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Xia S, Chen E, Zhang Y. Integrated Molecular Modeling and Machine Learning for Drug Design. J Chem Theory Comput 2023; 19:7478-7495. [PMID: 37883810 PMCID: PMC10653122 DOI: 10.1021/acs.jctc.3c00814] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/28/2023]
Abstract
Modern therapeutic development often involves several stages that are interconnected, and multiple iterations are usually required to bring a new drug to the market. Computational approaches have increasingly become an indispensable part of helping reduce the time and cost of the research and development of new drugs. In this Perspective, we summarize our recent efforts on integrating molecular modeling and machine learning to develop computational tools for modulator design, including a pocket-guided rational design approach based on AlphaSpace to target protein-protein interactions, delta machine learning scoring functions for protein-ligand docking as well as virtual screening, and state-of-the-art deep learning models to predict calculated and experimental molecular properties based on molecular mechanics optimized geometries. Meanwhile, we discuss remaining challenges and promising directions for further development and use a retrospective example of FDA approved kinase inhibitor Erlotinib to demonstrate the use of these newly developed computational tools.
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Affiliation(s)
- Song Xia
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Eric Chen
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Yingkai Zhang
- Department
of Chemistry, New York University, New York, New York 10003, United States
- Simons
Center for Computational Physical Chemistry at New York University, New York, New York 10003, United States
- NYU-ECNU
Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
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2
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Nguyen DT, Pham NK, Nguyen XT, Luu TXT, Nguyen Luong QN. Ultrasound accelerated solvent-free condensation reaction of rhodanines and carbonyls using Amberlyst 26 as a green and efficient base catalyst. J Sulphur Chem 2023. [DOI: 10.1080/17415993.2023.2173008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Duc-Thuan Nguyen
- Faculty of Chemistry, University of Science, Ho Chi Minh City, Vietnam
| | - Ngoc-Khoi Pham
- Faculty of Chemistry, University of Science, Ho Chi Minh City, Vietnam
| | - Xuan-Triet Nguyen
- Faculty of Chemistry, University of Science, Ho Chi Minh City, Vietnam
| | - Thi Xuan Thi Luu
- Faculty of Chemistry, University of Science, Ho Chi Minh City, Vietnam
- Department of Chemistry, Vietnam National University, Ho Chi Minh City, Vietnam
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3
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Yang C, Chen EA, Zhang Y. Protein-Ligand Docking in the Machine-Learning Era. Molecules 2022; 27:4568. [PMID: 35889440 PMCID: PMC9323102 DOI: 10.3390/molecules27144568] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 07/14/2022] [Indexed: 11/16/2022] Open
Abstract
Molecular docking plays a significant role in early-stage drug discovery, from structure-based virtual screening (VS) to hit-to-lead optimization, and its capability and predictive power is critically dependent on the protein-ligand scoring function. In this review, we give a broad overview of recent scoring function development, as well as the docking-based applications in drug discovery. We outline the strategies and resources available for structure-based VS and discuss the assessment and development of classical and machine learning protein-ligand scoring functions. In particular, we highlight the recent progress of machine learning scoring function ranging from descriptor-based models to deep learning approaches. We also discuss the general workflow and docking protocols of structure-based VS, such as structure preparation, binding site detection, docking strategies, and post-docking filter/re-scoring, as well as a case study on the large-scale docking-based VS test on the LIT-PCBA data set.
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Affiliation(s)
- Chao Yang
- Department of Chemistry, New York University, New York, NY 10003, USA; (C.Y.); (E.A.C.)
| | - Eric Anthony Chen
- Department of Chemistry, New York University, New York, NY 10003, USA; (C.Y.); (E.A.C.)
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, NY 10003, USA; (C.Y.); (E.A.C.)
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
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4
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Egu SA, Ali I, Khan KM, Chigurupati S, Qureshi U, Salar U, Taha M, Felemban SG, Venugopal V, Ul-Haq Z. Syntheses, in vitro, and in silico studies of rhodanine-based schiff bases as potential α-amylase inhibitors and radicals (DPPH and ABTS) scavengers. Mol Divers 2022; 27:767-791. [PMID: 35604512 DOI: 10.1007/s11030-022-10454-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 04/27/2022] [Indexed: 10/18/2022]
Abstract
A two-step reaction method was used to synthesize a series of rhodanine-based Schiff bases (2-33) that were characterized using spectroscopic techniques. All compounds were assessed for α-amylase inhibitory and radical scavenging (DPPH and ABTS) activities. In comparison to the standard acarbose (IC50 = 9.08 ± 0.07 µM), all compounds demonstrated good to moderate α-amylase inhibitory activity (IC50 = 10.91 ± 0.08-61.89 ± 0.102 µM). Compounds also demonstrated significantly higher DPPH (IC50 = 10.33 ± 0.02-96.65 ± 0.03 µM) and ABTS (IC50 = 12.01 ± 0.12-97.47 ± 0.13 µM) radical scavenging activities than ascorbic acid (DPPH, IC50 = 15.08 ± 0.03 µM; ABTS, IC50 = 16.09 ± 0.17 µM). The limited structure-activity relationship (SAR) suggests that the position and nature of the substituted groups on the phenyl ring have a vital role in varying inhibitory potential. Among the series, compounds with an electron-withdrawing group at the para position showed the highest potency. Kinetic studies revealed that the compounds followed a competitive mode of inhibition. Molecular docking results are found to agree with experimental findings, showing that compounds reside in the active pocket due to the main rhodanine moiety.
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5
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Rhodanine scaffold: A review of antidiabetic potential and structure-activity relationships (SAR). MEDICINE IN DRUG DISCOVERY 2022. [DOI: 10.1016/j.medidd.2022.100131] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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6
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Joon S, Singla RK, Shen B. In Silico Drug Discovery for Treatment of Virus Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1368:73-93. [DOI: 10.1007/978-981-16-8969-7_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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7
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Wu WJ, Xia CL, Ou SJ, Yang Y, Ma YF, Hou YL, Yang QP, Zhang J, Li JW, Qi Y, Xu CP. Novel Elongator Protein 2 Inhibitors Mitigating Tumor Necrosis Factor- α Induced Osteogenic Differentiation Inhibition. BIOMED RESEARCH INTERNATIONAL 2021; 2021:3664564. [PMID: 34853789 PMCID: PMC8629650 DOI: 10.1155/2021/3664564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/12/2021] [Indexed: 11/17/2022]
Abstract
Tumor necrosis factor-α is a common cytokine that increases in inflammatory processes, slows the differentiation of bone formation, and induces osteodystrophy in the long-term inflammatory microenvironment. Our previous study confirmed that the Elongation protein 2 (ELP2) plays a significant role in osteogenesis and osteogenic differentiation, which is considered a drug discovery target in diseases related to bone formation and differentiation. In this study, we applied an in silico virtual screening method to select molecules that bind to the ELP2 protein from a chemical drug molecule library and obtained 95 candidates. Then, we included 11 candidates by observing the docking patterns and the noncovalent bonds. The binding affinity of the ELP2 protein with the candidate compounds was examined by SPR analysis, and 5 out of 11 compounds performed good binding affinity to the mouse ELP2 protein. After in vitro cell differentiation assay, candidates 2# and 5# were shown to reduce differentiation inhibition after tumor necrosis factor-α stimulation, allowing further optimization and development for potential clinical treatment of inflammation-mediated orthopedic diseases.
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Affiliation(s)
- Wen-Jiao Wu
- Department of Medical Research Center, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, China
| | - Chang-Liang Xia
- Department of Orthopaedics, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, China
| | - Shuan-Ji Ou
- Department of Orthopaedics, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, China
| | - Yang Yang
- Department of Orthopaedics, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, China
| | - Yun-Fei Ma
- Department of Orthopaedics and Traumatology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yi-Long Hou
- Department of Orthopaedics and Traumatology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Qing-Po Yang
- Department of Orthopaedics, The First People's Hospital of Kashgar Prefecture, Kashgar, Xinjiang, China
| | - Jun Zhang
- Department of Orthopaedics, The First People's Hospital of Kashgar Prefecture, Kashgar, Xinjiang, China
| | - Jian-Wei Li
- Department of Orthopaedics, Shenzhen Shekou People's Hospital, Shenzhen, Guangdong, China
| | - Yong Qi
- Department of Orthopaedics, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, China
| | - Chang-Peng Xu
- Department of Orthopaedics, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, China
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Skoreński M, Sieńczyk M. The Fellowship of Privileged Scaffolds-One Structure to Inhibit Them All. Pharmaceuticals (Basel) 2021; 14:ph14111164. [PMID: 34832946 PMCID: PMC8622370 DOI: 10.3390/ph14111164] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/09/2021] [Accepted: 11/11/2021] [Indexed: 12/22/2022] Open
Abstract
Over the past few years, the application of privileged structure has emerged as a powerful approach to the discovery of new biologically active molecules. Privileged structures are molecular scaffolds with binding properties to the range of different biological targets. Moreover, privileged structures typically exhibit good drug-like properties, thus assuring more drug-like properties of modified compound. Our main objective is to discuss the privileged structures used for the development of antiviral agents.
