1
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Wang Z. Novel diarylpyrimidine subtypes as HIV-1 nonnucleoside reverse transcriptase inhibitors with improved resistance profile. J Med Virol 2024; 96:e29553. [PMID: 38516803 DOI: 10.1002/jmv.29553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 03/06/2024] [Indexed: 03/23/2024]
Affiliation(s)
- Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota, USA
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2
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De Clercq E. Selected Milestones in Antiviral Drug Development. Viruses 2024; 16:169. [PMID: 38399945 PMCID: PMC10891914 DOI: 10.3390/v16020169] [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: 11/27/2023] [Revised: 01/16/2024] [Accepted: 01/16/2024] [Indexed: 02/25/2024] Open
Abstract
This review article will describe the (wide) variety of approaches that I envisaged to develop a specific therapy for viral infections: (i) interferon and its inducers, (ii) HSV, VZV and CMV inhibitors, (iii) NRTIs (nucleoside reverse transcriptase inhibitors), NtRTIs (nucleotide reverse transcriptase inhibitors) and NNRTIs (non-nucleoside reverse transcriptase inhibitors) as HIV inhibitors, (iv) NtRTIs as HBV inhibitors, and finally, (v) the transition of an HIV inhibitor to a stem cell mobilizer, as exemplified by AMD-3100 (Mozobil®).
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Affiliation(s)
- Erik De Clercq
- Rega Institute for Medical Research, KU Leuven, Herestraat 49, B-3000 Leuven, Belgium
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3
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Jadaun P, Seniya C, Pal SK, Kumar S, Kumar P, Nema V, Kulkarni SS, Mukherjee A. Elucidation of Antiviral and Antioxidant Potential of C-Phycocyanin against HIV-1 Infection through In Silico and In Vitro Approaches. Antioxidants (Basel) 2022; 11:antiox11101942. [PMID: 36290665 PMCID: PMC9598530 DOI: 10.3390/antiox11101942] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/23/2022] [Accepted: 09/24/2022] [Indexed: 11/16/2022] Open
Abstract
Antiretroviral therapy is the single existing therapy for patients infected with HIV; however, it has drawbacks in terms of toxicity and resistance. Thus, there is a continuous need to explore safe and efficacious anti-retroviral agents. C-Phycocyanin (C-PC) is a phycobiliprotein, which has been known for various biological properties; however, its effect on HIV-1 replication needs revelation. This study aimed to identify the inhibitory effects of C-PC on HIV-1 using in vitro and in silico approaches and to assess its role in the generation of mitochondrial reactive oxygen species (ROS) during HIV-1 infection. In vitro anti-HIV-1 activity of C-PC was assessed on TZM-bl cells through luciferase gene assay against four different clades of HIV-1 strains in a dose-dependent manner. Results were confirmed in PBMCs, using the HIV-1 p24 antigen assay. Strong associations between C-PC and HIV-1 proteins were observed through in silico molecular simulation-based interactions, and the in vitro mechanistic study confirmed its target by inhibition of reverse transcriptase and protease enzymes. Additionally, the generation of mitochondrial ROS was detected by the MitoSOX and DCF-DA probe through confocal microscopy. Furthermore, our results confirmed that C-PC treatment notably subdued the fluorescence in the presence of the virus, thus reduction of ROS and the activation of caspase-3/7 in HIV-1-infected cells. Overall, our study suggests C-PC as a potent and broad in vitro antiviral and antioxidant agent against HIV-1 infection.
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Affiliation(s)
- Pratiksha Jadaun
- ICMR-National AIDS Research Institute, Pune 411026, MH, India
- Correspondence: (P.J.); (A.M.)
| | | | | | - Sanjit Kumar
- Vellore Institute of Technology, Vellore 632014, TN, India
| | - Pramod Kumar
- ICMR-National Institute of Cancer Prevention and Research, Noida 201301, UP, India
| | - Vijay Nema
- ICMR-National AIDS Research Institute, Pune 411026, MH, India
| | | | - Anupam Mukherjee
- ICMR-National AIDS Research Institute, Pune 411026, MH, India
- Correspondence: (P.J.); (A.M.)
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4
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Insights into HIV-1 Reverse Transcriptase (RT) Inhibition and Drug Resistance from Thirty Years of Structural Studies. Viruses 2022; 14:v14051027. [PMID: 35632767 PMCID: PMC9148108 DOI: 10.3390/v14051027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 02/01/2023] Open
Abstract
The enzyme reverse transcriptase (RT) plays a central role in the life cycle of human immunodeficiency virus (HIV), and RT has been an important drug target. Elucidations of the RT structures trapping and detailing the enzyme at various functional and conformational states by X-ray crystallography have been instrumental for understanding RT activities, inhibition, and drug resistance. The structures have contributed to anti-HIV drug development. Currently, two classes of RT inhibitors are in clinical use. These are nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs). However, the error-prone viral replication generates variants that frequently develop resistance to the available drugs, thus warranting a continued effort to seek more effective treatment options. RT also provides multiple additional potential druggable sites. Recently, the use of single-particle cryogenic electron microscopy (cryo-EM) enabled obtaining structures of NNRTI-inhibited HIV-1 RT/dsRNA initiation and RT/dsDNA elongation complexes that were unsuccessful by X-ray crystallography. The cryo-EM platform for the structural study of RT has been established to aid drug design. In this article, we review the roles of structural biology in understanding and targeting HIV RT in the past three decades and the recent structural insights of RT, using cryo-EM.
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5
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Wang Z, Cherukupalli S, Xie M, Wang W, Jiang X, Jia R, Pannecouque C, De Clercq E, Kang D, Zhan P, Liu X. Contemporary Medicinal Chemistry Strategies for the Discovery and Development of Novel HIV-1 Non-nucleoside Reverse Transcriptase Inhibitors. J Med Chem 2022; 65:3729-3757. [PMID: 35175760 DOI: 10.1021/acs.jmedchem.1c01758] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Currently, HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs) are a major component of the highly active anti-retroviral therapy (HAART) regimen. However, the occurrence of drug-resistant strains and adverse reactions after long-term usage have inevitably compromised the clinical application of NNRTIs. Therefore, the development of novel inhibitors with distinct anti-resistance profiles and better pharmacological properties is still an enormous challenge. Herein, we summarize state-of-the-art medicinal chemistry strategies for the discovery of potent NNRTIs, such as structure-based design strategies, contemporary computer-aided drug design, covalent-binding strategies, and the application of multi-target-directed ligands. The strategies described here will facilitate the identification of promising HIV-1 NNRTIs.
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Affiliation(s)
- Zhao Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Srinivasulu Cherukupalli
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Minghui Xie
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Wenbo Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Xiangyi Jiang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Ruifang Jia
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China.,China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China.,China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China.,China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
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6
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Ismail MMF, Ayoup MS. Review on fluorinated nucleoside/non-nucleoside FDA-approved antiviral drugs. RSC Adv 2022; 12:31032-31045. [PMID: 36348998 PMCID: PMC9620415 DOI: 10.1039/d2ra05370e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 10/13/2022] [Indexed: 11/07/2022] Open
Abstract
FDA-approved antiviral agents represent an important class that has attracted attention in recent years to combat current and future threats of viral pandemics. Fluorine ameliorates the electronic, lipophilic and steric problems of drugs. Additionally, fluorine can prolong drug activity and improve metabolic stability, thereby, modifying their pharmacodynamic and pharmacokinetic character. Herein, we summarized the fluorinated FDA-approved antiviral agents, dealing with biological aspects, mechanisms of action, and synthetic pathways. FDA-approved antiviral agents represent an important class that has attracted attention in recent years to combat current and future threats of viral pandemics.![]()
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Affiliation(s)
- Magda M. F. Ismail
- Department of Pharmaceutical Medicinal Chemistry and Drug Design, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo 11754, Egypt
| | - Mohammed Salah Ayoup
- Department of Chemistry, Faculty of Science, Alexandria University, P. O. Box 426, Alexandria 21321, Egypt
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7
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Cilento ME, Kirby KA, Sarafianos SG. Avoiding Drug Resistance in HIV Reverse Transcriptase. Chem Rev 2021; 121:3271-3296. [PMID: 33507067 DOI: 10.1021/acs.chemrev.0c00967] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
HIV reverse transcriptase (RT) is an enzyme that plays a major role in the replication cycle of HIV and has been a key target of anti-HIV drug development efforts. Because of the high genetic diversity of the virus, mutations in RT can impart resistance to various RT inhibitors. As the prevalence of drug resistance mutations is on the rise, it is necessary to design strategies that will lead to drugs less susceptible to resistance. Here we provide an in-depth review of HIV reverse transcriptase, current RT inhibitors, novel RT inhibitors, and mechanisms of drug resistance. We also present novel strategies that can be useful to overcome RT's ability to escape therapies through drug resistance. While resistance may not be completely avoidable, designing drugs based on the strategies and principles discussed in this review could decrease the prevalence of drug resistance.
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Affiliation(s)
- Maria E Cilento
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States.,Children's Healthcare of Atlanta, Atlanta, Georgia 30307, United States
| | - Karen A Kirby
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States.,Children's Healthcare of Atlanta, Atlanta, Georgia 30307, United States
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States.,Children's Healthcare of Atlanta, Atlanta, Georgia 30307, United States
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8
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Ferreira Pimentel LC, Cunha AC, Boas Hoelz LV, Canzian HF, Leite Firmino Marinho DI, Boechat N, Bastos MM. Phenylamino-pyrimidine (PAP) Privileged Structure: Synthesis and Medicinal Applications. Curr Top Med Chem 2020; 20:227-243. [DOI: 10.2174/1568026620666200124094949] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/17/2019] [Accepted: 12/25/2019] [Indexed: 12/23/2022]
Abstract
The phenylamino-pyrimidine (PAP) nucleus has been demonstrated to be useful for the development of new drugs and is present in a wide variety of antiretroviral agents and tyrosine kinase inhibitors (TKIs). This review aims to evaluate the application of PAP derivatives in drugs and other bioactive compounds. It was concluded that PAP derivatives are still worth exploring, as they may provide highly competitive ATP TKI’s with nano/picomolar activity.
