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

Proc Natl Acad Sci U S A. 2025 May 20;122(20):e2425052122. doi: 10.1073/pnas.2425052122. Epub 2025 May 16.

Abstract

Methylthioadenosine phosphorylase (MTAP) gene deletions are frequent in human cancers. Loss of MTAP 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 MTAP-deleted cells and in transplanted tumors while sparing MTAP-expressing counterparts, leading to specific suppression of viability in MTAP-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 MTAP-deleted cancers.

Keywords: DNA-encoded library screens; PRMT5; cancer.

MeSH terms

  • Animals
  • Cell Line, Tumor
  • DNA* / genetics
  • Deoxyadenosines
  • Enzyme Inhibitors* / chemistry
  • Enzyme Inhibitors* / pharmacology
  • Gene Library
  • Humans
  • Mice
  • Protein-Arginine N-Methyltransferases* / antagonists & inhibitors
  • Protein-Arginine N-Methyltransferases* / chemistry
  • Protein-Arginine N-Methyltransferases* / genetics
  • Protein-Arginine N-Methyltransferases* / metabolism
  • Purine-Nucleoside Phosphorylase* / genetics
  • Purine-Nucleoside Phosphorylase* / metabolism
  • Thionucleosides* / chemistry
  • Thionucleosides* / metabolism
  • Thionucleosides* / pharmacology

Substances

  • Protein-Arginine N-Methyltransferases
  • PRMT5 protein, human
  • 5'-methylthioadenosine phosphorylase
  • Purine-Nucleoside Phosphorylase
  • Thionucleosides
  • 5'-methylthioadenosine
  • DNA
  • Enzyme Inhibitors
  • Deoxyadenosines