Novel Compounds to Inactivate Oncogenic Fusion Proteins

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DESCRIPTION (provided by applicant): Chemotherapy-resistant leukemias and sarcomas contain tumor-specific chromosomal translocations that encode fusion-proteins and these fusion-proteins are expressed only in the tumor. A fusion-protein provides significant tumor target specificity and increases the likelihood that novel therapies targeting the fusion-protein will be both effective and lack non-specific toxicity. Many of the tumor-specific fusion-proteins that function as transcription factors are disordered proteins. Disordered proteins lack the rigid alpha-helical or beta sheet structures required for structure-based drug design. While disordered proteins require a more empiric approach to the discovery of small molecule protein-protein interaction inhibitors, the biochemical properties of disordered proteins may actually favor the success of protein-protein interaction inhibitors. We will develop a novel paradigm to inhibit the protein-protein interaction of an oncogenic fusion protein. The Ewing's Sarcoma Family of Tumors (ESFT) contains a characteristic translocation, t(11:22), which leads to the oncogenic, fusion-protein, transcription factor EWS-FLI1. Therapies that inactivate EWS-FLI1 might address the significant problem of recurrent disease for patients. Since EWS-FLI1 lacks intrinsic enzymatic activity, and is a disordered protein, we will create novel protein-protein interaction inhibitors to block EWS-FLI1 binding to critical protein partners. We identified RNA Helicase A (RHA, p150), a DEAD/H family member that modulates gene expression, as a critical partner of EWS-FLI1. EWS-FLI1 binds to a unique region of RHA that is NOT involved in non-malignant RHA transcriptional modulation. A peptide mimic of this binding region inhibits EWS- FLI1 binding to RHA and we have discovered a lead compound, NSC635437, which has significant structural homology with the peptide mimic. A derivative small molecule of NSC635437, YK-4-279, blocks RHA binding to EWS-FLI1 and induces apoptosis in ESFT cells. We hypothesize that the interaction of RHA with EWS- FLI1 results in a potent transcriptional activator/coactivator complex, which amplifies the functions of both proteins and drives the malignant phenotype of ESFT. Our approach will develop reagents that prevent the binding of EWS-FLI1 to RHA, both to address our hypothesis and create a new therapeutic agent. We will accomplish our objectives by examining the effects of blocking RHA from enhancing EWS-FLI1 function, first using a peptide and then with small molecule protein-protein interaction inhibitors. We will work together with Dr. Milton Brown, a highly regarded medicinal chemist, to chemically optimize our lead compound. Our work has broad applicability to a larger group of tumors, serving as a new paradigm for developmental therapeutics. This paradigm to create small molecule inhibitors of EWS-FLI1 could be used for other translocation-defined malignancies such as chemotherapy-resistant carcinomas, sarcomas and leukemias. Therefore, future work would have a strong potential for a positive impact upon many patients with difficult to treat tumors leading to reduced mortality and morbidity.