1
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Luo ML, Zhao Q, He XH, Xie X, Zhu HP, You FM, Peng C, Zhan G, Huang W. Research progress of indole-fused derivatives as allosteric modulators: Opportunities for drug development. Biomed Pharmacother 2023; 162:114574. [PMID: 36996677 DOI: 10.1016/j.biopha.2023.114574] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/12/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
Allosteric modulation is a direct and effective method for regulating the function of biological macromolecules, which play vital roles in various cellular activities. Unlike orthosteric modulators, allosteric modulators bind to sites distant from the protein's orthosteric/active site and can have specific effects on the protein's function or activity without competing with endogenous ligands. Compared to traditional orthosteric modulators, allosteric modulators offer several advantages, including reduced side effects, greater specificity, and lower toxicity, making them a promising strategy for developing novel drugs. Indole-fused architectures are widely distributed in natural products and bioactive drug leads, displaying diverse biological activities that attract the interest of both chemists and biologists in drug discovery. Currently, an increasing number of indole-fused compounds have exhibited potent activities in allosteric modulation. In this review, we provide a brief summary of examples of allosteric modulators based on the indole-fused complex architecture, highlighting the strategies for drug design/discovery and the structure-activity relationships of allosteric modulators from the perspective of medicinal chemistry.
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2
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Ouvry G. Recent applications of seven-membered rings in drug design. Bioorg Med Chem 2022; 57:116650. [PMID: 35123178 DOI: 10.1016/j.bmc.2022.116650] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 01/28/2023]
Abstract
This short review aims at highlighting recent design strategies hinged on using seven-membered rings. Analyses of the different selected examples coupled with torsion profiles derived from the CCDC suggest some of these strategies could have broad applications.
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Affiliation(s)
- Gilles Ouvry
- Evotec (U.K.) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, UK
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3
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Pan G, Lu L, Zhuang W, Huang Q. Synthesis of Indole-Fused Six-, Seven-, or Eight-Membered N,O-Heterocycles via Rhodium-Catalyzed NH-Indole-Directed C-H Acetoxylation/Hydrolysis/Annulation. J Org Chem 2021; 86:16753-16763. [PMID: 34756052 DOI: 10.1021/acs.joc.1c01982] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We report herein the facile synthesis of indole-fused six-, seven-, or eight-membered N,O-heterocycles through rhodium-catalyzed C-H acetoxylation/hydrolysis/annulation. The notable features of this method include C-H acetoxylation using NH-indole as the intrinsic directing group, high functional group compatibility, and construction of indole-fused medium-sized rings.
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Affiliation(s)
- Guoshuai Pan
- Fujian Key Laboratory of Polymer Materials, College of Chemistry & Materials Science, Fujian Normal University, Fuzhou, Fujian 350007, P. R. China
| | - Leipeng Lu
- Fujian Key Laboratory of Polymer Materials, College of Chemistry & Materials Science, Fujian Normal University, Fuzhou, Fujian 350007, P. R. China
| | - Weihui Zhuang
- Fujian Key Laboratory of Polymer Materials, College of Chemistry & Materials Science, Fujian Normal University, Fuzhou, Fujian 350007, P. R. China
| | - Qiufeng Huang
- Fujian Key Laboratory of Polymer Materials, College of Chemistry & Materials Science, Fujian Normal University, Fuzhou, Fujian 350007, P. R. China.,Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fuzhou, Fujian 35007, P.R. China
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4
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Kazmierski WM, Miriyala N, Johnson DK, Baskaran S. The Discovery of Conformationally Constrained Bicyclic Peptidomimetics as Potent Hepatitis C NS5A Inhibitors. ACS Med Chem Lett 2021; 12:1649-1655. [PMID: 34790290 PMCID: PMC8591741 DOI: 10.1021/acsmedchemlett.1c00391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Indexed: 01/03/2023] Open
Abstract
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HCV NS5A inhibitors are the backbone
of directly acting antiviral
treatments against the hepatitis C virus (HCV). While these therapies
are generally highly curative, they are less effective in some specific
HCV patient populations. In the search for broader-acting HCV NS5A
inhibitors that address these needs, we explored conformational restrictions
imposed by the [7,5]-azabicyclic lactam moiety incorporated into daclatasvir
(1) and related HCV NS5A inhibitors. Unexpectedly, compound 5 was identified as a potent HCV genotype 1a and 1b inhibitor.
Molecular modeling of 5 bound to HCV genotype 1a suggested
that the use of the conformationally restricted lactam moiety might
have resulted in reorientation of its N-terminal carbamate to expose
a new interaction with the NS5A pocket located between amino acids
P97 and Y93, which was not easily accessible to 1. The
results also suggest new chemistry directions that exploit the interactions
with the P97–Y93 site toward new and potentially improved HCV
NS5A inhibitors.
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Affiliation(s)
- Wieslaw M. Kazmierski
- GlaxoSmithKline, 5 Moore Drive, Research Triangle Park, North Carolina 27709-3398, United States
| | - Nagaraju Miriyala
- GlaxoSmithKline, 5 Moore Drive, Research Triangle Park, North Carolina 27709-3398, United States
| | - David K. Johnson
- Computational Chemical Biology Core and Molecular Graphics and Modeling Laboratory, University of Kansas, Lawrence, Kansas 66047, United States
| | - Sam Baskaran
- GlaxoSmithKline, 5 Moore Drive, Research Triangle Park, North Carolina 27709-3398, United States
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5
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Zhao Y, Li S, Fan Y, Guo X, Jiao X, Tian L, Sun X. Synthesis of 10
H
‐Indolo[1,2‐
a
]indole Derivatives
via
Intramolecular Cycloaddition and H‐Migration. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yulei Zhao
- School of Chemistry and Chemical Engineering Qufu Normal University Jining Shi, Qufu 273165 China
| | - Shuai Li
- School of Chemistry and Chemical Engineering Qufu Normal University Jining Shi, Qufu 273165 China
| | - Yuhang Fan
- School of Chemistry and Chemical Engineering Qufu Normal University Jining Shi, Qufu 273165 China
| | - Xuqiang Guo
- School of Chemistry and Chemical Engineering Qufu Normal University Jining Shi, Qufu 273165 China
| | - Xin Jiao
- School of Chemistry and Chemical Engineering Qufu Normal University Jining Shi, Qufu 273165 China
| | - Laijin Tian
- School of Chemistry and Chemical Engineering Qufu Normal University Jining Shi, Qufu 273165 China
| | - Xuejun Sun
- School of Chemistry and Chemical Engineering Qufu Normal University Jining Shi, Qufu 273165 China
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6
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Fukuda T, Anzai M, Nakahara A, Yamashita K, Matsukura K, Ishibashi F, Oku Y, Nishiya N, Uehara Y, Iwao M. Synthesis and evaluation of azalamellarin N and its A-ring-modified analogues as non-covalent inhibitors of the EGFR T790M/L858R mutant. Bioorg Med Chem 2021; 34:116039. [PMID: 33556869 DOI: 10.1016/j.bmc.2021.116039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 01/17/2021] [Accepted: 01/19/2021] [Indexed: 11/17/2022]
Abstract
Azalamellarin N, a synthetic lactam congener of the marine natural product lamellarin N, and its A-ring-modified analogues were synthesized and evaluated as potent and non-covalent inhibitors of the drug-resistant epidermal growth factor receptor T790M/L858R mutant. An in vitro tyrosine kinase assay indicated that the inhibitory activities of the synthetic azalamellarin analogues were higher than those of the corresponding lamellarins. The azalamellarin analogue bearing two 3-(dimethylamino)propoxy groups at C20- and C21-positions exhibited the highest activity and selectivity against the mutant kinase [IC50 (T790M/L858R) = 1.7 nM; IC50 (WT) = 4.6 nM]. The inhibitory activity was attributed to the hydrogen bonding interaction between the lactam NH group of the B-ring and carbonyl group of a methionine residue.
