Here we present WIDOCK, a virtual screening protocol that supports the selection of
diverse electrophiles as covalent inhibitors by incorporating ligand reactivity towards
cysteine residues into AutoDock4. WIDOCK applies the reactive docking method (Backus
et al. in Nature 534:570–574, 2016) and extends it into a virtual screening tool by
introducing facile experimental or computational parametrization and a ligand focused
evaluation scheme together with a retrospective and prospective validation against
various therapeutically relevant targets. Parameters accounting for ligand reactivity
are derived from experimental reaction kinetic data or alternatively from computed
reaction barriers. The performance of this docking protocol was first evaluated by
investigating compound series with diverse warhead chemotypes against KRASG12C,
MurA and cathepsin B. In addition, WIDOCK was challenged on larger electrophilic libraries
screened against OTUB2 and NUDT7. These retrospective analyses showed high sensitivity
in retrieving experimental actives, by also leading to superior ROC curves, AUC values
and better enrichments than the standard covalent docking tool available in AutoDock4
when compound collections with diverse warheads were investigated. Finally, we applied
WIDOCK for the prospective identification of covalent human MAO-A inhibitors acting
via a new mechanism by binding to Cys323. The inhibitory activity of several predicted
compounds was experimentally confirmed and the labelling of Cys323 was proved by subsequent
MS/MS measurements. These findings demonstrate the usefulness of WIDOCK as a warhead-sensitive,
covalent virtual screening protocol.
