Structural basis for IL-1α recognition by a modified DNA aptamer that specifically inhibits IL-1α signaling

IL-1α is an essential cytokine that contributes to inflammatory responses and is implicated in various forms of pathogenesis and cancer. Here we report a naphthyl modified DNA aptamer that specifically binds IL-1α and inhibits its signaling pathway. By solving the crystal structure of the IL-1α/aptamer, we provide a high-resolution structure of this critical cytokine and we reveal its functional interaction interface with high-affinity ligands. The non-helical aptamer, which represents a highly compact nucleic acid structure, contains a wealth of new conformational features, including an unknown form of G-quadruplex. The IL-1α/aptamer interface is composed of unusual polar and hydrophobic elements, along with an elaborate hydrogen bonding network that is mediated by sodium ion. IL-1α uses the same interface to interact with both the aptamer and its cognate receptor IL-1RI, thereby suggesting a novel route to immunomodulatory therapeutics.

The cytokine interleukin 1α (IL-1α) plays an important role in inflammatory processes. Here the authors use SELEX to generate a modified DNA aptamer which specifically binds IL-1α, present the structure of the IL-1α/aptamer complex and show that this aptamer inhibits the IL-1α signaling pathway.

Abstract 1798: Identification of pan-Trk inhibitors for the treatment of Trk-driven cancers

The Trk family of genes, which includes trkA/NTRK1, trkB/NTRK2 and trkC/NTRK3, encode the tyrosine kinase receptors for the neurotrophin family of nerve growth factors. Deregulated kinase activity of trk family members is associated with human cancer. Oncogenic translocations involving trkC kinase domain have been identified in AML, salivary gland carcinoma, adult secretory breast cancer, congenital fibrosarcoma, and pediatric nephroma. Oncogenic trkA translocations have been reported in papillary thyroid and colorectal cancers. We have identified orally bioavailable, potent and selective ATP-competitive inhibitors of the trk family of receptor tyrosine kinases and are developing these for the treatment of Trk-driven cancers. AR523 is a pan-Trk inhibitor which demonstrates similar activity against TrkA, TrkB and TrkC receptors in a cell based assay (IC50 ∼10 nM). In a screen at 1 µM against a panel of 230 kinases, AR523 inhibited only three additional kinases more than 50% (TNK2, Bmx and Txk). In cell culture AR523 was found to exhibit selective anti-proliferative activity toward the cell line KM12, which harbors the oncogenic TPM-TrkA translocation, while exhibiting no activity toward HT29, a cell line with no trk gene rearrangements. Studies in mice engrafted with KM12 tumors revealed significant anti-tumor and pharmacodynamic activity of AR523. Administration of a single oral dose of AR523 reduced tyrosine phosphorylation of TrkA by nearly 80% at twelve hours after dosing. Parallel analysis of Akt and Erk revealed reduced phosphorylation of these downstream effectors. Administration of 100 mg AR523 daily for two weeks to mice with KM12 xenografts produced mean tumor growth inhibition of 86% and a mean of 42% tumor regression. AR523 exhibits dose dependent inhibition of tumor growth at 10 and 30 mg/kg in KM12 xenografts with 54 and 72% TGI respectively. AR523 was well-tolerated, causing no weight loss or deaths compared with vehicle control. Increasingly Trk mutations have been shown to be activating and the use of Trk inhibitors may provide a new therapeutic strategy for targeted treatment.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1798. doi:1538-7445.AM2012-1798

Chk1 inhibition and Wee1 inhibition combine synergistically to impede cellular proliferation

