SMYD3 protein degraders in HPV-negative head and neck squamous cell carcinoma.

Despite the introduction of immunotherapy in treating HPV-negative head and neck squamous cell carcinoma, the overall outlook remains unfavorable. Researchers have found that SET and MYND containing 3 (SMYD3), a protein methyltransferase, is frequently overexpressed in approximately 60% of these tumors. SMYD3 contributes to cell proliferation, invasion, and resistance to immunotherapy by regulating the expression of specific genes.

Although commercially available SMYD3 inhibitors, EPZ031686 and BAY-6035, have shown no in vitro effectiveness, this suggests that SMYD3 likely influences oncogenic activities through mechanisms unrelated to its enzymatic function. To target SMYD3 more effectively, a series of protein degradation targeting chimeras (PROTACs) were developed.

When tested at extremely low concentrations in HPV-negative HNSCC cell lines, these PROTACs successfully degraded SMYD3, leading to a substantial reduction in cell proliferation and invasion. One of the most promising compounds, IAP-08, achieved a DC50 of approximately 177nM and demonstrated a Dmax of around 90%. IAP-08 also formed a ternary complex with SMYD3 and the XIAP E3 ligase.

Its favorable pharmacokinetic profile in vivo further supports its potential for future clinical development. Mass spectrometry confirmed IAP-08's high specificity for SMYD3. Depletion of SMYD3 using IAP-08 in HNSCC cells revealed changes in genes related to the cell cycle, EMT, and type I IFN response, indicating that SMYD3's oncogenic activity is more effectively suppressed through PROTAC-mediated depletion compared to its inhibition.