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Zhang K, Zhang YJ, Li M, Pannecouque C, De Clercq E, Wang S, Chen FE. Deciphering the enigmas of non-nucleoside reverse transcriptase inhibitors (NNRTIs): A medicinal chemistry expedition towards combating HIV drug resistance. Med Res Rev 2024. [PMID: 39188075 DOI: 10.1002/med.22080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/11/2024] [Accepted: 08/13/2024] [Indexed: 08/28/2024]
Abstract
The pivotal involvement of reverse transcriptase activity in the pathogenesis of the progressive HIV virus has stimulated gradual advancements in drug discovery initiatives spanning three decades. Consequently, nonnucleoside reverse transcriptase inhibitors (NNRTIs) have emerged as a preeminent category of therapeutic agents for HIV management. Academic institutions and pharmaceutical companies have developed numerous NNRTIs, an essential component of antiretroviral therapy. Six NNRTIs have received Food and Drug Administration approval and are widely used in clinical practice, significantly improving the quality of HIV patients. However, the rapid emergence of drug resistance has limited the effectiveness of these medications, underscoring the necessity for perpetual research and development of novel therapeutic alternatives. To supplement the existing literatures on NNRTIs, a comprehensive review has been compiled to synthesize this extensive dataset into a comprehensible format for the medicinal chemistry community. In this review, a thorough investigation and meticulous analysis were conducted on the progressions achieved in NNRTIs within the past 8 years (2016-2023), and the experiences and insights gained in the development of inhibitors with varying chemical structures were also summarized. The provision of a crucial point of reference for the development of wide-ranging anti-HIV medications is anticipated.
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Affiliation(s)
- Kun Zhang
- Department of Chemistry, Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, Shanghai, China
- Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, China
- Institute of Pharmaceutical Research and School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Yu-Jie Zhang
- Department of Chemistry, Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, Shanghai, China
- Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, China
- Institute of Pharmaceutical Research and School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Min Li
- Institute of Pharmaceutical Research and School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Christophe Pannecouque
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Erik De Clercq
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Shuai Wang
- Department of Chemistry, Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, Shanghai, China
- Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, China
| | - Fen-Er Chen
- Department of Chemistry, Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, Shanghai, China
- Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, China
- Institute of Pharmaceutical Research and School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
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2
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Jyoti Maiti N, Ganguly S, Choowongkomon K, Seetaha S, Saehlee S, Aiebchun T. Synthesis, in vitro Anti-HIV-1RT evaluation, molecular modeling, DFT and acute oral toxicity studies of some benzotriazole derivatives. J Struct Biol 2024; 216:108094. [PMID: 38653343 DOI: 10.1016/j.jsb.2024.108094] [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: 01/31/2024] [Revised: 04/19/2024] [Accepted: 04/20/2024] [Indexed: 04/25/2024]
Abstract
This study synthesized and evaluated a series of benzotriazole derivatives denoted 3(a-j) and 6(a-j) for their anti-HIV-1 RT activities compared to the standard drug efavirenz. Notably, compound 3 h, followed closely by 6 h, exhibited significant anti-HIV-1 RT efficacy relative to the standard drug. In vivo oral toxicity studies were conducted for the most active compound 3 h, confirming its nontoxic nature to ascertain the safety profile. By employing molecular docking techniques, we explored the potential interactions between the synthesized compounds (ligands) and a target biomolecule (protein)(PDB ID 1RT2) at the molecular level. We undertook the molecular dynamics study of 3 h, the most active compound, within the active binding pocket of the cocrystallized structure of HIV-1 RT (PDB ID 1RT2). We aimed to learn more about how biomolecular systems behave, interact, and change at the atomic or molecular level over time. Finally, the DFT-derived HOMO and LUMO orbitals, as well as analysis of the molecular electrostatic potential map, aid in discerning the reactivity characteristics of our molecule.
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Affiliation(s)
- Nigam Jyoti Maiti
- Department of Pharmaceutical Sciences, Birla Institute of Technology, Mesra, Ranchi 835215, Jharkhand, India
| | - Swastika Ganguly
- Department of Pharmaceutical Sciences, Birla Institute of Technology, Mesra, Ranchi 835215, Jharkhand, India.
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Pahon - Yothin Road, Chatuchak, Bangkok 10900, Thailand.
| | - Supaphorn Seetaha
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Pahon - Yothin Road, Chatuchak, Bangkok 10900, Thailand
| | - Siriwan Saehlee
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Pahon - Yothin Road, Chatuchak, Bangkok 10900, Thailand
| | - Thitinan Aiebchun
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Pahon - Yothin Road, Chatuchak, Bangkok 10900, Thailand
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3
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Singh AK, Kumar A, Arora S, Kumar R, Verma A, Khalilullah H, Jaremko M, Emwas AH, Kumar P. Current insights and molecular docking studies of HIV-1 reverse transcriptase inhibitors. Chem Biol Drug Des 2024; 103:e14372. [PMID: 37817296 DOI: 10.1111/cbdd.14372] [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: 03/21/2023] [Revised: 08/12/2023] [Accepted: 09/22/2023] [Indexed: 10/12/2023]
Abstract
Human immunodeficiency virus (HIV) causes acquired immunodeficiency syndrome (AIDS), a lethal disease that is prevalent worldwide. According to the Joint United Nations Programme on HIV/AIDS (UNAIDS) data, 38.4 million people worldwide were living with HIV in 2021. Viral reverse transcriptase (RT) is an excellent target for drug intervention. Nucleoside reverse transcriptase inhibitors (NRTIs) were the first class of approved antiretroviral drugs. Later, a new type of non-nucleoside reverse transcriptase inhibitors (NNRTIs) were approved as anti-HIV drugs. Zidovudine, didanosine, and stavudine are FDA-approved NRTIs, while nevirapine, efavirenz, and delavirdine are FDA-approved NNRTIs. Several agents are in clinical trials, including apricitabine, racivir, elvucitabine, doravirine, dapivirine, and elsulfavirine. This review addresses HIV-1 structure, replication cycle, reverse transcription, and HIV drug targets. This study focuses on NRTIs and NNRTIs, their binding sites, mechanisms of action, FDA-approved drugs and drugs in clinical trials, their resistance and adverse effects, their molecular docking studies, and highly active antiretroviral therapy (HAART).
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Affiliation(s)
- Ankit Kumar Singh
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, Punjab, India
| | - Adarsh Kumar
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, Punjab, India
| | - Sahil Arora
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, Punjab, India
| | - Raj Kumar
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, Punjab, India
| | - Amita Verma
- Department of Pharmaceutical Sciences, Bioorganic and Medicinal Chemistry Research Laboratory, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, Uttar Pradesh, India
| | - Habibullah Khalilullah
- Department of Pharmaceutical Chemistry and Pharmacognosy, Unaizah College of Pharmacy, Qassim University, Unayzah, Saudi Arabia
| | - Mariusz Jaremko
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Abdul-Hamid Emwas
- Core Labs, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Pradeep Kumar
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, Punjab, India
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4
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Loaiza JD, Chvatal-Medina M, Hernandez JC, Rugeles MT. Integrase inhibitors: current protagonists in antiretroviral therapy. Immunotherapy 2023; 15:1477-1495. [PMID: 37822251 DOI: 10.2217/imt-2023-0011] [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] [Indexed: 10/13/2023] Open
Abstract
Since HIV was identified as the etiological agent of AIDS, there have been significant advances in antiretroviral therapy (ART) that has reduced morbidity/mortality. Still, the viral genome's high mutation rate, suboptimal ART regimens, incomplete adherence to therapy and poor control of the viral load generate variants resistant to multiple drugs. Licensing over 30 anti-HIV drugs worldwide, including integrase inhibitors, has marked a milestone since they are potent and well-tolerated drugs. In addition, they favor a faster recovery of CD4+ T cells. They also increase the diversity profile of the gut microbiota and reduce inflammatory markers. All of these highlight the importance of including them in different ART regimens.