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9
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Malik AA, Chotpatiwetchkul W, Phanus-Umporn C, Nantasenamat C, Charoenkwan P, Shoombuatong W. StackHCV: a web-based integrative machine-learning framework for large-scale identification of hepatitis C virus NS5B inhibitors. J Comput Aided Mol Des 2021; 35:1037-1053. [PMID: 34622387 DOI: 10.1007/s10822-021-00418-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/17/2021] [Indexed: 01/07/2023]
Abstract
Fast and accurate identification of inhibitors with potency against HCV NS5B polymerase is currently a challenging task. As conventional experimental methods is the gold standard method for the design and development of new HCV inhibitors, they often require costly investment of time and resources. In this study, we develop a novel machine learning-based meta-predictor (termed StackHCV) for accurate and large-scale identification of HCV inhibitors. Unlike the existing method, which is based on single-feature-based approach, we first constructed a pool of various baseline models by employing a wide range of heterogeneous molecular fingerprints with five popular machine learning algorithms (k-nearest neighbor, multi-layer perceptron, partial least squares, random forest and support vectors machine). Secondly, we integrated these baseline models in order to develop the final meta-based model by means of the stacking strategy. Extensive benchmarking experiments showed that StackHCV achieved a more accurate and stable performance as compared to its constituent baseline models on the training dataset and also outperformed the existing predictor on the independent test dataset. To facilitate the high-throughput identification of HCV inhibitors, we built a web server that can be freely accessed at http://camt.pythonanywhere.com/StackHCV . It is expected that StackHCV could be a useful tool for fast and precise identification of potential drugs against HCV NS5B particularly for liver cancer therapy and other clinical applications.
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Affiliation(s)
- Aijaz Ahmad Malik
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, 10700, Thailand
| | - Warot Chotpatiwetchkul
- Applied Computational Chemistry Research Unit, Department of Chemistry, School of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand
| | - Chuleeporn Phanus-Umporn
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, 10700, Thailand
| | - Chanin Nantasenamat
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, 10700, Thailand
| | - Phasit Charoenkwan
- Modern Management and Information Technology, College of Arts, Media and Technology, Chiang Mai University, Chiang Mai, 50200, Thailand.
| | - Watshara Shoombuatong
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, 10700, Thailand.
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Mermer A. The Importance of Rhodanine Scaffold in Medicinal Chemistry: A Comprehensive Overview. Mini Rev Med Chem 2021; 21:738-789. [PMID: 33334286 DOI: 10.2174/1389557521666201217144954] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 09/21/2020] [Accepted: 10/07/2020] [Indexed: 11/22/2022]
Abstract
After the clinical use of epalrestat that contains a rhodanine ring, in type II diabetes mellitus and diabetic complications, rhodanin-based compounds have become an important class of heterocyclic in the field of medicinal chemistry. Various modifications to the rhodanine ring have led to a broad spectrum of biological activity of these compounds. Synthesis of rhodanine derivatives, depended on advenced throughput scanning hits, frequently causes potent and selective modulators of targeted enzymes or receptors, which apply their pharmacological activities through different mechanisms of action. Rhodanine-based compounds will likely stay a privileged scaffold in drug discovery because of different probability of chemical modifications of the rhodanine ring. We have, therefore reviewed their biological activities and structure activity relationship.
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Affiliation(s)
- Arif Mermer
- Department of Biotechnology, Hamidiye Health Science Institute, University of Health Sciences Turkey, 34668, İstanbul, Turkey
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11
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Facile synthesis of 5-arylidene rhodanine derivatives using Na2SO3 as an eco-friendly catalyst. Access to 2-mercapto-3-aryl-acrylic acids and a benzoxaborole derivative. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2020.152690] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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12
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Chen T, Xiong H, Yang JF, Zhu XL, Qu RY, Yang GF. Diaryl Ether: A Privileged Scaffold for Drug and Agrochemical Discovery. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:9839-9877. [PMID: 32786826 DOI: 10.1021/acs.jafc.0c03369] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Diaryl ether (DE) is a functional scaffold existing widely both in natural products (NPs) and synthetic organic compounds. Statistically, DE is the second most popular and enduring scaffold within the numerous medicinal chemistry and agrochemical reports. Given its unique physicochemical properties and potential biological activities, DE nucleus is recognized as a fundamental element of medicinal and agrochemical agents aimed at different biological targets. Its drug-like derivatives have been extensively synthesized with interesting biological features including anticancer, anti-inflammatory, antiviral, antibacterial, antimalarial, herbicidal, fungicidal, insecticidal, and so on. In this review, we highlight the medicinal and agrochemical versatility of the DE motif according to the published information in the past decade and comprehensively give a summary of the target recognition, structure-activity relationship (SAR), and mechanism of action of its analogues. It is expected that this profile may provide valuable guidance for the discovery of new active ingredients both in drug and pesticide research.
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Affiliation(s)
- Tao Chen
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Hao Xiong
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Jing-Fang Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Xiao-Lei Zhu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Ren-Yu Qu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
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13
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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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14
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Ali I, Lone MN, Alothman ZA, Badjah AY, Alanazi AG. Spectroscopic and In Silico DNA Binding Studies on the Interaction of Some New N-Substituted Rhodanines with Calf-thymus DNA: In Vitro Anticancer Activities. Anticancer Agents Med Chem 2019; 19:425-433. [PMID: 30277166 DOI: 10.2174/1871520618666181002131125] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 03/25/2018] [Accepted: 08/28/2018] [Indexed: 01/13/2023]
Abstract
BACKGROUND In this era of science, cancer is a black dot on the face of humankind. Consequently, the search of promising anticancer agents continues. AIMS Here we designed and synthesized new N-substituted rhodanines (RD1-7), evaluated their multispectroscopic interaction with calf thymus DNA, in silico and anticancer studies against MDA-MB-231cancer cell line. METHODS By MTT assay rhodanine RD1 was found to be the most potent with IC50 value of 72.61 μM. In addition, DNA binding studies (UV-vis and fluorescence) revealed strong binding affinity of RD1-7 with DNA (Kb in the range of 1.5-7.4 × 105 M-1). Moreover, molecular docking study, experimental DNA binding and anticancer studies are all well agreed to each other. RESULTS It was observed that H-bonding and hydrophobic attractions were responsible for stability of DNAcompound adducts. Besides, the reported rhodanines (RD1-7) were found as minor groove binders of DNA. Concisely, RD1-7 indicated promising pharmacological properties and hence, shows auspicious future for the development of novel anticancer agents. CONCLUSION The reported rhodanines showed excellent anticancer properties. Therefore, the described rhodanines may be used as potential anticancer agents in the future.