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Affiliation(s)
- Luiz Claudio Ferreira Pimentel
- Fundacao Oswaldo Cruz, Instituto de Tecnologia em Farmacos, Farmanguinhos - Fiocruz, Laboratório de Sintese de Farmacos - LASFAR, Manguinhos, CEP 21041-250, Rio de Janeiro, RJ, Brazil
| | - Anna Claudia Cunha
- Universidade Federal Fluminense, Departamento de Quimica Organica, Campus do Valonguinho, CEP 24020-150, Niteroi, RJ, Brazil
| | - Lucas Villas Boas Hoelz
- Fundacao Oswaldo Cruz, Instituto de Tecnologia em Farmacos, Farmanguinhos - Fiocruz, Laboratório de Sintese de Farmacos - LASFAR, Manguinhos, CEP 21041-250, Rio de Janeiro, RJ, Brazil
| | - Henayle Fernandes Canzian
- Fundacao Oswaldo Cruz, Instituto de Tecnologia em Farmacos, Farmanguinhos - Fiocruz, Laboratório de Sintese de Farmacos - LASFAR, Manguinhos, CEP 21041-250, Rio de Janeiro, RJ, Brazil
| | - Debora Inacio Leite Firmino Marinho
- Fundacao Oswaldo Cruz, Instituto de Tecnologia em Farmacos, Farmanguinhos - Fiocruz, Laboratório de Sintese de Farmacos - LASFAR, Manguinhos, CEP 21041-250, Rio de Janeiro, RJ, Brazil
| | - Nubia Boechat
- Fundacao Oswaldo Cruz, Instituto de Tecnologia em Farmacos, Farmanguinhos - Fiocruz, Laboratório de Sintese de Farmacos - LASFAR, Manguinhos, CEP 21041-250, Rio de Janeiro, RJ, Brazil
| | - Monica Macedo Bastos
- Fundacao Oswaldo Cruz, Instituto de Tecnologia em Farmacos, Farmanguinhos - Fiocruz, Laboratório de Sintese de Farmacos - LASFAR, Manguinhos, CEP 21041-250, Rio de Janeiro, RJ, Brazil
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9
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El-Hussieny M, El-Sayed NF, Ewies EF, Ibrahim NM, Mahran MRH, Fouad MA. Synthesis, molecular docking and biological evaluation of 2-(thiophen-2-yl)-1H-indoles as potent HIV-1 non-nucleoside reverse transcriptase inhibitors. Bioorg Chem 2019; 95:103521. [PMID: 31884145 DOI: 10.1016/j.bioorg.2019.103521] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/10/2019] [Accepted: 12/17/2019] [Indexed: 10/25/2022]
Abstract
New 2-(thiophen-2-yl)-1H-indole derivatives bearing hydrophobic substituents at the 3-position were designed, synthesized and evaluated for their inhibition of HIV-1 reverse transcriptase (RT) enzyme. Dialkylphosphites (2a-c) or trialkylphosphites (3a-c) were reacted with 2-(thiophen-2-yl)-1H-indole-3-carbaldehyde (1) yielding the corresponding α-hydroxyphosphonate adducts (7a-7c). The reaction of compound 1 with the ylidenetriphenylphosphoranes (4a-4c) proceeds via Wittig mechanism giving the corresponding ethylenes (E, 8a-c). Compounds 8b,c were equally obtained upon reacting aldehyde 1 with the appropriate dialkylphosphonates 5a,b under the Horner-Wittig reaction conditions. On the other hand, the reaction of aldehyde 1 with diethyl cyanomethylene phosphonate (5c) yielded a mixture of the E-ethylene 10 and the cyanovinyl phosphonate 11. The thioaldehyde 12 was obtained upon refluxing aldehyde 1 with the Lawesson's reagent (LR, 6a) or with the Japanese reagent (JR, 6b) in dry toluene. Upon evaluation of HIV-1 Reverse Transcriptase enzyme inhibition, compound 8b (IC50 = 2.93 nM) exhibited the superior HIV-1 RT inhibition and its potency was about 3-folds that of Efavirenz (IC50 = 6.03 nM). Also, compounds 9a (IC50 = 4.09 nM) and 12 (IC50 = 3.54 nM) showed significantly higher inhibition potency. Moreover, compounds 7b (IC50 = 7.48 nM), and 8a (IC50 = 4.55 nM) showed potency not significantly different from that of Efavirenz. Molecular docking experiments on these potent compounds was in accordance with the in vitro data and confirmed binding of these compounds to the enzyme through ring-stacking and hydrogen bond interactions. According to these results, the new molecules would serve as potent HIV-1 NNRTIs inhibitors.
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Affiliation(s)
- Marwa El-Hussieny
- Organometallic and Organometalloid Chemistry Department, National Research Centre, 33 El-Bohouth St. (former El Tahrir St.), P.O. 12622, Dokki, Giza, Egypt
| | - Naglaa F El-Sayed
- Organometallic and Organometalloid Chemistry Department, National Research Centre, 33 El-Bohouth St. (former El Tahrir St.), P.O. 12622, Dokki, Giza, Egypt
| | - Ewies F Ewies
- Organometallic and Organometalloid Chemistry Department, National Research Centre, 33 El-Bohouth St. (former El Tahrir St.), P.O. 12622, Dokki, Giza, Egypt.
| | - Nabila M Ibrahim
- Organometallic and Organometalloid Chemistry Department, National Research Centre, 33 El-Bohouth St. (former El Tahrir St.), P.O. 12622, Dokki, Giza, Egypt
| | - Mohamed R H Mahran
- Organometallic and Organometalloid Chemistry Department, National Research Centre, 33 El-Bohouth St. (former El Tahrir St.), P.O. 12622, Dokki, Giza, Egypt
| | - Marwa A Fouad
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini St., Cairo 11562, Egypt.
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10
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Huang YM, Alharbi NS, Sun B, Shantharam CS, Rakesh KP, Qin HL. Synthetic routes and structure-activity relationships (SAR) of anti-HIV agents: A key review. Eur J Med Chem 2019; 181:111566. [PMID: 31401538 DOI: 10.1016/j.ejmech.2019.111566] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 07/25/2019] [Accepted: 07/26/2019] [Indexed: 01/05/2023]
Abstract
The worldwide increase of AIDS, an epidemic infection in constant development has an essential and still requires potent antiretroviral chemotherapeutic agents for reducing the integer of deaths caused by HIV. Thus, there is an urgent need for new anti-HIV drug candidates with increased strength, new targets, superior pharmacokinetic properties, and compact side effects. From this viewpoint, we first review present strategies of anti-HIV drug innovation and the synthesis of heterocyclic or natural compound as anti-HIV agents for facilitating the development of more influential and successful anti-HIV agents.
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Affiliation(s)
- Yu-Mei Huang
- Department of Pharmaceutical Engineering, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 205 Luoshi Road, Wuhan, 430070, PR China
| | - Njud S Alharbi
- Biotechnology Research Group, Deportment of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Bing Sun
- Department of Pharmaceutical Engineering, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 205 Luoshi Road, Wuhan, 430070, PR China.
| | - C S Shantharam
- Department of Chemistry, Pooja Bhagavath Memorial Mahajana Education Centre, Mysuru, 570016, Karnataka, India
| | - K P Rakesh
- Department of Pharmaceutical Engineering, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 205 Luoshi Road, Wuhan, 430070, PR China.
| | - Hua-Li Qin
- Department of Pharmaceutical Engineering, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 205 Luoshi Road, Wuhan, 430070, PR China.
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11
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Romeo R, Iannazzo D, Veltri L, Gabriele B, Macchi B, Frezza C, Marino-Merlo F, Giofrè SV. Pyrimidine 2,4-Diones in the Design of New HIV RT Inhibitors. Molecules 2019; 24:E1718. [PMID: 31052607 PMCID: PMC6539630 DOI: 10.3390/molecules24091718] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/18/2019] [Accepted: 04/30/2019] [Indexed: 01/01/2023] Open
Abstract
The pyrimidine nucleus is a versatile core in the development of antiretroviral agents. On this basis, a series of pyrimidine-2,4-diones linked to an isoxazolidine nucleus have been synthesized and tested as nucleoside analogs, endowed with potential anti-HIV (human immunodeficiency virus) activity. Compounds 6a-c, characterized by the presence of an ethereal group at C-3, show HIV reverse transcriptase (RT) inhibitor activity in the nanomolar range as well as HIV-infection inhibitor activity in the low micromolar with no toxicity. In the same context, compound 7b shows only a negligible inhibition of RT HIV.
