Break-induced replication (BIR) is a specific type of DNA repair mechanism that is responsible for telomere elongation in telomerase-negative cancer cells. This Alternative Lengthening of Telomeres (ALT) is required for viability in approximately 10% of all carcinomas and at least 40% of soft tissue sarcomas. More interestingly, normal somatic cells seem to contain factors that repress the ALT mechanism and prevent their telomeres from being maintained by ALT activity. In recent studies, the BLM-TOP3A-RMI1/2 (BTR) complex has been shown to play a big role in the BIR mechanism and FANCM, a DNA translocase protein, is essential for attenuating its activity through interaction with RMI1 and RMI2. Furthermore, this protein-protein interaction (PPI) was demonstrated to be vital for ALT+ cancers and disrupting it resulted in excessive break-induced telomere synthesis and subsequent cell death.
The MM2 domain on FANCM has been reported to be responsible for this particular PPI and the co-crystal structure of this domain with its binding partners – the RMI proteins – has been revealed. Notably, the crystallographic data resolved the presence of only 12 MM2 residues, bound to a surface comprised of elements from both RMI1 and RMI2. Thus, this 12 AA stretch with a remarkably extended conformation was considered the key lead to the inhibition of the FANCM-BTR interaction that is lethal for ALT+ cancer cells but not for healthy human cells.
Peptide-based macrocycles, with the right size and functionality to bind protein interfaces, have emerged as an ideal strategy for targeting such PPIs with high potency and selectivity. Thus, this presented work comprises a combination of two parallel approach for discovering macrocyclic peptide inhibitors that disrupt the FANCM-BTR interaction: rational structure-based design using the 12 AA stretch on MM2, and selection of potent cyclic peptide binders using the mRNA-display technology RaPID as a complementary powerful approach.