PURPOSE Preclinical studies demonstrated that ATR inhibition can exploit synthetic lethality (eg, in cancer cells with impaired compensatory DNA damage responses through ATM loss) as monotherapy and combined with DNA-damaging drugs such as carboplatin. PATIENTS AND METHODS This phase I trial assessed the ATR inhibitor M6620 (VX-970) as monotherapy (once or twice weekly) and combined with carboplatin (carboplatin on day 1 and M6620 on days 2 and 9 in 21-day cycles). Primary objectives were safety, tolerability, and maximum tolerated dose; secondary objectives included pharmacokinetics and antitumor activity; exploratory objectives included pharmacodynamics in timed paired tumor biopsies. RESULTS Forty patients were enrolled; 17 received M6620 monotherapy, which was safe and well tolerated. The recommended phase II dose (RP2D) for once- or twice-weekly administration was 240 mg/m 2 . A patient with metastatic colorectal cancer harboring molecular aberrations, including ATM loss and an ARID1A mutation, achieved RECISTv1.1 complete response and maintained this response, with a progression-free survival of 29 months at last assessment. Twenty-three patients received M6620 with carboplatin, with mechanism-based hematologic toxicities at higher doses, requiring dose delays and reductions. The RP2D for combination therapy was M6620 90 mg/m 2 with carboplatin AUC5. A patient with advanced germline BRCA1 ovarian cancer achieved RECISTv1.1 partial response and Gynecologic Cancer Intergroup CA125 response despite being platinum refractory and PARP inhibitor resistant. An additional 15 patients had RECISTv1.1 stable disease as best response. Pharmacokinetics were dose proportional and exceeded preclinical efficacious levels. Pharmacodynamic studies demonstrated substantial inhibition of phosphorylation of CHK1, the downstream ATR substrate. CONCLUSION To our knowledge, this report is the first of an ATR inhibitor as monotherapy and combined with carboplatin. M6620 was well tolerated, with target engagement and preliminary antitumor responses observed.

Chromosome instability (CIN) is deleterious to normal cells because of the burden of aneuploidy. However, most human solid tumors have an abnormal karyotype implying that gain and loss of chromosomes by cancer cells confers a selective advantage. CIN can be induced in the mouse by inactivating the spindle assembly checkpoint. This is lethal in the germline but we show here that adult T cells and hepatocytes can survive conditional inactivation of the Mad2l1 SAC gene and resulting CIN. This causes rapid onset of acute lymphoblastic leukemia (T-ALL) and progressive development of hepatocellular carcinoma (HCC), both lethal diseases. The resulting DNA copy number variation and patterns of chromosome loss and gain are tumor-type specific, suggesting differential selective pressures on the two tumor cell types.

2504 Background: ATR is a regulator of cellular responses to replication stress, where it signals DNA damage repair by homologous recombination. Many cells depend on ATR to survive DNA damage. VX-970 is a potent, selective ATR inhibitor with marked preclinical antitumor activity in combo with chemotherapy. Methods: Patients (pts) with advanced cancers were enrolled in 2 parts. Part A: N=1 pt cohorts received VX-970 QW; 3 + 3 cohorts were commenced if ³ G2 drug-related toxicities occurred. Part B: 3 + 3 pt cohorts received CP on d1 + VX-970 on d2 and 9 in 21-day cycles. Timed pre- and post-VX-970 tumor biopsies were assessed for pS345 CHK1 levels by IHC in part B. Hematologic toxicities were modeled for pts in part B. Results: 26 pts were treated; M/F 10/16, ECOG PS 0/1: 9/17. Median age: 66 yrs (range 49-76 years). VX-970 was generally well tolerated as mono or CP combo with mainly G1-2 toxicities. CP dose delays and reductions occurred in 3/3 pts (B1); 2/2 pts (B2); 0/3 pts (B3); 1/6 pts (B4) due to neutropenia and/or thrombocytopenia. Clinical data were consistent with toxicity modeling that predicted probabilities of ≤5% G4 neutropenia and <1% thrombocytopenia at B4. Recommended phase 2 doses (RP2D) were DL A3 (mono) and B4 (CP combo). VX-970 PK was dose proportional with no CP interaction. VX-970 PK exposures at combo RP2D led to tumor regression in mouse models. Tumor biopsy studies showed decreased pCHK1 by 73-90% after VX-970. In part A, a pt with ATM loss colorectal cancer had RECIST complete response (19 mths+) and 4 pts had RECIST stable disease (SD). In part B: a pt with germline BRCA1 mutant and platinum-refractory, PARP inhibitor-resistant ovarian cancer with a somatic Y220C TP53 mutation had RECIST partial response for 6 mths and 8 pts had RECIST SD. Conclusions: VX-970 is generally well tolerated as mono and in CP combo with early evidence of PD and antitumor activity. VX-970 is now being tested in phase 2 combo trials and as mono in pts with DNA repair defects. Clinical trial information: 2013. Clinical trial information: #8209;005100. Clinical trial information: #8209;34.Dose Level (DL) VX-970 dose (mg/m2) CP dose (AUC) # pts Dose limiting toxicities A1 60 - 1 - A2 120 - 2 - A3 240 - 1 - A4 480 - 7 - B1 240 5 3 Febrile neutropenia B2 120 5 3 Hypersensitivity B3 120 4 3 - B4 90 5 6 Febrile neutropenia

