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Corona A, Meleddu R, Delelis O, Subra F, Cottiglia F, Esposito F, Distinto S, Maccioni E, Tramontano E. 5-Nitro-3-(2-(4-phenylthiazol-2-yl)hydrazineylidene)indolin-2-one derivatives inhibit HIV-1 replication by a multitarget mechanism of action. Front Cell Infect Microbiol 2023; 13:1193280. [PMID: 37424782 PMCID: PMC10328743 DOI: 10.3389/fcimb.2023.1193280] [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: 03/24/2023] [Accepted: 05/25/2023] [Indexed: 07/11/2023] Open
Abstract
In the effort to identify and develop new HIV-1 inhibitors endowed with innovative mechanisms, we focused our attention on the possibility to target more than one viral encoded enzymatic function with a single molecule. In this respect, we have previously identified by virtual screening a new indolinone-based scaffold for dual allosteric inhibitors targeting both reverse transcriptase-associated functions: polymerase and RNase H. Pursuing with the structural optimization of these dual inhibitors, we synthesized a series of 35 new 3-[2-(4-aryl-1,3-thiazol-2-ylidene)hydrazin-1-ylidene]1-indol-2-one and 3-[3-methyl-4-arylthiazol-2-ylidene)hydrazine-1-ylidene)indolin-2-one derivatives, which maintain their dual inhibitory activity in the low micromolar range. Interestingly, compounds 1a, 3a, 10a, and 9b are able to block HIV-1 replication with EC50 < 20 µM. Mechanism of action studies showed that such compounds could block HIV-1 integrase. In particular, compound 10a is the most promising for further multitarget compound development.
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Affiliation(s)
- Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Rita Meleddu
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Olivier Delelis
- Laboratory of Biology and Applied Pharmacology (LBPA), Ecole Normale Supérieure (ENS) Cachan, Centre National de la Recherche Scientifique (CNRS), Cachan, France
| | - Frederic Subra
- Laboratory of Biology and Applied Pharmacology (LBPA), Ecole Normale Supérieure (ENS) Cachan, Centre National de la Recherche Scientifique (CNRS), Cachan, France
| | - Filippo Cottiglia
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Simona Distinto
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Elias Maccioni
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
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2
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Losada N, Ruiz FX, Curreli F, Gruber K, Pilch A, Das K, Debnath AK, Arnold E. HIV-1 gp120 Antagonists Also Inhibit HIV-1 Reverse Transcriptase by Bridging the NNRTI and NRTI Sites. J Med Chem 2021; 64:16530-16540. [PMID: 34735153 PMCID: PMC10655131 DOI: 10.1021/acs.jmedchem.1c01104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
HIV-1 infection is typically treated using ≥2 drugs, including at least one HIV-1 reverse transcriptase (RT) inhibitor. Drugs targeting RT comprise nucleos(t)ide RT inhibitors (NRTIs) and non-nucleoside RT inhibitors (NNRTIs). NRTI-triphosphates bind at the polymerase active site and, following incorporation, inhibit DNA elongation. NNRTIs bind at an allosteric pocket ∼10 Å away from the polymerase active site. This study focuses on compounds ("NBD derivatives") originally developed to bind to HIV-1 gp120, some of which inhibit RT. We have determined crystal structures of three NBD compounds in complex with HIV-1 RT, correlating with RT enzyme inhibition and antiviral activity, to develop structure-activity relationships. Intriguingly, these compounds bridge the dNTP and NNRTI-binding sites and inhibit the polymerase activity of RT in the enzymatic assays (IC50 < 5 μM). Two of the lead compounds, NBD-14189 and NBD-14270, show potent antiviral activity (EC50 < 200 nM), and NBD-14270 shows low cytotoxicity (CC50 > 100 μM).
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Affiliation(s)
- Natalie Losada
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854, USA
| | - Francesc X. Ruiz
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854, USA
| | - Francesca Curreli
- Laboratory of Molecular Modeling & Drug Design, Lindsley F. Kimball Research Institute, New York Blood Center, New York, 10065, USA
| | - Kevin Gruber
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854, USA
| | - Alyssa Pilch
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, 08854, USA
| | - Kalyan Das
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, 08854, USA
| | - Asim K. Debnath
- Laboratory of Molecular Modeling & Drug Design, Lindsley F. Kimball Research Institute, New York Blood Center, New York, 10065, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854, USA
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Shrivastava N, Husain A, Rashid M, Alsabeelah NF, Karim S, Siddiqui NA. Recent Advances Towards Treatment of HIV: Synthesis and SAR Studies. Mini Rev Med Chem 2021; 21:471-499. [PMID: 30864523 DOI: 10.2174/1389557519666190312170158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 03/03/2019] [Accepted: 03/06/2019] [Indexed: 11/22/2022]
Abstract
In the present study, authors want to encourage the research exertions through structureactivity relationship for the identification of effective molecules for the treatment of Human immunodeficiency virus because nowadays AIDS is considered as one of the main causes of death in human beings. A diversity of biological resources has been searched and developed for the treatment of HIV but unfortunately, until now, no medicine is found to be fully effective and safe for the cure of patients. Human immunodeficiency virus is a type of lentivirus which causes the infection of HIV and once it enters the human body, it stays for a longer period of time triggering immunodeficiency syndrome. For searching and developing new potent and effective anti-HIV molecules, medicinal chemists have engaged in countless targets with the structure-activity relationship (SAR) of molecules and on this basis, many antiretroviral therapies have been developed to cure HIV infection. Most of these new searched molecules have been found to be clinically active against various types of AIDS patient and auxiliary research in this area may lead to better treatment in the near future. This article encompasses and highlights the recent advancement of innumerable inhibitors laterally through synthetic, semi-synthetic and structure-activity relationship approaches.
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Affiliation(s)
- Neelima Shrivastava
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard (Hamdard University), New Delhi 110062, India
| | - Asif Husain
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard (Hamdard University), New Delhi 110062, India
| | - Mohammad Rashid
- College of Pharmacy and Dentistry, Buraydah Colleges, Buraydah, Al-Qassim 31717, Saudi Arabia
| | - Nimer Fehaid Alsabeelah
- College of Pharmacy and Dentistry, Buraydah Colleges, Buraydah, Al-Qassim 31717, Saudi Arabia
| | - Shahid Karim
- Department of Pharmacology, College of Medicine, King Abdul Aziz University, Jeddah 21589, Saudi Arabia
| | - Nasir Ali Siddiqui
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
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4
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Meleddu R, Corona A, Distinto S, Cottiglia F, Deplano S, Sequeira L, Secci D, Onali A, Sanna E, Esposito F, Cirone I, Ortuso F, Alcaro S, Tramontano E, Mátyus P, Maccioni E. Exploring New Scaffolds for the Dual Inhibition of HIV-1 RT Polymerase and Ribonuclease Associated Functions. Molecules 2021; 26:molecules26133821. [PMID: 34201561 PMCID: PMC8270338 DOI: 10.3390/molecules26133821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/30/2021] [Accepted: 06/18/2021] [Indexed: 12/12/2022] Open
Abstract
Current therapeutic protocols for the treatment of HIV infection consist of the combination of diverse anti-retroviral drugs in order to reduce the selection of resistant mutants and to allow for the use of lower doses of each single agent to reduce toxicity. However, avoiding drugs interactions and patient compliance are issues not fully accomplished so far. Pursuing on our investigation on potential anti HIV multi-target agents we have designed and synthesized a small library of biphenylhydrazo 4-arylthiazoles derivatives and evaluated to investigate the ability of the new derivatives to simultaneously inhibit both associated functions of HIV reverse transcriptase. All compounds were active towards the two functions, although at different concentrations. The substitution pattern on the biphenyl moiety appears relevant to determine the activity. In particular, compound 2-{3-[(2-{4-[4-(hydroxynitroso)phenyl]-1,3-thiazol-2-yl} hydrazin-1-ylidene) methyl]-4-methoxyphenyl} benzamide bromide (EMAC2063) was the most potent towards RNaseH (IC50 = 4.5 mM)- and RDDP (IC50 = 8.0 mM) HIV RT-associated functions.
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Affiliation(s)
- Rita Meleddu
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Simona Distinto
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Filippo Cottiglia
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Serenella Deplano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Lisa Sequeira
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Daniela Secci
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Alessia Onali
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Erica Sanna
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Italo Cirone
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Francesco Ortuso
- Dipartimento di Scienze della Salute, Università Magna Graecia di Catanzaro, Campus ‘S. Venuta’, Viale Europa, 88100 Catanzaro, Italy; (F.O.); (S.A.)
