Biology-directed and in silico-aided design liberates a potent, simplified and ipomoeassin-F-derived Sec61 inhibitor

The macrocyclic small molecule inhibitor ipomoeassin F (Ipom-F) binds to the central Sec61α subunit of the Sec61 complex and induces cytotoxicity by disrupting multiple aspects of Sec61-mediated protein biogenesis at the endoplasmic reticulum (ER). Here, we show that the integrity of the Ipom-F macrocycle is not required either for Sec61 inhibition in vitro or the induction of cell death, which is abrogated in cells expressing a resistance-conferring Sec61α mutant. We conclude that Ipom-F and its open-chain analogues interact with Sec61α via its mycolactone binding site and/or lateral gate, thereby occluding the normal Sec61-mediated pathway for membrane protein insertion at the ER. Using biology-directed and in silico-aided design, we have revolutionised the production of Ipom-F to yield open-chain analogue 3; a potent, simplified and synthetically accessible Ipom-F-derived Sec61 inhibitor. We present 3 as a lead compound for the generation of new protein translocation probes and future therapeutic development.