Applying ultra-accelerated quantum chemical molecular dynamics technique for the evaluation of ligand protein interactions

摘要

Ligand–protein interactions have been studied using several chemical information techniques including quantum chemical methods that are applied to truncated systems composed of the ligand molecule and the surrounding amino acids of the receptor. Fragmented quantum molecular chemical studies are also a choice to study the enzyme–ligand system holistically, however there are still restrictions on the number of water molecules that can be included in a study of this nature. In this work we adopt a completely different approach to study ligand–protein interactions accounting explicitly for as many solvent molecules as possible and without the need for a fragmented calculation. Furthermore, we embed our quantum chemical calculations within a molecular dynamics framework that enables a fundamentally fast system for quantum chemical molecular dynamic simulations (QCMD). Central to this new system for QCMD is the tight binding QC system, newly developed in our laboratories, which combined with the MD paradigm results in an ultra-accelerated QCMD method for protein–ligand interaction evaluations. We have applied our newly developed system to the dihydrofolate reductase (DHFR)–methotrexate (MTX) system. We show how the proposed method leads us to new insights into the main interactions that bind MTX to the enzyme, mainly the interaction between the amino group of MTX and Asp27 of DHFR, as well as MTX amino group with Thr113 of DHFR, which have been only elucidated experimentally to date. Keywords Quantum chemical molecular dynamics (QCMD) calculation - Dihydrofolate reductase - Methotrexate - Enzyme - Density functional theory