HIV-1 protease with 10 lopinavir and darunavir resistance mutations exhibits altered inhibition, str

Wong-Sam, Andres; Wang, Yuan-Fang; Kneller, Daniel W.; Kovalevsky, Andrey Y.; Ghosh, Arun K.; Harrison, Robert W.; Weber, Irene T.

doi:10.1016/j.jmgm.2022.108315

HIV-1 protease with 10 lopinavir and darunavir resistance mutations exhibits altered inhibition, str

Journal Article · 01 December 2022 · J. Mol. Graph. Model.

DOI:https://doi.org/10.1016/j.jmgm.2022.108315· OSTI ID:1901175

Wong-Sam, Andres; Wang, Yuan-Fang; Kneller, Daniel W.; Kovalevsky, Andrey Y.; Ghosh, Arun K.; Harrison, Robert W.; Weber, Irene T.

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: DOE - Office Of Science; National Institutes of Health (NIH)

OSTI ID:: 1901175

Journal Information:: J. Mol. Graph. Model., Vol. 117

Country of Publication:: United States

Language:: ENGLISH

References (72)

Cabotegravir for HIV Prevention in Cisgender Men and Transgender Women Landovitz, Raphael J.; Donnell, Deborah; Clement, Meredith E. New England Journal of Medicine, Vol. 385, Issue 7 https://doi.org/10.1056/NEJMoa2101016	journal	August 2021
Current and Novel Inhibitors of HIV Protease Pokorná, Jana; Machala, Ladislav; Řezáčová, Pavlína Viruses, Vol. 1, Issue 3 https://doi.org/10.3390/v1031209	journal	December 2009
Molecular basis of human immunodeficiency virus type 1 drug resistance: Overview and recent developments Menéndez-Arias, Luis Antiviral Research, Vol. 98, Issue 1 https://doi.org/10.1016/j.antiviral.2013.01.007	journal	April 2013
Retroviral proteases and their roles in virion maturation Konvalinka, Jan; Kräusslich, Hans-Georg; Müller, Barbara Virology, Vol. 479-480 https://doi.org/10.1016/j.virol.2015.03.021	journal	May 2015
Improving Viral Protease Inhibitors to Counter Drug Resistance Kurt Yilmaz, Nese; Swanstrom, Ronald; Schiffer, Celia A. Trends in Microbiology, Vol. 24, Issue 7 https://doi.org/10.1016/j.tim.2016.03.010	journal	July 2016
Conformational flexibility in the flap domains of ligand-free HIV protease Heaslet, Holly; Rosenfeld, Robin; Giffin, Mike Acta Crystallographica Section D Biological Crystallography, Vol. 63, Issue 8 https://doi.org/10.1107/S0907444907029125	journal	July 2007
Drug Resistance Conferred by Mutations Outside the Active Site through Alterations in the Dynamic and Structural Ensemble of HIV-1 Protease Ragland, Debra A.; Nalivaika, Ellen A.; Nalam, Madhavi N. L. Journal of the American Chemical Society, Vol. 136, Issue 34 https://doi.org/10.1021/ja504096m	journal	August 2014
HIV-1 protease inhibitors: effects on HIV-2 replication and resistance Menéndez-Arias, Luis; Tözsér, József Trends in Pharmacological Sciences, Vol. 29, Issue 1 https://doi.org/10.1016/j.tips.2007.10.013	journal	January 2008
Highly resistant HIV-1 proteases and strategies for their inhibition Weber, Irene T.; Kneller, Daniel W.; Wong-Sam, Andres Future Medicinal Chemistry, Vol. 7, Issue 8 https://doi.org/10.4155/fmc.15.44	journal	June 2015
HIV Protease: Historical Perspective and Current Research Weber, Irene T.; Wang, Yuan-Fang; Harrison, Robert W. Viruses, Vol. 13, Issue 5 https://doi.org/10.3390/v13050839	journal	May 2021
Thermodynamic and structural analysis of HIV protease resistance to darunavir - analysis of heavily mutated patient-derived HIV-1 proteases Kožíšek, Milan; Lepšík, Martin; Grantz Šašková, Klára FEBS Journal, Vol. 281, Issue 7 https://doi.org/10.1111/febs.12743	journal	February 2014
Picomolar to Micromolar: Elucidating the Role of Distal Mutations in HIV-1 Protease in Conferring Drug Resistance Henes, Mina; Lockbaum, Gordon J.; Kosovrasti, Klajdi ACS Chemical Biology, Vol. 14, Issue 11 https://doi.org/10.1021/acschembio.9b00370	journal	July 2019
