ArticleScientific reports2014
Revealing origin of decrease in potency of darunavir and amprenavir against HIV-2 relative to HIV-1 protease by molecular dynamics simulations.
Article in Scientific reports, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 75 citations in OpenAlex.
- Phenotypic impacts of treatment-selected mutations in HIV-2 protease on darunavir and lopinavir susceptibility: Evaluating genotypic HIV-2 drug resistance tools.PLOS global public health · 2026Article
- Exploration of questionable backbone conformations in crystallographic structure models using a structural alphabet.Acta crystallographica. Section D, Structural biology · 2025Article
- Theoretical Study of the Influence of K20N Glycosylation on the Dynamic Behavior of Im7 Protein.Molecules (Basel, Switzerland) · 2025Article
- Computational screening combined with well-tempered metadynamics simulations identifies potential TMPRSS2 inhibitors.Scientific reports · 2024Article
- Role of CSF1R 550th-tryptophan in kusunokinin and CSF1R inhibitor binding and ligand-induced structural effect.Scientific reports · 2024Article
- FMO-guided design of darunavir analogs as HIV-1 protease inhibitors.Scientific reports · 2024Article
- Acquired HIV-1 Protease Conformational Flexibility Associated with Lopinavir Failure May Shape the Outcome of Darunavir Therapy after Antiretroviral Therapy Switch.Biomolecules · 2021Article
- Structural Impacts of Drug-Resistance Mutations Appearing in HIV-2 Protease.Molecules (Basel, Switzerland) · 2021Article
- Insights into the biased activity of dextromethorphan and haloperidol towards SARS-CoV-2 NSP6: in silico binding mechanistic analysis.Journal of molecular medicine (Berlin, Germany) · 2020Article
- Impacts of drug resistance mutations on the structural asymmetry of the HIV-2 protease.BMC molecular and cell biology · 2020Article
- Effective estimation of the inhibitor affinity of HIV-1 proteaseRSC advances · 2020Article
- Interactive molecular dynamics in virtual reality for accurate flexible protein-ligand docking.PloS one · 2020Article
- Combating the Coronavirus Pandemic: Early Detection, Medical Treatment, and a Concerted Effort by the Global Community.Research (Washington, D.C.) · 2020Review
- Structural and binding insights into HIV-1 protease and P2-ligand interactions through molecular dynamics simulations, binding free energy and principal component analysis.Journal of molecular graphics & modelling · 2019Article
- Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations.Nucleic acids research · 2019Article
- Exploration of the effect of sequence variations located inside the binding pocket of HIV-1 and HIV-2 proteases.Scientific reports · 2018Article
- Analysis of the HIV-2 protease's adaptation to various ligands: characterization of backbone asymmetry using a structural alphabet.Scientific reports · 2018Article
- Exploring the Reasons for Decrease in Binding Affinity of HIV-2 Against HIV-1 Protease Complex Using Interaction Entropy Under Polarized Force Field.Frontiers in chemistry · 2018Article
- Application of conventional molecular dynamics simulation in evaluating the stability of apomyoglobin in urea solution.Scientific reports · 2017Article
- In silico approach to explore the disruption in the molecular mechanism of human hyaluronidase 1 by mutant E268K that directs Natowicz syndrome.European biophysics journal : EBJ · 2017Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Clinical inhibitors Darunavir (DRV) and Amprenavir (APV) are less effective on HIV-2 protease (PR2) than on HIV-1 protease (PR1). To identify molecular basis associated with the lower inhibition, molecular dynamics (MD) simulations and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) calculations were performed to investigate the effectiveness of the PR1 inhibitors DRV and APV against PR1/PR2. The rank of predicted binding free energies agrees with the experimental determined one. Moreover, our results show that two inhibitors bind less strongly to PR2 than to PR1, again in agreement with the experimental findings. The decrease in binding free energies for PR2 relative to PR1 is found to arise from the reduction of the van der Waals interactions induced by the structural adjustment of the triple mutant V32I, I47V and V82I. This result is further supported by the difference between the van der Waals interactions of inhibitors with each residue in PR2 and in PR1. The results from the principle component analysis suggest that inhibitor binding tends to make the flaps of PR2 close and the one of PR1 open. We expect that this study can theoretically provide significant guidance and dynamics information for the design of potent dual inhibitors targeting PR1/PR2.
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