Biomolecular Simulations of Halogen Bonds with a GROMOS Force Field

Journal of Chemical Theory and Computation
Rafael NunesPaulo J Costa

Abstract

Halogen bonds (XBs) are non-covalent interactions in which halogens (X), acting as electrophiles, interact with Lewis bases. XBs are able to mediate protein-ligand recognition and therefore play an important role in rational drug design. In this context, the development of molecular modeling tools that can tackle XBs is paramount. XBs are predominantly explained by the existence of a positive region on the electrostatic potential of X named the σ-hole. Typically, with molecular mechanics force fields, this region is modeled using a charged extra point (EP) linked to X along the R-X covalent bond axis. In this work, we developed the first EP-based strategy for GROMOS force fields (specifically GROMOS 54A7) using bacteriophage T4 lysozyme in complex with both iodobenzene and iodopentafluorobenzene as a prototype system. Several EP parametrization schemes were tested by adding a virtual interaction site to ligand topologies retrieved from the Automated Topology Builder (ATB) and Repository. Contrary to previous approaches using other force fields, our analysis is based on the capability of each parametrization scheme to sample XBs during MD simulations. Our results indicate that the implementation of an EP at a distance from iodin...Continue Reading

References

Sep 15, 1988·Physical Review A: General Physics·A D Becke
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Apr 1, 2003·Journal of Computational Chemistry·Maurizio CossiVincenzo Barone
Apr 30, 2004·Journal of Computational Chemistry·Junmei WangDavid A Case
May 4, 2004·Chembiochem : a European Journal of Chemical Biology·Grégori GerebtzoffAnna Seelig
Jul 21, 2004·Journal of Computational Chemistry·Chris OostenbrinkWilfred F van Gunsteren
Nov 24, 2004·Proceedings of the National Academy of Sciences of the United States of America·Pascal AuffingerP Shing Ho
Oct 8, 2005·Journal of Computational Chemistry·David Van Der SpoelHerman J C Berendsen
Feb 7, 2006·Journal of Molecular Graphics & Modelling·Junmei WangDavid A Case
Jan 11, 2007·The Journal of Chemical Physics·Giovanni BussiMichele Parrinello
Apr 11, 2009·Journal of Medicinal Chemistry·Yunxiang LuWeiliang Zhu
Sep 26, 2009·The Journal of Physical Chemistry. B·Sara R R Campos, António M Baptista
Jan 23, 2010·Protein Science : a Publication of the Protein Society·Walter A BaaseBrian W Matthews
Dec 25, 2010·Angewandte Chemie·Leo A HardeggerFrançois Diederich
Mar 3, 2011·Chemical Society Reviews·Emilio ParisiniGiancarlo Terraneo
Apr 1, 2009·Nature Chemistry·Andrea Regier VothP Shing Ho
May 3, 2011·European Biophysics Journal : EBJ·Nathan SchmidWilfred F van Gunsteren
May 21, 2011·Journal of Computational Chemistry·Mahmoud A A Ibrahim
Oct 4, 2011·Physical Chemistry Chemical Physics : PCCP·Stefano RendineMaurizio Sironi
Jan 18, 2012·Angewandte Chemie·Antonio CaballeroPaul D Beer
May 31, 2012·Journal of Molecular Modeling·Mahmoud A A Ibrahim
Aug 4, 2012·Chemical Society Reviews·Thomas M BealeMark S Taylor
Aug 7, 2012·Journal of Computer-aided Molecular Design·Rainer WilckenFrank M Boeckler
Nov 14, 2012·Journal of Medicinal Chemistry·Rainer WilckenFrank M Boeckler
Dec 12, 2012·Protein Science : a Publication of the Protein Society·Matthew R ScholfieldP Shing Ho
Dec 22, 2012·Chemical Communications : Chem Comm·Michal KolářAgnieszka K Bronowska
Jan 19, 2013·Journal of Chemical Theory and Computation·William L Jorgensen, Patric Schyman
Feb 19, 2013·Journal of Chemical Theory and Computation·Maria M ReifChris Oostenbrink
Mar 16, 2013·Angewandte Chemie·Lydia C GildayPaul D Beer
Oct 17, 2013·Journal of Chemical Information and Modeling·Andreas LangeFrank M Boeckler
Jan 1, 2014·Journal of Chemical Information and Modeling·Zhijian XuWeiliang Zhu
Jan 31, 2014·Journal of Computer-aided Molecular Design·Katarzyna B KoziaraAlan E Mark
Feb 4, 2014·The Journal of Physical Chemistry. B·Xiaojiao MuPengyu Ren
Oct 23, 2014·Journal of Computer-aided Molecular Design·Cristian Celis-BarrosGerald Zapata-Torres
Jul 15, 2015·Chemical Reviews·Lydia C GildayPaul D Beer
Aug 20, 2015·ACS Medicinal Chemistry Letters·Mònica RosaGregorio Valencia
Oct 1, 2015·The Journal of Physical Chemistry. B·Archita N S AdluriChristopher N Rowley
Oct 16, 2015·Journal of Medicinal Chemistry·Melissa Coates Ford, P Shing Ho
Nov 20, 2015·Journal of Chemical Theory and Computation·Edward HarderRichard A Friesner
Oct 9, 2012·Journal of Chemical Theory and Computation·Maria M ReifChris Oostenbrink
Apr 10, 2012·Journal of Chemical Theory and Computation·Michal Kolář, Pavel Hobza
Dec 13, 2011·Journal of Chemical Theory and Computation·Alpeshkumar K MaldeAlan E Mark

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Citations

May 28, 2019·Expert Opinion on Drug Discovery·Paulo J CostaDiogo Vila-Viçosa
Oct 23, 2020·The Journal of Chemical Physics·Steve Scheiner
Mar 10, 2021·Journal of the American Chemical Society·Rafael Santana NunesPaulo J Costa
Jun 30, 2021·Journal of Chemical Information and Modeling·Andreia Fortuna, Paulo J Costa
May 27, 2020·Journal of Chemical Information and Modeling·Zhengdan ZhuWeiliang Zhu
May 31, 2019·Journal of Chemical Theory and Computation·Rafael NunesPaulo J Costa

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