Discovery and optimization of 1-(1H-indol-1-yl)ethanone derivatives as CBP/EP300 bromodomain inhibitors for the treatment of castration-resistant prostate cancer

The CREB (cAMP responsive element binding protein) binding protein (CBP) and its homolog EP300 have emerged as new therapeutic targets for the treatment of cancer and inflammatory diseases. Here we report the identification, optimization and evaluation of 1-(1H-indol-1-yl)ethanone derivatives as CBP/EP300 inhibitors starting from fragment-based virtual screening (FBVS). A cocrystal structure of the inhibitor (22e) in complex with CBP provides a solid structural basis for further optimization. The most potent compound 32h binds to the CBP bromodomain and has an IC₅₀ value of 0.037 μM in the AlphaScreen assay which was 2 times more potent than the reported CBP bromodomain inhibitor SGC-CBP30 in our hands. 32h also exhibit high selectivity for CBP/EP300 over other bromodomain-containing proteins. Notably, the ester derivative (29h) of compound 32h markedly inhibits cell growth in several prostate cancer cell lines including LNCaP, 22Rv1 and LNCaP derived C4-2B. Compound 29h suppresses the mRNA expression of full length AR (AR-FL), AR target genes and other oncogene in LNCaP cells. 29h also reduces the expression of PSA, the biomarker of prostate cancer. CBP/EP300 inhibitor 29h represents a promising lead compound for the development of new therapeutics for the treatment of castration-resistant prostate cancer.

Abstract A157: Antitumor activity of tarloxotinib, a hypoxia-activated EGFR TKI, in patient-derived lung cancer cell lines harboring EGFR exon 20 insertions

Tarloxotinib (TRLX) is a prodrug that releases an irreversible EGFR/HER2 tyrosine kinase inhibitor (TRLX-TKI) under pathophysiologically hypoxic conditions. Non-small cell lung cancer (NSCLC) has been characterized as a hypoxic disease and approximately 15% of lung adenocarcinomas harbor EGFR mutations. While most EGFR mutations predict for response to several FDA-approved tyrosine kinase inhibitors, in-frame insertions in exon 20 of EGFR are activating mutations in the tyrosine kinase domain that have significantly decreased sensitivity to EGFR inhibitors and currently have no approved targeted therapies. We derived and characterized three human lung adenocarcinoma cell lines with different EGFR exon 20 insertions in order to accelerate development of targeted therapies for this mutation class. Using these novel cell lines, we evaluated tarloxotinib as a therapeutic agent for tumors harboring this type of mutations. We demonstrate that our three patient-derived cell lines: CUTO14 (p.A767_V769dupASV), CUTO17 (p.N771_H773dupNPH), and CUTO18 (p.S768_770dupSVD) are dependent on EGFR for cell proliferation using shRNA-mediated knockdown. Our results show that EGFR exon 20 insertion cell lines are resistant to gefitinib; however, treatment with afatinib or TRLX-TKI reduces cell proliferation and signaling in a similar manner. The IC50 values for the three cell lines were 203nM, 89nM, and 709 nM for afatinib and 208nM, 33nM, and 345nM for TRLX-TKI, respectively. The prodrug form of tarloxitinib has minimal effect on cell proliferation in these models, consistent with the necessity for hypoxia-induced activation (to TRLX-TKI). Importantly, we evaluated the effect of tarloxotinib in vivo using murine xenograft models of CUTO14 and CUTO17. After four weeks of treatment, afatinib did not alter tumor growth compared to untreated tumors, whereas treatment with tarloxotinib induced significant tumor regression. The in vivo data suggest that the activated TKI of tarloxitinib is accumulating to biologically active concentrations in tumors following cleavage of tarlxoxotinib under hypoxic conditions. We conclude that our EGFR exon 20 insertions cell lines represent novel models for the investigation of therapeutic strategies for this mutation class. These cell lines have the ability to develop tumors in vivo and show reduced sensitivity to current EGFR TKIs, mimicking the lack of response in patients with these mutations. Finally, we demonstrate that tarloxotinib can overcome intrinsic EGFR exon 20 mutation resistance to standard EGFR TKIs.

