Chemical Biology and Drug Design
Chemical Biology and Drug Design
5 years ago

Molecular basis for covalent inhibition of glyceraldehyde-3-phosphate dehydrogenase by a 2-phenoxy-1,4-naphthoquinone small molecule

Molecular basis for covalent inhibition of glyceraldehyde-3-phosphate dehydrogenase by a 2-phenoxy-1,4-naphthoquinone small molecule
Mirko Zaffagnini, Romana Fato, Paola Conti, Gianluca Paredi, Elisa Uliassi, Stefano Bruno, Christian Bergamini, Marcel Kaiser, Andrea Cavalli, Maria Paola Costi, Marilena Margiotta, Riccardo Amorati, Maria Laura Bolognesi, Federica Prati
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) has recently gained attention as an antiprotozoan and anticancer drug target. We have previously identified 2-phenoxy-1,4-naphthoquinone as an inhibitor of both Trypanosoma brucei and human GAPDH. Herein, through multiple chemical, biochemical, and biological studies, and through the design of analogs, we confirmed the formation of a covalent adduct, we clarified the inhibition mechanism, and we demonstrated antitrypanosomal, antiplasmodial, and cytotoxic activities in cell cultures. The overall results lent support to the hypothesis that 2-phenoxy-1,4-naphthoquinone binds the GAPDH catalytic cysteine covalently through a phenolate displacement mechanism. By investigating the reactivity of 2-phenoxy-1,4-naphthoquinone and its analogs with four GAPDH homologs, we showed that the covalent inhibition is not preceded by the formation of a strong non-covalent complex. However, an up to fivefold difference in inactivation rates among homologs hinted at structural or electrostatic differences of their active sites that could be exploited to further design kinetically selective inhibitors. Moreover, we preliminarily showed that 2-phenoxy-1,4-naphthoquinone displays selectivity for GAPDHs over two other cysteine-dependent enzymes, supporting its suitability as a warhead starting fragment for the design of novel inhibitors. Herein, using multiple chemical and biological approaches and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) orthologs, we report on the ability of 2-phenoxy-1,4-naphthoquinone (1) to act as a covalent GAPDH inhibitor, by a cysteine trapping mechanism. Chemical probes 2–4 allowed us to further investigate the proposed mechanism of interaction. Moreover, we preliminarily evaluated the selectivity of 1 over other two thiol-dependent enzymes, supporting its suitability as a warhead fragment for GAPDH inhibitor design.

Publisher URL: http://onlinelibrary.wiley.com/resolve/doi

DOI: 10.1111/cbdd.12941

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