Metadynamics simulations of ligands binding to protein surfaces: a novel tool for rational drug design

Ke Zuo, Agata Kranjc, Riccardo Capelli, Giulia Rossetti, Rachel Nechushtai, Paolo Carloni*

*Corresponding author for this work

Research output: Contribution to journalReview articlepeer-review

1 Scopus citations

Abstract

Structure-based drug design protocols may encounter difficulties to investigate poses when the biomolecular targets do not exhibit typical binding pockets. In this study, by providing two concrete examples from our labs, we suggest that the combination of metadynamics free energy methods (validated against affinity measurements), along with experimental structural information (by X-ray crystallography and NMR), can help to identify the poses of ligands on protein surfaces. The simulation workflow proposed here was implemented in a widely used code, namely GROMACS, and it could straightforwardly be applied to various drug-design campaigns targeting ligands’ binding to protein surfaces.

Original languageAmerican English
Pages (from-to)13819-13824
Number of pages6
JournalPhysical Chemistry Chemical Physics
Volume25
Issue number20
DOIs
StatePublished - 5 May 2023

Bibliographical note

Publisher Copyright:
© 2023 The Royal Society of Chemistry.

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