HIV-1 Protease with 20 Mutations Exhibits Extreme Resistance to Clinical Inhibitors through Coordinated Structural Rearrangements Agniswamy, Johnson; Shen, Chen-Hsiang; Aniana, Annie Biochemistry, Vol. 51, Issue 13 https://doi.org/10.1021/bi2018317	journal	March 2012
The higher barrier of darunavir and tipranavir resistance for HIV-1 protease Wang, Yong; Liu, Zhigang; Brunzelle, Joseph S. Biochemical and Biophysical Research Communications, Vol. 412, Issue 4 https://doi.org/10.1016/j.bbrc.2011.08.045	journal	September 2011
Molecular Determinants of Epistasis in HIV-1 Protease: Elucidating the Interdependence of L89V and L90M Mutations in Resistance Henes, Mina; Kosovrasti, Klajdi; Lockbaum, Gordon J. Biochemistry, Vol. 58, Issue 35 https://doi.org/10.1021/acs.biochem.9b00446	journal	August 2019
Structural Studies of a Rationally Selected Multi-Drug Resistant HIV-1 Protease Reveal Synergistic Effect of Distal Mutations on Flap Dynamics Agniswamy, Johnson; Louis, John M.; Roche, Julien PLOS ONE, Vol. 11, Issue 12 https://doi.org/10.1371/journal.pone.0168616	journal	December 2016
Revertant mutation V48G alters conformational dynamics of highly drug resistant HIV protease PRS17 Burnaman, Shelley H.; Kneller, Daniel W.; Wang, Yuan-Fang Journal of Molecular Graphics and Modelling, Vol. 108 https://doi.org/10.1016/j.jmgm.2021.108005	journal	November 2021
Highly drug‐resistant HIV‐1 protease reveals decreased intra‐subunit interactions due to clusters of mutations Kneller, Daniel W.; Agniswamy, Johnson; Harrison, Robert W. The FEBS Journal, Vol. 287, Issue 15 https://doi.org/10.1111/febs.15207	journal	January 2020
Conformational variation of an extreme drug resistant mutant of HIV protease Shen, Chen-Hsiang; Chang, Yu-Chung; Agniswamy, Johnson Journal of Molecular Graphics and Modelling, Vol. 62 https://doi.org/10.1016/j.jmgm.2015.09.006	journal	November 2015
Evolution under Drug Pressure Remodels the Folding Free-Energy Landscape of Mature HIV-1 Protease Louis, John M.; Roche, Julien Journal of Molecular Biology, Vol. 428, Issue 13 https://doi.org/10.1016/j.jmb.2016.05.005	journal	July 2016
Human immunodeficiency virus reverse transcriptase and protease sequence database Rhee, S. -Y. Nucleic Acids Research, Vol. 31, Issue 1 https://doi.org/10.1093/nar/gkg100	journal	January 2003
Rationale and Uses of a Public HIV Drug‐Resistance Database Shafer, Robert W. The Journal of Infectious Diseases, Vol. 194, Issue s1 https://doi.org/10.1086/505356	journal	September 2006
HIV-1 Protease Mutations and Protease Inhibitor Cross-Resistance Rhee, Soo-Yon; Taylor, Jonathan; Fessel, W. Jeffrey Antimicrobial Agents and Chemotherapy, Vol. 54, Issue 10 https://doi.org/10.1128/AAC.00574-10	journal	October 2010
Influence of Flanking Sequences on the Dimer Stability of Human Immunodeficiency Virus Type 1 Protease ^† Wondrak, Ewald M.; Louis, John M. Biochemistry, Vol. 35, Issue 39 https://doi.org/10.1021/bi960984y	journal	January 1996
Structural and kinetic analysis of drug resistant mutants of HIV-1 protease Mahalingam, Bhuvaneshwari; Louis, John M.; Reed, Charles C. European Journal of Biochemistry, Vol. 263, Issue 1 https://doi.org/10.1046/j.1432-1327.1999.00514.x	journal	July 1999
Highly Drug-Resistant HIV-1 Protease Mutant PRS17 Shows Enhanced Binding to Substrate Analogues Agniswamy, Johnson; Kneller, Daniel W.; Brothers, Rowan ACS Omega, Vol. 4, Issue 5 https://doi.org/10.1021/acsomega.9b00683	journal	May 2019
Drug Resistance Mutation L76V Alters Nonpolar Interactions at the Flap–Core Interface of HIV-1 Protease Wong-Sam, Andres; Wang, Yuan-Fang; Zhang, Ying ACS Omega, Vol. 3, Issue 9 https://doi.org/10.1021/acsomega.8b01683	journal	September 2018
Structural studies of antiviral inhibitor with HIV-1 protease bearing drug resistant substitutions of V32I, I47V and V82I Pawar, Shrikant; Wang, Yuan-Fang; Wong-Sam, Andres Biochemical and Biophysical Research Communications, Vol. 514, Issue 3 https://doi.org/10.1016/j.bbrc.2019.05.064	journal	June 2019
