ArticleScientific reports2020
Inhibition of the activity of HIV-1 protease through antibody binding and mutations probed by molecular dynamics simulations.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 31 citations in OpenAlex.
- Ligand Versatility and Resistance Mechanism of Monotherapy-Grade HIV-1 Protease Inhibitor GRL-142 Binding the Multidrug Resistant Variant p51: Insights from 1 μs MD Simulations.Journal of chemical information and modeling · 2026Article
- Highly Potent Phosphinic HIV‑1 Protease Inhibitors: Synthesis, In Vitro Evaluation, and Docking Studies.ACS omega · 2025Article
- Integrative Computational Approaches for Understanding Drug Resistance in HIV-1 Protease Subtype C.Viruses · 2025Review
- Structural and Functional Studies on HIV Protease: Mechanism of Action, Subtypes, Inhibitors, and Drug Resistance.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Integrating Explicit and Implicit Fullerene Models into UNRES Force Field for Protein Interaction Studies.Molecules (Basel, Switzerland) · 2024Article
- Structural and quantum chemical basis for OCP-mediated quenching of phycobilisomes.Science advances · 2024Article
- FMO-guided design of darunavir analogs as HIV-1 protease inhibitors.Scientific reports · 2024Article
- Mechanism of drug resistance in HIV-1 protease subtype C in the presence of Atazanavir.Current research in structural biology · 2024Article
- The structural, dynamic, and thermodynamic basis of darunavir resistance of a heavily mutated HIV-1 protease using molecular dynamics simulation.Frontiers in molecular biosciences · 2022Article
- Sampling of Protein Conformational Space Using Hybrid Simulations: A Critical Assessment of Recent Methods.Frontiers in molecular biosciences · 2022Article
- In silico molecular docking analysis for repurposing approved antiviral drugs against SARS-CoV-2 main protease.Biochemistry and biophysics reports · 2021Article
- Article
- Progress in the Research and Development of Anti-COVID-19 Drugs.Frontiers in public health · 2020Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
HIV-1 protease is an essential enzyme in the life cycle of the HIV-1 virus. The conformational dynamics of the flap region of the protease is critical for the ligand binding mechanism, as well as for the catalytic activity. The monoclonal antibody F11.2.32 raised against HIV-1 protease inhibits its activity on binding. We have studied the conformational dynamics of protease in its free, inhibitor ritonavir and antibody bound forms using molecular dynamics simulations. We find that upon Ab binding to the epitope region (residues 36-46) of protease, the overall flexibility of the protease is decreased including the flap region and the active site, which is similar to the decrease in flexibility observed by inhibitor binding to the protease. This suggests an allosteric mechanism to inhibit protease activity. Further, the protease mutants G40E and G40R are known to have decreased activity and were also subjected to MD simulations. We find that the loss of flexibility in the mutants is similar to that observed in the protease bound to the Ab/inhibitor. These insights highlight the role played by dynamics in the function of the protease and how control of flexibility through Ab binding and site specific mutations can inhibit protease activity.
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