The PRMT5-MEP50 methyltransferase is a major target for anticancer drug discovery, and modulators of its interactions with different regulatory proteins are in high demand because they modulate PRMT5 substrate selectivity.
We describe a strategy for the development of a PRMT5/adaptor protein PPI inhibitor, which includes the design and synthesis of macrocyclic peptides based on the motif for the interaction of PRMT5 with its adaptor protein RioK1. After the initial exploration of different macrocycle sizes and cyclization linkages, analysis of a peptide library identified hot spots for the variation of the amino acid structure. The incorporation of nonproteinogenic amino acids into the macrocyclic peptide led to a potent cyclic PRMT5 binding peptide (Ki = 66 nM), which selectively inhibits the interaction of PRMT5 with the adaptor proteins RioK1 and pICln (IC50 = 654 nM) but not with the alternative adaptor protein MEP50. The inhibitor is a promising tool for further biological investigation of this intriguing protein interface.
J. Med. Chem., 2022, 65, 15300
(A) Heterooctameric PRMT5-MEP50 complex with PBM peptides bound to the TIM barrel domains. The full PRMT5-MEP50 complex can bind four PBM peptides (one per PRMT5 protomer) and has four active sites (one per PRMT5 protomer). The image is shown as a superposition of the PDB structures 7BOC and 4GQB. (B) Complex of the TIM barrel with a RioK1-derived peptide bound to the PBM groove (PDB ID/7BOC). The blue dashed line indicates the envisaged macrocyclization site. (C) Computational models of exemplary macrocycles overlaid on the linear peptide structure (wheat). A macrocycle with a 4-atom-long amide linker (5, green, first panel), a 4-atom-long unsaturated RCM linker (13 in trans, blue, second panel and cis, pink, third panel), and a 5-atom-long saturated linker (21, purple, fourth panel).