities of 2-phenylindole derivatives in recent 20 years. Bioorg Chem 2023; 132:106342. [PMID: 36621157 DOI: 10.1016/j.bioorg.2023.106342] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/05/2022] [Accepted: 01/02/2023] [Indexed: 01/05/2023]
Abstract
The privileged structure binds to multiple receptors with high affinity, which is helpful to the development of new bioactive compounds. Indole is classified as a privileged structure, which may be one of the most important structural categories in drug discovery. As a special subset of indole compounds, 2-phenylindole seems to be one of most promising forerunners of drug development. In this paper, 106 articles were referenced to review the structural changes, biological activities and structure-activity relationship of compounds in recent 20 years, and classified them according to their pharmacological activities, from several aspects, including anticancer, antibacterial, anti-inflammatory, analgesic, antiviral, anti-parasite, the biological activities target to central nervous system, et al. It also points out the importance of artificial intelligence (AI) technology in discovery of new 2-phenylindole compounds in a broader prospect. This review will provide some ideas for researchers to develop new indole drugs.
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Huang M, Saragih M, Tambunan USF. In silico Antivirus Repurposing and its Modification to Organoselenium Compounds as SARS-CoV-2 Spike Inhibitors. Pak J Biol Sci 2023; 26:81-90. [PMID: 37265039 DOI: 10.3923/pjbs.2023.81.90] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
<b>Background and Objective:</b> The COVID-19, which has been circulating since late 2019, is caused by SARS-CoV-2. Because of its high infectivity, this virus has spread widely throughout the world. Spike glycoprotein is one of the proteins found in SARS-CoV-2. Spike glycoproteins directly affect infection by forming ACE-2 receptors on host cells. Inhibiting glycoprotein spikes could be one method of treating COVID-19. In this study, the antivirus marketed as a database will be repurposed into an antiviral SARS-CoV-2 and the selected compounds will be modified to become organoselenium compounds. <b>Materials and Methods:</b> The research was carried out using <i>in silico</i> methods, such as rigid docking and flexible docking. To obtain information about the interaction between spike glycoprotein and ligands, MOE 2014.09 was used to perform the molecular docking simulation. <b>Results:</b> The analysis of binding energy values was used to select the ten best ligands from the first stage of the molecular docking simulation, which was then modified according to the previous QSAR study to produce 96 new molecules. The second stage of molecular docking simulation was performed with modified molecules. The best-modified ligand was chosen by analyzing the ADME-Tox property, RMSD value and binding energy value. <b>Conclusion:</b> The best three unmodified ligands, Ombitasvir, Elbasvir and Ledipasvir, have a binding energy value of -15.8065, -15.3842 and -15.1255 kcal mol<sup>1</sup>, respectively and the best three modified ligands ModL1, ModL2 and ModL3 has a binding value of -15.6716, -13.9489 and -13.2951 kcal mol<sup>1</sup>, respectively with an RMSD value of 1.7109 Å, 2.3179 Å and 1.7836 Å.
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Qin Z, Yan A. QSAR studies on hepatitis C virus NS5A protein tetracyclic inhibitors in wild type and mutants by CoMFA and CoMSIA. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2020; 31:281-311. [PMID: 32208783 DOI: 10.1080/1062936x.2020.1740889] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/07/2020] [Indexed: 06/10/2023]
Abstract
Several 3D-QSAR models were built based on 196 hepatitis C virus (HCV) NS5A protein inhibitors. The bioactivity values EC90 for three types of inhibitors, the wild type (GT1a) and two mutants (GT1a Y93H and GT1a L31V), were collected to build three datasets. The programs OMEGA and ROCS were used for generating conformations and aligning molecules of the dataset, respectively. Each dataset was randomly divided into a training set and a test set three times to reduce the contingency of only one random selection. QSAR models were computed by comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). For the datasets GT1a, GT1a Y93H, and GT1a L31V, the best models CoMFA-INDX, CoMSIA-SEHA, and CoMSIA-SEHA showed an r2 value of 0.682 ± 0.033, 0.779 ± 0.036, and 0.782 ± 0.022 on the test sets, respectively. From the contour maps of the three best models, we summarized the favourable and unfavourable substituents on the tetracyclic core, the Z group, the proline group, and the valine group of inhibitors. We guessed the mutants could change the electrostatic surfaces of the wild type active pocket. In addition, we used ECFP analyses to find important substructures and could intuitively understand the results from QSAR models.
