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Probing the nonribosomal peptide synthetase epimerization domain via rationally designed suicide inhibitors

Abstract

Nonribosomal peptides (NRPs) represent a class of biologically active natural products that contain a great deal of functional and therapeutic diversity. They are produced by both prokaryotes and eukaryotes from large, multidomain megaenzymes called nonribosomal peptide synthetases (NRPSs). Many of these NRPs contain D-amino acids that provide a great deal of physiological importance to their functionality. Incorporation of D- amino acids into the NRP natural product often occurs through integrated epimerization (E) domains that catalyze racemization of the C[alpha] position of a PCP-tethered L- amino acid. Several small molecule probes have been rationally designed in order to investigate the mechanism as well as gain insight into intradomain communication of E domains. [alpha]-Chlorvinylglycine 10 and [beta], [gamma]-phenylethynylglycine 15 are proposed to form a reactive allene intermediate in situ upon catalysis of the E domain that can be rapidly attacked by an active-site base. Utilizing the diketopiperazine condensation assay, we have demonstrated that probe 10 acts as an inhibitor of the E domain of the initiation module, grsA, of the gramicidin S synthetase. Inhibition of E domain activity suggests covalent crosslinking of the E domain and its proximal PCP partner, allowing insight into protein interactions that regulate NRP biosynthesis

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