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Affiliation(s)
- Tsutomu Fukuda
- Environmental Protection Center, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan.
| | - Mizuho Anzai
- Division of Chemistry and Materials Science, Graduate School of Engineering, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Akane Nakahara
- Division of Chemistry and Materials Science, Graduate School of Engineering, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Kentaro Yamashita
- Division of Chemistry and Materials Science, Graduate School of Engineering, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Kazuaki Matsukura
- Division of Marine Life Science and Biochemistry, Graduate School of Fisheries and Environmental Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Fumito Ishibashi
- Division of Marine Life Science and Biochemistry, Graduate School of Fisheries and Environmental Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Yusuke Oku
- Department of Integrated Information for Pharmaceutical Sciences, Iwate Medical University School of Pharmacy, 1-1-1 Idaidori, Yahaba-cho, Shiwa-gun, Iwate 028-3694, Japan
| | - Naoyuki Nishiya
- Department of Integrated Information for Pharmaceutical Sciences, Iwate Medical University School of Pharmacy, 1-1-1 Idaidori, Yahaba-cho, Shiwa-gun, Iwate 028-3694, Japan
| | - Yoshimasa Uehara
- Department of Integrated Information for Pharmaceutical Sciences, Iwate Medical University School of Pharmacy, 1-1-1 Idaidori, Yahaba-cho, Shiwa-gun, Iwate 028-3694, Japan
| | - Masatomo Iwao
- Division of Chemistry and Materials Science, Graduate School of Engineering, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
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7
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Iioka R, Yorozu K, Sakai Y, Kawai R, Hatae N, Takashima K, Tanabe G, Wasada H, Yoshimatsu M. Synthesis of Azepino[1,2‐
a
]indole‐10‐amines via [6+1] Annulation of Ynenitriles with Reformatsky Reagent. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Ryoya Iioka
- Department of Chemistry Faculty of Education Gifu University Yanagido 1–1 501-1193 Gifu Japan
| | - Kohei Yorozu
- Department of Chemistry Faculty of Education Gifu University Yanagido 1–1 501-1193 Gifu Japan
| | - Yoko Sakai
- Department of Chemistry Faculty of Education Gifu University Yanagido 1–1 501-1193 Gifu Japan
| | - Rika Kawai
- Department of Chemistry Faculty of Education Gifu University Yanagido 1–1 501-1193 Gifu Japan
| | - Noriyuki Hatae
- Faculty of Pharmaceutical Sciences Yokohama University of Pharmacy 601 Matano, Totsuka-ku 245-0066 Yokohama Kanagawa Japan
| | - Katsuki Takashima
- Faculty of Pharmacy Kinki University 3-4-1 Kowakae 577-8502 Higashi-osaka Osaka Japan
| | - Genzoh Tanabe
- Faculty of Pharmacy Kinki University 3-4-1 Kowakae 577-8502 Higashi-osaka Osaka Japan
| | - Hiroaki Wasada
- Department of Chemistry Faculty of Regional Study Gifu University Yanagido 1–1 501-1193 Gifu Japan
| | - Mitsuhiro Yoshimatsu
- Department of Chemistry Faculty of Education Gifu University Yanagido 1–1 501-1193 Gifu Japan
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8
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Ohuchi S, Koyama H, Shigehisa H. Catalytic Synthesis of Cyclic Guanidines via Hydrogen Atom Transfer and Radical-Polar Crossover. ACS Catal 2021. [DOI: 10.1021/acscatal.0c05359] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Shunya Ohuchi
- Faculty of Pharmacy, Musashino University, 1-1-20 Shinmachi, Nishitokyo-shi, Tokyo 202-8585, Japan
| | - Hiroki Koyama
- Faculty of Pharmacy, Musashino University, 1-1-20 Shinmachi, Nishitokyo-shi, Tokyo 202-8585, Japan
| | - Hiroki Shigehisa
- Faculty of Pharmacy, Musashino University, 1-1-20 Shinmachi, Nishitokyo-shi, Tokyo 202-8585, Japan
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9
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Qin Y, Zhuang W, Guo X, Zhang X, Huang Q. Rhodium-catalyzed direct C H amination of 2-arylindoles and 7-arylindoles with free amines. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2020.152686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Khalid H, Landry KB, Ijaz B, Ashfaq UA, Ahmed M, Kanwal A, Froeyen M, Mirza MU. Discovery of novel Hepatitis C virus inhibitor targeting multiple allosteric sites of NS5B polymerase. INFECTION GENETICS AND EVOLUTION 2020; 84:104371. [PMID: 32485331 DOI: 10.1016/j.meegid.2020.104371] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 05/13/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023]
Abstract
HCV is a viral infection posing a severe global threat when left untreated progress to end-stage liver disease, including cirrhosis and HCC. The NS5B polymerase of HCV is the most potent target that harbors four allosteric binding sites that could interfere with the HCV infection. We present the discovery of a novel synthetic compound that harbors the potential of NS5B polymerase inhibition. All eight compounds belonging to the benzothiazine family of heterocycles displayed no cellular cytotoxicity in HepG2 cells at nontoxic dose concentration (200 μM). Subsequently, among eight compounds of the series, merely compound 5b exhibited significant inhibition of the expression of the HCV NS5B gene as compared to DMSO control in semi-quantitative PCR. Based on our western blot result, 5b at the range of 50, 100 and 200 μM induced 20, 40, and 70% inhibition of NS5B protein respectively. To estimate the binding potential, 5b was docked at respective allosteric sites followed by molecular dynamics (MD) simulations for a period of 20 ns. In addition, binding free energy calculation by MM-GB/PBSA method revealed a conserved interaction profile of residues lining the allosteric sites in agreement with the reported NS5B co-crystallized inhibitors. The presented results provide important information about a novel compound 5b which may facilitate the the discovery of novel inhibitors that tends to target multiple sites on NS5B polymerase.
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Affiliation(s)
- Hina Khalid
- Department of Bioinformatics and Biotechnology, Government College University, 38000 Faisalabad, Pakistan
| | - Koloko Brice Landry
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Bushra Ijaz
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University, 38000 Faisalabad, Pakistan.
| | - Matloob Ahmed
- Department of Chemistry, Government College University, 38000 Faisalabad, Pakistan
| | - Afshan Kanwal
- Department of Chemistry, Government College University, 38000 Faisalabad, Pakistan
| | - Matheus Froeyen
- Department of Pharmaceutical Sciences, REGA Institute for Medical Research, Medicinal Chemistry, University of Leuven, 3000 Leuven, Belgium
| | - Muhammad Usman Mirza
- Department of Pharmaceutical Sciences, REGA Institute for Medical Research, Medicinal Chemistry, University of Leuven, 3000 Leuven, Belgium
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11
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Malik AA, Phanus-Umporn C, Schaduangrat N, Shoombuatong W, Isarankura-Na-Ayudhya C, Nantasenamat C. HCVpred: A web server for predicting the bioactivity of hepatitis C virus NS5B inhibitors. J Comput Chem 2020; 41:1820-1834. [PMID: 32449536 DOI: 10.1002/jcc.26223] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/10/2020] [Accepted: 04/28/2020] [Indexed: 02/06/2023]
Abstract
Hepatitis C virus (HCV) is one of the major causes of liver disease affecting an estimated 170 million people culminating in 300,000 deaths from cirrhosis or liver cancer. NS5B is one of three potential therapeutic targets against HCV (i.e., the other two being NS3/4A and NS5A) that is central to viral replication. In this study, we developed a classification structure-activity relationship (CSAR) model for identifying substructures giving rise to anti-HCV activities among a set of 578 non-redundant compounds. NS5B inhibitors were described by a set of 12 fingerprint descriptors and predictive models were constructed from 100 independent data splits using the random forest algorithm. The modelability (MODI index) of the data set was determined to be robust with a value of 0.88 exceeding established threshold of 0.65. The predictive performance was deduced by the accuracy, sensitivity, specificity, and Matthews correlation coefficient, which was found to be statistically robust (i.e., the former three parameters afforded values in excess of 0.8 while the latter statistical parameter provided a value >0.7). An in-depth analysis of the top 20 important descriptors revealed that aromatic ring and alkyl side chains are important for NS5B inhibition. Finally, the predictive model is deployed as a publicly accessible HCVpred web server (available at http://codes.bio/hcvpred/) that would allow users to predict the biological activity as being active or inactive against HCV NS5B. Thus, the knowledge and web server presented herein can be used in the design of more potent and specific drugs against the HCV NS5B.