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Affiliation(s)
- Imran Ali
- Department of Chemistry, College of Sciences, Taibah University, Al-Medina Al-Munawara-41477, Saudi Arabia.,Department of Chemistry, Jamia Millia Islamia (Central University), New Delhi-110025, India
| | - Mohammad N Lone
- Department of Chemistry, College of Sciences, Taibah University, Al-Medina Al-Munawara-41477, Saudi Arabia
| | - Zeid A Alothman
- Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ahmad Y Badjah
- Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdullah G Alanazi
- Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
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15
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Sabahi-Agabager L, Nasiri F. One-pot, solvent-free facile stereoselective synthesis of rhodanine–furan hybrids from renewable resources. J Sulphur Chem 2019. [DOI: 10.1080/17415993.2019.1702196] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
| | - Farough Nasiri
- Department of Applied Chemistry, University of Mohaghegh Ardabili, Ardabil, Iran
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16
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Abstract
Aim: Mucormycosis (zygomycosis) is a rare fungal infection that affects humans (40–100% mortality). Rhizopus oryzae is the primary fungus responsible for 70% of mucormycosis cases. RNA-dependent RNA polymerase (RdRp) is a vital enzyme accountable for the RNA polymerization process in different organisms, including R. oryzae. Blocking this enzyme has been previously reported as a successful strategy to eradicate viral infections. Materials & methods: AutoDock Vina is utilized for the calculation of binding affinities of Sofosbuvir, Ribavirin and uridine triphosphate nucleotide to the fungal RdRp model built by homology modeling (no solved structures available). Results: Sofosbuvir shows excellent binding affinity to the fungal RdRp in silico. Conclusion: In this study, R. oryzae RdRp is suggested to be a possible protein target against the nucleotide inhibitor, Sofosbuvir.
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Affiliation(s)
- Abdo A Elfiky
- Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt
- College of Applied Medical Sciences, University of Al-Jouf, Sakakah, Saudi Arabia
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17
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Hassan GS, Georgey HH, Mohammed EZ, Omar FA. Anti-hepatitis-C virus activity and QSAR study of certain thiazolidinone and thiazolotriazine derivatives as potential NS5B polymerase inhibitors. Eur J Med Chem 2019; 184:111747. [PMID: 31604164 DOI: 10.1016/j.ejmech.2019.111747] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/02/2019] [Accepted: 09/27/2019] [Indexed: 02/07/2023]
Abstract
The present study reports on evaluation of anti-HCV activity and QSAR of certain arylidenethiazolidinone derivatives as potential inhibitors of HCV-NS5B polymerase. The pursued compounds involving, 5-aryliden-3-arylacetamidothiazolidin-2,4-diones 4-6(a-f), 5-arylidine-2-(N-arylacetamido)-iminothiazolidin-4-one (10) and their rigid counterparts 5-arylidinethiazolotriazines 13-15(a-f), were synthesized and their structures confirmed by spectral and elemental analyses. The results of NS5B polymerase inhibition assay revealed compound 4e, as the most active inhibitor (IC50 = 0.035 μM), which is four folds greater than that of the reference agent, VCH-759, (IC50 = 0.14 μM). Meanwhile, compounds 4b, 4c, 5a, and 5c, and 13b, 14e and 15c displayed equipotency to 2 folds higher activity than VCH-759 (IC50 values: 0.085, 0.14, 0.14, 0.10, 0.12, 0.09 and 0.07 μM, respectively). Assessment of the anti-HCV activity (GT1a) using human hepatoma cell line (Huh-7.5) illustrates superior activity of 4e (EC50 = 3.80 μM) relative to VCH-759 (EC50 = 5.29 μM). Cytotoxicity evaluation on, Transformed normal cell lines (Human Liver Epithelial-2, THLE-2 and Proximal Tubular Epithelial, RPTEC/TERT1), demonstrate enhanced safety profile of 4e (CC50 = 102.77, 161.37 μM, respectively) compared to VCH-759 (CC50 = 61.83, 81.28 μM, respectively). Molecular docking of the synthesized derivatives to NS5B polymerase allosteric site (PDB: 2HWH) showed similar binding modes to that of the co-crystallized ligand. Moreover, QSAR models were established for the studied thiazolidinones and thiazolotriazines to investigate the molecular characteristics contributing to the observed NS5B polymerase inhibition activity. The obtained results inspire further investigations of thiazolidinones and thiazolotriazine aiming at affording more potent, safe and orally active non-nucleoside NS5B polymerase inhibitors as anti-HCV drug candidates.
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Affiliation(s)
- Ghaneya S Hassan
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt; Pharmaceutical Chemistry Department, Faculty of Pharmacy, Badr University, Cairo, 11829, Egypt
| | - Hanan H Georgey
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt.
| | - Esraa Z Mohammed
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, October 6 University, Giza, 12585, Egypt
| | - Farghaly A Omar
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, October 6 University, Giza, 12585, Egypt
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Synthesis and Cytotoxic Activity against K562 and MCF7 Cell Lines of Some N-(5-Arylidene-4-oxo-2-thioxothiazolidin-3-yl)-2-((4-oxo-3-phenyl-3,4-dihydroquinazoline-2-yl)thio)acetamide Compounds. J CHEM-NY 2019. [DOI: 10.1155/2019/1492316] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Ethyl 2-((4-oxo-3-phenyl-3,4-dihydroquinazolin-2-yl)thio)acetate (3) which was synthesized starting from anthranilic acid (1) via 2-thioxo-3-phenylquinazolin-4(3H)-one (2) reacted with hydrazine hydrate to afford 2-((4-oxo-3-phenyl-3,4-dihydroquinazolin-2-yl)thio)acetohydrazide (4). Reaction of (4) with thiocarbonyl-bis-thioglycolic acid gave a new compound nameN-(4-oxo-2-thioxothiazolidin-3-yl)-2-((4-oxo-3-phenyl-3,4-dihydroquinazolin-2-yl)thio)acetamide (5). Knoevenagel condensation of (5) with appropriate aldehydes gave fourteen (Z)-N-(5-arylidene-4-oxo-2-thioxothiazolidin-3-yl)-2-((4-oxo-3-phenyl-3,4-dihydroquinazolin-2-yl)thio)acetamide compounds (6a–o) with moderate yield. The chemical structure of the compounds was elucidated on the basis of IR,1H-NMR,13C-NMR, and HR-MS spectral data. The 5-arylidene-2-thioxothiazolidinone compounds exhibited mild-to-moderate cytotoxic activity against both K562 (chronic myelogenous leukemia) cells and MCF7 (breast cancer) cells.
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Baharfar R, Tarahomi M, Azimi R. Efficient Multicomponent Synthesis of Novel Rhodanine Based Amide Derivatives. ORG PREP PROCED INT 2019. [DOI: 10.1080/00304948.2019.1653130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- R. Baharfar
- Faculty of Chemistry, University of Mazandaran, P. O. Box 4741695447, Babolsar, Iran
| | - M. Tarahomi
- Faculty of Chemistry, University of Mazandaran, P. O. Box 4741695447, Babolsar, Iran
| | - R. Azimi
- Research Institute of Forests and Rangelands, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
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20
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Mousavi SM, Zarei M, Hashemi SA, Babapoor A, Amani AM. A conceptual review of rhodanine: current applications of antiviral drugs, anticancer and antimicrobial activities. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2019; 47:1132-1148. [DOI: 10.1080/21691401.2019.1573824] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Seyyed Mojtaba Mousavi
- Department of Medical Nanotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Maryam Zarei
- Department of Medical Nanotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyyed Alireza Hashemi
- Department of Medical Nanotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Aziz Babapoor
- Department of Chemical Engineering, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Ali Mohammad Amani
- Department of Medical Nanotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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21
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Tejchman W, Orwat B, Korona-Głowniak I, Barbasz A, Kownacki I, Latacz G, Handzlik J, Żesławska E, Malm A. Highly efficient microwave synthesis of rhodanine and 2-thiohydantoin derivatives and determination of relationships between their chemical structures and antibacterial activity. RSC Adv 2019; 9:39367-39380. [PMID: 35540630 PMCID: PMC9076067 DOI: 10.1039/c9ra08690k] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 11/15/2019] [Indexed: 11/21/2022] Open
Abstract
Here we report studies on the synthesis of 12 new heterocyclic derivatives that differ in three structural motifs and the simultaneous evaluation of the impact of these three variables on the biological properties. The examined compounds are based on rhodanine and 2-thiohydantoin cores equipped with hydrogen or carboxymethyl substituents at the N-3 position and linked to a triphenylamine moiety through 1,4-phenylene, 1,4-naphthalenylene and 1,9-anthracenylene spacers at the C-5 position of the heterocycles. All the compounds were synthesized very quickly, selectively and in high yields according to the developed microwave-assisted Knoevenagel condensation protocol, and they were characterized thoroughly with NMR, FT-IR and ESI-HRMS techniques. The derivatives were tested for their activity against selected strains of Gram-positive and Gram-negative bacteria and yeast. Two compounds showed good activity against Gram-positive bacteria, and all of them showed low cytotoxicity against three cell lines of the human immune system. Based on membrane permeability assays it was demonstrated that the active compounds do not penetrate the cell membrane, and thus they must act on the bacterial cell surface. Finally, we proved that the evaluated structure modifications had a synergistic effect and the simultaneous presence of a 1,4-phenylene spacer and carboxymethyl group at N-3 caused the highest boost in antimicrobial activity. An efficient microwave-assisted synthesis of rhodanine and 2-thiohydantoin derivatives, and the correlation between their chemical structure and biological properties is reported.![]()