Citation Format: Adriana Estrada-Bernal, Andrea E. Doak, Anh T. Le, Hengbo Zhu, Nan Chen, Shevan Silva, Jeff B. Smaill, Adam V. Patterson, Robert C. Doebele. Antitumor activity of tarloxotinib, a hypoxia-activated EGFR TKI, in patient-derived lung cancer cell lines harboring EGFR exon 20 insertions [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr A157.

2-Aminopyrimidine Derivatives as New Selective Fibroblast Growth Factor Receptor 4 (FGFR4) Inhibitors

A series of 2-aminopyrimidine derivatives were designed and synthesized as highly selective FGFR4 inhibitors. One of the most promising compounds 2n tightly bound FGFR4 with a K_d value of 3.3 nM and potently inhibited its enzymatic activity with an IC₅₀ value of 2.6 nM, but completely spared FGFR1/2/3. The compound selectively suppressed proliferation of breast cancer cells harboring dysregulated FGFR4 signaling with an IC₅₀ value of 0.38 μM. Furthermore, 2n exhibited extraordinary target specificity in a Kinome-wide screen against 468 kinases, with S(35) and S(10) selectivity scores of 0.01 and 0.007 at 1.0 μM, respectively.

Rational design of an AKR1C3-resistant analog of PR-104 for enzyme-prodrug therapy

The clinical stage anti-cancer agent PR-104 has potential utility as a cytotoxic prodrug for exogenous bacterial nitroreductases expressed from replicating vector platforms. However substrate selectivity is compromised due to metabolism by the human one- and two-electron oxidoreductases cytochrome P450 oxidoreductase (POR) and aldo-keto reductase 1C3 (AKR1C3). Using rational drug design we developed a novel mono-nitro analog of PR-104A that is essentially free of this off-target activity in vitro and in vivo. Unlike PR-104A, there was no biologically relevant cytotoxicity in cells engineered to express AKR1C3 or POR, under aerobic or anoxic conditions, respectively. We screened this inert prodrug analog, SN34507, against a type I bacterial nitroreductase library and identified E. coli NfsA as an efficient bioactivator using a DNA damage response assay and recombinant enzyme kinetics. Expression of E. coli NfsA in human colorectal cancer cells led to selective cytotoxicity to SN34507 that was associated with cell cycle arrest and generated a robust 'bystander effect' at tissue-like cell densities when only 3% of cells were NfsA positive. Anti-tumor activity of SN35539, the phosphate pre-prodrug of SN34507, was established in 'mixed' tumors harboring a minority of NfsA-positive cells and demonstrated marked tumor control following heterogeneous suicide gene expression. These experiments demonstrate that off-target metabolism of PR-104 can be avoided and identify the suicide gene/prodrug partnership of E. coli NfsA/SN35539 as a promising combination for development in armed vectors.

Advancing Clostridia to Clinical Trial: Past Lessons and Recent Progress

Most solid cancers contain regions of necrotic tissue. The extent of necrosis is associated with poor survival, most likely because it reflects aggressive tumour outgrowth and inflammation. Intravenously injected spores of anaerobic bacteria from the genus Clostridium infiltrate and selectively germinate in these necrotic regions, providing cancer-specific colonisation. The specificity of this system was first demonstrated over 60 years ago and evidence of colonisation has been confirmed in multiple tumour models. The use of "armed" clostridia, such as in Clostridium Directed Enzyme Prodrug Therapy (CDEPT), may help to overcome some of the described deficiencies of using wild-type clostridia for treatment of cancer, such as tumour regrowth from a well-vascularised outer rim of viable cells. Successful preclinical evaluation of a transferable gene that metabolises both clinical stage positron emission tomography (PET) imaging agents (for whole body vector visualisation) as well as chemotherapy prodrugs (for conditional enhancement of efficacy) would be a valuable early step towards the prospect of "armed" clostridia entering clinical evaluation. The ability to target the immunosuppressive hypoxic tumour microenvironment using CDEPT may offer potential for synergy with recently developed immunotherapy strategies. Ultimately, clostridia may be most efficacious when combined with conventional therapies, such as radiotherapy, that sterilise viable aerobic tumour cells.