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Affiliation(s)
- John D Loaiza
- Grupo Inmunovirología, Facultad de medicina, Universidad de Antioquia, Medellín, 050010, Colombia
| | - Mateo Chvatal-Medina
- Grupo Inmunovirología, Facultad de medicina, Universidad de Antioquia, Medellín, 050010, Colombia
| | - Juan C Hernandez
- Infettare, Facultad de medicina, Universidad Cooperativa de Colombia, Medellín, 050012, Colombia
| | - Maria T Rugeles
- Grupo Inmunovirología, Facultad de medicina, Universidad de Antioquia, Medellín, 050010, Colombia
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5
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Structure-directed expansion of biphenyl-pyridone derivatives as potent non-nucleoside reverse transcriptase inhibitors with significantly improved potency and safety. CHINESE CHEM LETT 2023. [DOI: 10.1016/j.cclet.2023.108261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
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6
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Singh VK, Mishra R, Kumari P, Som A, Yadav AK, Ram NK, Kumar P, Schols D, Singh RK. In Silico Design, Synthesis and Anti-HIV Activity of Quinoline Derivatives as Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs)r. Comput Biol Chem 2022; 98:107675. [DOI: 10.1016/j.compbiolchem.2022.107675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/23/2022] [Accepted: 03/29/2022] [Indexed: 12/23/2022]
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7
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Molecular Modeling for a Comparative Analysis of Interactions Between 2LTRZFP and 2-LTR-Circle Junctions. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-021-10175-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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8
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Ding L, Zhuang C, Chen F. Druggability modification strategies of the diarylpyrimidine-type non-nucleoside reverse transcriptase inhibitors. Med Res Rev 2021; 41:1255-1290. [PMID: 33497504 DOI: 10.1002/med.21760] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/04/2020] [Accepted: 11/18/2020] [Indexed: 12/20/2022]
Abstract
Drug discovery of human immunodeficiency virus (HIV) is a hot field in medicinal chemistry community for many years. The diarylpyrimidines (DAPYs) are the second-generation non-nucleoside reverse transcriptase inhibitors (NNRTIs) targeting reverse transcriptase, playing a great irreplaceable role in HIV transcriptional therapy. However, fast-growing drug-resistant mutations as nonnegligible challenge are still unpredictably appeared in the clinical practice, leading to deactivate or reduce the existing drugs. In the last 20 years, more and more novel DAPY derivatives have developed with the purpose to counter the mutants. Nevertheless, most of them have dissatisfactory pharmacokinetics (PK) or poor antiviral activity toward resistant mutant strains. In this article, we will analyze the NNRTI derivatives with promising druggability, and summarize a series of druggability modification strategies to improve the antiviral activity, reduce toxicity and improve the PK properties in recent years. The prospects of DAPYs and the directions for future efforts will be discussed.
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Affiliation(s)
- Li Ding
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, Shanghai, China.,Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, China
| | - Chunlin Zhuang
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, Shanghai, China.,Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, China
| | - Fener Chen
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, Shanghai, China.,Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, China.,Institute of Pharmaceutical Science and Technology, Zhejiang University of Technology, Hangzhou, China
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9
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Insuasty D, Castillo J, Becerra D, Rojas H, Abonia R. Synthesis of Biologically Active Molecules through Multicomponent Reactions. Molecules 2020; 25:E505. [PMID: 31991635 PMCID: PMC7038231 DOI: 10.3390/molecules25030505] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 01/18/2020] [Accepted: 01/20/2020] [Indexed: 02/02/2023] Open
Abstract
Focusing on the literature progress since 2002, the present review explores the highly significant role that multicomponent reactions (MCRs) have played as a very important tool for expedite synthesis of a vast number of organic molecules, but also, highlights the fact that many of such molecules are biologically active or at least have been submitted to any biological screen. The selected papers covered in this review must meet two mandatory requirements: (1) the reported products should be obtained via a multicomponent reaction; (2) the reported products should be biologically actives or at least tested for any biological property. Given the diversity of synthetic approaches utilized in MCRs, the highly diverse nature of the biological activities evaluated for the synthesized compounds, and considering their huge structural variability, much of the reported data are organized into concise schemes and tables to facilitate comparison, and to underscore the key points of this review.
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Affiliation(s)
- Daniel Insuasty
- Grupo de Investigación en Química y Biología, Departamento de Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia 1569, Barranquilla Atlántico 081007, Colombia;
| | - Juan Castillo
- Grupo de Catálisis, Escuela de Ciencias Químicas, Universidad Pedagógica y Tecnológica de Colombia UPTC, Avenida Central del Norte 39-115, Tunja 150003, Colombia; (J.C.); (D.B.); (H.R.)
- Bioorganic Compounds Research Group, Department of Chemistry, Universidad de los Andes, Carrera 1 No. 18A-10, Bogotá 111711, Colombia
| | - Diana Becerra
- Grupo de Catálisis, Escuela de Ciencias Químicas, Universidad Pedagógica y Tecnológica de Colombia UPTC, Avenida Central del Norte 39-115, Tunja 150003, Colombia; (J.C.); (D.B.); (H.R.)
| | - Hugo Rojas
- Grupo de Catálisis, Escuela de Ciencias Químicas, Universidad Pedagógica y Tecnológica de Colombia UPTC, Avenida Central del Norte 39-115, Tunja 150003, Colombia; (J.C.); (D.B.); (H.R.)
| | - Rodrigo Abonia
- Research Group of Heterocyclic Compounds, Department of Chemistry, Universidad del Valle, Cali A. A. 25360, Colombia
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10
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Daipule K, Goud NS, Sethi A, Gurrapu S, Mamidala E, Alvala M. Synthesis, molecular docking simulation, and biological evaluation studies of novel amide and ether conjugates of 2,3‐diaryl‐1,3‐thiazolidin‐4‐ones. J Heterocycl Chem 2019. [DOI: 10.1002/jhet.3819] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Komal Daipule
- Department of Medicinal ChemistryNational Institute of Pharmaceutical Education and Research—Hyderabad Hyderabad India
| | - Nerella Sridhar Goud
- Department of Medicinal ChemistryNational Institute of Pharmaceutical Education and Research—Hyderabad Hyderabad India
| | - Aaftaab Sethi
- Department of Medicinal ChemistryNational Institute of Pharmaceutical Education and Research—Hyderabad Hyderabad India
| | | | | | - Mallika Alvala
- Department of Medicinal ChemistryNational Institute of Pharmaceutical Education and Research—Hyderabad Hyderabad India
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11
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The Effects of Statistical Multiplicity of Infection on Virus Quantification and Infectivity Assays. Biophys J 2019; 114:2974-2985. [PMID: 29925033 DOI: 10.1016/j.bpj.2018.05.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 03/24/2018] [Accepted: 05/02/2018] [Indexed: 12/28/2022] Open
Abstract
Many biological assays are employed in virology to quantify parameters of interest. Two such classes of assays, virus quantification assays (VQAs) and infectivity assays (IAs), aim to estimate the number of viruses present in a solution and the ability of a viral strain to successfully infect a host cell, respectively. VQAs operate at extremely dilute concentrations, and results can be subject to stochastic variability in virus-cell interactions. At the other extreme, high viral-particle concentrations are used in IAs, resulting in large numbers of viruses infecting each cell, enough for measurable change in total transcription activity. Furthermore, host cells can be infected at any concentration regime by multiple particles, resulting in a statistical multiplicity of infection and yielding potentially significant variability in the assay signal and parameter estimates. We develop probabilistic models for statistical multiplicity of infection at low and high viral-particle-concentration limits and apply them to the plaque (VQA), endpoint dilution (VQA), and luciferase reporter (IA) assays. A web-based tool implementing our models and analysis is also developed and presented. We test our proposed new methods for inferring experimental parameters from data using numerical simulations and show improvement on existing procedures in all limits.
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12
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Yadav M, Srivastava R, Naaz F, Singh A, Verma R, Singh RK. In silico studies on new oxathiadiazoles as potential anti-HIV agents. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2018.12.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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13
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Che Z, Tian Y, Liu S, Hu M, Chen G. Synthesis and in vitro anti-HIV-1 evaluation of some N-arylsulfonyl-3-formylindoles. BRAZ J PHARM SCI 2018. [DOI: 10.1590/s2175-97902018000317044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Zhiping Che
- Henan University of Science and Technology, China
| | - Yuee Tian
- Henan University of Science and Technology, China
| | | | - Mei Hu
- Henan University of Science and Technology, China
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14
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Che Z, Tian Y, Liu S, Jiang J, Hu M, Chen G. Microwave-Assisted Expeditious Synthesis of 2-Alkyl-2-( N-arylsulfonylindol-3-yl)-3- N-acyl-5-aryl-1,3,4-oxadiazolines Catalyzed by HgCl₂ under Solvent-Free Conditions as Potential Anti-HIV-1 Agents. Molecules 2018; 23:E2936. [PMID: 30423803 PMCID: PMC6278315 DOI: 10.3390/molecules23112936] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/03/2018] [Accepted: 11/09/2018] [Indexed: 01/19/2023] Open
Abstract
A series of 2-alkyl-2-(N-arylsulfonylindol-3-yl)-3-N-acyl-5-aryl-1,3,4-oxadiazolines were expeditious prepared under microwave-assisted, catalyzed by HgCl₂ and solvent-free conditions. This method has the advantage of low catalyst loading and recovering catalyst, ease reaction and repaid reaction times, easy separation products and excellent yields, and more conducive to the large-scale synthesis products. Furthermore, compounds 3s, 3y, 3a', 3b', 3f', 3i', 3q', and 3r' exhibited more potent anti-HIV-1 activity with EC50 values of 3.35, 6.12, 3.63, 9.54, 1.79, 0.51, 3.00, and 4.01 μg/mL, and TI values of 32.66, >32.68, 31.22, 13.94, 24.27, 39.59, 26.01, and 24.51, respectively. Especially compound 3i' displayed the highest anti-HIV-1 activity with TI values of 39.59.
