51
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Jordaan MA, Singh P, Martincigh BS. A combined TD-DFT and spectroscopic investigation of the solute-solvent interactions of efavirenz. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 157:204-210. [PMID: 26773263 DOI: 10.1016/j.saa.2015.12.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 08/06/2015] [Accepted: 12/06/2015] [Indexed: 06/05/2023]
Abstract
Efavirenz, commercially known as Sustiva® or Stocrin®, is a first-line antiretroviral treatment for HIV/AIDS. The clinical efficacy of efavirenz is, however, hindered by its solubility. We sought to investigate the solute-solvent effects of efavirenz by means of a combined qualitative study implementing UV-visible spectrophotometry, (1)H NMR spectroscopy and time-dependent density functional theory (TD-DFT) calculations. The UV spectrum displayed two main absorbance maxima, band I and band II at 246-260 and 291-295 nm, respectively. A general bathochromic shift was noticed from the non-polar solvent cyclohexane to the most polar solvent DMSO (≈13.69 nm) in band I and a smaller bathochromic (≈2.17 nm) and hyperchromic shift was observed in band II. We propose that these observations are due to the role of the amino (NH) and carbonyl (CO) functionalities which induce charge-transfer and intra- and inter-molecular hydrogen bonding. The aromatic and amine protons showed the most deshielded effects in the observed chemical shifts (δ) in the more polar DMSO-d6 solvent relative to CDCl3. The (1)H NMR chemical shifts observed are due to the increased delocalization of the lone pair electrons of the amino nitrogen with increased polarity of the more polar DMSO solvent. The theoretical reproduction of the UV and (1)H NMR spectra by means of TD-DFT is in good agreement with the experimental results.
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Affiliation(s)
- Maryam A Jordaan
- School of Chemistry and Physics, University of KwaZulu-Natal, Westville Campus, Private Bag X54001, Durban 4000, South Africa.
| | - Parvesh Singh
- School of Chemistry and Physics, University of KwaZulu-Natal, Westville Campus, Private Bag X54001, Durban 4000, South Africa
| | - Bice S Martincigh
- School of Chemistry and Physics, University of KwaZulu-Natal, Westville Campus, Private Bag X54001, Durban 4000, South Africa
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52
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Jesus R, Rabelo A, Figueiredo R, Cides da Silva L, Codentino I, Fantini M, Araújo G, Araújo A, Mesquita M. Synthesis and application of the MCM-41 and SBA-15 as matrices for in vitro efavirenz release study. J Drug Deliv Sci Technol 2016. [DOI: 10.1016/j.jddst.2015.11.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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53
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An in-silico approach aimed to clarify the role of Y181C and K103N HIV-1 reverse transcriptase mutations versus Indole Aryl Sulphones. J Mol Graph Model 2016; 63:49-56. [DOI: 10.1016/j.jmgm.2015.11.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 11/19/2015] [Accepted: 11/20/2015] [Indexed: 12/20/2022]
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54
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Efavirenz a nonnucleoside reverse transcriptase inhibitor of first-generation: Approaches based on its medicinal chemistry. Eur J Med Chem 2016; 108:455-465. [DOI: 10.1016/j.ejmech.2015.11.025] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 11/12/2015] [Accepted: 11/17/2015] [Indexed: 11/21/2022]
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55
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Vite-Caritino H, Méndez-Lucio O, Reyes H, Cabrera A, Chávez D, Medina-Franco JL. Advances in the development of pyridinone derivatives as non-nucleoside reverse transcriptase inhibitors. RSC Adv 2016. [DOI: 10.1039/c5ra25722k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Medicinal chemistry, computational design and biological screening have advanced pyridin-2(1H)-one derivatives as a promising class of non-nucleoside reverse transcriptase inhibitors for the treatment of HIV/AIDS.
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Affiliation(s)
- Hugo Vite-Caritino
- Facultad de Química
- Departamento de Farmacia
- Universidad Nacional Autónoma de México
- Mexico City 04510
- Mexico
| | - Oscar Méndez-Lucio
- Unilever Centre for Molecular Science Informatics
- Department of Chemistry
- University of Cambridge
- Cambridge CB2 1EW
- UK
| | - Héctor Reyes
- Centro de Graduados e Investigación en Química del Instituto Tecnológico de Tijuana
- Tijuana
- Mexico
| | - Alberto Cabrera
- Centro de Graduados e Investigación en Química del Instituto Tecnológico de Tijuana
- Tijuana
- Mexico
| | - Daniel Chávez
- Centro de Graduados e Investigación en Química del Instituto Tecnológico de Tijuana
- Tijuana
- Mexico
| | - José L. Medina-Franco
- Facultad de Química
- Departamento de Farmacia
- Universidad Nacional Autónoma de México
- Mexico City 04510
- Mexico
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56
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A computational investigation of the photochemical oxaziridine and amide conversion process of open-chain conjugated nitrone with electron-withdrawing trifluoromethyl group on nitrogen. J CHEM SCI 2015. [DOI: 10.1007/s12039-015-0941-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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57
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Gray WT, Frey KM, Laskey SB, Mislak AC, Spasov KA, Lee WG, Bollini M, Siliciano RF, Jorgensen WL, Anderson KS. Potent Inhibitors Active against HIV Reverse Transcriptase with K101P, a Mutation Conferring Rilpivirine Resistance. ACS Med Chem Lett 2015; 6:1075-9. [PMID: 26487915 DOI: 10.1021/acsmedchemlett.5b00254] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/31/2015] [Indexed: 11/29/2022] Open
Abstract
Catechol diether compounds have nanomolar antiviral and enzymatic activity against HIV with reverse transcriptase (RT) variants containing K101P, a mutation that confers high-level resistance to FDA-approved non-nucleoside inhibitors efavirenz and rilpivirine. Kinetic data suggests that RT (K101P) variants are as catalytically fit as wild-type and thus can potentially increase in the viral population as more antiviral regimens include efavirenz or rilpivirine. Comparison of wild-type structures and a new crystal structure of RT (K101P) in complex with a leading compound confirms that the K101P mutation is not a liability for the catechol diethers while suggesting that key interactions are lost with efavirenz and rilpivirine.