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università Magna Graecia di Catanzaro, Campus ‘S. Venuta’, Viale Europa, 88100 Catanzaro, Italy; (F.O.); (S.A.)
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Péter Mátyus
- Institute of Digital Health Sciences, Faculty of Health and Public Services, Semmelweis University, Ferenc tér 15, 1094 Budapest, Hungary;
| | - Elias Maccioni
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
- Correspondence: ; Tel.: +39-070-6758744
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5
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Large Multidomain Protein NMR: HIV-1 Reverse Transcriptase Precursor in Solution. Int J Mol Sci 2020; 21:ijms21249545. [PMID: 33333923 PMCID: PMC7765405 DOI: 10.3390/ijms21249545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/10/2020] [Accepted: 12/12/2020] [Indexed: 11/17/2022] Open
Abstract
NMR studies of large proteins, over 100 kDa, in solution are technically challenging and, therefore, of considerable interest in the biophysics field. The challenge arises because the molecular tumbling of a protein in solution considerably slows as molecular mass increases, reducing the ability to detect resonances. In fact, the typical 1H-13C or 1H-15N correlation spectrum of a large protein, using a 13C- or 15N-uniformly labeled protein, shows severe line-broadening and signal overlap. Selective isotope labeling of methyl groups is a useful strategy to reduce these issues, however, the reduction in the number of signals that goes hand-in-hand with such a strategy is, in turn, disadvantageous for characterizing the overall features of the protein. When domain motion exists in large proteins, the domain motion differently affects backbone amide signals and methyl groups. Thus, the use of multiple NMR probes, such as 1H, 19F, 13C, and 15N, is ideal to gain overall structural or dynamical information for large proteins. We discuss the utility of observing different NMR nuclei when characterizing a large protein, namely, the 66 kDa multi-domain HIV-1 reverse transcriptase that forms a homodimer in solution. Importantly, we present a biophysical approach, complemented by biochemical assays, to understand not only the homodimer, p66/p66, but also the conformational changes that contribute to its maturation to a heterodimer, p66/p51, upon HIV-1 protease cleavage.
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6
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Alaoui MAE, Fartah SE, Alaoui N, Fahime EME, Habsaoui A. Molecular docking analysis of flavonoid compounds with HIV-1 Reverse transcriptase for the identification of potential effective inhibitors. Bioinformation 2019; 15:646-656. [PMID: 31787814 PMCID: PMC6859701 DOI: 10.6026/97320630015646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/07/2019] [Accepted: 10/08/2019] [Indexed: 11/23/2022] Open
Abstract
It is of interest to elucidate the binding mode analysis of 18 sulphonated flavones in the non nucleoside inhibitory binding pocket of the HIV-1 reverse transcriptase (PDB ID: 1RTD).
We further compared them with the known Non Nucleosidic Reverse Transcriptase Inhibitors (NNRTI) drug molecules such as delaviridine, nevirapine and etravirine. Molecular docking studies
of sulphonated flavones were performed in the binding pocket of reverse transcriptase using the PatchDock server. The flavones have different binding energies with RT and the atomic contact
energy (ACE) value of sulfonated flavones range from-389 to-231 Kcal/mol while docking of the commercialized NNRTI showed the ACE value range from -486 to -224 Kcal/mol. This shows that
most sulfonated flavones have ACE similar to the known NNRTI. Thus, seven compounds (FS-6, FS-7, FS-8, FS-9, FS-14, FS-15, FS-17) were reported as potent, selective, orally bio available,
and nontoxic lead based on ADMET screening and effective binding analysis in the active site of the reverse transcriptase (PDB ID: 1RTD) for further consideration. We further document that
compounds (FS-1, FS-10, FS-4 and FS-12) have unfavorable binding features to be considered as leads.
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Affiliation(s)
- My Abdelaziz El Alaoui
- Functional Genomic Platform, UATRS, Center for Scientific and Technical Research [CNRST], ZIP 10000 Rabat, Morocco.,Laboratory of Genetics and Biometry, Faculty of Sciences, Ibn Tofail University, Kenitra, Morocco
| | - Souad El Fartah
- engineering and environment laboratory, Modeling and Application LIMEMA, Faculty of Science - University Ibn Tofail ,Kenitra .B.P 133 Kenitra 14000, Morocco
| | - Najwa Alaoui
- Research Team in Molecular Virology and Oncobiology, Faculty of Medicine and Pharmacy, University Mohammed V in Rabat, Av. Mohamed Belarbi El Alaoui, ZIP 6203, Rabat, Morocco
| | - El Mostapha El Fahime
- Functional Genomic Platform, UATRS, Center for Scientific and Technical Research [CNRST], ZIP 10000 Rabat, Morocco
| | - Amar Habsaoui
- engineering and environment laboratory, Modeling and Application LIMEMA, Faculty of Science - University Ibn Tofail ,Kenitra .B.P 133 Kenitra 14000, Morocco
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Massari S, Corona A, Distinto S, Desantis J, Caredda A, Sabatini S, Manfroni G, Felicetti T, Cecchetti V, Pannecouque C, Maccioni E, Tramontano E, Tabarrini O. From cycloheptathiophene-3-carboxamide to oxazinone-based derivatives as allosteric HIV-1 ribonuclease H inhibitors. J Enzyme Inhib Med Chem 2019; 34:55-74. [PMID: 30362381 PMCID: PMC6211256 DOI: 10.1080/14756366.2018.1523901] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/11/2018] [Accepted: 09/11/2018] [Indexed: 11/30/2022] Open
Abstract
The paper focussed on a step-by-step structural modification of a cycloheptathiophene-3-carboxamide derivative recently identified by us as reverse transcriptase (RT)-associated ribonuclease H (RNase H) inhibitor. In particular, its conversion to a 2-aryl-cycloheptathienoozaxinone derivative and the successive thorough exploration of both 2-aromatic and cycloheptathieno moieties led to identify oxazinone-based compounds as new anti-RNase H chemotypes. The presence of the catechol moiety at the C-2 position of the scaffold emerged as critical to achieve potent anti-RNase H activity, which also encompassed anti-RNA dependent DNA polymerase (RDDP) activity for the tricyclic derivatives. Benzothienooxazinone derivative 22 resulted the most potent dual inhibitor exhibiting IC50s of 0.53 and 2.90 μM against the RNase H and RDDP functions. Mutagenesis and docking studies suggested that compound 22 binds two allosteric pockets within the RT, one located between the RNase H active site and the primer grip region and the other close to the DNA polymerase catalytic centre.
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Affiliation(s)
- Serena Massari
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Cagliari, Italy
| | - Simona Distinto
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Cagliari, Italy
| | - Jenny Desantis
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Alessia Caredda
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Cagliari, Italy
| | - Stefano Sabatini
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Giuseppe Manfroni
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Tommaso Felicetti
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Violetta Cecchetti
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, K.U. Leuven, Leuven, Belgium
| | - Elias Maccioni
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Cagliari, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Cagliari, Italy
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Italy
| | - Oriana Tabarrini
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
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8
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Xi Z, Wang Z, Sarafianos SG, Myshakina NS, Ishima R. Determinants of Active-Site Inhibitor Interaction with HIV-1 RNase H. ACS Infect Dis 2019; 5:1963-1974. [PMID: 31577424 DOI: 10.1021/acsinfecdis.9b00300] [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] [Indexed: 02/06/2023]
Abstract
The ribonuclease H (RNH) activity of HIV-1 reverse transcriptase (RT) is essential for viral replication and can be a target for drug development. Yet, no RNH inhibitor to date has substantial antiviral activity to allow advancement into clinical development. Herein, we describe our characterization of the detailed binding mechanisms of RNH active-site inhibitors, YLC2-155 and ZW566, that bind to the RNH domain through divalent metal ions, using NMR, molecular docking, and quantum mechanical calculations. In the presence of Mg2+, NMR spectra of RNH exhibited split (two) resonances for some residues upon inhibitor binding, suggesting two binding modes, an observation consistent with the docking results. The relative populations of the two binding conformers were independent of inhibitor or Mg2+ concentration, with one conformation consistently more favored. In our docking study, one distinctive pose of ZW566 showed more interactions with surrounding residues of RNH compared to the analogous binding pose of YLC2-155. Inhibitor titration experiments revealed a lower dissociation constant for ZW566 compared to YLC2-155, in agreement with its higher inhibitory activity. Mg2+ titration data also indicated a stronger dependence on Mg2+ for the RNH interaction with ZW566 compared to YLC2-155. Combined docking and quantum mechanical calculation results suggest that stronger metal coordination as well as more protein-inhibitor interactions may account for the higher binding affinity of ZW566. These findings support the idea that strategies for the development of potent competitive active site RNH inhibitors should take into account not only metal-inhibitor coordination but also protein-inhibitor interaction and conformational selectivity.
