Post-Catalytic Complexes with Emtricitabine or Stavudine and HIV-1 Reverse Transcriptase Reveal New Mechanistic Insights for Nucleotide Incorporation and Drug Resistance

Bertoletti, N; Chan, A.; Schinazi, R.; Anderson, K.

doi:10.3390/molecules25204868

Post-Catalytic Complexes with Emtricitabine or Stavudine and HIV-1 Reverse Transcriptase Reveal New Mechanistic Insights for Nucleotide Incorporation and Drug Resistance

Journal Article · 01 January 2022 · Molecules

DOI:https://doi.org/10.3390/molecules25204868· OSTI ID:1760499

Bertoletti, N; Chan, A.; Schinazi, R.; Anderson, K.

Research Organization:: Brookhaven National Laboratory (BNL), Upton, NY (United States)

Sponsoring Organization:: ~OTHER

DOE Contract Number:: SC0012704

OSTI ID:: 1760499

Report Number(s):: BNL-220847-2021-JACI

Journal Information:: Molecules, Journal Name: Molecules Journal Issue: 20 Vol. 25; ISSN 1420-3049

Country of Publication:: United States

Language:: English

References (43)

Structural basis of HIV inhibition by translocation-defective RT inhibitor 4′-ethynyl-2-fluoro-2′-deoxyadenosine (EFdA) Salie, Zhe Li; Kirby, Karen A.; Michailidis, Eleftherios Proceedings of the National Academy of Sciences, Vol. 113, Issue 33 https://doi.org/10.1073/pnas.1605223113	journal	August 2016
Collaboration gets the most out of software Morin, Andrew; Eisenbraun, Ben; Key, Jason eLife, Vol. 2 https://doi.org/10.7554/eLife.01456	journal	September 2013
Probing the Molecular Mechanisms of AZT Drug Resistance Mediated by HIV-1 Reverse Transcriptase Using a Transient Kinetic Analysis ^† Ray, Adrian S.; Murakami, Eisuke; Basavapathruni, Aravind Biochemistry, Vol. 42, Issue 29 https://doi.org/10.1021/bi034435l	journal	July 2003
Mechanism of inhibition of HIV-1 reverse transcriptase by nonnucleoside inhibitors Spence, R.; Kati, W.; Anderson, K. Science, Vol. 267, Issue 5200 https://doi.org/10.1126/science.7532321	journal	February 1995
Structural basis of HIV-1 resistance to AZT by excision Tu, Xiongying; Das, Kalyan; Han, Qianwei Nature Structural & Molecular Biology, Vol. 17, Issue 10 https://doi.org/10.1038/nsmb.1908	journal	September 2010
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
Mechanistic Studies Comparing the Incorporation of (+) and (−) Isomers of 3TCTP by HIV-1 Reverse Transcriptase ^† Feng, Joy Y.; Anderson, Karen S. Biochemistry, Vol. 38, Issue 1 https://doi.org/10.1021/bi982340r	journal	January 1999
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Crystal Structures of Clinically Relevant Lys103Asn/Tyr181Cys Double Mutant HIV-1 Reverse Transcriptase in Complexes with ATP and Non-nucleoside Inhibitor HBY 097 Das, Kalyan; Sarafianos, Stefan G.; Clark, Arthur D. Journal of Molecular Biology, Vol. 365, Issue 1 https://doi.org/10.1016/j.jmb.2006.08.097	journal	January 2007
Advances in understanding the initiation of HIV-1 reverse transcription Krupkin, Miri; Jackson, Lynnette Nthenya; Ha, Betty Current Opinion in Structural Biology, Vol. 65 https://doi.org/10.1016/j.sbi.2020.07.005	journal	December 2020
Relationship between Antiviral Activity and Host Toxicity: Comparison of the Incorporation Efficiencies of 2',3'-Dideoxy-5-Fluoro-3'-Thiacytidine-Triphosphate Analogs by Human Immunodeficiency Virus Type 1 Reverse Transcriptase and Human Mitochondrial DNA Polymerase Feng, J. Y.; Murakami, E.; Zorca, S. M. Antimicrobial Agents and Chemotherapy, Vol. 48, Issue 4 https://doi.org/10.1128/AAC.48.4.1300-1306.2004	journal	March 2004
Elucidating molecular interactions of L-nucleotides with HIV-1 reverse transcriptase and mechanism of M184V-caused drug resistance Hung, Magdeleine; Tokarsky, E. John; Lagpacan, Leanna Communications Biology, Vol. 2, Issue 1 https://doi.org/10.1038/s42003-019-0706-x	journal	December 2019
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
