1
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Darsaraee M, Kaveh S, Mani-Varnosfaderani A, Neiband MS. General structure-activity/selectivity relationship patterns for the inhibitors of the chemokine receptors (CCR1/CCR2/CCR4/CCR5) with application for virtual screening of PubChem database. J Biomol Struct Dyn 2024; 42:8781-8799. [PMID: 37599469 DOI: 10.1080/07391102.2023.2248255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 08/08/2023] [Indexed: 08/22/2023]
Abstract
CC chemokine receptors (CCRs) form a crucial subfamily of G protein-linked receptors that play a distinct role in the onset and progression of various life-threatening diseases. The main aim of this research is to derive general structure-activity relationship (SAR) patterns to describe the selectivity and activity of CCR inhibitors. To this end, a total of 7332 molecules related to the inhibition of CCR1, CCR2, CCR4, and CCR5 were collected from the Binding Database and analyzed using machine learning techniques. A diverse set of 450 molecular descriptors was calculated for each molecule, and the molecules were classified based on their therapeutic targets and activities. The variable importance in the projection (VIP) approach was used to select discriminatory molecular features, and classification models were developed using supervised Kohonen networks (SKN) and counter-propagation artificial neural networks (CPANN). The reliability and predictability of the models were estimated using 10-fold cross-validation, an external validation set, and an applicability domain approach. We were able to identify different sets of molecular descriptors for discriminating between active and inactive molecules and model the selectivity of inhibitors towards different CCRs. The sensitivities of the predictions for the external test set for the SKN models ranged from 0.827-0.873. Finally, the developed classification models were used to screen approximately 2 million random molecules from the PubChem database, with average values for areas under the receiver operating characteristic curves ranging from 0.78-0.96 for SKN models and 0.75-0.89 for CPANN models.Communicated by Ramaswamy H. Sarma.
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MESH Headings
- Structure-Activity Relationship
- Humans
- Databases, Chemical
- Receptors, CCR1/antagonists & inhibitors
- Receptors, CCR1/chemistry
- Receptors, CCR1/metabolism
- Receptors, CCR5/chemistry
- Receptors, CCR5/metabolism
- Receptors, CCR/antagonists & inhibitors
- Receptors, CCR/chemistry
- Receptors, CCR/metabolism
- Receptors, CCR2/antagonists & inhibitors
- Receptors, CCR2/chemistry
- Receptors, CCR2/metabolism
- Receptors, Chemokine/antagonists & inhibitors
- Receptors, Chemokine/chemistry
- Receptors, Chemokine/metabolism
- Models, Molecular
- Neural Networks, Computer
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Affiliation(s)
- M Darsaraee
- Chemometrics and Cheminformatics Laboratory, Department of Analytical Chemistry, Tarbiat Modares University, Tehran, Iran
| | - S Kaveh
- Chemometrics and Cheminformatics Laboratory, Department of Analytical Chemistry, Tarbiat Modares University, Tehran, Iran
| | - A Mani-Varnosfaderani
- Chemometrics and Cheminformatics Laboratory, Department of Analytical Chemistry, Tarbiat Modares University, Tehran, Iran
| | - M S Neiband
- Department of Chemistry, Payame Noor University (PNU), Tehran, Iran
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2
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He Y, Zhou J, Gao H, Liu C, Zhan P, Liu X. Broad-spectrum antiviral strategy: Host-targeting antivirals against emerging and re-emerging viruses. Eur J Med Chem 2024; 265:116069. [PMID: 38160620 DOI: 10.1016/j.ejmech.2023.116069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/06/2023] [Accepted: 12/16/2023] [Indexed: 01/03/2024]
Abstract
Viral infections are amongst the most prevalent diseases that pose a significant threat to human health. Targeting viral proteins or host factors represents two primary strategies for the development of antiviral drugs. In contrast to virus-targeting antivirals (VTAs), host-targeting antivirals (HTAs) offer advantages in terms of overcoming drug resistance and effectively combating a wide range of viruses, including newly emerging ones. Therefore, targeting host factors emerges as an extremely promising strategy with the potential to address critical challenges faced by VTAs. In recent years, extensive research has been conducted on the discovery and development of HTAs, leading to the approval of maraviroc, a chemokine receptor type 5 (CCR5) antagonist used for the treatment of HIV-1 infected individuals, with several other potential treatments in various stages of development for different viral infections. This review systematically summarizes advancements made in medicinal chemistry regarding various host targets and classifies them into four distinct catagories based on their involvement in the viral life cycle: virus attachment and entry, biosynthesis, nuclear import and export, and viral release.