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Affiliation(s)
- Waldemar Tejchman
- Department of Chemistry
- Institute of Biology
- Pedagogical University of Cracow
- 30-084 Kraków
- Poland
| | - Bartosz Orwat
- Faculty of Chemistry
- Adam Mickiewicz University
- 61-614 Poznań
- Poland
- Centre for Advanced Technology
| | | | - Anna Barbasz
- Department of Chemistry
- Institute of Biology
- Pedagogical University of Cracow
- 30-084 Kraków
- Poland
| | - Ireneusz Kownacki
- Faculty of Chemistry
- Adam Mickiewicz University
- 61-614 Poznań
- Poland
- Centre for Advanced Technology
| | - Gniewomir Latacz
- Department of Technology and Biotechnology of Drugs
- Jagiellonian University Medical College
- 30-688 Kraków
- Poland
| | - Jadwiga Handzlik
- Department of Technology and Biotechnology of Drugs
- Jagiellonian University Medical College
- 30-688 Kraków
- Poland
| | - Ewa Żesławska
- Department of Chemistry
- Institute of Biology
- Pedagogical University of Cracow
- 30-084 Kraków
- Poland
| | - Anna Malm
- Department of Pharmaceutical Microbiology
- Medical University of Lublin
- 20-093 Lublin
- Poland
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22
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Ashraf MU, Iman K, Khalid MF, Salman HM, Shafi T, Rafi M, Javaid N, Hussain R, Ahmad F, Shahzad-Ul-Hussan S, Mirza S, Shafiq M, Afzal S, Hamera S, Anwar S, Qazi R, Idrees M, Qureshi SA, Chaudhary SU. Evolution of efficacious pangenotypic hepatitis C virus therapies. Med Res Rev 2018; 39:1091-1136. [PMID: 30506705 DOI: 10.1002/med.21554] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 10/11/2018] [Accepted: 10/11/2018] [Indexed: 12/12/2022]
Abstract
Hepatitis C compromises the quality of life of more than 350 million individuals worldwide. Over the last decade, therapeutic regimens for treating hepatitis C virus (HCV) infections have undergone rapid advancements. Initially, structure-based drug design was used to develop molecules that inhibit viral enzymes. Subsequently, establishment of cell-based replicon systems enabled investigations into various stages of HCV life cycle including its entry, replication, translation, and assembly, as well as role of host proteins. Collectively, these approaches have facilitated identification of important molecules that are deemed essential for HCV life cycle. The expanded set of putative virus and host-encoded targets has brought us one step closer to developing robust strategies for efficacious, pangenotypic, and well-tolerated medicines against HCV. Herein, we provide an overview of the development of various classes of virus and host-directed therapies that are currently in use along with others that are undergoing clinical evaluation.
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Affiliation(s)
- Muhammad Usman Ashraf
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan.,Virology Laboratory, Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Kanzal Iman
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Muhammad Farhan Khalid
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan.,Department of Biomedical Engineering, University of Engineering and Technology, Lahore, Pakistan
| | - Hafiz Muhammad Salman
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan.,Plant Biotechnology Laboratory, Institute of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Talha Shafi
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Momal Rafi
- Department of Statistics, University of Gujrat, Gujrat, Pakistan
| | - Nida Javaid
- Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Rashid Hussain
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Fayyaz Ahmad
- Department of Statistics, University of Gujrat, Gujrat, Pakistan
| | | | - Shaper Mirza
- Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Muhammad Shafiq
- Plant Biotechnology Laboratory, Institute of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Samia Afzal
- Virology Laboratory, Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Sadia Hamera
- Department of Plant Genetics, Institute of Life Sciences, University of Rostock, Germany
| | - Saima Anwar
- Department of Biomedical Engineering, University of Engineering and Technology, Lahore, Pakistan
| | - Romena Qazi
- Department of Pathology, Shaukat Khanum Memorial Cancer Hospital & Research Centre, Lahore, Pakistan
| | - Muhammad Idrees
- Virology Laboratory, Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.,Hazara University, Mansehra, Pakistan
| | - Sohail A Qureshi
- Institute of Integrative Biosciences, CECOS-University of Information Technology and Emerging Sciences, Peshawar, Pakistan
| | - Safee Ullah Chaudhary
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
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23
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Zhang D, Markoulides MS, Stepanovs D, Rydzik AM, El-Hussein A, Bon C, Kamps JJAG, Umland KD, Collins PM, Cahill ST, Wang DY, von Delft F, Brem J, McDonough MA, Schofield CJ. Structure activity relationship studies on rhodanines and derived enethiol inhibitors of metallo-β-lactamases. Bioorg Med Chem 2018; 26:2928-2936. [PMID: 29655609 PMCID: PMC6008492 DOI: 10.1016/j.bmc.2018.02.043] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 02/20/2018] [Accepted: 02/22/2018] [Indexed: 12/14/2022]
Abstract
Metallo-β-lactamases (MBLs) enable bacterial resistance to almost all classes of β-lactam antibiotics. We report studies on enethiol containing MBL inhibitors, which were prepared by rhodanine hydrolysis. The enethiols inhibit MBLs from different subclasses. Crystallographic analyses reveal that the enethiol sulphur displaces the di-Zn(II) ion bridging 'hydrolytic' water. In some, but not all, cases biophysical analyses provide evidence that rhodanine/enethiol inhibition involves formation of a ternary MBL enethiol rhodanine complex. The results demonstrate how low molecular weight active site Zn(II) chelating compounds can inhibit a range of clinically relevant MBLs and provide additional evidence for the potential of rhodanines to be hydrolysed to potent inhibitors of MBL protein fold and, maybe, other metallo-enzymes, perhaps contributing to the complex biological effects of rhodanines. The results imply that any medicinal chemistry studies employing rhodanines (and related scaffolds) as inhibitors should as a matter of course include testing of their hydrolysis products.
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Affiliation(s)
- Dong Zhang
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Marios S Markoulides
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Dmitrijs Stepanovs
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Anna M Rydzik
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Ahmed El-Hussein
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom; The National Institute of Laser Enhanced Science, Cairo University, Egypt
| | - Corentin Bon
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Jos J A G Kamps
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Klaus-Daniel Umland
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Patrick M Collins
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Samuel T Cahill
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - David Y Wang
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Frank von Delft
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom; Structural Genomics Consortium (SGC), University of Oxford, Oxford, OX3 7DQ, UK; (e)Department of Biochemistry, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Jürgen Brem
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Michael A McDonough
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Christopher J Schofield
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom.
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25
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Balasubramanian K, Patil VM. Quantum molecular modeling of hepatitis C virus inhibition through non-structural protein 5B polymerase receptor binding of C 5-arylidene rhodanines. Comput Biol Chem 2018; 73:147-158. [PMID: 29486389 DOI: 10.1016/j.compbiolchem.2018.01.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 01/09/2018] [Accepted: 01/23/2018] [Indexed: 11/25/2022]
Abstract
We have carried out high-level quantum chemical computations followed by molecular docking studies on a set of 17C5-arylidene rhodanine isomers to provide insights into the binding modes with different reported binding pockets of the nonstructural protein 5B (NS5B) polymerase that contribute to the hepatitis C virus (HCV) inhibition. We optimized the multi-target profile of the selected rhodanine analogs to investigate potential non-nucleotide inhibitors (NNIs) by quantum chemical optimization of the 18 isomers followed by docking with quantum chemically optimized structures of each isomer with NS5B polymerase at multiple binding pockets. The binding affinities of the PP-I, PP-II and TP-II pockets of NS5B polymerase were analyzed for all the 17 isomers of 2-[(5Z)-5-(2,4-dichlorobenzylidene)-4-oxo-2-thioxo-1,3-thiazolidin-3-yl]-3-phenylpropanoic acid. On the basis of binding propensity at the different pockets and inhibitor constants, we ranked these isomers as potential candidates for the HCV inhibition. We have identified four isomers as promising NNIs of NS5B polymerase with comparable binding and inhibition to the standard (1,3) dichloro substituted isomer that exhibits in vitro activity and several other isomers as candidates in a "multi-targeted drug" approach.