Abstract Proficient repair of DNA damage is a cause of the poor response many patients experience when treated with commonly used DNA-damaging drugs such as cisplatin, carboplatin and gemcitabine. The protein kinase ataxia telangiectasia mutated and Rad3 related (ATR) is recruited to DNA damage lesions caused by such drugs during the S and G2 phase of cell cycle, where it coordinates a series of responses including checkpoint activation and DNA repair by homologous recombination. Inhibition of ATR potentiates the cytotoxic activity of DNA damaging drugs in many cancer cells. In stark contrast, non-cancer cells survive inhibition of ATR with just transient growth arrest. Cancer cells carrying common defects in a compensatory repair pathway mediated by the kinase ataxia telangiectasia mutated (ATM) and its principle substrate, p53, are especially sensitive to ATR inhibition. Two ATR inhibitors are in clinical development in combination with DNA damaging drugs, however a comprehensive assessment of dose schedule considerations has not been reported. In pre-clinical models, the efficacy of an ATR inhibitor in combination with multiple DNA damaging drugs was shown to be dependent on dose schedule. In vitro, transient exposure of cancer cells to an ATR inhibitor (2 hours) was highly effective when added after the DNA damaging drug. Maximum activity was observed when addition of the ATR inhibitor was timed to coincide with peak accumulation of cells in S-phase and concomitant activation of ATR (P-Chk1), following treatment with the DNA damaging drug. In mouse xenograft models, strong synergistic activity was achieved from just a single dose of the ATR inhibitor given once per cycle of the DNA damaging drug. Optimal efficacy was achieved by administering the ATR inhibitor 12-24 hours after the DNA damaging drug. Dosing the ATR inhibitor prior to, or greater than 48 hours after, the DNA damaging drug provided limited benefit. On this schedule, addition of the ATR inhibitor had minimal impact on the tolerability profile of the DNA damaging drug. VX-970, the first-in-class ATR inhibitor, is being assessed as monotherapy and in combination with gemcitabine, cisplatin and carboplatin in Ph1/2 clinical studies. Based on pre-clinical data, VX-970 is being dosed approximately 24 hours after the DNA damaging drug. Preliminary tumor biomarker data from three patients showed high P-Chk1 24 hours after treatment with carboplatin, which is inhibited by VX-970. These data suggest the importance of dose scheduling on the efficacy of ATR inhibitors and DNA damaging drug combinations and inform the design of ongoing clinical studies. Citation Format: John Pollard, Phil Reaper, Adele Peek, Stuart Hughes, Scott Gladwell, Julie Jones, Peter Chiu, Mark Wood, Crystal Tolman, Mac Johnson, Peter Littlewood, Marina Penney, Katherine McDermott, Brian Hare, Scott Z. Fields, Mohammed Asmal, Brent O’Carrigan, Timothy A. Yap. Defining optimal dose schedules for ATR inhibitors in combination with DNA damaging drugs: Informing clinical studies of VX-970, the first-in-class ATR inhibitor. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3717.