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Affiliation(s)
- Zhiping Che
- Laboratory of Pharmaceutical Design & Synthesis, Department of Plant Protection, College of Forestry, Henan University of Science and Technology, Luoyang 471003, China.
| | - Yuee Tian
- Laboratory of Pharmaceutical Design & Synthesis, Department of Plant Protection, College of Forestry, Henan University of Science and Technology, Luoyang 471003, China.
| | - Shengming Liu
- Laboratory of Pharmaceutical Design & Synthesis, Department of Plant Protection, College of Forestry, Henan University of Science and Technology, Luoyang 471003, China.
| | - Jia Jiang
- Laboratory of Pharmaceutical Design & Synthesis, Department of Plant Protection, College of Forestry, Henan University of Science and Technology, Luoyang 471003, China.
| | - Mei Hu
- Laboratory of Pharmaceutical Design & Synthesis, Department of Plant Protection, College of Forestry, Henan University of Science and Technology, Luoyang 471003, China.
| | - Genqiang Chen
- Laboratory of Pharmaceutical Design & Synthesis, Department of Plant Protection, College of Forestry, Henan University of Science and Technology, Luoyang 471003, China.
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15
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Synthesis, docking, ADMET prediction, cytotoxicity and antimicrobial activity of oxathiadiazole derivatives. Comput Biol Chem 2018; 77:226-239. [PMID: 30366286 DOI: 10.1016/j.compbiolchem.2018.10.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/29/2018] [Accepted: 10/10/2018] [Indexed: 11/23/2022]
Abstract
A series of molecules bearing oxathiadiazole, a five membered heterocyclic ring has been designed, synthesized and screened for antimicrobial activity. Molecules, 1a, 1b, 1d, 3a-b and 4a-b were found to be highly active (MIC value upto 1.5 μg/mL) against different human pathogens, namely S. aureus, B. cerus, P. aeruginosa and E. coli. Some of the compounds, 1a, 1b and 1d have also shown the antifungal activity (MIC value upto 6.2 μg/mL) against Candida albicans, Candida glubrate and Candida crusei. During in vitro cytotoxicity study, the oxathiadiazole derivatives showed less toxicity than the reference used against PBM, CEM and Vero (African green monkey kidney) cell lines. Docking studies suggested that all designed ligands interacted well within active site of PDF enzyme (PDB ID: 1G2A). Oxathiadiazole ring of all ligands formed H-bond with amino acid Leu91 at a distance ranging between 2.5-2.8 Å and also exhibited π - + and π - π interactions with amino acid residues Arg97 and His132, respectively. In silico ADMET evaluations of compounds showed more than 90% intestinal absorption for all compounds except 4b (87.45%), which too was greater than the reference drugs sulfamethoxazole (76.46%) and chloramphenicol (69.94%). TOPKAT results also supported the lower cytotoxicity of all compounds.
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16
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Combining New Non-Nucleoside Reverse Transcriptase Inhibitors (RTIs) with AZT Results in Strong Synergism against Multi-RTI-Resistant HIV-1 Strains. Molecules 2018; 23:molecules23071599. [PMID: 30004408 PMCID: PMC6099689 DOI: 10.3390/molecules23071599] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 06/21/2018] [Accepted: 06/28/2018] [Indexed: 12/31/2022] Open
Abstract
Reverse transcriptase inhibitors (RTIs), including nucleoside RTIs (NRTIs) and non-nucleoside RTIs (NNRTIs), are critical antiretroviral drugs for the treatment of human immunodeficiency virus (HIV) infection. Emergence of multi-RTI resistance calls for the development of more potent therapeutics or regimens against RTI-resistant strains. Here, we demonstrated that combining azidothymidine (AZT) with a new NNRTIs under development, diarylpyridine (DAPA)-2e, diarylanilin (DAAN)-14h, or DAAN-15h, resulted in strong synergism against infection by divergent HIV-1 strains, including those resistant to NRTIs and NNRTIs, suggesting the potential for developing these novel NNRTIs as salvage therapy for HIV/acquired immune deficiency syndrome (AIDS) patients.
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17
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Naaz F, Srivastava R, Singh A, Singh N, Verma R, Singh VK, Singh RK. Molecular modeling, synthesis, antibacterial and cytotoxicity evaluation of sulfonamide derivatives of benzimidazole, indazole, benzothiazole and thiazole. Bioorg Med Chem 2018; 26:3414-3428. [DOI: 10.1016/j.bmc.2018.05.015] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 05/01/2018] [Accepted: 05/10/2018] [Indexed: 11/27/2022]
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18
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Bala J, Chinnapaiyan S, Dutta RK, Unwalla H. Aptamers in HIV research diagnosis and therapy. RNA Biol 2018; 15:327-337. [PMID: 29431588 PMCID: PMC5927724 DOI: 10.1080/15476286.2017.1414131] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/07/2017] [Accepted: 12/03/2017] [Indexed: 12/30/2022] Open
Abstract
Aptamers are high affinity single-stranded nucleic acid or protein ligands which exhibit specificity and avidity comparable to, or exceeding that of antibodies and can be generated against most targets. The functionality of aptamers is based on their unique tertiary structure, complexity and their ability to attain unique binding pockets by folding. Aptamers are selected in vitro by a process called Systematic Evolution of Ligands by Exponential enrichment (SELEX). The Kd values for the selected aptamer are often in the picomolar to low nanomolar range. Stable and nontoxic aptamers could be selected for a wide range of ligands including small molecules to large proteins. Aptamers have shown tremendous potential and have found multipurpose application in the field of therapeutic, diagnostic, biosensor and bio-imaging. While their mechanism of action can be similar to that of monoclonal antibodies, aptamers provide additional advantages in terms of production cost, simpler regulatory approval and lower immunogenicity as they are synthesized chemically. Human immunodeficiency virus (HIV) is the primary cause of acquired immune deficiency syndrome (AIDS), which causes significant morbidity and mortality with a significant consequent decrease in the quality of patient's lives. While cART has led to good viral control, people living with HIV now suffer from non-HIV comorbidities due to viral protein expression that cannot be controlled by cART. Hence pathophysiological mechanisms that govern these comorbidities with a focus on therapies that neutralize these HIV effects gained increased attention. Recent advances in HIV/AIDS research have identified several molecular targets and for the development of therapeutic and diagnostic using aptamers against HIV/AIDS. This review presents recent advances in aptamers technology for potential application in HIV diagnostics and therapeutics towards improving the quality of life of people living with HIV.
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Affiliation(s)
- Jyoti Bala
- Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Srinivasan Chinnapaiyan
- Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Rajib Kumar Dutta
- Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Hoshang Unwalla
- Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
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Che Z, Tian Y, Liu S, Hu M, Chen G. Discovery of N-arylsulfonyl-3-acylindole benzoyl hydrazone derivatives as anti-HIV-1 agents. BRAZ J PHARM SCI 2018. [DOI: 10.1590/s2175-97902018000417543] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Zhiping Che
- Henan University of Science and Technology, People′s Republic of China
| | - Yuee Tian
- Henan University of Science and Technology, People′s Republic of China
| | - Shengming Liu
- Henan University of Science and Technology, People′s Republic of China
| | - Mei Hu
- Henan University of Science and Technology, People′s Republic of China
| | - Genqiang Chen
- Henan University of Science and Technology, People′s Republic of China
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20
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Zhou Z, Liu T, Kang D, Huo Z, Wu G, Daelemans D, De Clercq E, Pannecouque C, Zhan P, Liu X. Discovery of novel diarylpyrimidines as potent HIV-1 NNRTIs by investigating the chemical space of a less explored “hydrophobic channel”. Org Biomol Chem 2018; 16:1014-1028. [DOI: 10.1039/c7ob02828h] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We described the identification of novel HIV-1 NNRTIs via exploration of the chemical space of a seldom explored “hydrophobic channel”.