Inhibition of the checkpoint kinase Chk1, both as a monotherapy and in combination with DNA damaging cytotoxics, is a promising therapeutic approach for the treatment of a wide array of human cancers. However, much remains to be elucidated in regard to the patient populations that will respond best to a Chk1 inhibitor and the optimal therapeutics to combine with a Chk1 inhibitor. In an effort to discover sensitizing mutations and novel combination strategies for Chk1 inhibition, an siRNA screen was performed in combination with the selective Chk1 inhibitor AR458323. This screen employed a custom made library of siRNAs targeting 195 genes, most of which are involved in cell-cycle control or DNA damage repair. One of the most prominent and consistent hits across runs of the screen performed in three different cancer cell lines was Wee1 kinase. MK-1775 is a small molecule inhibitor of Wee1 that is currently in early stage clinical trials. In confirmation of the results obtained from the siRNA screen, AR458323 and MK-1775 synergistically inhibited proliferation in multiple cancer cell types. This antiproliferative effect correlated with a synergistic induction of apoptosis. In cellular mechanistic studies, the combination of the two molecules resulted in dramatic decreases in inhibitory phosphorylation of cyclin-dependent kinases, an increase in DNA damage, alterations in cell-cycle profile, and collapse of DNA synthesis. In conclusion, the clinical combination of a Chk1 inhibitor and a Wee1 inhibitor holds promise as an effective treatment strategy for cancer.

Single-agent inhibition of Chk1 is antiproliferative in human cancer cell lines in vitro and inhibits tumor xenograft growth in vivo

Chk1 is a serine/threonine kinase that plays several important roles in the cellular response to genotoxic stress. Since many current standard-of-care therapies for human cancer directly damage DNA or inhibit DNA synthesis, there is interest in using small molecule inhibitors of Chk1 to potentiate their clinical activity. Additionally, Chk1 is known to be critically involved in cell cycle progression of unperturbed cells. Therefore, it is plausible that treatment with a Chkl inhibitor alone could also be an efficacious cancer therapy. Here we report that Chk1-A, a potent and highly selective small molecule inhibitor of Chk1, is antiproliferative as a single agent in a variety of human cancer cell lines in vitro. The inhibition of proliferation is associated with collapse of DNA replication and apoptosis. Rapid decreases in inhibitory phosphorylation of CDKs and a concomitant increase in CDK kinase activity and chromatin loading of Cdc45 suggest that the antiproliferative and proapoptotic activity of Chk1-A is at least in part due to deregulation of DNA synthesis. We extend these in vitro studies by demonstrating that Chk1-A inhibits the growth of tumor xenografts in vivo in a treatment regimen that is well tolerated. Together, these results suggest that single-agent inhibition of Chk1 may be an effective treatment strategy for selected human malignancies.

Abstract 2939: Chk1 inhibition and Wee1 inhibition combine synergistically to inhibit cellular proliferation

Inhibition of the checkpoint kinase Chk1, both as a monotherapy and in combination with DNA damaging cytotoxics, is a promising therapeutic strategy for human cancer. However, much remains to be learned in regard to the patient populations that will respond best to a Chk1 inhibitor and the optimal therapeutics to combine with a Chk1 inhibitor. In an effort to discover sensitizing mutations and novel combination strategies for Chk1 inhibition, we performed a synthetic lethality siRNA screen with the selective Chk1 inhibitor Chk1-A. This screen employed a custom made library of siRNAs against 197 genes (3 siRNAs per gene), most of which are involved in cell-cycle control or DNA damage repair. One of the most prominent and consistent hits across runs of the screen performed in PC3, LNCaP, and A549 cell lines was Wee1 kinase. MK-1775 is a small molecule inhibitor of Wee1 that is currently in early stage clinical trials. In confirmation of the results obtained from the siRNA screen, we found that Chk1-A and MK-1775 synergistically inhibited proliferation in multiple cell types. The combination of the two molecules resulted in up to a 5-fold enhancement of anti-proliferative activity compared to what would be expected from pure additivity. This anti-proliferative synergy correlated with a synergistic induction of apoptosis. We explored the mechanism of the impressive synergy by examining the cellular and biochemical effects of the Chk1-A and MK-1775 combination. We found that co-treatment with the two inhibitors resulted in dramatic decreases in inhibitory phosphorylation of cyclin-dependent kinases 1 and 2, increases in DNA damage, and the collapse of DNA replication. In conclusion, the combination of a Chk1 inhibitor and a Wee1 inhibitor may be an effective treatment strategy for cancer.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2939. doi:10.1158/1538-7445.AM2011-2939