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Affiliation(s)
- Zhaoyong Xi
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, 516 Delaware Street SE, PWB 7-215,
MMC 204, Minneapolis, Minnesota 55455, United States
| | - Stefan G. Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Nataliya S. Myshakina
- Department of Natural Science, Chatham University, Woodland Road, Pittsburgh, Pennsylvania 15232, United States
| | - Rieko Ishima
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15260, United States
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9
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Wang Y, Yan F, Jia Q, Dai Y, Wang Q. Quantitative structure-activity relationship of anti-HIV integrase and reverse transcriptase inhibitors using norm indexes. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2017; 28:1025-1044. [PMID: 29157005 DOI: 10.1080/1062936x.2017.1397055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 10/23/2017] [Indexed: 06/07/2023]
Abstract
The development of new and safe anti-human immunodeficiency virus (anti-HIV) drugs has been an urgent task for medical research recently. Herein, based on the norm-index descriptors proposed in this work and previous works, a couple of models were developed for investigating the quantitative structure-activity/toxicity relationship (QSAR/QSTR) of dual-target anti-HIV integrase (IN) and reverse transcriptase (RT) inhibitors. The validation results proved that the developed models were stable and reliable, both in statistical quality and predictive capacity. Moreover, potential dual-target inhibitors with high activity and low toxicity were deduced from the developed models; molecular docking results indicated that these inhibitors could interact with some important residues of HIV IN and RT through H-bonding. Accordingly, the norm indexes descriptors proposed by this work might be helpful for the research and development of dual-target anti-HIV drugs.
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Affiliation(s)
- Y Wang
- a School of Chemical Engineering and Material Science , Tianjin University of Science and Technology , Tianjin , PR China
| | - F Yan
- a School of Chemical Engineering and Material Science , Tianjin University of Science and Technology , Tianjin , PR China
| | - Q Jia
- b School of Marine and Environmental Science , Tianjin University of Science and Technology , Tianjin , PR China
| | - Y Dai
- c School of Bioengineering , Tianjin University of Science and Technology , Tianjin , PR China
| | - Q Wang
- a School of Chemical Engineering and Material Science , Tianjin University of Science and Technology , Tianjin , PR China
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10
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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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11
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Gu SX, Xue P, Ju XL, Zhu YY. Advances in rationally designed dual inhibitors of HIV-1 reverse transcriptase and integrase. Bioorg Med Chem 2016; 24:5007-5016. [PMID: 27658796 DOI: 10.1016/j.bmc.2016.09.025] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 09/09/2016] [Accepted: 09/10/2016] [Indexed: 01/07/2023]
Abstract
Reverse transcriptase (RT) and integrase (IN) are two indispensable enzymes in human immunodeficiency virus type 1 (HIV-1) replication. RT is responsible for the transformation of the single-stranded RNA viral genome into double-stranded DNA, and IN catalyzes the integration of viral DNA into the host DNA. Although highly active antiretroviral therapy (HAART) combining nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs/NtRTIs) with nonnucleoside reverse transcriptase inhibitors (NNRTIs) or protease inhibitors (PIs) could suppress successfully HIV viral load and reduce evidently the mortality of HIV infected people, it involves the difficulty of perfect adherence, and other drawbacks such as viral rebound, toxicities and multi-drug resistances. Recently, rational drug design has become a dominant technique for the development of multi-target drugs. And the rationally designed dual inhibitors of HIV-1 RT and IN have become a hot topic of anti-HIV research. In this review, the advances in rationally designed dual inhibitors of HIV-1 RT and IN were summarized, including structurally diverse inhibitors, their structure-activity relationship (SAR) studies as well as binding mode analysis.
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Affiliation(s)
- Shuang-Xi Gu
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430073, China.
| | - Ping Xue
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430073, China
| | - Xiu-Lian Ju
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430073, China
| | - Yuan-Yuan Zhu
- School of Chemistry and Environmental Engineering, Wuhan Institute of Technology, Wuhan 430073, China.
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12
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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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13
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Ribonuclease H/DNA Polymerase HIV-1 Reverse Transcriptase Dual Inhibitor: Mechanistic Studies on the Allosteric Mode of Action of Isatin-Based Compound RMNC6. PLoS One 2016; 11:e0147225. [PMID: 26800261 PMCID: PMC4723341 DOI: 10.1371/journal.pone.0147225] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 12/30/2015] [Indexed: 12/11/2022] Open
Abstract
The DNA polymerase and ribonuclease H (RNase H) activities of human immunodeficiency virus type 1 (HIV-1) are needed for the replication of the viral genome and are validated drug targets. However, there are no approved drugs inhibiting RNase H and the efficiency of DNA polymerase inhibitors can be diminished by the presence of drug resistance mutations. In this context, drugs inhibiting both activities could represent a significant advance towards better anti-HIV therapies. We report on the mechanisms of allosteric inhibition of a newly synthesized isatin-based compound designated as RMNC6 that showed IC50 values of 1.4 and 9.8 μM on HIV-1 RT-associated RNase H and polymerase activities, respectively. Blind docking studies predict that RMNC6 could bind two different pockets in the RT: one in the DNA polymerase domain (partially overlapping the non-nucleoside RT inhibitor [NNRTI] binding pocket), and a second one close to the RNase H active site. Enzymatic studies showed that RMNC6 interferes with efavirenz (an approved NNRTI) in its binding to the RT polymerase domain, although NNRTI resistance-associated mutations such as K103N, Y181C and Y188L had a minor impact on RT susceptibility to RMNC6. In addition, despite being naturally resistant to NNRTIs, the polymerase activity of HIV-1 group O RT was efficiently inhibited by RMNC6. The compound was also an inhibitor of the RNase H activity of wild-type HIV-1 group O RT, although we observed a 6.5-fold increase in the IC50 in comparison with the prototypic HIV-1 group M subtype B enzyme. Mutagenesis studies showed that RT RNase H domain residues Asn474 and Tyr501, and in a lesser extent Ala502 and Ala508, are critical for RMNC6 inhibition of the endonuclease activity of the RT, without affecting its DNA polymerization activity. Our results show that RMNC6 acts as a dual inhibitor with allosteric sites in the DNA polymerase and the RNase H domains of HIV-1 RT.
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Wang J, Lu P, Wang Y. Copper-catalyzed multi-component synthesis of acrylamidines and benzoimidazoles. Org Chem Front 2015. [DOI: 10.1039/c5qo00196j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Acrylamidines were synthesized via the copper-catalyzed three-component reaction of propargyl acetates, sulfonyl azides and amines, which are readily accessible materials.
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Affiliation(s)
- Jinjin Wang
- Department of Chemistry
- Zhejiang University
- Hangzhou 310027
- P. R. China
| | - Ping Lu
- Department of Chemistry
- Zhejiang University
- Hangzhou 310027
- P. R. China
| | - Yanguang Wang
- Department of Chemistry
- Zhejiang University
- Hangzhou 310027
- P. R. China
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15
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Singh K, Flores JA, Kirby KA, Neogi U, Sonnerborg A, Hachiya A, Das K, Arnold E, McArthur C, Parniak M, Sarafianos SG. Drug resistance in non-B subtype HIV-1: impact of HIV-1 reverse transcriptase inhibitors. Viruses 2014; 6:3535-62. [PMID: 25254383 PMCID: PMC4189038 DOI: 10.3390/v6093535] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 09/09/2014] [Accepted: 09/09/2014] [Indexed: 01/20/2023] Open
Abstract
Human immunodeficiency virus (HIV) causes approximately 2.5 million new infections every year, and nearly 1.6 million patients succumb to HIV each year. Several factors, including cross-species transmission and error-prone replication have resulted in extraordinary genetic diversity of HIV groups. One of these groups, known as group M (main) contains nine subtypes (A-D, F-H and J-K) and causes ~95% of all HIV infections. Most reported data on susceptibility and resistance to anti-HIV therapies are from subtype B HIV infections, which are prevalent in developed countries but account for only ~12% of all global HIV infections, whereas non-B subtype HIV infections that account for ~88% of all HIV infections are prevalent primarily in low and middle-income countries. Although the treatments for subtype B infections are generally effective against non-B subtype infections, there are differences in response to therapies. Here, we review how polymorphisms, transmission efficiency of drug-resistant strains, and differences in genetic barrier for drug resistance can differentially alter the response to reverse transcriptase-targeting therapies in various subtypes.