Estimating KI values for tight binding inhibitors from dose-response plots Copeland, Robert A.; Lombardo, Diane; Giannaras, John Bioorganic & Medicinal Chemistry Letters, Vol. 5, Issue 17 https://doi.org/10.1016/0960-894X(95)00330-V	journal	September 1995
[20] Processing of X-ray diffraction data collected in oscillation mode Otwinowski, Zbyszek; Minor, Wladek Macromolecular Crystallography Part A, 307-326 https://doi.org/10.1016/S0076-6879(97)76066-X	book	January 1997
A graphical user interface to the CCP 4 program suite Potterton, Elizabeth; Briggs, Peter; Turkenburg, Maria Acta Crystallographica Section D Biological Crystallography, Vol. 59, Issue 7 https://doi.org/10.1107/S0907444903008126	journal	June 2003
Molecular replacement with MOLREP Vagin, Alexei; Teplyakov, Alexei Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1 https://doi.org/10.1107/S0907444909042589	journal	December 2009
Overview of the CCP 4 suite and current developments Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444910045749	journal	March 2011
Amprenavir complexes with HIV-1 protease and its drug-resistant mutants altering hydrophobic clusters: HIV protease mutants altering hydrophobic clusters Shen, Chen-Hsiang; Wang, Yuan-Fang; Kovalevsky, Andrey Y. FEBS Journal, Vol. 277, Issue 18 https://doi.org/10.1111/j.1742-4658.2010.07771.x	journal	August 2010
A short history of SHELX Sheldrick, George M. Acta Crystallographica Section A Foundations of Crystallography, Vol. 64, Issue 1, p. 112-122 https://doi.org/10.1107/S0108767307043930	journal	December 2007
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
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
Refinement of Macromolecular Structures by the Maximum-Likelihood Method Murshudov, G. N.; Vagin, A. A.; Dodson, E. J. Acta Crystallographica Section D Biological Crystallography, Vol. 53, Issue 3 https://doi.org/10.1107/S0907444996012255	journal	May 1997
Ultra-high Resolution Crystal Structure of HIV-1 Protease Mutant Reveals Two Binding Sites for Clinical Inhibitor TMC114 Kovalevsky, Andrey Y.; Liu, Fengling; Leshchenko, Sofiya Journal of Molecular Biology, Vol. 363, Issue 1 https://doi.org/10.1016/j.jmb.2006.08.007	journal	October 2006
GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers Abraham, Mark James; Murtola, Teemu; Schulz, Roland SoftwareX, Vol. 1-2 https://doi.org/10.1016/j.softx.2015.06.001	journal	September 2015
CHARMM36m: an improved force field for folded and intrinsically disordered proteins Huang, Jing; Rauscher, Sarah; Nawrocki, Grzegorz Nature Methods, Vol. 14, Issue 1 https://doi.org/10.1038/nmeth.4067	journal	November 2016
Comparison of simple potential functions for simulating liquid water Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D. The Journal of Chemical Physics, Vol. 79, Issue 2 https://doi.org/10.1063/1.445869	journal	July 1983
Canonical sampling through velocity rescaling Bussi, Giovanni; Donadio, Davide; Parrinello, Michele The Journal of Chemical Physics, Vol. 126, Issue 1 https://doi.org/10.1063/1.2408420	journal	January 2007
Molecular dynamics with coupling to an external bath Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F. The Journal of Chemical Physics, Vol. 81, Issue 8 https://doi.org/10.1063/1.448118	journal	October 1984
A molecular dynamics method for simulations in the canonical ensemble Nosé, Shūichi Molecular Physics, Vol. 52, Issue 2 https://doi.org/10.1080/00268978400101201	journal	June 1984
Canonical dynamics: Equilibrium phase-space distributions Hoover, William G. Physical Review A, Vol. 31, Issue 3 https://doi.org/10.1103/PhysRevA.31.1695	journal	March 1985
Polymorphic transitions in single crystals: A new molecular dynamics method Parrinello, M.; Rahman, A. Journal of Applied Physics, Vol. 52, Issue 12 https://doi.org/10.1063/1.328693	journal	December 1981