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Affiliation(s)
- Yong He
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan, 250012, Shandong Province, PR China
| | - Jiahui Zhou
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan, 250012, Shandong Province, PR China
| | - Huizhan Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan, 250012, Shandong Province, PR China
| | - Chuanfeng Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan, 250012, Shandong Province, PR China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan, 250012, Shandong Province, PR China.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan, 250012, Shandong Province, PR China.
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3
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Design, synthesis, characterization and analysis of anti-inflammatory properties of novel N-(benzo[d]thiazol-2-yl)-2-[phenyl(2-(piperidin-1-yl) ethylamino] benzamides and N-(benzo[d]thiazol-2-yl)-2-[phenyl (2-morpholino) ethylamino] benzamides derivatives through in vitro and in silico approach. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2022. [DOI: 10.1007/s13738-022-02719-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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4
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Suttisintong K, Kaewchangwat N, Thanayupong E, Nerungsi C, Srikun O, Pungpo P. Recent Progress in the Development of HIV-1 Entry Inhibitors: From Small Molecules to Potent Anti-HIV Agents. Curr Top Med Chem 2019; 19:1599-1620. [DOI: 10.2174/1568026619666190712204050] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 06/07/2019] [Accepted: 06/21/2019] [Indexed: 01/21/2023]
Abstract
Viral entry, the first process in the reproduction of viruses, primarily involves attachment of the viral envelope proteins to membranes of the host cell. The crucial components that play an important role in viral entry include viral surface glycoprotein gp120, viral transmembrane glycoprotein gp41, host cell glycoprotein (CD4), and host cell chemokine receptors (CCR5 and CXCR4). Inhibition of the multiple molecular interactions of these components can restrain viruses, such as HIV-1, from fusion with the host cell, blocking them from reproducing. This review article specifically focuses on the recent progress in the development of small-molecule HIV-1 entry inhibitors and incorporates important aspects of their structural modification that lead to the discovery of new molecular scaffolds with more potency.
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Affiliation(s)
- Khomson Suttisintong
- National Nanotechnology Center (NANOTEC), National Science and Technology, Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Narongpol Kaewchangwat
- National Nanotechnology Center (NANOTEC), National Science and Technology, Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Eknarin Thanayupong
- National Nanotechnology Center (NANOTEC), National Science and Technology, Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Chakkrapan Nerungsi
- The Government Pharmaceutical Organization, 75/1 Rama VI Road, Ratchathewi, Bangkok 10400, Thailand
| | - Onsiri Srikun
- The Government Pharmaceutical Organization, 75/1 Rama VI Road, Ratchathewi, Bangkok 10400, Thailand
| | - Pornpan Pungpo
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, 85 Sathonlamark Road, Warinchamrap, Ubon Ratchathani 34190, Thailand
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5
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Zabiulla Z, Malojirao VH, Mohammed YHE, Thirusangu P, Prabhakar BT, Khanum SA. Synthesis, molecular docking, and apoptogenic efficacy of novel N-heterocycle analogs to target B-cell lymphoma 2/X-linked inhibitors of apoptosis proteins to regress melanoma. Med Chem Res 2019. [DOI: 10.1007/s00044-019-02357-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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6
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Byrappa S, Rachaiah K, Kotian SY, Balaraju Y, Prabhuswamimath SC, Rai KML, Salimath BP. Synthesis and Screening of Pro-apoptotic and Angio-inhibitory Activity of Novel Benzisoxazole Derivatives both In Vitro and In Vivo. Anticancer Agents Med Chem 2019; 19:827-839. [PMID: 30648522 DOI: 10.2174/1871520619666190114170621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 12/21/2018] [Accepted: 01/28/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Triple Negative Breast Cancer (TNBC) tends to be more aggressive than other types of breast cancer. Resistance to chemotherapy is a major obstacle hence there is a significant need for new antineoplastic drugs with multi-target potency. Numerous Benzoisoxazole moieties have been found to possess a broad spectrum of pharmacological activities. In the present study, we have synthesized 9 novel derivatives of Benzisoxazole 7(a-i) and screened them for their biological potential. METHODS Chemical synthesis, Mass spectrometry (HRMS), cell proliferation and cytotoxicity assay, wound healing assay, flow cytometry and nuclear staining. Angio-inhibitory activity assessed by corneal micropocket assay and in vivo peritoneal angiogenesis assay. RESULTS The Benzisoxazole derivatives 7(a-i) were synthesized and screened for their biological potency by both in vitro and in vivo experimental models. Among the series, compound 3-(1-((3-(3(Benzyloxy)-4-methoxyphenyl)- 4,5-dihydroisoxazole-5-yl)methyl)piperidine-4-yl)6-fluorobenzo[d] isoxazole (7e) was found to be most promising, with an average IC50 value of 50.36 ± 1.7 µM in MTT assay and showed 81.3% cell death. The compound 7e also showed 60-70% inhibition on a recombinant Metastasis-Associated protein (MTA1) induced proliferation and cell migration in MDAMB-231 cells, which is known to play a major role in angiogenesis. The anti-tumour studies inferred the regression of tumour activity. This was due to inhibition of neovascularization and evoking apoptosis process as assessed by corneal vascularization, peritoneal angiogenesis and apoptotic hallmarks in 7e treated cells. CONCLUSION These findings not only show the biological efficacy of compound 7e but it is also an effective beginning to explore the mechanism of metastasis and cancer therapy strategy targeting MTA1. The observed biological activity makes compound 7e an attractive drug candidate.