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Affiliation(s)
- Roberto Romeo
- Dipartimento di Scienze chimiche, biologiche, farmaceutiche ed ambientali, Università di Messina, Via S.S. Annunziata, 98168 Messina, Italy.
| | - Daniela Iannazzo
- Dipartimento di Ingegneria, Università di Messina, Contrada Di Dio, 98166 Messina, Italy.
| | - Lucia Veltri
- Dipartimento di Chimica e tecnologie chimiche, Università della Calabria,Via P. Bucci 12/C, 87036 Arcavacata di Rende, Italy.
| | - Bartolo Gabriele
- Dipartimento di Chimica e tecnologie chimiche, Università della Calabria,Via P. Bucci 12/C, 87036 Arcavacata di Rende, Italy.
| | - Beatrice Macchi
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma "Tor Vergata", 00133 Roma, Italy.
| | - Caterina Frezza
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma "Tor Vergata", 00133 Roma, Italy.
| | | | - Salvatore V Giofrè
- Dipartimento di Scienze chimiche, biologiche, farmaceutiche ed ambientali, Università di Messina, Via S.S. Annunziata, 98168 Messina, Italy.
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12
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Abstract
Fifty years of research (1968-2018) toward the identification of selective antiviral drugs have been primarily focused on antiviral compounds active against DNA viruses (HSV, VZV, CMV, HBV) and retroviruses (HIV). For the treatment of HSV infections the aminoacyl esters of acyclovir were designed, and valacyclovir became the successor of acyclovir in the treatment of HSV and VZV infections. BVDU (brivudin) still stands out as the most potent among the marketed compounds for the treatment of VZV infections (i.e., herpes zoster). In the treatment of HIV infections 10 tenofovir-based drug combinations have been marketed, and tenofovir disoproxil fumarate (TDF) and tenofovir alafenamide (TAF) have also proved effective in the treatment of HBV infections. As a spin-off of our anti-HIV research, a CXCR4 antagonist AMD-3100 was found to be therapeutically useful as a stem cell mobilizer, and has since 10 years been approved for the treatment of some hematological malignancies.
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Affiliation(s)
- Erik De Clercq
- Department of Microbiology and Immunology, Rega Institute for Medical Research , KU Leuven , Herestraat 49 , 3000 Leuven , Belgium
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13
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DeStefano JJ. Non-nucleoside Reverse Transcriptase Inhibitors Inhibit Reverse Transcriptase through a Mutually Exclusive Interaction with Divalent Cation-dNTP Complexes. Biochemistry 2019; 58:2176-2187. [PMID: 30900874 DOI: 10.1021/acs.biochem.9b00028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Non-nucleoside reverse transcriptase inhibitors (NNRTIs) are considered noncompetitive inhibitors that structurally alter reverse transcriptase (RT) and dramatically decrease catalysis. In this report, biochemical analysis with various divalent cations was used to demonstrate that NNRTIs and divalent cation-dNTP complexes are mutually exclusive, inhibiting each other's binding to RT/primer/template (RT-P/T) complexes. The binding of catalytically competent divalent cation-dNTP complexes to RT-P/T was measured with Mg2+, Mn2+, Zn2+, Co2+, and Ni2+ using Ca2+, a noncatalytic cation, for displacement. Binding strength order was Mn2+ ≈ Zn2+ ≫ Co2+ > Mg2+ ≈ Ni2+. Consistent with but not exclusive to mutually exclusive binding, primer extension assays showed that stronger divalent cation-dNTP complexes were more resistant to NNRTIs (efavirenz (EFV), rilpivirine (RPV), and nevirapine (NVP)). Filtration assays demonstrated that divalent cation-dNTP complexes inhibited the binding of 14C-labeled EFV to RT-P/T with stronger binding complexes formed with Mn2+ inhibiting more potently than those with Mg2+. Conversely, filter binding assays demonstrated that EFV inhibited 3H-labeled dNTP binding to RT-P/T complexes with displacement of Mn2+-dNTP complexes requiring much greater concentrations of EFV than the more weakly bound Mg2+-dNTP complexes. EFV bound relatively weakly to the NNRTI resistant K103N RT; but, binding was modestly enhanced in the presence of P/T, and EFV was easily displaced by divalent cation-dNTP complexes. This suggests that K103N overcomes EFV inhibition mostly by binding more weakly to the drug and is in contrast to other reports that indicate K103N has little to no effect on drug or dNTP binding. Overall, this biochemical analysis supports recent biophysical analyses of NNRTI-RT interactions that indicate mutually exclusive binding.
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Affiliation(s)
- Jeffrey J DeStefano
- Department of Cell Biology and Molecular Genetics and the Maryland Pathogen Research Institute , University of Maryland , College Park , Maryland 20742 , United States
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14
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Namasivayam V, Vanangamudi M, Kramer VG, Kurup S, Zhan P, Liu X, Kongsted J, Byrareddy SN. The Journey of HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs) from Lab to Clinic. J Med Chem 2018; 62:4851-4883. [PMID: 30516990 DOI: 10.1021/acs.jmedchem.8b00843] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Human immunodeficiency virus (HIV) infection is now pandemic. Targeting HIV-1 reverse transcriptase (HIV-1 RT) has been considered as one of the most successful targets for the development of anti-HIV treatment. Among the HIV-1 RT inhibitors, non-nucleoside reverse transcriptase inhibitors (NNRTIs) have gained a definitive place due to their unique antiviral potency, high specificity, and low toxicity in antiretroviral combination therapies used to treat HIV. Until now, >50 structurally diverse classes of compounds have been reported as NNRTIs. Among them, six NNRTIs were approved for HIV-1 treatment, namely, nevirapine (NVP), delavirdine (DLV), efavirenz (EFV), etravirine (ETR), rilpivirine (RPV), and doravirine (DOR). In this perspective, we focus on the six NNRTIs and lessons learned from their journey through development to clinical studies. It demonstrates the obligatory need of understanding the physicochemical and biological principles (lead optimization), resistance mutations, synthesis, and clinical requirements for drugs.
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Affiliation(s)
- Vigneshwaran Namasivayam
- Pharmaceutical Institute, Pharmaceutical Chemistry II , University of Bonn , 53121 Bonn , Germany
| | - Murugesan Vanangamudi
- Department of Medicinal and Pharmaceutical Chemistry , Sree Vidyanikethan College of Pharmacy , Tirupathi , Andhra Pradesh 517102 , India
| | | | - Sonali Kurup
- College of Pharmacy , Roosevelt University , Schaumburg , Illinois 60173 , United States
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , Jinan 250012 , P.R. 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 , Jinan 250012 , P.R. China
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , DK-5230 , Odense M , Denmark
| | - Siddappa N Byrareddy
- Department of Pharmacology and Experimental Neuroscience , University of Nebraska Medical Center , Omaha 68198-5880 , United States
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15
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Yang Y, Kang D, Nguyen LA, Smithline ZB, Pannecouque C, Zhan P, Liu X, Steitz TA. Structural basis for potent and broad inhibition of HIV-1 RT by thiophene[3,2- d]pyrimidine non-nucleoside inhibitors. eLife 2018; 7:e36340. [PMID: 30044217 PMCID: PMC6080946 DOI: 10.7554/elife.36340] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 07/18/2018] [Indexed: 12/18/2022] Open
Abstract
Rapid generation of drug-resistant mutations in HIV-1 reverse transcriptase (RT), a prime target for anti-HIV therapy, poses a major impediment to effective anti-HIV treatment. Our previous efforts have led to the development of two novel non-nucleoside reverse transcriptase inhibitors (NNRTIs) with piperidine-substituted thiophene[3,2-d]pyrimidine scaffolds, compounds K-5a2 and 25a, which demonstrate highly potent anti-HIV-1 activities and improved resistance profiles compared with etravirine and rilpivirine, respectively. Here, we have determined the crystal structures of HIV-1 wild-type (WT) RT and seven RT variants bearing prevalent drug-resistant mutations in complex with K-5a2 or 25a at ~2 Å resolution. These high-resolution structures illustrate the molecular details of the extensive hydrophobic interactions and the network of main chain hydrogen bonds formed between the NNRTIs and the RT inhibitor-binding pocket, and provide valuable insights into the favorable structural features that can be employed for designing NNRTIs that are broadly active against drug-resistant HIV-1 variants.
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Affiliation(s)
- Yang Yang
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenUnited States
- Howard Hughes Medical InstituteYale UniversityNew HavenUnited States
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical SciencesShandong UniversityJinanChina
| | - Laura A Nguyen
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenUnited States
| | - Zachary B Smithline
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenUnited States
| | | | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical SciencesShandong UniversityJinanChina
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical SciencesShandong UniversityJinanChina
| | - Thomas A Steitz
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenUnited States
- Howard Hughes Medical InstituteYale UniversityNew HavenUnited States
- Department of ChemistryYale UniversityNew HavenUnited States
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16
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Valuev-Elliston VT, Kochetkov SN. Novel HIV-1 Non-nucleoside Reverse Transcriptase Inhibitors: A Combinatorial Approach. BIOCHEMISTRY (MOSCOW) 2018. [PMID: 29523068 DOI: 10.1134/s0006297917130107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Highly active antiretroviral therapy (HAART) is one of the most effective means for fighting against HIV-infection. HAART primarily targets HIV-1 reverse transcriptase (RT), and 14 of 28 compounds approved by the FDA as anti-HIV drugs act on this enzyme. HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs) hold a special place among HIV RT inhibitors owing to their high specificity and unique mode of action. Nonetheless, these drugs show a tendency to decrease their efficacy due to high HIV-1 variability and formation of resistant virus strains tolerant to clinically applied HIV NNRTIs. A combinatorial approach based on varying substituents within various fragments of the parent molecule that results in development of highly potent compounds is one of the approaches aimed at designing novel HIV NNRTIs. Generation of HIV NNRTIs based on pyrimidine derivatives explicitly exemplifies this approach, which is discussed in this review.
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Affiliation(s)
- V T Valuev-Elliston
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.