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Affiliation(s)
- William T. Gray
- Department
of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States
| | - Kathleen M. Frey
- Department
of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States
| | - Sarah B. Laskey
- Department
of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Andrea C. Mislak
- Department
of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States
| | - Krasimir A. Spasov
- Department
of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States
| | - Won-Gil Lee
- Department
of Chemistry, Yale University, New Haven, Connecticut 06530-8107, United States
| | - Mariela Bollini
- Department
of Chemistry, Yale University, New Haven, Connecticut 06530-8107, United States
| | - Robert F. Siliciano
- Department
of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Howard Hughes Medical Institute, Baltimore, Maryland 21205, United States
| | - William L. Jorgensen
- Department
of Chemistry, Yale University, New Haven, Connecticut 06530-8107, United States
| | - Karen S. Anderson
- Department
of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States
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58
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Tao R, Yin XJ, Wang KH, Niu YZ, Wang YL, Huang DF, Su YP, Wang JX, Hu YL, Fu Y, Du ZY. Solvent free synthesis of trifluoromethyl tertiary alcohols by cross Aldol reaction. CHINESE CHEM LETT 2015. [DOI: 10.1016/j.cclet.2015.04.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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59
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Direct C–N bond cleavage of N-vinyl or N-allyl arylamines: a metal-free strategy for N-devinylation and N-deallylation. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.05.042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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60
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Goswami D, Tuske S, Pascal BD, Bauman JD, Patel D, Arnold E, Griffin PR. Differential isotopic enrichment to facilitate characterization of asymmetric multimeric proteins using hydrogen/deuterium exchange mass spectrometry. Anal Chem 2015; 87:4015-4022. [PMID: 25763479 DOI: 10.1021/acs.analchem.5b00372] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrogen/deuterium exchange (HDX) coupled to mass spectrometry has emerged as a powerful tool for analyzing the conformational dynamics of protein-ligand and protein-protein interactions. Recent advances in instrumentation and methodology have expanded the utility of HDX for the analysis of large and complex proteins; however, asymmetric dimers with shared amino acid sequence present a unique challenge for HDX because assignment of peptides with identical sequence to their subunit of origin remains ambiguous. Here we report the use of differential isotopic labeling to facilitate HDX analysis of multimers using HIV-1 reverse transcriptase (RT) as a model. RT is an asymmetric heterodimer of 51 kDa (p51) and 66 kDa (p66) subunits. The first 440 residues of p51 and p66 are identical. In this study differentially labeled RT was reconstituted from isotopically enriched ((15)N-labeled) p51 and unlabeled p66. To enable detection of (15)N-deuterated RT peptides, the software HDX Workbench was modified to follow a 100% (15)N model. Our results demonstrated that (15)N enrichment of p51 did not affect its conformational dynamics compared to unlabeled p51, but (15)N-labeled p51 did show different conformational dynamics than p66 in the RT heterodimer. Differential HDX-MS of isotopically labeled RT in the presence of the non-nucleoside reverse transcriptase inhibitor (NNRTI) efavirenz (EFV) showed subunit-specific perturbation in the rate of HDX consistent with previously published results and the RT-EFV cocrystal structure.
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Affiliation(s)
- Devrishi Goswami
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL 33458.USA
| | - Steve Tuske
- Center for Advanced Biotechnology and Medicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Bruce D Pascal
- Informatics Core, The Scripps Research Institute, Jupiter, FL 33458.USA
| | - Joseph D Bauman
- Center for Advanced Biotechnology and Medicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Disha Patel
- Center for Advanced Biotechnology and Medicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Patrick R Griffin
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL 33458.USA
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61
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Yang X, Wu T, Phipps R, Toste FD. Advances in catalytic enantioselective fluorination, mono-, di-, and trifluoromethylation, and trifluoromethylthiolation reactions. Chem Rev 2015; 115:826-70. [PMID: 25337896 PMCID: PMC4311656 DOI: 10.1021/cr500277b] [Citation(s) in RCA: 1084] [Impact Index Per Article: 120.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Indexed: 12/18/2022]
Affiliation(s)
| | | | | | - F. Dean Toste
- Department of Chemistry, University
of California, Berkeley, California 94720, United States
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62
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Famiglini V, La Regina G, Coluccia A, Pelliccia S, Brancale A, Maga G, Crespan E, Badia R, Riveira-Muñoz E, Esté JA, Ferretti R, Cirilli R, Zamperini C, Botta M, Schols D, Limongelli V, Agostino B, Novellino E, Silvestri R. Indolylarylsulfones carrying a heterocyclic tail as very potent and broad spectrum HIV-1 non-nucleoside reverse transcriptase inhibitors. J Med Chem 2014; 57:9945-57. [PMID: 25418038 DOI: 10.1021/jm5011622] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We synthesized new indolylarylsulfone (IAS) derivatives carrying a heterocyclic tail at the indole-2-carboxamide nitrogen as potential anti-HIV/AIDS agents. Several new IASs yielded EC50 values <1.0 nM against HIV-1 WT and mutant strains in MT-4 cells. The (R)-11 enantiomer proved to be exceptionally potent against the whole viral panel; in the reverse transcriptase (RT) screening assay, it was remarkably superior to NVP and EFV and comparable to ETV. The binding poses were consistent with the one previously described for the IAS non-nucleoside reverse transcriptase inhibitors. Docking studies showed that the methyl group of (R)-11 points toward the cleft created by the K103N mutation, different from the corresponding group of (S)-11. By calculating the solvent-accessible surface, we observed that the exposed area of RT in complex with (S)-11 was larger than the area of the (R)-11 complex. Compounds 6 and 16 and enantiomer (R)-11 represent novel robust lead compounds of the IAS class.
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Affiliation(s)
- Valeria Famiglini
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma , Piazzale Aldo Moro 5, I-00185 Roma, Italy
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63
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Iyidogan P, Anderson KS. Current perspectives on HIV-1 antiretroviral drug resistance. Viruses 2014; 6:4095-139. [PMID: 25341668 PMCID: PMC4213579 DOI: 10.3390/v6104095] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 10/08/2014] [Accepted: 10/20/2014] [Indexed: 11/18/2022] Open
Abstract
Current advancements in antiretroviral therapy (ART) have turned HIV-1 infection into a chronic and manageable disease. However, treatment is only effective until HIV-1 develops resistance against the administered drugs. The most recent antiretroviral drugs have become superior at delaying the evolution of acquired drug resistance. In this review, the viral fitness and its correlation to HIV-1 mutation rates and drug resistance are discussed while emphasizing the concept of lethal mutagenesis as an alternative therapy. The development of resistance to the different classes of approved drugs and the importance of monitoring antiretroviral drug resistance are also summarized briefly.
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Affiliation(s)
- Pinar Iyidogan
- Department of Pharmacology, School of Medicine, Yale University, New Haven, CT 06520, USA.
| | - Karen S Anderson
- Department of Pharmacology, School of Medicine, Yale University, New Haven, CT 06520, USA.
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64
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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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65
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Schauer GD, Huber KD, Leuba SH, Sluis-Cremer N. Mechanism of allosteric inhibition of HIV-1 reverse transcriptase revealed by single-molecule and ensemble fluorescence. Nucleic Acids Res 2014; 42:11687-96. [PMID: 25232099 PMCID: PMC4191400 DOI: 10.1093/nar/gku819] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Non-nucleoside reverse transcriptase (RT) inhibitors (NNRTIs) are routinely used to treat HIV-1 infection, yet their mechanism of action remains unclear despite intensive investigation. In this study, we developed complementary single-molecule fluorescence and ensemble fluorescence anisotropy approaches to discover how NNRTIs modulate the intra-molecular conformational changes and inter-molecular dynamics of RT-template/primer (T/P) and RT–T/P–dNTP complexes. We found that NNRTI binding to RT induces opening of the fingers and thumb subdomains, which increases the dynamic sliding motion of the enzyme on the T/P and reduces dNTP binding affinity. Further, efavirenz promotes formation of the E138-K101 salt bridge between the p51 and p66 subunits of RT, which contributes to opening of the thumb/fingers subdomains. Engineering a more polar salt bridge between p51 and p66 resulted in even greater increases in the thumb/fingers opening, RT sliding, dNTP binding disruption and in vitro and in vivo RT inhibition than were observed with wild-type RT. We also observed that K103N, a clinically relevant NNRTI resistance mutation, does not prevent binding between efavirenz and RT-T/P but instead allows formation of a stable and productive RT–T/P–dNTP complex, possibly through disruption of the E138-K101 salt bridge. Collectively, these data describe unique structure–activity–resistance relationships that could be exploited for drug development.