Abstract A67: Preclinical efficacy of tarloxotinib bromide (TH-4000), a hypoxia-activated EGFR/HER2 inhibitor: rationale for clinical evaluation in EGFR mutant, T790M-negative NSCLC following progression on EGFR-TKI therapy

Tarloxotinib bromide (T) is a prodrug that releases an irreversible EGFR/HER2 inhibitor (T-TKI) under hypoxic conditions. NSCLC is known to be a hypoxic disease and wild type (WT) EGFR is upregulated by multiple hypoxia-driven mechanisms (Curr Pharm Des, 19:907). Mutant EGFR NSCLC is commonly heterozygous and may result in maintenance of WT EGFR signalling (Can Sci, 103:1946; PloS One 8:e54170). Clinical studies indicate NSCLC patients harbouring WT/mut heterozygous EGFR have significantly poorer ORR, PFS and OS on treatment with EGFR-TKI (Can Sci, 99:929). Other mechanisms of resistance to EGFR-TKI include 50-60% with T790M EGFR mutation, 8-13% with HER2 amplification, while 15-20% lack identifiable mutation/amplification events (Nat Rev Clin Onc, 11:473). The combination of cetuximab/afatinib provides an ORR of 25% and PFS of 4.6 months in T790M-negative NSCLC suggesting the persistence of HER signalling plays a role in resistance. However the high proportion of Grade 3/4 toxicity seen with cetuximab/afatinib indicates an opportunity for dose-intensification with an improved therapeutic index (Can Discov, 4:1). In addition, early clinical data on resistance to the 3rd Gen (WT EGFR-sparing) TKI rociletinib, fails to identify further mutations by NGS in some patients and describes reversion to EGFR-WT (T790) status (Can Discov, 5:713). Collectively these data support the hypothesis that WT EGFR heterozygosity may be a mechanism of resistance to current EGFR-TKI.

Current EGFR-TKI lack the therapeutic index to silence WT EGFR signalling in tumors due to on-target skin/GI toxicities (Ann Oncol 18:761). Therefore we sought to examine the potency of T-TKI relative to erlotinib, afatinib and AZD9291 in five human cancer cell lines expressing WT EGFR (H1838, H2073, H1648, H125 and A431). In antiproliferative assays T-TKI was more dose-potent than erlotinib (25- to 110-fold) afatinib (4- to 32-fold) and AZD9291 (120- to 71-fold). This activity correlated with inhibition of WT EGFR phosphorylation and downstream MAPK signalling. We used a prototypic WT EGFR driven xenograft model (A431) to benchmark T activity against each EGFR-TKI by ‘retrotranslation’ of reported plasma exposure for each agent in human subjects back to the xenograft model. Only treatment with clinically relevant doses and schedules of T was associated with tumor regression and durable inhibition of WT EGFR tumor phosphorylation. Consistent with these findings, T treatment can also regress the WT EGFR NSCLC tumor models H125 and H1648, demonstrating T provides the necessary therapeutic index to inhibit WT EGFR in vivo. The transfection of WT EGFR into mutant EGFR NSCLC line PC9 (vs GFP control) conferred TGFα dependent induction of p-EGFR that was supressed by T-TKI but resistant to inhibition by erlotinib, afatinib or AZD9291. This was associated with reduced antiproliferative activity for EGFR-TKIs. Collectively these data indicate T-TKI is a dose-potent inhibitor of WT EGFR signalling and the prodrug T may possess the therapeutic index to silence WT EGFR signalling in xenograft models at plasma exposure levels achieved in a human Ph1 trial. T is under investigation in a Phase 2 clinical trial for EGFR mutant, T790M-negative, NSCLC patients who have progressed on EGFR-TKI (NCT02454842).

Citation Format: Shevan Silva, Victoria Jackson, Christopher Guise, Maria Abbattista, Matthew Bull, Angus Grey, Robert Anderson, Amir Ashoorzadeh, Charles Hart, Tillman Pearce, Adam V. Patterson, Jeff B. Smaill. Preclinical efficacy of tarloxotinib bromide (TH-4000), a hypoxia-activated EGFR/HER2 inhibitor: rationale for clinical evaluation in EGFR mutant, T790M-negative NSCLC following progression on EGFR-TKI therapy. [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 A67.