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Affiliation(s)
- Aijaz Ahmad Malik
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Chuleeporn Phanus-Umporn
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Nalini Schaduangrat
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Watshara Shoombuatong
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | | | - Chanin Nantasenamat
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
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12
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Hu W, Teng F, Hu H, Luo S, Zhu Q. Pd-Catalyzed C(sp 2)-H Imidoylative Annulation: A General Approach To Construct Dibenzoox(di)azepines. J Org Chem 2019; 84:6524-6535. [PMID: 31050283 DOI: 10.1021/acs.joc.9b00683] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A general method to construct the scaffolds of dibenzooxazepine and dibenzodiazepine, through Pd-catalyzed isocyanide insertion and intramolecular C(sp2)-H activation, has been developed. This is the first example of seven-membered heterocycle formation by C-H imidoylative annulation.
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Affiliation(s)
- Weiming Hu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health , Chinese Academy of Sciences , 190 Kaiyuan Avenue , Guangzhou 510530 , China.,University of Chinese Academy of Sciences, No. 19(A) Yuquan Road , Shijingshan District, Beijing 100049 , China
| | - Fan Teng
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health , Chinese Academy of Sciences , 190 Kaiyuan Avenue , Guangzhou 510530 , China.,University of Chinese Academy of Sciences, No. 19(A) Yuquan Road , Shijingshan District, Beijing 100049 , China
| | - Huaanzi Hu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health , Chinese Academy of Sciences , 190 Kaiyuan Avenue , Guangzhou 510530 , China.,University of Chinese Academy of Sciences, No. 19(A) Yuquan Road , Shijingshan District, Beijing 100049 , China
| | - Shuang Luo
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health , Chinese Academy of Sciences , 190 Kaiyuan Avenue , Guangzhou 510530 , China.,University of Chinese Academy of Sciences, No. 19(A) Yuquan Road , Shijingshan District, Beijing 100049 , China
| | - Qiang Zhu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health , Chinese Academy of Sciences , 190 Kaiyuan Avenue , Guangzhou 510530 , China.,University of Chinese Academy of Sciences, No. 19(A) Yuquan Road , Shijingshan District, Beijing 100049 , China
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13
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Polamreddy P, Vishwakarma V, Arumugam P, Bheemanati R, Esram P, Mahto MK, Kacker P. Discovery of hit molecules targeting allosteric site of hepatitis C virus NS5B polymerase. J Biomol Struct Dyn 2019; 38:1448-1466. [PMID: 31007134 DOI: 10.1080/07391102.2019.1608864] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Nonstructural protein 5B (NS5B), the RNA-dependent RNA polymerase of Hepatitis C Virus (HCV), plays a key role in viral amplification and is an attractive and most explored target for discovery of new therapeutic agents for Hepatitis C. Though safe and effective, NS5B inhibitors were launched in 2013 (Sovaldi) and 2014 (Harvoni, Viekira Pak), the high price tags of these medications limit their use among poor people in developing countries. Hence, still there exists a need for cost-effective and short duration anti-HCV agents especially those targeting niche patient population who were non-respondent to earlier therapies or with comorbid conditions. The present study describes the discovery of novel non-nucleoside (NNI) inhibitors of NS5B using a series of rational drug design techniques such as virtual screening, scaffold matching and molecular docking. 2D and 3D structure based virtual screening technique identified 300 hit compounds. Top 20 hits were screened out from identified hits using molecular docking technique. Four molecules, that are representative of 20 hits were evaluated for binding affinity under in vitro conditions using surface plasmon resonance-based assay and the results emphasized that compound with CoCoCo ID: 412075 could exhibit good binding response toward NS5B and could be a potential candidate as NS5B inhibitor.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Prasanthi Polamreddy
- Centre for Nanoscience and Nanotechnology, Sathyabama Institute of Science and Technology, Chennai, India.,Excelra Knowledge Solutions Pvt Ltd, Hyderabad, India
| | - Vinita Vishwakarma
- Centre for Nanoscience and Nanotechnology, Sathyabama Institute of Science and Technology, Chennai, India
| | | | | | | | | | - Puneet Kacker
- Excelra Knowledge Solutions Pvt Ltd, Hyderabad, India
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14
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Wang Z, Chen Z, Li J, Huang J, Zheng C, Liu JP. Combined 3D-QSAR, molecular docking and molecular dynamics study on the benzimidazole inhibitors targeting HCV NS5B polymerase. J Biomol Struct Dyn 2019; 38:1071-1082. [PMID: 30915896 DOI: 10.1080/07391102.2019.1593244] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The hepatitis C virus (HCV)-infected population has continued to grow during recent years, and novel HCV antiviral agents are urgently needed. In this work, a combined theoretical study was performed on the HCV non-structural 5B (NS5B) polymerase and 53 benzimidazole inhibitors. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were carried out with ligand-based and receptor-based alignments. Ligand-based QSAR models (cross-validated q2 of 0.918 for CoMFA and 0.825 for CoMSIA) were found to be superior to receptor-based approaches (cross-validated q2 of 0.765 for CoMFA and 0.740 for CoMSIA). Based on the most predictive CoMFA and CoMSIA models, the structural features that were essential for the inhibitory activity of benzimidazoles were characterized. A molecular dynamics study revealed that the induced fit effect between NS5B and its substrate may be responsible for the inferiority of the receptor-based CoMFA and CoMSIA models. The binding-free energy calculated using the MM/PBSA method correlated well with the experimental results and revealed that the van der Waals and electrostatic interactions most contributed to the binding. In addition, energetically favorable NS5B residues were identified by the per-residue decomposition of binding-free energy. The results presented in this work provide meaningful information for the design of novel benzimidazole inhibitors targeting the NS5B polymerase.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zhiguo Wang
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Zhenming Chen
- Laboratory of Biocatalysis, College of Life & Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Jianfeng Li
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Jing Huang
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Chenni Zheng
- Laboratory of Biocatalysis, College of Life & Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Jun-Ping Liu
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China.,Department of Immunology, Central Eastern Clinical School, Monash University, Melbourne, Vitoria, Australia.,Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
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15
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Cummings MD, Sekharan S. Structure-Based Macrocycle Design in Small-Molecule Drug Discovery and Simple Metrics To Identify Opportunities for Macrocyclization of Small-Molecule Ligands. J Med Chem 2019; 62:6843-6853. [DOI: 10.1021/acs.jmedchem.8b01985] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Maxwell D. Cummings
- Janssen Research and Development, LLC, Welsh and McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Sivakumar Sekharan
- Cambridge Crystallographic Data Centre, 252 Nassau Street, Princeton, New Jersey 08542, United States
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16
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Dreger A, Kharwb O, Agoglitta O, Bülbül EF, Melesina J, Sippl W, Holl R. Chiral Pool Synthesis, Biological Evaluation and Molecular Docking Studies ofC‐Furanosidic LpxC Inhibitors. ChemMedChem 2019; 14:871-886. [DOI: 10.1002/cmdc.201900068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Indexed: 01/15/2023]
Affiliation(s)
- Alexander Dreger
- Department of Chemistry, Institute of Organic ChemistryUniversity of Hamburg Martin-Luther-King Platz 6 20146 Hamburg Germany
- German Center for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems Germany
| | - Omar Kharwb
- Institute of Pharmaceutical and Medicinal ChemistryUniversity of Münster Corrensstr. 48 48149 Münster Germany
| | - Oriana Agoglitta
- Department of Chemistry, Institute of Organic ChemistryUniversity of Hamburg Martin-Luther-King Platz 6 20146 Hamburg Germany
- German Center for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems Germany
- NRW Graduate School of ChemistryUniversity of Münster Germany
| | - Emre F. Bülbül
- Institute of PharmacyMartin Luther University of Halle-Wittenberg Wolfgang-Langenbeck Str. 4 06120 Halle/Saale Germany
| | - Jelena Melesina
