Structure Based Design of Pol-theta inhibitors

Acute myeloid leukemia (AML) is the most frequently diagnosed form of acute leukemia in adults, and standard of care treatment involving chemotherapy and/or stem cell transplantation only cures 30-40% of patients. Recent studies show that AMLs with FLT3 receptor activating internal tandem duplication (ITD) mutations (FLT3(ITD)- positive AMLs) become defective in the BRCA1/2 pathway of homologous recombination (HR) following treatment with tyrosine kinase inhibitors (TKi). BRCA-deficiency confers strong sensitivity to DNA damage and/or DNA repair inhibition, and thus presents a promising new therapeutic strategy for AML. We discovered that BRCA-deficient leukemia cells are hyper-dependent on the DNA repair enzyme DNA polymerase theta (Polθ), which is dispensable for normal cells and mice. Polθ is involved in translesion synthesis and the microhomology-mediated end-joining (MMEJ) double-strand break (DSB) repair pathway. Our leading small- molecule Polθ inhibitor (Polθi) kills AML patient cells co-treated with the TKi quizartinib which causes BRCA-deficiency, whereas quizartinib and Polθi as single agents shows significantly less killing. These data demonstrate the Polθi + TKi combination as a promising therapeutic strategy for FLT3(ITD)-positive AML. Polθi also shows preferential killing of other BRCA-deficient leukemias (ALL, CML) in vitro and in vivo, especially in combination with TKi. In summary, our data discover Polθ as a novel drug target in leukemia, and demonstrate Polθi + TKi as a promising therapeutic strategy, especially in aggressive FLT3(ITD)-positive AML. In phase I, Recombination Therapeutics, LLC (RTx), a start-up precision oncology company, plans to increase the potency of our leading Polθi as a novel treatment for FLT3(IDT)-positive AML using X-ray crystallography and structure based optimization/design by developing the following Aims: 1. To solve the co-crystal structure of Polθ-DNA- Polθi ternary complexes; 2. To optimize Polθi using structure based optimization/design.In Phase II, RTx aims to achieve the following goals: 1. Further develop our leading Polθi drug candidate by achieving more favorable ADME and pharmacokinetic parameters; 2. Characterize optimized Polθi in combination with TKi in FLT3(IDT)-positive AML animal models in vivo.Acute myeloid leukemia (AML) is the most frequently diagnosed form of acute leukemia in adults, and standard of care treatment involving chemotherapy and/or stem cell transplantation only cures 30-40% of patients. We discovered DNA polymerase theta (Polθ) as a novel drug target in AML possessing FLT3 receptor mutations, and AML deficient in homology-directed DNA repair (HDR). Recombination Therapeutics, LLC, a precision oncology start-up company, plans to advance our leading Polθ inhibitor as a novel therapeutic for AML using structure based design/optimization.