Targeting Protein Pockets with Halogen Bonds: The Role of the Halogen Environment

J Chem Inf Model. 2022 Dec 26;62(24):6494-6507. doi: 10.1021/acs.jcim.2c00475. Epub 2022 Aug 31.

Abstract

Protein pockets that form a halogen bond (X-bond) with a halogenated ligand molecule simultaneously form other (mainly hydrophobic) interactions with the halogen atom that can be considered as its "X-bond environment" (XBenv). Most studies in the field have focused on the X-bond, with the properties of the XBenv usually overlooked. In this work, we derived a protocol that evaluates the XBenv strength as a measure of the propensity of a protein pocket to host an X-bond. The charge density-based topological descriptors in combination with machine learning tools were employed to predict formation and strength of the interactions that conform the XBenv as a function of their geometrical parameters. On the basis of these results, we propose that the XBenv can be used as a footprint to judge the chance of a protein pocket to form an X-bond.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Halogens* / chemistry
  • Ligands
  • Proteins* / chemistry

Substances

  • Halogens
  • Proteins
  • Ligands