Docking, molecular dynamics and QM/MM studies to delineate the mode of binding of CucurbitacinE to F-actin

[Display omitted] •The binding mode of CurcurbitacinE (CurE) in F-actin and it mechanisms is presented in this paper.•Docking, molecular dynamics followed by QM/MM shows the detailed transition state model for the Michael reaction.•CurE allosterically modulates ADP and stabilizes F-actin structure that could affect the nucleotide exchange and depolymerization of F-actin.•The proposed binding mode of CurE is in an unexplored small molecule binding site of actin•Therefore, it should be the starting point for structure based drug discovery initiatives specific to this site and mechanism. CucurbitacinE (CurE) has been known to bind covalently to F-actin and inhibit depolymerization. However, the mode of binding of CurE to F-actin and the consequent changes in the F-actin dynamics have not been studied. Through quantum mechanical/molecular mechanical (QM/MM) and density function theory (DFT) simulations after the molecular dynamics (MD) simulations of the docked complex of F-actin and CurE, a detailed transition state (TS) model for the Michael reaction is proposed. The TS model shows nucleophilic attack of the sulphur of Cys257 at the β-carbon of Michael Acceptor of CurE producing an enol intermediate that forms a covalent bond with CurE. The MD results show a clear difference between the structure of the F-actin in free form and F-actin complexed with CurE. CurE affects the conformation of the nucleotide binding pocket increasing the binding affinity between F-actin and ADP, which in turn could affect the nucleotide exchange. CurE binding also limits the correlated displacement of the relatively flexible domain 1 of F-actin causing the protein to retain a flat structure and to transform into a stable “tense” state. This structural transition could inhibit depolymerization of F-actin. In conclusion, CurE allosterically modulates ADP and stabilizes F-actin structure, thereby affecting nucleotide exchange and depolymerization of F-actin.