- Institute of PharmacyMartin Luther University of Halle-Wittenberg Wolfgang-Langenbeck Str. 4 06120 Halle/Saale Germany
| | - Wolfgang Sippl
- Institute of PharmacyMartin Luther University of Halle-Wittenberg Wolfgang-Langenbeck Str. 4 06120 Halle/Saale Germany
| | - Ralph Holl
- Department of Chemistry, Institute of Organic ChemistryUniversity of Hamburg Martin-Luther-King Platz 6 20146 Hamburg Germany
- German Center for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems Germany
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17
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Alam K, Kim JG, Kang DY, Park JK. Regiodivergent Trifluoromethanesulfonic Acid‐Promoted Cycloisomerizations of Ynenamines to Fused Indoles. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201801506] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Khyarul Alam
- The Department of Chemistry and Chemistry Institute of Functional MaterialsPusan National University Busan 46241 Korea
| | - Jin Gyeong Kim
- The Department of Chemistry and Chemistry Institute of Functional MaterialsPusan National University Busan 46241 Korea
| | - Dong Yun Kang
- The Department of Chemistry and Chemistry Institute of Functional MaterialsPusan National University Busan 46241 Korea
| | - Jin Kyoon Park
- The Department of Chemistry and Chemistry Institute of Functional MaterialsPusan National University Busan 46241 Korea
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18
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Shan XH, Yang B, Zheng HX, Qu JP, Kang YB. Phenanthroline-tBuOK Promoted Intramolecular C–H Arylation of Indoles with ArI under Transition-Metal-Free Conditions. Org Lett 2018; 20:7898-7901. [DOI: 10.1021/acs.orglett.8b03449] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Xiang-Huan Shan
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Bo Yang
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Hong-Xing Zheng
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jian-Ping Qu
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, China
| | - Yan-Biao Kang
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
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19
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Virelli M, Moroni E, Colombo G, Fiengo L, Porta A, Ackermann L, Zanoni G. Expedient Access to 2-Benzazepines by Palladium-Catalyzed C−H Activation: Identification of a Unique Hsp90 Inhibitor Scaffold. Chemistry 2018; 24:16516-16520. [DOI: 10.1002/chem.201804244] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Matteo Virelli
- Department of Chemistry; University of Pavia; Viale Taramelli 10 27100 Pavia Italy
| | | | - Giorgio Colombo
- Department of Chemistry; University of Pavia; Viale Taramelli 10 27100 Pavia Italy
- Istituto di Chimica del Riconoscimento Molecolare; CNR; Via Mario Bianco 9 20131 Milano Italy
| | - Lorenzo Fiengo
- Department of Pharmacy; University of Salerno; Via Giovanni Paolo II, 132 84084 Fisciano Italy
| | - Alessio Porta
- Department of Chemistry; University of Pavia; Viale Taramelli 10 27100 Pavia Italy
| | - Lutz Ackermann
- Department of Chemistry; University of Pavia; Viale Taramelli 10 27100 Pavia Italy
- Institut für Organische und Biomolekulare Chemie; Georg-August-Universität Göttingen; Tammannstraße 2 37077 Göttingen Germany
| | - Giuseppe Zanoni
- Department of Chemistry; University of Pavia; Viale Taramelli 10 27100 Pavia Italy
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20
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Bien J, Davulcu A, DelMonte AJ, Fraunhoffer KJ, Gao Z, Hang C, Hsiao Y, Hu W, Katipally K, Littke A, Pedro A, Qiu Y, Sandoval M, Schild R, Soltani M, Tedesco A, Vanyo D, Vemishetti P, Waltermire RE. The First Kilogram Synthesis of Beclabuvir, an HCV NS5B Polymerase Inhibitor. Org Process Res Dev 2018. [DOI: 10.1021/acs.oprd.8b00214] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Jeffrey Bien
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Akin Davulcu
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Albert J. DelMonte
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Kenneth J. Fraunhoffer
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Zhinong Gao
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Chao Hang
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Yi Hsiao
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Wenhao Hu
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Kishta Katipally
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Adam Littke
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Aghogho Pedro
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Yuping Qiu
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Maria Sandoval
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Richard Schild
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Michelle Soltani
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Anthony Tedesco
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Dale Vanyo
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Purushotham Vemishetti
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Robert E. Waltermire
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
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21
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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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22
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Tomakinian T, Hamdan HA, Denizot N, Guillot R, Baltaze JP, Kouklovsky C, Vincent G. Evaluation of an NIS-Mediated Oxidative Cyclisation of Phenol-Containing N
-Acyltryptamine Precursors towards Phalarine: Synthesis of 4′,5′-Dihydrospiro[indole-3,6′-[1,3]oxazine]s. European J Org Chem 2017. [DOI: 10.1002/ejoc.201601563] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Terry Tomakinian
- Univ Paris Sud; CNRS; Université Paris-Saclay; Institut de Chimie moléculaire et des Matériaux d'Orsay (ICMMO); Equipe Méthodologie, Synthèse et molécules Thérapeutique (MS&MT); Bat. 410 91405 Orsay France
| | - Hussein Abou Hamdan
- Univ Paris Sud; CNRS; Université Paris-Saclay; Institut de Chimie moléculaire et des Matériaux d'Orsay (ICMMO); Equipe Méthodologie, Synthèse et molécules Thérapeutique (MS&MT); Bat. 410 91405 Orsay France
| | - Natacha Denizot
- Univ Paris Sud; CNRS; Université Paris-Saclay; Institut de Chimie moléculaire et des Matériaux d'Orsay (ICMMO); Equipe Méthodologie, Synthèse et molécules Thérapeutique (MS&MT); Bat. 410 91405 Orsay France
| | - Régis Guillot
- Univ Paris Sud; CNRS; Université Paris-Saclay; Institut de Chimie moléculaire et des Matériaux d'Orsay (ICMMO); Equipe Méthodologie, Synthèse et molécules Thérapeutique (MS&MT); Bat. 410 91405 Orsay France
| | - Jean-Pierre Baltaze
- Univ Paris Sud; CNRS; Université Paris-Saclay; Institut de Chimie moléculaire et des Matériaux d'Orsay (ICMMO); Equipe Méthodologie, Synthèse et molécules Thérapeutique (MS&MT); Bat. 410 91405 Orsay France
| | - Cyrille Kouklovsky
- Univ Paris Sud; CNRS; Université Paris-Saclay; Institut de Chimie moléculaire et des Matériaux d'Orsay (ICMMO); Equipe Méthodologie, Synthèse et molécules Thérapeutique (MS&MT); Bat. 410 91405 Orsay France
| | - Guillaume Vincent
- Univ Paris Sud; CNRS; Université Paris-Saclay; Institut de Chimie moléculaire et des Matériaux d'Orsay (ICMMO); Equipe Méthodologie, Synthèse et molécules Thérapeutique (MS&MT); Bat. 410 91405 Orsay France
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23
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Siraiwa S, Suzuki A, Katoh R, Saito Y. Design and synthesis of a novel fluorescent benzo[g]imidazo[4,5-c]quinoline nucleoside for monitoring base-pair-induced protonation with cytosine: distinguishing cytosine via changes in the intensity and wavelength of fluorescence. Org Biomol Chem 2016; 14:3934-42. [PMID: 27044927 DOI: 10.1039/c6ob00494f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A novel fluorescent benzo[g]imidazo[4,5-c]quinoline nucleoside (BIQ)A (1) comprising a 3-deaza-2'-deoxyadenosine skeleton was developed and used to monitor (BIQ)A-C base-pair formation in oligodeoxynucleotide (ODN) duplexes. The newly synthesized (BIQ)A exhibited distinct photophysical properties associated with its protonated/deprotonated forms (monomer: pKa 6.2) via dramatic changes in its absorption and fluorescence spectra. In ODN duplexes, the induced protonation of (BIQ)A occurred, even under alkalescent conditions when cytosine was the opposite base on the complementary strand; the resulting (BIQ)A-C base pairs were stable. By monitoring the protonation of (BIQ)A under neutral and alkalescent conditions, we could clearly discriminate cytosine through spectral changes in absorption and fluorescence. Similarly, we found that the demonstrated 3-deaza-2'-deoxyadenosine (3z)A forms a stable base pair with cytosine via N(1) protonation in ODN duplexes under neutral and acidic conditions (pH < 7.0). At lower pH values, (3z)A-containing ODNs could clearly discriminate cytosine through melting temperature (Tm) measurements. Therefore, ODN probes containing indicator nucleosides, such as (BIQ)A and (3z)A, exhibit great potential as bioprobes for genetic analysis and structural studies of nucleic acids.
