Estimation of ligand receptor binding affinity from the fluctuation of their interface

概要

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It is necessary for the understanding of protein interactions or in silico drug designs to accurately estimate ligand-receptor affinity. The energy calculation based on the electrostatic force, van der Waals force, and solvation effect is a direct method of computing the magnitude of the interaction between ligand and receptor. By this conventional method, however, it is difficult to estimate a slight difference in binding affinity with sufficient accuracy. We propose a novel concept for the evaluation of binding affinity between a ligand and its receptor by functionalizing the fluctuation at the ligand-receptor interface. This method enables an adequate estimation with a high accuracy compared with the conventional energetic approach. Human immunodeficiency virus type 1 (HIV-1) protease and its inhibitor are used to explain how binding affinity is extracted from the fluctuation in interfacial energy, and a combination of an antigen and its antibody is examined to demonstrate the compatibility between the estimation from the interfacial fluctuation and the experimentally measured binding energy.
2005-10-10