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Affiliation(s)
- Kamalendra Singh
- Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
| | - Jacqueline A Flores
- Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
| | - Karen A Kirby
- Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm 141 86, Sweden.
| | - Anders Sonnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm 141 86, Sweden.
| | - Atsuko Hachiya
- Clinical Research Center, Department of Infectious Diseases and Immunology, National Hospital Organization, Nagoya Medical Center, Nagoya 460-0001, Japan.
| | - Kalyan Das
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854, USA.
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854, USA.
| | - Carole McArthur
- Department of Oral and Craniofacial Science , School of Dentistry, University of Missouri, Kansas City, MO 64108, USA.
| | - Michael Parniak
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
| | - Stefan G Sarafianos
- Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
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16
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Meleddu R, Cannas V, Distinto S, Sarais G, Del Vecchio C, Esposito F, Bianco G, Corona A, Cottiglia F, Alcaro S, Parolin C, Artese A, Scalise D, Fresta M, Arridu A, Ortuso F, Maccioni E, Tramontano E. Design, synthesis, and biological evaluation of 1,3-diarylpropenones as dual inhibitors of HIV-1 reverse transcriptase. ChemMedChem 2014; 9:1869-79. [PMID: 24850787 DOI: 10.1002/cmdc.201402015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Indexed: 12/12/2022]
Abstract
A small library of 1,3-diarylpropenones was designed and synthesized as dual inhibitors of both HIV-1 reverse transcriptase (RT) DNA polymerase (DP) and ribonuclease H (RNase H) associated functions. Compounds were assayed on these enzyme activities, which highlighted dual inhibition properties in the low-micromolar range. Interestingly, mutations in the non-nucleoside RT inhibitor binding pocket strongly affected RNase H inhibition by the propenone derivatives without decreasing their capacity to inhibit DP activity, which suggests long-range RT structural effects. Biochemical and computational studies indicated that the propenone derivatives bind two different interdependent allosteric pockets.
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Affiliation(s)
- Rita Meleddu
- Department of Life and Environmental Sciences, University of Cagliari, Via Ospedale 72, 09124 Cagliari (Italy)
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17
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Kang D, Song Y, Chen W, Zhan P, Liu X. “Old Dogs with New Tricks”: exploiting alternative mechanisms of action and new drug design strategies for clinically validated HIV targets. MOLECULAR BIOSYSTEMS 2014; 10:1998-2022. [DOI: 10.1039/c4mb00147h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Wadford DA, Kauffman RC, Deere JD, Aoki ST, Stanton RA, Higgins J, Van Rompay KKA, Villalobos A, Nettles JH, Schinazi RF, Pedersen NC, North TW. Variation of human immunodeficiency virus type-1 reverse transcriptase within the simian immunodeficiency virus genome of RT-SHIV. PLoS One 2014; 9:e86997. [PMID: 24498008 PMCID: PMC3909041 DOI: 10.1371/journal.pone.0086997] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 12/17/2013] [Indexed: 11/25/2022] Open
Abstract
RT-SHIV is a chimera of simian immunodeficiency virus (SIV) containing the reverse transcriptase (RT)-encoding region of human immunodeficiency virus type 1 (HIV-1) within the backbone of SIVmac239. It has been used in a non-human primate model for studies of non-nucleoside RT inhibitors (NNRTI) and highly active antiretroviral therapy (HAART). We and others have identified several mutations that arise in the "foreign" HIV-1 RT of RT-SHIV during in vivo replication. In this study we catalogued amino acid substitutions in the HIV-1 RT and in regions of the SIV backbone with which RT interacts that emerged 30 weeks post-infection from seven RT-SHIV-infected rhesus macaques. The virus set points varied from relatively high virus load, moderate virus load, to undetectable virus load. The G196R substitution in RT was detected from 6 of 7 animals at week 4 post-infection and remained in virus from 4 of 6 animals at week 30. Virus from four high virus load animals showed several common mutations within RT, including L74V or V75L, G196R, L214F, and K275R. The foreign RT from high virus load isolates exhibited as much variation as that of the highly variable envelope surface glycoprotein, and 10-fold higher than that of the native RT of SIVmac239. Isolates from moderate virus load animals showed much less variation in the foreign RT than the high virus load isolates. No variation was found in SIVmac239 genes known to interact with RT. Our results demonstrate substantial adaptation of the foreign HIV-1 RT in RT-SHIV-infected macaques, which most likely reflects selective pressure upon the foreign RT to attain optimal activity within the context of the chimeric RT-SHIV and the rhesus macaque host.
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Affiliation(s)
- Debra A. Wadford
- Center for Comparative Medicine, University of California Davis, Davis, California, United States of America
| | - Robert C. Kauffman
- Center for Comparative Medicine, University of California Davis, Davis, California, United States of America
| | - Jesse D. Deere
- Center for Comparative Medicine, University of California Davis, Davis, California, United States of America
| | - Scott T. Aoki
- Center for Comparative Medicine, University of California Davis, Davis, California, United States of America
| | - Richard A. Stanton
- Children's Center for Drug Discovery (CDD), Departments of Pediatrics and Biomedical Informatics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Joanne Higgins
- Center for Comparative Medicine, University of California Davis, Davis, California, United States of America
| | - Koen K. A. Van Rompay
- California National Primate Research Center, University of California Davis, Davis, California, United States of America
| | - Andradi Villalobos
- Center for Comparative Medicine, University of California Davis, Davis, California, United States of America
| | - James H. Nettles
- Children's Center for Drug Discovery (CDD), Departments of Pediatrics and Biomedical Informatics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Raymond F. Schinazi
- Emory University School of Medicine, Veterans Affairs Medical Center, Decatur, Georgia, United States of America
| | - Niels C. Pedersen
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Thomas W. North
- Center for Comparative Medicine, University of California Davis, Davis, California, United States of America
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
- * E-mail:
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19
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Bellucci L, Angeli L, Tafi A, Radi M, Botta M. Unconventional plasticity of HIV-1 reverse transcriptase: how inhibitors could open a connection "gate" between allosteric and catalytic sites. J Chem Inf Model 2013; 53:3117-22. [PMID: 24256065 DOI: 10.1021/ci400414s] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Targeted molecular dynamics (TMD) simulations allowed for identifying the chemical/structural features of the nucleotide-competitive HIV-1 inhibitor DAVP-1, which is responsible for the disruption of the T-shape motif between Try183 and Trp229 of the reverse transcriptase (RT). DAVP-1 promoted the opening of a connection "gate" between allosteric and catalytic sites of HIV-1 RT, thus explaining its peculiar mechanism of action and providing useful insights to develop novel nucleotide-competitive RT inhibitors.
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Affiliation(s)
- Luca Bellucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via Aldo Moro 2, 53100 Siena, Italy
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20
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Chen T, Romesberg FE. Directed polymerase evolution. FEBS Lett 2013; 588:219-29. [PMID: 24211837 DOI: 10.1016/j.febslet.2013.10.040] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2013] [Revised: 10/28/2013] [Accepted: 10/29/2013] [Indexed: 12/23/2022]
Abstract
Polymerases evolved in nature to synthesize DNA and RNA, and they underlie the storage and flow of genetic information in all cells. The availability of these enzymes for use at the bench has driven a revolution in biotechnology and medicinal research; however, polymerases did not evolve to function efficiently under the conditions required for some applications and their high substrate fidelity precludes their use for most applications that involve modified substrates. To circumvent these limitations, researchers have turned to directed evolution to tailor the properties and/or substrate repertoire of polymerases for different applications, and several systems have been developed for this purpose. These systems draw on different methods of creating a pool of randomly mutated polymerases and are differentiated by the process used to isolate the most fit members. A variety of polymerases have been evolved, providing new or improved functionality, as well as interesting new insight into the factors governing activity.
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Affiliation(s)
- Tingjian Chen
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Floyd E Romesberg
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States.
