Nucleotide inhibitors as precision medicine in breast cancer

Breast cancer is the most frequently diagnosed cancer in women, and 15-20% of patients have triple negative breast cancer (TNBC) which results in a 70% mortality rate within 5 years of diagnosis. 10-15% of TNBC patients possess heritable mutations in the BRCA1/BRCA2 tumor suppressor genes which promote homologous recombination (HR) of DNA double-strand breaks (DSBs). BRCA-mutated cells are highly susceptible to DNA damage and DNA repair inhibitors. Although Poly (ADP) ribose polymerase inhibitors (PARPi) cause synthetic lethality in BRCA-deficient cells by suppressing DNA repair and inducing DNA damage, resistance has become a major problem in the clinic. Thus, there is an urgent need for developing additional druggable targets. The DNA repair protein DNA polymerase theta (Polq) is a promising drug target since it is essential for the proliferation of BRCA-mutated cancer cells, but is dispensable for normal cells and mice. Moreover, high Polq expression levels correspond to a poor clinical outcome for the majority (70%) of breast cancer patients. Hence, Polq represents an ideal drug target for eradicating BRCA-mutated breast cancer cells.Nucleoside analog chain terminators have been widely used as FDA approved prodrugs to successfully target polymerases for the treatment of viruses (i.e. HIV and Hepatitis C). Once these analogs are incorporated by the target polymerase (as their triphosphate active metabolite), nucleic acid synthesis becomes terminated. Here, we discovered 2’,3’-dideoxyribonucleoside triphosphates (ddNTPs; chain terminators) as potent nucleotide Polq inhibitors (NPolqi). Remarkably, ddNTPs show absolutely no inhibition of replicative Pols d and e or repair Pols k and h, and show a ~3-fold selectivity for Polq over mitochondrial Polg. These data demonstrate the unexpected finding that replicative Pols are completely resistant to ddNTPs, whereas Polq prefers these chain terminators over canonical dNTPs. Cellular data demonstrate that 2’,3’-dideoxycytosine (ddC), an FDA approved HIV prodrug (Zalcitabine), preferentially kills BRCA1-mutated TNBC cells, with little toxicity in BRCA1-wild-type (WT) cells. ddC also acts in combination with FDA approved olaparib to kill PARPi resistant BRCA1-WT TNBC cells. ddC therefore serves as an initial scaffold for developing novel NPolqi. Recombination Therapeutics, LLC (RTx), a start-up company focusing on precision oncology, will further develop ddC as a novel, potent and selective NPolqi by developing the following Aims: 1. To optimize the potency and selectivity of NPolqi; 2. To test the efficacy of optimized prodrug NPolqi in breast cancer xenograft models. In summary, we expect that these Phase I studies will develop a novel Polq nucleotide inhibitor for provisional patent filing, and demonstrate its ability to halt/slow the growth of breast cancer tumors exhibiting BRCA1 mutations and PARPi resistance.10-15% of triple negative breast cancer (TNBC) patients possess heritable mutations in the BRCA1/BRCA2 tumor suppressor genes which makes these cells highly susceptible to DNA damage and DNA repair inhibitors. DNA polymerase theta (Polq) is a promising drug target in BRCA-mutated TNBC since it is essential for the proliferation of BRCA1/2-mutated cancer cells, but is dispensable for normal cells and mice. Recombination Therapeutics, LLC, a precision oncology start-up company, aims to develop novel nucleotide Polq inhibitors for treating BRCA-mutated and BRCA-wild-type TNBC as a single agent and in combination with PARP inhibitors, respectively.