4ll3 › Citations

Thermodynamic and structural analysis of HIV protease resistance to darunavir - analysis of heavily mutated patient-derived HIV-1 proteases.

Kožíšek M, Lepšík M, Grantz Šašková K, Brynda J, Konvalinka J, Rezáčová P
FEBS J 281 1834-47 (2014)
Cited: 37 times
EuropePMC logo PMID: 24785545

Abstract

We report enzymologic, thermodynamic and structural analyses of a series of six clinically derived mutant HIV proteases (PR) resistant to darunavir. As many as 20 mutations in the resistant PRs decreased the binding affinity of darunavir by up to 13 000-fold, mostly because of a less favorable enthalpy of binding that was only partially compensated by the entropic contribution. X-ray structure analysis suggested that the drop in enthalpy of darunavir binding to resistant PR species was mostly the result of a decrease in the number of hydrogen bonds and a loosening of the fit between the inhibitor and the mutated enzymes. The favorable entropic contribution to darunavir binding to mutated PR variants correlated with a larger burial of the nonpolar solvent-accessible surface area upon inhibitor binding. We show that even very dramatic changes in the PR sequence leading to the loss of hydrogen bonds with the inhibitor could be partially compensated by the entropy contribution as a result of the burial of the larger nonpolar surface area of the mutated HIV PRs.

Reviews - 4ll3 mentioned but not cited (3)

  1. Viral proteases as therapeutic targets. Majerová T, Konvalinka J. Mol Aspects Med 88 101159 (2022)
  2. Regulation of Retroviral and SARS-CoV-2 Protease Dimerization and Activity through Reversible Oxidation. Davis DA, Bulut H, Shrestha P, Mitsuya H, Yarchoan R. Antioxidants (Basel) 11 2054 (2022)
  3. Comprehending the Structure, Dynamics, and Mechanism of Action of Drug-Resistant HIV Protease. Dakshinamoorthy A, Asmita A, Senapati S. ACS Omega 8 9748-9763 (2023)

Articles - 4ll3 mentioned but not cited (17)

  1. Anti-HIV drug repurposing against SARS-CoV-2. Sang P, Tian SH, Meng ZH, Yang LQ. RSC Adv 10 15775-15783 (2020)
  2. Class A G Protein-Coupled Receptor Antagonist Famotidine as a Therapeutic Alternative Against SARS-CoV2: An In Silico Analysis. Ortega JT, Serrano ML, Jastrzebska B. Biomolecules 10 E954 (2020)
  3. Webina: an open-source library and web app that runs AutoDock Vina entirely in the web browser. Kochnev Y, Hellemann E, Cassidy KC, Durrant JD. Bioinformatics 36 4513-4515 (2020)
  4. Thermodynamic and structural analysis of HIV protease resistance to darunavir - analysis of heavily mutated patient-derived HIV-1 proteases. Kožíšek M, Lepšík M, Grantz Šašková K, Brynda J, Konvalinka J, Rezáčová P. FEBS J 281 1834-1847 (2014)
  5. LigBuilder V3: A Multi-Target de novo Drug Design Approach. Yuan Y, Pei J, Lai L. Front Chem 8 142 (2020)
  6. Predominance of positive epistasis among drug resistance-associated mutations in HIV-1 protease. Zhang TH, Dai L, Barton JP, Du Y, Tan Y, Pang W, Chakraborty AK, Lloyd-Smith JO, Sun R. PLoS Genet 16 e1009009 (2020)
  7. Structural analyses of 2015-updated drug-resistant mutations in HIV-1 protease: an implication of protease inhibitor cross-resistance. Su CT, Ling WL, Lua WH, Haw YX, Gan SK. BMC Bioinformatics 17 500 (2016)
  8. Dimer Interface Organization is a Main Determinant of Intermonomeric Interactions and Correlates with Evolutionary Relationships of Retroviral and Retroviral-Like Ddi1 and Ddi2 Proteases. Mótyán JA, Miczi M, Tőzsér J. Int J Mol Sci 21 E1352 (2020)
  9. research-article Structural Similarity of SARS-CoV2 Mpro and HCV NS3/4A Proteases Suggests New Approaches for Identifying Existing Drugs Useful as COVID-19 Therapeutics. Bafna K, Krug RM, Montelione GT. ChemRxiv (2020)
  10. Exploring the Reasons for Decrease in Binding Affinity of HIV-2 Against HIV-1 Protease Complex Using Interaction Entropy Under Polarized Force Field. Cong Y, Li Y, Jin K, Zhong S, Zhang JZH, Li H, Duan L. Front Chem 6 380 (2018)
  11. The L33F darunavir resistance mutation acts as a molecular anchor reducing the flexibility of the HIV-1 protease 30s and 80s loops. Kuiper BD, Keusch BJ, Dewdney TG, Chordia P, Ross K, Brunzelle JS, Kovari IA, MacArthur R, Salimnia H, Kovari LC. Biochem Biophys Rep 2 160-165 (2015)
  12. FPocketWeb: protein pocket hunting in a web browser. Kochnev Y, Durrant JD. J Cheminform 14 58 (2022)
  13. Limits to detecting epistasis in the fitness landscape of HIV. Biswas A, Haldane A, Levy RM. PLoS One 17 e0262314 (2022)
  14. Quantum-Chemical Quasi-Docking for Molecular Dynamics Calculations. Sulimov A, Kutov D, Ilin I, Sulimov V. Nanomaterials (Basel) 12 274 (2022)
  15. Towards designing of a potential new HIV-1 protease inhibitor using QSAR study in combination with Molecular docking and Molecular dynamics simulations. Baassi M, Moussaoui M, Soufi H, Rajkhowa S, Sharma A, Sinha S, Belaaouad S. PLoS One 18 e0284539 (2023)
  16. Computer-Aided Prediction of the Interactions of Viral Proteases with Antiviral Drugs: Antiviral Potential of Broad-Spectrum Drugs. Ren P, Li S, Wang S, Zhang X, Bai F. Molecules 29 225 (2023)
  17. FMO-guided design of darunavir analogs as HIV-1 protease inhibitors. Chuntakaruk H, Hengphasatporn K, Shigeta Y, Aonbangkhen C, Lee VS, Khotavivattana T, Rungrotmongkol T, Hannongbua S. Sci Rep 14 3639 (2024)