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Affiliation(s)
- Grant D Schauer
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh School of Medicine, Hillman Cancer Center, 5117 Centre Avenue, Pittsburgh, PA 15213, USA Department of Cell Biology, University of Pittsburgh School of Medicine, Hillman Cancer Center, 5117 Centre Avenue, Pittsburgh, PA 15213, USA
| | - Kelly D Huber
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Scaife Hall, 3550 Terrace Street, Pittsburgh, PA 15261, USA
| | - Sanford H Leuba
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh School of Medicine, Hillman Cancer Center, 5117 Centre Avenue, Pittsburgh, PA 15213, USA Department of Cell Biology, University of Pittsburgh School of Medicine, Hillman Cancer Center, 5117 Centre Avenue, Pittsburgh, PA 15213, USA
| | - Nicolas Sluis-Cremer
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Scaife Hall, 3550 Terrace Street, Pittsburgh, PA 15261, USA
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66
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Krzemińska A, Paneth P, Moliner V, Świderek K. Binding Isotope Effects as a Tool for Distinguishing Hydrophobic and Hydrophilic Binding Sites of HIV-1 RT. J Phys Chem B 2014; 119:917-27. [DOI: 10.1021/jp506119h] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Agnieszka Krzemińska
- Institute
of Applied Radiation Chemistry, Lodz University of Technology, 90-924 Lodz, Poland
| | - Piotr Paneth
- Institute
of Applied Radiation Chemistry, Lodz University of Technology, 90-924 Lodz, Poland
| | - Vicent Moliner
- Departament
de Química Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
| | - Katarzyna Świderek
- Institute
of Applied Radiation Chemistry, Lodz University of Technology, 90-924 Lodz, Poland
- Departament
de Química Física, Universitat de València, 46100 Burjassot, Spain
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67
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68
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Famiglini V, La Regina G, Coluccia A, Pelliccia S, Brancale A, Maga G, Crespan E, Badia R, Clotet B, Esté JA, Cirilli R, Novellino E, Silvestri R. New indolylarylsulfones as highly potent and broad spectrum HIV-1 non-nucleoside reverse transcriptase inhibitors. Eur J Med Chem 2014; 80:101-11. [PMID: 24769348 DOI: 10.1016/j.ejmech.2014.04.027] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 03/04/2014] [Accepted: 04/07/2014] [Indexed: 10/25/2022]
Abstract
New indolylarylsulfone HIV-1 NNRTIs were synthesized to evaluate unexplored substitutions of the benzyl/phenylethyl group linked at the indole-2-carboxamide. Against the NL4-3 HIV-1 WT strain, 17 out 20 compounds were superior to NVP and EFV. Several compounds inhibited the K103N HIV-1 mutant strain at nanomolar concentration and were superior to EFV. Some derivatives were superior to EFV against the Y181C and L100I HIV-1 mutant strains. Against the NL4-3 HIV-1 strain, the enantiomers 24 and 25 showed small differences of activity. In contrast, 24 turned out significantly more potent than 25 against the whole panel of mutant HIV-1 strains. The docking studies suggested that the difference in the observed inhibitory activities of 24 and 25 against the K03N mutation could be due to a kinetic rather than affinity differences.
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Affiliation(s)
- Valeria Famiglini
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Giuseppe La Regina
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, I-00185 Roma, Italy.
| | - Antonio Coluccia
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Sveva Pelliccia
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Andrea Brancale
- Welsh School of Pharmacy, Cardiff University, King Edward VII Avenue, Cardiff CF10 3NB, UK
| | - Giovanni Maga
- Institute of Molecular Genetics IGM-CNR, National Research Council, via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Emmanuele Crespan
- Institute of Molecular Genetics IGM-CNR, National Research Council, via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Roger Badia
- AIDS Research Institute - IrsiCaixa, Hospitals Germans Trias i Pujol, Universitat Autonóma de Barcelona, 08916 Badalona, Spain
| | - Bonaventura Clotet
- AIDS Research Institute - IrsiCaixa, Hospitals Germans Trias i Pujol, Universitat Autonóma de Barcelona, 08916 Badalona, Spain
| | - José A Esté
- AIDS Research Institute - IrsiCaixa, Hospitals Germans Trias i Pujol, Universitat Autonóma de Barcelona, 08916 Badalona, Spain
| | - Roberto Cirilli
- Istituto Superiore di Sanità, Dipartimento del Farmaco, Viale Regina Elena 299, I-00161 Roma, Italy
| | - Ettore Novellino
- Dipartimento di Farmacia, Università di Napoli Federico II, Via Domenico Montesano 49, I-80131, Napoli, Italy
| | - Romano Silvestri
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, I-00185 Roma, Italy.
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69
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Wang Y, Huang C, Kang Y. Incorporation of ligand–receptor binding‐site models and transistor‐based sensors for resolving dissociation constants and number of binding sites. IET Nanobiotechnol 2014; 8:10-7. [DOI: 10.1049/iet-nbt.2013.0031] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Yu‐Lin Wang
- Institute of Nanoengineering and MicrosystemsNational Tsing Hua UniversityHsinchu 30013Taiwan
| | - Chih‐Cheng Huang
- Institute of Nanoengineering and MicrosystemsNational Tsing Hua UniversityHsinchu 30013Taiwan
| | - Yen‐Wen Kang
- Institute of Nanoengineering and MicrosystemsNational Tsing Hua UniversityHsinchu 30013Taiwan
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70
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Zheng X, Mueller GA, DeRose EF, London RE. Protein-mediated antagonism between HIV reverse transcriptase ligands nevirapine and MgATP. Biophys J 2014; 104:2695-705. [PMID: 23790378 DOI: 10.1016/j.bpj.2013.04.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 04/07/2013] [Accepted: 04/10/2013] [Indexed: 11/27/2022] Open
Abstract
Nonnucleoside reverse transcriptase inhibitors (NNRTIs) play a central role in the treatment of AIDS, but their mechanisms of action are incompletely understood. The interaction of the NNRTI nevirapine (NVP) with HIV-1 reverse transcriptase (RT) is characterized by a preference for the open conformation of the fingers/thumb subdomains, and a reported variation of three orders of magnitude between the binding affinity of NVP for RT in the presence or absence of primer/template DNA. To investigate the relationship between conformation and ligand binding, we evaluated the use of methionine NMR probes positioned near the tip of the fingers or thumb subdomains. Such probes would be expected to be sensitive to changes in the local environment depending on the fractions of open and closed RT. Comparisons of the NMR spectra of three conservative mutations, I63M, L74M, and L289M, indicated that M63 showed the greatest shift sensitivity to the addition of NVP. The exchange kinetics of the M63 resonance are fast on the chemical shift timescale, but become slow in the presence of NVP due to the slow binding of RT with the inhibitor. The simplest model consistent with this behavior involves a rapid open/closed equilibrium coupled with a slow interaction of the inhibitor with the open conformation. Studies of RT in the presence of both NVP and MgATP indicate a strong negative cooperativity. Binding of MgATP reduces the fraction of RT bound to NVP, as indicated by the intensity of the NVP-perturbed M230 resonance, and enhances the dissociation rate constant of the NVP, resulting in an increase of the open/closed interconversion rate, so that the M63 resonance moves into the fast/intermediate-exchange regime. Protein-mediated interactions appear to explain most of the affinity variation of NVP for RT.
