MTA-cooperative PRMT5 inhibitors from cofactor-directed DNA-encoded library screens.

Andersson, Jan; Cowland, Sanne; Vestergaard, Mikkel; Yang, Yajing; Liu, Siyuan; Fang, Xie; Mukund, Susmith; Ghimire-Rijal, Sudipa et al. · Proc Natl Acad Sci U S A · 2025

basic_science · Level V

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Abstract

Methylthioadenosine phosphorylase (<i>MTAP</i>) gene deletions are frequent in human cancers. Loss of <i>MTAP</i> leads to significantly increased cellular levels of methylthioadenosine (MTA), a cellular metabolite and specific inhibitor of the cell-essential enzyme Protein Arginine Methyltransferase-5 (PRMT5). Using a cofactor-directed screening strategy and DNA-encoded libraries, we identify a class of PRMT5 inhibitors that cooperatively inhibit PRMT5 in the presence of MTA. An optimized inhibitor, AM-9934, selectively inhibits PRMT5 in <i>MTAP</i>-deleted cells and in transplanted tumors while sparing <i>MTAP</i>-expressing counterparts, leading to specific suppression of viability in <i>MTAP</i>-deleted cells. Structural studies show that AM-9934 occupies the arginine substrate pocket of MTA-bound PRMT5. This study introduces a broadly applicable method for directed DNA-encoded library screening toward a desired mechanistic outcome and highlights MTA-selective PRMT5 inhibition as an attractive therapeutic strategy with a potentially broad therapeutic index in patients with <i>MTAP</i>-deleted cancers.

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