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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

preprint
submitted on 31.12.2020, 21:33 and posted on 04.01.2021, 13:02 by Prashant Kumar, Paulina Dominiak

Computational analysis of protein-ligand interactions is of crucial importance for drug discovery. Assessment of ligand binding energy allows us to have a glimpse on the potential of a small organic molecule to be a ligand to the binding site of a protein target. Available scoring functions such as in docking programs, we could say that they all rely on equations that sum each type of protein-ligand interactions to model the binding affinity. Most of the scoring functions consider electrostatic interactions involving the protein and the ligand. Electrostatic interactions contribute one of the most important part of total interaction energies 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 paper, complexes of HIV-1 protease with inhibitor molecules (JE-2147 and Darunavir) have been analysed using charge densities from a transferable aspherical-atom data bank. Moreover, we analyse the electrostatic interaction energy for an ensemble of structures using molecular dynamic simulation to highlight the main features related to the importance of this interaction for binding affinity.

Funding

National Centre of Science (Poland) PRELUDIUM No. UMO-2014/13/N/ST4/03851

History

Email Address of Submitting Author

pkumar@chem.uw.edu.pl

Institution

University of Warsaw

Country

Poland

ORCID For Submitting Author

0000-0001-5154-1059

Declaration of Conflict of Interest

The authors declare no competing financial interest.

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