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Evaluating QM/MM Free Energy Surfaces for Ranking Cysteine Protease Covalent Inhibitors
Clauber H S da Costa1, Vinícius Bonatto2, Alberto M Dos Santos1
1Laboratório de Planejamento e Desenvolvimento de Fármacos , Universidade Federal do Pará , Rua Augusto Correa S/N , 66075-110 Belém , PA , Brazil.
Abstract:
One tactic for cysteine protease inhibition is to form a covalent bond between an electrophilic atom of the inhibitor and the thiol of the catalytic cysteine. In this study, we evaluate the reaction free energy obtained from a hybrid quantum mechanical/molecular mechanical (QM/MM) free energy profile as a predictor of affinity for reversible, covalent inhibitors of rhodesain. We demonstrate that the reaction free energy calculated with the PM6/MM potential is in agreement with the experimental data and suggest that the free energy profile for covalent bond formation in a protein environment may be a useful tool for the inhibitor design.
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