Extending the MMPBSA method to membrane proteins: Addressing conformational changes upon ligand binding to P2Y12R

Membrane proteins play crucial roles in biological signaling and represent key targets in drug discovery, garnering significant experimental and computational attention. Recent advances in computational screening techniques have enabled the development of more accurate and efficient binding affinity calculation methods. Among these, the Molecular Mechanics Poisson Boltzmann Surface Area (MMPBSA) method has gained widespread adoption in large-scale simulations due to its computational efficiency. However, its application to membrane protein-ligand systems remains less developed compared to globular protein systems, primarily due to the additional complexity introduced by the membrane environment. In this study, we present enhanced capabilities in Amber that provide flexible and automatic options for calculating membrane placement parameters. Furthermore, we present the first application of ensemble simulations, combined with a multi-trajectory approach and entropy corrections, to enhance MMPBSA calculations for membrane protein systems. This novel methodology is particularly advantageous for systems exhibiting large ligand-induced conformational changes, significantly improving accuracy and sampling depth compared to traditional single-trajectory methods. We validate our approach using the human purinergic platelet receptor P2Y12R as a model system, chosen for its well-documented agonist-induced conformational changes and extensive experimental data, making it an ideal candidate for evaluating our enhanced simulation protocol.