Structure-Guided Optimization of Replication Protein A (RPA)–DNA Interaction Inhibitors

Replication protein A (RPA) is the major human single stranded DNA (ssDNA)-binding protein, playing essential roles in DNA replication, repair, recombination, and DNA-damage response (DDR). Inhibition of RPA–DNA interactions represents a therapeutic strategy for cancer drug discovery and has great potential to provide single agent anticancer activity and to synergize with both common DNA damaging chemotherapeutics and newer targeted anticancer agents. In this letter, a new series of analogues based on our previously reported TDRL-551 (4) compound were designed to improve potency and physicochemical properties. Molecular docking studies guided molecular insights, and further SAR exploration led to the identification of a series of novel compounds with low micromolar RPA inhibitory activity, increased solubility, and excellent cellular up-take. Among a series of analogues, compounds 43, 44, 45, and 46 hold promise for further development of novel anticancer agents

In Vivo Targeting Replication Protein A for Cancer Therapy

Replication protein A (RPA) plays essential roles in DNA replication, repair, recombination, and the DNA damage response (DDR). Retrospective analysis of lung cancer patient data demonstrates high RPA expression as a negative prognostic biomarker for overall survival in smoking-related lung cancers. Similarly, relative expression of RPA is a predictive marker for response to chemotherapy. These observations are consistent with the increase in RPA expression serving as an adaptive mechanism that allows tolerance of the genotoxic stress resulting from carcinogen exposure. We have developed second-generation RPA inhibitors (RPAis) that block the RPA-DNA interaction and optimized formulation for in vivo analyses. Data demonstrate that unlike first-generation RPAis, second-generation molecules show increased cellular permeability and induce cell death via apoptosis. Second-generation RPAis elicit single-agent in vitro anticancer activity across a broad spectrum of cancers, and the cellular response suggests existence of a threshold before chemical RPA exhaustion induces cell death. Chemical RPA inhibition potentiates the anticancer activity of a series of DDR inhibitors and traditional DNA-damaging cancer therapeutics. Consistent with chemical RPA exhaustion, we demonstrate that the effects of RPAi on replication fork dynamics are similar to other known DDR inhibitors. An optimized formulation of RPAi NERx 329 was developed that resulted in single-agent anticancer activity in two non-small cell lung cancer models. These data demonstrate a unique mechanism of action of RPAis eliciting a state of chemical RPA exhaustion and suggest they will provide an effective therapeutic option for difficult-to-treat lung cancers

Discovery and development of novel DNA-PK inhibitors by targeting the unique Ku–DNA interaction

DNA-dependent protein kinase (DNA-PK) plays a critical role in the non-homologous end joining (NHEJ) repair pathway and the DNA damage response (DDR). DNA-PK has therefore been pursued for the development of anti-cancer therapeutics in combination with ionizing radiation (IR). We report the discovery of a new class of DNA-PK inhibitors that act via a novel mechanism of action, inhibition of the Ku-DNA interaction. We have developed a series of highly potent and specific Ku-DNA binding inhibitors (Ku-DBi's) that block the Ku-DNA interaction and inhibit DNA-PK kinase activity. Ku-DBi's directly interact with the Ku and inhibit in vitro NHEJ, cellular NHEJ, and potentiate the cellular activity of radiomimetic agents and IR. Analysis of Ku-null cells demonstrates that Ku-DBi's cellular activity is a direct result of Ku inhibition, as Ku-null cells are insensitive to Ku-DBi's. The utility of Ku-DBi's was also revealed in a CRISPR gene-editing model where we demonstrate that the efficiency of gene insertion events was increased in cells pre-treated with Ku-DBi's, consistent with inhibition of NHEJ and activation of homologous recombination to facilitate gene insertion. These data demonstrate the discovery and application of new series of compounds that modulate DNA repair pathways via a unique mechanism of action

Abstract 1406: Design and synthesis of novel cardiac glycosides by targeting the DNA damage response for cancer therapy

