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Singh AK, Kumar A, Arora S, Kumar R, Verma A, Khalilullah H, Jaremko M, Emwas AH, Kumar P. Current insights and molecular docking studies of HIV-1 reverse transcriptase inhibitors. Chem Biol Drug Des 2024; 103:e14372. [PMID: 37817296 DOI: 10.1111/cbdd.14372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 08/12/2023] [Accepted: 09/22/2023] [Indexed: 10/12/2023]
Abstract
Human immunodeficiency virus (HIV) causes acquired immunodeficiency syndrome (AIDS), a lethal disease that is prevalent worldwide. According to the Joint United Nations Programme on HIV/AIDS (UNAIDS) data, 38.4 million people worldwide were living with HIV in 2021. Viral reverse transcriptase (RT) is an excellent target for drug intervention. Nucleoside reverse transcriptase inhibitors (NRTIs) were the first class of approved antiretroviral drugs. Later, a new type of non-nucleoside reverse transcriptase inhibitors (NNRTIs) were approved as anti-HIV drugs. Zidovudine, didanosine, and stavudine are FDA-approved NRTIs, while nevirapine, efavirenz, and delavirdine are FDA-approved NNRTIs. Several agents are in clinical trials, including apricitabine, racivir, elvucitabine, doravirine, dapivirine, and elsulfavirine. This review addresses HIV-1 structure, replication cycle, reverse transcription, and HIV drug targets. This study focuses on NRTIs and NNRTIs, their binding sites, mechanisms of action, FDA-approved drugs and drugs in clinical trials, their resistance and adverse effects, their molecular docking studies, and highly active antiretroviral therapy (HAART).
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Affiliation(s)
- Ankit Kumar Singh
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, Punjab, India
| | - Adarsh Kumar
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, Punjab, India
| | - Sahil Arora
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, Punjab, India
| | - Raj Kumar
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, Punjab, India
| | - Amita Verma
- Department of Pharmaceutical Sciences, Bioorganic and Medicinal Chemistry Research Laboratory, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, Uttar Pradesh, India
| | - Habibullah Khalilullah
- Department of Pharmaceutical Chemistry and Pharmacognosy, Unaizah College of Pharmacy, Qassim University, Unayzah, Saudi Arabia
| | - Mariusz Jaremko
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Abdul-Hamid Emwas
- Core Labs, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Pradeep Kumar
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, Punjab, India
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Li L, Hu J, Fu Y, Shi X, Du H, Xu J, Chen N. Direct Regioselective C-H Cyanation of Purines. Molecules 2023; 28:molecules28030914. [PMID: 36770582 PMCID: PMC9920237 DOI: 10.3390/molecules28030914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/13/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
A direct regioselective C-H cyanation of purines was developed through a sequential triflic anhydride activation, nucleophilic cyanation with TMSCN, followed by a process of base-mediated elimination of triflous acid (CF3SO2H). In most cases, the direct C-H cyanation occurred on the electron-rich imidazole motif of purines, affording 8-cyanated purine derivatives in moderate to excellent yields. Various functional groups, including allyl, alkynyl, ketone, ester, nitro et al. were tolerated and acted as a C8 directing group. The electron-donating 6-diethylamino, as C2-directing group substituent, can switch the regioselectivity of purine from 8- to 2-position, enabling the synthesis of 8- and 2-cyano 6-dialkylaminopurines from corresponding 6-chloropurine in different reaction order. Further functional manipulations of the cyano group allow the conversions of 8-cyanopurines to corresponding purine amides, imidates, imidothioates, imidamides, oxazolines, and isothiazoles.