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Affiliation(s)
- Shogo Siraiwa
- Department of Chemical Biology and Applied Chemistry, College of Engineering, Nihon University, Koriyama, Fukushima 963-8642, Japan.
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24
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Nasiri AH, Saxena K, Bats JW, Nasiri HR, Schwalbe H. Biophysical investigation and conformational analysis of p38α kinase inhibitor doramapimod and its analogues. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00262e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Doramapimod (BIRB 796) is a potent inhibitor of p38α nitrogen-activated protein kinase. By using biophysical methods, a clear correlation between kinase binding and the torsion angle θ of doramapimod analogues was found, highlighting the importance of inhibitor conformation for protein binding.
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Affiliation(s)
- Amir H. Nasiri
- Institute of Organic Chemistry and Chemical Biology
- Center for Biomolecular Magnetic Resonance (BMRZ)
- Johann Wolfgang Goethe-University Frankfurt
- D-60438 Frankfurt am Main
- Germany
| | - Krishna Saxena
- Institute of Organic Chemistry and Chemical Biology
- Center for Biomolecular Magnetic Resonance (BMRZ)
- Johann Wolfgang Goethe-University Frankfurt
- D-60438 Frankfurt am Main
- Germany
| | - Jan W. Bats
- Institute of Organic Chemistry and Chemical Biology
- Center for Biomolecular Magnetic Resonance (BMRZ)
- Johann Wolfgang Goethe-University Frankfurt
- D-60438 Frankfurt am Main
- Germany
| | - Hamid R. Nasiri
- Institute of Organic Chemistry and Chemical Biology
- Center for Biomolecular Magnetic Resonance (BMRZ)
- Johann Wolfgang Goethe-University Frankfurt
- D-60438 Frankfurt am Main
- Germany
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology
- Center for Biomolecular Magnetic Resonance (BMRZ)
- Johann Wolfgang Goethe-University Frankfurt
- D-60438 Frankfurt am Main
- Germany
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25
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Lin W, Yang L, Chai SC, Lu Y, Chen T. Development of CINPA1 analogs as novel and potent inverse agonists of constitutive androstane receptor. Eur J Med Chem 2015; 108:505-528. [PMID: 26717202 DOI: 10.1016/j.ejmech.2015.12.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Revised: 12/01/2015] [Accepted: 12/10/2015] [Indexed: 11/30/2022]
Abstract
Constitutive androstane receptor (CAR, NR1I3) and pregnane X receptor (PXR, NR1I2) are master regulators of endobiotic and xenobiotic metabolism and disposition. Because CAR is constitutively active in certain cellular contexts, inhibiting CAR might reduce drug-induced hepatotoxicity and resensitize drug-resistant cancer cells to chemotherapeutic drugs. We recently reported a novel CAR inhibitor/inverse agonist CINPA1 (11). Here, we have obtained or designed 54 analogs of CINPA1 and used a time-resolved fluorescence resonance energy transfer (TR-FRET) assay to evaluate their CAR inhibition potency. Many of the 54 analogs showed CAR inverse agonistic activities higher than those of CINPA1, which has an IC50 value of 687 nM. Among them, 72 has an IC50 value of 11.7 nM, which is about 59-fold more potent than CINPA1 and over 10-fold more potent than clotrimazole (an IC50 value of 126.9 nM), the most potent CAR inverse agonist in a biochemical assay previously reported by others. Docking studies provide a molecular explanation of the structure-activity relationship (SAR) observed experimentally. To our knowledge, this effort is the first chemistry endeavor in designing and identifying potent CAR inverse agonists based on a novel chemical scaffold, leading to 72 as the most potent CAR inverse agonist so far. The 54 chemicals presented are novel and unique tools for characterizing CAR's function, and the SAR information gained from these 54 analogs could guide future efforts to develop improved CAR inverse agonists.
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Affiliation(s)
- Wenwei Lin
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 1000, Memphis, TN 38105, United States
| | - Lei Yang
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 1000, Memphis, TN 38105, United States
| | - Sergio C Chai
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 1000, Memphis, TN 38105, United States
| | - Yan Lu
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 1000, Memphis, TN 38105, United States
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 1000, Memphis, TN 38105, United States.
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26
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Discovery of HCV NS5B thumb site I inhibitors: Core-refining from benzimidazole to indole scaffold. Eur J Med Chem 2015; 94:218-28. [DOI: 10.1016/j.ejmech.2015.03.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Revised: 03/03/2015] [Accepted: 03/04/2015] [Indexed: 11/18/2022]
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27
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Mirza MU, Ghori NUH, Ikram N, Adil AR, Manzoor S. Pharmacoinformatics approach for investigation of alternative potential hepatitis C virus nonstructural protein 5B inhibitors. Drug Des Devel Ther 2015; 9:1825-41. [PMID: 25848219 PMCID: PMC4383224 DOI: 10.2147/dddt.s75886] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Hepatitis C virus (HCV) is one of the major viruses affecting the world today. It is a highly variable virus, having a rapid reproduction and evolution rate. The variability of genomes is due to hasty replication catalyzed by nonstructural protein 5B (NS5B) which is also a potential target site for the development of anti-HCV agents. Recently, the US Food and Drug Administration approved sofosbuvir as a novel oral NS5B inhibitor for the treatment of HCV. Unfortunately, it is much highlighted for its pricing issues. Hence, there is an urgent need to scrutinize alternate therapies against HCV that are available at affordable price and do not have associated side effects. Such a need is crucial especially in underdeveloped countries. The search for various new bioactive compounds from plants is a key part of pharmaceutical research. In the current study, we applied a pharmacoinformatics-based approach for the identification of active plant-derived compounds against NS5B. The results were compared to docking results of sofosbuvir. The lead compounds with high-binding ligands were further analyzed for pharmacokinetic and pharmacodynamic parameters based on in silico absorption, distribution, metabolism, excretion, and toxicity (ADMET) profile. The results showed the potential alternative lead compounds that can be developed into commercial drugs having high binding energy and promising ADMET properties.
