HSF1 Pathway Inhibitor Clinical Candidate (CCT361814/NXP800) Developed from a Phenotypic Screen as a Potential Treatment for Refractory Ovarian Cancer and Other Malignancies

CCT251236 1, a potent chemical probe, was previously developed from a cell-based phenotypic high-throughput screen (HTS) to discover inhibitors of transcription mediated by HSF1, a transcription factor that supports malignancy. Owing to its activity against models of refractory human ovarian cancer, 1 was progressed into lead optimization. The reduction of P-glycoprotein efflux became a focus of early compound optimization; central ring halogen substitution was demonstrated by matched molecular pair analysis to be an effective strategy to mitigate this liability. Further multiparameter optimization led to the design of the clinical candidate, CCT361814/NXP800 22, a potent and orally bioavailable fluorobisamide, which caused tumor regression in a human ovarian adenocarcinoma xenograft model with on-pathway biomarker modulation and a clean in vitro safety profile. Following its favorable dose prediction to human, 22 has now progressed to phase 1 clinical trial as a potential future treatment for refractory ovarian cancer and other malignancies.

Discovery of potent and selective HER2 inhibitors with efficacy against HER2 exon 20 insertion-driven tumors, which preserve wild-type EGFR signaling

Oncogenic alterations in human epidermal growth factor receptor 2 (HER2) occur in approximately 2% of patients with non-small cell lung cancer and predominantly affect the tyrosine kinase domain and cluster in exon 20 of the ERBB2 gene. Most clinical-grade tyrosine kinase inhibitors are limited by either insufficient selectivity against wild-type (WT) epidermal growth factor receptor (EGFR), which is a major cause of dose-limiting toxicity or by potency against HER2 exon 20 mutant variants. Here we report the discovery of covalent tyrosine kinase inhibitors that potently inhibit HER2 exon 20 mutants while sparing WT EGFR, which reduce tumor cell survival and proliferation in vitro and result in regressions in preclinical xenograft models of HER2 exon 20 mutant non-small cell lung cancer, concomitant with inhibition of downstream HER2 signaling. Our results suggest that HER2 exon 20 insertion-driven tumors can be effectively treated by a potent and highly selective HER2 inhibitor while sparing WT EGFR, paving the way for clinical translation.

Chemoenzymatic one-pot reaction from carboxylic acid to nitrile via oxime

We report a new chemoenzymatic cascade starting with aldehyde synthesis by carboxylic acid reductase (CAR) followed by chemical in situ oxime formation. The final step to the nitrile is catalyzed by aldoxime dehydratase (Oxd). Full conversions of phenylacetic acid and hexanoic acid were achieved in a two-phase mode.

We report a new chemoenzymatic cascade starting with aldehyde synthesis by carboxylic acid reductase (CAR) followed by chemical in situ oxime formation and enzymatic dehydration by aldoxime dehydratase (Oxd).

Abstract 1472: Novel EGFR WT sparing, HER2 selective inhibitors for the treatment of HER2 exon 20 insertion driven tumors address a clear unmet medical need

Activating mutations in ERBB2 receptors are tractable oncogenes in 2-3% of NSCLC patients for whom no approved targeted therapies are available. In this indication, oncogenic mutations in HER2 predominantly affect the tyrosine kinase domain and cluster in exon 20 of the ERBB2 gene. We initiated a drug discovery program aiming at discovering novel HER2 selective inhibitors sparing EGFR WT activity. Focus was set on the most frequent HER2 mutation (ERBB2 A775 insYVMA), which is least sensitive to current compounds tested in clinical trials. Here, we report the identification and pharmacological characterization of novel selective HER2 exon 20 mutation TKIs that differ from currently tested TKIs such as poziotinib, TAK-788 or BDTX-189. We could demonstrate that selective inhibition of oncogenic HER2 signaling abrogates oncogenic signaling in in vitro models. Cell survival and proliferation was reduced, which translated into tumor regressions in preclinical CRISPR engineered xenotransplantation models of HER2 exon 20 mutants. The in vivo efficacy was confirmed in patient-derived tumor models. Our results suggest that HER2 exon 20 insertions can be effectively treated by a potent and highly selective HER2 inhibitor that spares EGFR wild type. These findings warrant the upcoming clinical testing in HER2 mutant NSCLC patients in order to effectively treat this aggressive type of cancer.

