Identification of defactinib derivatives targeting focal adhesion kinase using ensemble docking, molecular dynamics simulations and binding free energy calculations

Abstract

Focal adhesion kinase (FAK) belongs to the nonreceptor tyrosine kinases, which selectively phosphorylate tyrosine residues on substrate proteins. FAK is associated with bladder, esophageal, gastric, neck, breast, ovarian and lung cancers. Thus, FAK has been considered as a potential target for tumor treatment. Currently, there are six adenosine triphosphate (ATP)-competitive FAK inhibitors tested in clinical trials but no approved inhibitors targeting FAK. Defactinib (VS-6063) is a second-generation FAK inhibitor with an IC₅₀ of 0.6 nM. The binding model of VS-6063 with FAK may provide a reference model for developing new antitumor FAK-targeting drugs. In this study, the VS-6063/FAK binding model was constructed using ensemble docking and molecular dynamics simulations. Furthermore, the molecular mechanics/generalized Born (GB) surface area (MM/GBSA) method was employed to estimate the binding free energy between VS-6063 and FAK. The key residues involved in VS-6063/FAK binding were also determined using per-residue energy decomposition analysis. Based on the binding model, VS-6063 could be separated into seven regions to enhance its binding affinity with FAK. Meanwhile, 60 novel defactinib-based compounds were designed and verified using ensemble docking. Overall, the present study improves our understanding of the binding mechanism of human FAK with VS-6063 and provides new insights into future drug designs targeting FAK.

Communicated by Ramaswamy H. Sarma

Keywords:

• Binding mechanism
• defactinib
• FAK inhibitor
• focal adhesion kinase
• free energy calculation
• VS-6063
• molecular dynamics simulations

Acknowledgments

Certain data were obtained from the National Supercomputing Center of Guangzhou and the Chengdu Supercomputing Center. The authors thank Editage (www.editage.cn) for English language editing.

Disclosure statement

The authors declare no conflicts of interest.

Author contributions

Conceptualization, C.G. and M.S.; methodology, Q.L. and M.S.; software, M.S. and C.G.; validation, C.G., J.X. and M.S.; formal analysis, F.M. and M.S.; investigation, Q.L. and M.S.; resources, Q.L.; data curation, X.X. and M.S.; writing—original draft preparation, M.S.; writing—review and editing, C.G. and M.S.; visualization, Q.L. and M.S.; supervision, M.S. and C.G.; project administration, M.S. and C.G.; funding acquisition, C.G. All authors have read and agreed to the published version of the manuscript.

Data availability statement

Not applicable.

Additional information

Funding

The research was funded by Chengdu Municipal Health Commission, grant number 2021063, and The First Affiliated Hospital of Chengdu Medical College High-level Talents Research Start-up Fund, grant number 140013.