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Combining Molecular Dynamic Information and an Aspherical-Atom Data Bank in the Evaluation of the Electrostatic Interaction Energy in Multimeric Protein-Ligand Complex: A Case Study for HIV-1 Protease

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dc.abstract.enComputational analysis of protein–ligand interactions is of crucial importance for drug discovery. Assessment of ligand binding energy allows us to have a glimpse of the potential of a small organic molecule to be a ligand to the binding site of a protein target. Available scoring func-tions, such as in docking programs, all rely on equations that sum each type of protein–ligand interactions in order to predict the binding affinity. Most of the scoring functions consider electrostatic interactions involving the protein and the ligand. Electrostatic interactions constitute one of the most important part of total interactions between macromolecules. Unlike dispersion forces, they are highly directional and therefore dominate the nature of molecular packing in crystals and in biological complexes and contribute significantly to differences in inhibition strength among related enzyme inhibitors. In this study, complexes of HIV‐1 protease with inhibitor molecules (JE‐2147 and darunavir) were analyzed by using charge densities from the transferable aspherical‐atom University at Buffalo Databank (UBDB). Moreover, we analyzed the electrostatic interaction energy for an ensemble of structures, using molecular dynamic simulations to highlight the main features of electrostatic interactions important for binding affinity.
dc.affiliationUniwersytet Warszawski
dc.contributor.authorKumar, Prashant
dc.contributor.authorDominiak, Paulina
dc.date.accessioned2024-01-24T19:49:37Z
dc.date.available2024-01-24T19:49:37Z
dc.date.issued2021
dc.description.accesstimeAT_PUBLICATION
dc.description.financePublikacja bezkosztowa
dc.description.number13
dc.description.versionFINAL_PUBLISHED
dc.description.volume26
dc.identifier.doi10.3390/MOLECULES26133872
dc.identifier.issn1420-3049
dc.identifier.urihttps://repozytorium.uw.edu.pl//handle/item/103281
dc.identifier.weblinkhttps://www.mdpi.com/1420-3049/26/13/3872/pdf
dc.languageeng
dc.pbn.affiliationchemical sciences
dc.relation.ispartofMolecules
dc.relation.pages3872
dc.rightsCC-BY
dc.sciencecloudnosend
dc.subject.enElectrostatic interactions
dc.subject.enProtein–ligand interactions
dc.subject.enQuantum crystallography
dc.titleCombining Molecular Dynamic Information and an Aspherical-Atom Data Bank in the Evaluation of the Electrostatic Interaction Energy in Multimeric Protein-Ligand Complex: A Case Study for HIV-1 Protease
dc.typeJournalArticle
dspace.entity.typePublication