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Affiliation(s)
- Xunhai Zheng
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
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71
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Turpin JA. The next generation of HIV/AIDS drugs: novel and developmental antiHIV drugs and targets. Expert Rev Anti Infect Ther 2014; 1:97-128. [PMID: 15482105 DOI: 10.1586/14787210.1.1.97] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
There are presently 42 million people worldwide living with HIV/AIDS, the majority of which have limited access to antiretrovirals. Even if worldwide penetration was possible, our current chemotherapeutic strategies still suffer from issues of cost, patient compliance, deleterious acute and chronic side effects, emerging single and multidrug resistance, and generalized treatment and economic issues. Even our best antiretroviral therapeutic strategy, highly active antiretroviral therapy (HAART), falls short of completely suppressing HIV replication. Therefore, expansion of current therapeutic options by discovering new antiretrovirals and targets will be critical in the coming years. This review addresses the current status of reverse transcriptase and protease inhibitor development, and summarizes the progress in emerging classes of HIV inhibitors, including entry (T-20, T-1249), coreceptor (SCH-C, SCH-D), integrase (beta-Diketos) and p7 nucleocapsid Zn finger inhibitors (thioesters and PATEs). In addition, the processes of virus entry, PIC transport to the nucleus, HIV interaction with nuclear pores, Tat function, Rev function and virus budding (Tsg101 and ubiquitination) are examined, and proof of concept inhibitors and potential antiviral targets discussed.
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Affiliation(s)
- Jim A Turpin
- HowPin Consulting International, PO Box B Frederick, MD 21705, USA.
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72
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Bilska-Markowska M, Rapp M, Siodła T, Katrusiak A, Hoffmann M, Koroniak H. Tri- and tetrafluoropropionamides derived from chiral secondary amines – synthesis and the conformational studies. NEW J CHEM 2014. [DOI: 10.1039/c4nj00317a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The trifluoromethyl group placed in the α position to the CO group impacts the conformation around F–C–CO bond.
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Affiliation(s)
| | - Magdalena Rapp
- Faculty of Chemistry
- Adam Mickiewicz University in Poznań
- 61-614 Poznań, Poland
| | - Tomasz Siodła
- Faculty of Chemistry
- Adam Mickiewicz University in Poznań
- 61-614 Poznań, Poland
| | - Andrzej Katrusiak
- Faculty of Chemistry
- Adam Mickiewicz University in Poznań
- 61-614 Poznań, Poland
| | - Marcin Hoffmann
- Faculty of Chemistry
- Adam Mickiewicz University in Poznań
- 61-614 Poznań, Poland
| | - Henryk Koroniak
- Faculty of Chemistry
- Adam Mickiewicz University in Poznań
- 61-614 Poznań, Poland
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73
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Zhou J, Ba M, Wang B, Zhou H, Bie J, Fu D, Cao Y, Xu B, Guo Y. Synthesis and biological evaluation of novel quinoxalinone-based HIV-1 reverse transcriptase inhibitors. MEDCHEMCOMM 2014. [DOI: 10.1039/c3md00337j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of novel quinoxalinone derivatives were identified as potent anti-HIV-1 agents with IC50 values at 10−8 μmol L−1 level.
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Affiliation(s)
- Jie Zhou
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation
- Institute of Materia Medica
- Chinese Academy of Medical Sciences & Peking Union Medical College
- Beijing, China
| | - Mingyu Ba
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation
- Institute of Materia Medica
- Chinese Academy of Medical Sciences & Peking Union Medical College
- Beijing, China
| | - Bo Wang
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation
- Institute of Materia Medica
- Chinese Academy of Medical Sciences & Peking Union Medical College
- Beijing, China
- Hebei University of Science and Technology
| | - Haibo Zhou
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation
- Institute of Materia Medica
- Chinese Academy of Medical Sciences & Peking Union Medical College
- Beijing, China
| | - Jianbo Bie
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation
- Institute of Materia Medica
- Chinese Academy of Medical Sciences & Peking Union Medical College
- Beijing, China
| | - Decai Fu
- Hebei University of Science and Technology
- Shijiazhuang, China
| | - Yingli Cao
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation
- Institute of Materia Medica
- Chinese Academy of Medical Sciences & Peking Union Medical College
- Beijing, China
| | - Bailing Xu
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation
- Institute of Materia Medica
- Chinese Academy of Medical Sciences & Peking Union Medical College
- Beijing, China
| | - Ying Guo
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation
- Institute of Materia Medica
- Chinese Academy of Medical Sciences & Peking Union Medical College
- Beijing, China
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74
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Nenajdenko V. Fluorine-Containing Diazines in Medicinal Chemistry and Agrochemistry. FLUORINE IN HETEROCYCLIC CHEMISTRY VOLUME 2 2014. [PMCID: PMC7121506 DOI: 10.1007/978-3-319-04435-4_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The combination of a fluorine atom and a diazine ring, which both possess unique structural and chemical features, can generate new relevant building blocks for the discovery of efficient fluorinated biologically active agents. Herein we give a comprehensive review on the biological activity and synthesis of fluorine containing, pyrimidine, pyrazine and pyridazine derivatives with relevance to medicinal and agrochemistry.
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75
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Arylsulfone-based HIV-1 non-nucleoside reverse transcriptase inhibitors. Future Med Chem 2013; 5:2141-56. [DOI: 10.4155/fmc.13.174] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs) represent one of the most significant classes of drugs for the treatment of AIDS/HIV infection. Over the past two decades several potent arylsulfone-based HIV-1 NNRTIs and related analogs have been developed. This review provides an essential overview of the structure–activity relationships of the arylsulfone-based HIV-1 NNRTIs. Furthermore, structural information useful for the design and development of new sulfur containing NNRTIs with enhanced antiretroviral activity against HIV-1 wild type and clinically relevant drug resistant HIV-1 mutant strains will be discussed.