Citation Format: Ralph A. Neumüller, Birgit Wilding, Dirk Scharn, Dietrich Böse, Valeria Santoro, Daniel Gerlach, Peter Ettmayer, Thomas Gerstberger, Julian Fuchs, Matthias Treu, Stephan Zahn, Anke Baum, Paolo Chetta, Mark Pearson, Darryl B. McConnell, Norbert Kraut, Flavio Solca. Novel EGFR WT sparing, HER2 selective inhibitors for the treatment of HER2 exon 20 insertion driven tumors address a clear unmet medical need [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1472.

Investigating the phosphinic acid tripeptide mimetic DG013A as a tool compound inhibitor of the M1-aminopeptidase ERAP1

ERAP1 is a zinc-dependent M1-aminopeptidase that trims lipophilic amino acids from the N-terminus of peptides. Owing to its importance in the processing of antigens and regulation of the adaptive immune response, dysregulation of the highly polymorphic ERAP1 has been implicated in autoimmune disease and cancer. To test this hypothesis and establish the role of ERAP1 in these disease areas, high affinity, cell permeable and selective chemical probes are essential. DG013A 1, is a phosphinic acid tripeptide mimetic inhibitor with reported low nanomolar affinity for ERAP1. However, this chemotype is a privileged structure for binding to various metal-dependent peptidases and contains a highly charged phosphinic acid moiety, so it was unclear whether it would display the high selectivity and passive permeability required for a chemical probe. Therefore, we designed a new stereoselective route to synthesize a library of DG013A 1 analogues to determine the suitability of this compound as a cellular chemical probe to validate ERAP1 as a drug discovery target.

Privileged Structures and Polypharmacology within and between Protein Families

Polypharmacology is often a key contributor to the efficacy of a drug, but is also a potential risk. We investigated two hits discovered via a cell-based phenotypic screen, the CDK9 inhibitor CCT250006 (1) and the pirin ligand CCT245232 (2), to establish methodology to elucidate their secondary protein targets. Using computational pocket-based analysis, we discovered intrafamily polypharmacology for our kinase inhibitor, despite little overall sequence identity. The interfamily polypharmacology of 2 with B-Raf was used to discover a novel pirin ligand from a very small but privileged compound library despite no apparent ligand or binding site similarity. Our data demonstrates that in areas of drug discovery where intrafamily polypharmacology is often an issue, ligand dissimilarity cannot necessarily be used to assume different off-target profiles and that understanding interfamily polypharmacology will be important in the future to reduce the risk of idiopathic toxicity and in the design of screening libraries.

Abstract 2976: Confirmation of in-cell target engagement using the proteolysis targeting chimeras (PROTACs) against pirin