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Affiliation(s)
- Zhongxia Zhou
- Department of Medicinal Chemistry
- Key Laboratory of Chemical Biology (Ministry of Education)
- School of Pharmaceutical Sciences
- Shandong University
- 250012 Jinan
| | - Tao Liu
- Department of Medicinal Chemistry
- Key Laboratory of Chemical Biology (Ministry of Education)
- School of Pharmaceutical Sciences
- Shandong University
- 250012 Jinan
| | - Dongwei Kang
- Department of Medicinal Chemistry
- Key Laboratory of Chemical Biology (Ministry of Education)
- School of Pharmaceutical Sciences
- Shandong University
- 250012 Jinan
| | - Zhipeng Huo
- Department of Medicinal Chemistry
- Key Laboratory of Chemical Biology (Ministry of Education)
- School of Pharmaceutical Sciences
- Shandong University
- 250012 Jinan
| | - Gaochan Wu
- Department of Medicinal Chemistry
- Key Laboratory of Chemical Biology (Ministry of Education)
- School of Pharmaceutical Sciences
- Shandong University
- 250012 Jinan
| | - Dirk Daelemans
- Rega Institute for Medical Research
- K.U.Leuven
- B-3000 Leuven
- Belgium
| | - Erik De Clercq
- Rega Institute for Medical Research
- K.U.Leuven
- B-3000 Leuven
- Belgium
| | | | - Peng Zhan
- Department of Medicinal Chemistry
- Key Laboratory of Chemical Biology (Ministry of Education)
- School of Pharmaceutical Sciences
- Shandong University
- 250012 Jinan
| | - Xinyong Liu
- Department of Medicinal Chemistry
- Key Laboratory of Chemical Biology (Ministry of Education)
- School of Pharmaceutical Sciences
- Shandong University
- 250012 Jinan
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21
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Wan Y, Tian Y, Wang W, Gu S, Ju X, Liu G. In silico studies of diarylpyridine derivatives as novel HIV-1 NNRTIs using docking-based 3D-QSAR, molecular dynamics, and pharmacophore modeling approaches. RSC Adv 2018; 8:40529-40543. [PMID: 35557880 PMCID: PMC9091378 DOI: 10.1039/c8ra06475j] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 11/26/2018] [Indexed: 11/22/2022] Open
Abstract
A series of novel diarylpyridine derivatives has recently been identified as HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs), and most of them exhibited potent activities against HIV-1 strains, with EC50 values in the low nanomolar range. However, the three-dimensional quantitative structure–activity relationships (3D-QSARs) and pharmacophore characteristics of these compounds remain to be studied. In the present study, forty-two diarylpyridine derivatives were firstly docked into HIV-1 reverse transcriptase, and molecular dynamics (10 ns) simulations were further performed to validate the reliability of the docking results, which indicated that residues Lys101, Tyr181, Tyr188, Phe227, and Trp229 might play important roles in binding with these diarylpyridines. The “U”-shaped docking conformations of all compounds were then used to construct 3D-QSAR and pharmacophore models. The satisfactory statistical parameters of CoMFA (qloo2 = 0.665, rncv2 = 0.989, rpred2 = 0.962, etc.) and CoMSIA (qloo2 = 0.727, rncv2 = 0.988, rpred2 = 0.912, etc.) models demonstrated that both constructed models had excellent predictability, and their contour maps gave insights into the structural requirements of the diarylpyridines for the anti-HIV-1 activity. A docking-conformation-based pharmacophore model, containing three hydrophobic centers, three hydrogen-bond acceptors, and three hydrogen-bond donors, was also established. The observations in this study might provide important information for the rational design and development of novel HIV-1 NNRTIs. Computational modeling approaches were successfully applied to a series of diarylpyridine derivatives as novel HIV-1 NNRTIs.![]()
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Affiliation(s)
- Youlan Wan
- Key Laboratory for Green Chemical Process of Ministry of Education
- School of Chemical Engineering and Pharmacy
- Wuhan Institute of Technology
- Wuhan 430205
- P. R. China
| | - Yafeng Tian
- Key Laboratory for Green Chemical Process of Ministry of Education
- School of Chemical Engineering and Pharmacy
- Wuhan Institute of Technology
- Wuhan 430205
- P. R. China
| | - Wenjie Wang
- Key Laboratory for Green Chemical Process of Ministry of Education
- School of Chemical Engineering and Pharmacy
- Wuhan Institute of Technology
- Wuhan 430205
- P. R. China
| | - Shuangxi Gu
- Key Laboratory for Green Chemical Process of Ministry of Education
- School of Chemical Engineering and Pharmacy
- Wuhan Institute of Technology
- Wuhan 430205
- P. R. China
| | - Xiulian Ju
- Key Laboratory for Green Chemical Process of Ministry of Education
- School of Chemical Engineering and Pharmacy
- Wuhan Institute of Technology
- Wuhan 430205
- P. R. China
| | - Genyan Liu
- Key Laboratory for Green Chemical Process of Ministry of Education
- School of Chemical Engineering and Pharmacy
- Wuhan Institute of Technology
- Wuhan 430205
- P. R. China
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22
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Xu Z, Liu R, Guan H. Dual-target inhibitor screening against thrombin and factor Xa simultaneously by mass spectrometry. Anal Chim Acta 2017; 990:1-10. [PMID: 29029731 DOI: 10.1016/j.aca.2017.07.063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 07/19/2017] [Accepted: 07/28/2017] [Indexed: 12/12/2022]
Abstract
An accurate, rapid, and cost-effective methodology for enzyme assay is highly demanded to screen the effect of compounds on target at the molecular level. Thrombin (EC 3.4.21.5) and factor Xa (FXa, EC 3.4.21.6) have been identified as the critical targets for the development of potential drugs with anticoagulant activity. In this study, a rapid, sensitive and accurate assay based on UHPLC-MS/MS method has been developed for inhibitor screening against thrombin and factor Xa simultaneously. For thrombin and factor Xa, the Michaelis-Menten constants (Km) were calculated to be 6.14 and 57.27 μM, respectively. The inhibition constants (Ki) for two known inhibitors, argatroban and rivaroxaban, were determined to be 16.23 and 0.41 nM, respectively. The assay was further validated through the determination of a high Z' factor value of 0.89. Finally, the developed assay was applied to screen a chemical library against two enzymes. Three hit compounds belonging to a class of sulfated polysaccharides were identified and their targets of inhibition action were further evaluated. The results indicated that the dual-target assay by UHPLC-MS/MS analysis could be used as a reliable method for screening anticoagulant agents.
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Affiliation(s)
- Zhe Xu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts, Innovation Center for Marine Drugs Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266273, China; Marine Biomedical Research Institute of Qingdao, Qingdao 266271, China.
| | - Ruonan Liu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Qingdao 266003, China
| | - Huashi Guan
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts, Innovation Center for Marine Drugs Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266273, China; Marine Biomedical Research Institute of Qingdao, Qingdao 266271, China
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23
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Samanta PN, Das KK. Inhibition activities of catechol diether based non-nucleoside inhibitors against the HIV reverse transcriptase variants: Insights from molecular docking and ONIOM calculations. J Mol Graph Model 2017. [DOI: 10.1016/j.jmgm.2017.06.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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24
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ANN QSAR workflow for predicting the inhibition of HIV-1 reverse transcriptase by pyridinone non-nucleoside derivatives. Future Med Chem 2017; 9:1175-1191. [DOI: 10.4155/fmc-2017-0040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aim: Pyridinone derivatives have high potency against non-nucleoside reverse transcriptase inhibitor (NNRTI)-resistant human immunodeficiency virus type-1 strains. Quantitative structure–activity relationship (QSAR) studies on a series of pyridinone derivatives acting as NNRTIs are very important in designing the next generation of NNRTIs. Methodology & results: The QSAR models were developed using linear (single and forward stepwise) and combined nonlinear artificial neural network (ANN) approaches. ANN provided QSAR model with highly correlating values of 0.963, 0.964, 0.920 and 0.917, corresponding to the biological activity pIC50 of the training, validation, testing and all samples, respectively. Conclusion: The nonlinear ANN-QSAR model based on the topological polarizability, geometrical steric, hydrophobicity and substituted benzene functional group indices might be able to help for designing novel pyridinone NNRTIs.