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Howlader H, Suzol SH, Blanco K, Martin‐Rafa L, Laverde EE, Liu Y, Wnuk SF. Purine Nucleosides with a Reactive (
β
‐Iodovinyl)sulfone or a (
β
‐Keto)sulfone Group at the C8 Position and Their Polymerase‐Catalyzed Incorporation into DNA. ASIAN J ORG CHEM 2022. [DOI: 10.1002/ajoc.202100764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hasan Howlader
- Department of Chemistry and Biochemistryan Florida International University Miami Florida 33199 U.S.A
| | - Sazzad H. Suzol
- Department of Chemistry and Biochemistryan Florida International University Miami Florida 33199 U.S.A
| | - Kevin Blanco
- Department of Chemistry and Biochemistryan Florida International University Miami Florida 33199 U.S.A
| | - Lilian Martin‐Rafa
- Department of Chemistry and Biochemistryan Florida International University Miami Florida 33199 U.S.A
| | - Eduardo E. Laverde
- Department of Chemistry and Biochemistryan Florida International University Miami Florida 33199 U.S.A
| | - Yuan Liu
- Department of Chemistry and Biochemistryan Florida International University Miami Florida 33199 U.S.A
- Biomolecular Sciences Institute Florida International University Miami Florida 33199 U.S.A
| | - Stanislaw F. Wnuk
- Department of Chemistry and Biochemistryan Florida International University Miami Florida 33199 U.S.A
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Wen Z, Tuttle PR, Howlader AH, Vasilyeva A, Gonzalez L, Tangar A, Lei R, Laverde EE, Liu Y, Miksovska J, Wnuk SF. Fluorescent 5-Pyrimidine and 8-Purine Nucleosides Modified with an N-Unsubstituted 1,2,3-Triazol-4-yl Moiety. J Org Chem 2019; 84:3624-3631. [PMID: 30806513 DOI: 10.1021/acs.joc.8b03135] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Cu(I)- or Ag(I)-catalyzed cycloaddition between 8-ethynyladenine or guanine nucleosides and TMSN3 gave 8-(1- H-1,2,3-triazol-4-yl) nucleosides in good yields. On the other hand, reactions of 5-ethynyluracil or cytosine nucleosides with TMSN3 led to the chemoselective formation of triazoles via Cu(I)-catalyzed cycloaddition or vinyl azides via Ag(I)-catalyzed hydroazidation. These nucleosides with a minimalistic triazolyl modification showed excellent fluorescent properties with 8-(1- H-1,2,3-triazol-4-yl)-2'-deoxyadenosine (8-TrzdA), exhibiting a quantum yield of 44%. The 8-TrzdA 5'-triphosphate was incorporated into duplex DNA containing a one-nucleotide gap by DNA polymerase β.
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Affiliation(s)
- Zhiwei Wen
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| | - Paloma R Tuttle
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| | - A Hasan Howlader
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| | - Anna Vasilyeva
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| | - Laura Gonzalez
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| | - Antonija Tangar
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| | - Ruipeng Lei
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| | - Eduardo E Laverde
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| | - Yuan Liu
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| | - Jaroslava Miksovska
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| | - Stanislaw F Wnuk
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
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Dimopoulou A, Manta S, Parmenopoulou V, Kollatos N, Christidou O, Triantakonstanti VV, Schols D, Komiotis D. An easy microwave-assisted synthesis of C8-alkynyl adenine pyranonucleosides as novel cytotoxic antitumor agents. Front Chem 2015; 3:21. [PMID: 25853123 PMCID: PMC4369668 DOI: 10.3389/fchem.2015.00021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 03/05/2015] [Indexed: 11/13/2022] Open
Abstract
We describe the synthesis of C8-alkynyl adenine pyranonucleosides 4, 5, and 8-phenylethynyl-adenine (II), via Sonogashira cross-coupling reaction under microwave irradiation. Compounds 4e and II were less cytostatic than 5-fluorouracil (almost an order of magnitude) against murine leukemia (L1210) and human cervix carcinoma (HeLa) cells, while the same compounds proved to be more active than 5-fluorouracil against human lymphocyte (CEM) cells.
