Structure and function of prodrug-activating peptidases

Abi Family Protein, DidK, Is Involved in the Maturation of Anticancer Depsipeptide, Didemnin B

“…The previously identified maturation enzymes in nonribosomal peptide biosynthesis mainly include the βlactamase family proteins such as ClbP in colibactin biosynthesis, peptide transporters harboring a β-lactamase domain such as ZmaM in zwittermicin A biosynthesis, the peptidase M28 family proteins such as SfmE in saframycin biosynthesis, and penicillin amidase PvdQ in pyoverdine biosynthesis (Table S1). 2,5,7,8,11 However, none of these maturation enzyme-like proteins were found to be encoded in the didemnin BGC. 13 Previous sequence analysis of the open reading frames adjacent to the didA−J operon revealed two hydrolytic enzymes (orf 2, orf14), and we then examined their involvement in didemnin B maturation by gene knockout.…”

“…Their major strategies include prodrug mechanism, chemical modification of natural products by resistant enzymes, removal of toxic substances from the cells by efflux pumps, isolation of the active molecules from their targets by recruiting self-protection proteins, and modification of the natural product binding targets . For the prodrug mechanism, a nontoxic precursor of the toxin is usually assembled in the cytoplasm and exported from cell following the conversion to its active product. , …”

“…Some known examples of nonribosomal peptides/polyketides (NRPs/PKs) that undergo prodrug activation include colibactin, xenocoumacin, zwittermicin, amicoumacin, edeine A1, nocardicin G, paenilamicin B1, saframycin, naphthyridinomycin, and pyoverdine (Figure ). − Notably, these natural products are linked to their cleavable moiety, often a fatty acyl or aminoacyl group via an amide bond except naphthyridinomycin, which employs an ester bond. Most of the identified cleaving enzymes are peptidases, particularly β-lactamase (PF00144) family proteins which are often encoded in the relevant biosynthetic gene clusters (BGCs). ,, Analogously, a prodrug maturation step was proposed in the biosynthesis of didemnin B, but the corresponding maturation enzyme remained unknown …”

“…1 For the prodrug mechanism, a nontoxic precursor of the toxin is usually assembled in the cytoplasm and exported from cell following the conversion to its active product. 1,2 The natural prodrug activation mechanism is commonly found in the biosynthetic pathways for ribosomally synthesized and post-translationally modified peptides, but is less common for thio-templated nonribosomal peptide synthetase/polyketide synthase (NRPS/PKS)-derived natural products. 3 Some known examples of nonribosomal peptides/polyketides (NRPs/PKs) that undergo prodrug activation include colibactin, xenocoumacin, zwittermicin, amicoumacin, edeine A1, nocardicin G, paenilamicin B1, saframycin, naphthyridinomycin, and pyoverdine (Figure 1).…”

“…Most of the identified cleaving enzymes are peptidases, particularly βlactamase (PF00144) family proteins which are often encoded in the relevant biosynthetic gene clusters (BGCs). 2,11,12 Analogously, a prodrug maturation step was proposed in the biosynthesis of didemnin B, but the corresponding maturation enzyme remained unknown. 13 Didemnin B is a marine-derived depsipeptide with potent antiviral and anticancer activities.…”