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76
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Chen W, Zhan P, De Clercq E, Pannecouque C, Balzarini J, Jiang X, Liu X. Design, synthesis and biological evaluation of N2,N4-disubstituted-1,1,3-trioxo-2H,4H-pyrrolo[1,2-b][1,2,4,6]thiatriazine derivatives as HIV-1 NNRTIs. Bioorg Med Chem 2013; 21:7091-100. [DOI: 10.1016/j.bmc.2013.09.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Revised: 09/03/2013] [Accepted: 09/04/2013] [Indexed: 11/15/2022]
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77
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Sakakibara N, Hamasaki T, Baba M, Demizu Y, Kurihara M, Irie K, Iwai M, Asada E, Kato Y, Maruyama T. Synthesis and evaluation of novel 3-(3,5-dimethylbenzyl)uracil analogs as potential anti-HIV-1 agents. Bioorg Med Chem 2013; 21:5900-6. [DOI: 10.1016/j.bmc.2013.06.061] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 06/25/2013] [Accepted: 06/25/2013] [Indexed: 11/15/2022]
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78
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Seckler JM, Leioatts N, Miao H, Grossfield A. The interplay of structure and dynamics: insights from a survey of HIV-1 reverse transcriptase crystal structures. Proteins 2013; 81:1792-801. [PMID: 23720322 DOI: 10.1002/prot.24325] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 04/12/2013] [Accepted: 04/19/2013] [Indexed: 11/07/2022]
Abstract
HIV-1 reverse transcriptase (RT) is a critical drug target for HIV treatment, and understanding the exact mechanisms of its function and inhibition would significantly accelerate the development of new anti-HIV drugs. It is well known that structure plays a critical role in protein function, but for RT, structural information has proven to be insufficient-despite enormous effort-to explain the mechanism of inhibition and drug resistance of non-nucleoside RT inhibitors. We hypothesize that the missing link is dynamics, information about the motions of the system. However, many of the techniques that give the best information about dynamics, such as solution nuclear magnetic resonance and molecular dynamics simulations, cannot be easily applied to a protein as large as RT. As an alternative, we combine elastic network modeling with simultaneous hierarchical clustering of structural and dynamic data. We present an extensive survey of the dynamics of RT bound to a variety of ligands and with a number of mutations, revealing a novel mechanism for drug resistance to non-nucleoside RT inhibitors. Hydrophobic core mutations restore active-state motion to multiple functionally significant regions of HIV-1 RT. This model arises out of a combination of structural and dynamic information, rather than exclusively from one or the other.
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Affiliation(s)
- James M Seckler
- Department of Biostatistics and Computational Biology, University of Rochester, Rochester, New York
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79
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Kawai H, Mizuta S, Tokunaga E, Shibata N. Cinchona alkaloid/TMAF combination: Enantioselective trifluoromethylation of aryl aldehydes. J Fluor Chem 2013. [DOI: 10.1016/j.jfluchem.2013.01.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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80
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Debnath U, Verma S, Jain S, Katti SB, Prabhakar YS. Pyridones as NNRTIs against HIV-1 mutants: 3D-QSAR and protein informatics. J Comput Aided Mol Des 2013; 27:637-54. [DOI: 10.1007/s10822-013-9667-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 07/14/2013] [Indexed: 11/27/2022]
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81
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Lapkouski M, Tian L, Miller JT, Le Grice SFJ, Yang W. Complexes of HIV-1 RT, NNRTI and RNA/DNA hybrid reveal a structure compatible with RNA degradation. Nat Struct Mol Biol 2013; 20:230-236. [PMID: 23314251 PMCID: PMC3973182 DOI: 10.1038/nsmb.2485] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 12/05/2012] [Indexed: 11/25/2022]
Abstract
Structures of type-1 human immunodeficiency virus (HIV-1) reverse transcriptase (RT) have been determined in several forms, but only one contains an RNA/DNA hybrid. Here we report three structures of HIV-1 RT complexed with a non-nucleotide RT inhibitor (NNRTI) and an RNA/DNA hybrid. In the presence of an NNRTI, the RNA/DNA structure differs from all prior nucleic acid bound to RT including the RNA/DNA hybrid. The enzyme structure also differs from all previous RT–DNA complexes. As a result, the hybrid has ready access to the RNase H active site. These observations indicate that an RT–nucleic acid complex may adopt two structural states, one competent for DNA polymerization and the other for RNA degradation. RT mutations that confer drug resistance but are distant from the inhibitor-binding sites often map to the unique RT–hybrid interface that undergoes conformational changes between two catalytic states.
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Affiliation(s)
- Mikalai Lapkouski
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lan Tian
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jennifer T Miller
- HIV Drug Resistance Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Stuart F J Le Grice
- HIV Drug Resistance Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Wei Yang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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82
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Protein-free efavirenz concentrations in cerebrospinal fluid and blood plasma are equivalent: applying the law of mass action to predict protein-free drug concentration. Antimicrob Agents Chemother 2013; 57:1409-14. [PMID: 23295919 DOI: 10.1128/aac.02329-12] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Efavirenz (EFV) is one of the most commonly prescribed antiretroviral drugs (ARVs) for the treatment of HIV. Highly protein-bound drugs, like EFV, have limited central nervous system (CNS) penetration when measured using total drug concentration gradients between blood plasma (BP) and cerebrospinal fluid (CSF). However, the more relevant pharmacologically active protein-free drug concentrations are rarely assessed directly in clinical studies. Using paired BP and CSF samples obtained from 13 subjects on an EFV-containing regimen, both the protein-free and total concentrations of EFV were determined. Despite a median (interquartile range [IQR]) total EFV BP/CSF concentration ratio of 134 (116 to 198), the protein-free EFV BP/CSF concentration ratio was 1.20 (0.97 to 2.12). EFV median (IQR) protein binding was 99.78% (99.74 to 99.80%) in BP and 76.19% (74.47 to 77.15%) in CSF. In addition, using the law of mass action and an in vitro-derived EFV-human serum albumin dissociation constant, we have demonstrated that the predicted median (IQR) protein-free concentration in BP, 4.59 ng/ml (4.02 to 9.44 ng/ml), compared well to that observed in BP, 4.77 ng/ml (3.68 to 6.75 ng/ml). Similar results were also observed in CSF and seminal plasma. This method provides a useful predictive tool for estimating protein binding in varied anatomic compartments. Our results of equivalent protein-free EFV concentrations in BP and CSF do not support prior concerns of the CNS as a pharmacological sanctuary from EFV. As CSF penetration of ARVs may increase our understanding of HIV-associated neurological dysfunction and antiretroviral effect, assessment of protein-free CSF concentrations of other highly protein-bound ARVs is warranted.