Reviews citing this publication (4)

  1. Retroviral proteases and their roles in virion maturation. Konvalinka J, Kräusslich HG, Müller B. Virology 479-480 403-417 (2015)
  2. Highly resistant HIV-1 proteases and strategies for their inhibition. Weber IT, Kneller DW, Wong-Sam A. Future Med Chem 7 1023-1038 (2015)
  3. HIV Protease: Historical Perspective and Current Research. Weber IT, Wang YF, Harrison RW. Viruses 13 839 (2021)
  4. Decoding HIV resistance: from genotype to therapy. Weber IT, Harrison RW. Future Med Chem 9 1529-1538 (2017)

Articles citing this publication (13)

  1. Elucidating the Interdependence of Drug Resistance from Combinations of Mutations. Ragland DA, Whitfield TW, Lee SK, Swanstrom R, Zeldovich KB, Kurt-Yilmaz N, Schiffer CA. J Chem Theory Comput 13 5671-5682 (2017)
  2. Structural Adaptation of Darunavir Analogues against Primary Mutations in HIV-1 Protease. Lockbaum GJ, Leidner F, Rusere LN, Henes M, Kosovrasti K, Nachum GS, Nalivaika EA, Ali A, Yilmaz NK, Schiffer CA. ACS Infect Dis 5 316-325 (2019)
  3. Effects of Hinge-region Natural Polymorphisms on Human Immunodeficiency Virus-Type 1 Protease Structure, Dynamics, and Drug Pressure Evolution. Liu Z, Huang X, Hu L, Pham L, Poole KM, Tang Y, Mahon BP, Tang W, Li K, Goldfarb NE, Dunn BM, McKenna R, Fanucci GE. J Biol Chem 291 22741-22756 (2016)
  4. Estimation of the Binding Free Energy of AC1NX476 to HIV-1 Protease Wild Type and Mutations Using Free Energy Perturbation Method. Ngo ST, Mai BK, Hiep DM, Li MS. Chem Biol Drug Des 86 546-558 (2015)
  5. Darunavir-Resistant HIV-1 Protease Constructs Uphold a Conformational Selection Hypothesis for Drug Resistance. Liu Z, Tran TT, Pham L, Hu L, Bentz K, Savin DA, Fanucci GE. Viruses 12 E1275 (2020)
  6. Off-Target-Based Design of Selective HIV-1 PROTEASE Inhibitors. La Monica G, Lauria A, Bono A, Martorana A. Int J Mol Sci 22 6070 (2021)
  7. Structural and binding insights into HIV-1 protease and P2-ligand interactions through molecular dynamics simulations, binding free energy and principal component analysis. Karnati KR, Wang Y. J Mol Graph Model 92 112-122 (2019)
  8. Kinetic, thermodynamic and structural analysis of tamiphosphor binding to neuraminidase of H1N1 (2009) pandemic influenza. Albiñana CB, Machara A, Řezáčová P, Pachl P, Konvalinka J, Kožíšek M. Eur J Med Chem 121 100-109 (2016)
  9. Diversity-Oriented Synthesis of Diol-Based Peptidomimetics as Potential HIV Protease Inhibitors and Antitumor Agents. Vadhadiya PM, Jean MA, Bouzriba C, Tremblay T, Lagüe P, Fortin S, Boukouvalas J, Giguère D. Chembiochem (2018)
  10. HIV-1 protease with 10 lopinavir and darunavir resistance mutations exhibits altered inhibition, structural rearrangements and extreme dynamics. Wong-Sam A, Wang YF, Kneller DW, Kovalevsky AY, Ghosh AK, Harrison RW, Weber IT. J Mol Graph Model 117 108315 (2022)
  11. Metabolome profiling and molecular docking analysis revealed the metabolic differences and potential pharmacological mechanisms of the inflorescence and succulent stem of Cistanche deserticola. Sun X, Zheng Y, Tian L, Miao Y, Zeng T, Jiang Y, Pei J, Ahmad B, Huang L. RSC Adv 11 27226-27245 (2021)
  12. Structural determinants for subnanomolar inhibition of the secreted aspartic protease Sapp1p from Candida parapsilosis. Dostál J, Brynda J, Vaňková L, Zia SR, Pichová I, Heidingsfeld O, Lepšík M. J Enzyme Inhib Med Chem 36 914-921 (2021)
  13. The structural, dynamic, and thermodynamic basis of darunavir resistance of a heavily mutated HIV-1 protease using molecular dynamics simulation. Shabanpour Y, Sajjadi S, Behmard E, Abdolmaleki P, Keihan AH. Front Mol Biosci 9 927373 (2022)


Quick links