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Affiliation(s)
- Sathish Byrappa
- Department of Studies in Chemistry, University of Mysore, Manasagangotri, Mysore 570 006, India
| | - Kavitha Rachaiah
- Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysore 570 006, India
| | - Sumana Y Kotian
- Department of Studies in Chemistry, University of Mysore, Manasagangotri, Mysore 570 006, India
| | - Yashaswini Balaraju
- Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysore 570 006, India
| | | | - Kuriya M L Rai
- Department of Studies in Chemistry, University of Mysore, Manasagangotri, Mysore 570 006, India
| | - Bharathi P Salimath
- Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysore 570 006, India
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7
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Peng P, Chen H, Zhu Y, Wang Z, Li J, Luo RH, Wang J, Chen L, Yang LM, Jiang H, Xie X, Wu B, Zheng YT, Liu H. Structure-Based Design of 1-Heteroaryl-1,3-propanediamine Derivatives as a Novel Series of CC-Chemokine Receptor 5 Antagonists. J Med Chem 2018; 61:9621-9636. [DOI: 10.1021/acs.jmedchem.8b01077] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Panfeng Peng
- University of Chinese Academy of Sciences, Number 19A Yuquan Road, Beijing 100049, China
| | - Huan Chen
- Key Laboratory of Bioactive Peptides of Yunnan Province, Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- University of Chinese Academy of Sciences, Number 19A Yuquan Road, Beijing 100049, China
| | - Ya Zhu
- University of Chinese Academy of Sciences, Number 19A Yuquan Road, Beijing 100049, China
| | - Zhilong Wang
- University of Chinese Academy of Sciences, Number 19A Yuquan Road, Beijing 100049, China
| | - Jian Li
- University of Chinese Academy of Sciences, Number 19A Yuquan Road, Beijing 100049, China
| | - Rong-Hua Luo
- Key Laboratory of Bioactive Peptides of Yunnan Province, Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- University of Chinese Academy of Sciences, Number 19A Yuquan Road, Beijing 100049, China
| | - Jiang Wang
- University of Chinese Academy of Sciences, Number 19A Yuquan Road, Beijing 100049, China
| | - Liang Chen
- University of Chinese Academy of Sciences, Number 19A Yuquan Road, Beijing 100049, China
| | - Liu-Meng Yang
- Key Laboratory of Bioactive Peptides of Yunnan Province, Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- University of Chinese Academy of Sciences, Number 19A Yuquan Road, Beijing 100049, China
| | - Hualiang Jiang
- University of Chinese Academy of Sciences, Number 19A Yuquan Road, Beijing 100049, China
| | - Xin Xie
- University of Chinese Academy of Sciences, Number 19A Yuquan Road, Beijing 100049, China
| | - Beili Wu
- University of Chinese Academy of Sciences, Number 19A Yuquan Road, Beijing 100049, China
| | - Yong-Tang Zheng
- Key Laboratory of Bioactive Peptides of Yunnan Province, Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- University of Chinese Academy of Sciences, Number 19A Yuquan Road, Beijing 100049, China
| | - Hong Liu
- University of Chinese Academy of Sciences, Number 19A Yuquan Road, Beijing 100049, China
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8
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Zhu YP, Mampuys P, Sergeyev S, Ballet S, Maes BUW. Amine Activation:N-Arylamino Acid Amide Synthesis from Isothioureas and Amino Acids. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201700134] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Yan-Ping Zhu
- Organic Synthesis, Department of Chemistry; University of Antwerp; Groenenborgerlaan 171, B- 2020 Antwerp Belgium
| | - Pieter Mampuys
- Organic Synthesis, Department of Chemistry; University of Antwerp; Groenenborgerlaan 171, B- 2020 Antwerp Belgium
| | - Sergey Sergeyev
- Organic Synthesis, Department of Chemistry; University of Antwerp; Groenenborgerlaan 171, B- 2020 Antwerp Belgium
| | - Steven Ballet
- Research Group of Organic Chemistry; Departments of Bioengineering Sciences and Chemistry; Vrije Universiteit Brussel; Pleinlaan 2, B- 1050 Brussels Belgium
| | - Bert U. W. Maes
- Organic Synthesis, Department of Chemistry; University of Antwerp; Groenenborgerlaan 171, B- 2020 Antwerp Belgium
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9
