Fragment-based targeting of EMT-mediated resistance in EGFR-mutant lung cancer

Targeted therapy provides significant clinical benefit to patients with lung cancers driven by EGFR mutations. However, many patients develop non-genomic mechanisms of resistance for which we lack therapeutic strategies, such as epithelial-to-mesenchymal transition (EMT). To identify new targets and molecules that target EMT-mediated resistance, we will use fragment-like chemical probes that have a distinct advantage over larger drug-like molecules due to their smaller size and simpler structures which allow them to engage target binding sites usually inaccessible to more developed molecules. Fragments can identify novel targets and probe uncharted biological target space, which is significantly larger than what is interrogated by comparable numbers of lead-like molecules. Only a small proportion of the chemical space is currently being used and fragments can significantly broaden the biological target space. Fragments identified to bind to proteins of interest can be chemically modified for lead optimization. Using an optimized fragment-based drug discovery approach that allows for probing a significantly larger biological target space, we expect to identify unique targets for EMTmediated resistance to EGFR inhibitors. At the same time, our approach will identify chemical leads engaging these targets for future dedicated drug discovery programs. Aim 1: To discover new proteins, and their ligands, associated with EMT-mediated resistance to EGFR tyrosine kinase inhibitors (TKIs) and validate their functional role in resistant cells. We hypothesize that chemical proteomics with fragment-like probes that generate stable covalent bonds will enable detection of a previously untapped target space that has functional relevance for these cells. Using multiple EGFR-mutant parental/sensitive and TKI-resistant cell pair models with EMTmediated resistance, we will map the target binding space and then through a predetermined prioritization schema, evaluate target modulation using CRISPR inhibition and activation and target expression in human tumors. Aim 2: To identify chemical hit compounds, and identify and validate novel and selective actionable targets for EGFR TKI-resistant cells. The objective of this aim is to identify new active chemical compounds for EGFR TKI-resistant EMT cells. We hypothesize that cellular viability screening of fragment-like molecules will identify new selective lead compounds. We will identify EGFR TKI resistant targets using chemical proteomics in the appropriate cells, genetically validate them in vitro and in vivo and determine human tumor expression. Binding site identification and medicinal chemistry will optimize target binding and inhibition. This aim will provide chemical starting points for the identification of novel targets and new drug discovery opportunities in EGFR TKI resistant cells. The expected outcome of this research is the identification of novel druggable and unique cancer and/or subtype-specific targets for EGFR TKI-resistant lung cancer cells. The chemical matter will serve as starting points for developing new therapeutics to overcome EMT-mediated drug resistance. This project will use mice due to the experiment duration and the tumor microenvironment that is only present in the animal model. Project Number: 1R21CA302981-01A1 | Fiscal Year: 2026 | NIH Institute/Center: National Cancer Institute (NCI) | Principal Investigator: Uwe Rix (+1 co-PI) | Institution: H. LEE MOFFITT CANCER CTR & RES INST, TAMPA, FL | Award Amount: $433,256 | Activity Code: R21 | Study Section: Special Emphasis Panel[ZRG1 CTH-J (81)] View on NIH RePORTER: https://reporter.nih.gov/project-details/11371307