TCB Publications - Abstract

Yui Tik Pang, Anna Pavlova, Emad Tajkhorshid, and James C. Gumbart. Parameterization of a drug molecule with a halogen σ-hole particle using ffTK: Implementation, testing, and comparison. Journal of Chemical Physics, 153:164104, 2020.

PANG2020-ET Halogen atoms are widely used in drug molecules to improve their binding affinity for the receptor proteins. Many of the examples involve “halogen bonding” between the molecule and the binding site, which is a directional interaction between a halogen atom and a nucleophilic atom. Such an interaction is induced by an electron cloud shift of the halogen atom toward its covalently bonded neighbor to form the $\sigma$- bond, leaving a small electrostatic positive region opposite to the bond called the “$\sigma$-hole.” To mimic the effect of the $\sigma$-hole in the Chemistry at Harvard Molecular Mechanics (CHARMM) Q4 non- polarizable force field, recently CGenFF added a positively charged massless particle to halogen atoms, positioned at the opposite side of the carbon–halogen bond. This particle is referred to as a lone pair (LP) particle because it uses the lone pair implementation in the CHARMM force field. Here, we have added support for LP particles to ffTK, an automated force field parameterization toolkit widely distributed as a plugin to the molecular visualization software. We demonstrate the updated optimization process using an example halogenated drug molecule, AT130, which is a capsid assembly modulator targeting the hepatitis B virus. Our results indicate that parameterization with the LP particle significantly improves the accuracy of the electrostatic response of the molecule, especially around the halogen atom. Although the inclusion of the LP particle does not produce a prominent effect on the interactions between the molecule and its target protein, the protein–ligand binding performance is greatly improved by optimization of the parameters.

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