Identification of a peptide inhibitor for the histone methyltransferase WHSC1

Morrison, Michael J.; Boriack-Sjodin, P.A.; Swinger, Kerren K.; Wigle, Tim J.; Sadalge, D; Kuntz, Kevin W.; Scott, Margaret Porter; Janzen, William P.; Chesworth, Richard; Duncan, Kenneth W.; Harvey, Darren M.; Lampe, John W.; Mitchell, Lorna H.; Copeland, Robert A.

doi:10.1371/journal.pone.0197082

Cited by 23 publications

(17 citation statements)

References 55 publications

(58 reference statements)

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“…The catalytic segment of NSD3 folds into a compact structure ( Fig. 1h ) as reported previously 5 – 7 . In the NCP-bound NSD3 C -E1181K/T1232A complex, two kinds of complex particles exhibiting NCP-NSD3 ratios of 1:1 and 1:2 were observed.…”

supporting

confidence: 69%

“…Given activating mutations and up-regulation of NSD proteins can both drive tumor progression 1 , 2 , the NSD family of histone lysine methyltransferases are viewed as promising targets for the treatment of several cancer types. Indeed, extensive efforts have been made to identify inhibitors to target the catalytic domain of NSD proteins prior to the resolution of an NCP-bound activating complex structure 5 , 7 , 24 – 26 . The molecular mechanisms shown in this study should provide valuable information for drug design and development in treating NSD-associated neoplastic diseases.…”

mentioning

confidence: 99%

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Molecular basis of nucleosomal H3K36 methylation by NSD methyltransferases

Tian

Yuan

et al. 2020

Nature

128

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The NSD family histone methyltransferases, including NSD1, NSD2 and NSD3, play crucial roles in chromatin regulation and are implicated in oncogenesis 1 , 2 . NSD enzymes exhibit an auto-inhibitory state that is relieved by nucleosome engagement, allowing for H3K36 di-methylation catalysis 3 – 7 . However, the molecular basis underlying this mechanism is largely unknown. Here, we have solved the cryo-EM structures of NSD2 and NSD3 bound to mononucleosomes at atomic resolution. We find that NSD2/3 mononucleosome engagement causes DNA near the linker region to unwrap, which facilitates insertion of their catalytic core in-between the histone octamer and the unwrapped segment of DNA. A network of DNA- and histone-specific contacts between the nucleosome and NSD2/3 precisely define the enzymes’ position on the nucleosome, explaining the methylation specificity for H3K36. Further, NSD-nucleosome intermolecular contacts are altered by several recurrent cancer-associated NSD2/3 mutations. NSDs harboring these mutations are catalytically hyperactive in vitro and in cells, and their ectopic expression promotes cancer cell proliferation and xenograft tumor growth. Together, our research provides molecular insights into the nucleosome-based recognition and modification mechanisms of NSD2 and NSD3, which should uncover strategies for therapeutic targeting of the NSD family of proteins.

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supporting

confidence: 69%

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confidence: 99%

Molecular basis of nucleosomal H3K36 methylation by NSD methyltransferases

Tian

Yuan

et al. 2020

Nature

128

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“…As such, NSD SET domain inhibitors described to date are either very weak 12 , nonselective and without validated binding to the NSD SET domains 13 , or are SAM analogs (e.g. sinefungin) 14 or peptides 15 lacking cellular activity. Therefore, development of drug-like small molecule inhibitors of NSDs with on-target activity in cancer cells remains a major challenge.…”

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confidence: 99%

Covalent inhibition of NSD1 histone methyltransferase

et al. 2020

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The NSD family of histone methyltransferases is associated with various malignancies, including aggressive acute leukemia with NUP98-NSD1 translocation. While NSD proteins represent attractive drug targets, their catalytic SET domains exist in autoinhibited conformation, presenting significant challenges for inhibitor development. Here, we employed a fragment-based screening strategy followed by chemical optimization, which resulted in development of the first-in-class irreversible small molecule inhibitors of the NSD1 SET domain. The crystal structure of NSD1 in complex with covalently bound ligand reveals conformational change in the autoinhibitory loop of the SET domain and formation of a channel-like pocket suitable for targeting with small molecules. Our covalent lead, compound BT5, demonstrates on-target activity in NUP98-NSD1 leukemia cells, including inhibition of H3K36 dimethylation and downregulation of target genes, and impairs colony formation in NUP98-NSD1 patient sample. This study will facilitate development of the next generation of potent and selective inhibitors of the NSD histone methyltransferases.

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“…Structure-activity relationships have been reported for sinefungin analogs, the most potent of which inhibited the SET domains of NSD2 (IC 50 ϭ 1.8 M) and SETD2 (IC 50 ϭ 0.29 M) (41). Also, a peptide inhibitor of NSD2, PTD2 (IC 50 ϭ 3-22 M), has been reported that was derived from the histone H4 sequence (43).…”

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confidence: 99%

High-throughput screening with nucleosome substrate identifies small-molecule inhibitors of the human histone lysine methyltransferase NSD2

Coussens

Kales

Henderson

et al. 2018

Journal of Biological Chemistry

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The histone lysine methyltransferase nuclear receptor-binding SET domain protein 2 (NSD2, also known as WHSC1/MMSET) is an epigenetic modifier and is thought to play a driving role in oncogenesis. Both NSD2 overexpression and point mutations that increase its catalytic activity are associated with several human cancers. Although NSD2 is an attractive therapeutic target, no potent, selective, and bioactive small molecule inhibitors of NSD2 have been reported to date, possibly due to the challenges of developing high-throughput assays for NSD2. Here, to establish a platform for the discovery and development of selective NSD2 inhibitors, we optimized and implemented multiple assays. We performed quantitative high-throughput screening with full-length WT NSD2 and a nucleosome substrate against a diverse collection of bioactive small molecules comprising 16,251 compounds. We further interrogated 174 inhibitory compounds identified in the primary screen with orthogonal and counter assays and with activity assays based on the clinically relevant NSD2 variants E1099K and T1150A. We selected five confirmed inhibitors for follow-up, which included a radiolabeled validation assay, surface plasmon resonance studies, methyltransferase profiling, and histone methylation in cells. We found that all five NSD2 inhibitors bind the catalytic SET domain and one exhibited apparent activity in cells, validating the workflow and providing a template for identifying selective NSD2 inhibitors. In summary, we have established a robust discovery pipeline for identifying potent NSD2 inhibitors from small-molecule libraries.

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Identification of a peptide inhibitor for the histone methyltransferase WHSC1

Cited by 23 publications

References 55 publications

Molecular basis of nucleosomal H3K36 methylation by NSD methyltransferases

Molecular basis of nucleosomal H3K36 methylation by NSD methyltransferases

Covalent inhibition of NSD1 histone methyltransferase

High-throughput screening with nucleosome substrate identifies small-molecule inhibitors of the human histone lysine methyltransferase NSD2

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