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17
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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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18
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Corona A, Onnis V, Deplano A, Bianco G, Demurtas M, Distinto S, Cheng YC, Alcaro S, Esposito F, Tramontano E. Design, synthesis and antiviral evaluation of novel heteroarylcarbothioamide derivatives as dual inhibitors of HIV-1 reverse transcriptase-associated RNase H and RDDP functions. Pathog Dis 2017; 75:3943645. [PMID: 28859311 PMCID: PMC6433301 DOI: 10.1093/femspd/ftx078] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 07/08/2017] [Indexed: 11/14/2022] Open
Abstract
In the continuous effort to identify new HIV-1 inhibitors endowed with innovative mechanisms, the dual inhibition of different viral functions would provide a significant advantage against drug-resistant variants. The HIV-1 reverse transcriptase (RT)-associated ribonuclease H (RNase H) is the only viral-encoded enzymatic activity that still lacks an efficient inhibitor. We synthesized a library of 3,5-diamino-N-aryl-1H-pyrazole-4-carbothioamide and 4-amino-5-benzoyl-N-phenyl-2-(substituted-amino)-1H-pyrrole-3-carbothioamide derivatives and tested them against RNase H activity. We identified the pyrazolecarbothioamide derivative A15, able to inhibit viral replication and both RNase H and RNA-dependent DNA polymerase (RDDP) RT-associated activities in the low micromolar range. Docking simulations hypothesized its binding to two RT pockets. Site-directed mutagenesis experiments showed that, with respect to wt RT, V108A substitution strongly reduced A15 IC50 values (12.6-fold for RNase H inhibition and 4.7-fold for RDDP), while substitution A502F caused a 9.0-fold increase in its IC50 value for RNase H, not affecting the RDDP inhibition, reinforcing the hypothesis of a dual-site inhibition. Moreover, A15 retained good inhibition potency against three non-nucleoside RT inhibitor (NNRTI)-resistant enzymes, confirming a mode of action unrelated to NNRTIs and suggesting its potential as a lead compound for development of new HIV-1 RT dual inhibitors active against drug-resistant viruses.
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Affiliation(s)
- Angela Corona
- Dipartimento di Scienze della Vita e dell’Ambiente, Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato (Cagliari), Italy
| | - Valentina Onnis
- Dipartimento di Scienze della Vita e dell’Ambiente, Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato (Cagliari), Italy
| | - Alessandro Deplano
- Dipartimento di Scienze della Vita e dell’Ambiente, Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato (Cagliari), Italy
| | - Giulia Bianco
- Dipartimento di Scienze della Vita e dell’Ambiente, Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato (Cagliari), Italy
| | - Monica Demurtas
- Dipartimento di Scienze della Vita e dell’Ambiente, Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato (Cagliari), Italy
| | - Simona Distinto
- Dipartimento di Scienze della Vita e dell’Ambiente, Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato (Cagliari), Italy
| | - Yung-Chi Cheng
- Department of Pharmacology, Yale University Medical School, New Haven, CT 06520, USA
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Francesca Esposito
- Dipartimento di Scienze della Vita e dell’Ambiente, Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato (Cagliari), Italy
| | - Enzo Tramontano
- Dipartimento di Scienze della Vita e dell’Ambiente, Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato (Cagliari), Italy
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19
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Nováková L, Pavlík J, Chrenková L, Martinec O, Červený L. Current antiviral drugs and their analysis in biological materials - Part II: Antivirals against hepatitis and HIV viruses. J Pharm Biomed Anal 2017; 147:378-399. [PMID: 29031512 DOI: 10.1016/j.jpba.2017.07.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 07/01/2017] [Indexed: 12/18/2022]
Abstract
This review is a Part II of the series aiming to provide comprehensive overview of currently used antiviral drugs and to show modern approaches to their analysis. While in the Part I antivirals against herpes viruses and antivirals against respiratory viruses were addressed, this part concerns antivirals against hepatitis viruses (B and C) and human immunodeficiency virus (HIV). Many novel antivirals against hepatitis C virus (HCV) and HIV have been introduced into the clinical practice over the last decade. The recent broadening portfolio of these groups of antivirals is reflected in increasing number of developed analytical methods required to meet the needs of clinical terrain. Part II summarizes the mechanisms of action of antivirals against hepatitis B virus (HBV), HCV, and HIV, their use in clinical practice, and analytical methods for individual classes. It also provides expert opinion on state of art in the field of bioanalysis of these drugs. Analytical methods reflect novelty of these chemical structures and use by far the most current approaches, such as simple and high-throughput sample preparation and fast separation, often by means of UHPLC-MS/MS. Proper method validation based on requirements of bioanalytical guidelines is an inherent part of the developed methods.
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Affiliation(s)
- Lucie Nováková
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203, 500 05 Hradec Králové, Czech Republic.
| | - Jakub Pavlík
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
| | - Lucia Chrenková
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
| | - Ondřej Martinec
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
| | - Lukáš Červený
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
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20
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Chamorro C, Camarasa MJ, Pérez-Pérez MJ, de Clercq E, Balzarini J, Félix AS. An Approach towards the Synthesis of Potential Metal-Chelating TSAO-T Derivatives as Bidentate Inhibitors of Human Immunodeficiency virus Type 1 Reverse Transcriptase. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029800900505] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Novel derivatives of the potent human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) inhibitor TSAO-T have been designed, synthesized and tested for their in vitro antiretro-viral activity against HIV. These TSAO-T derivatives have been designed as potential bidentate inhibitors of HIV-1 RT, which combine in their structure the functionality of a non-nucleoside RT inhibitor (TSAO-T) and a bivalent ion-chelating moiety (a β-diketone moiety) linked through an appropriate spacer to the N-3 of thymine of TSAO-T . Some of the new compounds have an anti-HIV-1 activity comparable to that of the parent compound TSAO-T, but display a markedly increased antiviral selectivity. There was a clear relationship between antiviral activity and the length of the spacer group that links the TSAO molecule with the chelating moiety. A shorter spacer invariably resulted in increased antiviral potency. None of the TSAO-T derivatives were endowed with anti-HIV-2 activity.
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Affiliation(s)
- C Chamorro
- Instituto de Química Médica (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - M-J Camarasa
- Instituto de Química Médica (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - M-J Pérez-Pérez
- Instituto de Química Médica (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - E de Clercq
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
| | - J Balzarini
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
| | - A San Félix
- Instituto de Química Médica (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
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21
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Meleddu R, Distinto S, Corona A, Tramontano E, Bianco G, Melis C, Cottiglia F, Maccioni E. Isatin thiazoline hybrids as dual inhibitors of HIV-1 reverse transcriptase. J Enzyme Inhib Med Chem 2016; 32:130-136. [PMID: 27766892 PMCID: PMC6010014 DOI: 10.1080/14756366.2016.1238366] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
A series of 3-3-{2-[2-3-methyl-4-phenyl-2,3-dihydro-1,3-thiazol-2-ylidene]hydrazin-1-ylidene-2,3-dihydro-1H-indol-2-one derivatives has been designed and synthesized to study their activity on both HIV-1 (Human Immunodeficiency Virus type 1) RT (Reverse Transcriptase) associated functions. These derivatives are analogs of previously reported series whose biological activity and mode of action have been investigated. In this work we investigated the influence of the introduction of a methyl group in the position 3 of the dihydrothiazole ring and of a chlorine atom in the position 5 of the isatin nucleus. The new synthesized compounds are active towards both DNA polymerase and ribonuclease H in the µM range. The nature of the aromatic group in the position 4 of the thiazole was relevant in determining the biological activity.
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Affiliation(s)
- Rita Meleddu
- a Department of Life and Environmental Sciences , University of Cagliari , Cagliari , Italy
| | - Simona Distinto
- a Department of Life and Environmental Sciences , University of Cagliari , Cagliari , Italy
| | - Angela Corona
- b Department of Life and Environmental Sciences , University of Cagliari, Cittadella Universitaria di Monserrato , Cagliari , Italy
| | - Enzo Tramontano
- b Department of Life and Environmental Sciences , University of Cagliari, Cittadella Universitaria di Monserrato , Cagliari , Italy
| | - Giulia Bianco
- a Department of Life and Environmental Sciences , University of Cagliari , Cagliari , Italy
| | - Claudia Melis
- a Department of Life and Environmental Sciences , University of Cagliari , Cagliari , Italy
| | - Filippo Cottiglia
- a Department of Life and Environmental Sciences , University of Cagliari , Cagliari , Italy
| | - Elias Maccioni
- a Department of Life and Environmental Sciences , University of Cagliari , Cagliari , Italy
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22
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Mechanistic Study of Common Non-Nucleoside Reverse Transcriptase Inhibitor-Resistant Mutations with K103N and Y181C Substitutions. Viruses 2016; 8:v8100263. [PMID: 27669286 PMCID: PMC5086599 DOI: 10.3390/v8100263] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 09/15/2016] [Accepted: 09/16/2016] [Indexed: 12/30/2022] Open
Abstract
Non-nucleoside reverse transcriptase inhibitors (NNRTIs) are a mainstay of therapy for human immunodeficiency type 1 virus (HIV-1) infections. However, their effectiveness can be hampered by the emergence of resistant mutations. To aid in designing effective NNRTIs against the resistant mutants, it is important to understand the resistance mechanism of the mutations. Here, we investigate the mechanism of the two most prevalent NNRTI-associated mutations with K103N or Y181C substitution. Virus and reverse transcriptase (RT) with K103N/Y188F, K103A, or K103E substitutions and with Y181F, Y188F, or Y181F/Y188F substitutions were employed to study the resistance mechanism of the K103N and Y181C mutants, respectively. Results showed that the virus and RT with K103N/Y188F substitutions displayed similar resistance levels to the virus and RT with K103N substitution versus NNRTIs. Virus and RT containing Y181F, Y188F, or Y181F/Y188F substitution exhibited either enhanced or similar susceptibility to NNRTIs compared with the wild type (WT) virus. These results suggest that the hydrogen bond between N103 and Y188 may not play an important role in the resistance of the K103N variant to NNRTIs. Furthermore, the results from the studies with the Y181 or Y188 variant provide the direct evidence that aromatic π-π stacking plays a crucial role in the binding of NNRTIs to RT.
