Scaffold Hopping and Optimization of Small Molecule Soluble Adenyl Cyclase Inhibitors Led by Free Energy Perturbation

Free energy perturbation is a computational technique that can be used to predict how small changes to an inhibitor structure will affect the binding free energy to its target. In this paper, we describe the utility of free energy perturbation with FEP+ in the hit-to-lead stage of a drug discovery project targeting soluble adenyl cyclase. The project was structurally enabled by X-ray crystallography throughout. We employed free energy perturbation to first scaffold hop to a preferable chemotype and then optimize the binding affinity to sub-nanomolar levels while retaining druglike properties. The results illustrate that effective use of free energy perturbation can enable a drug discovery campaign to progress rapidly from hit to lead, facilitating proof-of-concept studies that enable target validation.

Automated summary

Free energy perturbation is used to predict the effects of small changes to an inhibitor structure on the binding free energy. This paper focuses on its utility in the hit-to-lead stage of a drug discovery project targeting soluble adenyl cyclase. X-ray crystallography was used throughout the project to enable structural analysis. The results demonstrate that free energy perturbation can facilitate the rapid progress of a drug discovery campaign, enabling proof-of-concept studies for target validation.