Pre-clinical activity of PR-104 as monotherapy and in combination with sorafenib in hepatocellular carcinoma

PR-104 is a clinical stage bioreductive prodrug that is converted in vivo to its cognate alcohol, PR-104A. This dinitrobenzamide mustard is reduced to activated DNA cross-linking metabolites (hydroxylamine PR-104H and amine PR-104M) under hypoxia by one-electron reductases and independently of hypoxia by the 2-electron reductase aldo-keto reductase 1C3 (AKR1C3). High expression of AKR1C3, along with extensive hypoxia, suggested the potential of PR-104 for treatment of hepatocellular carcinoma (HCC). However, a phase IB trial with sorafenib demonstrated significant toxicity that was ascribed in part to reduced PR-104A clearance, likely reflecting compromised glucuronidation in patients with advanced HCC. Here, we evaluate the activity of PR-104 in HCC xenografts (HepG2, PLC/PRF/5, SNU-398, Hep3B) in mice, which do not significantly glucuronidate PR-104A. Cell line differences in sensitivity to PR-104A in vitro under aerobic conditions could be accounted for by differences in both expression of AKR1C3 (high in HepG2 and PLC/PRF/5) and sensitivity to the major active metabolite PR-104H, to which PLC/PRF/5 was relatively resistant, while hypoxic selectivity of PR-104A cytotoxicity and reductive metabolism was greatest in the low-AKR1C3 SNU-398 and Hep3B lines. Expression of AKR1C3 in HepG2 and PLC/PRF/5 xenografts was in the range seen in 21 human HCC specimens. PR-104 monotherapy elicited significant reductions in growth of Hep3B and HepG2 xenografts, and the combination with sorafenib was significantly active in all 4 xenograft models. The results suggest that better-tolerated analogs of PR-104, without a glucuronidation liability, may have the potential to exploit AKR1C3 and/or hypoxia in HCC in humans.

Synthesis and cytotoxicity of pyranonaphthoquinone natural product analogues under bioreductive conditions

We have synthesised a focused library of derivatives of natural products containing the pyranonaphthoquinone moiety including the first report of such a scaffold with an appended tetrazole functionality. Examples include kalafungin derivatives as well as analogues of nanaomycin and eleutherin. These compounds were assessed for cytotoxic activation by breast cancer cell lines engineered to express the prototypic human one- and two-electron quinone bioreductive enzymes, NADPH: cytochrome P450 oxidoreductase (POR) and

NAD(P)H

quinoneoxidoreductase 1 (NQO1; DT-diaphorase), respectively. Several compounds were observed to be cytotoxic at sub-micromolar level and a pattern of increased aerobic potency was observed in cells over expressing POR. A subset of analogues was assessed under anoxic conditions, where cytotoxicity was reduced, implicating redox cycling as a major mechanism of toxicity. The substrate specificity for reductive enzymes is relevant to the future design of bioreductive prodrugs to treat cancer.

Identification of one-electron reductases that activate both the hypoxia prodrug SN30000 and diagnostic probe EF5

SN30000 is a second-generation benzotriazine-N-oxide hypoxia-activated prodrug scheduled for clinical trial. Previously we showed that covalent binding of the hypoxia probe EF5 predicts metabolic activation of SN30000 in a panel of cancer cell lines under anoxia, suggesting that they are activated by the same reductases. However the identity of these reductases is unknown. Here, we test whether forced expression of nine oxidoreductases with known or suspected roles in bioreductive prodrug metabolism (AKR1C3, CYB5R3, FDXR, MTRR, NDOR1, NOS2A, NQO1, NQO2 and POR) enhances oxic or anoxic reduction of SN30000 and EF5 by HCT116 cells. Covalent binding of (14)C-EF5 and reduction of SN30000 to its 1-oxide and nor-oxide metabolites was highly selective for anoxia in all lines, with significantly elevated anoxic metabolism of both compounds in lines over-expressing POR, MTRR, NOS2A or NDOR1. There was a strong correlation between EF5 binding and SN30000 metabolism under anoxia across the cell lines (R(2)=0.84, p=0.0001). Antiproliferative potency of SN30000 under anoxia was increased most strongly by overexpression of MTRR and POR. Transcript abundance in human tumours, evaluated using public domain mRNA expression data, was highest for MTRR, followed by POR, NOS2A and NDOR1, with little variation between tumour types. Immunostaining of tissue microarrays demonstrated variable MTRR protein expression across 517 human cancers with most displaying low expression. In conclusion, we have identified four diflavin reductases (POR, MTRR, NOS2A and NDOR1) capable of reducing both SN30000 and EF5, further supporting use of 2-nitroimidazole probes to predict the ability of hypoxic cells to activate SN30000.

