Multiresolution non-covalent interaction analysis for ligand–protein promolecular electron density distributions

Abstract

Nowadays, the topology of electron density (ED) distributions as well as the non-covalent interaction (NCI) analysis of reduced density gradient (RDG) distributions, are extensively used to characterize intermolecular contacts. Here, topological and NCI-based analyses are combined for the multiresolution study of the intermolecular interactions occurring in a drug-protein system (PDB access code: 3UNK). The method involves the search for the critical points (CP) of the well-known PASA model developed by Carbo-Dorca and co-workers, and the minima in the corresponding RDG grids. The CP-based representation of the intermolecular contacts enriches the geometry-based interactions found using a Web server. The stability of the intermolecular interactions is studied by following their corresponding CP trajectory in space at several degrees of the ED smoothing, and by the evaluation of the local potential energy density (LPDE). It is observed that several RDG minima are located at the meeting point of CP trajectories initiated in the unsmoothed ED distribution. At high smoothing levels, the accumulation of ED charges at the ligand–protein interface progressively emerges and is detected through the study of the Laplacian values at the CPs and RDG minima. In parallel, the distance-dependency of the LPED values is less and less clear while the density-dependency is favored. The CP networks and their descriptors are seen as a signature of the ligand–protein arrangement, which is proposed to be further used in the characterization of ligand–protein stackings obtained from, e.g., crystal structures, docking calculations, Molecular Dynamics simulations, and pharmacophore designs.