Glycoside Hydrolase Catalysis: Do Substrates and Mechanism-Based Covalent Inhibitors React via Matching Transition States?

In this study, we look at how a catalytically efficient α-galactosidase stabilizes transition state (TS) charge delocalization for substrate hydrolysis. We then assess whether covalent inhibition of the enzyme by three types mechanism-based inhibitors occurs via similar modes TS stabilization. show, using Bartlett-type linear free energy relationships, that good correlations are obtained between catalytic efficiencies (kcat/Km and/or kinact/Ki) enzyme-catalyzed reactions natural and activated galactoside substrates representatives families classical inhibitors: 2-deoxy-2-fluoroglycoside, allylic carbasugars, an epoxy carbasugar. Of note, show glycoside carbasugars display log(rate)–log(rate) unity (slope ≈ 1), observation consistent with them having identical positive stabilization SN1-like glycosylation pseudo-glycosylation TSs, respectively. contrast, 2-deoxy-2-fluoroglycoside react different mechanism (SN2), while strained carbasugar inactivates traversing in which hydrolase inactivation has significantly lower degree to those substrates. To add weight these conclusions, computed landscapes their associated galactosylation pseudo-galactosylation TSs QM/MM molecular dynamics methods whole solvated enzyme.