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25
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Lu YY, Cheng HX, Wang X, Wang XW, Liu JY, Li P, Lou YQ, Li J, Lu C, Zhang GL. Identification of cytochrome P450s involved in the metabolism of 6-benzyl-1-benzyloxymethyl-5-iodouracil (W-1) using human recombinant enzymes and rat liver microsomes in vitro. Xenobiotica 2016; 47:667-672. [PMID: 27910729 DOI: 10.1080/00498254.2016.1217365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
1. The aim of this study was to identify the hepatic metabolic enzymes, which involved in the biotransformation of 6-benzyl-1-benzyloxymethyl-5-iodouracil (W-1), a novel non-nucleoside reverse transcriptase inhibitor (NNRTI) in rat and human in vitro. 2. The parent drug of W-1 was incubated with rat liver microsomes (RLMs) or recombinant CYPs (CYP1A2, CYP2A6, CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6, CYP2E1, CYP3A4, and CYP3A5, respectively) in the presence or absence of nicotinamide adeninedinucleotide phosphate (NADPH)-regenerating system. The metabolites of W-1 were analyzed with liquid chromatography-ion trap-time of flight-mass spectrometry (LC-IT-TOF-MS). 3. The parent drug of W-1 was metabolized in a NADPH-dependent manner in RLMs. The kinetic parameters of prototype W-1 including Km, Vmax, and CLint were 2.3 μM, 3.3 nmol/min/mg protein, and 1.4 mL/min/mg protein, respectively. Two metabolites M1 and M2 were observed in shorter retention times (2.988 and 3.188 min) with a higher molecular ion at m/z 463.0160 (both M1 and M2) than that of the W-1 parent drug (6.158 min with m/z 447.0218). The CYP selective inhibition and recombinant enzymes also showed that two hydroxyl metabolites M1 and M2 are mainly mediated by CYP2C19 and CYP3A4. 4. The identification of CYPs involved in W-1 biotransformation is important to understand and minimize, if possible, the potential of drug-drug interactions.
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Affiliation(s)
- Ying-Yuan Lu
- a Department of Pharmacology , School of Basic Medical Science, Beijing (Peking) University , Beijing , PR China
| | - Hai-Xu Cheng
- a Department of Pharmacology , School of Basic Medical Science, Beijing (Peking) University , Beijing , PR China
| | - Xin Wang
- a Department of Pharmacology , School of Basic Medical Science, Beijing (Peking) University , Beijing , PR China
| | - Xiao-Wei Wang
- b Department of Chemical Biology , School of Pharmaceutical Sciences, Beijing (Peking) University , Beijing , PR China
| | - Jun-Yi Liu
- b Department of Chemical Biology , School of Pharmaceutical Sciences, Beijing (Peking) University , Beijing , PR China
| | - Pu Li
- a Department of Pharmacology , School of Basic Medical Science, Beijing (Peking) University , Beijing , PR China
| | - Ya-Qing Lou
- a Department of Pharmacology , School of Basic Medical Science, Beijing (Peking) University , Beijing , PR China
| | - Jun Li
- c State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Beijing (Peking) University , Beijing , PR China , and
| | - Chuang Lu
- d Department of Drug Metabolism & Pharmacokinetics , Biogen , Cambridge , MA , USA
| | - Guo-Liang Zhang
- a Department of Pharmacology , School of Basic Medical Science, Beijing (Peking) University , Beijing , PR China
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26
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Design and anti-HIV activity of arylsulphonamides as non-nucleoside reverse transcriptase inhibitors. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1707-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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27
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Synthesis, crystal structure, anti-HIV, and antiproliferative activity of new oxadiazole and thiazole analogs. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1669-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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28
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Mistry B, D'Orsogna MR, Webb NE, Lee B, Chou T. Quantifying the Sensitivity of HIV-1 Viral Entry to Receptor and Coreceptor Expression. J Phys Chem B 2016; 120:6189-99. [PMID: 27137677 DOI: 10.1021/acs.jpcb.6b02102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Infection by many viruses begins with fusion of viral and cellular lipid membranes, followed by entry of viral contents into the target cell and ultimately, after many biochemical steps, integration of viral DNA into that of the host cell. The early steps of membrane fusion and viral capsid entry are mediated by adsorption to the cell surface, and receptor and coreceptor binding. HIV-1 specifically targets CD4+ helper T-cells of the human immune system and binds to the receptor CD4 and coreceptor CCR5 before fusion is initiated. Previous experiments have been performed using a cell line (293-Affinofile) in which the expressions of CD4 and CCR5 concentration were independently controlled. After exposure to HIV-1 of various strains, the resulting infectivity was measured through the fraction of infected cells. To design and evaluate the effectiveness of drug therapies that target the inhibition of the entry processes, an accurate functional relationship between the CD4/CCR5 concentrations and infectivity is desired in order to more quantitatively analyze experimental data. We propose three kinetic models describing the possible mechanistic processes involved in HIV entry and fit their predictions to infectivity measurements, contrasting and comparing different outcomes. Our approach allows interpretation of the clustering of infectivity of different strains of HIV-1 in the space of mechanistic kinetic parameters. Our model fitting also allows inference of nontrivial stoichiometries of receptor and coreceptor binding and provides a framework through which to quantitatively investigate the effectiveness of fusion inhibitors and neutralizing antibodies.
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Affiliation(s)
- Bhaven Mistry
- Department of Biomathematics, University of California , Los Angeles, California 90095, United States
| | - Maria R D'Orsogna
- Department of Biomathematics, University of California , Los Angeles, California 90095, United States.,Department of Mathematics, California State University , Northridge, California 91330, United States
| | - Nicholas E Webb
- Department of Infectious Disease, Children's Hospital Los Angeles , Los Angeles, California 90027, United States
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Tom Chou
- Department of Biomathematics, University of California , Los Angeles, California 90095, United States.,Department of Mathematics, University of California , Los Angeles, California 90095, United States
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29
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Bonache MC, Chamorro C, Lobatón E, De Clercq E, Balzarini J, Velázquez S, Camarasa MJ, San-Félix A. Structure-Activity Relationship Studies on a Novel Family of Specific HIV-1 Reverse Transcriptase Inhibitors. ACTA ACUST UNITED AC 2016; 14:249-62. [PMID: 14694988 DOI: 10.1177/095632020301400504] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We have previously reported the discovery and preliminary structure-activity relationships of a new class of specific HIV-1 reverse transcriptase (RT) inhibitors whose prototype compound is the 1-[2′,5′-bis- O-( tert-butyldimethylsilyl)-β-D-ribofuranosyl]-3- N-[(carboxy) methyl]-thymine. In an attempt to increase the inhibitory efficacy against HIV-1 RT of this new class of nucleosides, and to further explore the structural features required for anti-HIV-1 activity, different types of modifications have been carried out on the prototype compound. These include substitution of the tert-butyldimethylsilyl groups by other liphophilic groups, replacement of the carboxy group at the N-3 position of the nucleobase by other functional groups, change in the length of the spacer between the thymine and the carboxylic acid residue and substitution of the thymine moiety by other pyrimidine (uracil, 5-ethyluracil) or purine (hypoxanthine) nucleobases. In addition, the most salient structural features of this new class of HIV-1-specific nucleosides have been incorporated into classical HIV RT nucleoside inhibitors such as ddI, AZT, d4T. Our studies demonstrate that both the carboxymethyl moiety at the nucleobase and tert-butyldimethylsilyl groups at the sugar are important structural components since deletion of either of them is detrimental to the antiviral activity.
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Lu YY, Wang XW, Wang X, Dai WB, Zhang Q, Li P, Lou YQ, Lu C, Liu JY, Zhang GL. Profile of disposition, tissue distribution and excretion of the novel anti-human immunodeficiency virus (HIV) agent W-1 in rats. Arch Pharm Res 2016; 39:970-7. [DOI: 10.1007/s12272-016-0727-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 02/27/2016] [Indexed: 10/21/2022]
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31
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Yang J, Chen W, Kang D, Lu X, Li X, Liu Z, Huang B, Daelemans D, Pannecouque C, De Clercq E, Zhan P, Liu X. Design, synthesis and anti-HIV evaluation of novel diarylpyridine derivatives targeting the entrance channel of NNRTI binding pocket. Eur J Med Chem 2015; 109:294-304. [PMID: 26802545 DOI: 10.1016/j.ejmech.2015.11.039] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 11/20/2015] [Accepted: 11/21/2015] [Indexed: 11/26/2022]
Abstract
The development of novel NNRTIs with activity against variants of HIV-1RT is crucial for overcoming treatment failure. In the present study, a series of novel 6-substituted diarylpyridine derivatives targeting the entrance channel of the NNIBP of RT were designed through a molecular hybridization strategy. Encouragingly, these new diarylpyridine derivatives were found to be active against wild-type (WT) HIV-1 with an EC50 values ranging from 0.035 μM to 1.99 μM. Nearly half of them exhibited more potent inhibitory activities in cellular assays than the control drug nevirapine (NVP). Notably, three most promising compounds If (EC50 = 35 nM), Ia (EC50 = 43 nM) and IIa (EC50 = 41 nM) showed high potency against WT and were comparable to the reference drug delavirdine (DLV) (EC50 = 33 nM). Moreover, compounds Ib, IIb and IIh displayed effective activity against the most common clinically observed single and double-mutated HIV-1 strains in micromolar concentrations. In particular, the inhibition of IIb against the K103N mutation (EC50 = 49 nM), which confers resistance to a wide variety of NNRTIs, was about 140 times more effective than NVP (EC50 = 6.78 μM), 50 times more than DLV (EC50 = 2.48 μM) and about 3 times more than EFV (EC50 = 0.12 μM), indicating that the newly designed compounds have great potential to be further developed as new anti-HIV-1 agents. Preliminary structure-activity relationships (SARs) and molecular modeling of the new diarylpyridine derivatives were discussed in detail.