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21
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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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22
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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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23
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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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Zhan P, Chen X, Li D, Fang Z, De Clercq E, Liu X. HIV-1 NNRTIs: structural diversity, pharmacophore similarity, and implications for drug design. Med Res Rev 2011; 33 Suppl 1:E1-72. [PMID: 21523792 DOI: 10.1002/med.20241] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nonnucleoside reverse transcriptase inhibitors (NNRTIs) nowadays represent very potent and most promising anti-AIDS agents that specifically target the HIV-1 reverse transcriptase (RT). However, the effectiveness of NNRTI drugs can be hampered by rapid emergence of drug-resistant viruses and severe side effects upon long-term use. Therefore, there is an urgent need to develop novel, highly potent NNRTIs with broad spectrum antiviral activity and improved pharmacokinetic properties, and more efficient strategies that facilitate and shorten the drug discovery process would be extremely beneficial. Fortunately, the structural diversity of NNRTIs provided a wide space for novel lead discovery, and the pharmacophore similarity of NNRTIs gave valuable hints for lead discovery and optimization. More importantly, with the continued efforts in the development of computational tools and increased crystallographic information on RT/NNRTI complexes, structure-based approaches using a combination of traditional medicinal chemistry, structural biology, and computational chemistry are being used increasingly in the design of NNRTIs. First, this review covers two decades of research and development for various NNRTI families based on their chemical scaffolds, and then describes the structural similarity of NNRTIs. We have attempted to assemble a comprehensive overview of the general approaches in NNRTI lead discovery and optimization reported in the literature during the last decade. The successful applications of medicinal chemistry strategies, crystallography, and computational tools for designing novel NNRTIs are highlighted. Future directions for research are also outlined.
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Affiliation(s)
- Peng Zhan
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong, PR China
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Götte M. Initiation of HIV reverse transcription: is enzyme flipping required? Viruses 2011; 3:331-335. [PMID: 21994735 PMCID: PMC3185700 DOI: 10.3390/v3040331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 04/01/2011] [Accepted: 04/01/2011] [Indexed: 12/03/2022] Open
Abstract
Liu and colleagues have recently studied dynamic changes in the orientation of HIV reverse transcriptase (RT) on its nucleic acid substrate during initiation of DNA synthesis. The authors employed a single molecule FRET assay and revealed the existence of an equilibrium between polymerase-competent and “flipped” polymerase-incompetent orientations. RT flipping correlates with enzyme pausing during initiation, while the transition to the processive elongation phase correlates with increases in the population of polymerase-competent complexes. The potential biological significance of these findings is discussed in this commentary in lieu of the entire process of reverse transcription.
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Affiliation(s)
- Matthias Götte
- Department of Microbiology and Immunology, McGill University, Duff Medical Building (D-6), 3775 University St., Montreal, QC, H3A 2B4, Canada; E-Mail: ; Tel.: +1-514-398-1365; Fax: +1-514-398-7052
- Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6, Canada
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26
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Esposito F, Kharlamova T, Distinto S, Zinzula L, Cheng YC, Dutschman G, Floris G, Markt P, Corona A, Tramontano E. Alizarine derivatives as new dual inhibitors of the HIV-1 reverse transcriptase-associated DNA polymerase and RNase H activities effective also on the RNase H activity of non-nucleoside resistant reverse transcriptases. FEBS J 2011; 278:1444-57. [PMID: 21348941 DOI: 10.1111/j.1742-4658.2011.08057.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
HIV-1 reverse transcriptase (RT) has two associated activities, DNA polymerase and RNase H, both essential for viral replication and validated drug targets. Although all RT inhibitors approved for therapy target DNA polymerase activity, the search for new RT inhibitors that target the RNase H function and are possibly active on RTs resistant to the known non-nucleoside inhibitors (NNRTI) is a viable approach for anti-HIV drug development. In this study, several alizarine derivatives were synthesized and tested for both HIV-1 RT-associated activities. Alizarine analogues K-49 and KNA-53 showed IC(50) values for both RT-associated functions of ∼ 10 μm. When tested on the K103N RT, both derivatives inhibited the RT-associated functions equally, whereas when tested on the Y181C RT, KNA-53 inhibited the RNase H function and was inactive on the polymerase function. Mechanism of action studies showed that these derivatives do not intercalate into DNA and do not chelate the divalent cofactor Mg(2+) . Kinetic studies demonstrated that they are noncompetitive inhibitors, they do not bind to the RNase H active site or to the classical NNRTI binding pocket, even though efavirenz binding negatively influenced K-49/KNA-53 binding and vice versa. This behavior suggested that the alizarine derivatives binding site might be close to the NNRTI binding pocket. Docking experiments and molecular dynamic simulation confirmed the experimental data and the ability of these compounds to occupy a binding pocket close to the NNRTI site.
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Affiliation(s)
- Francesca Esposito
- Department of Applied Sciences in Biosystems, University of Cagliari, Cagliari, Italy
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27
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Alonso J, Halland N, Nazaré M, R'kyek O, Urmann M, Lindenschmidt A. A Direct, Regioselective Palladium-Catalyzed Synthesis of N-Substituted Benzimidazoles and Imidazopyridines. European J Org Chem 2010. [DOI: 10.1002/ejoc.201001423] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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28
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Li Z, Zhang H, Li Y, Zhang J, Chen HF. Drug resistant mechanism of diaryltriazine analog inhibitors of HIV-1 reverse transcriptase using molecular dynamics simulation and 3D-QSAR. Chem Biol Drug Des 2010; 77:63-74. [PMID: 21134218 DOI: 10.1111/j.1747-0285.2010.01049.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: 11/30/2022]
Abstract
Diaryltriazine inhibitors have highly potent and effective bioactivities for the wild type of HIV-1 reverse transcription. To design new drug of antimutant HIV-1 reverse transcriptase, the mechanism of drug resistance for four types of mutants was revealed. Molecular dynamics simulations suggest that Lys101, Leu100, Lys103, Tyr181, and Tyr188 are key residues. Different mutants of key residues may have different interaction modes and lead to different drug resistances. Then, CoMFA and CoMSIA methods were employed to construct 3D quantitative structure-activity relationship models. These models were evaluated by test set compounds. These models can be used to make quantitative prediction of their bioactivities for lead compounds before resorting to in vitro and in vivo experimentation.
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Affiliation(s)
- Zeng Li
- College of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, China
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29
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Active site binding modes of dimeric phloroglucinols for HIV-1 reverse transcriptase, protease and integrase. Bioorg Med Chem Lett 2010; 20:4427-31. [DOI: 10.1016/j.bmcl.2010.06.057] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 06/03/2010] [Accepted: 06/09/2010] [Indexed: 11/18/2022]
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30
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Freisz S, Bec G, Radi M, Wolff P, Crespan E, Angeli L, Dumas P, Maga G, Botta M, Ennifar E. Crystal structure of HIV-1 reverse transcriptase bound to a non-nucleoside inhibitor with a novel mechanism of action. Angew Chem Int Ed Engl 2010; 49:1805-8. [PMID: 20135654 DOI: 10.1002/anie.200905651] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Séverine Freisz
- Architecture et réactivité de l'ARN, Université de Strasbourg, CNRS, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg, France
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31
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Freisz S, Bec G, Radi M, Wolff P, Crespan E, Angeli L, Dumas P, Maga G, Botta M, Ennifar E. Crystal Structure of HIV-1 Reverse Transcriptase Bound to a Non-Nucleoside Inhibitor with a Novel Mechanism of Action. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200905651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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32
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Abstract
HIV-1 Reverse Transcriptase (HIV-1 RT) has been the target of numerous approved anti-AIDS drugs that are key components of Highly Active Anti-Retroviral Therapies (HAART). It remains the target of extensive structural studies that continue unabated for almost twenty years. The crystal structures of wild-type or drug-resistant mutant HIV RTs in the unliganded form or in complex with substrates and/or drugs have offered valuable glimpses into the enzyme’s folding and its interactions with DNA and dNTP substrates, as well as with nucleos(t)ide reverse transcriptase inhibitor (NRTI) and non-nucleoside reverse transcriptase inhibitor (NNRTIs) drugs. These studies have been used to interpret a large body of biochemical results and have paved the way for innovative biochemical experiments designed to elucidate the mechanisms of catalysis and drug inhibition of polymerase and RNase H functions of RT. In turn, the combined use of structural biology and biochemical approaches has led to the discovery of novel mechanisms of drug resistance and has contributed to the design of new drugs with improved potency and ability to suppress multi-drug resistant strains.