LINCS: A linear constraint solver for molecular simulations Hess, Berk; Bekker, Henk; Berendsen, Herman J. C. Journal of Computational Chemistry, Vol. 18, Issue 12 https://doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H	journal	September 1997
P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation Hess, Berk Journal of Chemical Theory and Computation, Vol. 4, Issue 1 https://doi.org/10.1021/ct700200b	journal	December 2007
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems Darden, Tom; York, Darrin; Pedersen, Lee The Journal of Chemical Physics, Vol. 98, Issue 12 https://doi.org/10.1063/1.464397	journal	June 1993
Potent antiviral HIV-1 protease inhibitor combats highly drug resistant mutant PR20 Kneller, Daniel W.; Agniswamy, Johnson; Ghosh, Arun K. Biochemical and Biophysical Research Communications, Vol. 519, Issue 1 https://doi.org/10.1016/j.bbrc.2019.08.126	journal	October 2019
The L76V Drug Resistance Mutation Decreases the Dimer Stability and Rate of Autoprocessing of HIV-1 Protease by Reducing Internal Hydrophobic Contacts Louis, John M.; Zhang, Ying; Sayer, Jane M. Biochemistry, Vol. 50, Issue 21 https://doi.org/10.1021/bi200033z	journal	May 2011
Unique Thermodynamic Response of Tipranavir to Human Immunodeficiency Virus Type 1 Protease Drug Resistance Mutations Muzammil, S.; Armstrong, A. A.; Kang, L. W. Journal of Virology, Vol. 81, Issue 10 https://doi.org/10.1128/JVI.02706-06	journal	May 2007
HIV/AIDS epidemiology Todd, Charles The Lancet, Vol. 356, Issue 9238 https://doi.org/10.1016/S0140-6736(05)74270-7	journal	October 2000
Probing Multidrug-Resistance and Protein-Ligand Interactions with Oxatricyclic Designed Ligands in HIV-1 Protease Inhibitors Ghosh, Arun K.; Xu, Chun-Xiao; Rao, Kalapala Venkateswara ChemMedChem, Vol. 5, Issue 11 https://doi.org/10.1002/cmdc.201000318	journal	September 2010
Novel P2 Tris-tetrahydrofuran Group in Antiviral Compound 1 (GRL-0519) Fills the S2 Binding Pocket of Selected Mutants of HIV-1 Protease Zhang, Hongmei; Wang, Yuan-Fang; Shen, Chen-Hsiang Journal of Medicinal Chemistry, Vol. 56, Issue 3 https://doi.org/10.1021/jm301519z	journal	January 2013
Extreme Multidrug Resistant HIV-1 Protease with 20 Mutations Is Resistant to Novel Protease Inhibitors with P1′-Pyrrolidinone or P2-Tris-tetrahydrofuran Agniswamy, Johnson; Shen, Chen-Hsiang; Wang, Yuan-Fang Journal of Medicinal Chemistry, Vol. 56, Issue 10 https://doi.org/10.1021/jm400231v	journal	May 2013
Contribution of the 80s loop of HIV-1 protease to the multidrug-resistance mechanism: crystallographic study of MDR769 HIV-1 protease variants Yedidi, Ravikiran S.; Proteasa, Georghe; Martinez, Jorge L. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 6 https://doi.org/10.1107/S0907444911011541	journal	May 2011
Mutations in HIV-1 gag and pol Compensate for the Loss of Viral Fitness Caused by a Highly Mutated Protease Kožíšek, Milan; Henke, Sandra; Šašková, Klára Grantz Antimicrobial Agents and Chemotherapy, Vol. 56, Issue 8 https://doi.org/10.1128/AAC.00465-12	journal	May 2012
Non-active site mutants of HIV-1 protease influence resistance and sensitisation towards protease inhibitors Bastys, Tomas; Gapsys, Vytautas; Walter, Hauke Retrovirology, Vol. 17, Issue 1 https://doi.org/10.1186/s12977-020-00520-6	journal	May 2020
Effects of Hinge-region Natural Polymorphisms on Human Immunodeficiency Virus-Type 1 Protease Structure, Dynamics, and Drug Pressure Evolution Liu, Zhanglong; Huang, Xi; Hu, Lingna Journal of Biological Chemistry, Vol. 291, Issue 43 https://doi.org/10.1074/jbc.M116.747568	journal	October 2016
The Role of Select Subtype Polymorphisms on HIV-1 Protease Conformational Sampling and Dynamics Huang, Xi; Britto, Manuel D.; Kear-Scott, Jamie L. Journal of Biological Chemistry, Vol. 289, Issue 24 https://doi.org/10.1074/jbc.M114.571836	journal	June 2014
