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Improved Estimation of Protein-Ligand Binding Free Energy by Using the Ligand-Entropy and Mobility of Water Molecules
Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan
Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
* Author to whom correspondence should be addressed.
Received: 27 February 2013; in revised form: 17 April 2013 / Accepted: 17 April 2013 / Published: 26 April 2013
Abstract: We previously developed the direct interaction approximation (DIA) method to estimate the protein-ligand binding free energy (DG). The DIA method estimates the DG value based on the direct van der Waals and electrostatic interaction energies between the protein and the ligand. In the current study, the effect of the entropy of the ligand was introduced with protein dynamic properties by molecular dynamics simulations, and the interaction between each residue of the protein and the ligand was also weighted considering the hydration of each residue. The molecular dynamics simulation of the apo target protein gave the hydration effect of each residue, under the assumption that the residues, which strongly bind the water molecules, are important in the protein-ligand binding. These two effects improved the reliability of the DIA method. In fact, the parameters used in the DIA became independent of the target protein. The averaged error of DG estimation was 1.3 kcal/mol and the correlation coefficient between the experimental DG value and the calculated DG value was 0.75.
Keywords: protein-ligand docking; molecular dynamics simulation; protein-ligand binding free energy
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MDPI and ACS Style
Fukunishi, Y.; Nakamura, H. Improved Estimation of Protein-Ligand Binding Free Energy by Using the Ligand-Entropy and Mobility of Water Molecules. Pharmaceuticals 2013, 6, 604-622.
Fukunishi Y, Nakamura H. Improved Estimation of Protein-Ligand Binding Free Energy by Using the Ligand-Entropy and Mobility of Water Molecules. Pharmaceuticals. 2013; 6(5):604-622.
Fukunishi, Yoshifumi; Nakamura, Haruki. 2013. "Improved Estimation of Protein-Ligand Binding Free Energy by Using the Ligand-Entropy and Mobility of Water Molecules." Pharmaceuticals 6, no. 5: 604-622.