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Affiliation(s)
- Jiapei Yang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong, PR China
| | - Wenmin Chen
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong, PR China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong, PR China
| | - Xueyi Lu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong, PR China
| | - Xiao Li
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong, PR China
| | - Zhaoqiang Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong, PR China
| | - Boshi Huang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong, PR China
| | - Dirk Daelemans
- Rega Institute for Medical Research, K.U.Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Christophe Pannecouque
- Rega Institute for Medical Research, K.U.Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Erik De Clercq
- Rega Institute for Medical Research, K.U.Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong, PR China.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong, PR China.
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32
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Kumari G, Singh RK. Molecular Modeling, Synthesis, and Anti-HIV Activity of Novel Isoindolinedione Analogues as Potent Non-nucleoside Reverse Transcriptase Inhibitors. Chem Biol Drug Des 2015. [DOI: 10.1111/cbdd.12620] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Garima Kumari
- Nucleic Acids and Antiviral Research Laboratory; Department of Chemistry; University of Allahabad; Allahabad India
| | - Ramendra K. Singh
- Nucleic Acids and Antiviral Research Laboratory; Department of Chemistry; University of Allahabad; Allahabad India
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33
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Bai R, Zhang XJ, Li YL, Liu JP, Zhang HB, Xiao WL, Pu JX, Sun HD, Zheng YT, Liu LX. SJP-L-5, a novel small-molecule compound, inhibits HIV-1 infection by blocking viral DNA nuclear entry. BMC Microbiol 2015; 15:274. [PMID: 26630969 PMCID: PMC4667461 DOI: 10.1186/s12866-015-0605-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 11/24/2015] [Indexed: 11/15/2022] Open
Abstract
Background Small-molecule compounds that inhibit human immunodeficiency virus type 1 (HIV-1) infection can be used not only as drug candidates, but also as reagents to dissect the life cycle of the virus. Thus, it is desirable to have an arsenal of such compounds that inhibit HIV-1 infection by various mechanisms. Until now, only a few small-molecule compounds that inhibit nuclear entry of viral DNA have been documented. Results We identified a novel, small-molecule compound, SJP-L-5, that inhibits HIV-1 infection. SJP-L-5 is a nitrogen-containing, biphenyl compound whose synthesis was based on the dibenzocyclooctadiene lignan gomisin M2, an anti-HIV bioactive compound isolated from Schisandra micrantha A. C. Smith. SJP-L-5 displayed relatively low cytotoxicity (50 % cytoxicity concentrations were greater than 200 μg/ml) and high antiviral activity against a variety of HIV strains (50 % effective concentrations (EC50)) of HIV-1 laboratory-adapted strains ranged from 0.16–0.97 μg/ml; EC50s of primary isolates ranged from 1.96–5.33 μg/ml). Analyses of the viral DNA synthesis indicated that SJP-L-5 specifically blocks the entry of the HIV-1 pre-integration complex (PIC) into the nucleus. Further results implicated that SJP-L-5 inhibits the disassembly of HIV-1 particulate capsid in the cytoplasm of the infected cells. Conclusions SJP-L-5 is a novel small-molecule compound that inhibits HIV-1 nuclear entry by blocking the disassembly of the viral core. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0605-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ru Bai
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China.
| | - Xing-Jie Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and the Kunming Institute of Zoology of the Chinese Academy of Sciences, Kunming, 650223, P. R. China.
| | - Yan-Li Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China.
| | - Jing-Ping Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, P. R. China.
| | - Hong-Bin Zhang
- Key Laboratory of Medicinal Chemistry for Natural Resources, Ministry of Education, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, P. R. China.
| | - Wei-Lie Xiao
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, P. R. China.
| | - Jian-Xin Pu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, P. R. China.
| | - Han-Dong Sun
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, P. R. China.
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and the Kunming Institute of Zoology of the Chinese Academy of Sciences, Kunming, 650223, P. R. China.
| | - Li-Xin Liu
- Sun Yat-Sen University, Guangzhou, 510275, P. R. China.
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Sahu KK, Hatakeyama N, Miyamoto A. Theoretical investigation of the interactions in binding pocket of Reverse Transcriptase. Saudi J Biol Sci 2015; 22:719-24. [PMID: 26586999 PMCID: PMC4625139 DOI: 10.1016/j.sjbs.2014.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 12/11/2014] [Accepted: 12/16/2014] [Indexed: 11/28/2022] Open
Abstract
Interactions in proteins have been studied using several chemical information techniques including quantum chemical methods that are applied to truncated systems composed of the ligand molecule and the surrounding amino acids of the receptor. In this work we adopt an approach to study these interactions accounting for as many as possible explicit solvent molecules and without the need of a fragmented calculation. Furthermore, we embed our quantum chemical calculations within a molecular dynamics framework that enables a fundamentally fast system for quantum molecular dynamic simulations (QCMD). Central to this new system for QCMD is the tight binding QC system, newly developed in our laboratories, and which combined with the MD paradigm results in an ultra accelerated QCMD method for protein–ligand interaction evaluations. We have applied our newly developed method to the Nevirapine (NVP)–Reverse Transcriptase (RT) system. We show how the proposed method leads us to new findings. The advanced QCMD was applied to a system of RT with NVP and it has led to the knowledge of specific groups and atoms that interact with surrounding amino acids of RT and help in drug binding. The information derived from this calculation may be used in designing drugs for NVP resistant virus strains that have binding capability like NVP.
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Affiliation(s)
| | - Nozomu Hatakeyama
- New Industry Creation Hatchery Center, Tohoku University, Sendai, Japan
| | - Akira Miyamoto
- New Industry Creation Hatchery Center, Tohoku University, Sendai, Japan
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Seniya C, Yadav A, Khan GJ, Sah NK. In-silico Studies Show Potent Inhibition of HIV-1 Reverse Transcriptase Activity by a Herbal Drug. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2015; 12:1355-1364. [PMID: 26671807 DOI: 10.1109/tcbb.2015.2415771] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Acquired immunodeficiency syndrome (AIDS) is a life threatening disease of the human immune system caused by human immunodeficiency virus (HIV). Effective inhibition of reverse transcriptase activity is a prominent, clinically viable approach for the treatment of AIDS. Few non-nucleoside reverse transcriptase inhibitors (NNRTIs) have been approved by the United States Food and Drug Administration (US FDA) as drugs for AIDS. In order to enhance therapeutic options against AIDS we examined novel herbal compounds of 4-thiazolidinone and its derivatives that are known to have remarkable antiviral potency. Our molecular docking and simulation experiments have identified one such herbal molecule known as (5E)-3-(2-aminoethyl)-5-benzylidene-1, 3-thiazolidine-2,4-dione that may bind HIV-1RT with high affinity to cause noncompetitive inhibition. Results are also compared with other US FDA approved drugs. Long de novo simulations and docking study suggest that the ligand (5E)-3-(2-aminoethyl)-5-benzylidene-1, 3-thiazolidine-2,4-dione (CID: 1656714) has strong binding interactions with Asp113, Asp110, Asp185 and Asp186 amino acids, all of which belong to one or the other catalytic pockets of HIV-1RT. It is expected that these interactions could be critical in the inhibitory activity of the HIV-1RT. Therefore, this study provides an evidence for consideration of (5E)-3-(2-aminoethyl)-5-benzylidene-1, 3-thiazolidine-2,4-dione as a valuable natural molecule in the treatment and prevention of HIV-associated disorders.
