Assessment of Reversibility for Covalent Cysteine Protease Inhibitors Using Quantum Mechanics/Molecular Mechanics Free Energy Surfaces

We have used molecular dynamics (MD) simulations with
hybrid quantum
mechanics/molecular mechanics (QM/MM) potentials to investigate the
reaction mechanism for covalent inhibition of cathepsin K and assess
the reversibility of inhibition. The computed free energy profiles
suggest that a nucleophilic attack by the catalytic cysteine on the
inhibitor warhead and proton transfer from the catalytic histidine
occur in a concerted manner. The results indicate that the reaction
is more strongly exergonic for the alkyne-based inhibitors, which
bind irreversibly to cathepsin K, than for the nitrile-based inhibitor
odanacatib, which binds reversibly. Gas-phase energies were also calculated
for the addition of methanethiol to structural prototypes for a number
of warheads of interest in cysteine protease inhibitor design in order
to assess electrophilicity. The approaches presented in this study
are particularly applicable to assessment of novel warheads, and computed
transition state geometries can be incorporated into molecular models
for covalent docking.