Toward a high-throughput screening platform for directed evolution of enzymes that activate genotoxic prodrugs

Engineering of enzymes to more efficiently activate genotoxic prodrugs holds great potential for improving anticancer gene or antibody therapies. We report the development of a new, GFP-based, high-throughput screening platform to enable engineering of prodrug-activating enzymes by directed evolution. By fusing an inducible SOS promoter to an engineered GFP reporter gene, we were able to measure levels of DNA damage in intact Escherichia coli and separate cell populations by fluorescence activating cell sorting (FACS). In two FACS iterations, we were able to achieve a 90,000-fold enrichment of a functional prodrug-activating nitroreductase from a null library background.

Characterisation of radicals formed by the triazine 1,4-dioxide hypoxia-activated prodrug, SN30000

The radical species underlying the activity of the bioreductive anticancer prodrug, SN30000, have been identified by electron paramagnetic resonance and pulse radiolysis techniques. Spin-trapping experiments indicate both an aryl-type radical and an oxidising radical, trapped as a carbon-centred radical, are formed from the protonated radical anion of SN30000. The carbon-centred radical, produced upon the one-electron oxidation of the 2-electron reduced metabolite of SN30000, oxidises 2-deoxyribose, a model for the site of damage on DNA which leads to double strand breaks. Calculations using density functional theory support the assignments made.

Bioreductive prodrugs as cancer therapeutics: targeting tumor hypoxia

Hypoxia, a state of low oxygen, is a common feature of solid tumors and is associated with disease progression as well as resistance to radiotherapy and certain chemotherapeutic drugs. Hypoxic regions in tumors, therefore, represent attractive targets for cancer therapy. To date, five distinct classes of bioreactive prodrugs have been developed to target hypoxic cells in solid tumors. These hypoxia-activated prodrugs, including nitro compounds, N-oxides, quinones, and metal complexes, generally share a common mechanism of activation whereby they are reduced by intracellular oxidoreductases in an oxygen-sensitive manner to form cytotoxins. Several examples including PR-104, TH-302, and EO9 are currently undergoing phase II and phase III clinical evaluation. In this review, we discuss the nature of tumor hypoxia as a therapeutic target, focusing on the development of bioreductive prodrugs. We also describe the current knowledge of how each prodrug class is activated and detail the clinical progress of leading examples.

Zinc finger nuclease knock-out of NADPH:cytochrome P450 oxidoreductase (POR) in human tumor cell lines demonstrates that hypoxia-activated prodrugs differ in POR dependence

Hypoxia, a ubiquitous feature of tumors, can be exploited by hypoxia-activated prodrugs (HAP) that are substrates for one-electron reduction in the absence of oxygen. NADPH:cytochrome P450 oxidoreductase (POR) is considered one of the major enzymes responsible, based on studies using purified enzyme or forced overexpression in cell lines. To examine the role of POR in HAP activation at endogenous levels of expression, POR knock-outs were generated in HCT116 and SiHa cells by targeted mutation of exon 8 using zinc finger nucleases. Absolute quantitation by proteotypic peptide mass spectrometry of DNA sequence-confirmed multiallelic mutants demonstrated expression of proteins with residual one-electron reductase activity in some clones and identified two (Hko2 from HCT116 and S2ko1 from SiHa) that were functionally null by multiple criteria. Sensitivities of the clones to 11 HAP (six nitroaromatics, three benzotriazine N-oxides, and two quinones) were compared with wild-type and POR-overexpressing cells. All except the quinones were potentiated by POR overexpression. Knocking out POR had a marked effect on antiproliferative activity of the 5-nitroquinoline SN24349 in both genetic backgrounds after anoxic exposure but little or no effect on activity of most other HAP, including the clinical stage 2-nitroimidazole mustard TH-302, dinitrobenzamide mustard PR-104A, and benzotriazine N-oxide SN30000. Clonogenic cell killing and reductive metabolism of PR-104A and SN30000 under anoxia also showed little change in the POR knock-outs. Thus, although POR expression is a potential biomarker of sensitivity to some HAP, identification of other one-electron reductases responsible for HAP activation is needed for their rational clinical development.