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Affiliation(s)
- Z Qin
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, PR China
| | - A Yan
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, PR China
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Yu W, Hu B, Zhong B, Hao J, Lei Z, Agrawal S, Rokosz L, Liu R, Chen S, Asante-Appiah E, Kozlowski JA. Discovery of novel pan-genotypic HCV NS5A inhibitors containing a novel tetracyclic core. Bioorg Med Chem Lett 2019; 29:700-706. [PMID: 30711390 DOI: 10.1016/j.bmcl.2019.01.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 01/06/2019] [Accepted: 01/24/2019] [Indexed: 11/16/2022]
Abstract
A series of novel tetracyclic core-containing HCV NS5A inhibitors has been discovered. Incorporation of tetrahydropyran-substituted amino acid moiety improved their potency and yielded HCV NS5A inhibitors with a minimum potency shift from the GT1a strain compared to other genotypes and mutants. Compounds 53 and 54 showed the best potency profile and had reasonable half-times in rat PK studies. However, further optimization of their oral bioavailability is still needed in order to advance them for further development. [BMCL ABSTRACT] ©2000 Elsevier Science Ltd. All rights reserved.
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Affiliation(s)
- Wensheng Yu
- Merck & Co., Inc, 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA.
| | - Bin Hu
- WuXi AppTec, 288 Fute Zhong Road, Shanghai 200131, China
| | - Bin Zhong
- WuXi AppTec, 288 Fute Zhong Road, Shanghai 200131, China
| | - Jinglai Hao
- WuXi AppTec, 288 Fute Zhong Road, Shanghai 200131, China
| | - Zhixin Lei
- WuXi AppTec, 288 Fute Zhong Road, Shanghai 200131, China
| | - Sony Agrawal
- Merck & Co., Inc, 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Laura Rokosz
- Merck & Co., Inc, 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Rong Liu
- Merck & Co., Inc, 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Shiying Chen
- Merck & Co., Inc, 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA
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Asante-Appiah E, Liu R, Curry S, McMonagle P, Agrawal S, Carr D, Rokosz L, Lahser F, Bystol K, Chase R, Black S, Ferrari E, Ingravallo P, Tong L, Yu W, Kozlowski J. In Vitro Antiviral Profile of Ruzasvir, a Potent and Pangenotype Inhibitor of Hepatitis C Virus NS5A. Antimicrob Agents Chemother 2018; 62:e01280-18. [PMID: 30150466 PMCID: PMC6201069 DOI: 10.1128/aac.01280-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 08/13/2018] [Indexed: 12/13/2022] Open
Abstract
Inhibition of NS5A has emerged as an attractive strategy to intervene in hepatitis C virus (HCV) replication. Ruzasvir (formerly MK-8408) was developed as a novel NS5A inhibitor to improve upon the potency and barrier to resistance of early compounds. Ruzasvir inhibited HCV RNA replication with 50% effective concentrations (EC50s) of 1 to 4 pM in Huh7 or Huh7.5 cells bearing replicons for HCV genotype 1 (GT1) to GT7. The antiviral activity was modestly (10-fold) reduced in the presence of 40% normal human serum. The picomolar potency in replicon cells extended to sequences of clinical isolates available in public databases that were synthesized and tested as replicons. In GT1a, ruzasvir inhibited common NS5A resistance-associated substitutions (RASs), with the exception of M28G. De novo resistance selection studies identified pathways with certain amino acid substitutions at residues 28, 30, 31, and 93 across genotypes. Substitutions at position 93 were more common in GT1 to -4, while changes at position 31 emerged frequently in GT5 and -6. With the exception of GT4, the reintroduction of selected RASs conferred a ≥100-fold potency reduction in the antiviral activity of ruzasvir. Common RASs from other classes of direct-acting antiviral agents (DAAs) did not confer cross-resistance to ruzasvir. The interaction of ruzasvir with an NS3/4A protease inhibitor (grazoprevir) and an NS5B polymerase prodrug (uprifosbuvir) was additive to synergistic, with no evidence of antagonism or cytotoxicity. The antiviral profile of ruzasvir supported its further evaluation in human trials in combination with grazoprevir and uprifosbuvir.
