Discovery and Computational Studies of Potent Covalent Kinase Inhibitors with α‑Substituent Electrophiles Targeting Cysteine

Both reversible noncovalent inhibitors and irreversible
covalent
inhibitors targeting tyrosine kinases have their disadvantages. The
reversible covalent inhibitors with electrophilic group cyanoacrylamide
as warheads reacting with cysteine residues could solve the dilemmas.
However, there are still several unresolved issues regarding the electrophilic
groups. In this manuscript, a series of EGFR inhibitors with double
electron-withdrawing substituents introduced into the Cα position on the olefin bond were designed and synthesized. The binding
structures and characteristics of inhibitors with the kinase in both
the first noncovalent binding phase and the second covalent binding
step were explored and combined with molecular docking and molecular
dynamics simulations. Then, the reverse β-elimination reactions
of the thiol-Michael adducts were investigated by applying density
functional theory calculations. In addition, the effects of different
electrophilic substituents of Cα on the binding between
the inhibitors and kinase were elucidated. The results suggested that
the electrophilicity and size of the electron-withdrawing groups play
an important role in the specific interactions during the reaction.
The compounds with the electron-withdrawing groups that had medium
electrostatic and steric complementarity to the kinase active site
could cooperatively stabilize the complexes and showed relatively
good potent activities in the kinase assay experiment. The mechanical
and structural information in this study could enhance our understanding
of the functioning of the electron-withdrawing groups in the covalent
inhibitors. The results might help to design efficient cysteine targeting
inhibitors in the future.