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Affiliation(s)
- Athina Dimopoulou
- Laboratory of Bioorganic Chemistry, Department of Biochemistry and Biotechnology, University of Thessaly Larissa, Greece
| | - Stella Manta
- Laboratory of Bioorganic Chemistry, Department of Biochemistry and Biotechnology, University of Thessaly Larissa, Greece
| | - Vanessa Parmenopoulou
- Laboratory of Bioorganic Chemistry, Department of Biochemistry and Biotechnology, University of Thessaly Larissa, Greece
| | - Nikolaos Kollatos
- Laboratory of Bioorganic Chemistry, Department of Biochemistry and Biotechnology, University of Thessaly Larissa, Greece
| | - Ourania Christidou
- Laboratory of Bioorganic Chemistry, Department of Biochemistry and Biotechnology, University of Thessaly Larissa, Greece
| | - Virginia V Triantakonstanti
- Laboratory of Organic Chemistry, Department of Chemistry, Aristotle University of Thessaloniki Thessaloniki, Greece
| | - Dominique Schols
- Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven Leuven, Belgium
| | - Dimitri Komiotis
- Laboratory of Bioorganic Chemistry, Department of Biochemistry and Biotechnology, University of Thessaly Larissa, Greece
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Vivet-Boudou V, Isel C, El Safadi Y, Smyth RP, Laumond G, Moog C, Paillart JC, Marquet R. Evaluation of anti-HIV-1 mutagenic nucleoside analogues. J Biol Chem 2014; 290:371-83. [PMID: 25398876 DOI: 10.1074/jbc.m114.616383] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Because of their high mutation rates, RNA viruses and retroviruses replicate close to the threshold of viability. Their existence as quasi-species has pioneered the concept of "lethal mutagenesis" that prompted us to synthesize pyrimidine nucleoside analogues with antiviral activity in cell culture consistent with an accumulation of deleterious mutations in the HIV-1 genome. However, testing all potentially mutagenic compounds in cell-based assays is tedious and costly. Here, we describe two simple in vitro biophysical/biochemical assays that allow prediction of the mutagenic potential of deoxyribonucleoside analogues. The first assay compares the thermal stabilities of matched and mismatched base pairs in DNA duplexes containing or not the nucleoside analogues as follows. A promising candidate should display a small destabilization of the matched base pair compared with the natural nucleoside and the smallest gap possible between the stabilities of the matched and mismatched base pairs. From this assay, we predicted that two of our compounds, 5-hydroxymethyl-2'-deoxyuridine and 5-hydroxymethyl-2'-deoxycytidine, should be mutagenic. The second in vitro reverse transcription assay assesses DNA synthesis opposite nucleoside analogues inserted into a template strand and subsequent extension of the newly synthesized base pairs. Once again, only 5-hydroxymethyl-2'-deoxyuridine and 5-hydroxymethyl-2'-deoxycytidine are predicted to be efficient mutagens. The predictive potential of our fast and easy first line screens was confirmed by detailed analysis of the mutation spectrum induced by the compounds in cell culture because only compounds 5-hydroxymethyl-2'-deoxyuridine and 5-hydroxymethyl-2'-deoxycytidine were found to increase the mutation frequency by 3.1- and 3.4-fold, respectively.
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Affiliation(s)
- Valérie Vivet-Boudou
- From the Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg Cedex and
| | - Catherine Isel
- From the Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg Cedex and
| | - Yazan El Safadi
- From the Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg Cedex and
| | - Redmond P Smyth
- From the Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg Cedex and
| | - Géraldine Laumond
- the Unité INSERM 748, Université de Strasbourg, Institut de Virologie, 67000 Strasbourg, France
| | - Christiane Moog
- the Unité INSERM 748, Université de Strasbourg, Institut de Virologie, 67000 Strasbourg, France
| | - Jean-Christophe Paillart
- From the Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg Cedex and
| | - Roland Marquet
- From the Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg Cedex and
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HIV-1 Reverse Transcriptase Still Remains a New Drug Target: Structure, Function, Classical Inhibitors, and New Inhibitors with Innovative Mechanisms of Actions. Mol Biol Int 2012; 2012:586401. [PMID: 22778958 PMCID: PMC3388302 DOI: 10.1155/2012/586401] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 04/03/2012] [Indexed: 12/21/2022] Open
Abstract
During the retrotranscription process, characteristic of all retroviruses, the viral ssRNA genome is converted into integration-competent dsDNA. This process is accomplished by the virus-coded reverse transcriptase (RT) protein, which is a primary target in the current treatments for HIV-1 infection. In particular, in the approved therapeutic regimens two classes of drugs target RT, namely, nucleoside RT inhibitors (NRTIs) and nonnucleoside RT inhibitors (NNRTIs). Both classes inhibit the RT-associated polymerase activity: the NRTIs compete with the natural dNTP substrate and act as chain terminators, while the NNRTIs bind to an allosteric pocket and inhibit polymerization noncompetitively. In addition to these two classes, other RT inhibitors (RTIs) that target RT by distinct mechanisms have been identified and are currently under development. These include translocation-defective RTIs, delayed chain terminators RTIs, lethal mutagenesis RTIs, dinucleotide tetraphosphates, nucleotide-competing RTIs, pyrophosphate analogs, RT-associated RNase H function inhibitors, and dual activities inhibitors. This paper describes the HIV-1 RT function and molecular structure, illustrates the currently approved RTIs, and focuses on the mechanisms of action of the newer classes of RTIs.
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