Nemzeti Gyógyszerkutatási és Fejlesztési Laboratórium(PharmaLab) Támogató: NKFIH
Heterocyclic thiones have recently been identified as reversible covalent warheads,
consistent with their mild electrophilic nature. Little is known so far about their
mechanism of action in labelling nucleophilic sidechains, especially cysteines. The
vast number of tractable cysteines promotes a wide range of target proteins to examine;
however, our focus was put on functional cysteines. We chose the main protease of
SARS‐CoV‐2 harboring Cys145 at the active site that is a structurally characterized
and clinically validated target of covalent inhibitors. We screened an in‐house, cysteine‐targeting
covalent inhibitor library which resulted in several covalent fragment hits with benzoxazole,
benzothiazole and benzimidazole cores. Thione derivatives and Michael acceptors were
selected for further investigations with the objective of exploring the mechanism
of inhibition of the thiones and using the thoroughly characterized Michael acceptors
for benchmarking our studies. Classical and hybrid quantum mechanical/molecular mechanical
(QM/MM) molecular dynamics simulations were carried out that revealed a new mechanism
of covalent cysteine labelling by thione derivatives, which was supported by QM and
free energy calculations and by a wide range of experimental results. Our study shows
that the molecular recognition step plays a crucial role in the overall binding of
both sets of molecules.