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23
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Santos LH, Ferreira RS, Caffarena ER. Computational drug design strategies applied to the modelling of human immunodeficiency virus-1 reverse transcriptase inhibitors. Mem Inst Oswaldo Cruz 2016; 110:847-64. [PMID: 26560977 PMCID: PMC4660614 DOI: 10.1590/0074-02760150239] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 09/08/2015] [Indexed: 01/05/2023] Open
Abstract
Reverse transcriptase (RT) is a multifunctional enzyme in the human immunodeficiency
virus (HIV)-1 life cycle and represents a primary target for drug discovery efforts
against HIV-1 infection. Two classes of RT inhibitors, the nucleoside RT inhibitors
(NRTIs) and the nonnucleoside transcriptase inhibitors are prominently used in the
highly active antiretroviral therapy in combination with other anti-HIV drugs.
However, the rapid emergence of drug-resistant viral strains has limited the
successful rate of the anti-HIV agents. Computational methods are a significant part
of the drug design process and indispensable to study drug resistance. In this
review, recent advances in computer-aided drug design for the rational design of new
compounds against HIV-1 RT using methods such as molecular docking, molecular
dynamics, free energy calculations, quantitative structure-activity relationships,
pharmacophore modelling and absorption, distribution, metabolism, excretion and
toxicity prediction are discussed. Successful applications of these methodologies are
also highlighted.
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Affiliation(s)
| | - Rafaela Salgado Ferreira
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
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24
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Elgaher WAM, Sharma KK, Haupenthal J, Saladini F, Pires M, Real E, Mély Y, Hartmann RW. Discovery and Structure-Based Optimization of 2-Ureidothiophene-3-carboxylic Acids as Dual Bacterial RNA Polymerase and Viral Reverse Transcriptase Inhibitors. J Med Chem 2016; 59:7212-22. [PMID: 27339173 DOI: 10.1021/acs.jmedchem.6b00730] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We are concerned with the development of novel anti-infectives with dual antibacterial and antiretroviral activities for MRSA/HIV-1 co-infection. To achieve this goal, we exploited for the first time the mechanistic function similarity between the bacterial RNA polymerase (RNAP) "switch region" and the viral non-nucleoside reverse transcriptase inhibitor (NNRTI) binding site. Starting from our previously discovered RNAP inhibitors, we managed to develop potent RT inhibitors effective against several resistant HIV-1 strains with maintained or enhanced RNAP inhibitory properties following a structure-based design approach. A quantitative structure-activity relationship (QSAR) analysis revealed distinct molecular features necessary for RT inhibition. Furthermore, mode of action (MoA) studies revealed that these compounds inhibit RT noncompetitively, through a new mechanism via closing of the RT clamp. In addition, the novel RNAP/RT inhibitors are characterized by a potent antibacterial activity against S. aureus and in cellulo antiretroviral activity against NNRTI-resistant strains. In HeLa and HEK 293 cells, the compounds showed only marginal cytotoxicity.
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Affiliation(s)
- Walid A M Elgaher
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); and Pharmaceutical and Medicinal Chemistry, Saarland University , Campus E8.1, 66123 Saarbrücken, Germany
| | - Kamal K Sharma
- Laboratoire de Biophotonique et Pharmacologie, Faculté de Pharmacie, UMR 7213 CNRS, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Jörg Haupenthal
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); and Pharmaceutical and Medicinal Chemistry, Saarland University , Campus E8.1, 66123 Saarbrücken, Germany
| | - Francesco Saladini
- Department of Medical Biotechnologies, University of Siena , Viale Mario Bracci 16, 53100 Siena, Italy
| | - Manuel Pires
- Laboratoire de Biophotonique et Pharmacologie, Faculté de Pharmacie, UMR 7213 CNRS, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Eleonore Real
- Laboratoire de Biophotonique et Pharmacologie, Faculté de Pharmacie, UMR 7213 CNRS, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Yves Mély
- Laboratoire de Biophotonique et Pharmacologie, Faculté de Pharmacie, UMR 7213 CNRS, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Rolf W Hartmann
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); and Pharmaceutical and Medicinal Chemistry, Saarland University , Campus E8.1, 66123 Saarbrücken, Germany
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25
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Abstract
Since the first antiviral drug, idoxuridine, was approved in 1963, 90 antiviral drugs categorized into 13 functional groups have been formally approved for the treatment of the following 9 human infectious diseases: (i) HIV infections (protease inhibitors, integrase inhibitors, entry inhibitors, nucleoside reverse transcriptase inhibitors, nonnucleoside reverse transcriptase inhibitors, and acyclic nucleoside phosphonate analogues), (ii) hepatitis B virus (HBV) infections (lamivudine, interferons, nucleoside analogues, and acyclic nucleoside phosphonate analogues), (iii) hepatitis C virus (HCV) infections (ribavirin, interferons, NS3/4A protease inhibitors, NS5A inhibitors, and NS5B polymerase inhibitors), (iv) herpesvirus infections (5-substituted 2'-deoxyuridine analogues, entry inhibitors, nucleoside analogues, pyrophosphate analogues, and acyclic guanosine analogues), (v) influenza virus infections (ribavirin, matrix 2 protein inhibitors, RNA polymerase inhibitors, and neuraminidase inhibitors), (vi) human cytomegalovirus infections (acyclic guanosine analogues, acyclic nucleoside phosphonate analogues, pyrophosphate analogues, and oligonucleotides), (vii) varicella-zoster virus infections (acyclic guanosine analogues, nucleoside analogues, 5-substituted 2'-deoxyuridine analogues, and antibodies), (viii) respiratory syncytial virus infections (ribavirin and antibodies), and (ix) external anogenital warts caused by human papillomavirus infections (imiquimod, sinecatechins, and podofilox). Here, we present for the first time a comprehensive overview of antiviral drugs approved over the past 50 years, shedding light on the development of effective antiviral treatments against current and emerging infectious diseases worldwide.
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Affiliation(s)
- Erik De Clercq
- KU Leuven-University of Leuven, Rega Institute for Medical Research, Department of Microbiology and Immunology, Leuven, Belgium
| | - Guangdi Li
- KU Leuven-University of Leuven, Rega Institute for Medical Research, Department of Microbiology and Immunology, Leuven, Belgium Department of Metabolism and Endocrinology, Metabolic Syndrome Research Center, Key Laboratory of Diabetes Immunology, Ministry of Education, National Clinical Research Center for Metabolic Diseases, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
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26
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Chimirri A, Grasso S, Molica C, Monforte AM, Monforte P, Zappalà M, Bruno G, Nicolò F, Witvrouw M, Jonckeere H, Balzarini J, De Clercq E. Structural Features and Anti-Human Immunodeficiency Virus (HIV) Activity of the Isomers of 1-(2′,6′-Difluorophenyl)-1H,3H-Thiazolo[3,4-a]Benzimidazole, a Potent Non-Nucleoside HIV-1 Reverse Transcriptase Inhibitor. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029700800409] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The structural features, including the absolute configuration, of the enantiomers of 1-(2′,6′-difluorophenyl)-1 H,3 H-thiazolo[3,4- a]benzimidazole (TBZ; NSC 625487), the lead compound of a new class of human immunodeficiency virus type 1 (HIV-1) non-nucleoside reverse transcriptase inhibitors (NNRTIs), are described. Diffractometric analysis revealed that TBZ, like other NNRTIs, assumes a butterfly-like conformation in which the phenyl ring at C1 is in an orthogonal orientation relative to the thiazolobenzimidazole system, and the 2′,6′-fluorine atoms form two intramolecular hydrogen bonds with H1 and one of the methylene protons at C3, respectively. The stereochemistry in solution, as confirmed by lanthanide shift reagent-assisted ‘H NMR, paralleled the situation present in the solid state. The in vitro anti-HIV activity of the two enantiomers was also evaluated and the results obtained showed that the R-(+) is more active than the S-(−) isomer in inhibiting HIV-1 replication. Resistance and cross-resistance to other NNRTIs as well as inhibitory effects on HIV-1 reverse transcriptase activity are also reported.
