Electrostatic Complementarity as a Fast and Effective Tool to Optimize Binding and Selectivity of Protein–Ligand Complexes

• Published in: Journal of medicinal chemistry Vol. 62; no. 6; pp. 3036 - 3050
• Main Authors: Bauer, Matthias R, Mackey, Mark D
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 28.03.2019
• Subjects: Drug Design; Ligands; Protein Binding; Proteins - chemistry; Static Electricity; Structure-Activity Relationship
• ISSN: 0022-2623; 1520-4804
• DOI: 10.1021/acs.jmedchem.8b01925

Electrostatic interactions between small molecules and their respective receptors are essential for molecular recognition and are also key contributors to the binding free energy. Assessing the electrostatic match of protein–ligand complexes therefore provides important insights into why ligands bind and what can be changed to improve binding. Ideally, the ligand and protein electrostatic potentials at the protein–ligand interaction interface should maximize their complementarity while minimizing desolvation penalties. In this work, we present a fast and efficient tool to calculate and visualize the electrostatic complementarity (EC) of protein–ligand complexes. We compiled benchmark sets demonstrating electrostatically driven structure-activity relationships (SAR) from literature data, including kinase, protein−protein interaction, and GPCR targets, and used these to demonstrate that the EC method can visualize, rationalize, and predict electrostatically driven ligand affinity changes and help to predict compound selectivity. The methodology presented here for the analysis of EC is a powerful and versatile tool for drug design.