We recently reported the identification of the original bisamide lead compound CCT251236 as an inhibitor of the HSF1 stress pathway with a high affinity for the putative transcription factor co-regulator, pirin (SPR KD=44nM) (Cheeseman et al., J Med Chem, 60; 180-201, 2017). Pirin is a highly conserved non-heme iron-binding regulatory protein that is a member of the functionally diverse cupin superfamily, but has no known enzymatic function or biomarkers of activity. To understand further this poorly characterized protein and to confirm that CCT251236 binds to pirin within living cells, we conceived and optimized a heterobifunctional protein degradation probe using the proteolysis targeting chimeras (PROTACs; CCT367766) comprising a pirin-binding moiety linked to the cereblon-targeting ligand thalidomide. This PROTAC molecule was designed to recruit pirin to the E3 ubiquitin ligase cereblon resulting in the ubiquitylation and degradation of pirin. Negative control probes lacking binding to pirin (CCT367857) or cereblon (CCT367936) were also designed and synthesized. We demonstrated a concentration-dependent depletion of pirin protein from as low as 0.5nM and as early as 2 hr treatment of SKOV3 human ovarian cancer cells with the PROTAC. The negative controls CCT367857 and CCT367936 exhibited no pirin depletion at equimolar concentrations. At higher concentrations of the active probe, a hook effect is observed, consistent with the formation of a ternary complex. Degradation of pirin by the PROTAC was confirmed to be proteasome-dependent by rescue of depletion following pre-incubation with the proteasome inhibitor MG132. In addition, the PROTAC could not induce pirin degradation in CRISPR/cas9 cereblon knockout SKOV3 cells, confirming dependence on cereblon. Pre-treatment with the bisamide compound CCT251236 or free thalidomide abrogated the PROTAC-induced pirin degradation, consistent with pirin and cereblon engagement. Finally, to estimate the cellular selectivity of the PROTAC to pirin in an unbiased manner, we carried out whole proteome mass spectrometry in SKOV3 cells. From 8547 quantifiable proteins identified, only pirin (2.3-fold reduction) displayed a statistically significant (Padj<0.05) difference in protein expression, indicating impressive selectivity. In summary, we have designed a PROTAC as an intracellular probe against a poorly understood molecular target, pirin. This approach has allowed us to confirm in-cell target engagement of our bisamide lead CCT251236 with pirin and validates CCT367766 as a PROTAC tool to further study this largely unexplored protein. Our results also provide a systematic approach for the use of the powerful PROTAC technology to investigate potential and poorly understood cancer drug targets.

Citation Format: Swee Y. Sharp, Nicola E. Chessum, John J. Caldwell, Marissa V. Powers, A Elisa Pasqua, Birgit Wilding, Ian Collins, Bugra Ozer, Martin Rowlands, Mark Stubbs, Rosemary Burke, Rob L. van Montfort, Matthew D. Cheeseman, Paul A. Clarke, Paul Workman, Keith Jones. Confirmation of in-cell target engagement using the proteolysis targeting chimeras (PROTACs) against pirin [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2976.

Demonstrating In-Cell Target Engagement Using a Pirin Protein Degradation Probe (CCT367766)

Demonstrating intracellular protein target engagement is an essential step in the development and progression of new chemical probes and potential small molecule therapeutics. However, this can be particularly challenging for poorly studied and noncatalytic proteins, as robust proximal biomarkers are rarely known. To confirm that our recently discovered chemical probe 1 (CCT251236) binds the putative transcription factor regulator pirin in living cells, we developed a heterobifunctional protein degradation probe. Focusing on linker design and physicochemical properties, we generated a highly active probe 16 (CCT367766) in only three iterations, validating our efficient strategy for degradation probe design against nonvalidated protein targets.

Abstract LB-304: Discovery of chemical probe CCT251236: An orally bioavailable efficacious pirin ligand from an HSF1 phenotypic screen

