CrypToth: Cryptic pocket detection through mixed-solvent molecular dynamics simulations based topological data analysis

Some functional proteins undergo conformational changes to expose hidden binding sites when a binding molecule approaches their surface. Such binding sites are called cryptic sites and are important targets for drug discovery. However, it is still difficult to correctly predict cryptic sites. Therefore, we introduce a new method, CrypToth, for the precise identification of cryptic sites utilizing the persistent homology method. This method integrates topological data analysis and mixed-solvent molecular dynamics (MSMD) simulations. To identify hotspots corresponding to cryptic sites, we conducted MSMD simulations using six probes with different chemical properties: benzene, isopropanol, phenol, imidazole, acetonitrile, and ethylene glycol. Subsequently, we applied our topological data analysis method to rank hotspots based on the possibility of harboring cryptic sites. Evaluation of CrypToth using nine target proteins containing well-defined cryptic sites revealed its superior performance compared to recent machine-learning methods. As a result, in 7 out of 9 cases, hotspots associated with cryptic sites were ranked highest. CrypToth can explore hotspots on the protein surface favorable to ligand binding using MSMD simulations with six different probes and then identify hotspots corresponding to cryptic sites by assessing the proteins conformational variability using the topological data analysis. This synergistic approach facilitates the prediction of cryptic sites with high accuracy.