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Review

Application of MM-PBSA Methods in Virtual Screening

1
Department of Pharmacy, University of Pisa, 56126 Pisa, Italy
2
Department of Molecular science and Nanosystems, University Ca’ Foscari of Venice, 30170 Venice, Italy
3
Pathology unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081 Aviano, Italy
*
Author to whom correspondence should be addressed.
Academic Editor: Giosuè Costa
Molecules 2020, 25(8), 1971; https://doi.org/10.3390/molecules25081971
Received: 30 March 2020 / Revised: 17 April 2020 / Accepted: 21 April 2020 / Published: 23 April 2020
(This article belongs to the Special Issue Computational Methods in Drug Design and Food Chemistry)
Computer-aided drug design techniques are today largely applied in medicinal chemistry. In particular, receptor-based virtual screening (VS) studies, in which molecular docking represents the gold standard in silico approach, constitute a powerful strategy for identifying novel hit compounds active against the desired target receptor. Nevertheless, the need for improving the ability of docking in discriminating true active ligands from inactive compounds, thus boosting VS hit rates, is still pressing. In this context, the use of binding free energy evaluation approaches can represent a profitable tool for rescoring ligand-protein complexes predicted by docking based on more reliable estimations of ligand-protein binding affinities than those obtained with simple scoring functions. In the present review, we focused our attention on the Molecular Mechanics-Poisson Boltzman Surface Area (MM-PBSA) method for the calculation of binding free energies and its application in VS studies. We provided examples of successful applications of this method in VS campaigns and evaluation studies in which the reliability of this approach has been assessed, thus providing useful guidelines for employing this approach in VS. View Full-Text
Keywords: virtual screening; MM-PBSA; rescoring; docking virtual screening; MM-PBSA; rescoring; docking
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MDPI and ACS Style

Poli, G.; Granchi, C.; Rizzolio, F.; Tuccinardi, T. Application of MM-PBSA Methods in Virtual Screening. Molecules 2020, 25, 1971. https://doi.org/10.3390/molecules25081971

AMA Style

Poli G, Granchi C, Rizzolio F, Tuccinardi T. Application of MM-PBSA Methods in Virtual Screening. Molecules. 2020; 25(8):1971. https://doi.org/10.3390/molecules25081971

Chicago/Turabian Style

Poli, Giulio, Carlotta Granchi, Flavio Rizzolio, and Tiziano Tuccinardi. 2020. "Application of MM-PBSA Methods in Virtual Screening" Molecules 25, no. 8: 1971. https://doi.org/10.3390/molecules25081971

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