Abstract 3055: Targeting the MKK3/MYC protein-protein interaction to overcome drug resistance in MYC-driven cancers

Abstract MYC is a central oncogenic transcription factor that drives tumor progression in multiple cancer types, including triple-negative breast cancer (TNBC) and non-small cell lung cancer (NSCLC). However, direct MYC inhibition remains highly challenging due to its intrinsically disordered structure and lack of defined drug-binding pockets. We uncovered a novel mechanism of MYC activation through a direct protein-protein interaction (PPI) with mitogen-activated protein kinase kinase 3 (MKK3). Integrative bioinformatics analyses using our AVERON platform revealed that elevated levels of the MKK3/MYC complex significantly correlate with poor clinical outcomes in TNBC and lung cancer, particularly in patient subsets with high MYC dependency. To define the functional consequences of the PPI, we combined genetic perturbation, chemical biology, and clinical genomics analyses. MKK3 silencing reduced the viability of TNBC and NSCLC cells, and these effects were recapitulated with small-molecule MKK3/MYC PPI inhibitors (MMPins), identified through our TR-FRET ultra-high-throughput screening campaign. Disruption of the MKK3/MYC PPI destabilized MYC and suppressed MYC-driven transcriptional programs. Furthermore, MKK3/MYC PPI inhibition is correlated with the downregulation of lactate dehydrogenase A (LDHA), a key mediator of glycolytic reprogramming and a well-established driver of drug resistance. In TNBC models, MKK3/MYC PPI inhibition reduced LDHA expression and blocked the glycolytic flux that fuels MYC-dependent growth. In NSCLC, MMPins restored apoptotic sensitivity in EGFR TKI-resistant cells and, when combined with osimertinib, significantly suppressed tumor growth in vivo. Together, these findings define the MKK3/MYC PPI as a mechanistic driver of LDHA-mediated metabolic adaptation and drug resistance. Pharmacological disruption of this interaction offers a promising therapeutic strategy to suppress MYC-dependent oncogenic networks, reverse resistance phenotypes, and improve outcomes in MYC-driven cancers. Acknowledgments: This work was supported in part by the Emory Center for New Medicines Therapeutic Advancement Award (A.A.I), Mary Kay Foundation Grant for Cancer Research (A.A.I), the NCI’s Informatics Technology for Cancer Research (ITCR) Program (R21CA274620, A.A.I.), NCI Emory Lung Cancer SPORE (P50CA217691, H.F.), NCI P01CA257906 (H.F.), Career Enhancement Program (A.A.I., P50CA217691), Winship Cancer Institute (NIH 5P30CA138292). We thank the Emory University Undergraduate Research Program in Biology. Citation Format: Payton Fleming, Elsa Bildtsen, Zhen Chen, Eric J. Miller, Yuhong Du, Shi-Yong Sun, Haian Fu, Andrey A. Ivanov. Targeting the MKK3/MYC protein-protein interaction to overcome drug resistance in MYC-driven cancers abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 3055.