Abstract B278: PR610: A novel hypoxia-selective tyrosine kinase inhibitor in phase I clinical trial

PR610 is a hypoxia-selective irreversible Human Epidermal Growth Factor Receptor (HER) family inhibitor currently in phase I clinical trials in New Zealand and the USA (clinical trial ID NCT01631279). The prodrug PR610 releases the TKI (Tyrosine Kinase Inhibitor) PR610E, a picomolar irreversible inhibitor of EGFR (HER1), under oxygen-limiting conditions typically found in solid tumors. Human neoplastic cell lines exposed to PR610 show an anoxia-selective anti-proliferative response that is associated with G1 arrest and induction of apoptosis arising from inhibition of EGFR auto-phosphorylation and downstream silencing of associated signal transduction pathways. PR610 is optimized for long tumor residency (T½ >2 days); in a preclinical model of erlotinib-resistant NSCLC, a single injection of PR610 produces profound, global shutdown of signal transduction via EGFRT790M/L858R. Tumor PR610E concentrations were above cellular anti-proliferative IC50 concentrations for over 5 days, being more than sufficient to induce apoptosis via “oncogenic shock”.

Pharmacokinetic (PK) studies of PR610 show significant differences in species toxicokinetics. Both the rat and dog preclinical toxicology models display considerable systemic conversion of PR610 to PR610E (6% - 30% and 24% - 29% of prodrug AUC, respectively) with attendant symptoms of EGFR inhibition including acneiform skin rash and diarrhea. In contrast NIH-III nude mice display minimal circulating TKI (PR610E) relative to PR610 (1.5% - 1.7% of AUC) consistent with a substantially improved tolerance as judged by PR610 plasma AUCinf at the maximum tolerated dose (MTD). Human subjects from the phase I clinical trial consistently experience the lowest systemic levels of PR610E (Mean 1.06% ± 0.69%; range 0.34% - 2.7%; n=20) across dose levels ranging from 10 - 150 mg/m2. Notably, a dose of 150 mg/m2 in human subjects produces a PR610 plasma AUCinf equivalent to that measured for 30 mg/kg PR610 in NIH-III mice, a dose that is active in several HER-dependent subcutaneous tumor xenograft models. Collectively, these data indicate that PR610 has the desirable characteristics of a deactivated prodrug in human subjects and preclinical models predict that an active dose range has been reached in the phase I trial. PR610 is a first-in-class hypoxia-selective EGFR/HER2 inhibitor with exciting clinical potential.

Citation Information: Mol Cancer Ther 2013;12(11 Suppl):B278.

Citation Format: Adam V. Patterson, Jagdish Jaiswal, Kendall Carlin, Maria R. Abbattista, Christopher P. Guise, Shevan Silva, Ho Lee, Guo-Liang Lu, Robert F. Anderson, Teresa J. Melink, John C. Gutheil, Jeff B. Smaill. PR610: A novel hypoxia-selective tyrosine kinase inhibitor in phase I clinical trial. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr B278.

Pseudomonas aeruginosa NfsB and nitro-CBI-DEI--a promising enzyme/prodrug combination for gene directed enzyme prodrug therapy

BACKGROUND

The nitro-chloromethylbenzindoline prodrug nitro-CBI-DEI appears a promising candidate for the anti-cancer strategy gene-directed enzyme prodrug therapy, based on its ability to be converted to a highly cytotoxic cell-permeable derivative by the nitroreductase NfsB from Escherichia coli. However, relative to some other nitroaromatic prodrugs, nitro-CBI-DEI is a poor substrate for E. coli NfsB. To address this limitation we evaluated other nitroreductase candidates from E. coli and Pseudomonas aeruginosa.

FINDINGS

Initial screens of candidate genes in the E. coli reporter strain SOS-R2 identified two additional nitroreductases, E. coli NfsA and P. aeruginosa NfsB, as being more effective activators of nitro-CBI-DEI than E. coli NfsB. In monolayer cytotoxicity assays, human colon carcinoma (HCT-116) cells transfected with P. aeruginosa NfsB were >4.5-fold more sensitive to nitro-CBI-DEI than cells expressing either E. coli enzyme, and 23.5-fold more sensitive than untransfected HCT-116. In three dimensional mixed cell cultures, not only were the P. aeruginosa NfsB expressing cells 540-fold more sensitive to nitro-CBI-DEI than pure cultures of untransfected HCT-116, the activated drug that they generated also displayed an unprecedented local bystander effect.