Abstract Cardiac Glycosides (CGs) are used to treat congestive heart disease. Their application has since been extended to cancer treatment. While the mechanism of action is still unknown, it was previously believed that Na+/K+ ATPase might play a crucial role in cancer mitigation. However, we recently reported that cardiac glycosides could specifically enhance the anti-cancer effect of chemotherapy in KRAS mutant lung cancer by inhibiting the DNA Damage Response (DDR), and these effects were independent of the Na+/K+ ATPase. Mechanistically, we showed that cardiac glycosides induced the degradation of UHRF1, an important player in promoting DNA double strand break (DSB) repair through homologous recombination. These results suggest the promise of derivatizing cardiac glycosides into potential chemo sensitizing agents. Yet, one of the major challenges with these compounds is their cardiotoxicity. This has created a need for developing a strategy to generate less cardiotoxic drugs that are effective in inhibiting the DNA damage response to safe and effective anticancer activity. Herein we report a multi-step synthetic route utilizing k-strophanthidin as the initial building block. A systematic structural design was applied that included modification of the sugar moiety, glycoside linker, stereochemistry, and lactone ring to create a library of O-glycosides and MeON-neoglycosides. These molecules were screened for anti-cancer properties by exploring their influence on the signaling/expression of various downstream kinases in the DDR pathway. We discovered the inhibitory activity of O-glycosides to be more potent than the MeON-neoglycosides or benzylidene-lactone modified compounds. These results demonstrate the ability to chemically synthesize CG derivatives to optimize for anticancer activity with the goal of identifying less cardiotoxic CGs. Citation Format: Diana Ainembabazi, Xinran Geng, Navnath Gavande, YouWei Zhang, John Turchi. Design and synthesis of novel cardiac glycosides by targeting the DNA damage response for cancer therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1406.</jats:p

Abstract B34: Development of novel small molecule inhibitors targeting DNA repair proteins

Abstract More than 1.6 million new cases of cancer will be diagnosed in the US in 2016 and a third of these will be from solid tumor of the lung, pancreas, breast, and ovary. These cancers represent a continuing clinical challenge in treatment and together account for over 250,000 deaths in the US alone, representing over 40% of all cancer deaths. There are limited therapeutic options for these patients, and targeted and combination therapies remain necessary for treating these aggressive cancers. The opportunity exists to exploit recent scientific advances in our knowledge of the underlying biology behind these cancers to create novel targeted therapeutics to dramatically enhance patient response to therapy and ultimately survival. To this end, we have developed a series of novel small chemical molecules that disrupt critical protein-DNA interactions in the nucleotide excision and non-homologous end joining DNA repair pathways. It is well understood that various cancer treatments like cisplatin, etoposide and ionizing radiation impart their chemotherapeutic effect by the formation of direct DNA damage which block DNA replication and transcription culminating in apoptosis. It is also well established that repair of this DNA damage by various DNA repair pathways reduces the effectiveness of chemo- or radio- therapy. It is our contention, borne out by analysis of clinical data to be presented on the development of our DNA repair inhibitors, that inhibition of these DNA repair pathways sensitizes these difficult to treat cancers to traditional DNA-damaging therapy. We anticipate both direct mechanisms of action on the repair pathways and synthetic lethal interactions can be exploited for therapeutic benefit. The series of novel small molecule inhibitors that we have developed targeting DNA repair proteins exhibit single-agent anti-cancer activity in cancer cell lines, and potentiate cellular sensitivity to chemotherapy and ionizing radiation treatment. Our data demonstrate that this class of inhibitors can be further developed as anti-cancer therapeutics with considerable potential to be used in conjunction with radiation therapy and other cancer therapies that induce DNA damage. Citation Format: Katherine S. Pawelczak, Navnath Gavande, Pamela VanderVere-Carozza, John Turchi. Development of novel small molecule inhibitors targeting DNA repair proteins [abstract]. In: Proceedings of the AACR Special Conference on DNA Repair: Tumor Development and Therapeutic Response; 2016 Nov 2-5; Montreal, QC, Canada. Philadelphia (PA): AACR; Mol Cancer Res 2017;15(4_Suppl):Abstract nr B34.</jats:p

Antidepressant, anticonvulsant and antinociceptive effects of 3'-methoxy-6-methylflavone and 3'-hydroxy-6-methylflavone may involve GABAergic mechanisms