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Affiliation(s)
- Ernest Asante-Appiah
- Department of Infectious Diseases, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Rong Liu
- Department of Infectious Diseases, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Stephanie Curry
- Department of Infectious Diseases, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Patricia McMonagle
- Department of Infectious Diseases, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Sony Agrawal
- Department of In Vitro Pharmacology, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Donna Carr
- Department of In Vitro Pharmacology, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Laura Rokosz
- Department of In Vitro Pharmacology, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Frederick Lahser
- Department of Infectious Diseases, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Karin Bystol
- Department of Infectious Diseases, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Robert Chase
- Department of Infectious Diseases, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Stuart Black
- Department of Infectious Diseases, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Eric Ferrari
- Department of Infectious Diseases, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Paul Ingravallo
- Department of Infectious Diseases, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Ling Tong
- Department of Medicinal Chemistry, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Wensheng Yu
- Department of Medicinal Chemistry, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Joseph Kozlowski
- Department of Medicinal Chemistry, Merck & Co., Inc., Kenilworth, New Jersey, USA
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Grande F, Occhiuzzi MA, Ioele G, Ragno G, Garofalo A. Benzopyrroloxazines containing a bridgehead nitrogen atom as promising scaffolds for the achievement of biologically active agents. Eur J Med Chem 2018; 151:121-144. [DOI: 10.1016/j.ejmech.2018.03.061] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/09/2018] [Accepted: 03/20/2018] [Indexed: 12/28/2022]
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Yu W, Tong L, Selyutin O, Chen L, Hu B, Zhong B, Hao J, Ji T, Zan S, Yin J, Ruck RT, Curry S, McMonagle P, Agrawal S, Rokosz L, Carr D, Ingravallo P, Bystol K, Lahser F, Liu R, Chen S, Feng KI, Cartwright M, Asante-Appiah E, Kozlowski JA. Discovery of MK-6169, a Potent Pan-Genotype Hepatitis C Virus NS5A Inhibitor with Optimized Activity against Common Resistance-Associated Substitutions. J Med Chem 2018; 61:3984-4003. [PMID: 29681153 DOI: 10.1021/acs.jmedchem.7b01927] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We describe the discovery of MK-6169, a potent and pan-genotype hepatitis C virus NS5A inhibitor with optimized activity against common resistance-associated substitutions. SAR studies around the combination of changes to both the valine and aminal carbon region of elbasvir led to the discovery of a series of compounds with substantially improved potency against common resistance-associated substitutions in the major genotypes, as well as good pharmacokinetics in both rat and dog. Through further optimization of key leads from this effort, MK-6169 (21) was discovered as a preclinical candidate for further development.
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Affiliation(s)
| | | | | | | | - Bin Hu
- WuXi AppTec , 288 Fute Zhong Road , Shanghai 200131 , China
| | - Bin Zhong
- WuXi AppTec , 288 Fute Zhong Road , Shanghai 200131 , China
| | - Jinglai Hao
- WuXi AppTec , 288 Fute Zhong Road , Shanghai 200131 , China
| | - Tao Ji
- WuXi AppTec , 288 Fute Zhong Road , Shanghai 200131 , China
| | - Shuai Zan
- WuXi AppTec , 288 Fute Zhong Road , Shanghai 200131 , China
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Tong L, Yu W, Chen L, Selyutin O, Dwyer MP, Nair AG, Mazzola R, Kim JH, Sha D, Yin J, Ruck RT, Davies IW, Hu B, Zhong B, Hao J, Ji T, Zan S, Liu R, Agrawal S, Xia E, Curry S, McMonagle P, Bystol K, Lahser F, Carr D, Rokosz L, Ingravallo P, Chen S, Feng KI, Cartwright M, Asante-Appiah E, Kozlowski JA. Discovery of Ruzasvir (MK-8408): A Potent, Pan-Genotype HCV NS5A Inhibitor with Optimized Activity against Common Resistance-Associated Polymorphisms. J Med Chem 2016; 60:290-306. [PMID: 27808515 DOI: 10.1021/acs.jmedchem.6b01310] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We describe the research that led to the discovery of compound 40 (ruzasvir, MK-8408), a pan-genotypic HCV nonstructural protein 5A (NS5A) inhibitor with a "flat" GT1 mutant profile. This NS5A inhibitor contains a unique tetracyclic indole core while maintaining the imidazole-proline-valine Moc motifs of our previous NS5A inhibitors. Compound 40 is currently in early clinical trials and is under evaluation as part of an all-oral DAA regimen for the treatment of chronic HCV infection.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Bin Hu
