Self‐Immolation of a Bacterial Dehydratase Enzyme by its Epoxide Product

• Published in: Chemistry : a European journal Vol. 26; no. 36; pp. 8035 - 8044
• Main Authors: Lence, Emilio, Maneiro, María, Sanz‐Gaitero, Marta, Raaij, Mark J., Thompson, Paul, Hawkins, Alastair R., González‐Bello, Concepción
• Format: Journal Article
• Language: English
• Published: WEINHEIM Wiley 26.06.2020; Wiley Subscription Services, Inc
• Subjects: Chemical modification; Chemistry; Chemistry, Multidisciplinary; Computer applications; Crystallography; Dehydration; Design modifications; enzymatic mechanisms; Enzymes; epoxide proforms; Lysine; lysine-covalent modification; Molecular dynamics; Physical Sciences; Quantum mechanics; reaction intermediates; Science & Technology; structural enzymology; Virulence; I DEHYDROQUINASE; enzymatic mechanisms; MECHANISM; ACTIVE-SITE; ESCHERICHIA-COLI; DRUG DISCOVERY; VACCINE; structural enzymology; CHEMICAL-MODIFICATION; epoxide proforms; lysine-covalent modification; TARGETING VIRULENCE; SUBSTRATE; QM/MM METHODS; reaction intermediates; Enzymatic mechanisms; Reaction intermediates; Lysine-covalent modification; Structural enzymology
• ISSN: 0947-6539; 1521-3765; 1521-3765
• DOI: 10.1002/chem.202000759

Disabling the bacterial capacity to cause infection is an innovative approach that has attracted significant attention to fight against superbugs. A relevant target for anti‐virulence drug discovery is the type I dehydroquinase (DHQ1) enzyme. It was shown that the 2‐hydroxyethylammonium derivative 3 has in vitro activity since it causes the covalent modification of the catalytic lysine residue of DHQ1. As this compound does not bear reactive electrophilic centers, how the chemical modification occurs is intriguing. We report here an integrated approach, which involves biochemical studies, X‐ray crystallography and computational studies on the reaction path using combined quantum mechanics/molecular mechanics Umbrella Sampling Molecular Dynamics, that evidences that DHQ1 catalyzes its self‐immolation by transforming the unreactive 2‐hydroxyethylammonium group in 3 into an epoxide that triggers the lysine covalent modification. This finding might open opportunities for the design of lysine‐targeted irreversible inhibitors bearing a 2‐hydroxyethylammonium moiety as an epoxide proform, which to our knowledge has not been reported previously. Enzyme self‐immolation: Catalyzing the generation of an epoxide from a 2‐hydroxyethylammonium proform triggers the self‐destruction of a dehydratase enzyme involved in bacterial virulence. Evidences of this lethal enzyme catalyzed process from incubations and MALDI studies with designed ligands, protein X‐ray crystallography and computational studies on the reaction path are provided.