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Kotoulas SS, Kojić VV, Bogdanović GM, Koumbis AE. Synthesis of novel pyrimidine apiothionucleosides and in vitro evaluation of their cytotoxicity. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.03.089] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Lu YY, Wang X, Wang XW, Liu JY, Li P, Ren H, Lou YQ, Lu C, Zhang GL. Development and validation of a high performance liquid chromatography method for determination of 6-benzyl-1-benzyloxymethyl-5-iodouracil (W-1), a novel non-nucleoside reverse transcriptase inhibitor and its application to a pharmacokinetic study in rats. Biomed Chromatogr 2015; 29:1548-52. [DOI: 10.1002/bmc.3457] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 01/21/2015] [Accepted: 02/15/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Ying-Yuan Lu
- Department of Pharmacology, Basic Medical School; Beijing (Peking) University; Beijing 100191 People's Republic of China
| | - Xin Wang
- Department of Pharmacology, Basic Medical School; Beijing (Peking) University; Beijing 100191 People's Republic of China
| | - Xiao-Wei Wang
- Department of Chemical Biology, School of Pharmaceutical Sciences; Beijing (Peking) University; Beijing 100191 People's Republic of China
| | - Jun-Yi Liu
- Department of Chemical Biology, School of Pharmaceutical Sciences; Beijing (Peking) University; Beijing 100191 People's Republic of China
| | - Pu Li
- Department of Pharmacology, Basic Medical School; Beijing (Peking) University; Beijing 100191 People's Republic of China
| | - Hong Ren
- Department of Pharmacology, Basic Medical School; Beijing (Peking) University; Beijing 100191 People's Republic of China
| | - Ya-Qing Lou
- Department of Pharmacology, Basic Medical School; Beijing (Peking) University; Beijing 100191 People's Republic of China
| | - Chuang Lu
- Millennium Pharmaceuticals-Takeda; Cambridge Massachusetts USA
| | - Guo-Liang Zhang
- Department of Pharmacology, Basic Medical School; Beijing (Peking) University; Beijing 100191 People's Republic of China
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Han X, Wu H, Dong C, Tien P, Xie W, Wu S, Zhou HB. Halolactones are potent HIV-1 non-nucleoside reverse transcriptase inhibitors. RSC Adv 2015. [DOI: 10.1039/c4ra11087k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Halolactones with an isobenzofuran-1(3H)-one core structure have been developed as efficient non-nucleoside reverse transcriptase inhibitors (NNRTIs). The best compound 13a showed excellent potency against WT HIV-1 with a low EC50 value of 0.45 μM.
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Affiliation(s)
- Xin Han
- State Key Laboratory of Virology
- Wuhan University School of Pharmaceutical Sciences
- Wuhan
- China
| | - Haoming Wu
- College of Life Sciences
- Wuhan University
- Wuhan
- China
| | - Chune Dong
- State Key Laboratory of Virology
- Wuhan University School of Pharmaceutical Sciences
- Wuhan
- China
| | - Po Tien
- College of Life Sciences
- Wuhan University
- Wuhan
- China
| | - Wei Xie
- Key Laboratory of Gene Engineering of the Ministry of Education
- State Key Laboratory for Biocontrol
- School of Life Sciences
- The Sun Yat-Sen University
- Guangzhou 510275
| | - Shuwen Wu
- College of Life Sciences
- Wuhan University
- Wuhan
- China
| | - Hai-Bing Zhou
- State Key Laboratory of Virology
- Wuhan University School of Pharmaceutical Sciences
- Wuhan
- China
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Iyidogan P, Anderson KS. Current perspectives on HIV-1 antiretroviral drug resistance. Viruses 2014; 6:4095-139. [PMID: 25341668 PMCID: PMC4213579 DOI: 10.3390/v6104095] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 10/08/2014] [Accepted: 10/20/2014] [Indexed: 11/18/2022] Open
Abstract
Current advancements in antiretroviral therapy (ART) have turned HIV-1 infection into a chronic and manageable disease. However, treatment is only effective until HIV-1 develops resistance against the administered drugs. The most recent antiretroviral drugs have become superior at delaying the evolution of acquired drug resistance. In this review, the viral fitness and its correlation to HIV-1 mutation rates and drug resistance are discussed while emphasizing the concept of lethal mutagenesis as an alternative therapy. The development of resistance to the different classes of approved drugs and the importance of monitoring antiretroviral drug resistance are also summarized briefly.
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Affiliation(s)
- Pinar Iyidogan
- Department of Pharmacology, School of Medicine, Yale University, New Haven, CT 06520, USA.
| | - Karen S Anderson
- Department of Pharmacology, School of Medicine, Yale University, New Haven, CT 06520, USA.
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40
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Singh A, Yadav D, Yadav M, Dhamanage A, Kulkarni S, Singh RK. Molecular Modeling, Synthesis and Biological Evaluation ofN-Heteroaryl Compounds as Reverse Transcriptase Inhibitors Against HIV-1. Chem Biol Drug Des 2014; 85:336-47. [DOI: 10.1111/cbdd.12397] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 07/08/2014] [Accepted: 07/12/2014] [Indexed: 01/20/2023]
Affiliation(s)
- Anuradha Singh
- Nucleic Acids and Antiviral Research Laboratory; Department of Chemistry; University of Allahabad; Allahabad 211002 India
| | - Dipti Yadav
- Nucleic Acids and Antiviral Research Laboratory; Department of Chemistry; University of Allahabad; Allahabad 211002 India
| | - Madhu Yadav
- Nucleic Acids and Antiviral Research Laboratory; Department of Chemistry; University of Allahabad; Allahabad 211002 India
| | - Ashwini Dhamanage
- Department of Virology; National AIDS Research Institute; Pune 411026 India
| | - Smita Kulkarni
- Department of Virology; National AIDS Research Institute; Pune 411026 India
| | - Ramendra K. Singh
- Nucleic Acids and Antiviral Research Laboratory; Department of Chemistry; University of Allahabad; Allahabad 211002 India
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Kumar S, Tiwari M. Topomer-CoMFA-based predictive modelling on 2,3-diaryl-substituted-1,3-thiazolidin-4-ones as non-nucleoside reverse transcriptase inhibitors. Med Chem Res 2014. [DOI: 10.1007/s00044-014-1105-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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42
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Van Schoubroeck B, Van Loock M, Ivens T, Dehertogh P, Jochmans D, Dams G. Identification of HIV-1 reverse transcriptase inhibitors using a scintillation proximity assay. Methods Mol Biol 2014; 1030:19-24. [PMID: 23821257 DOI: 10.1007/978-1-62703-484-5_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) converts the viral single-stranded RNA into double-stranded DNA. The inhibition of reverse transcription in the viral life cycle has proven its efficacy as a clinically relevant antiviral target, but the appearance of resistance mutations remains a major cause of treatment failure and stresses the continuous need for new antiviral compounds. In this chapter, we describe an HIV-1 RT scintillation proximity assay (SPA) to identify inhibitors of the RT. The assay uses an RNA/DNA (poly(rA)/oligo(dT)) template/primer bound to SPA beads, which contain scintillant. Reverse transcriptase extends the primer by incorporating [(3)H]dTTP and dTTP, which results in light production by the scintillant in the bead. Compounds that inhibit reverse transcriptase will prevent the incorporation of tritiated dTTP resulting in a reduction of emitted light compared to the untreated controls.
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Wildum S, Paulsen D, Thede K, Ruebsamen-Schaeff H, Zimmermann H. In vitro and in vivo activities of AIC292, a novel HIV-1 nonnucleoside reverse transcriptase inhibitor. Antimicrob Agents Chemother 2013; 57:5320-9. [PMID: 23959304 PMCID: PMC3811302 DOI: 10.1128/aac.01377-13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 08/07/2013] [Indexed: 11/20/2022] Open
Abstract
Nonnucleoside reverse transcriptase inhibitors (NNRTIs) are important and frequently used elements of highly active antiretroviral therapy (HAART) for the treatment of human immunodeficiency virus type 1 (HIV-1) infection. However, the development of drug resistance, as well as the side effects of existing drugs, defines a medical need for novel NNRTIs with excellent tolerability, improved activity against NNRTI-resistant viruses, and a low barrier to resistance. Within the chemical class of diarylpyrazole-[imidazolidinone]-carboxamides, AIC292 was identified as a promising novel HIV-1 NNRTI and has successfully completed single-dose clinical phase I studies. Here, we report on the antiviral activity of AIC292, evaluated in vitro against wild-type and NNRTI-resistant HIV-1 isolates and in vivo using an engineered mouse xenograft model. AIC292 inhibited wild-type HIV-1 laboratory strains at low nanomolar concentrations, was well tolerated in different cell lines, and showed excellent selectivity in a lead profiling screen. In addition, activity of AIC292 could be demonstrated against a broad panel of wild-type HIV-1 group M and group O clinical isolates. AIC292 also retained activity against viruses harboring NNRTI resistance-associated mutations (RAMs), including the most prevalent variants, K103N, Y181C, and G190A. Interestingly, viruses bearing the L100I RAM were hypersusceptible to AIC292. Two-drug combination assays showed no antagonistic interactions between AIC292 and representative marketed HIV drugs with regard to antiviral activity. Furthermore, AIC292 displayed potent antiviral in vivo efficacy in a mouse xenograft model when applied once daily. Taken together, these data show that AIC292 represents a molecule with the antiviral properties of a novel NNRTI for the treatment of HIV-1 infection.
