Identification and structural characterization of a novel PCNA-interacting small molecule scaffold

Proliferating cell nuclear antigen (PCNA) plays essential roles in DNA replication, repair, transcription, and cell-cycle regulation, making it an attractive yet historically difficult target in cancer therapy. Building on our development of AOH1996, a first-in-class small molecule currently in Phase I clinical evaluation for solid and liquid tumors, we sought to identify additional PCNA-interacting chemotypes that could expand therapeutic opportunities and inform next-generation inhibitor design. Using an artificial intelligence-guided computer-aided drug discovery workflow, we screened more than ten million drug-like compounds and prioritized candidates through differential scanning fluorimetry. This approach led to the identification of COH005, a previously unreported small-molecule scaffold that binds PCNA. X-ray crystallography demonstrated that COH005 engages the major PCNA-interacting-protein (PIP)-box binding pocket, a critical interface for PCNA-mediated protein-protein interactions. Cellular thermal shift assays (CETSA) validated direct COH005-PCNA engagement in cells similar to clinical IND, AOH1996. To assess selectivity, we performed protein-structure frustration analysis comparing COH005 interactions with PCNA against an unrelated anti-target, revealing energetically favorable binding unique to PCNA. Together, these studies establish COH005 as a novel PCNA-interacting scaffold with strong potential for therapeutic development. This work provides a structural and mechanistic foundation for designing next-generation PCNA-targeted agents with improved specificity and pharmacological properties.