A New Method for Navigating Optimal Direction for Pulling Ligand from Binding Pocket: Application to Ranking Binding Affinity by Steered Molecular Dynamics

• Published in: Journal of chemical information and modeling Vol. 55; no. 12; pp. 2731 - 2738
• Main Authors: Vuong, Quan Van, Nguyen, Tin Trung, Li, Mai Suan
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 28.12.2015
• Subjects: Binding Sites; Biochemistry; Chemistry Techniques, Analytical - methods; Correlation analysis; Humans; Ligands; Molecular Dynamics Simulation; Molecules; Protein Binding; Thermodynamics; Thrombin - chemistry
• ISSN: 1549-9596; 1549-960X
• DOI: 10.1021/acs.jcim.5b00386

In this paper we present a new method for finding the optimal path for pulling a ligand from the binding pocket using steered molecular dynamics (SMD). Scoring function is defined as the steric hindrance caused by a receptor to ligand movement. Then the optimal path corresponds to the minimum of this scoring function. We call the new method MSH (Minimal Steric Hindrance). Contrary to existing navigation methods, our approach takes into account the geometry of the ligand while other methods including CAVER only consider the ligand as a sphere with a given radius. Using three different target + receptor sets, we have shown that the rupture force F max and nonequilibrium work W pull obtained based on the MSH method show a much higher correlation with experimental data on binding free energies compared to CAVER. Furthermore, W pull was found to be a better indicator for binding affinity than F max. Thus, the new MSH method is a reliable tool for obtaining the best direction for ligand exiting from the binding site. Its combination with the standard SMD technique can provide reasonable results for ranking binding affinities using W pull as a scoring function.