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Affiliation(s)
| | - Vaishali M Patil
- Department of Pharmaceutical Chemistry, KIET School of Pharmacy, KIET Group of Institutions, Ghaziabad, Uttar Pradesh, India.
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26
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Kaminskyy D, Kryshchyshyn A, Lesyk R. 5-Ene-4-thiazolidinones - An efficient tool in medicinal chemistry. Eur J Med Chem 2017; 140:542-594. [PMID: 28987611 PMCID: PMC7111298 DOI: 10.1016/j.ejmech.2017.09.031] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 07/14/2017] [Accepted: 09/17/2017] [Indexed: 02/02/2023]
Abstract
The presented review is an attempt to summarize a huge volume of data on 5-ene-4-thiazolidinones being a widely studied class of small molecules used in modern organic and medicinal chemistry. The manuscript covers approaches to the synthesis of 5-ene-4-thiazolidinone derivatives: modification of the C5 position of the basic core; synthesis of the target compounds in the one-pot or multistage reactions or transformation of other related heterocycles. The most prominent pharmacological profiles of 5-ene derivatives of different 4-thiazolidinone subtypes belonging to hit-, lead-compounds, drug-candidates and drugs as well as the most studied targets have been discussed. Currently target compounds (especially 5-en-rhodanines) are assigned as frequent hitters or pan-assay interference compounds (PAINS) within high-throughput screening campaigns. Nevertheless, the crucial impact of the presence/nature of C5 substituent (namely 5-ene) on the pharmacological effects of 5-ene-4-thiazolidinones was confirmed by the numerous listed findings from the original articles. The main directions for active 5-ene-4-thiazolidinones optimization have been shown: i) complication of the fragment in the C5 position; ii) introduction of the substituents in the N3 position (especially fragments with carboxylic group or its derivatives); iii) annealing in complex heterocyclic systems; iv) combination with other pharmacologically attractive fragments within hybrid pharmacophore approach. Moreover, the utilization of 5-ene-4-thiazolidinones in the synthesis of complex compounds with potent pharmacological application is described. The chemical transformations cover mainly the reactions which involve the exocyclic double bond in C5 position of the main core and correspond to the abovementioned direction of the 5-ene-4-thiazolidinone modification.
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Affiliation(s)
- Danylo Kaminskyy
- Department of Pharmaceutical, Organic and Bioorganic Chemistry, Danylo Halytsky Lviv National Medical University, Pekarska 69, Lviv-10, 79010, Ukraine
| | - Anna Kryshchyshyn
- Department of Pharmaceutical, Organic and Bioorganic Chemistry, Danylo Halytsky Lviv National Medical University, Pekarska 69, Lviv-10, 79010, Ukraine
| | - Roman Lesyk
- Department of Pharmaceutical, Organic and Bioorganic Chemistry, Danylo Halytsky Lviv National Medical University, Pekarska 69, Lviv-10, 79010, Ukraine.
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Kaminskyy D, Kryshchyshyn A, Lesyk R. Recent developments with rhodanine as a scaffold for drug discovery. Expert Opin Drug Discov 2017; 12:1233-1252. [PMID: 29019278 DOI: 10.1080/17460441.2017.1388370] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Rhodanines, as one of the 4-thiazolidinones subtypes, are recognized as privileged heterocycles in medicinal chemistry. The main achievements include the development of drug-like molecules with numerous biological activities as well as approved drugs. Among rhodanines, 5-ene-rhodanines are of special interest, and are often claimed as pan assay interference compounds due to Michael acceptor functionality. Areas covered: Herein, the synthetic protocols for rhodanines and their transformation are reviewed. Biological activity is briefly discussed as well as biotargets, mode of actions and optimization directions. Furthermore, the utilization of 5-ene-rhodanines in Michael additions are discussed while both pro and contra arguments have been outlined within medicinal chemistry application. Expert opinion: Rhodanines remain privileged heterocycles in drug discovery. They are accessible building blocks for optimization and transformation into related heterocycles, simplified analogues and fused heterocycles with a thiazolidine framework. Michael acceptor functionality, as well as the thesis about low selectivity towards biotargets of rhodanines, must be confirmed experimentally and it cannot be based on just the presence of conjugated α,β-unsaturated carbonyl. Moreover, the positive aspects of Michael acceptors must be considered as well as their multitarget properties. New criteria for target affinity must be found. In conclusion, rhodanines are generally not problematic per se.
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Affiliation(s)
- Danylo Kaminskyy
- a Department of Pharmaceutical, Organic and Bioorganic Chemistry , Danylo Halytsky Lviv National Medical University , Lviv-10 , Ukraine
| | - Anna Kryshchyshyn
- a Department of Pharmaceutical, Organic and Bioorganic Chemistry , Danylo Halytsky Lviv National Medical University , Lviv-10 , Ukraine
| | - Roman Lesyk
- a Department of Pharmaceutical, Organic and Bioorganic Chemistry , Danylo Halytsky Lviv National Medical University , Lviv-10 , Ukraine
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28
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Devi NS, Devi N. Synthesis of rhodanine-derived enaminones in aqueous medium. SYNTHETIC COMMUN 2017. [DOI: 10.1080/00397911.2017.1319486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- N. S. Devi
- Department of Chemistry, Cotton College, Guwahati, Assam
| | - Nirada Devi
- Department of Chemistry, Cotton College, Guwahati, Assam
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29
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Elfiky AA, Ismail AM. Molecular modeling and docking revealed superiority of IDX-184 as HCV polymerase inhibitor. Future Virol 2017. [DOI: 10.2217/fvl-2017-0027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: IDX-184 is a nonstructural 5b nucleoside inhibitor (NI) that was under clinical trials against HCV. This work adopts a molecular modeling approach in order to study the interaction between IDX-184 and HCV polymerase from four different genotypes. Methods: Comparisons to the native nucleotide (Guanosine triphosphate) and other NIs were performed using interaction descriptors, calculated using semiempirical quantum mechanics and molecular docking. Results: IDX-184 shows potent binding to the active site of the polymerases. In addition, IDX-184 was better than Sofosbuvir and Ribavirin when docked into polymerase active site (even with experimentally solved structure). Conclusion: Analysis of the interaction descriptors and docking complexes suggests IDX-184 as a superior NI against the studied HCV subtypes.
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Affiliation(s)
- Abdo A Elfiky
- Biophysics Department, Faculty of Sciences, Cairo University, PO Box 12613, Giza, Egypt
- Quantitative Life Science Department, The Abdus Salam International Center for Theoretical Physics, Strada Costiera, 11 I34151, Trieste, Italy
| | - Alaa M Ismail
- Biophysics Department, Faculty of Sciences, Cairo University, PO Box 12613, Giza, Egypt
- Biochemistry Department, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, T6G 2R3, AB, Canada
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30
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Ganesan A, Barakat K. Applications of computer-aided approaches in the development of hepatitis C antiviral agents. Expert Opin Drug Discov 2017; 12:407-425. [PMID: 28164720 DOI: 10.1080/17460441.2017.1291628] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
INTRODUCTION Hepatitis C virus (HCV) is a global health problem that causes several chronic life-threatening liver diseases. The numbers of people affected by HCV are rising annually. Since 2011, the FDA has approved several anti-HCV drugs; while many other promising HCV drugs are currently in late clinical trials. Areas covered: This review discusses the applications of different computational approaches in HCV drug design. Expert opinion: Molecular docking and virtual screening approaches have emerged as a low-cost tool to screen large databases and identify potential small-molecule hits against HCV targets. Ligand-based approaches are useful for filtering-out compounds with rich physicochemical properties to inhibit HCV targets. Molecular dynamics (MD) remains a useful tool in optimizing the ligand-protein complexes and understand the ligand binding modes and drug resistance mechanisms in HCV. Despite their varied roles, the application of in-silico approaches in HCV drug design is still in its infancy. A more mature application should aim at modelling the whole HCV replicon in its active form and help to identify new effective druggable sites within the replicon system. With more technological advancements, the roles of computer-aided methods are only going to increase several folds in the development of next-generation HCV drugs.
