MFAG

Abstract

Background: Undruggable proteins are particularly relevant in cancer, as they can act as drivers, precursors, and progression factors. Intrinsically disordered proteins (IDPs) are undruggable by definition due to the lack of a stable drug-binding pocket. These proteins lack a fixed three-dimensional structure, are more extended, and exhibit extreme dynamic or “fuzzy” behavior. Many IDPs are oncogenes or tumor suppressors, but their functions in cancer are poorly understood. Molecular recognition data, essential for structure-based drug design, is not available for fuzzy complexes. Therefore, studying IDP-binding molecules that retain selectivity without off-target toxicity is crucial. Hypothesis: Direct approaches, where small molecules directly inhibit binding sites, are ineffective for IDPs due to their large interfaces. Indirect strategies targeting druggable allosteric pockets are more effective in controlling the behavior of disordered domains in fuzzy complexes, potentially rewiring their interaction network. The unprecedented accuracy in protein structure prediction achieved by AlphaFold enables a rational approach to studying allosterism in cancer-associated proteins, focusing on neglected cases such as IDPs and fuzzy complexes. Aims: The project aims to: i) characterize proteins from childhood malignant neoplasms, focusing on recurrent cancer targets and undruggable targets that can be treated through allosteric communication mechanisms; ii) study the allosteric communication between globular and disordered domains in these proteins; iii) characterize the globular and disordered domains of the identified targets; iv) investigate how the rewiring of the interactome of disordered domains is triggered by allosteric modulators in various cell lines and conditions. Experimental Design: Allosteric communication, binding pocket location, ligand effectors, and the interactome of disordered domains will first be studied in silico to prioritize cancer-associated proteins. The selected ligands will be experimentally validated using DSF and NMR. The rewiring of the interactome, influenced by allosteric communication and ligands, will be analyzed using comparative mass spectrometry experiments. Expected Results: The project aims to reveal the molecular details driving cancer onset. Specifically, it will provide a library of undruggable targets annotated with their function in cancer cell lines, binding partners, participating pathways, and information on allosteric regulation. A candidate fuzzy protein complex identified in the initial phase will be experimentally characterized. All results will be integrated into public databases. Impact on Cancer: According to the NIH, approximately 10,000 new cases of childhood cancer are diagnosed annually, with a 10% mortality rate, making it a leading cause of disease-related death. The most common subtypes are leukemias, brain tumors, and lymphomas. The binding regions and models identified in this project will complement current knowledge and provide additional tools for physicians to understand why certain therapies are ineffective in poorly characterized cancers like childhood malignant neoplasms.

Funded by AIRC, the Italian Association for Cancer Research