Targeting Post-translational Modifications in Squamous Cell Carcinomas

Figure 1. X-ray co-structure of NAcM-OPT (green) bound to DCN1 (gray) (PDB:5V86), disrupting the key interactions with the N-terminally acetylated portion of UBE2M (pink).

Squamous Cell Carcinomas (SCC) including those of the lung, esophagus, and head and neck, cause over one third of cancer-related deaths. with poor survival rates (ca. 16% for lung). Thus, there is a pressing need to develop novel approaches to treat SCC.  DCN1 is amplified in >40% of lung SCC and associated with malignant transformation, metastasis, and poorer patient survival rates. DCN1 binds to the acetylated N-terminus of UBC12 (an E2 enzyme for the ubiquitin-like protein (UBL) NEDD8) and the “Cullin (or CUL)” family of proteins to act as a co-E3 promoting NEDD8 modification of CULs which activates them to regulate ubiquitination of a wide range of clients.

The goal of this this project is to discover and develop inhibitors that block the interaction of the Defective in Cullin Neddylation 1 (DCN1) and UBE2M proteins, thereby preventing their activation of the cullin RING ubiquitin ligases (CRL’s). Because the CRL’s ultimately control ubiquitination of many diverse proteins, thus regulating their stability, intracellular localization, and function specific DCN1-UBE2M interaction inhibitors have the potential to selectively regulate key signaling networks.

This project is a collaboration with Brenda Schulman’s laboratory at St Jude/MPI (discoverer of the DCN mechanism) and Bhuv Singh’s laboratory at MSKCC (Discoverer of  DCN1 (aka SCCRO).  Their studies show that DCN1 activity depends on a ≈350 Å3 pocket in the DCN1 oncoprotein binding to UBE2M’s acetylated N-terminal methionine (Figure 1).

In 2017, together with the Schulman and Singh labs, we reported the first selective small molecule inhibitors of the DCN1-UBE2M interaction (Figure 2).1,2,3  Our current inhibitor set includes an orally bioavailable reversible inhibitor (NAcM-OPT), an irreversible inhibitor (NAcM-COV), and a structurally related negative control (NAcM-NEG).   We are currently using these and another structurally unrelated scaffold4 to dissect the effects of acute pharmacologic inhibition of the DCN1-UBE2M interaction on the NEDD8/CUL pathway in both cellular and in vivo models.

Figure 2. N-terminal acetyl Methionine inhibiting (NAcM) Chemical Probes

References

  1. Kim HS, Hammill JT, Scott DC, Chen Y, Min J, Rector J, Singh B, Schulman BA, Guy RK. Discovery of Novel Pyrazolo-pyridone DCN1 Inhibitors Controlling Cullin Neddylation. J Med Chem. 2019 Sep 26;62(18):8429-8442. doi: 10.1021/acs.jmedchem.9b00410. Epub 2019 Sep 13. PMID: 31465221; PMCID: PMC7228038.
  2. Hammill JT, Scott DC, Min J, Connelly MC, Holbrook G, Zhu F, Matheny A, Yang L, Singh B, Schulman BA, Guy RK. Piperidinyl Ureas Chemically Control Defective in Cullin Neddylation 1 (DCN1)-Mediated Cullin Neddylation. J Med Chem. 2018 Apr 12;61(7):2680-2693. PMID: 29547696; PMCID: PMC5898815.
  3. Hammill JT, Bhasin D, Scott DC, Min J, Chen Y, Lu Y, Yang L, Kim HS, Connelly MC, Hammill C, Holbrook G, Jeffries C, Singh B, Schulman BA, Guy RK. Discovery of an Orally Bioavailable Inhibitor of Defective in Cullin Neddylation 1 (DCN1)-Mediated Cullin Neddylation. J Med Chem. 2018 Apr 12;61(7):2694-2706. PMID: 29547693; PMCID: PMC5914176.
  4. Scott DC*, Hammill JT*, Min J, Rhee DY, Connelly M, Sviderskiy VO, Bhasin D, Chen Y, Ong SS, Chai SC, Goktug AN, Huang G, Monda JK, Low J, Kim HS, Paulo JA, Cannon JR, Shelat AA, Chen T, Kelsall IR, Alpi AF, Pagala V, Wang X, Peng J, Singh B, Harper JW, Schulman BA, Guy RK. Blocking an N-terminal acetylation-dependent protein interaction inhibits an E3 ligase. Nat Chem Biol. 2017 Aug;13(8):850-857. PMID: 28581483; PMCID: PMC5577376. *Co-first authorship

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