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Affiliation(s)
- A Chimirri
- Departimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy
| | - S Grasso
- Departimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy
| | - C Molica
- Departimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy
| | - A-M Monforte
- Departimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy
| | - P Monforte
- Departimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy
| | - M Zappalà
- Departimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy
| | - G Bruno
- Dipartimento di Chimica Inorganica, Analitica e Struttura Molecolare, Università di Messina, Salita Sperone 31, 98166 Messina, Italy
| | - F Nicolò
- Dipartimento di Chimica Inorganica, Analitica e Struttura Molecolare, Università di Messina, Salita Sperone 31, 98166 Messina, Italy
| | - M Witvrouw
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, B-3000, Leuven, Belgium
| | - H Jonckeere
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, B-3000, Leuven, Belgium
| | - J Balzarini
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, B-3000, Leuven, Belgium
| | - E De Clercq
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, B-3000, Leuven, Belgium
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27
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Zhang Z, Hamatake R, Hong Z. Clinical Utility of Current NNRTIs and Perspectives of New Agents in This Class under Development. ACTA ACUST UNITED AC 2016; 15:121-34. [PMID: 15266894 DOI: 10.1177/095632020401500302] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Highly active antiretroviral therapy (HAART) has significantly reduced the number of deaths caused by AIDS. However, the antiviral efficacy of HAART comprising protease inhibitors (PIs) and nucleoside reverse transcriptase inhibitors (NRTIs) is frequently accompanied by a decrease in patients' quality of life. PI-based therapies often fail due to poor adherence caused by heavy pill burden, complex dosing schedules and undesirable side effects. The current trend is to switch from PI-based to PI-sparing regimens consisting of non-nucleoside reverse transcriptase inhibitors (NNRTIs) and NRTIs. Despite some encouraging results from NNRTI-containing therapies, two major concerns in using the currently available NNRTIs remain: 1) low genetic barrier to the emergence of resistance and 2) cross-resistance due to single mutations that often render the whole class of NNRTIs ineffective. Clearly, new and improved NNRTIs are needed to address these concerns.
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Affiliation(s)
- Zhijun Zhang
- Drug Discovery, Valeant Pharmaceuticals International, Costa Mesa, Calif., USA.
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28
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Jernigan RL, Bahar I, Covell DG, Atilgan AR, Erman B, Flatow DT. Relating the Structure of HIV-1 Reverse Transcriptase to Its Processing Step. J Biomol Struct Dyn 2016; 17 Suppl 1:49-55. [PMID: 22607406 DOI: 10.1080/07391102.2000.10506603] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Abstract By treating an enzyme as a coarse-grained uniform block of material, utilizing only the α-Carbon positions, the normal modes of motion can be obtained. For reverse transcriptase the slower of these motions are suggestive of being involved in the processing step, where the RNA or DNA strand is copied onto a new DNA strand at a polymerase site, and the RNA strand is subsequently cut up at the distant Ribonuclease H site. The slowest mode of motion involves hinge bending about a site midway between the polymerase and Ribonuclease H sites, suggesting that it can push or pull the RNA strand between these two sites. Pulling the nucleic acid strand would require tight binding to the RNase H site. The next slowest mode involves a hinge that opens and closes the protein like a clamp, which could facilitate the release of the nucleic acids for their step-wise progression. The third mode could rotate the substrate. An overall description of the step-wise processing step would involve close coordination among these steps. Results suggest that the smaller p51 subunit serves only as ballast to support the various modes of motion involving the different parts of the p66 subunit.
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Affiliation(s)
- R L Jernigan
- a Molecular Structure Section, Laboratory of Experimental and Computational Biology, Division of Basic Sciences , National Cancer Institute, National Institutes of Health , MSC 5677 , Bethesda , MD , 20892-5677
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29
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Hameed A, Abdullah MI, Ahmed E, Sharif A, Irfan A, Masood S. Anti-HIV cytotoxicity enzyme inhibition and molecular docking studies of quinoline based chalcones as potential non-nucleoside reverse transcriptase inhibitors (NNRT). Bioorg Chem 2016; 65:175-82. [PMID: 26964017 DOI: 10.1016/j.bioorg.2016.02.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 02/24/2016] [Accepted: 02/25/2016] [Indexed: 11/20/2022]
Abstract
A series of fourteen (A1 - A14) qunioline based chalcones were screened for reverse transcriptase inhibitors (RT) and found potentially active against RT. Bioassay, theoretical and dockings studies with RT (the enzyme required for reverse transcription of viral RNA) results showed that the type and positions of the substituents seemed to be critical for their inhibition against RT. The bromo and chloro substituted chalcone displayed high degree of inhibition against RT. The A4 andA6 showed high interaction with RT, contributing high free binding energy (ΔG -9.30 and -9.13kcal) and RT inhibition value (IC50 0.10μg/ml and 0.11μg/ml).
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Affiliation(s)
- Asima Hameed
- Institute of Chemistry, University of the Punjab, Lahore, P.O 54590, Pakistan
| | | | - Ejaz Ahmed
- Institute of Chemistry, University of the Punjab, Lahore, P.O 54590, Pakistan.
| | - Ahsan Sharif
- Institute of Chemistry, University of the Punjab, Lahore, P.O 54590, Pakistan
| | - Ahmad Irfan
- Department of Chemistry, Faculty of Science, King Khalid University, Abha 61413, P.O. Box 9004, Saudi Arabia; Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha 61413, P.O. Box 9004, Saudi Arabia
| | - Sara Masood
- Sheikh Zayed Madical College & Hospital Rahim Yar Khan, Pakistan
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30
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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: 3] [Impact Index Per Article: 0.3] [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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31
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Patel RV, Park SW. Pyrroloaryls and pyrroloheteroaryls: Inhibitors of the HIV fusion/attachment, reverse transcriptase and integrase. Bioorg Med Chem 2015; 23:5247-63. [PMID: 26116177 DOI: 10.1016/j.bmc.2015.06.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Revised: 06/04/2015] [Accepted: 06/05/2015] [Indexed: 02/01/2023]
Abstract
Heterocyclic compounds execute a very important role in drug design and discovery. This article provides the basic milestones of the research for pyrroloaryl and pyrroloheteroaryl based components targeting HIV viral replication cycle. Anti-HIV activity is elaborated for several classes of pyrrolo-compounds as pyrrolopyridines, pyrrolopyrimidines, pyrrolopyridazines, pyrrolobenzodiazepinones, pyrrolobenzothiazepines, pyrrolobenzoxazepinones, pyrrolophenanthridines, pyrroloquinoxalines, pyrrolotriazines, pyrroloquinolines, pyrrolopyrazinones, pyrrolothiatriazines, arylthiopyrroles and pyrrolopyrazolones targeting two essential HIV enzymes, reverse transcriptase and integrase as well as attachment/fusion of HIV virons to the host CD-4 cell. Such attempts were resulted in a discovery of highly potent anti-HIV agents suitable for clinical trials, for example, BMS-378806, BMS-585248, BMS-626529, BMS-663068, BMS-488043 and BMS-663749, etc. as anti-HIV attachment agents, triciribine, QX432, BI-1 and BI-2 as HIV RT inhibitors which are in preclinical or clinical development. Mechanism of action of compounds presented in this article towards the suppression of HIV attachment/fusion as well as against the activities of HIV enzymes reverse transcriptase and integrase has been discussed. Relationships of new compounds' molecular framework and HIV viral target has been overviewed in order to facilitate further construction of promising anti-HIV agents in future drug discovery process.
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Affiliation(s)
- Rahul V Patel
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany ASCR & Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic.
| | - Se Won Park
- Organic Research Laboratory, Department of Bioresources and Food Science, College of Life and Environmental Sciences, Konkuk University, Seoul 143 701, South Korea
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32
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Vlachakis D, Bencurova E, Papangelopoulos N, Kossida S. Current state-of-the-art molecular dynamics methods and applications. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 94:269-313. [PMID: 24629189 DOI: 10.1016/b978-0-12-800168-4.00007-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Molecular dynamics simulations are used to describe the patterns, strength, and properties of protein behavior, drug-receptor interactions, the solvation of molecules, the conformational changes that a protein or molecule may undergo under various conditions, and other events that require the systematic evaluation of molecular properties in dynamic molecular systems. Only few years ago proteins were considered to be rigid body structures with very limited conformational flexibility. However, it is now clear that proteins are highly dynamic structures, the internal organization of which is the key to their 3D spatial arrangement and hence biological function. The study of protein dynamics in the lab is a very complicated, expensive, and time-consuming process. Therefore, a lot of effort and hope lies with the computers and the in silico study of protein structure and molecular dynamics. Herein, an effort has been made to describe the ever-evolving field of molecular dynamics, the different algorithms, and force fields that are being used as well as to provide some insight on what the near future holds for this auspicious field of computational structural biology.
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Affiliation(s)
- Dimitrios Vlachakis
- Bioinformatics & Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Elena Bencurova
- Bioinformatics & Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Athens, Greece; Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Kosice, Slovakia
| | - Nikitas Papangelopoulos
- Bioinformatics & Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Sophia Kossida
- Bioinformatics & Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Athens, Greece.
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33
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Molecular docking studies of marine diterpenes as inhibitors of wild-type and mutants HIV-1 reverse transcriptase. Mar Drugs 2013; 11:4127-43. [PMID: 24172210 PMCID: PMC3853719 DOI: 10.3390/md11114127] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 09/11/2013] [Accepted: 10/02/2013] [Indexed: 11/30/2022] Open
Abstract
AIDS is a pandemic responsible for more than 35 million deaths. The emergence of resistant mutations due to drug use is the biggest cause of treatment failure. Marine organisms are sources of different molecules, some of which offer promising HIV-1 reverse transcriptase (RT) inhibitory activity, such as the diterpenes dolabelladienotriol (THD, IC50 = 16.5 µM), (6R)-6-hydroxydichotoma-3,14-diene-1,17-dial (HDD, IC50 = 10 µM) and (6R)-6-acetoxydichotoma-3,14-diene-1,17-dial (ADD, IC50 = 35 µM), isolated from a brown algae of the genus Dictyota, showing low toxicity. In this work, we evaluated the structure-activity relationship (SAR) of THD, HDD and ADD as anti HIV-1 RT, using a molecular modeling approach. The analyses of stereoelectronic parameters revealed a direct relationship between activity and HOMO (Highest Occupied Molecular Orbital)-LUMO (Lowest Unoccupied Molecular Orbital) gap (ELUMO–EHOMO), where antiviral profile increases with larger HOMO-LUMO gap values. We also performed molecular docking studies of THD into HIV-1 RT wild-type and 12 different mutants, which showed a seahorse conformation, hydrophobic interactions and hydrogen bonds with important residues of the binding pocket. Based on in vitro experiments and docking studies, we demonstrated that mutations have little influence in positioning and interactions of THD. Following a rational drug design, we suggest a modification of THD to improve its biological activity.
