ArticleJournal of chemical information and modeling2009
Prediction of potency of protease inhibitors using free energy simulations with polarizable quantum mechanics-based ligand charges and a hybrid water model.
Article in Journal of chemical information and modeling, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 78 citations in OpenAlex.
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- Discovery of Histone Deacetylase Inhibitor Using Molecular Modeling and Free Energy Calculations.ACS omega · 2022Article
- Identification of Potent and Selective JAK1 Lead Compounds Through Ligand-Based Drug Design Approaches.Frontiers in pharmacology · 2022Article
- Exploring the Resistance Mechanisms of Distal D835V Mutation in FLT3 to Inhibitors.Oxidative medicine and cellular longevity · 2022Article
- Structure-Based Virtual Screening Reveals Ibrutinib and Zanubrutinib as Potential Repurposed Drugs against COVID-19.International journal of molecular sciences · 2021Article
- Evaluating Iso-Mukaadial Acetate and Ursolic Acid Acetate asBiomolecules · 2019Article
- Inhibition of Oncogenic Kinases: An In Vitro Validated Computational Approach Identified Potential Multi-Target Anticancer Compounds.Biomolecules · 2019Article
- A theoretical insight to understand the molecular mechanism of dual target ligand CTA-018 in the chronic kidney disease pathogenesis.PloS one · 2018Article
- Exploring the Carbamazepine Interaction with Human Pregnane X Receptor and Effect on ABCC2 Using in Vitro and in Silico Approach.Pharmaceutical research · 2017Article
- Towards Celiac-safe foods: Decreasing the affinity of transglutaminase 2 for gliadin by addition of ascorbyl palmitate and ZnClScientific reports · 2017Article
- In Silico Screening, Alanine Mutation, and DFT Approaches for Identification of NS2B/NS3 Protease Inhibitors.Biochemistry research international · 2016Article
- Examine the characterization of biofilm formation and inhibition by targeting SrtA mechanism in Bacillus subtilis: a combined experimental and theoretical study.Journal of molecular modeling · 2014Article
- Effect of explicit water molecules on ligand-binding affinities calculated with the MM/GBSA approach.Journal of molecular modeling · 2014Article
- Binding affinity prediction with property-encoded shape distribution signatures.Journal of chemical information and modeling · 2010Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
Reliable and robust prediction of the binding affinity for drug molecules continues to be a daunting challenge. We simulated the binding interactions and free energy of binding of nine protease inhibitors (PIs) with wild-type and various mutant proteases by performing GBSA simulations in which each PI's partial charge was determined by quantum mechanics (QM) and the partial charge accounts for the polarization induced by the protease environment. We employed a hybrid solvation model that retains selected explicit water molecules in the protein with surface-generalized Born (SGB) implicit solvent. We examined the correlation of the free energy with the antiviral potency of PIs with regard to amino acid substitutions in protease. The GBSA free energy thus simulated showed strong correlations (r > 0.75) with antiviral IC(50) values of PIs when amino acid substitutions were present in the protease active site. We also simulated the binding free energy of PIs with P2-bis-tetrahydrofuranylurethane (bis-THF) or related cores, utilizing a bis-THF-containing protease crystal structure as a template. The free energy showed a strong correlation (r = 0.93) with experimentally determined anti-HIV-1 potency. The present data suggest that the presence of selected explicit water in protein and protein polarization-induced quantum charges for the inhibitor, compared to lack of explicit water and a static force-field-based charge model, can serve as an improved lead optimization tool and warrants further exploration.
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