Structure of HIV-1 reverse transcriptase/d4TTP complex: Novel DNA cross-linking site and pH-dependent conformational changes: RT/d4TTP structure with novel DNA cross-link Martinez, Sergio E.; Bauman, Joseph D.; Das, Kalyan Protein Science, Vol. 28, Issue 3 https://doi.org/10.1002/pro.3559	journal	December 2018
The CCP4 suite programs for protein crystallography No authors listed Acta Crystallographica Section D Biological Crystallography, Vol. 50, Issue 5, p. 760-763 https://doi.org/10.1107/S0907444994003112	journal	September 1994
Structure of a Covalently Trapped Catalytic Complex of HIV-1 Reverse Transcriptase: Implications for Drug Resistance Huang, H. Science, Vol. 282, Issue 5394 https://doi.org/10.1126/science.282.5394.1669	journal	November 1998
Mechanism of Inhibition of the Human Immunodeficiency Virus Type 1 Reverse Transcriptase by d4TTP: an Equivalent Incorporation Efficiency Relative to the Natural Substrate dTTP Vaccaro, J. A.; Parnell, K. M.; Terezakis, S. A. Antimicrobial Agents and Chemotherapy, Vol. 44, Issue 1 https://doi.org/10.1128/AAC.44.1.217-221.2000	journal	January 2000
Solvent content of protein crystals Matthews, B. W. Journal of Molecular Biology, Vol. 33, Issue 2 https://doi.org/10.1016/0022-2836(68)90205-2	journal	April 1968
Evolving understanding of HIV-1 reverse transcriptase structure, function, inhibition, and resistance Xavier RUIZ, Francesc; Arnold, Eddy Current Opinion in Structural Biology, Vol. 61 https://doi.org/10.1016/j.sbi.2019.11.011	journal	April 2020
4′-Ethynyl-2-fluoro-2′-deoxyadenosine, MK-8591: a novel HIV-1 reverse transcriptase translocation inhibitor Markowitz, Martin; Sarafianos, Stefan G. Current Opinion in HIV and AIDS, Vol. 13, Issue 4 https://doi.org/10.1097/COH.0000000000000467	journal	January 2018
Mechanism and fidelity of HIV reverse transcriptase. Kati, W. M.; Johnson, K. A.; Jerva, L. F. Journal of Biological Chemistry, Vol. 267, Issue 36 https://doi.org/10.1016/S0021-9258(18)35706-5	journal	December 1992
Long term adverse effects related to nucleoside reverse transcriptase inhibitors: Clinical impact of mitochondrial toxicity Maagaard, Anne; Kvale, Dag Scandinavian Journal of Infectious Diseases, Vol. 41, Issue 11-12 https://doi.org/10.3109/00365540903186181	journal	January 2009
Structural insights into the recognition of nucleoside reverse transcriptase inhibitors by HIV‐1 reverse transcriptase: First crystal structures with reverse transcriptase and the active triphosphate forms of lamivudine and emtricitabine Bertoletti, Nicole; Chan, Albert H.; Schinazi, Raymond F. Protein Science https://doi.org/10.1002/pro.3681	journal	August 2019
Nucleotide Reverse Transcriptase Inhibitors: A Thorough Review, Present Status and Future Perspective as HIV Therapeutics Holec, Ashley D.; Mandal, Subhra; Prathipati, Pavan Kumar Current HIV Research, Vol. 15, Issue 6 https://doi.org/10.2174/1570162X15666171120110145	journal	January 2018
TLSMD web server for the generation of multi-group TLS models Painter, Jay; Merritt, Ethan A. Journal of Applied Crystallography, Vol. 39, Issue 1 https://doi.org/10.1107/S0021889805038987	journal	January 2006
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
Nonnucleoside Inhibitor Binding Affects the Interactions of the Fingers Subdomain of Human Immunodeficiency Virus Type 1 Reverse Transcriptase with DNA Peletskaya, E. N.; Kogon, A. A.; Tuske, S. Journal of Virology, Vol. 78, Issue 7 https://doi.org/10.1128/JVI.78.7.3387-3397.2004	journal	March 2004
Trapping HIV-1 Reverse Transcriptase Before and After Translocation on DNA Sarafianos, Stefan G.; Clark, Arthur D.; Tuske, Steve Journal of Biological Chemistry, Vol. 278, Issue 18 https://doi.org/10.1074/jbc.M212911200	journal	January 2003
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
Matthews coefficient probabilities: Improved estimates for unit cell contents of proteins, DNA, and protein-nucleic acid complex crystals Kantardjieff, Katherine A.; Rupp, Bernhard Protein Science, Vol. 12, Issue 9 https://doi.org/10.1110/ps.0350503	journal	September 2003