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Kim MB, Giesler KE, Tahirovic YA, Truax VM, Liotta DC, Wilson LJ. CCR5 receptor antagonists in preclinical to phase II clinical development for treatment of HIV. Expert Opin Investig Drugs 2016; 25:1377-1392. [PMID: 27791451 PMCID: PMC5776690 DOI: 10.1080/13543784.2016.1254615] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION The chemokine receptor CCR5 has garnered significant attention in recent years as a target to treat HIV infection largely due to the approval and success of the drug Maraviroc. The side effects and inefficiencies with other first generation agents led to failed clinical trials, prompting the development of newer CCR5 antagonists. Areas covered: This review aims to survey the current status of 'next generation' CCR5 antagonists in the preclinical pipeline with an emphasis on emerging agents for the treatment of HIV infection. These efforts have culminated in the identification of advanced second-generation agents to reach the clinic and the dual CCR5/CCR2 antagonist Cenicriviroc as the most advanced currently in phase II clinical studies. Expert opinion: The clinical success of CCR5 inhibitors for treatment of HIV infection has rested largely on studies of Maraviroc and a second-generation dual CCR5/CCR2 antagonist Cenicriviroc. Although research efforts identified several promising preclinical candidates, these were dropped during early clinical studies. Despite patient access to Maraviroc, there is insufficient enthusiasm surrounding its use as front-line therapy for treatment of HIV. The non-HIV infection related development activities for Maraviroc and Cenicriviroc may help drive future interests.
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Affiliation(s)
- Michelle B Kim
- a Department of Chemistry , Emory University , Atlanta , GA , USA
| | - Kyle E Giesler
- a Department of Chemistry , Emory University , Atlanta , GA , USA
| | | | - Valarie M Truax
- a Department of Chemistry , Emory University , Atlanta , GA , USA
| | - Dennis C Liotta
- a Department of Chemistry , Emory University , Atlanta , GA , USA
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Mostafa GA, Ghabbour HA. Crystal structure of 1-(3-chloropropyl)piperidin-1-ium tetraphenylborate, C 32H 37BClN. Z KRIST-NEW CRYST ST 2016. [DOI: 10.1515/ncrs-2016-0035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
C32H37BClN, monoclinic, P21/n (no. 14), a = 15.7303(6) Å, b = 9.1129(3) Å, c = 19.9295(8) Å, β = 109.143(2)°, V = 2698.9(2) Å3, Z = 4, R
gt
(F) = 0.0483, wR
ref
(F
2
) = 0.1265, T = 100 K.
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Hu S, Wang Z, Hou T, Ma X, Li J, Liu T, Xie X, Hu Y. Design, synthesis, and biological evaluation of novel 2-methylpiperazine derivatives as potent CCR5 antagonists. Bioorg Med Chem 2014; 23:1157-68. [PMID: 25638498 DOI: 10.1016/j.bmc.2014.12.052] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 12/19/2014] [Accepted: 12/20/2014] [Indexed: 11/16/2022]
Abstract
Three series of novel 2-methylpiperazine derivatives were designed and synthesized using a fragment-assembly strategy. Among them, six compounds (13, 16, 18, 22, 33, and 36) showed potent activity against CCR5 comparable to that of the positive control, maraviroc, in calcium mobilization assay. Moreover, some compounds were selected and further tested for their antiviral activity in HIV-1 single cycle assay. As a result, four compounds (13, 16, 33, and 36) showed antiviral activity at the nanomolar level. Additionally, the potent four compounds showed no cytotoxicity at a concentration of 10μM.
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Affiliation(s)
- Suwen Hu
- ZJU-ENS Joint Laboratory of Medicinal Chemistry, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhilong Wang
- State Key Laboratory of Drug Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Tingjun Hou
- ZJU-ENS Joint Laboratory of Medicinal Chemistry, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China
| | - Xiaodong Ma
- ZJU-ENS Joint Laboratory of Medicinal Chemistry, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jing Li
- State Key Laboratory of Drug Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Tao Liu
- ZJU-ENS Joint Laboratory of Medicinal Chemistry, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Xin Xie
- State Key Laboratory of Drug Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Yongzhou Hu
- ZJU-ENS Joint Laboratory of Medicinal Chemistry, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
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