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Affiliation(s)
- Aravindhan Ganesan
- a Faculty of Pharmacy and Pharmaceutical Sciences , University of Alberta , Edmonton , Canada
| | - Khaled Barakat
- a Faculty of Pharmacy and Pharmaceutical Sciences , University of Alberta , Edmonton , Canada
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31
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Thai KM, Dong QH, Nguyen TTL, Le DP, Le MT, Tran TD. Computational Approaches for the Discovery of Novel Hepatitis C Virus NS3/4A and NS5B Inhibitors. Oncology 2017. [DOI: 10.4018/978-1-5225-0549-5.ch017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nonstructural 5B (NS5B) polymerase and Nonstructural 3/4A (NS3/4A) protease have proven to be promising targets for the development of anti-HCV (Hepatitis C Virus) agents. The NS5B polymerase is of paramount importance in HCV viral replication; therefore, employing NS5B inhibitors was considered an effective way for the treatment of HCV. Identifying inhibitors against NS3/4A serine protease represents another attractive approach applied in anti-HCV drug discovery, which is evidenced by its crucial role of in the biogenesis of the viral replication activity. In this chapter, many different computational approaches including Quantitative Structure-Activity Relationship (QSAR) and virtual screening in anti-HCV drug discovery were considered and discussed in detail. Virtual Screening (VS) techniques, including ligand-based and structure-based, and QSAR have been utilized for the discovery of NS5B inhibitors. Moreover, using various in silico protocols and workflows, a number of studies have been conducted with an aim of identifying potential NS3/4A blockage agents.
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Affiliation(s)
| | | | | | - Duy-Phong Le
- University of Medicine and Pharmacy at HCMC, Vietnam
| | - Minh-Tri Le
- University of Medicine and Pharmacy at HCMC, Vietnam
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32
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Krátký M, Štěpánková Š, Vorčáková K, Vinšová J. Synthesis and in vitro evaluation of novel rhodanine derivatives as potential cholinesterase inhibitors. Bioorg Chem 2016; 68:23-9. [DOI: 10.1016/j.bioorg.2016.07.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/28/2016] [Accepted: 07/06/2016] [Indexed: 12/21/2022]
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33
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Zelisko NI. New thiopyrano[2,3-d][1,3]thiazole derivatives as potential antiviral agents. UKRAINIAN BIOCHEMICAL JOURNAL 2016. [DOI: 10.15407/ubj88.si01.105] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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34
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Subhedar DD, Shaikh MH, Nawale L, Yeware A, Sarkar D, Shingate BB. [Et3NH][HSO4] catalyzed efficient synthesis of 5-arylidene-rhodanine conjugates and their antitubercular activity. RESEARCH ON CHEMICAL INTERMEDIATES 2016. [DOI: 10.1007/s11164-016-2484-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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35
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Fernandes TDA, Manvar D, Domingos JLO, Basu A, Nichols DB, Kaushik-Basu N, Costa PRR. 5-Carba-pterocarpens: A new scaffold with anti-HCV activity. Eur J Med Chem 2016; 112:33-38. [PMID: 26874742 DOI: 10.1016/j.ejmech.2016.02.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Revised: 02/03/2016] [Accepted: 02/04/2016] [Indexed: 01/01/2023]
Abstract
The synthesis of a series of 5-carba-pterocarpens derivatives involving the cyclization of α-aryl-α-tetralones is described. Several compounds demonstrated potent activity and selectivity in vitro against HCV replicon reporter cells. The best profile in Huh7/Rep-Feo1b replicon reporter cells was observed with 2h (EC50 = 5.5 μM/SI = 20), while 2e was the most active in Huh7.5-FGR-JC1-Rluc2A replicon reporter cells (EC50 = 1.5 μM/SI = 70). Hydroxy groups at A- and D-rings are essential for anti-HCV activity, and substitutions in the A-ring at positions 3 and 4 resulted in enhanced activity of the compounds.
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Affiliation(s)
- Talita de A Fernandes
- Laboratório de Química Bioorgânica, Instituto de Pesquisas de Produtos Naturais, Universidade Federal do Rio de Janeiro, Centro de Ciências da Saúde, Bloco H, Ilha da Cidade Universitária, 21941-590 Rio de Janeiro, RJ, Brazil
| | - Dinesh Manvar
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers-The State University of New Jersey, 185 South Orange Avenue, New Jersey 07103, USA
| | - Jorge L O Domingos
- Departamento de Química Orgânica, Centro de Tecnologia e Ciências, Universidade do Estado do Rio de Janeiro, Rua São Francisco Xavier 524, Pav. Haroldo Lisboa da Cunha - s 406 - Maracanã, 20550-900 Rio de Janeiro, RJ, Brazil
| | - Amartya Basu
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers-The State University of New Jersey, 185 South Orange Avenue, New Jersey 07103, USA
| | - Daniel Brian Nichols
- Department of Biological Sciences, Seton Hall University, 400 South Orange Avenue, New Jersey, 07079, USA
| | - Neerja Kaushik-Basu
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers-The State University of New Jersey, 185 South Orange Avenue, New Jersey 07103, USA.
| | - Paulo R R Costa
- Laboratório de Química Bioorgânica, Instituto de Pesquisas de Produtos Naturais, Universidade Federal do Rio de Janeiro, Centro de Ciências da Saúde, Bloco H, Ilha da Cidade Universitária, 21941-590 Rio de Janeiro, RJ, Brazil.
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36
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Wei Y, Li J, Qing J, Huang M, Wu M, Gao F, Li D, Hong Z, Kong L, Huang W, Lin J. Discovery of Novel Hepatitis C Virus NS5B Polymerase Inhibitors by Combining Random Forest, Multiple e-Pharmacophore Modeling and Docking. PLoS One 2016; 11:e0148181. [PMID: 26845440 PMCID: PMC4742222 DOI: 10.1371/journal.pone.0148181] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 01/14/2016] [Indexed: 02/07/2023] Open
Abstract
The NS5B polymerase is one of the most attractive targets for developing new drugs to block Hepatitis C virus (HCV) infection. We describe the discovery of novel potent HCV NS5B polymerase inhibitors by employing a virtual screening (VS) approach, which is based on random forest (RB-VS), e-pharmacophore (PB-VS), and docking (DB-VS) methods. In the RB-VS stage, after feature selection, a model with 16 descriptors was used. In the PB-VS stage, six energy-based pharmacophore (e-pharmacophore) models from different crystal structures of the NS5B polymerase with ligands binding at the palm I, thumb I and thumb II regions were used. In the DB-VS stage, the Glide SP and XP docking protocols with default parameters were employed. In the virtual screening approach, the RB-VS, PB-VS and DB-VS methods were applied in increasing order of complexity to screen the InterBioScreen database. From the final hits, we selected 5 compounds for further anti-HCV activity and cellular cytotoxicity assay. All 5 compounds were found to inhibit NS5B polymerase with IC50 values of 2.01-23.84 μM and displayed anti-HCV activities with EC50 values ranging from 1.61 to 21.88 μM, and all compounds displayed no cellular cytotoxicity (CC50 > 100 μM) except compound N2, which displayed weak cytotoxicity with a CC50 value of 51.3 μM. The hit compound N2 had the best antiviral activity against HCV, with a selective index of 32.1. The 5 hit compounds with new scaffolds could potentially serve as NS5B polymerase inhibitors through further optimization and development.
