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

• 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.

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