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83
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Zhang C, Zhuang DM, Li J, Chen SY, Du XL, Wang JY, Li JY, Jiang B, Yao JH. Diverse reactivity in microwave-promoted catalyst-free coupling of substituted anilines with ethyl trifluoropyruvate and biological evaluation. Org Biomol Chem 2013; 11:5621-33. [DOI: 10.1039/c3ob40650d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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84
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Electrochemical oxidation and determination of antiretroviral drug nevirapine based on uracil-modified carbon paste electrode. J APPL ELECTROCHEM 2012. [DOI: 10.1007/s10800-012-0516-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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85
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Global Conformational Dynamics of HIV-1 Reverse Transcriptase Bound to Non-Nucleoside Inhibitors. BIOLOGY 2012; 1:222-44. [PMID: 24832224 PMCID: PMC4009785 DOI: 10.3390/biology1020222] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 07/16/2012] [Accepted: 07/17/2012] [Indexed: 11/16/2022]
Abstract
HIV-1 Reverse Transcriptase (RT) is a multifunctional enzyme responsible for the transcription of the RNA genome of the HIV virus into DNA suitable for incorporation within the DNA of human host cells. Its crucial role in the viral life cycle has made it one of the major targets for antiretroviral drug therapy. The Non-Nucleoside RT Inhibitor (NNRTI) class of drugs binds allosterically to the enzyme, affecting many aspects of its activity. We use both coarse grained network models and atomistic molecular dynamics to explore the changes in protein dynamics induced by NNRTI binding. We identify changes in the flexibility and conformation of residue Glu396 in the RNaseH primer grip which could provide an explanation for the acceleration in RNaseH cleavage rate observed experimentally in NNRTI bound HIV-1 RT. We further suggest a plausible path for conformational and dynamic changes to be communicated from the vicinity of the NNRTI binding pocket to the RNaseH at the other end of the enzyme.
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86
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Ballante F, Musmuca I, Marshall GR, Ragno R. Comprehensive model of wild-type and mutant HIV-1 reverse transciptases. J Comput Aided Mol Des 2012; 26:907-19. [DOI: 10.1007/s10822-012-9586-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Accepted: 06/28/2012] [Indexed: 10/28/2022]
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87
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Maes M, Loyter A, Friedler A. Peptides that inhibit HIV-1 integrase by blocking its protein-protein interactions. FEBS J 2012; 279:2795-809. [PMID: 22742518 DOI: 10.1111/j.1742-4658.2012.08680.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
HIV-1 integrase (IN) is one of the key enzymes in the viral replication cycle. It mediates the integration of viral cDNA into the host cell genome. IN activity requires interactions with several viral and cellular proteins, as well as IN oligomerization. Inhibition of IN is an important target for the development of anti-HIV therapies, but there is currently only one anti-HIV drug used in the clinic that targets IN. Several other small-molecule anti-IN drug leads are either undergoing clinical trials or in earlier stages of development. These molecules specifically inhibit one of the IN-mediated reactions necessary for successful integration. However, small-molecule inhibitors of protein-protein interactions are difficult to develop. In this review, we focus on peptides that inhibit IN. Peptides have advantages over small-molecule inhibitors of protein-protein interactions: they can mimic the structures of the binding domains within proteins, and are large enough to competitively inhibit protein-protein interactions. The development of peptides that bind IN and inhibit its protein-protein interactions will increase our understanding of the IN mode of action, and lead to the development of new drug leads, such as small molecules derived from these peptides, for better anti-HIV therapy.
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Affiliation(s)
- Michal Maes
- Institute of Chemistry, The Hebrew University of Jerusalem, Israel
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88
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Hassam M, Basson AE, Liotta DC, Morris L, van Otterlo WAL, Pelly SC. Novel Cyclopropyl-Indole Derivatives as HIV Non-Nucleoside Reverse Transcriptase Inhibitors. ACS Med Chem Lett 2012; 3:470-5. [PMID: 24900496 DOI: 10.1021/ml3000462] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 05/02/2012] [Indexed: 11/28/2022] Open
Abstract
The HIV pandemic represents one of the most serious diseases to face mankind in both a social and economic context, with many developing nations being the worst afflicted. Due to ongoing resistance issues associated with the disease, the design and synthesis of anti-HIV agents presents a constant challenge for medicinal chemists. Utilizing molecular modeling, we have designed a series of novel cyclopropyl indole derivatives as HIV non-nucleoside reverse transcriptase inhibitors and carried out their preparation. These compounds facilitate a double hydrogen bonding interaction to Lys101 and efficiently occupy the hydrophobic pockets in the regions of Tyr181/188 and Val179. Several of these compounds inhibited HIV replication as effectively as nevirapine when tested in a phenotypic assay.
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Affiliation(s)
- Mohammad Hassam
- Department
of Chemistry and
Polymer Science, Stellenbosch University, Western Cape, South Africa
| | - Adriaan E. Basson
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Dennis C. Liotta
- Department of Chemistry, Emory University, Atlanta, Georgia, United States
| | - Lynn Morris
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Willem A. L. van Otterlo
- Department
of Chemistry and
Polymer Science, Stellenbosch University, Western Cape, South Africa
| | - Stephen C. Pelly
- Department
of Chemistry and
Polymer Science, Stellenbosch University, Western Cape, South Africa
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89
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Reynolds C, de Koning CB, Pelly SC, van Otterlo WAL, Bode ML. In search of a treatment for HIV--current therapies and the role of non-nucleoside reverse transcriptase inhibitors (NNRTIs). Chem Soc Rev 2012; 41:4657-70. [PMID: 22618809 DOI: 10.1039/c2cs35058k] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The human immunodeficiency virus (HIV) causes AIDS (acquired immune deficiency syndrome), a disease in which the immune system progressively deteriorates, making sufferers vulnerable to all manner of opportunistic infections. Currently, world-wide there are estimated to be 34 million people living with HIV, with the vast majority of these living in sub-Saharan Africa. Therefore, an important research focus is development of new drugs that can be used in the treatment of HIV/AIDS. This review gives an overview of the disease and addresses the drugs currently used for treatment, with specific emphasis on new developments within the class of allosteric non-nucleoside reverse transcriptase inhibitors (NNRTIs).
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Affiliation(s)
- Chevonne Reynolds
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Private Bag 3, PO WITS, 2050, South Africa
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90
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Ordonez P, Hamasaki T, Isono Y, Sakakibara N, Ikejiri M, Maruyama T, Baba M. Anti-human immunodeficiency virus type 1 activity of novel 6-substituted 1-benzyl-3-(3,5-dimethylbenzyl)uracil derivatives. Antimicrob Agents Chemother 2012; 56:2581-9. [PMID: 22290950 PMCID: PMC3346622 DOI: 10.1128/aac.06307-11] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Accepted: 01/24/2012] [Indexed: 11/20/2022] Open
Abstract
Nonnucleoside reverse transcriptase (RT) inhibitors (NNRTIs) are important components of current combination therapies for human immunodeficiency virus type 1 (HIV-1) infection. In screening of chemical libraries, we found 6-azido-1-benzyl-3-(3,5-dimethylbenzyl)uracil (AzBBU) and 6-amino-1-benzyl-3-(3,5-dimethylbenzyl)uracil (AmBBU) to be highly active and selective inhibitors of HIV-1 replication in vitro. To determine the resistance profiles of these compounds, we conducted a long-term culture of HIV-1-infected MT-4 cells with escalating concentrations of each compound. After serial passages of the infected cells, escape viruses were obtained, and they were more than 500-fold resistant to the uracil derivatives compared to the wild type. Sequence analysis was conducted for RT of the escape viruses at passages 12 and 24. The amino acid mutation Y181C in the polymerase domain of RT was detected for all escape viruses. Docking studies using the crystal structure of RT showed that AmBBU requires the amino acid residues Leu100, Val106, Tyr181, and Trp229 for exerting its inhibitory effect on HIV-1. Four additional amino acid changes (K451R, R461K, T468P, and D471N) were identified in the RNase H domain of RT; however, their precise role in the acquisition of resistance is still unclear. In conclusion, the initial mutation Y181C seems sufficient for the acquisition of resistance to the uracil derivatives AzBBU and AmBBU. Further studies are required to determine the precise role of each mutation in the acquisition of HIV-1 resistance.