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33
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Paris KA, Haq O, Felts AK, Das K, Arnold E, Levy RM. Conformational landscape of the human immunodeficiency virus type 1 reverse transcriptase non-nucleoside inhibitor binding pocket: lessons for inhibitor design from a cluster analysis of many crystal structures. J Med Chem 2009; 52:6413-20. [PMID: 19827836 PMCID: PMC3182518 DOI: 10.1021/jm900854h] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Clustering of 99 available X-ray crystal structures of HIV-1 reverse transcriptase (RT) at the flexible non-nucleoside inhibitor binding pocket (NNIBP) provides information about features of the conformational landscape for binding non-nucleoside inhibitors (NNRTIs), including effects of mutation and crystal forms. The ensemble of NNIBP conformations is separated into eight discrete clusters based primarily on the position of the functionally important primer grip, the displacement of which is believed to be one of the mechanisms of inhibition of RT. Two of these clusters are populated by structures in which the primer grip exhibits novel conformations that differ from the predominant cluster by over 4 A and are induced by the unique inhibitors capravirine and rilpivirine/TMC278. This work identifies a new conformation of the NNIBP that may be used to design NNRTIs. It can also be used to guide more complete exploration of the NNIBP free energy landscape using advanced sampling techniques.
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Affiliation(s)
- Kristina A. Paris
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
- BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Omar Haq
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
- BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Anthony K. Felts
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
- BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Kalyan Das
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Eddy Arnold
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Ronald M. Levy
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
- BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, New Jersey 08854, USA
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34
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Nichols SE, Domaoal RA, Thakur VV, Tirado-Rives J, Anderson KS, Jorgensen WL. Discovery of wild-type and Y181C mutant non-nucleoside HIV-1 reverse transcriptase inhibitors using virtual screening with multiple protein structures. J Chem Inf Model 2009; 49:1272-9. [PMID: 19374380 DOI: 10.1021/ci900068k] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To discover non-nucleoside inhibitors of HIV-1 reverse transcriptase (NNRTIs) that are effective against both wild-type (WT) virus and variants that encode the clinically troublesome Tyr181Cys (Y181C) RT mutation, virtual screening by docking was carried out using three RT structures and more than 2 million commercially available compounds. Two of the structures are for WT-virus with different conformations of Tyr181, while the third structure incorporates the Y181C modification. Eventually nine compounds were purchased and assayed. Three of the compounds show low-micromolar antiviral activity toward either or both the wild-type and Y181C HIV-1 strains. The study illustrates a viable protocol to seek anti-HIV agents with enhanced resistance profiles.
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Affiliation(s)
- Sara E Nichols
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06511, USA
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35
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Radi M, Maga G, Alongi M, Angeli L, Samuele A, Zanoli S, Bellucci L, Tafi A, Casaluce G, Giorgi G, Armand-Ugon M, Gonzalez E, Esté JA, Baltzinger M, Bec G, Dumas P, Ennifar E, Botta M. Discovery of Chiral Cyclopropyl Dihydro-Alkylthio-Benzyl-Oxopyrimidine (S-DABO) Derivatives as Potent HIV-1 Reverse Transcriptase Inhibitors with High Activity Against Clinically Relevant Mutants. J Med Chem 2009; 52:840-51. [DOI: 10.1021/jm801330n] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marco Radi
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
| | - Giovanni Maga
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
| | - Maddalena Alongi
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
| | - Lucilla Angeli
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
| | - Alberta Samuele
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
| | - Samantha Zanoli
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
| | - Luca Bellucci
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
| | - Andrea Tafi
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
| | - Gianni Casaluce
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
| | - Gianluca Giorgi
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
| | - Mercedes Armand-Ugon
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
| | - Emmanuel Gonzalez
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
| | - José A. Esté
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
| | - Mireille Baltzinger
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
| | - Guillaume Bec
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
| | - Philippe Dumas
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
| | - Eric Ennifar
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
| | - Maurizio Botta
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
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36
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Hawtrey A, Pieterse A, van Zyl J, Van der Bijl P, Van der Merwe M, Nel W, Ariatti M. Studies on the inhibition of Moloney murine leukemia virus reverse transcriptase by N-tritylamino acids and N-tritylamino acid-nucleotide compounds. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 27:1011-23. [PMID: 18711664 DOI: 10.1080/15257770802271698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
N-Acylated derivatives of 8-(6-aminohexyl) amino-adenosine-5 '-phosphate were prepared and studied with regard to their effect on DNA synthesis by the Moloney leukemia virus reverse transcriptase. N-palmitoyl and N-nicotinyl derivatives and bis-8-(6-aminohexyl) amino-5'-AMP inhibited the enzyme partially using poly (rA).oligo d(pT)(16-18) as template-primer with [(3)H]dTTP. In order to increase hydrophobicity in the acyl component tethered to the 8-(6-aminohexyl) amino group on the adenine nucleotide, N-trityl-L-phenylalanine and the N-trityl derivatives of the o, m, and p-fluoro-DL-phenylalanine were initially examined for inhibition of the enzyme using the above template-primer system. The compounds all inhibited the reverse transcriptase with IC(50) values of approximately 60-80 microM. However, when N-trityl-m-fluoro-DL-phenylalanine was coupled to the nucleotide 8-(6-aminohexyl) amino-adenosine-5'-phosphate, the inhibitory activity of this compound increased significantly (IC(50) = 5 microM).
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Affiliation(s)
- Arthur Hawtrey
- Division of Pharmacology, Department of Medicine, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
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37
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Srivab P, Hannongbua S. A Study of the Binding Energies of Efavirenz to Wild-Type and K103N/Y181C HIV-1 Reverse Transcriptase Based on the ONIOM Method. ChemMedChem 2008; 3:803-11. [DOI: 10.1002/cmdc.200700181] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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38
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Ren J, Stammers DK. Structural basis for drug resistance mechanisms for non-nucleoside inhibitors of HIV reverse transcriptase. Virus Res 2008; 134:157-70. [PMID: 18313784 DOI: 10.1016/j.virusres.2007.12.018] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2007] [Revised: 12/21/2007] [Accepted: 12/21/2007] [Indexed: 11/25/2022]
Abstract
The selection of drug resistant virus is a significant obstacle to the continued successful treatment of HIV infection. Reverse transcriptase is the target for numerous approved anti-HIV drugs including both nucleoside inhibitor (NRTI) and non-nucleosides (NNRTI). The many available crystal structures of RT reveal that, generally, in relation to their binding sites NRTI resistance mutations are generally more distally positioned, whilst for NNRTIs mutations are clustered. Such clustering implies a direct stereochemical basis for NNRTI resistance mechanisms, which is indeed observed in many cases such as the loss of key ring stacking interactions with inhibitors via mutations at Tyr181 and Tyr188. However, there are also indirect resistance mechanisms observed, e.g. V108I (via perturbation of Tyr188 and Tyr181) and K103N (apo-enzyme stabilisation). The resistance mechanism can be NNRTI-dependent as is the case for K101E where either indirect (nevirapine) or direct effects (efavirenz) apply. Structural studies have contributed to the design of newer generation NNRTIs and identified a number of features which may contribute to their much improved resistance profiles. Such factors include reduced interactions with Tyr181, the presence of inhibitor/main-chain H-bonds and ability to undergo conformational flexing and rearrangement within the mutated drug site.
