SPONGE-FEP: An Automated Relative Binding Free Energy Calculation Accelerated by Selective Integrated Tempering Sampling

Computer-aided drug discovery (CADD) utilizes computational methods to accelerate the identification and optimization of potential drug candidates. Free energy perturbation (FEP) and thermodynamic integration (TI) play a critical role in predicting differences in protein binding affinities between drug molecules. Here, we implement SPONGE-FEP, which incorporates selective integrated tempering sampling (SITS) to enhance sampling efficiency and contains an automated workflow for relative binding free energy (RBFE) calculations. We first provide an overview of the workflow, which encompasses the generation of a perturbation map, alchemical free energy calculations, and cycle closure analysis. Two case studies were then performed to demonstrate the enhanced sampling of conformational states of ligands and proteins during the alchemical transformation process. The results show that the refined SITS method in SPONGE-FEP can significantly improve the sampling efficiency of rare events and the performance of RBFE predictions. Three series of comparative RBFE tests were conducted to demonstrate the accuracy of SPONGE-FEP, which is comparable to FEP+, using an average computation time of 4 h for a pair of ligands on an A100 GPU device.