Optimal description of a protein structure in terms of multiple groups undergoing TLS motion Painter, Jay; Merritt, Ethan A. Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 4 https://doi.org/10.1107/S0907444906005270	journal	March 2006
Structures of HIV-1 reverse transcriptase with pre- and post-translocation AZTMP-terminated DNA Sarafianos, S. G. The EMBO Journal, Vol. 21, Issue 23 https://doi.org/10.1093/emboj/cdf637	journal	December 2002
HIV-1 reverse transcriptase and antiviral drug resistance. Part 2 Das, Kalyan; Arnold, Eddy Current Opinion in Virology, Vol. 3, Issue 2 https://doi.org/10.1016/j.coviro.2013.03.014	journal	April 2013
A mechanism for all polymerases Steitz, Thomas A. Nature, Vol. 391, Issue 6664 https://doi.org/10.1038/34542	journal	January 1998
Mechanistic studies show that (-)-FTC-TP is a better inhibitor of HIV-1 reverse transcriptase than 3TC-TP Feng, Joy Y.; Shi, Junxing; Schinazi, Raymond F. The FASEB Journal, Vol. 13, Issue 12 https://doi.org/10.1096/fasebj.13.12.1511	journal	September 1999
Targets for Inhibition of HIV Replication: Entry, Enzyme Action, Release and Maturation Sierra, Saleta; Walter, Hauke Intervirology, Vol. 55, Issue 2 https://doi.org/10.1159/000331995	journal	January 2012
The HIV therapy market Gubernick, Steven I.; Félix, Nuno; Lee, Dolim Nature Reviews Drug Discovery, Vol. 15, Issue 7 https://doi.org/10.1038/nrd.2016.69	journal	June 2016
electronic Ligand Builder and Optimization Workbench ( eLBOW ): a tool for ligand coordinate and restraint generation Moriarty, Nigel W.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Acta Crystallographica Section D Biological Crystallography, Vol. 65, Issue 10 https://doi.org/10.1107/S0907444909029436	journal	September 2009
HIV-1 reverse transcriptase and antiviral drug resistance. Part 1 Das, Kalyan; Arnold, Eddy Current Opinion in Virology, Vol. 3, Issue 2 https://doi.org/10.1016/j.coviro.2013.03.012	journal	April 2013
The Role of Nucleotide Excision by Reverse Transcriptase in HIV Drug Resistance Acosta-Hoyos, Antonio J.; Scott, Walter A. Viruses, Vol. 2, Issue 2 https://doi.org/10.3390/v2020372	journal	January 2010
Structural features in common of HBV and HIV-1 resistance against chirally-distinct nucleoside analogues entecavir and lamivudine Yasutake, Yoshiaki; Hattori, Shin-ichiro; Tamura, Noriko Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-59775-w	journal	February 2020
Architecture of an HIV-1 reverse transcriptase initiation complex Larsen, Kevin P.; Mathiharan, Yamuna Kalyani; Kappel, Kalli Nature, Vol. 557, Issue 7703 https://doi.org/10.1038/s41586-018-0055-9	journal	April 2018
Interactions of enantiomers of 2′,3′-didehydro-2′,3′-dideoxy-fluorocytidine with wild type and M184V mutant HIV-1 reverse transcriptase Ray, A.; Murakami, E.; Peterson, C. Antiviral Research, Vol. 56, Issue 3 https://doi.org/10.1016/S0166-3542(02)00102-X	journal	December 2002

Similar Records

Post-Catalytic Complexes with Emtricitabine or Stavudine and HIV-1 Reverse Transcriptase Reveal New Mechanistic Insights for Nucleotide Incorporation and Drug Resistance

Journal Article · 2020 · Molecules · OSTI ID:1691541

Structural Insights into HIV Reverse Transcriptase Mutations Q151M and Q151M Complex That Confer Multinucleoside Drug Resistance

Journal Article · 2017 · Antimicrobial Agents and Chemotherapy · OSTI ID:1409612

Structural insights into the recognition of nucleoside reverse transcriptase inhibitors by HIV‐1 reverse transcriptase: First crystal structures with reverse transcriptase and the active triphosphate forms of lamivudine and emtricitabine

Journal Article · 2019 · Protein Science · OSTI ID:1547084

Related Subjects

99 GENERAL AND MISCELLANEOUS

Post-Catalytic Complexes with Emtricitabine or Stavudine and HIV-1 Reverse Transcriptase Reveal New Mechanistic Insights for Nucleotide Incorporation and Drug Resistance

Citation Formats

References (43)

Similar Records

Related Subjects