Proficient repair of DNA damage is important for cancer cell survival and is a leading cause for the poor response many patients experience when treated with DNA-damaging drugs or ionizing radiation. The protein kinase ataxia telangiectasia mutated and Rad3 related (ATR) regulates an important DNA damage response pathway that is most commonly activated by replication stress (RS). RS arises during S-phase when the cell9s DNA replication machinery attempts to copy through an unresolved damage lesion. Such events are common after cells are treated with DNA-damaging agents. Unresolved RS often leads to double strand breaks, which in turn may cause DNA mutations, chromosomal rearrangements or cell death. Pre-clinical data suggests a reliance on ATR for survival is a common feature in cancer cells. This may occur when there are defects in other DNA damage repair pathways or high levels of background RS. VX-970 is the first potent (Ki VX-970 is currently in Phase 1 clinical studies as monotherapy and in combination with gemcitabine, cisplatin and carboplatin. Note: This abstract was not presented at the meeting. Citation Format: John Pollard, Philip Reaper, Julie Jones, Christopher Barnes, Scott Gladwell, Stuart Hughes, Adele Peak, Hakim Djeha, Amy Hall, David Newsome, Yuxin Wang, Diane Boucher, Brenda Eustace, Yong Gu, Brian Hare, Mac Johnson, Sean Milton, Cheryl Murphy, Darin Takemoto, Crystal Tolman, Mark Wood, Brinley Furey, Marina Penney, Howard Li, Christopher Defranco, Mohammed Asmal, Scott Fields. VX-970, the first-in-class inhibitor of the DNA damage repair enzyme ATR. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1644. doi:10.1158/1538-7445.AM2015-1644

This data article contains Supplementary material for a published research article describing a whole-blood proteomic signature that predicts treatment outcome for subjects infected with hepatitis C virus (HCV) [1]. The proteomic signature is derived from whole-blood samples from subjects infected with HCV. The article includes detailed experimental and computational methods used in the analysis. The article also includes tables of demographic and other information about the subjects. Finally, the article includes several figures and tables showing detailed results of the analyses (e.g. lists of identified proteins and coefficients/ROC curves for the regression models).

Platinum-based DNA-damaging chemotherapy is standard-of-care for most patients with lung cancer but outcomes remain poor. This has been attributed, in part, to the highly effective repair network known as the DNA-damage response (DDR). ATR kinase is a critical regulator of this pathway, and its inhibition has been shown to sensitize some cancer, but not normal, cells in vitro to DNA damaging agents. However, there are limited in vivo proof-of-concept data for ATR inhibition. To address this we profiled VX-970, the first clinical ATR inhibitor, in a series of in vitro and in vivo lung cancer models and compared it with an inhibitor of the downstream kinase Chk1. VX-970 markedly sensitized a large proportion of a lung cancer cell line and primary tumor panel in vitro to multiple DNA damaging drugs with clear differences to Chk1 inhibition observed. In vivo VX-970 blocked ATR activity in tumors and dramatically enhanced the efficacy of cisplatin across a panel of patient derived primary lung xenografts. The combination led to complete tumor growth inhibition in three cisplatin-insensitive models and durable tumor regression in a cisplatin-sensitive model. These data provide a strong rationale for the clinical evaluation of VX-970 in lung cancer patients.

Abstract DNA damaging agents have been the cornerstone of cancer therapy for decades yet they provide only modest benefit for most patients. For example, standard of care for patients with non-small cell lung cancer (NSCLC) is dominated by the use of platinating drugs and ionizing radiation (IR), however outcome remains very poor with 5-year survival rates of <15% for patients that present with advanced disease. Such poor responses to DNA damaging treatment reflects, in part, the efficient repair of DNA damage via a complex signaling and repair network known as the DNA damage response (DDR). The DDR detects double strand breaks and replication stress, the most lethal forms of DNA damage, and acts to enforce checkpoints to halt cell cycle progression, and to stimulate repair. Key regulators of the DDR are the phosphoinositol 3-kinase-like serine/threonine protein kinase (PIKK) family members ATR and ATM. Recent pre-clinical data has suggested that a reliance on ATR for survival from DNA damage may be a common feature of cancer. This can arise either as a consequence of high replicative stress, for example from expression of certain oncogenes, from a hypoxic microenvironment, or from defects elsewhere in DNA damage surveillance and repair pathways. Most notably inhibition of ATR has been shown to be synthetic lethal with loss of the ATM-p53 pathway. In NSCLC defective ATM signaling, from loss of ATM expression or from defects in p53 has been reported in about 50% of tumors. Here we describe the comprehensive in vitro and in vivo profile for VE-822 a novel highly potent and selective inhibitor of ATR. VE-822 potently inhibits ATR in biochemical assays with Ki <0.3nM and in cell assays with IC50 of 20nM. Against a large panel of NSCLC lines, low concentrations of VE-822 sensitized many lines to the cytotoxic effects of multiple DNA damaging agents; for example >90% of lines showed >3-fold shifts in IC50 for cisplatin in the presence of VE-822, with ~50% of lines showing >10-fold increases in cisplatin cytotoxicity. In contrast normal cells tolerate inhibition of ATR. In a panel of mouse xenograft models, derived from various primary human NSCLC tumor tissues, oral or IV administration of VE-822 strongly sensitized tumors to cisplatin treatment. In many cases, combinations including VE-822 led to tumor regression or extensive tumor growth delay. Inhibition of ATR activity and accumulation of DNA damage by VE-822 was observed coincident with efficacy. When administered alone or in combination with cisplatin VE-822 was well tolerated in mice at doses that block ATR activity. These data support the potential for ATR inhibitors to substantially increase the efficacy of standard-of-care agents in diseases such as NSCLC. Citation Format: Diane Boucher, Peter Charlton, Jean-Damien Charrier, Brinley Furey, Yong Gu, Amy Hall, Brian Hare, Howard Li, Sean Milton, Cheryl Murphy, Philip Reaper, Darin Takemoto, Taturo Udagawa, Yuxin Wang, Mark Wood, John Pollard. Comprehensive preclinical evaluation of VE-822, the first ATR-targeted drug candidate: a novel approach to transforming the efficacy of DNA damaging agents. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-299. doi:10.1158/1538-7445.AM2013-LB-299

