Simultaneous refinement of inaccurate local regions and overall structure in the CASP12 protein model refinement experiment.

Advances in protein model refinement techniques are required as diverse sources of protein structure information are available from low-resolution experiments or informatics-based computations such as cryo-EM, NMR, homology models, or predicted residue contacts. Given semi-reliable or incomplete structural information, structure quality of a protein model has to be improved by ab initio methods such as energy-based simulation. In this study, we describe a new automatic refinement server method designed to improve locally inaccurate regions and overall structure simultaneously. Locally inaccurate regions may occur in protein structures due to non-convergent or missing information in template structures used in homology modeling or due to intrinsic structural flexibilities not resolved by experimental techniques. However, such variable or dynamic regions often play important functional roles by participating in interactions with other biomolecules or in transitions between different functional states. The new refinement method introduced here utilizes diverse types of geometric operators which drive both local and global changes, and the effect of structure changes and relaxations are accumulated. This resulted in consistent refinement of both local and global structural features. Performance of this method in CASP12 is discussed.

Free energy perturbation (FEP)-guided scaffold hopping.

Scaffold hopping refers to computer-aided screening for active compounds with different structures against the same receptor to enrich privileged scaffolds, which is a topic of high interest in organic and medicinal chemistry. However, most approaches cannot efficiently predict the potency level of candidates after scaffold hopping. Herein, we identified potent PDE5 inhibitors with a novel scaffold via a free energy perturbation (FEP)-guided scaffold-hopping strategy, and FEP shows great advantages to precisely predict the theoretical binding potencies ΔG FEP between ligands and their target, which were more consistent with the experimental binding potencies ΔG EXP (the mean absolute deviations | Δ G FEP - Δ G EXP |  < 2 kcal/mol) than those ΔG MM-PBSA or ΔG MM-GBSA predicted by the MM-PBSA or MM-GBSA method. Lead L12 had an IC50 of 8.7 nmol/L and exhibited a different binding pattern in its crystal structure with PDE5 from the famous starting drug tadalafil. Our work provides the first report via the FEP-guided scaffold hopping strategy for potent inhibitor discovery with a novel scaffold, implying that it will have a variety of future applications in rational molecular design and drug discovery.