Heat shock factor 1 (HSF1) was originally identified as a master regulator of the classical ‘cytoprotective’ heat shock response. However, a large body of evidence has now verified the importance of HSF1 to tumorigenesis and cancer progression. HSF1 is activated by various elements of the cancer state, reprogramming the transcriptome in a way that is overlapping with, but distinct from, the canonical heat-shock response. Also, there is a strong correlation between the expression of activated HSF1 in tumors and adverse clinical outcomes. This evidence indicates that the inhibition of HSF1-mediated transcription could be a viable strategy in cancer treatment. Inhibiting the HSF1 stress pathway represents an attempt at targeting non-oncogene addiction and proteotoxic stress, which has been proposed to be advantageous. However, HSF1 is a ligandless transcription factor and is unlikely to be amenable to standard drug discovery strategies and direct inhibition with small molecules. Therefore, we proposed that inhibitors of HSF1-mediated transcription, which antagonize the HSF1 pathway but without necessarily binding directly to HSF1, could be discovered and developed via a cell-based phenotypic screen. We carried out a high throughput Arrayscan assay of 200,000 compounds to measure the inhibition of HSF1-mediated HSP72 expression stimulated by pre-treatment with an HSP90 inhibitor. We identified a singleton hit with a bisamide core, CCT245232. This compound showed potent growth inhibition in a range of human cancer cell lines but had poor physicochemical properties leading to an unacceptable pharmacokinetic profile. Improvement of the physicochemical properties of CCT245232 whilst maintaining potency versus our cell-based assays led to the orally bioavailable tool compound CCT251236. This compound shows potent growth inhibition (GI50 values in low nanomolar range) of human ovarian cancer cell lines in vitro and good efficacy against human ovarian cancer xenografts in nude mice in vivo. We applied chemo-proteomic strategies to identify the molecular target using a probe based on CCT251236 and discovered pirin as a high affinity molecular target. Binding of CCT251236 to recombinant pirin was confirmed in biophysical assays. CCT251236 recapitulates the reported anti-migratory phenotype for a pirin ligand although binding to pirin alone does not explain the cellular phenotype observed with our chemical tool. We are currently using CCT251236 as a chemical probe while further optimizing its properties to identify a clinical candidate.

Citation Format: Matthew D. Cheeseman, Nicola E. Chessum, Carl S. Rye, Elisa A. Pasqua, Michael J. Tucker, Birgit Wilding, Lindsay E. Evans, Susan Lepri, Meirion Richards, Swee Y. Sharp, Salyha Ali, Martin Rowlands, Lisa O'Fee, Asadh Miah, Angela Hayes, Alan T. Henley, Marissa Powers, Robert te Poele, Emmanuel De Billy, Loredana Pellegrino, Florence Raynaud, Rosemary Burke, Robert L. van Montfort, Suzanne A. Eccles, Keith Jones, Paul Workman. Discovery of chemical probe CCT251236: An orally bioavailable efficacious pirin ligand from an HSF1 phenotypic screen [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-304. doi:10.1158/1538-7445.AM2017-LB-304

Discovery of a Chemical Probe Bisamide (CCT251236): An Orally Bioavailable Efficacious Pirin Ligand from a Heat Shock Transcription Factor 1 (HSF1) Phenotypic Screen

Phenotypic screens, which focus on measuring and quantifying discrete cellular changes rather than affinity for individual recombinant proteins, have recently attracted renewed interest as an efficient strategy for drug discovery. In this article, we describe the discovery of a new chemical probe, bisamide (CCT251236), identified using an unbiased phenotypic screen to detect inhibitors of the HSF1 stress pathway. The chemical probe is orally bioavailable and displays efficacy in a human ovarian carcinoma xenograft model. By developing cell-based SAR and using chemical proteomics, we identified pirin as a high affinity molecular target, which was confirmed by SPR and crystallography.

Kinetic Analysis and Probing with Substrate Analogues of the Reaction Pathway of the Nitrile Reductase QueF from Escherichia coli

The enzyme QueF catalyzes a four-electron reduction of a nitrile group into an amine, the only reaction of this kind known in biology. In nature, QueF converts 7-cyano-7-deazaguanine (preQ₀) into 7-aminomethyl-7-deazaguanine (preQ₁) for the biosynthesis of the tRNA-inserted nucleoside queuosine. The proposed QueF mechanism involves a covalent thioimide adduct between preQ₀ and a cysteine nucleophile in the enzyme, and this adduct is subsequently converted into preQ₁ in two NADPH-dependent reduction steps. Here, we show that the Escherichia coli QueF binds preQ₀ in a strongly exothermic process (ΔH = -80.3 kJ/mol; -TΔS = 37.9 kJ/mol, K_d = 39 nm) whereby the thioimide adduct is formed with half-of-the-sites reactivity in the homodimeric enzyme. Both steps of preQ₀ reduction involve transfer of the 4-pro-R-hydrogen from NADPH. They proceed about 4-7-fold more slowly than trapping of the enzyme-bound preQ₀ as covalent thioimide (1.63 s^-1) and are thus mainly rate-limiting for the enzyme's k_cat (=0.12 s^-1). Kinetic studies combined with simulation reveal a large primary deuterium kinetic isotope effect of 3.3 on the covalent thioimide reduction and a smaller kinetic isotope effect of 1.8 on the imine reduction to preQ₁ 7-Formyl-7-deazaguanine, a carbonyl analogue of the imine intermediate, was synthesized chemically and is shown to be recognized by QueF as weak ligand for binding (ΔH = -2.3 kJ/mol; -TΔS = -19.5 kJ/mol) but not as substrate for reduction or oxidation. A model of QueF substrate recognition and a catalytic pathway for the enzyme are proposed based on these data.