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Affiliation(s)
- Muhammad Usman Mirza
- Centre for Research in Molecular Medicine (CRiMM), The University of Lahore, Lahore, Pakistan
| | - Noor-Ul-Huda Ghori
- Atta-ur-Rehman School of Applied Biosciences (ASAB), National University of Science and Technology, Islamabad, Pakistan
| | - Nazia Ikram
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore, Lahore, Pakistan
| | - Abdur Rehman Adil
- Centre for Excellence in Molecular Biology (CEMB), The University of Punjab, Lahore, Pakistan
| | - Sadia Manzoor
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore, Lahore, Pakistan
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28
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Naoe S, Saito T, Uchiyama M, Oishi S, Fujii N, Ohno H. Direct Construction of Fused Indoles by Gold-Catalyzed Cascade Cyclization of Conjugated Diynes. Org Lett 2015; 17:1774-7. [DOI: 10.1021/acs.orglett.5b00550] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Saori Naoe
- Graduate School
of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tatsuo Saito
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-0033, Japan
| | - Masanobu Uchiyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-0033, Japan
| | - Shinya Oishi
- Graduate School
of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Nobutaka Fujii
- Graduate School
of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroaki Ohno
- Graduate School
of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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29
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Fuentes N, Kong W, Fernández-Sánchez L, Merino E, Nevado C. Cyclization Cascades via N-Amidyl Radicals toward Highly Functionalized Heterocyclic Scaffolds. J Am Chem Soc 2015; 137:964-73. [DOI: 10.1021/ja5115858] [Citation(s) in RCA: 315] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Noelia Fuentes
- Department of Chemistry, University of Zürich, Winterthurerstrasse
190, 8057 Zürich, Switzerland
| | - Wangqing Kong
- Department of Chemistry, University of Zürich, Winterthurerstrasse
190, 8057 Zürich, Switzerland
| | - Luis Fernández-Sánchez
- Department of Chemistry, University of Zürich, Winterthurerstrasse
190, 8057 Zürich, Switzerland
| | - Estíbaliz Merino
- Department of Chemistry, University of Zürich, Winterthurerstrasse
190, 8057 Zürich, Switzerland
| | - Cristina Nevado
- Department of Chemistry, University of Zürich, Winterthurerstrasse
190, 8057 Zürich, Switzerland
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30
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Meguellati A, Ahmed-Belkacem A, Yi W, Haudecoeur R, Crouillère M, Brillet R, Pawlotsky JM, Boumendjel A, Peuchmaur M. B-ring modified aurones as promising allosteric inhibitors of hepatitis C virus RNA-dependent RNA polymerase. Eur J Med Chem 2014; 80:579-92. [DOI: 10.1016/j.ejmech.2014.04.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 03/31/2014] [Accepted: 04/03/2014] [Indexed: 01/21/2023]
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31
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LaPlante SR, Bös M, Brochu C, Chabot C, Coulombe R, Gillard JR, Jakalian A, Poirier M, Rancourt J, Stammers T, Thavonekham B, Beaulieu PL, Kukolj G, Tsantrizos YS. Conformation-based restrictions and scaffold replacements in the design of hepatitis C virus polymerase inhibitors: discovery of deleobuvir (BI 207127). J Med Chem 2013; 57:1845-54. [PMID: 24159919 DOI: 10.1021/jm4011862] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Conformational restrictions of flexible torsion angles were used to guide the identification of new chemotypes of HCV NS5B inhibitors. Sites for rigidification were based on an acquired conformational understanding of compound binding requirements and the roles of substituents in the free and bound states. Chemical bioisosteres of amide bonds were explored to improve cell-based potency. Examples are shown, including the design concept that led to the discovery of the phase III clinical candidate deleobuvir (BI 207127). The structure-based strategies employed have general utility in drug design.
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Affiliation(s)
- Steven R LaPlante
- Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd. , 2100 Cunard Street, Laval, Quebec, Canada H7S 2G5
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32
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Cummings MD, Lin TI, Hu L, Tahri A, McGowan D, Amssoms K, Last S, Devogelaere B, Rouan MC, Vijgen L, Berke JM, Dehertogh P, Fransen E, Cleiren E, van der Helm L, Fanning G, Nyanguile O, Simmen K, Van Remoortere P, Raboisson P, Vendeville S. Discovery and Early Development of TMC647055, a Non-Nucleoside Inhibitor of the Hepatitis C Virus NS5B Polymerase. J Med Chem 2013; 57:1880-92. [DOI: 10.1021/jm401396p] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Maxwell D. Cummings
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Tse-I Lin
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Lili Hu
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Abdellah Tahri
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - David McGowan
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Katie Amssoms
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Stefaan Last
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Benoit Devogelaere
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Marie-Claude Rouan
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Leen Vijgen
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Jan Martin Berke
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Pascale Dehertogh
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Els Fransen
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Erna Cleiren
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Liesbet van der Helm
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Gregory Fanning
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Origène Nyanguile
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Kenny Simmen
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Pieter Van Remoortere
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Pierre Raboisson
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Sandrine Vendeville
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
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Ando I, Ogura N, Toyonaga Y, Hirahara K, Shibata T, Noguchi T. JTK-853, a novel non-nucleoside hepatitis C virus polymerase inhibitor, demonstrates a high genetic barrier to resistance in vitro. Intervirology 2013; 56:302-9. [PMID: 24008863 DOI: 10.1159/000351141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 04/04/2013] [Indexed: 11/19/2022] Open
Abstract
JTK-853 is a novel, non-nucleoside, palm site-binding hepatitis C virus (HCV) polymerase inhibitor that has demonstrated antiviral activity in HCV-infected patients during 3 days of treatment. To estimate the genetic barrier of JTK-853 to resistance in vitro, colony formation assays were conducted using HCV replicon cells (genotypes 1a and 1b). The colony formation assays revealed that the numbers of resistant colonies for JTK-853 were much lower than those for other direct-acting antivirals, including palm site- or thumb pocket-binding non-nucleoside HCV polymerase inhibitors (NNIs), an NS5A inhibitor (NS5Ai), and a protease inhibitor (PI). Furthermore, the numbers of resistant colonies for JTK-853 in combination with the NS5Ai or PI were lower than those for other combinations of NS5Ai + NNI, and NS5Ai + PI. Our findings demonstrate that JTK-853 has a high genetic barrier to resistance, and suggest that its combination therapies will be potent in suppressing the emergence of drug resistance in HCV-infected patients.
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Affiliation(s)
- I Ando
- Central Pharmaceutical Research Institute, Japan Tobacco Inc., Osaka, Japan
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34
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He S, Li P, Dai X, McComas CC, Huang H, Zhan C, Chang L, Liu Y, Chen S, Lai Z, Liu H, Yin J, Dang Q, Xiao D, Zorn N, Peng X, Nargund RP, Palani A. A general approach to substituted 6H-pyrido[2′,3′:5,6] [1,3]oxazino[3,4-a]indole via cyclization from an indoline precursor followed by re-aromatization. Tetrahedron Lett 2013. [DOI: 10.1016/j.tetlet.2013.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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35
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Beaulieu PL. Design and Development of NS5B Polymerase Non‐nucleoside Inhibitors for the Treatment of Hepatitis C Virus Infection. SUCCESSFUL STRATEGIES FOR THE DISCOVERY OF ANTIVIRAL DRUGS 2013. [DOI: 10.1039/9781849737814-00248] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The hepatitis C virus (HCV) infects an estimated 130–170 million people worldwide and is associated with life‐threatening liver diseases. The recent introduction of the first two HCV direct‐acting antivirals (DAAs) as a complement to the interferon/ribavirin standard of care has provided patients with improved outcomes. Still, 25–30% of subjects infected with genotype 1 HCV do not respond adequately to treatment owing to the emergence of resistant virus and many suffer from severe side effects. A paradigm shift towards the development of interferon‐free combinations of DAAs with complementary modes of action is currently taking place. Virally encoded proteins and enzymes have become the target of HCV drug discovery efforts and several promising new agents are currently being evaluated in the clinic for treatment of chronic HCV infection. The NS5B RNA‐dependent RNA polymerase is responsible for replication of viral RNA and plays a pivotal role in the virus life cycle. NS5B is undoubtedly the most druggable HCV target and is susceptible to several classes of allosteric inhibitors that bind to four distinct sites on the enzyme. This chapter describes successful strategies that have led to the discovery of HCV NS5B antivirals. It is divided according to allosteric sites and describes how each of the known families of inhibitors was discovered, characterized and optimized to provide clinical candidates. When available, the strategies adopted by medicinal chemists to optimize initial leads and address challenges and liabilities encountered on the path to candidate selection are described, along with reported clinical outcomes.
