Bioengineering of syrbactin megasynthetases for immunoproteasome inhibitor production

The natural product (NP) class of syrbactins are potent proteasome inhibitors produced by hybrids of non-ribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs). Here, we describe the stepwise reassembly of an entire NRPS/PKS hybrid to produce a new syrbactin derivative by utilizing the recently described “eXchange Unit between Thiolation domains” (XUTs) approach. Remarkably, XUT-based engineering allowed the direct assembly of PKS and NRPS modules to introduce an α,β-unsaturated Michael system in a macrolactam moiety, which represents the inhibitory warhead of syrbactins. The novel derivative was produced in E. coli, isolated, and examined for its ability to inhibit yeast (yCP), human constitutive (cCP), and immunoproteasome (iCP). The engineered NP maintained the inhibitory activities of the syrbactin class but, due to rational modifications, inhibited iCP most strongly. Moreover, analysis of the crystal structure of yCP in complex with the derivative revealed further design strategies for even more specific iCP inhibition.