NUP98-fusion oncogenes (FO) are associated with several pediatric hematological malignancies characterized by poor prognosis. There is a great need for new therapeutic strategies to treat NUP98 FO-driven leukemias. To support Project 1, the Chemistry Core will design focused compound libraries including FDA drugs, preclinical compounds and chemical probes and provide chemistry support to identify compounds that effectively inhibit the NUP98-fusions, or block critical interactions in cell models as proposed in Project 1. To support Project 4, we will optimize the screening hits for potency, selectivity, and drug-like properties to deliver KDM5A-PHD3 inhibitors that meet the criteria for in vitro and in vivo chemical probes. In addition, we will utilize small molecule inhibitors/binders of KDM5A-PHD3 to develop PROTACs (PROteolysis-TArgeting Chimaera) targeting KDM5A PHD3 and selectively degrading NUP98-KDM5A. We propose to evaluate, further optimize, select and formulate compounds for pre-clinical in vivo efficacy evaluation proposed in Project 4. The Chemistry Core consists of three highly integrated teams that collectively provide state-of-the-art chemical probe design, synthesis, and evaluation capabilities: the Analytical Chemistry Center (ATC) provides an extensive battery of analytical methods to evaluate compound chemical, biophysical and ADME properties, and routinely elucidates structures of metabolites and other unknown molecules, develops highly customized bioanalytical methods, and formulations for in vivo studies. The Medicinal Chemistry Center (MCC) focuses on identification and development of potent and selective chemical probes for proof-of-concept studies in cells and in vivo preclinical models. The Chemical Biology Center (CBC) applies advanced chemical biology methods to develop sophisticated chemical tools designed to map and interrogate disease-related biological pathways. The CBC chemical tool-box includes PROTACs, molecular glues, pool-down, photoactivatable and imaging probes. For example to support PROTAC platform CBC developed an FP-CRBN assay and built a library of >50 linker-E3 intermediates suitable for rapid ?click? chemistry-based synthesis of the final PROTAC target molecules.
Chemistry Core/Narrative The Chemistry Core consists of three highly integrated teams (Analytical Chemistry Center, Chemical Biology Center and Medicinal Chemistry Center) that collectively provide state-of-the-art chemical probe design, synthesis, and evaluation capabilities to support the identification of small molecules that effectively inhibit the activities of NUP98-fusions, or block critical interactions in cell models (Project 1), optimization of screening hits to deliver KDM5A-PHD3 inhibitors that meet in vitro and in vivo chemical probe criteria (Project 4), and development of PROTACs for the degradation of the NUP98-KDM5A by converting the tightest-binding, optimized molecules into PROTACs that cause specific degradation of the NUP98-KDM5A fusion oncoproteins. We will iteratively perform design, chemical synthesis, structural and biophysical evaluations, and tests of in vitro and cellular efficacy, to drive compound optimization.