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Affiliation(s)
- Pierre L. Beaulieu
- Boehringer Ingelheim (Canada) Ltd. 2100 Cunard Street, Laval, Québec Canada, H7S 2G5 resgeneral.lav@boehringer‐ingelheim.com
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36
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Asthana S, Shukla S, Vargiu AV, Ceccarelli M, Ruggerone P, Paglietti G, Marongiu ME, Blois S, Giliberti G, La Colla P. Different Molecular Mechanisms of Inhibition of Bovine Viral Diarrhea Virus and Hepatitis C Virus RNA-Dependent RNA Polymerases by a Novel Benzimidazole. Biochemistry 2013; 52:3752-64. [DOI: 10.1021/bi400107h] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Shailendra Asthana
- Dipartimento di Scienze Biomediche,
Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy
- Dipartimento di Scienze Fisiche,
Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy
| | - Saumya Shukla
- Dipartimento di Scienze Biomediche,
Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy
| | | | - Matteo Ceccarelli
- Dipartimento di Scienze Fisiche,
Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy
| | - Paolo Ruggerone
- Dipartimento di Scienze Fisiche,
Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy
| | - Giuseppe Paglietti
- Dipartimento di Scienze del
Farmaco, Università degli Studi di Sassari, Via Muroni 23/a, 07100 Sassari, Italy
| | - Maria E. Marongiu
- Dipartimento di Scienze Biomediche,
Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy
| | - Sylvain Blois
- Dipartimento di Scienze Biomediche,
Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy
| | - Gabriele Giliberti
- Dipartimento di Scienze Biomediche,
Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy
| | - Paolo La Colla
- Dipartimento di Scienze Biomediche,
Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy
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37
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Wang Y, Kirschner A, Fabian AK, Gopalakrishnan R, Kress C, Hoogeland B, Koch U, Kozany C, Bracher A, Hausch F. Increasing the efficiency of ligands for FK506-binding protein 51 by conformational control. J Med Chem 2013; 56:3922-35. [PMID: 23647266 DOI: 10.1021/jm400087k] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The design of efficient ligands remains a key challenge in drug discovery. In the quest for lead-like ligands for the FK506-binding protein 51 (FKBP51), we designed two new classes of bicyclic sulfonamides to probe the contribution of conformational energy in these ligands. The [4.3.1] scaffold had consistently higher affinity compared to the [3.3.1] or monocyclic scaffolds, which could be attributed to better preorganization of two key recognition motifs. Surprisingly, the binding of the rigid [4.3.1] scaffold was enthalpy-driven and entropically disfavored compared to the flexible analogues. Cocrystal structures at atomic resolution revealed that the sulfonamide nitrogen in the bicyclic scaffolds can accept an unusual hydrogen bond from Tyr(113) that mimics the putative FKBP transition state. This resulted in the first lead-like, functionally active ligand for FKBP51. Our work exemplifies how atom-efficient ligands can be achieved by careful conformational control even in very open and thus difficult binding sites such as FKBP51.
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Affiliation(s)
- Yansong Wang
- AG Chemical Genomics, Max Planck Institute of Psychiatry , Kraepelinstraße 2, 80804 Munich, Germany
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38
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Alorati AD, Gibb AD, Mullens PR, Stewart GW. An Efficient Process for the Large-Scale Synthesis of a 2,3,6-Trisubstituted Indole. Org Process Res Dev 2012. [DOI: 10.1021/op300303p] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anthony D. Alorati
- Global Process Chemistry, Merck Sharp & Dohme Ltd, Hertford Road, Hoddesdon, Hertfordshire EN11 9BU, United Kingdom
| | - Andrew D. Gibb
- Global Process Chemistry, Merck Sharp & Dohme Ltd, Hertford Road, Hoddesdon, Hertfordshire EN11 9BU, United Kingdom
| | - Peter R. Mullens
- Global Process Chemistry, Merck Sharp & Dohme Ltd, Hertford Road, Hoddesdon, Hertfordshire EN11 9BU, United Kingdom
| | - Gavin W. Stewart
- Global Process Chemistry, Merck Sharp & Dohme Ltd, Hertford Road, Hoddesdon, Hertfordshire EN11 9BU, United Kingdom
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Genotypic and phenotypic analyses of hepatitis C virus from patients treated with JTK-853 in a three-day monotherapy. Antimicrob Agents Chemother 2012; 57:436-44. [PMID: 23129048 DOI: 10.1128/aac.01432-12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
JTK-853, a palm site-binding NS5B nonnucleoside polymerase inhibitor, shows antiviral activity in vitro and in hepatitis C virus (HCV)-infected patients. Here, we report the results of genotypic and phenotypic analyses of resistant variants in 24 HCV genotype 1-infected patients who received JTK-853 (800, 1,200, or 1,600 mg twice daily or 1,200 mg three times daily) in a 3-day monotherapy. Viral resistance in NS5B was investigated using HCV RNA isolated from serum specimens from the patients. At the end of treatment (EOT) with JTK-853, the amino acid substitutions M414T (methionine [M] in position 414 at baseline was replaced with threonine [T] at EOT), C445R (cysteine [C] in position 445 at baseline was replaced with arginine [R] at EOT), Y448C/H (tyrosine [Y] in position 448 at baseline was replaced with cysteine [C] or histidine [H] at EOT), and L466F (leucine [L] in position 466 at baseline was replaced with phenylalanine [F] at EOT), which are known to be typical resistant variants of nonnucleoside polymerase inhibitors, were observed in a clonal sequencing analysis. These substitutions were also selected by a treatment with JTK-853 in vitro, and the 50% effective concentration of JTK-853 in the M414T-, C445F-, Y448H-, and L466V-harboring replicons attenuated the susceptibility by 44-, 5-, 6-, and 21-fold, respectively, compared with that in the wild-type replicon (Con1). These findings suggest that amino acid substitutions of M414T, C445R, Y448C/H, and L466F are thought to be viral resistance mutations in HCV-infected patients receiving JTK-853 in a 3-day monotherapy.
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40
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Davis BC, Thorpe IF. Thumb inhibitor binding eliminates functionally important dynamics in the hepatitis C virus RNA polymerase. Proteins 2012; 81:40-52. [PMID: 22855387 DOI: 10.1002/prot.24154] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/12/2012] [Accepted: 07/23/2012] [Indexed: 11/09/2022]
Abstract
Hepatitis C virus (HCV) has infected almost 200 million people worldwide, typically causing chronic liver damage and severe complications such as liver failure. Currently, there are few approved treatments for viral infection. Thus, the HCV RNA-dependent RNA polymerase (gene product NS5B) has emerged as an important target for small molecule therapeutics. Potential therapeutic agents include allosteric inhibitors that bind distal to the enzyme active site. While their mechanism of action is not conclusively known, it has been suggested that certain inhibitors prevent a conformational change in NS5B that is crucial for RNA replication. To gain insight into the molecular origin of long-range allosteric inhibition of NS5B, we employed molecular dynamics simulations of the enzyme with and without an inhibitor bound to the thumb domain. These studies indicate that the presence of an inhibitor in the thumb domain alters both the structure and internal motions of NS5B. Principal components analysis identified motions that are severely attenuated by inhibitor binding. These motions may have functional relevance by facilitating interactions between NS5B and RNA template or nascent RNA duplex, with presence of the ligand leading to enzyme conformations with narrower and thus less accessible RNA binding channels. This study provides the first evidence for a mechanistic basis of allosteric inhibition in NS5B. Moreover, we present evidence that allosteric inhibition of NS5B results from intrinsic features of the enzyme free energy landscape, suggesting a common mechanism for the action of diverse allosteric ligands.
