Correlating Predicted Reactivities with Experimental Inhibition Data of Covalent ChlaDUB1 Inhibitors

Covalent inhibition with electrophiles of suitable reactivity allows for prolonged inactivation of a targeted enzyme, in comparison to noncovalent inhibitors. To fine-tune covalently reacting groups, various computational workflows have been developed for reactivity prediction. Their results are typically evaluated based on in vitro assays that use cysteine, glutathione, or other model nucleophiles, but the relevance of the predictions for the situation in a particular enzyme environment remains under-investigated. Herein, we utilized a DFT-based computational method to assess the transferability of predicted reactivities to enzyme inhibition. For this, we designed and synthesized a set of covalent inhibitors of ChlaDUB1, a potential target to fight the pathogen Chlamydia trachomatis. We show that in the context of enzyme inhibition, geometrical congruence between ligands has to be taken into account when evaluating the reactivity of covalently reacting groups in respective drug discovery projects.