Abstract DNA damaging agents have been the cornerstone of solid cancer therapy for decades yet they provide only modest benefit for patients with many tumor types. This reflects, in part, the efficient repair of DNA damage via a complex signaling and repair network known as the DNA damage response (DDR). Key regulators of the DDR are the phosphoinositol 3-kinase-like serine/threonine protein kinase (PIKK) family members ATR, ATM and DNA-PK. The DDR acts to detect DNA lesions, enforce checkpoints to halt cell cycle progression, and stimulate repair. Recent data have shown that elements of the DDR are commonly defective in cancer cells. It is widely believed that these cells become dependent on the remaining DDR pathways for survival from DNA damage. Inhibitors have been reported for a number of DDR enzymes, including ATM, DNA-PK, CHK1 and PARP, however there are no reports of drug-like ATR inhibitors. Here we disclose the in vitro characterization of a potent and highly selective ATR inhibitor (VE-821). This compound selectively blocks ATR signaling in cells (IC50 = 0.7 µM), but has little impact on ATM or DNA-PK signaling (IC50 >10 µM). Treatment with 10 µM VE-821 for 144 h causes little cell death in normal cell lines (5-11 %) but markedly higher death in cancer cell lines (28-46 %). VE-821 also dramatically sensitizes many cancer cells to multiple classes of genotoxic agents including antimetabolites, topoisomerase inhibitors and crosslinking agents; with over 10-fold increases genotoxic potency observed in some cases. In a panel of 36 lung cancer cell lines, VE-821 sensitized the cytotoxic effect of cisplatin to a far greater magnitude and over a broader subset of these lines than potent inhibitors of ATM, Chk1, or PARP. In over half of these cell lines, the IC50 of cisplatin was reduced by greater than 5 fold upon the addition of VE-821. We show that a basis for the cancer-selective effects of VE-821 is a synthetic lethal interaction between loss of ATM signaling (a frequent event in cancer resulting from loss of function of proteins such as ATM or p53) and ATR inhibition when cells encounter DNA damage. In keeping with this, ATR inhibition does not sensitize normal cells (with functional ATM) to the cytotoxic effects of genotoxic therapy. In this case a compensatory DDR is activated that is associated with marked activation of ATM, which in turn leads to reversible checkpoint arrest and a strong survival response. These studies show for the first time that a selective ATR inhibitor can preferentially sensitize cancer cells to genotoxic drugs by exploiting a synthetic lethal interaction between ATM and ATR signaling. This underpins the broad potential of ATR inhibition as a highly promising new strategy to improve the efficacy of genotoxic therapy. 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 5491. doi:10.1158/1538-7445.AM2011-5491