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Affiliation(s)
- Jingshan Ren
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
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Ilina T, Parniak MA. Inhibitors of HIV-1 reverse transcriptase. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2008; 56:121-67. [PMID: 18086411 DOI: 10.1016/s1054-3589(07)56005-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Tatiana Ilina
- Department of Molecular Genetics and Biochemistry, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
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40
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Xia Q, Radzio J, Anderson KS, Sluis-Cremer N. Probing nonnucleoside inhibitor-induced active-site distortion in HIV-1 reverse transcriptase by transient kinetic analyses. Protein Sci 2007; 16:1728-37. [PMID: 17656585 PMCID: PMC2203366 DOI: 10.1110/ps.072829007] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Nonnucleoside reverse transcriptase inhibitors (NNRTI) are a group of structurally diverse compounds that bind to a single site in HIV-1 reverse transcriptase (RT), termed the NNRTI-binding pocket (NNRTI-BP). NNRTI binding to RT induces conformational changes in the enzyme that affect key elements of the polymerase active site and also the association between the two protein subunits. To determine which conformational changes contribute to the mechanism of inhibition of HIV-1 reverse transcription, we used transient kinetic analyses to probe the catalytic events that occur directly at the enzyme's polymerase active site when the NNRTI-BP was occupied by nevirapine, efavirenz, or delavirdine. Our results demonstrate that all NNRTI-RT-template/primer (NNRTI-RT-T/P) complexes displayed a metal-dependent increase in dNTP binding affinity (K(d) ) and a metal-independent decrease in the maximum rate of dNTP incorporation (k (pol)). The magnitude of the decrease in k (pol) was dependent on the NNRTI used in the assay: Efavirenz caused the largest decrease followed by delavirdine and then nevirapine. Analyses that were designed to probe direct effects on phosphodiester bond formation suggested that the NNRTI mediate their effects on the chemistry step of the DNA polymerization reaction via an indirect manner. Because each of the NNRTI analyzed in this study exerted largely similar phenotypic effects on single nucleotide addition reactions, whereas each of them are known to exert differential effects on RT dimerization, we conclude that the NNRTI effects on subunit association do not directly contribute to the kinetic mechanism of inhibition of DNA polymerization.
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Affiliation(s)
- Qing Xia
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
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41
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El Safadi Y, Vivet-Boudou V, Marquet R. HIV-1 reverse transcriptase inhibitors. Appl Microbiol Biotechnol 2007; 75:723-37. [PMID: 17370068 DOI: 10.1007/s00253-007-0919-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2007] [Revised: 02/28/2007] [Accepted: 03/01/2007] [Indexed: 10/23/2022]
Abstract
Reverse transcriptase (RT) is one of the three enzymes encoded by the human immunodeficiency virus type 1 (HIV-1), the etiological agent of AIDS. Together with protease inhibitors, drugs inhibiting the RNA- and DNA-dependant DNA polymerase activity of RT are the major components of highly active antiretroviral therapy (HAART), which has dramatically reduced mortality and morbidity of people living with HIV-1/AIDS in developed countries. In this study, we focus on RT inhibitors approved by the US Food and Drugs Administration (FDA) or in phases II and III clinical trials. RT inhibitors belong to two main classes acting by distinct mechanisms. Nucleoside RT inhibitors (NRTIs) lack a 3' hydroxyl group on their ribose or ribose mimic moiety and thus act as chain terminators. Non-NRTIs bind into a hydrophobic pocket close to the polymerase active site and inhibit the chemical step of the polymerization reaction. For each class of inhibitors, we review the mechanism of action, the resistance mechanisms selected by the virus, and the side effects of the drugs. We also discuss the main perspectives for the development of new RT inhibitors.
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Affiliation(s)
- Yazan El Safadi
- Architecture et Réactivité de l'ARN, Université Louis Pasteur, CNRS, IBMC, 15 rue René Descartes, 67084, Strasbourg cedex, France
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Himmel DM, Sarafianos SG, Dharmasena S, Hossain MM, McCoy-Simandle K, Ilina T, Clark AD, Knight JL, Julias JG, Clark PK, Krogh-Jespersen K, Levy RM, Hughes SH, Parniak MA, Arnold E. HIV-1 reverse transcriptase structure with RNase H inhibitor dihydroxy benzoyl naphthyl hydrazone bound at a novel site. ACS Chem Biol 2006; 1:702-12. [PMID: 17184135 PMCID: PMC2963427 DOI: 10.1021/cb600303y] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The rapid emergence of drug-resistant variants of human immunodeficiency virus, type 1 (HIV-1), has limited the efficacy of anti-acquired immune deficiency syndrome (AIDS) treatments, and new lead compounds that target novel binding sites are needed. We have determined the 3.15 A resolution crystal structure of HIV-1 reverse transcriptase (RT) complexed with dihydroxy benzoyl naphthyl hydrazone (DHBNH), an HIV-1 RT RNase H (RNH) inhibitor (RNHI). DHBNH is effective against a variety of drug-resistant HIV-1 RT mutants. While DHBNH has little effect on most aspects of RT-catalyzed DNA synthesis, at relatively high concentrations it does inhibit the initiation of RNA-primed DNA synthesis. Although primarily an RNHI, DHBNH binds >50 A away from the RNH active site, at a novel site near both the polymerase active site and the non-nucleoside RT inhibitor (NNRTI) binding pocket. When DHBNH binds, both Tyr181 and Tyr188 remain in the conformations seen in unliganded HIV-1 RT. DHBNH interacts with conserved residues (Asp186, Trp229) and has substantial interactions with the backbones of several less well-conserved residues. On the basis of this structure, we designed substituted DHBNH derivatives that interact with the NNRTI-binding pocket. These compounds inhibit both the polymerase and RNH activities of RT.
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Affiliation(s)
- Daniel M. Himmel
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-5627
| | - Stefan G. Sarafianos
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-5627
| | - Sanjeewa Dharmasena
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261-0001
| | - Mohammed M. Hossain
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261-0001
| | - Kessler McCoy-Simandle
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261-0001
| | - Tatiana Ilina
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261-0001
| | - Arthur D. Clark
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-5627
| | - Jennifer L. Knight
- Department of Chemistry and Chemical Biology and BIOMAPS Institute for Quantitative Biology, Rutgers University, Piscataway, New Jersey 08854-8066
| | - John G. Julias
- Basic Research Program, SAIC-Frederick, Inc., Frederick, Maryland 21702-1201
| | - Patrick K. Clark
- Basic Research Program, SAIC-Frederick, Inc., Frederick, Maryland 21702-1201
| | - Karsten Krogh-Jespersen
- Department of Chemistry and Chemical Biology and BIOMAPS Institute for Quantitative Biology, Rutgers University, Piscataway, New Jersey 08854-8066
| | - Ronald M. Levy
- Department of Chemistry and Chemical Biology and BIOMAPS Institute for Quantitative Biology, Rutgers University, Piscataway, New Jersey 08854-8066
| | - Stephen H. Hughes
- HIV Drug Resistance Program, NCI-Frederick, Building 539, Frederick, Maryland 21702-1201
| | - Michael A. Parniak
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261-0001
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-5627
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Zhang Z, Walker M, Xu W, Shim JH, Girardet JL, Hamatake RK, Hong Z. Novel nonnucleoside inhibitors that select nucleoside inhibitor resistance mutations in human immunodeficiency virus type 1 reverse transcriptase. Antimicrob Agents Chemother 2006; 50:2772-81. [PMID: 16870771 PMCID: PMC1538665 DOI: 10.1128/aac.00127-06] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mutations in and around the catalytic site of the reverse transcriptase (RT) of human immunodeficiency virus type 1 (HIV-1) are associated with resistance to nucleoside RT inhibitors (NRTIs), whereas changes in the hydrophobic pocket of the RT are attributed to nonnucleoside RT inhibitor (NNRTI) resistance. In this study, we report a novel series of nonnucleoside inhibitors of HIV-1, exemplified by VRX-329747 and VRX-413638, which inhibit both NNRTI- and NRTI-resistant HIV-1 isolates. Enzymatic studies indicated that these compounds are HIV-1 RT inhibitors. Surprisingly, however, following prolonged (6 months) tissue culture selection, this series of nonnucleoside inhibitors did not select NNRTI-resistant mutations in HIV-1 RT. Rather, four mutations (M41L, A62T/V, V118I, and M184V) known to cause resistance to NRTIs and two additional novel mutations (S68N and G112S) adjacent to the catalytic site of the enzyme were selected. Although the M184V mutation appears to be the initial mutation to establish resistance, this mutation alone confers only a two- to fourfold decrease in susceptibility to VRX-329747 and VRX-413638. At least two additional mutations must accumulate for significant resistance. Moreover, while VRX-329747-selected viruses are resistant to lamivudine and emtricitabine due to the M184V mutation, they remain susceptible to zidovudine, stavudine, dideoxyinosine, abacavir, tenofovir, and efavirenz. These results directly demonstrate that VRX-329747 and VRX-413638 are novel nonnucleoside inhibitors of HIV-1 RT with the potential to augment current therapies.
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Affiliation(s)
- Zhijun Zhang
- Drug Discovery, Valeant Research & Development, Costa Mesa, CA 92626, USA.