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Affiliation(s)
- Paula Ordonez
- Division of Antiviral Chemotherapy, Center for Chronic Viral Diseases, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Takayuki Hamasaki
- Division of Antiviral Chemotherapy, Center for Chronic Viral Diseases, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Yohei Isono
- Faculty of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, Sanuki, Japan
| | - Norikazu Sakakibara
- Faculty of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, Sanuki, Japan
| | - Masahiro Ikejiri
- Faculty of Pharmacy, Osaka Ohtani University, Tondabayashi, Japan
| | - Tokumi Maruyama
- Faculty of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, Sanuki, Japan
| | - Masanori Baba
- Division of Antiviral Chemotherapy, Center for Chronic Viral Diseases, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
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91
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Mishra S, Tandon P, Ayala AP. Study on the structure and vibrational spectra of efavirenz conformers using DFT: comparison to experimental data. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 88:116-123. [PMID: 22206896 DOI: 10.1016/j.saa.2011.12.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 12/04/2011] [Indexed: 05/31/2023]
Abstract
Efavirenz, (S)-6-chloro-4-(cyclopropylethynyl)-1,4-dihydro-4-(trifluoromethyl)-2H-3,1-benzoxazin-2-one, is an anti HIV agent belonging to the class of the non-nucleoside inhibitors of the HIV-1 virus reverse transcriptase. A systematic quantum chemical study of the possible conformations, their relative stabilities and vibrational spectra of efavirenz has been reported. Structural and spectral characteristics of efavirenz have been studied by vibrational spectroscopy and quantum chemical methods. Density functional theory (DFT) calculations for potential energy curve, optimized geometries and vibrational spectra have been carried out using 6-311++G(d,p) basis sets and B3LYP functionals. Based on these results, we have discussed the correlation between the vibrational modes and the crystalline structure of the most stable form of efavirenz. A complete analysis of the experimental infrared and Raman spectra has been reported on the basis of wavenumber of the vibrational bands and potential energy distribution. The infrared and the Raman spectra of the molecule based on DFT calculations show reasonable agreement with the experimental results. The calculated HOMO and LUMO energies shows that charge transfer occur within the molecule.
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Affiliation(s)
- Soni Mishra
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, India
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92
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Liu ZJ, Zhang F, Liu JT. Regiospecific and diastereoselective aldol reaction of chiral N-sulfinyl metalloenamines with α,β-unsaturated trifluoromethyl ketones: Asymmetric synthesis of tertiary trifluoromethyl allylic carbinols. J Fluor Chem 2012. [DOI: 10.1016/j.jfluchem.2011.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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93
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Minkara MS, Davis PH, Radhakrishnan ML. Multiple drugs and multiple targets: An analysis of the electrostatic determinants of binding between non-nucleoside HIV-1 reverse transcriptase inhibitors and variants of HIV-1 RT. Proteins 2011; 80:573-90. [DOI: 10.1002/prot.23221] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Revised: 09/13/2011] [Accepted: 10/06/2011] [Indexed: 11/09/2022]
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94
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Menéndez-Arias L, Betancor G, Matamoros T. HIV-1 reverse transcriptase connection subdomain mutations involved in resistance to approved non-nucleoside inhibitors. Antiviral Res 2011; 92:139-49. [DOI: 10.1016/j.antiviral.2011.08.020] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 08/19/2011] [Accepted: 08/22/2011] [Indexed: 11/25/2022]
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95
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Alcaro S, Alteri C, Artese A, Ceccherini-Silberstein F, Costa G, Ortuso F, Bertoli A, Forbici F, Santoro MM, Parrotta L, Flandre P, Masquelier B, Descamps D, Calvez V, Marcelin AG, Perno CF, Sing T, Svicher V. Docking analysis and resistance evaluation of clinically relevant mutations associated with the HIV-1 non-nucleoside reverse transcriptase inhibitors nevirapine, efavirenz and etravirine. ChemMedChem 2011; 6:2203-13. [PMID: 21953939 DOI: 10.1002/cmdc.201100362] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Indexed: 11/07/2022]
Abstract
An integrated computational and statistical approach was used to determine the association of non-nucleoside reverse transcriptase inhibitors (NNRTIs) nevirapine, efavirenz and etravirine with resistance mutations that cause therapeutic failure and their impact on NNRTI resistance. Mutations detected for nevirapine virological failure with a prevalence greater than 10% in the used patient set were: K103N, Y181C, G190A, and K101E. A support vector regression model, based on matched genotypic/phenotypic data (n=850), showed that among 6365 analyzed mutations, K103N, Y181C and G190A have the first, third, and sixth greatest significance for nevirapine resistance, respectively. The most common indicator of treatment failure for efavirenz was K103N mutation present in 56.7% of the patients where the drug failed, followed by V108I, L100I, and G190A. For efavirenz resistance, K103N, G190, and L100I have the first, fourth, and eighth greatest significance, respectively, as determined in support vector regression model. No positive interactions were observed among nevirapine resistance mutations, while a more complex situation was observed with treatment failure of efavirenz and etravirine, characterized by the accumulation of multiple mutations. Docking simulations and free energy analysis based on docking scores of mutated human immunodeficiency virus (HIV) RT complexes were used to evaluate the influence of selected mutations on drug recognition. Results from support vector regression were confirmed by docking analysis. In particular, for nevirapine and efavirenz, a single mutation K103N was associated with the most unfavorable energetic profile compared to the wild-type sequence. This is in line with recent clinical data reporting that diarylpyrimidine etravirine, a very potent third generation drug effective against a wide range of drug-resistant HIV-1 variants, shows increased affinity towards K103N/S mutants due to its high conformational flexibility.
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Affiliation(s)
- Stefano Alcaro
- Dipartimento di Scienze Farmacobiologiche, Università degli Studi Magna Graecia di Catanzaro, Complesso Ninì Barbieri, 88021 Roccelletta di Borgia (CZ), Italy
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96
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Nonnucleoside reverse transcriptase inhibitor-resistant HIV is stimulated by efavirenz during early stages of infection. J Virol 2011; 85:10861-73. [PMID: 21835788 DOI: 10.1128/jvi.05116-11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nonnucleoside reverse transcriptase inhibitors (NNRTIs) are potent and commonly prescribed antiviral agents used in combination therapy (CART) of human immunodeficiency virus type 1 (HIV-1) infection. The development of drug resistance is a major limitation of CART. Reverse transcriptase (RT) genotypes with the NNRTI resistance mutations K101E+G190S are highly resistant to efavirenz (EFV) and can develop during failure of EFV-containing regimens in patients. We have previously shown that virus with K101E+G190S mutations can replicate more efficiently in the presence of EFV than in its absence. In this study, we evaluated the underlying mechanism for drug-dependent stimulation, using a single-cycle cell culture assay in which EFV was added either during the infection or the virus production step. We determined that EFV stimulates K101E+G190S virus during early infection and does not affect late steps of virus replication, such as increasing the amount of active RT incorporated into virions. Additionally, we showed that another NNRTI, nevirapine (NVP), stimulated K101E+G190S virus replication during the early steps of infection similar to EFV, but that the newest NNRTI, etravirine (ETR), did not. We also showed that EFV stimulates K101E+Y188L and K101E+V106I virus, but not K101E+L100I, K101E+K103N, K101E+Y181C, or K101E+G190A virus, suggesting that the stimulation is mutation specific. Real-time PCR of reverse transcription intermediates showed that although the drug did not stimulate minus-strand transfer, it did stimulate minus-strand strong-stop DNA synthesis. Our results indicate that stimulation most likely occurs through a mechanism whereby NNRTIs stimulate priming or elongation of the tRNA.
