Sorting drug conformers in enzyme active sites: the XTB way.

Abstract

In the present study, we have used the MEI196 set of interaction energies to investigate low-cost computational chemistry approaches for the calculation of binding between a molecule and its environment. Density functional theory (DFT) methods, when used with the vDZP basis set, yield good agreement with the reference energies. On the other hand, semi-empirical methods are less accurate as expected. By examining different groups of systems within MEI196 that contain species of a similar nature, we find that chemical similarity leads to cancellation of errors in the calculation of relative binding energies. Importantly, the semi-empirical method GFN1-xTB (XTB1) yields reasonable results for this purpose. We have thus further assessed the performance of XTB1 for calculating relative energies of docking poses of substrates in enzyme active sites represented by cluster models or within the ONIOM protocol. The results support the observations on error cancellation. This paves the way for the use of XTB1 in parts of large-scale virtual screening workflows to accelerate the drug discovery process.