Rapid and accurate assessment of GPCR–ligand interactions Using the fragment molecular orbital-based density-functional tight-binding method

5 years ago

Rapid and accurate assessment of GPCR–ligand interactions Using the fragment molecular orbital-based density-functional tight-binding method

Alexander Heifetz, Dmitri G. Fedorov, Roger Robinson, Inaki Morao, Mike J. Bodkin, Andrea Townsend-Nicholson, Michelle Southey

The reliable and precise evaluation of receptor–ligand interactions and pair-interaction energy is an essential element of rational drug design. While quantum mechanical (QM) methods have been a promising means by which to achieve this, traditional QM is not applicable for large biological systems due to its high computational cost. Here, the fragment molecular orbital (FMO) method has been used to accelerate QM calculations, and by combining FMO with the density-functional tight-binding (DFTB) method we are able to decrease computational cost 1000 times, achieving results in seconds, instead of hours. We have applied FMO-DFTB to three different GPCR–ligand systems. Our results correlate well with site directed mutagenesis data and findings presented in the published literature, demonstrating that FMO-DFTB is a rapid and accurate means of GPCR–ligand interactions. © 2017 Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc. Total protein–ligand binding energies and individual residue contributions are rapidly and accurately estimated using the fragment molecular orbital method combined with density-functional tight-binding, as established on a set of experimental data for three typical G-protein coupled receptors. Both total binding energies and residue contributions are shown to strongly correlate with a standard quantum-mechanical method, Møller–Plesset perturbation theory. The approach has a high potential for drug discovery studies.

Publisher URL: http://onlinelibrary.wiley.com/resolve/doi

DOI: 10.1002/jcc.24850