- Department of Medicinal Chemistry, WuXi AppTec , Shanghai, 200131, China
| | - Bin Zhong
- Department of Medicinal Chemistry, WuXi AppTec , Shanghai, 200131, China
| | - Jinglai Hao
- Department of Medicinal Chemistry, WuXi AppTec , Shanghai, 200131, China
| | - Tao Ji
- Department of Medicinal Chemistry, WuXi AppTec , Shanghai, 200131, China
| | - Shuai Zan
- Department of Medicinal Chemistry, WuXi AppTec , Shanghai, 200131, China
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Yu W, Tong L, Hu B, Zhong B, Hao J, Ji T, Zan S, Coburn CA, Selyutin O, Chen L, Rokosz L, Agrawal S, Liu R, Curry S, McMonagle P, Ingravallo P, Asante-Appiah E, Chen S, Kozlowski JA. Discovery of Chromane Containing Hepatitis C Virus (HCV) NS5A Inhibitors with Improved Potency against Resistance-Associated Variants. J Med Chem 2016; 59:10228-10243. [PMID: 27792320 DOI: 10.1021/acs.jmedchem.6b01234] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The discovery of potent and pan-genotypic HCV NS5A inhibitors faces many challenges including the significant diversity among genotypes, substantial potency shift conferred on some key resistance-associated variants, inconsistent SARs between different genotypes and mutants, and the lacking of models of inhibitor/protein complexes for rational inhibitor design. As part of ongoing efforts on HCV NS5A inhibition at Merck, we now describe the discovery of a novel series of chromane containing NS5A inhibitors. SAR studies around the "Z" group of the tetracyclic indole scaffold explored fused bicyclic rings as alternates to the phenyl group of elbasvir (1, MK-8742) and identified novel chromane and 2,3-dihydrobenzofuran derivatives as "Z" group replacements offered good potency across all genotypes. This effort, incorporating the C-1 fluoro substitution at the tetracyclic indole core, led to the discovery of a new series of NS5A inhibitors, such as compounds 14 and 25-28, with significantly improved potency against resistance-associated variants, such as GT2b, GT1a Y93H, and GT1a L31V. Compound 14 also showed reasonable PK exposures in preclinical species (rat and dog).
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Affiliation(s)
- Wensheng Yu
- Department of Medicinal Chemistry, Merck Research Laboratories , 126 East Lincoln Avenue, Rahway New Jersey 07065, United States
| | - Ling Tong
- Department of Medicinal Chemistry, Merck Research Laboratories , 126 East Lincoln Avenue, Rahway New Jersey 07065, United States
| | - Bin Hu
- WuXi AppTec , 288 Fute Zhong Road, Shanghai, 200131, China
| | - Bin Zhong
- WuXi AppTec , 288 Fute Zhong Road, Shanghai, 200131, China
| | - Jinglai Hao
- WuXi AppTec , 288 Fute Zhong Road, Shanghai, 200131, China
| | - Tao Ji
- WuXi AppTec , 288 Fute Zhong Road, Shanghai, 200131, China
| | - Shuai Zan
- WuXi AppTec , 288 Fute Zhong Road, Shanghai, 200131, China
| | - Craig A Coburn
- Department of Medicinal Chemistry, Merck Research Laboratories , 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
| | - Oleg Selyutin
- Department of Medicinal Chemistry, Merck Research Laboratories , 126 East Lincoln Avenue, Rahway New Jersey 07065, United States
| | - Lei Chen
- Department of Medicinal Chemistry, Merck Research Laboratories , 126 East Lincoln Avenue, Rahway New Jersey 07065, United States
| | - Laura Rokosz
- Department of in Vitro Pharmacology, Merck Research Laboratories , 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Sony Agrawal
- Department of in Vitro Pharmacology, Merck Research Laboratories , 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Rong Liu
- Department of Infectious Diseases, Merck Research Laboratories , 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Stephanie Curry
- Department of Infectious Diseases, Merck Research Laboratories , 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Patricia McMonagle
- Department of Infectious Diseases, Merck Research Laboratories , 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Paul Ingravallo
- Department of Infectious Diseases, Merck Research Laboratories , 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Ernest Asante-Appiah
- Department of Infectious Diseases, Merck Research Laboratories , 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Shiying Chen
- Department of PPDM, Merck Research Laboratories , 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Joseph A Kozlowski
- Department of Medicinal Chemistry, Merck Research Laboratories , 126 East Lincoln Avenue, Rahway New Jersey 07065, United States
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