Computational Characterization of Structural Role of the Non-active Site Mutation M36I of Human Immunodeficiency Virus Type 1 Protease Ode, Hirotaka; Matsuyama, Shou; Hata, Masayuki Journal of Molecular Biology, Vol. 370, Issue 3 https://doi.org/10.1016/j.jmb.2007.04.081	journal	July 2007
Insights into amprenavir resistance in E35D HIV-1 protease mutation from molecular dynamics and binding free-energy calculations Meiselbach, Heike; Horn, Anselm H. C.; Harrer, Thomas Journal of Molecular Modeling, Vol. 13, Issue 2 https://doi.org/10.1007/s00894-006-0121-3	journal	June 2006
Unique Flap Conformation in an HIV-1 Protease with High-Level Darunavir Resistance Nakashima, Masaaki; Ode, Hirotaka; Suzuki, Koji Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00061	journal	February 2016
Darunavir-Resistant HIV-1 Protease Constructs Uphold a Conformational Selection Hypothesis for Drug Resistance Liu, Zhanglong; Tran, Trang T.; Pham, Linh Viruses, Vol. 12, Issue 11 https://doi.org/10.3390/v12111275	journal	November 2020
Multi-drug resistance profile of PR20 HIV-1 protease is attributed to distorted conformational and drug binding landscape: molecular dynamics insights Chetty, Sarentha; Bhakat, Soumendranath; Martin, Alberto J. M. Journal of Biomolecular Structure and Dynamics, Vol. 34, Issue 1 https://doi.org/10.1080/07391102.2015.1018326	journal	February 2015
Binding kinetics and substrate selectivity in HIV-1 protease−Gag interactions probed at atomic resolution by chemical exchange NMR Deshmukh, Lalit; Tugarinov, Vitali; Louis, John M. Proceedings of the National Academy of Sciences, Vol. 114, Issue 46 https://doi.org/10.1073/pnas.1716098114	journal	October 2017
Acquired HIV-1 Protease Conformational Flexibility Associated with Lopinavir Failure May Shape the Outcome of Darunavir Therapy after Antiretroviral Therapy Switch Eche, Simeon; Kumar, Ajit; Sonela, Nelson Biomolecules, Vol. 11, Issue 4 https://doi.org/10.3390/biom11040489	journal	March 2021
Gag-protease coevolution shapes the outcome of lopinavir-inclusive treatment regimens in chronically infected HIV-1 subtype C patients Marie, V.; Gordon, M. Bioinformatics, Vol. 35, Issue 18 https://doi.org/10.1093/bioinformatics/btz076	journal	February 2019
Understanding the co-evolutionary molecular mechanisms of resistance in the HIV-1 Gag and protease Marie, Veronna; Gordon, Michelle Journal of Biomolecular Structure and Dynamics https://doi.org/10.1080/07391102.2021.1950569	journal	July 2021
Structural Analysis of Human Immunodeficiency Virus Type 1 CRF01_AE Protease in Complex with the Substrate p1-p6 Bandaranayake, Rajintha M.; Prabu-Jeyabalan, Moses; Kakizawa, Junko Journal of Virology, Vol. 82, Issue 13 https://doi.org/10.1128/JVI.00018-08	journal	July 2008

Similar Records

HIV-1 protease with 10 lopinavir and darunavir resistance mutations exhibits altered inhibition, structural rearrangements and extreme dynamics

Journal Article · 2022 · Journal of Molecular Graphics and Modelling · OSTI ID:1887609

Wong-Sam, Andres; Wang, Yuan-Fang; Kneller, Daniel W.; +4 more

HIV-1 protease with 10 lopinavir and darunavir resistance mutations exhibits altered inhibition, structural rearrangements and extreme dynamics

Journal Article · 2022 · Journal of Molecular Graphics and Modelling · OSTI ID:1887649

Wong-Sam, Andres; Wang, Yuan-Fang; Kneller, Daniel W.; +4 more

Effect of Flap Mutations on Structure of HIV-1 Protease and Inhibition by Sanquinavir and Darunavir

Journal Article · 2008 · J. Mol. Biol. · OSTI ID:1006792

Liu, F; Kovalevsky, A; Tie, Y; +3 more

HIV-1 protease with 10 lopinavir and darunavir resistance mutations exhibits altered inhibition, str

Citation Formats

References (72)

Similar Records

Related Subjects