Discovery of NSD2-Degraders from Novel and Selective DEL Hits

NSD2 is a histone methyltransferase predominantly catalyzing di-methylation of histone H3 on lysine K36. Increased NSD2 activity due to mutations or fusion-events affecting the gene encoding NSD2 is considered an oncogenic event and a driver in various cancers, including multiple myelomas carrying t(4;14) chromosomal translocations and acute lymphoblastic leukemia's expressing the hyperactive NSD2 mutant E1099 K. Using DNA-encoded libraries, we have identified small molecule ligands that selectively and potently bind to the PWWP1 domain of NSD2, inhibit NSD2 binding to H3K36me2-bearing nucleosomes, but do not inhibit the methyltransferase activity. The ligands were subsequently converted to selective VHL1-recruiting NSD2 degraders and by using one of the most efficacious degraders in cell lines, we show that it leads to NSD2 degradation, decrease in K3 K36me2 levels and inhibition of cell proliferation. DNA-encoded small molecule libraries were employed to screen billions of molecules against NSD2. Hits were identified against the PWWP1 domain. One chemotype was converted into a VHL1/EloB/EloC E3 ligase PROTAC, which demonstrated selective and on-target degradation of NSD2 in cells. The binding MoA of compounds was elucidated by molecular docking and validated by subsequent single-point mutation studies.+image

Automated summary

This study identified small molecule ligands that can selectively and effectively bind to NSD2, and demonstrated that their conversion into degraders can degrade NSD2 and inhibit cell proliferation. These findings are important for understanding the role of NSD2 in cancer and developing novel therapeutic approaches.