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34
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Monroe JI, El-Nahal WG, Shirts MR. Investigating the mutation resistance of nonnucleoside inhibitors of HIV-RT using multiple microsecond atomistic simulations. Proteins 2013; 82:130-44. [PMID: 23775803 DOI: 10.1002/prot.24346] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 05/17/2013] [Accepted: 05/31/2013] [Indexed: 11/06/2022]
Abstract
Inhibiting HIV reverse transcriptase through the use of nonnucleoside reverse transcriptase inhibitors (NNRTIs) has become an essential component in drug regimens for the treatment of HIV. Older NNRTIs, such as nevirapine, are structurally rigid, exhibiting decreased inhibitory function on development of common mutations in the NNRTI-binding pocket, which is located around 10 Å from the catalytically active binding site. The newer generation of drugs, such as rilpivirine, are more flexible and resistant to binding pocket mutations but the mechanism by which they actually inhibit protein function and avoid mutations is not well-understood. To this end, we have performed 2-2.4 µs simulations with explicit solvent in an isobaric-isothermal ensemble of six different systems: apo wild-type, apo K103N/Y181C mutant, nevirapine-bound wild-type, nevirapine-bound mutant, rilpivirine-bound wild type, and rilpivirine-bound mutant. Analysis of protein conformations, principal components of motion, and mutual information between residues points to an inhibitory mechanism in which the primer grip stretches away from the catalytic triad of aspartic acids necessary for polymerization of HIV-encoding DNA, but is still unable to reveal a specific structural mechanism behind mutation resistance.
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Affiliation(s)
- Jacob I Monroe
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia
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35
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De Clercq E. Dancing with chemical formulae of antivirals: a personal account. Biochem Pharmacol 2013; 86:711-25. [PMID: 23876344 DOI: 10.1016/j.bcp.2013.07.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 07/08/2013] [Accepted: 07/08/2013] [Indexed: 02/08/2023]
Abstract
A chemical structure is a joy forever, and this is how I perceived the chemical structures of a number of antiviral compounds with which I have been personally acquainted over the past 3 decades: (1) amino acid esters of acyclovir (i.e. valaciclovir); (2) 5-substituted 2'-deoxyuridines (i.e. brivudin); (3) 2',3'-dideoxynucleoside analogues (i.e. stavudine); (4) acyclic nucleoside phosphonates (ANPs) (i.e. cidofovir, adefovir); (5) tenofovir disoproxil fumarate (TDF) and drug combinations therewith; (6) tenofovir alafenamide (TAF, GS-7340), a new phosphonoamidate prodrug of tenofovir; (7) pro-prodrugs of PMEG (i.e. GS-9191 and GS-9219); (8) new ANPs: O-DAPy and 5-aza-C phosphonates; (9) non-nucleoside reverse transcriptase inhibitors (NNRTIs): HEPT and TIBO derivatives; and (10) bicyclam derivatives (i.e. AMD3100).
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Affiliation(s)
- Erik De Clercq
- Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium.
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36
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Identifying chemicals with potential therapy of HIV based on protein-protein and protein-chemical interaction network. PLoS One 2013; 8:e65207. [PMID: 23762317 PMCID: PMC3675210 DOI: 10.1371/journal.pone.0065207] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 04/23/2013] [Indexed: 12/27/2022] Open
Abstract
Acquired immune deficiency syndrome (AIDS) is a severe infectious disease that causes a large number of deaths every year. Traditional anti-AIDS drugs directly targeting the HIV-1 encoded enzymes including reverse transcriptase (RT), protease (PR) and integrase (IN) usually suffer from drug resistance after a period of treatment and serious side effects. In recent years, the emergence of numerous useful information of protein-protein interactions (PPI) in the HIV life cycle and related inhibitors makes PPI a new way for antiviral drug intervention. In this study, we identified 26 core human proteins involved in PPI between HIV-1 and host, that have great potential for HIV therapy. In addition, 280 chemicals that interact with three HIV drugs targeting human proteins can also interact with these 26 core proteins. All these indicate that our method as presented in this paper is quite promising. The method may become a useful tool, or at least plays a complementary role to the existing method, for identifying novel anti-HIV drugs.
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37
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De Clercq E. Antiviral drug development--success and failure: a personal perspective with a Japanese connection. Antivir Chem Chemother 2013; 23:45-55. [PMID: 22992351 DOI: 10.3851/imp2396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2012] [Indexed: 12/29/2022] Open
Abstract
At the 25th International Conference on Antiviral Research, I received a special recognition for my contribution to the International Society of Antiviral Research over a period of 25 years (from 1987 until 2012). This review follows the theme of my presentation at that event, which comprised 10 reminiscences, all with a Japanese connection concerning the success, or otherwise, in the clinical development of: double- and single-stranded polynucleotides; suramin, a polysulfonate; dextran sulfate, a polysulfate; brivudin; BVaraU; 2',3'-dideoxynucleoside analogues; HEPT; adefovir and tenofovir; CXCR4 antagonists; and elvitegravir.
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Affiliation(s)
- Erik De Clercq
- Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.
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38
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Bailey CM, Sullivan TJ, Iyidogan P, Tirado-Rives J, Chung R, Ruiz-Caro J, Mohamed E, Jorgensen WL, Jorgensen W, Hunter R, Anderson KS. Bifunctional inhibition of human immunodeficiency virus type 1 reverse transcriptase: mechanism and proof-of-concept as a novel therapeutic design strategy. J Med Chem 2013; 56:3959-68. [PMID: 23659183 DOI: 10.1021/jm400160s] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) is a major target for currently approved anti-HIV drugs. These drugs are divided into two classes: nucleoside and non-nucleoside reverse transcriptase inhibitors (NRTIs and NNRTIs). This study illustrates the synthesis and biochemical evaluation of a novel bifunctional RT inhibitor utilizing d4T (NRTI) and a TMC-derivative (a diarylpyrimidine NNRTI) linked via a poly(ethylene glycol) (PEG) linker. HIV-1 RT successfully incorporates the triphosphate of d4T-4PEG-TMC bifunctional inhibitor in a base-specific manner. Moreover, this inhibitor demonstrates low nanomolar potency that has 4.3-fold and 4300-fold enhancement of polymerization inhibition in vitro relative to the parent TMC-derivative and d4T, respectively. This study serves as a proof-of-concept for the development and optimization of bifunctional RT inhibitors as potent inhibitors of HIV-1 viral replication.
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Affiliation(s)
- Christopher M Bailey
- Department of Pharmacology, School of Medicine, Yale University, New Haven, Connecticut 06520, USA
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39
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Das K, Arnold E. HIV-1 reverse transcriptase and antiviral drug resistance. Part 1. Curr Opin Virol 2013; 3:111-8. [PMID: 23602471 DOI: 10.1016/j.coviro.2013.03.012] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Revised: 02/27/2013] [Accepted: 03/20/2013] [Indexed: 10/26/2022]
Abstract
HIV-1 reverse transcriptase (RT) contributes to the development of resistance to all anti-AIDS drugs by introducing mutations into the viral genome. At the molecular level, mutations in RT result in resistance to RT inhibitors. Eight nucleoside/nucleotide analogs (NRTIs) and five non-nucleoside inhibitors (NNRTIs) are approved HIV-1 drugs. Structures of RT have been determined in complexes with substrates and/or inhibitors, and the structures have illuminated different conformational and functional states of the enzyme. Understanding the molecular mechanisms of resistance to NRTIs and NNRTIs, and their complex relationships, may help in designing new drugs that are periodically required to overcome existing as well as emerging trends of drug resistance.
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Affiliation(s)
- Kalyan Das
- Center for Advanced Biotechnology and Medicine (CABM), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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40
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Piao D, Basavapathruni A, Iyidogan P, Dai G, Hinz W, Ray AS, Murakami E, Feng JY, You F, Dutschman GE, Austin DJ, Parker KA, Anderson KS. Bifunctional inhibition of HIV-1 reverse transcriptase: a first step in designing a bifunctional triphosphate. Bioorg Med Chem Lett 2012; 23:1511-8. [PMID: 23380374 DOI: 10.1016/j.bmcl.2012.12.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2011] [Revised: 12/04/2012] [Accepted: 12/10/2012] [Indexed: 11/28/2022]
Abstract
The onset of resistance to approved anti-AIDS drugs by HIV necessitates the search for novel inhibitors of HIV-1 reverse transcriptase (RT). Developing single molecular agents concurrently occupying the nucleoside and nonnucleoside binding sites in RT is an intriguing idea but the proof of concept has so far been elusive. As a first step, we describe molecular modeling to guide focused chemical syntheses of conjugates having nucleoside (d4T) and nonnucleoside (TIBO) moieties tethered by a flexible polyethylene glycol (PEG) linker. A triphosphate of d4T-6PEG-TIBO conjugate was successfully synthesized that is recognized as a substrate by HIV-1 RT and incorporated into a double-stranded DNA.