Variants resistant to compounds specifically targeting HCV are observed in clinical trials. A multi-variant viral dynamic model was developed to quantify the evolution and in vivo fitness of variants in subjects dosed with monotherapy of an HCV protease inhibitor, telaprevir. Variant fitness was estimated using a model in which variants were selected by competition for shared limited replication space. Fitness was represented in the absence of telaprevir by different variant production rate constants and in the presence of telaprevir by additional antiviral blockage by telaprevir. Model parameters, including rate constants for viral production, clearance, and effective telaprevir concentration, were estimated from 1) plasma HCV RNA levels of subjects before, during, and after dosing, 2) post-dosing prevalence of plasma variants from subjects, and 3) sensitivity of variants to telaprevir in the HCV replicon. The model provided a good fit to plasma HCV RNA levels observed both during and after telaprevir dosing, as well as to variant prevalence observed after telaprevir dosing. After an initial sharp decline in HCV RNA levels during dosing with telaprevir, HCV RNA levels increased in some subjects. The model predicted this increase to be caused by pre-existing variants with sufficient fitness to expand once available replication space increased due to rapid clearance of wild-type (WT) virus. The average replicative fitness estimates in the absence of telaprevir ranged from 1% to 68% of WT fitness. Compared to the relative fitness method, the in vivo estimates from the viral dynamic model corresponded more closely to in vitro replicon data, as well as to qualitative behaviors observed in both on-dosing and long-term post-dosing clinical data. The modeling fitness estimates were robust in sensitivity analyses in which the restoration dynamics of replication space and assumptions of HCV mutation rates were varied.

We report herein the design and synthesis of 4-(benzimidazol-2-yl)-1,2,5-oxadiazol-3-amine derivatives as inhibitors of p70S6 kinase. Screening hits containing the 4-(benzimidazol-2-yl)-1,2,5-oxadiazol-3-ylamine scaffold were optimized for p70S6K potency and selectivity against related kinases. Structure-based design employing an active site homology model derived from PKA led to the preparation of benzimidazole 5-substituted compounds 26 and 27 as highly potent inhibitors (K(i) <1nM) of p70S6K, with >100-fold selectivity against PKA, ROCK and GSK3.

Background Telaprevir (TVR) is a hepatitis C virus (HCV) NS3.4A protease inhibitor that has exhibited antiviral activity in patients with HCV genotype 1 infection. The viral dynamics in patients dosed with TVR were compared with those reported for patients treated with interferon (IFN). Methods The dynamics of wild-type HCV genotype 1 in patients dosed with TVR monotherapy ( n=36) and TVR plus pegylated interferon (PEG-IFN)-α2a ( n=8) were quantified using a biphasic viral dynamic model. Results Patients dosed with either TVR monotherapy or TVR plus PEG-IFN-α2a had median first and second phase decreases of 12 per day and 1.1 per day, respectively. The second phase decrease was approximately 10-fold higher than reported values for IFN-based treatments ( P<0.0001). Patients dosed with TVR plus PEG-IFN-α2a had a median remaining viral production after blockage (1-ε) of -2.37 log10. In patients dosed with TVR mono-therapy, increased TVR dosage of the same schedule was related to better blockage. Conclusions These results suggested that TVR-based regimens for chronic HCV infection will lead to an early and more rapid viral decrease that could potentially result in higher sustained viral response rates as well as offer the potential for a reduced duration of treatment.

Magnetically oriented lipid/detergent bilayers arepotentially useful forstudies ofmembrane-associated mol- ecules andcomplexes using x-rayscattering andnuclear magnetic resonance(NMR). Toestablish whetherthesystemisa reasonable modelofa phospholipid bilayer, we havestudied thesystemusing x-raysolution scattering todetermine the bilayer thickness, interparticle spacing, andorientational parameters formagnetically oriented lipid bilayers. Themagnetically orientable samples contain thephospholipid L-a-dilauroylphosphatidylcholine (DLPC) andthebilesaltanalog 3-((3-cholami- dopropyl)dimethylammonio)-2-hydroxy-1 -propanesulfonate (CHAPSO) ina3:1molarratio in70% water(w/v) andaresimilar tomagnetically orientable samples usedasNMR mediaforstructural studies ofmembrane-associated molecules. A bilayer thickness of30A was determined fortheDLPC/CHAPSOparticles, whichisthesame asthebilayer thickness ofpureDLPC vesicles, suggesting thattheCHAPSO isnotgreatly perturbing thelipid bilayer. Thesedata, as wellas NMR dataon molecules incorporated intheoriented lipid particles, areconsistent withthesampleconsisting ofreasonably homogeneous andwelldispersed lipid particles. Finally, theorientational energyofthesamplesuggests thatthesizeofthecooperatively orienting unitinthesamples is2 x 107phospholipid molecules.