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45
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Synthesis and cytotoxic evaluation of novel pyrimidine deoxyapiothionucleosides. Bioorg Med Chem Lett 2013; 23:3364-7. [DOI: 10.1016/j.bmcl.2013.03.091] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Revised: 03/19/2013] [Accepted: 03/22/2013] [Indexed: 11/23/2022]
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Novikov MS, Valuev-Elliston VT, Babkov DA, Paramonova MP, Ivanov AV, Gavryushov SA, Khandazhinskaya AL, Kochetkov SN, Pannecouque C, Andrei G, Snoeck R, Balzarini J, Seley-Radtke KL. N1,N3-disubstituted uracils as nonnucleoside inhibitors of HIV-1 reverse transcriptase. Bioorg Med Chem 2013; 21:1150-8. [PMID: 23357038 PMCID: PMC7125863 DOI: 10.1016/j.bmc.2012.12.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 12/18/2012] [Accepted: 12/25/2012] [Indexed: 11/17/2022]
Abstract
A series of phenyloxyethyl and cinnamyl derivatives of substituted uracils were synthesized and found to exhibit potent activity against HIV-RT and HIV replication in cell culture. In general, the cinnamyl derivatives proved superior to the phenyloxyethyl derivatives, however 1-[2-(4-methylphenoxy)ethyl]-3-(3,5-dimethylbenzyl)uracil (19) exhibited the highest activity (EC(50)=0.27 μM) thus confirming that the 3-benzyluracil fragment in the NNRTI structure can be regarded as a functional analogue of the benzophenone pharmacophore typically found in NNRTIs.
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Affiliation(s)
- Mikhail S Novikov
- Department of Pharmaceutical & Toxicological Chemistry, Volgograd State Medical University, Pavshikh Bortsov Sq., 1, Volgograd 400131, Russia
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47
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Matyugina ES, Valuev-Elliston VT, Babkov DA, Novikov MS, Ivanov AV, Kochetkov SN, Balzarini J, Seley-Radtke KL, Khandazhinskaya AL. 5′-Nor carbocyclic nucleosides: unusual nonnucleoside inhibitors of HIV-1 reverse transcriptase. MEDCHEMCOMM 2013. [DOI: 10.1039/c3md00036b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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48
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Seniya C, Yadav A, Uchadia K, Kumar S, Sagar N, Shrivastava P, Shrivastava S, Wadhwa G. Molecular docking of (5E)-3-(2-aminoethyl)-5-(2- thienylmethylene)-1, 3-thiazolidine-2, 4-dione on HIV-1 reverse transcriptase: novel drug acting on enzyme. Bioinformation 2012; 8:678-83. [PMID: 23055609 PMCID: PMC3449371 DOI: 10.6026/97320630008678] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 07/05/2012] [Indexed: 11/23/2022] Open
Abstract
The study of Human immunodeficiency virus (HIV) in humans and animal models in last 31 years suggested that it is a causative agent of AIDS. This causes serious pandemic public health concern globally. It was reported that the HIV-1 reverse transcriptase (RT) played a critical role in the life cycle of HIV. Therefore, inhibition of HIV-1RT enzyme is one of the major and potential targets in the treatment of AIDS. The enzyme (HIV-1RT) was successfully targeted by non nucleotide reverse transcriptase inhibitors (NNRTIs). But frequent application of NNRTIs led drug resistance mutation on HIV infections. Therefore, there is a need to search new NNRTIs with appropriate pharmacophores. For the purpose, a virtually screened 3D model of unliganded HIV-1RT (1DLO) was explored. The unliganded HIV-1RT (1DLO) was docked with 4-thiazolidinone and its derivatives (ChemBank Database) by using AutoDock4. The best seven docking solutions complex were selected and analyzed by Ligplot. The analysis showed that derivative (5E)-3-(2- aminoethyl)-5-(2- thienylmethylene)-1, 3-thiazolidine-2, 4-dione (CID 3087795) has maximum potential against unliganded HIV-1RT (1DLO). The analysis was done on the basis of scoring and binding ability. The derivative (5E)-3-(2- aminoethyl)-5-(2- thienylmethylene)-1, 3-thiazolidine-2, 4-dione (CID 3087795) indicated minimum energy score and highest number of interactions with active site residue and could be a promising inhibitor for HIV-1 RT as Drug target.
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Affiliation(s)
- Chandrabhan Seniya
- Department of Biotechnology, Madhav Institute of Technology & Science Gwalior – 474005, M. P., India
| | - Ajay Yadav
- Department of Biotechnology, Madhav Institute of Technology & Science Gwalior – 474005, M. P., India
| | - Kuldeep Uchadia
- Department of Biotechnology, Madhav Institute of Technology & Science Gwalior – 474005, M. P., India
| | - Sanjay Kumar
- Department of Botany, Nagaland University, Headquarter Lumami, Nagaland- 798601, India
| | - Nitin Sagar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai-400076
| | - Priyanka Shrivastava
- Department of Biotechnology, Madhav Institute of Technology & Science Gwalior – 474005, M. P., India
| | - Shilpi Shrivastava
- Department of Biotechnology, Madhav Institute of Technology & Science Gwalior – 474005, M. P., India
| | - Gulshan Wadhwa
- Apex Bioinformatics Centre, Department of Biotechnology, Ministry of Science and Technology, CGO complex, Lodhi Road, New Delhi – 110 003, India
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Akyüz L, Sarıpınar E. Conformation depends on 4D-QSAR analysis using EC-GA method: pharmacophore identification and bioactivity prediction of TIBOs as non-nucleoside reverse transcriptase inhibitors. J Enzyme Inhib Med Chem 2012; 28:776-91. [PMID: 22591319 DOI: 10.3109/14756366.2012.684051] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The electron conformational and genetic algorithm methods (EC-GA) were integrated for the identification of the pharmacophore group and predicting the anti HIV-1 activity of tetrahydroimidazo[4,5,1-jk][1,4]benzodiazepinone (TIBO) derivatives. To reveal the pharmacophore group, each conformation of all compounds was arranged by electron conformational matrices of congruity. Multiple comparisons of these matrices, within given tolerances for high active and low active TIBO derivatives, allow the identification of the pharmacophore group that refers to the electron conformational submatrix of activity. The effects of conformations, internal and external validation were investigated by four different models based on an ensemble of conformers and a single conformer, both with and without a test set. Model 1 using an ensemble of conformers for the training (39 compounds) and test sets (13 compounds), obtained by the optimum seven parameters, gave satisfactory results (R²(training) = 0.878, R²(test)= 0.910, q² = 0.840, q²(ext1) = 0.926 and q²(ext2) = 0.900).
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Affiliation(s)
- Lalehan Akyüz
- Faculty of Science, Department of Chemistry, Erciyes University, Kayseri, Turkey
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50
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Mishra S, Tandon P, Ayala AP. Study on the structure and vibrational spectra of efavirenz conformers using DFT: comparison to experimental data. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 88:116-123. [PMID: 22206896 DOI: 10.1016/j.saa.2011.12.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 12/04/2011] [Indexed: 05/31/2023]
Abstract
Efavirenz, (S)-6-chloro-4-(cyclopropylethynyl)-1,4-dihydro-4-(trifluoromethyl)-2H-3,1-benzoxazin-2-one, is an anti HIV agent belonging to the class of the non-nucleoside inhibitors of the HIV-1 virus reverse transcriptase. A systematic quantum chemical study of the possible conformations, their relative stabilities and vibrational spectra of efavirenz has been reported. Structural and spectral characteristics of efavirenz have been studied by vibrational spectroscopy and quantum chemical methods. Density functional theory (DFT) calculations for potential energy curve, optimized geometries and vibrational spectra have been carried out using 6-311++G(d,p) basis sets and B3LYP functionals. Based on these results, we have discussed the correlation between the vibrational modes and the crystalline structure of the most stable form of efavirenz. A complete analysis of the experimental infrared and Raman spectra has been reported on the basis of wavenumber of the vibrational bands and potential energy distribution. The infrared and the Raman spectra of the molecule based on DFT calculations show reasonable agreement with the experimental results. The calculated HOMO and LUMO energies shows that charge transfer occur within the molecule.
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Affiliation(s)
- Soni Mishra
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, India
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