CONCLUSION

We posit that the discrepancy in the fold-sensitivity to nitro-CBI-DEI between the two and three dimensional cytotoxicity assays stems from loss of activated drug into the media in the monolayer cultures. This emphasises the importance of evaluating high-bystander GDEPT prodrugs in three dimensional models. The high cytotoxicity and bystander effect exhibited by the NfsB_Pa/nitro-CBI-DEI combination suggest that further preclinical development of this GDEPT pairing is warranted.

Abstract 2111: Identification of reductases capable of metabolic activation of hypoxia targeting prodrug SN30000 and hypoxia marker EF5

Background: SN30000 is a 2nd generation benzotriazine-N-oxide hypoxia-activated prodrug (tirapazamine analogue) and is currently in preclinical development. We have previously shown that reductive activation of the hypoxia marker EF5 and SN30000 are correlated across a panel of cancer cells under hypoxia (Wang et al, Clin Can Res 18:1684, 2012), suggesting that they are activated by the same reductases. The identities of these reductases are not known, except NADPH:cytochrome p450 oxidoreductase (POR). Further, knockout of POR in HCT116 and SiHa cell lines had little or no effect on reduction of either compound. Here, we utilise a previously reported panel of HCT116 isogenic cell lines (Guise et al, Can Res 70:1573, 2010; Mol Pharmacol 81:31, 2012) over-expressing nine oxidoreductases with known or suspected roles in bioreductive prodrug metabolism (AKR1C3, CYB5R, FDXR, MTRR, NDOR1, NOS2A, NQO1, NQO2 and POR) to identify reductases capable of reducing SN30000 and EF5. Methods: Drug metabolism rates under oxic and anoxic conditions were determined in each cell line. The metabolism of SN 30000 to its corresponding 1-oxide and nor-oxide metabolites were measured by LC/MS/MS and the reduction of EF5 by quantifying covalent protein binding of 14C-EF5. SN30000 anoxic cytotoxicity was determined by clonogenic assay. Oxidoreductase expression profiling in cancer patient samples was conducted using Oncomine Premium edition. Results: There was minimal reductive metabolism under oxic conditions (0.1 to 4.8% of anoxic values) for both compounds in all cell lines. Under anoxic conditions, 4 to 5 fold differences were obtained for EF5 and SN30000 across the 10 isogenic cell lines. Our results confirmed our previous observations that POR is one of the reductases capable for SN30000 and EF5 metabolism. In addition to POR, three other members of the diflavin oxidoreductase family (MTRR, NOS2A and NDOR1) had increased anoxic metabolism rates compared to the parental line for both SN30000 and EF5. There was a good correlation between EF5 binding and SN30000 anoxic metabolism across the cell lines (R2=0.78, p=0.0015). SN30000 cytotoxicity under anoxic conditions was also increased in the cells over-expressing POR, NDOR1, MTRR and NOS2A. Expression of these four reductases showed considerable variation between individual human tumour biopsies. In general, the ranking of transcript abundance between the four reductases was POR > MTRR > NOS2A ≈ NDOR1 in most cancer types. In breast cancer, expression of these reductases was similar in tumours with high and low expression of the hypoxia marker gene CA9. Conclusion: we have identified 4 flavoreductases (POR, MTRR, NOS2A and NDOR1) that are capable of activating both SN30000 and EF5 under anoxia when overexpressed in HCT116 cells. However it is not yet clear whether they play a significant role at basal levels of expression in cell lines or tumours.

Citation Format: Jingli Wang, Chris P. Guise, Huai-Ling Hsu, Daniel Hurley, William R. Wilson, Adam V. Patterson. Identification of reductases capable of metabolic activation of hypoxia targeting prodrug SN30000 and hypoxia marker EF5. [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 2111. doi:10.1158/1538-7445.AM2013-2111

Creation and screening of a multi-family bacterial oxidoreductase library to discover novel nitroreductases that efficiently activate the bioreductive prodrugs CB1954 and PR-104A

