Mechanistic Investigation of Cysteine-Targeted Covalent Inhibition of DJ-1 via MD, QM/MM, and SAPT Computations

DJ-1 is a multifunctional protein implicated in cancer and autosomal early onset Parkinson's disease. Cys106 of DJ-1 plays a crucial role in its biological functions. The inhibitor bonded to Cys106 needs to be developed with tight binding for the definitive characterization of DJ-1. In this study, we investigate the binding mechanisms of two classes of DJ-1's covalent ligands, isatins and α-chloroamides, using MD simulations, QM/MM calculations, and SAPT analyses. MD simulations indicated that the stable binding process of a ligand in protein would be beneficial to have a good starting point for its covalent binding to DJ-1 in relation to the inhibition. Moreover, the warhead of a covalent inhibitor should be a small group fitting in the narrow space around Cys106, adopting a stable binding pose to facilitate the formation of the C(warhead)–S(Cys106) bond in DJ-1. The covalent bond can enhance the stability of nonbonded interactions between the ligands and DJ-1 during MD simulations. Furthermore, QM/MM calculations demonstrated the two-step nucleophilic addition reaction to form the C(warhead)–S(Cys106) bond for the covalent bindings of isatins and the three-step nucleophilic substitution reaction for the covalent bindings of α-chloroamides in DJ-1. In both reactions, proton transfer from Cys106 to Glu18 is the first step with the highest energy barrier. The electronic characteristics of the phenyl moiety may exert a negligible influence on the formation of the C(warhead)–S(Cys106) bond for the covalent binding to DJ-1. Finally, SAPT analyses revealed the detailed electronic interactions of the compounds with key residues around the active pocket of DJ-1. All the studies shed light on binding mechanisms of covalent inhibitors in the target protein, providing useful clues for the drug design of bioactive compounds.