Discovery of Small-Molecule Antagonists of the PWWP Domain of NSD2

Abstract

Increased activity of the lysine methyltransferase NSD2 driven by translocation and activating mutations is associated with multiple myeloma and acute lymphoblastic leukemia, but no NSD2-targeting chemical probe has been reported to date. Here, we present the first antagonists that block the protein–protein interaction between the N-terminal PWWP domain of NSD2 and H3K36me2. Using virtual screening and experimental validation, we identified the small-molecule antagonist 3f, which binds to the NSD2-PWWP1 domain with a K d of 3.4 μM and abrogates histone H3K36me2 binding to the PWWP1 domain in cells. This study establishes an alternative approach to targeting NSD2 and provides a small-molecule antagonist that can be further optimized into a chemical probe to better understand the cellular function of this protein.

Targeting the Nuclear Receptor-Binding SET Domain Family of Histone Lysine Methyltransferases for Cancer Therapy: Recent Progress and Perspectives

“…Interestingly, as an alternative to SET domain NSD inhibitors, Berardi et al reported in silico derived small molecules that inhibited finger–finger interaction between PHDVC5HCH and C2HRNizp1 of NSD1. Likewise, some studies have reported the use of small molecules to interfere with the function of the PWWP domain as an alternative strategy for developing novel NSD inhibitors. , Compound 34 has been identified as the first potent small-molecule antagonist targeting the PWWP1 domain of NSD2, while another recent study reported the fragment-based discovery of a chemical probe 37 that displayed selective and potent antagonistic activity against the PWWP1 domains of NSD3 …”

“…Likewise, some studies have reported the use of small molecules to interfere with the function of the PWWP domain as an alternative strategy for developing novel NSD inhibitors. 26,32 Compound 34 has been identified as the first potent smallmolecule antagonist targeting the PWWP1 domain of NSD2, 32 while another recent study reported the fragment-based discovery of a chemical probe 37 that displayed selective and potent antagonistic activity against the PWWP1 domains of NSD3. 26 Recent studies indicate ongoing efforts to explore the structure and function of different NSD domains and PHD fingers to develop NSD-specific inhibitors as an alternative to catalytic SET domains of NSD methyltransferases.…”

“…Recently, Ferreira de Freitas et al 32 reported the discovery of 4-cyano-N-cyclopropyl-N-(thiophen-2-ylmethyl)benzamide (32) as the first small molecule antagonist that targets the PWWP1 domain of NSD2 (Figure 10). Using virtual screening and biophysical assays initially, they identified a chiral compound, 29, which showed selective interaction with the PWWP1 domain of NSD2 (K d = 41 μM).…”

“…Recent studies have demonstrated the discovery of small molecule chemical probes that inhibit NSD methylating activity. These probes target either their catalytic SET domain or other functional domains including the proline-tryptophan-tryptophan-proline (PWWP) domain and plant homeodomain (PHD) fingers of NSD proteins. ,,, Based on these recent studies, more promising studies on discovery of novel potent and selective NSD inhibitors to treat various cancers are expected in the near future.…”

From Hit Seeking to Magic Bullets: The Successful Union of Epigenetic and Fragment Based Drug Discovery (EPIDD + FBDD)

“…Recently, the Structural Genomics Consortium identified fragment 138 (Figure ) as a binder to the PWWP1 domain of NSD2 through virtual screening of ∼2 million commercially available compounds followed by SPR assays with 39 selected compounds . Further progress combined 2D similarity search of a virtual library of ∼8 million commercially available compounds generated by 3D shape matching with manually designed scaffold hopping.…”