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97
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Ibe S, Sugiura W. Clinical significance of HIV reverse-transcriptase inhibitor-resistance mutations. Future Microbiol 2011; 6:295-315. [PMID: 21449841 DOI: 10.2217/fmb.11.7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In this article, we summarize recent knowledge on drug-resistance mutations within HIV reverse transcriptase (RT). Several large-scale HIV-1 genotypic analyses have revealed that the most prevalent nucleos(t)ide analog RT inhibitor (NRTI)-resistance mutation is M184V/I followed by a series of thymidine analog-associated mutations: M41L, D67N, K70R, L210W, T215Y/F and K219Q/E. Among non-nucleoside RT inhibitor (NNRTI)-resistance mutations, K103N was frequently observed, followed by Y181C and G190A. Interestingly, V106M was identified in HIV-1 subtype C as a subtype-specific multi-NNRTI-resistance mutation. Regarding mutations in the HIV-1 RT C-terminal region, including the connection subdomain and RNase H domain, their clinical impacts are still controversial, although their effects on NRTI and NNRTI resistance have been confirmed in vitro. In HIV-2 infections, the high prevalence of the Q151M mutation associated with multi-NRTI resistance has been frequently observed.
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Affiliation(s)
- Shiro Ibe
- Department of Infection & Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
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98
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Scarth BJ, Ehteshami M, Beilhartz GL, Götte M. HIV-1 reverse transcriptase inhibitors: beyond classic nucleosides and non-nucleosides. Future Virol 2011. [DOI: 10.2217/fvl.11.35] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reverse transcriptase (RT) of HIV-1 remains an important target in current treatments of HIV-1 infection. Clinically available inhibitors of HIV-1 RT include nucleoside analog RT inhibitors and non-nucleoside RT inhibitors. Nucleoside analog RT inhibitors compete with the natural dNTP substrate and act as chain terminators, while non-nucleoside RT inhibitors bind to an allosteric pocket, inhibiting polymerization noncompetitively. In addition to these two classes of approved drugs, there are a number of RT inhibitors that target the enzyme in different ways. These include nonobligate chain terminators, nucleotide-competing RT inhibitors, pyrophosphate analogs and compounds that inhibit the RT-associated RNase H activity. Here, we review the mechanisms of action associated with these compounds and discuss opportunities and challenges in drug discovery and development efforts.
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Affiliation(s)
- Brian J Scarth
- Department of Microbiology & Immunology, McGill University, Montreal, Quebec, H3A 2B4, Canada
| | - Maryam Ehteshami
- Department of Microbiology & Immunology, McGill University, Montreal, Quebec, H3A 2B4, Canada
| | - Greg L Beilhartz
- Department of Microbiology & Immunology, McGill University, Montreal, Quebec, H3A 2B4, Canada
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99
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Das K, Bauman JD, Rim AS, Dharia C, Clark AD, Camarasa MJ, Balzarini J, Arnold E. Crystal structure of tert-butyldimethylsilyl-spiroaminooxathioledioxide-thymine (TSAO-T) in complex with HIV-1 reverse transcriptase (RT) redefines the elastic limits of the non-nucleoside inhibitor-binding pocket. J Med Chem 2011; 54:2727-37. [PMID: 21446702 PMCID: PMC3361896 DOI: 10.1021/jm101536x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
tert-Butyldimethylsilyl-spiroaminooxathioledioxide (TSAO) compounds have an embedded thymidine-analogue backbone; however, TSAO compounds invoke non-nucleoside RT inhibitor (NNRTI) resistance mutations. Our crystal structure of RT:7 (TSAO-T) complex shows that 7 binds inside the NNRTI-binding pocket, assuming a "dragon" shape, and interacts extensively with almost all the pocket residues. The structure also explains the structure-activity relationships and resistance data for TSAO compounds. The binding of 7 causes hyper-expansion of the pocket and significant rearrangement of RT subdomains. This nonoptimal complex formation is apparently responsible (1) for the lower stability of a RT (p66/p51) dimer and (2) for the lower potency of 7 despite of its extensive interactions with RT. However, the HIV-1 RT:7 structure reveals novel design features such as (1) interactions with the conserved Tyr183 from the YMDD-motif and (2) a possible way for an NNRTI to reach the polymerase active site that may be exploited in designing new NNRTIs.
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Affiliation(s)
- Kalyan Das
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Joseph D. Bauman
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Angela S. Rim
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Chhaya Dharia
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Arthur D. Clark
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - María-José Camarasa
- Instituto de Química Médica (C.S.I.C.). Juan de la Cierva 3, 28006 Madrid, Spain
| | - Jan Balzarini
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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100
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Seckler JM, Barkley MD, Wintrode PL. Allosteric suppression of HIV-1 reverse transcriptase structural dynamics upon inhibitor binding. Biophys J 2011; 100:144-53. [PMID: 21190666 DOI: 10.1016/j.bpj.2010.11.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Revised: 10/22/2010] [Accepted: 11/03/2010] [Indexed: 11/15/2022] Open
Abstract
Efavirenz is a second-generation nonnucleoside reverse transcriptase inhibitor (NNRTI) and a common component of clinically approved anti-AIDS regimens. NNRTIs are noncompetitive inhibitors that bind in a hydrophobic pocket in the p66 subunit of reverse transcriptase (RT) ∼10 Å from the polymerase active site. Hydrogen exchange mass spectrometry (HXMS) shows that efavirenz binding reduces molecular flexibility in multiple regions of RT heterodimer in addition to the NNRTI binding site. Of the 47 peptic fragments monitored by HXMS, 15 showed significantly altered H/D exchange rates in the presence of efavirenz. The slow cooperative unfolding of a β-sheet in the NNRTI binding pocket, which was previously observed in unliganded RT, is dramatically suppressed by efavirenz. HXMS also defines an extensive network of allosterically coupled sites, including four distinct regions of allosteric stabilization, and one region of allosteric destabilization. The effects of efavirenz binding extend > 60 Å from the NNRTI binding pocket. Allosteric changes to the structural dynamics propagate to the thumb and connection subdomains and RNase H domain of the p66 subunit as well as the thumb and palm subdomains of the p51 subunit. These allosteric regions may represent potential new drug targets.
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Affiliation(s)
- James M Seckler
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio, USA
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