Gaussian mapping of chemical fragments in ligand binding sites

Abstract

We present a new approach to automatically define a quasi-optimal minimal set of pharmacophoric points mapping the interaction properties of a user-defined ligand binding site. The method is based on a fitting algorithm where a grid of sampled interaction energies of the target protein with small chemical fragments in the binding site is approximated by a linear expansion of Gaussian functions. A heuristic approximation selects from this expansion the smallest possible set of Gaussians required to describe the interaction properties of the binding site within a prespecified accuracy. We have evaluated the performance of the approach by comparing the computed Gaussians with the positions of aromatic sites found in experimental protein–ligand complexes. For a set of 53 complexes, good correspondence is found in general. At a 95% significance level, ∼65% of the predicted interaction points have an aromatic binding site within 1.5 Å. We then studied the utility of these points in docking using the program DOCK. Short docking times, with an average of ∼0.18 s per conformer, are obtained, while retaining, both for rigid and flexible docking, the ability to sample native-like binding modes for the ligand. An average 4–5-fold speed-up in docking times and a similar success rate is estimated with respect to the standard DOCK protocol.

Abbreviations: RMSD – root mean square deviation; ASA – Atomic Shell Approximation; LSF – Least-Squares Fitting; 3D – three-dimensional; VDW – Van der Waals.