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Affiliation(s)
- Brittny C Davis
- Department of Chemistry and Biochemistry, University of Maryland-Baltimore County, Baltimore, Maryland 21250, USA
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41
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Haudecoeur R, Peuchmaur M, Ahmed-Belkacem A, Pawlotsky JM, Boumendjel A. Structure-Activity Relationships in the Development of Allosteric Hepatitis C Virus RNA-Dependent RNA Polymerase Inhibitors: Ten Years of Research. Med Res Rev 2012; 33:934-84. [DOI: 10.1002/med.21271] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Romain Haudecoeur
- Département de Pharmacochimie Moléculaire; Université de Grenoble/CNRS; UMR 5063, BP 53; 38041; Grenoble Cedex 9; France
| | - Marine Peuchmaur
- Département de Pharmacochimie Moléculaire; Université de Grenoble/CNRS; UMR 5063, BP 53; 38041; Grenoble Cedex 9; France
| | | | | | - Ahcène Boumendjel
- Département de Pharmacochimie Moléculaire; Université de Grenoble/CNRS; UMR 5063, BP 53; 38041; Grenoble Cedex 9; France
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42
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Finger-loop inhibitors of the HCV NS5b polymerase. Part 1: Discovery and optimization of novel 1,6- and 2,6-macrocyclic indole series. Bioorg Med Chem Lett 2012; 22:4431-6. [DOI: 10.1016/j.bmcl.2012.03.097] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 03/27/2012] [Accepted: 03/28/2012] [Indexed: 12/26/2022]
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43
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Vendeville S, Lin TI, Hu L, Tahri A, McGowan D, Cummings MD, Amssoms K, Canard M, Last S, Van den Steen I, Devogelaere B, Rouan MC, Vijgen L, Berke JM, Dehertogh P, Fransen E, Cleiren E, van der Helm L, Fanning G, Van Emelen K, Nyanguile O, Simmen K, Raboisson P. Finger loop inhibitors of the HCV NS5b polymerase. Part II. Optimization of tetracyclic indole-based macrocycle leading to the discovery of TMC647055. Bioorg Med Chem Lett 2012; 22:4437-43. [DOI: 10.1016/j.bmcl.2012.04.113] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Revised: 04/20/2012] [Accepted: 04/21/2012] [Indexed: 01/31/2023]
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44
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Preclinical characterization of JTK-853, a novel nonnucleoside inhibitor of the hepatitis C virus RNA-dependent RNA polymerase. Antimicrob Agents Chemother 2012; 56:4250-6. [PMID: 22615294 DOI: 10.1128/aac.00312-12] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
JTK-853 is a novel piperazine derivative nonnucleoside inhibitor of hepatitis C virus (HCV) RNA-dependent RNA polymerase. JTK-853 showed potent inhibitory activity against genotype 1 HCV polymerase, with a 50% inhibitory concentration in the nanomolar range, and showed potent antiviral activity against the genotype 1b replicon, with a 50% effective concentration of 0.035 μM. The presence of human serum at up to 40% had little effect on the antiviral activity of JTK-853. Structure analysis of HCV polymerase with JTK-853 revealed that JTK-853 associates with the palm site and β-hairpin region of HCV polymerase, and JTK-853 showed decreased antiviral activity against HCV replicons bearing the resistance mutations C316Y, M414T, Y452H, and L466V in the palm site region of HCV polymerase. JTK-853 showed an additive combination effect with other DAAs (direct antiviral agents), such as nucleoside polymerase inhibitor, thumb pocket-binding nonnucleoside polymerase inhibitor, NS5A inhibitor, and protease inhibitor. Collectively, these data demonstrate that JTK-853 is a potent and novel nonnucleoside palm site-binding HCV polymerase inhibitor, suggesting JTK-853 as a potentially useful agent in combination with other DAAs for treatment of HCV infections.
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45
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Ismail MA, Abou El Ella DA, Abouzid KA, Mahmoud AH. Integrated structure-based activity prediction model of benzothiadiazines on various genotypes of HCV NS5b polymerase (1a, 1b and 4) and its application in the discovery of new derivatives. Bioorg Med Chem 2012; 20:2455-78. [DOI: 10.1016/j.bmc.2012.01.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Revised: 12/25/2011] [Accepted: 01/05/2012] [Indexed: 02/06/2023]
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46
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Ding M, He F, Hudyma TW, Zheng X, Poss MA, Kadow JF, Beno BR, Rigat KL, Wang YK, Fridell RA, Lemm JA, Qiu D, Liu M, Voss S, Pelosi LA, Roberts SB, Gao M, Knipe J, Gentles RG. Synthesis and SAR studies of novel heteroaryl fused tetracyclic indole-diamide compounds: Potent allosteric inhibitors of the hepatitis C virus NS5B polymerase. Bioorg Med Chem Lett 2012; 22:2866-71. [DOI: 10.1016/j.bmcl.2012.02.063] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Accepted: 02/21/2012] [Indexed: 11/15/2022]
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47
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Cummings MD, Lin TI, Hu L, Tahri A, McGowan D, Amssoms K, Last S, Devogelaere B, Rouan MC, Vijgen L, Berke JM, Dehertogh P, Fransen E, Cleiren E, van der Helm L, Fanning G, Van Emelen K, Nyanguile O, Simmen K, Raboisson P, Vendeville S. Structure-Based Macrocyclization Yields Hepatitis C Virus NS5B Inhibitors with Improved Binding Affinities and Pharmacokinetic Properties. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201200110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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48
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Cummings MD, Lin TI, Hu L, Tahri A, McGowan D, Amssoms K, Last S, Devogelaere B, Rouan MC, Vijgen L, Berke JM, Dehertogh P, Fransen E, Cleiren E, van der Helm L, Fanning G, Van Emelen K, Nyanguile O, Simmen K, Raboisson P, Vendeville S. Structure-Based Macrocyclization Yields Hepatitis C Virus NS5B Inhibitors with Improved Binding Affinities and Pharmacokinetic Properties. Angew Chem Int Ed Engl 2012; 51:4637-40. [DOI: 10.1002/anie.201200110] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 02/07/2012] [Indexed: 11/11/2022]
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49
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Soto S, Vaz E, Dell'Aversana C, Álvarez R, Altucci L, de Lera ÁR. New synthetic approach to paullones and characterization of their SIRT1 inhibitory activity. Org Biomol Chem 2012; 10:2101-12. [PMID: 22286328 DOI: 10.1039/c2ob06695e] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A series of 7,12-dihydroindolo[3,2-d][1]benzazepine-6(5H)-ones (paullones) substituted at C9/C10 (Br) and C2 (Me, CF(3), CO(2)Me) have been synthesized by a one-pot Suzuki-Miyaura cross-coupling of an o-aminoarylboronic acid and methyl 2-iodoindoleacetate followed by intramolecular amide formation. Other approaches to the paullone scaffold based on Pd-catalyzed C-H activation were unsuccessful. In vitro enzymatic assay with recombinant human SIRT-1 indicated a strong inhibitory profile for the series, in particular the analogue with a methoxycarbonyl group at C2 and a bromine at C9. These compounds are, in general, inducers of granulocyte differentiation of the U937 acute leukemia cell line and cause a marked increase in pre-G1 of the cell cycle.
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Affiliation(s)
- Sara Soto
- Departamento de Química Orgánica, Facultade de Química, Universidade de Vigo, Lagoas-Marcosende, 36310 Vigo, Spain
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50
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Sofia MJ, Chang W, Furman PA, Mosley RT, Ross BS. Nucleoside, nucleotide, and non-nucleoside inhibitors of hepatitis C virus NS5B RNA-dependent RNA-polymerase. J Med Chem 2012; 55:2481-531. [PMID: 22185586 DOI: 10.1021/jm201384j] [Citation(s) in RCA: 217] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Michael J Sofia
- Pharmasset, Inc., 303A College Road East, Princeton, New Jersey 08540, United States.
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