BACKGROUND: GABAA receptors have been implicated in the pathophysiology of depression, epilepsy and pain disorders. The purpose of this study was to investigate two novel synthetic flavones, 3'-methoxy-6-methylflavone (3'-MeO6MF) and 3'-hydroxy-6-methylflavone (3'-OH6MF), for their effect on GABAA receptors and subsequently investigate their antidepressant, anticonvulsant and antinociceptive effects.METHODS: Recombinant GABAA receptor subunits were expressed in Xenopus oocytes and a two electrode voltage clamp technique was used for electrophysiological studies. The antidepressant and anticonvulsant activities were determined using forced swim (FST) and tail suspension tests (TST) and bicuculline (BIC)-induced seizures respectively. Furthermore, the antinociceptive activity was determined using tail immersion and hot plate tests.RESULTS: 3'-MeO6MF and 3'-OH6MF potentiated GABA-induced currents through ternary α1-2β1-3γ2L and binary α1β2 receptors indicating that the positive modulation by these flavonoids is not dependent on the γ subunit. In behavioral studies, 3'-MeO6MF and 3'-OH6MF (10-100mg/kg, ip) exerted significant antidepressant like effects in the FST and TST. 3'-MeO6MF (10-100mg/kg) and 3'-OH6MF (30 and 100mg/kg) also exhibited significant anticonvulsant effects in BIC-induced seizures, and antinociceptive activity in tail immersion and hot plate tests (*p&lt;0.05, **p&lt;0.01, ***p&lt;0.001). Furthermore, the antidepressant and antinociceptive activities of 3'-MeO6MF and 3'-OH6MF were partially ameliorated by co-administration of BIC (3mg/kg) suggesting the involvement of GABAergic mechanisms.CONCLUSION: The findings of this study suggest that 3'-MeO6MF and 3'-OH6MF exhibited significant antidepressant, anticonvulsant and antinociceptive effects mediated via interactions with GABAA receptors.</p

Abstract C58: Small molecule inhibitors targeting the interaction of xeroderma pigmentosum group A protein with cisplatin-damaged DNA

Abstract Targeting DNA repair and the DNA damage response for cancer therapy has recently gained increasing attention with inhibitors of the PI3-K-like kinases in early stage clinical trials. The utility of DNA repair inhibitors can be expanded by their use in combination treatment with DNA damaging chemotherapeutics including cisplatin. We have focused on directly targeting the DNA repair pathway responsible for repairing platinum-induced DNA damage, nucleotide excision repair (NER). We have selected the molecular target XPA, whose role is in the identification and verification of the sites of DNA damage. Clinical validation of XPA has been obtained where high XPA expression in lung, ovarian and lung cancer results in decreased efficacy of platinum therapy. We report the continued development of the X80 class of XPA small molecule inhibitors. In a two-step, iterative process we have identified critical structure activity relationships that have resulted in a 100-fold increase in potency with in vitro IC50 values below 1μM. Analyses of the SARs define the chemical and structural features that impact the interaction with XPA, cellular permeability and contribute to selectivity. Data demonstrate that the X80 class of inhibitors do not interact with DNA but directly bind the XPA protein. Recent production of a sub-fragment of the XPA protein will allow the identification of the direct binding domain to enable continued structure-based design of more potent XPA inhibitors. Supported by NIH grants R01CA180710 and R41CA162648 to JJT. Citation Format: Pamela S. VanderVere-Carozza, Navnath Gavande, Akaash Mishra, John J. Turchi. Small molecule inhibitors targeting the interaction of xeroderma pigmentosum group A protein with cisplatin-damaged DNA. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr C58.</jats:p

Targeting DNA-PK and the DNA Damage Response via Small Molecule Ku Inhibitors

The DNA dependent protein kinase (DNA-PK) is a validated target for cancer therapeutics that drives the DNA damage response (DDR) and plays a critical role as a primary sensor in the non-homologous end joining (NHEJ) DNA double strand break (DSB) repair pathway. Various anti-cancer therapeutic strategies mediate their cytotoxic effects by inducing DSBs, inducing ionizing radiation (IR), and clinical outcomes are directly related to the repair of DNA damage. Modulating the pathway responsible for repairing DSBs will have a profound impact on the efficacy of DNA damaging agents in the clinic. To date, development of inhibitors for DNA-PK has focused on targeting the active site with ATP mimetics. We have taken the novel and innovative approach to inhibiting DNA-PK via blocking the Ku 70/80 heterodimer interaction with DNA, a necessary step in DNA-PK activation. Exploiting this unique mechanism of kinase activa-tion, we have identified a series of highly potent and specific DNA-PK inhibitors that impart their inhibitory activity via disruption of the binding of Ku protein to DNA ends. This novel approach affords significant advantages to current approaches in kinase inhibition. Novel derivatives of our initial hit inhibit DNA-PK catalytic activity at nanomo-lar concentrations and potentiate cellular sensitivity to DSB-inducing agents like etopo-side and bleomycin. Data demonstrate that the cellular effects observed are a function of Ku inhibition and that this novel class of DNA-PK inhibitors can be further developed as anti-cancer therapeutics that can be used as an adjuvant to, or concomitant with radiotherapy and other cancer therapies that induce DNA damage