Two potentially complementary approaches to improve the anti-cancer strategy gene-directed enzyme prodrug therapy (GDEPT) are discovery of more efficient prodrug-activating enzymes, and development of more effective prodrugs. Here we demonstrate the utility of a flexible screening system based on the Escherichia coli SOS response to evaluate novel nitroreductase enzymes and prodrugs in concert. To achieve this, a library of 47 candidate genes representing 11 different oxidoreductase families was created and screened to identify the most efficient activators of two different nitroaromatic prodrugs, CB1954 and PR-104A. The most catalytically efficient nitroreductases were found in the NfsA and NfsB enzyme families, with NfsA homologues generally more active than NfsB. Some members of the AzoR, NemA and MdaB families also exhibited low-level activity with one or both prodrugs. The results of SOS screening in our optimised E. coli reporter strain SOS-R2 were generally predictive of the ability of nitroreductase candidates to sensitise E. coli to CB1954, and of the kcat/Km for each prodrug substrate at a purified protein level. However, we also found that not all nitroreductases express stably in human (HCT-116 colon carcinoma) cells, and that activity at a purified protein level did not necessarily predict activity in stably transfected HCT-116. These results highlight a need for all enzyme-prodrug partners for GDEPT to be assessed in the specific context of the vector and cell line that they are intended to target. Nonetheless, our oxidoreductase library and optimised screens provide valuable tools to identify preferred nitroreductase-prodrug combinations to advance to preclinical evaluation.

Single agent- and combination treatment with two targeted suicide gene therapy systems is effective in chemoresistant small cell lung cancer cells

BACKGROUND

Transcriptional targeted suicide gene (SG) therapy driven by the insulinoma-associated 1 (INSM1) promoter makes it possible to target suicide toxin production and cytotoxicity exclusively to small cell lung cancer (SCLC) cells and tumors. It remains to be determined whether acquired chemoresistance, as observed in the majority of SCLC patients, desensitizes SCLC cells to INSM1 promoter-driven SG therapy.

METHODS

A panel of SCLC cell lines resistant to clinically relevant chemotherapeutics was characterized regarding the expression of proteins involved in response to chemotherapy and regarding INSM1 promoter activity. Sensitivity towards INSM1 promoter-driven SG therapy was tested using different systems: Yeast cytosine deaminase-uracil phosphoribosyl transferase (YCD-YUPRT) in combination with the prodrug 5-fluorocytosine (5-FC) or Escherichia coli nitroreductase (NTR) together with the bromomustard prodrug SN27686.

RESULTS

The chemoresistant cell lines displayed heterogeneous expression profiles of molecules involved in multidrug resistance, apoptosis and survival pathways. Despite this, the INSM1 promoter activity was found to be unchanged or increased in SCLC chemoresistant cells and xenografts compared to chemosensitive variants. INSM1 promoter-driven SG therapy with YCD-YUPRT/5-FC or NTR/SN27686, was found to induce high levels of cytotoxicity in both chemosensitive and chemoresistant SCLC cells. Moreover, the combination of INSM1 promoter-driven YCD-YUPRT/5-FC therapy and chemotherapy, as well as the combination of INSM1 promoter-driven YCD-YUPRT/5-FC and NTR/SN27686 therapy, was observed to be superior to single agent therapy in chemoresistant SCLC cells.

CONCLUSIONS

Collectively, the present study demonstrates that targeted SG therapy is a potent therapeutic approach for chemoresistant SCLC patients, with the highest efficacy achieved when applied as combination SG therapy or in combination with standard chemotherapy.

Targeted mutagenesis of the Vibrio fischeri flavin reductase FRase I to improve activation of the anticancer prodrug CB1954

Phase I/II cancer gene therapy trials of the Escherichia coli nitroreductase NfsB in partnership with the prodrug CB1954 [5-(aziridin-1-yl)-2,4-dinitrobenzamide] have indicated that CB1954 toxicity is dose-limiting at concentrations far below the enzyme K(M). Here we report that the flavin reductase FRase I from Vibrio fischeri is also a CB1954 nitroreductase, which has a substantially lower apparent K(M) than E. coli NfsB. To enhance the activity of FRase I with CB1954 we used targeted mutagenesis and an E. coli SOS reporter strain to engineer single- and multi-residue variants that possess a substantially reduced apparent K(M) and an increased k(cat)/K(M) relative to the wild type enzyme. In a bacteria-delivered model for enzyme prodrug therapy, the engineered FRase I variants were able to kill human colon carcinoma (HCT-116) cells at significantly lower CB1954 concentrations than wild type FRase I or E. coli NfsB.