An investigation of nitrile transforming enzymes in the chemo-enzymatic synthesis of the taxol sidechain

Paclitaxel (taxol) is an antimicrotubule agent widely used in the treatment of cancer. Taxol is prepared in a semisynthetic route by coupling the N-benzoyl-(2R,3S)-3-phenylisoserine sidechain to the baccatin III core structure. Precursors of the taxol sidechain have previously been prepared in chemoenzymatic approaches using acylases, lipases, and reductases, mostly featuring the enantioselective, enzymatic step early in the reaction pathway. Here, nitrile hydrolysing enzymes, namely nitrile hydratases and nitrilases, are investigated for the enzymatic hydrolysis of two different sidechain precursors. Both sidechain precursors, an openchain α-hydroxy-β-amino nitrile and a cyanodihydrooxazole, are suitable for coupling to baccatin III directly after the enzymatic step. An extensive set of nitrilases and nitrile hydratases was screened towards their activity and selectivity in the hydrolysis of two taxol sidechain precursors and their epimers. A number of nitrilases and nitrile hydratases converted both sidechain precursors and their epimers.

The Nitrile-Forming Enzyme 7-Cyano-7-Deazaguanine Synthase from Geobacillus kaustophilus: A Reverse Nitrilase?

7-Cyano-7-deazaguanine synthase (E.C. 6.3.4.20) is an enzyme that catalyzes the formation of a nitrile from a carboxylic acid and ammonia at the expense of ATP. The protein from G. kaustophilus was heterologously expressed, and its biochemical characteristics were explored by using a newly developed HPLC-MS based assay, (31) P NMR, and a fluorescence-based thermal-shift assay. The protein showed the expected high thermostability, had a pH optimum at pH 9.5, and an apparent temperature optimum at 60 °C. We observed strict substrate specificity of QueC for the natural substrate 7-carboxy-7-deazaguanine, and determined AMP and pyrophosphate as co-products of preQ0.

Targeting the substrate binding site of E. coli nitrile reductase QueF by modeling, substrate and enzyme engineering

Nitrile reductase QueF catalyzes the reduction of 2-amino-5-cyanopyrrolo[2,3-d]pyrimidin-4-one (preQ0) to 2-amino-5-aminomethylpyrrolo[2,3-d]pyrimidin-4-one (preQ1) in the biosynthetic pathway of the hypermodified nucleoside queuosine. It is the only enzyme known to catalyze a reduction of a nitrile to its corresponding primary amine and could therefore expand the toolbox of biocatalytic reactions of nitriles. To evaluate this new oxidoreductase for application in biocatalytic reactions, investigation of its substrate scope is prerequisite. We report here an investigation of the active site binding properties and the substrate scope of nitrile reductase QueF from Escherichia coli. Screenings with simple nitrile structures revealed high substrate specificity. Consequently, binding interactions of the substrate to the active site were identified based on a new homology model of E. coli QueF and modeled complex structures of the natural and non-natural substrates. Various structural analogues of the natural substrate preQ0 were synthesized and screened with wild-type QueF from E. coli and several active site mutants. Two amino acid residues Cys190 and Asp197 were shown to play an essential role in the catalytic mechanism. Three non-natural substrates were identified and compared to the natural substrate regarding their specific activities by using wild-type and mutant nitrile reductase.