The core task in computational drug discovery is to accurately predict binding free energies in receptor-ligand systems for large libraries of putative binders. Here, the ABSINTH implicit solvent model and force field is extended to describe small, organic molecules and their interactions with proteins. We show that an automatic pipeline based on partitioning arbitrary molecules into substructures corresponding to model compounds with known free energies of solvation can be combined with the CHARMM general force field into a method that is successful at the two important challenges a scoring function faces in virtual screening work flows: it ranks known binders with correlation values rivaling that of comparable state-of-the-art methods, and it enriches true binders in a set of decoys. Our protocol introduces innovative modifications to common virtual screening workflows, notably the use of explicit ions as competitors and the integration over multiple protein and ligand species differing in their protonation states. We demonstrate the value of modifications to both the protocol and to ABSINTH itself. We conclude by discussing limitations of high-throughput implicit methods like the one proposed here.
BT - Journal of Chemical Information and Modeling C1 - 0258 DA - 2020 Sep 08 DO - 10.1021/acs.jcim.0c00558 IS - 10 J2 - J. Chem. Inf. Model. LA - eng M3 - Research Article N2 -The core task in computational drug discovery is to accurately predict binding free energies in receptor-ligand systems for large libraries of putative binders. Here, the ABSINTH implicit solvent model and force field is extended to describe small, organic molecules and their interactions with proteins. We show that an automatic pipeline based on partitioning arbitrary molecules into substructures corresponding to model compounds with known free energies of solvation can be combined with the CHARMM general force field into a method that is successful at the two important challenges a scoring function faces in virtual screening work flows: it ranks known binders with correlation values rivaling that of comparable state-of-the-art methods, and it enriches true binders in a set of decoys. Our protocol introduces innovative modifications to common virtual screening workflows, notably the use of explicit ions as competitors and the integration over multiple protein and ligand species differing in their protonation states. We demonstrate the value of modifications to both the protocol and to ABSINTH itself. We conclude by discussing limitations of high-throughput implicit methods like the one proposed here.
PY - 2020 SE - 5188 SP - 5188 EP - 5202 T2 - Journal of Chemical Information and Modeling TI - An ABSINTH-based protocol for predicting binding affinities between proteins and small molecules. VL - 60 SN - 1549-960X ER -