ArticleJournal of molecular modeling2014
Investigation on the mechanism for the binding and drug resistance of wild type and mutations of G86 residue in HIV-1 protease complexed with Darunavir by molecular dynamic simulation and free energy calculation.
Article in Journal of molecular modeling, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed, 35 citations in OpenAlex.
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- Theoretical Study on Zearalenol Compounds Binding with Wild Type Zearalenone Hydrolase and V153H Mutant.International journal of molecular sciences · 2018Article
- Effect of polarization on HIV-1protease and fluoro-substituted inhibitors binding energies by large scale molecular dynamics simulations.Scientific reports · 2017Article
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- Insights into resistance mechanism of the macrolide biosensor protein MphR(A) binding to macrolide antibiotic erythromycin by molecular dynamics simulation.Journal of computer-aided molecular design · 2015Article
- Effects of drug-resistant mutations on the dynamic properties of HIV-1 protease and inhibition by Amprenavir and Darunavir.Scientific reports · 2015Article
- Investigate the binding of catechins to trypsin using docking and molecular dynamics simulation.PloS one · 2015Article
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Authors and funding
5 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Residue Gly86 is considered as the highly conversed residue in the HIV-1 protease. In our work, the detailed binding free energies for the wild-type (WT) and mutated proteases binding to the TMC-114 are estimated to investigate the protein-inhibitor binding and drug resistance mechanism by molecule dynamic simulations and molecular mechanics Poisson Boltzmann surface area (MM-PBSA) method. The binding affinities between the mutants and inhibitor are different than that in the wild-type complex and the major resistance to Darunavir (DRV) of G86A and G86S originate from the electrostatic energy and entropy, respectively. Furthermore, free energy decomposition analysis for the WT and mutated complexes on the basis of per-residue indicates that the mutagenesis influences the energy contribution of the residue located at three regions: active site region (residue 24-32), the flap region, and the region around the mutated residue G86 (residue 79-88), especially the flap region. Finally, further hydrogen bonds and structure analysis are carried out to detect the relationship between the energy and conformation. In all, the G86 mutations change the flap region's conformation. The experimental results are in good agreement with available results.
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