Abstract 3874: Single-agent Chk1 inhibition is anti-proliferative in leukemia cells in vitro and in vivo

Chk1 is a serine/threonine kinase that plays important roles in the cellular response to genotoxic stress. For this reason, there is a great deal of interest in using inhibitors of Chk1 to potentiate the effects of DNA-damaging chemotherapeutics. In addition, multiple studies have demonstrated that Chk1 activity is essential during an unperturbed cell cycle to ensure proper DNA replication and maintain genomic integrity. Therefore, it is plausible that a Chk1 inhibitor could also be efficacious as a single-agent therapeutic for human cancer. Here we show that treatment with Chk1-A, a potent and selective inhibitor of Chk1, alone is anti-proliferative against a wide array of cancer cell lines with varying degrees of potency. We sought to understand the mechanisms by which Chk1 inhibition derives the observed anti-proliferative effect. Employing the human leukemia cell line HEL92.1.7, a line particularly sensitive to Chk1 inhibition in terms of proliferation, we characterized the biochemical and functional effects of Chk1-A treatment. We observed concentration-dependent increases in phosphorylation of H2A. X, Chk1, and Chk2, which are markers of DNA damage and cell-cycle checkpoint activation. These biochemical events correlated with S-phase accumulation and eventual apoptosis. In vivo, we found that HEL92.1.7 tumor xenografts were sensitive to oral administration of Chk1-A at a dose that was well tolerated. Together, these studies suggest that inhibition of Chk1 results in DNA damage that induces apoptosis and that use of a Chk1 inhibitor as a single-agent could be an effective strategy to treat certain types of human cancers.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3874.

Abstract B254: Extended target-coverage by selective Chk1 inhibitors enhances pharmacodynamic inhibition of Chk1 signaling and antitumor activity in vivo

Loss of coordination between cell cycle checkpoints and DNA damage repair is a fundamental feature tumor cells rely on for unregulated growth and developing chemotherapeutic resistance. The protein kinase Checkpoint kinase 1 (Chk1) is a sentinel molecule essential for cell cycle arrest at the S and G2M checkpoints, as well as regulating homologous recombination DNA repair. In tumor cells exposed to chemotherapy, Chk1 inhibition overrides cell cycle arrest and DNA repair functions, effectively driving tumor cells into a state of mitotic catastrophe and, ultimately, cell death. We have previously reported in schedule-dependence studies, using Chk1 inhibitors and irinotecan (CPT-11), that oral administration of Chk1 inhibitors allows for multi-day target-coverage, and thus continuous inhibition of Chk1 for a finite period of time, which maximizes anti-tumor efficacy. Here, we extend these studies and investigate the pharmacodynamic relationship to efficacy, as well as the specific biomarkers that are predictive of an anti-tumor effect, when Chk1 inhibitors are administered on a multi-day dosing schedule. Utilizing potent (IC50=24–27nM), selective, and orally bio-available small molecule Chk1 inhibitors of which Chk1-A and Chk1-C are representative, we find only modest inhibition of the functional biomarker phospho-cdc2, following a single dose of a Chk1 inhibitor. Alternatively, on multi-day Chk1 inhibitor dose schedules, we find dose-related pharmacodynamic inhibition of Chk1 signaling that is maximized at doses where we see significant tumor growth inhibition in efficacy experiments. Furthermore, multi-day dosing of Chk1 inhibitors induces marked inhibition of phospho-cdc2 and Rad51 protein levels, suggesting tumoricidal activity related to Chk1 inhibition is due to both checkpoint override and impairment of DNA damage repair. In human tumor xenografts administered combination therapy with gemcitabine, an orally-delivered Chk1 inhibitor dosed on a multi-day schedule shows superior efficacy over an IV administered compound. Taken together, our findings show a clear correlative relationship between pharmacodynamic target inhibition and anti-tumor activity that is exclusively achieved on multi-day dose schedules. These results demonstrate the need for prolonged Chk1 inhibition to provide robust pharmacodynamic inhibition and maximal anti-tumor efficacy.

Citation Information: Mol Cancer Ther 2009;8(12 Suppl):B254.