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Affiliation(s)
- Yu Wei
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300071, China
| | - Jinlong Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300071, China
- High-Throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biomedicine and Technology, Tianjin, 300457, China
| | - Jie Qing
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Mingjie Huang
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Ming Wu
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Fenghua Gao
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Dongmei Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300071, China
| | - Zhangyong Hong
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Lingbao Kong
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
- * E-mail: (JPL); (WH); (LK)
| | - Weiqiang Huang
- PracticaChem-China, Tianjin, 300192, PR China
- * E-mail: (JPL); (WH); (LK)
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300071, China
- High-Throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biomedicine and Technology, Tianjin, 300457, China
- * E-mail: (JPL); (WH); (LK)
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37
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Prediction of the ligands having the inhibitory activity against the HCV non-structural protein 5B polymerase. ASIAN PACIFIC JOURNAL OF TROPICAL DISEASE 2015. [DOI: 10.1016/s2222-1808(15)60906-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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Zhao C, Wang Y, Ma S. Recent advances on the synthesis of hepatitis C virus NS5B RNA-dependent RNA-polymerase inhibitors. Eur J Med Chem 2015; 102:188-214. [PMID: 26276434 DOI: 10.1016/j.ejmech.2015.07.046] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 07/23/2015] [Accepted: 07/28/2015] [Indexed: 02/07/2023]
Abstract
Hepatitis C is a viral liver infection considered as the major cause of cirrhosis and hepatocellular carcinoma (HCC). The HCV NS5B polymerase, an RNA-dependent RNA polymerase, is essential for HCV replication, which is able to catalyze the synthesis of positive (genomic) and negative (template) strand HCV RNA, but has no functional equivalent in mammalian cells. Therefore, the NS5B polymerase has emerged as an attractive target for the development of specifically targeted antiviral therapy for HCV (DAA, for direct-acting antivirals). Recently, a growing number of compounds have been reported as the NS5B polymerase inhibitors, some of which especially have been licensed in clinical trials. This review describes recent advances on the synthesis of the NS5B polymerase inhibitors, focusing on the merits and demerits of their synthetic methods. In particular, inspiration from the synthesis and the future direction of the NS5B polymerase inhibitors are highlighted.
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Affiliation(s)
- Can Zhao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, PR China
| | - Yinhu Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, PR China
| | - Shutao Ma
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, PR China.
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39
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Wei Y, Li J, Chen Z, Wang F, Huang W, Hong Z, Lin J. Multistage virtual screening and identification of novel HIV-1 protease inhibitors by integrating SVM, shape, pharmacophore and docking methods. Eur J Med Chem 2015; 101:409-18. [PMID: 26185005 DOI: 10.1016/j.ejmech.2015.06.054] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Revised: 06/28/2015] [Accepted: 06/29/2015] [Indexed: 11/30/2022]
Abstract
The HIV-1 protease has proven to be a crucial component of the HIV replication machinery and a reliable target for anti-HIV drug discovery. In this study, we applied an optimized hierarchical multistage virtual screening method targeting HIV-1 protease. The method sequentially applied SVM (Support Vector Machine), shape similarity, pharmacophore modeling and molecular docking. Using a validation set (270 positives, 155,996 negatives), the multistage virtual screening method showed a high hit rate and high enrichment factor of 80.47% and 465.75, respectively. Furthermore, this approach was applied to screen the National Cancer Institute database (NCI), which contains 260,000 molecules. From the final hit list, 6 molecules were selected for further testing in an in vitro HIV-1 protease inhibitory assay, and 2 molecules (NSC111887 and NSC121217) showed inhibitory potency against HIV-1 protease, with IC50 values of 62 μM and 162 μM, respectively. With further chemical development, these 2 molecules could potentially serve as HIV-1 protease inhibitors.
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Affiliation(s)
- Yu Wei
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, PR China; College of Pharmacy, Nankai University, Tianjin 300071, PR China
| | - Jinlong Li
- College of Pharmacy, Nankai University, Tianjin 300071, PR China
| | - Zeming Chen
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, PR China; College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Fengwei Wang
- Department of Oncology, Tianjin Union Medical Center, Tianjin 300180, PR China
| | | | - Zhangyong Hong
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, PR China; College of Life Sciences, Nankai University, Tianjin 300071, PR China.
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, PR China; College of Pharmacy, Nankai University, Tianjin 300071, PR China.
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40
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Vrontaki E, Melagraki G, Mavromoustakos T, Afantitis A. Searching for anthranilic acid-based thumb pocket 2 HCV NS5B polymerase inhibitors through a combination of molecular docking, 3D-QSAR and virtual screening. J Enzyme Inhib Med Chem 2015; 31:38-52. [PMID: 26060939 DOI: 10.3109/14756366.2014.1003925] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A combination of the following computational methods: (i) molecular docking, (ii) 3-D Quantitative Structure Activity Relationship Comparative Molecular Field Analysis (3D-QSAR CoMFA), (iii) similarity search and (iv) virtual screening using PubChem database was applied to identify new anthranilic acid-based inhibitors of hepatitis C virus (HCV) replication. A number of known inhibitors were initially docked into the "Thumb Pocket 2" allosteric site of the crystal structure of the enzyme HCV RNA-dependent RNA polymerase (NS5B GT1b). Then, the CoMFA fields were generated through a receptor-based alignment of docking poses to build a validated and stable 3D-QSAR CoMFA model. The proposed model can be first utilized to get insight into the molecular features that promote bioactivity, and then within a virtual screening procedure, it can be used to estimate the activity of novel potential bioactive compounds prior to their synthesis and biological tests.
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Affiliation(s)
- Eleni Vrontaki
- a Department of Chemoinformatics , NovaMechanics Ltd. , Nicosia , Cyprus and.,b Department of Chemistry, Laboratory of Organic Chemistry , University of Athens , Athens , Greece
| | - Georgia Melagraki
- a Department of Chemoinformatics , NovaMechanics Ltd. , Nicosia , Cyprus and
| | - Thomas Mavromoustakos
- b Department of Chemistry, Laboratory of Organic Chemistry , University of Athens , Athens , Greece
| | - Antreas Afantitis
- a Department of Chemoinformatics , NovaMechanics Ltd. , Nicosia , Cyprus and
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41
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Vrontaki E, Melagraki G, Mavromoustakos T, Afantitis A. Exploiting ChEMBL database to identify indole analogs as HCV replication inhibitors. Methods 2015; 71:4-13. [DOI: 10.1016/j.ymeth.2014.03.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Revised: 03/11/2014] [Accepted: 03/13/2014] [Indexed: 12/16/2022] Open
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42
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Synthesis and antibacterial activity of analogs of 5-arylidene-3-(4-methylcoumarin-7-yloxyacetylamino)-2-thioxo-1,3-thiazoli-din-4-one. Molecules 2014; 19:13577-86. [PMID: 25255757 PMCID: PMC6271709 DOI: 10.3390/molecules190913577] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 08/26/2014] [Accepted: 08/27/2014] [Indexed: 11/30/2022] Open
Abstract
In an effort to develop new antimicrobial agents, 3-(4-methylcoumarin-7-yloxyacetylamino)-2-thioxo-1,3-thiazolidin-4-one (4) was synthesized by reaction of thiocarbonylbisthioglycolic acid with ethyl (4-methyl-2-oxo-2H-chromen-7-yloxy)aceto- hydrazide (3), which was prepared in turn from 7-hydroxy-4-methylcoumarin (1). The condensation of compound 4 with different aromatic aldehydes afforded a series of 5-(arylidene)-3-(4-methylcoumarin-7-yloxyacetyl-amino)-2-thioxo-1,3-thiozolidin-4-one analogs 5a–h. The structures of these synthetic compounds were elucidated on the basis of IR, 1H-NMR and 13C-NMR spectral data and ESI-MS spectrometric analysis. Compounds 5a–h were examined for their antibacterial activity against several strains of Gram-positive and Gram-negative bacteria.
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43
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Barakat A, Al-Majid AM, AL-Najjar HJ, Mabkhot YN, Ghabbour HA, Fun HK. An efficient and green procedure for synthesis of rhodanine derivatives by aldol-thia-Michael protocol using aqueous diethylamine medium. RSC Adv 2014. [DOI: 10.1039/c3ra46551a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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44
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Küçükgüzel I, Satılmış G, Gurukumar KR, Basu A, Tatar E, Nichols DB, Talele TT, Kaushik-Basu N. 2-Heteroarylimino-5-arylidene-4-thiazolidinones as a new class of non-nucleoside inhibitors of HCV NS5B polymerase. Eur J Med Chem 2013; 69:931-41. [PMID: 24161679 DOI: 10.1016/j.ejmech.2013.08.043] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 08/27/2013] [Accepted: 08/31/2013] [Indexed: 12/09/2022]
Abstract
Hepatitis C virus (HCV) NS5B polymerase is an important and attractive target for the development of anti-HCV drugs. Here we report on the design, synthesis and evaluation of twenty-four novel allosteric inhibitors bearing the 4-thiazolidinone scaffold as inhibitors of HCV NS5B polymerase. Eleven compounds tested were found to inhibit HCV NS5B with IC₅₀ values ranging between 19.8 and 64.9 μM. Compound 24 was the most active of this series with an IC₅₀ of 5.6 μM. A number of these derivatives further exhibited strong inhibition against HCV 1b and 2a genotypes in cell based antiviral assays. Molecular docking analysis predicted that the thiazolidinone derivatives bind to the NS5B thumb pocket-II (TP-II). Our results suggest that further optimization of the thiazolidinone scaffold may be possible to yield new derivatives with improved enzyme- and cell-based activity.