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Affiliation(s)
- Dongyuan Piao
- Brown University, Department of Chemistry, Providence, RI 02912, United States
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41
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De Clercq E. Where rilpivirine meets with tenofovir, the start of a new anti-HIV drug combination era. Biochem Pharmacol 2012; 84:241-8. [DOI: 10.1016/j.bcp.2012.03.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 03/28/2012] [Accepted: 03/28/2012] [Indexed: 10/28/2022]
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42
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Wang X, Zhang J, Huang Y, Wang R, Zhang L, Qiao K, Li L, Liu C, Ouyang Y, Xu W, Zhang Z, Zhang L, Shao Y, Jiang S, Ma L, Liu J. Design, synthesis, and biological evaluation of 1-[(2-benzyloxyl/alkoxyl)methyl]-5-halo-6-aryluracils as potent HIV-1 non-nucleoside reverse transcriptase inhibitors with an improved drug resistance profile. J Med Chem 2012; 55:2242-50. [PMID: 22283377 DOI: 10.1021/jm201506e] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Because the emergence of drug-resistant mutants has limited the efficacy of non-nucleoside reverse transcriptase inhibitors (NNRTIs), it is essential to develop new antivirals with better drug resistance and pharmacokinetic profiles. Here we designed and synthesized a series of 1-[(2-benzyloxyl/alkoxyl)methyl]-5-halo-6-aryluracils, the HEPT analogues, and evaluated their biological activity using nevirapine and 18 (TNK-651) as reference compounds. Most of these compounds, especially 6b, 7b, 9b, 11b, and 7c, exhibited highly potent anti-HIV-1 activity against both wild-type and NNRTI-resistant HIV-1 strains. Compound 7b, which had the highest selectivity index (SI = 38 215), is more potent than nevirapine and 18. These results suggest that the introduction of a halogen at the C-5 position may contribute to the effectiveness of these compounds against RTI-resistant variants. In addition, meta substituents on the C-6 aromatic moiety could significantly enhance activity against NNRTI-resistant HIV-1 strains. These compounds can be further developed as next-generation NNRTIs with an improved antiviral efficacy and drug-resistance profile.
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Affiliation(s)
- Xiaowei Wang
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
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Li D, Zhan P, De Clercq E, Liu X. Strategies for the design of HIV-1 non-nucleoside reverse transcriptase inhibitors: lessons from the development of seven representative paradigms. J Med Chem 2012; 55:3595-613. [PMID: 22268494 DOI: 10.1021/jm200990c] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Dongyue Li
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, 44, West Culture Road, 250012, Jinan, Shandong, P. R. China
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44
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Romeo R, Giofrè SV, Macchi B, Balestrieri E, Mastino A, Merino P, Carnovale C, Romeo G, Chiacchio U. Truncated Reverse Isoxazolidinyl Nucleosides: A New Class of Allosteric HIV-1 Reverse Transcriptase Inhibitors. ChemMedChem 2012; 7:565-9. [DOI: 10.1002/cmdc.201200022] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Indexed: 01/03/2023]
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45
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Jalali-Heravi M, Ebrahimi-Najafabadi H. The use of ladder particle swarm optimisation for quantitative structure–activity relationship analysis of human immunodeficiency virus-1 integrase inhibitors. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2011.586347] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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46
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VAILIKHIT V, BUNSAWANSONG P, TECHASAKUL S, HANNONGBUA S. CONFORMATIONAL ANALYSIS OF NEVIRAPINE IN SOLUTIONS BASED ON NMR SPECTROSCOPY AND QUANTUM CHEMICAL CALCULATIONS. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633606002702] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The conformational analysis of HIV-1 Reverse Transcriptase Inhibitor, nevirapine, 11-cyclopropyl-5,-11dihydro-4-methyl-6H-dipyrido[3,2-b2′,3′-e][1,4]diazepin-6-one, was investigated using ab initio and density functional theory calculations. The fully optimized structures and rotational potential energies of the nitrogen and carbon bonds in the cyclopropyl ring (C15-N11-C17-C19, α) were examined in detail. Geometries obtained from all applied calculations show similarities to the complex structure with HIV-1 reverse transcriptase. To obtain more information on the structure, conformational minima of nevirapine, optimized at the B3LYP/6-31G** level, were calculated for the 1H, 13C, and 15N-NMR chemical shifts at the B3LYP/6-311++G** level using the GIAO approach in DMSO and chloroform IEFPCM solvation models. The calculated 1H, 13C-NMR chemical shifts agree well with the experimental data, which indicates that the geometry of nevirapine in solution is similar to that of the molecule in the inhibition complex. Solvation free energies (ΔG sol ) of nevirapine in DMSO and chloroform were also obtained.
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Affiliation(s)
- V. VAILIKHIT
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - P. BUNSAWANSONG
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - S. TECHASAKUL
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - S. HANNONGBUA
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
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Boyer J, Arnoult E, Médebielle M, Guillemont J, Unge J, Jochmans D. Difluoromethylbenzoxazole Pyrimidine Thioether Derivatives: A Novel Class of Potent Non-Nucleoside HIV-1 Reverse Transcriptase Inhibitors. J Med Chem 2011; 54:7974-85. [DOI: 10.1021/jm200766b] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jérémie Boyer
- Université de Lyon, Université Claude Bernard Lyon 1, Institut de
Chimie et Biochimie Moléculaires et Supramoléculaires
(ICBMS), UMR CNRS-UCBL-INSA, Equipe “Synthèse de Molécules
d’Intérêt Thérapeutique (SMITH)”,
Bâtiment Curien, 43 Boulevard du 11 Novembre 1918, F-69622
Villeurbanne, France
| | - Eric Arnoult
- Chemistry
Lead Antimicrobial Research, Janssen-Cilag/Tibotec, Campus de Maigremont BP615,
F-27106 Val de Reuil Cedex, France
| | - Maurice Médebielle
- Université de Lyon, Université Claude Bernard Lyon 1, Institut de
Chimie et Biochimie Moléculaires et Supramoléculaires
(ICBMS), UMR CNRS-UCBL-INSA, Equipe “Synthèse de Molécules
d’Intérêt Thérapeutique (SMITH)”,
Bâtiment Curien, 43 Boulevard du 11 Novembre 1918, F-69622
Villeurbanne, France
| | - Jérôme Guillemont
- Chemistry
Lead Antimicrobial Research, Janssen-Cilag/Tibotec, Campus de Maigremont BP615,
F-27106 Val de Reuil Cedex, France
| | - Johan Unge
- MAX-lab, Lund University, P.O. Box 118,
SE-221 00
Lund, Sweden
| | - Dirk Jochmans
- Tibotec-Virco BVBA, A Division of Janssen Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, BE-2340 Beerse, Belgium
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Davis CA, Parniak MA, Hughes SH. The effects of RNase H inhibitors and nevirapine on the susceptibility of HIV-1 to AZT and 3TC. Virology 2011; 419:64-71. [PMID: 21907380 DOI: 10.1016/j.virol.2011.08.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 06/04/2011] [Accepted: 08/17/2011] [Indexed: 11/19/2022]
Abstract
It was recently proposed that HIV RT mutations that decrease RNase H activity increase zidovudine (AZT) resistance by delaying the degradation of the RNA template, allowing more time for AZTMP excision from the 3' end of the viral DNA. This predicts that suboptimal concentrations of an RNase H Inhibitor (RNHI), which would decrease RNaseH activity, would decrease AZT susceptibility. Conversely, a suboptimal concentration of a nonnucleoside RT inhibitor (NNRTI) would decrease polymerase activity and increase AZT susceptibility. We determined the effect of several RNHIs and an NNRTI (nevirapine) on AZT and lamivudine (3TC) susceptibility with vectors that replicate using WT or AZT resistant RTs. Susceptibility to 3TC, which is not readily excised, did not change significantly. Nevirapine, and most RNHIs tested, had only small effects on the susceptibility of either HIV vector to AZT and 3TC. One RNHI, F0444-0019, increased the IC(50) for AZT for either vector by ~5-fold, which may be a concern.
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Affiliation(s)
- Caroline A Davis
- HIV Drug Resistance Program, National Cancer Institute at Frederick, Frederick, MD 21702-1201, USA
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Latha RS, Vijayaraj R, Singam ERA, Chitra K, Subramanian V. 3D-QSAR and docking studies on the HEPT derivatives of HIV-1 reverse transcriptase. Chem Biol Drug Des 2011; 78:418-26. [PMID: 21689378 DOI: 10.1111/j.1747-0285.2011.01162.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Three-dimensional Quantitative Structure Activity Relationship (3D-QSAR) has been derived for a set of HEPT derivatives of HIV-1 reverse transcriptase (RT) using Comparative Molecular Field Analysis (CoMFA). The CoMFA models have been developed using two different alignment procedures such as common substructure and bioactive conformation. The CoMFA model I is derived from a common substructure procedure that includes steric and electrostatic fields with the cross-validated q(2) and the non-cross-validated r(2) value of 0.86 and 0.97, respectively. The same for the CoMFA model II that is derived based on the bioactive conformation are 0.19 and 0.77, respectively. It is evident from the results that the common substructure-based alignment model has good statistical significance when compared with that of bioactive conformation for the selected systems in this study. The docking study revealed that the conformational flexibility observed at the R3 position favors different orientations of the substitution at the active site of HIV-1 RT and thereby leads to inconsistency in the CoMFA alignment based on bioactive conformation.
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50
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De Clercq E. From TIBO to Rilpivirine: The Chronicle of the Discovery of the Ideal Nonnucleoside Reverse Transcriptase Inhibitor. ANTIVIRAL DRUG STRATEGIES 2011. [DOI: 10.1002/9783527635955.ch15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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