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Freitas RF, Galembeck SE. Computational Study of the Interaction between TIBO Inhibitors and Y181 (C181), K101, and Y188 Amino Acids. J Phys Chem B 2006; 110:21287-98. [PMID: 17048958 DOI: 10.1021/jp063058u] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The non-nucleoside inhibitors of HIV-1 reverse transcriptase (NNRTIs) are an important class of drugs employed in anti-HIV chemotherapy. TIBO compounds, which belong to the NNRTIs class, are potent inhibitors of the HIV-1 reverse transcriptase enzyme (HIV-1 RT). However, mutations in the amino acids present in the active site of these inhibitors limit their clinical use. In this work, the intermolecular interactions taking place between compounds of the TIBO family and Y181 (C181), K101, and Y188 amino acids are investigated. For this purpose the coordinates of three RT crystalline structures complexed with TIBO were taken from PDB database, and were analyzed by means of the B3LYP/6-31+G(d,p) model. The natural bond orbital (NBO) and atoms in molecules (AIM) methods indicate that not only does the Y181C mutation lead to loss of favorable interactions between the TIBO side chains and tyrosine, but it also affects the interaction between the inhibitor and K101 and Y188. Results also revealed that the interaction between TIBO and K101 is stabilized by N-H...O and N-H...S hydrogen bonds. This is the first time that the presence of the latter hydrogen bond (N-H...S) is reported to play an important role in the stabilization of the interaction between TIBO and K101. In addition the NBO and natural population analyses (NPA) indicate that the 8 Cl-TIBO inhibitor presents a more effective interaction with the Y181, K101, and Y188 than that of 9 Cl-TIBO.
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Affiliation(s)
- Renato F Freitas
- Departamento de Química, FFCLRP, Universidade de São Paulo, 14040-901 Ribeirão Preto-SP, Brasil
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Das K, Sarafianos SG, Clark AD, Boyer PL, Hughes SH, Arnold E. Crystal structures of clinically relevant Lys103Asn/Tyr181Cys double mutant HIV-1 reverse transcriptase in complexes with ATP and non-nucleoside inhibitor HBY 097. J Mol Biol 2006; 365:77-89. [PMID: 17056061 DOI: 10.1016/j.jmb.2006.08.097] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2006] [Accepted: 08/22/2006] [Indexed: 11/16/2022]
Abstract
Lys103Asn and Tyr181Cys are the two mutations frequently observed in patients exposed to various non-nucleoside reverse transcriptase inhibitor drugs (NNRTIs). Human immunodeficiency virus (HIV) strains containing both reverse transcriptase (RT) mutations are resistant to all of the approved NNRTI drugs. We have determined crystal structures of Lys103Asn/Tyr181Cys mutant HIV-1 RT with and without a bound non-nucleoside inhibitor (HBY 097, (S)-4-isopropoxycarbonyl-6-methoxy-3-(methylthio-methyl)-3,4-dihydroquinoxalin-2(1H)-thione) at 3.0 A and 2.5 A resolution, respectively. The structure of the double mutant RT/HBY 097 complex shows a rearrangement of the isopropoxycarbonyl group of HBY 097 compared to its binding with wild-type RT. HBY 097 makes a hydrogen bond with the thiol group of Cys181 that helps the drug retain potency against the Tyr181Cys mutation. The structure of the unliganded double mutant HIV-1 RT showed that Lys103Asn mutation facilitates coordination of a sodium ion with Lys101 O, Asn103 N and O(delta1), Tyr188 O(eta), and two water molecules. The formation of the binding pocket requires the removal of the sodium ion. Although the RT alone and the RT/HBY 097 complex were crystallized in the presence of ATP, only the RT has an ATP coordinated with two Mn(2+) at the polymerase active site. The metal coordination mimics a reaction intermediate state in which complete octahedral coordination was observed for both metal ions. Asp186 coordinates at an axial position whereas the carboxylates of Asp110 and Asp185 are in the planes of coordination of both metal ions. The structures provide evidence that NNRTIs restrict the flexibility of the YMDD loop and prevent the catalytic aspartate residues from adopting their metal-binding conformations.
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Affiliation(s)
- Kalyan Das
- Center for Advanced Biotechnology and Medicine, Rutgers University, Department of Chemistry and Chemical Biology, Piscataway, NJ 08854, USA
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Ceccherini-Silberstein F, Gago F, Santoro M, Gori C, Svicher V, Rodríguez-Barrios F, d'Arrigo R, Ciccozzi M, Bertoli A, d'Arminio Monforte A, Balzarini J, Antinori A, Perno CF. High sequence conservation of human immunodeficiency virus type 1 reverse transcriptase under drug pressure despite the continuous appearance of mutations. J Virol 2005; 79:10718-29. [PMID: 16051864 PMCID: PMC1182657 DOI: 10.1128/jvi.79.16.10718-10729.2005] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To define the extent of sequence conservation in human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) in vivo, the first 320 amino acids of RT obtained from 2,236 plasma-derived samples from a well-defined cohort of 1,704 HIV-1-infected individuals (457 drug naïve and 1,247 drug treated) were analyzed and examined in structural terms. In naïve patients, 233 out of these 320 residues (73%) were conserved (<1% variability). The majority of invariant amino acids clustered into defined regions comprising between 5 and 29 consecutive residues. Of the nine longest invariant regions identified, some contained residues and domains critical for enzyme stability and function. In patients treated with RT inhibitors, despite profound drug pressure and the appearance of mutations primarily associated with resistance, 202 amino acids (63%) remained highly conserved and appeared mostly distributed in regions of variable length. This finding suggests that participation of consecutive residues in structural domains is strictly required for cooperative functions and sustainability of HIV-1 RT activity. Besides confirming the conservation of amino acids that are already known to be important for catalytic activity, stability of the heterodimer interface, and/or primer/template binding, the other 62 new invariable residues are now identified and mapped onto the three-dimensional structure of the enzyme. This new knowledge could be of help in the structure-based design of novel resistance-evading drugs.
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47
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Ren J, Stammers DK. HIV reverse transcriptase structures: designing new inhibitors and understanding mechanisms of drug resistance. Trends Pharmacol Sci 2005; 26:4-7. [PMID: 15629197 DOI: 10.1016/j.tips.2004.11.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
HIV reverse transcriptase (RT) is one of the main targets for the action of anti-AIDS drugs. The selection of drug-resistant HIV is a key problem in the continued treatment of the infection and thus new drugs are required. A significant body of information consisting of HIV-1 RT crystal structures with bound inhibitors has become available during the past several years, and, increasingly, such data will be of use in developing novel inhibitors. Two examples of crystal structures of HIV-1 RT with bound inhibitors have been published recently, one with the non-nucleoside CP94707 and the second with the nucleotide analogue drug tenofovir. Such structures will help the design of new drugs and improve our understanding of the mechanisms of resistance.
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Affiliation(s)
- Jingshan Ren
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
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48
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Abstract
DNA polymerases are molecular motors directing the synthesis of DNA from nucleotides. All polymerases have a common architectural framework consisting of three canonical subdomains termed the fingers, palm, and thumb subdomains. Kinetically, they cycle through various states corresponding to conformational transitions, which may or may not generate force. In this review, we present and discuss the kinetic, structural, and single-molecule works that have contributed to our understanding of DNA polymerase function.
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Affiliation(s)
- Paul J Rothwell
- Institute of Structural Molecular Biology, University College London and Birkbeck College, Malet Street, London WC1E 7HX, United Kingdom
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Aharoni A, Gaidukov L, Khersonsky O, McQ Gould S, Roodveldt C, Tawfik DS. The 'evolvability' of promiscuous protein functions. Nat Genet 2004; 37:73-6. [PMID: 15568024 DOI: 10.1038/ng1482] [Citation(s) in RCA: 621] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2004] [Accepted: 11/03/2004] [Indexed: 11/09/2022]
Abstract
How proteins with new functions (e.g., drug or antibiotic resistance or degradation of man-made chemicals) evolve in a matter of months or years is still unclear. This ability is dependent on the induction of new phenotypic traits by a small number of mutations (plasticity). But mutations often have deleterious effects on functions that are essential for survival. How are these seemingly conflicting demands met at the single-protein level? Results from directed laboratory evolution experiments indicate that the evolution of a new function is driven by mutations that have little effect on the native function but large effects on the promiscuous functions that serve as starting point. Thus, an evolving protein can initially acquire increased fitness for a new function without losing its original function. Gene duplication and the divergence of a completely new protein may then follow.
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Affiliation(s)
- Amir Aharoni
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
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