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Affiliation(s)
- Ilkay Küçükgüzel
- Marmara University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Haydarpaşa, 34668 İstanbul, Turkey.
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45
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Elfiky AA, Elshemey WM, Gawad WA, Desoky OS. Molecular modeling comparison of the performance of NS5b polymerase inhibitor (PSI-7977) on prevalent HCV genotypes. Protein J 2013; 32:75-80. [PMID: 23322006 DOI: 10.1007/s10930-013-9462-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The current available treatment for hepatitis C virus (HCV)-the causative of liver cirrhosis and development of liver cancer-is a dual therapy using modified interferon and ribavirin. While this regimen increases the sustained viral response rate up to 40-80 % in different genotypes, unfortunately, it is poorly tolerated by patients. PSI-7977, a prodrug for PSI-7409, is a Non-Structural 5b (NS5b) polymerase nucleoside inhibitor that is currently in phase III clinical trials. The activated PSI-7977 is a direct acting antiviral (DAA) drug that acts on NS5b polymerase of HCV through a coordination bond with the two Mg(+2) present at the GDD active site motif. The present work utilizes a molecular modeling approach for studying the interaction between the activated PSI-7977 and the 12 amino acids constituting a 5 Å region surrounding the GDD active triad motif for HCV genotypes 1a, 2b, 3b and 4a. The analysis of the interaction parameters suggests that PSI-7977 is probably a better DAA drug for HCV genotypes 1a and 3b rather than genotypes 2b and 4a.
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Affiliation(s)
- Abdo A Elfiky
- Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt.
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46
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Structure modeling and docking study of HCV NS5B-3a RNA polymerase for the identification of potent inhibitors. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0666-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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47
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Patel B, Krishnan R, Khadtare N, Gurukumar KR, Basu A, Arora P, Bhatt A, Patel MR, Dana D, Kumar S, Kaushik-Basu N, Talele TT. Design and synthesis of L- and D-phenylalanine derived rhodanines with novel C5-arylidenes as inhibitors of HCV NS5B polymerase. Bioorg Med Chem 2013; 21:3262-71. [PMID: 23598249 PMCID: PMC3651775 DOI: 10.1016/j.bmc.2013.03.041] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 03/01/2013] [Accepted: 03/09/2013] [Indexed: 10/27/2022]
Abstract
Hepatitis C virus (HCV) NS5B polymerase is a key target for anti-HCV therapeutics development. Herein, we report the synthesis and in vitro evaluation of anti-NS5B polymerase activity of a molecular hybrid of our previously reported lead compounds 1 (IC50=7.7 μM) and 2 (IC50=10.6 μM) as represented by hybrid compound 27 (IC50=6.7 μM). We have explored the optimal substituents on the terminal phenyl ring of the 3-phenoxybenzylidene moiety in 27, by generating a set of six analogs. This resulted in the identification of compound 34 with an IC50 of 2.6 μM. To probe the role of stereochemistry towards the observed biological activity, we synthesized and evaluated the D-isomers 41 (IC50=19.3 μM) and 45 (IC50=5.4 μM) as enantiomers of the l-isomers 27 and 34, respectively. The binding site of compounds 32 and 34 was mapped to palm pocket-I (PP-I) of NS5B. The docking models of 34 and 45 within the PP-I of NS5B were investigated to envisage the molecular mechanism of inhibition.
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Affiliation(s)
- Bhargav Patel
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, 8000 Utopia Parkway, Queens, NY 11439, USA
| | - Ramalingam Krishnan
- Department of Biochemistry and Molecular Biology, UMDNJ-New Jersey Medical School, 185 South Orange Avenue, Newark, NJ 07103, USA
| | - Nikhil Khadtare
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, 8000 Utopia Parkway, Queens, NY 11439, USA
| | - K. R. Gurukumar
- Department of Biochemistry and Molecular Biology, UMDNJ-New Jersey Medical School, 185 South Orange Avenue, Newark, NJ 07103, USA
| | - Amartya Basu
- Department of Biochemistry and Molecular Biology, UMDNJ-New Jersey Medical School, 185 South Orange Avenue, Newark, NJ 07103, USA
| | - Payal Arora
- Department of Biochemistry and Molecular Biology, UMDNJ-New Jersey Medical School, 185 South Orange Avenue, Newark, NJ 07103, USA
| | - Aaditya Bhatt
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, 8000 Utopia Parkway, Queens, NY 11439, USA
| | - Maulik R. Patel
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, 1275 York Ave, New York, NY 10021, USA
| | - Dibyendu Dana
- Department of Chemistry and Biochemistry, Queens College and the Graduate Center of the City University of New York, 65–30 Kissena Blvd., Flushing, NY 11367, USA
| | - Sanjai Kumar
- Department of Chemistry and Biochemistry, Queens College and the Graduate Center of the City University of New York, 65–30 Kissena Blvd., Flushing, NY 11367, USA
| | - Neerja Kaushik-Basu
- Department of Biochemistry and Molecular Biology, UMDNJ-New Jersey Medical School, 185 South Orange Avenue, Newark, NJ 07103, USA
| | - Tanaji T. Talele
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, 8000 Utopia Parkway, Queens, NY 11439, USA
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48
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Jin X, Zheng CJ, Song MX, Wu Y, Sun LP, Li YJ, Yu LJ, Piao HR. Synthesis and antimicrobial evaluation of l-phenylalanine-derived C5-substituted rhodanine and chalcone derivatives containing thiobarbituric acid or 2-thioxo-4-thiazolidinone. Eur J Med Chem 2012; 56:203-9. [DOI: 10.1016/j.ejmech.2012.08.026] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 08/17/2012] [Accepted: 08/20/2012] [Indexed: 10/27/2022]
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49
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Golub AG, Gurukumar KR, Basu A, Bdzhola VG, Bilokin Y, Yarmoluk SM, Lee JC, Talele TT, Nichols DB, Kaushik-Basu N. Discovery of new scaffolds for rational design of HCV NS5B polymerase inhibitors. Eur J Med Chem 2012; 58:258-64. [PMID: 23127989 DOI: 10.1016/j.ejmech.2012.09.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 09/05/2012] [Accepted: 09/07/2012] [Indexed: 02/02/2023]
Abstract
Hepatitis C virus (HCV) NS5B polymerase is a key target for the development of anti-HCV drugs. Here we report on the identification of novel allosteric inhibitors of HCV NS5B through a combination of structure-based virtual screening and in vitro NS5B inhibition assays. One hundred and sixty thousand compounds from the Otava database were virtually screened against the thiazolone inhibitor binding site on NS5B (thumb pocket-2, TP-2), resulting in a sequential down-sizing of the library by 2.7 orders of magnitude to yield 59 NS5B non-nucleoside inhibitor (NNI) candidates. In vitro evaluation of the NS5B inhibitory activity of the 59 selected compounds resulted in a 14% hit rate, yielding 8 novel structural scaffolds. Of these, compound 1 bearing a 4-hydrazinoquinazoline scaffold was the most active (IC(50) = 16.0 μM). The binding site of all 8 NNIs was mapped to TP-2 of NS5B as inferred by a decrease in their inhibition potency against the M423T NS5B mutant, employed as a screen for TP-2 site binders. At 100 μM concentration, none of the eight compounds exhibited any cytotoxicity, and all except compound 8 exhibited between 40 and 60% inhibition of intracellular NS5B polymerase activity in BHK-NS5B-FRLuc reporter cells. These inhibitor scaffolds will form the basis for future optimization and development of more potent NS5B inhibitors.
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Affiliation(s)
- Andriy G Golub
- Department of Combinatorial Chemistry, Institute of Molecular Biology and Genetics of the National Academy of Sciences of Ukraine, 150 Zabolotnogo Street, 03143 Kyiv, Ukraine
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50
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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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