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Mutations in estrogen receptor alpha (ERα) are detected in up to 30% of breast cancer patients who have relapsed during endocrine therapy. ERα mutations functionally confer resistance to existing classes of endocrine therapies, likely through gaining constitutive activity. The fact that current ER-directed therapies are only partially effective in the ERα mutant setting, and that a significant proportion of resistant breast cancer metastases continue to remain dependent on ERα signaling for growth/survival, highlights the critical need to develop the next generation of ERα antagonists that can overcome aberrant ERα activity. Using structure-based drug design approaches we have identified a novel class of ERα antagonist referred to as Selective ERα Covalent Antagonist (SERCA) that inactivate both wild-type and mutant ERα by targeting a unique cysteine residue that is not conserved among other steroid hormone receptors. Biophysical, biochemical and cellular analyses confirm the covalent mechanism of action, specific binding to ER and selective inhibition of ERα-dependent transcription of SERCAs. H3B-6545 is a highly selective SERCA that potently antagonizes wild-type and mutant ERα in biochemical and cell based assays demonstrating increased potency over standard of care and other experimental agents. In vivo, H3B-6545 shows superior efficacy to fulvestrant in the MCF-7 xenograft model with once daily oral dosing, achieving maximal antitumor activity at doses >10x below the maximum tolerated dose in mice. In addition, H3B-6545 shows superior antitumor activity to both tamoxifen and fulvestrant in patient derived xenograft models of breast cancer carrying estrogen receptor mutations. In summary, H3B-6545 is a first-in-class, orally available and selective ER covalent antagonist with a compelling pre-clinical profile that is being developed for the treatment of ERα positive breast cancer. Citation Format: Korpal M, Puyang X, Furman C, Zheng GZ, Banka D, Wu J, Zhang Z, Thomas M, Mackenzie C, Yao H, Rimkunas V, Kumar P, Caleb B, Karr C, Subramanian V, Irwin S, Larsen N, Vaillancourt F, Nguyen T-V, Davis A, Chan B, Hao MH, O'Shea M, Prajapati S, Agoulnik S, Kuznetsov G, Kumar N, Yu Y, Lai G, Hart A, Eckley S, Fekkes P, Bowser T, Joshi JJ, Selvaraj A, Wardell S, Norris J, Smith S, Reynolds D, Mitchell L, Wang J, Yu L, Kim A, Rioux N, Sahmoud T, Warmuth M, Smith PG, Zhu P. Development of a first-in-class oral selective ERα covalent antagonist (SERCA) for the treatment of ERαWT and ERαMUT breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P1-10-08.

Mutations in the estrogen receptor (ER) are detected in up to 30% of patients that initially respond but subsequently relaps to anti-endocrine therapies. ERα mutations, likely through constitutively activating ERα, can functionally confer resistance to existing classes of endocrine therapies. Current endocrine therapies are only partially effective in the ERα mutant setting and a significant proportion of endocrine-therapy resistant breast cancer metastases continue to remain dependent on ERα signaling for growth/survival indicating a critical need to develop the next generation of ERα antagonists that can overcome ERα wild-type and mutant activity. Here we describe a novel series of compounds with a unique mode of inhibition that potently target both wild-type and mutant ERα. These compounds are Selective Estrogen Receptor Covalent Antagonists (SERCAs) that inactivate the estrogen receptor by targeting a cysteine that is not present in other nuclear hormone receptors, leading to a unique biological and activity profile differentiated from Selective Estrogen Receptor Modulators (SERMs) and Selective Estrogen Receptor Degraders (SERDs). Using structure-based drug design approaches we have identified a first-in-class clinical candidate, H3B-6545. H3B-6545 is a highly selective small molecule that potently antagonizes wild-type and mutant ERα in biochemical and cell based assays. In vitro comparisons with standard of care and other experimental agents confirm increased cell potency of H3B-6545 under continuous as well as washout treatment conditions. In vivo, once daily oral dosing of H3B-6545 shows potent activity and superior efficacy to fulvestrant in the MCF-7 xenograft model with maximal antitumor activity at doses >10x below the maximum tolerated dose in mice. In addition, H3B-6545 shows superior antitumor activity to tamoxifen and fulvestrant in patient derived xenograft models of estrogen receptor positive breast cancer including models carrying ERα mutations In non-clinical safety studies in rat and monkeys, H3B-6545 is well tolerated across a broad dose range and at exposures that significantly exceed those required for efficacy in mouse xenograft models. In summary, H3B-6545 is a first-in-class, orally available and potent selective estrogen receptor covalent antagonist with a compelling preclinical efficacy and safety profile that is being developed for the treatment of breast cancer. Citation Format: Peter G. Smith, Xiaoling Puyang, Craig Furman, Guo Zhu Zheng, Deepti Banka, Michael Thomas, Vanitha Subramanian, Sean Irwin, Nicholas Larsen, Benjamin Caleb, Craig Karr, Jeremy Wu, Morgan O’Shea, Joyce Yang, Allison Davis, Amy Kim, Nathalie Rioux, Victoria Rimkunas, Huilan Yao, Crystal MacKenzie, Pavan Kumar, Sherri Smith, Sean Eckley, Andrew Hart, George Lai, Christopher Rowbottom, Peter Fekkes, Silvia Buonamici, Dominic Reynolds, Lihua Yu, Tarek Sahmoud, Markus Warmuth, Lorna Mitchell, Ping Zhu, Manav Korpal. Discovery and development of H3B-6545: A novel, oral, selective estrogen receptor covalent antagonist (SERCA) for the treatment of breast cancer [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 DDT01-04. doi:10.1158/1538-7445.AM2017-DDT01-04

SMYD3 has been implicated in a range of cancers; however, until now no potent selective small molecule inhibitors have been available for target validation studies. A novel oxindole series of SMYD3 inhibitors was identified through screening of the Epizyme proprietary histone methyltransferase-biased library. Potency optimization afforded two tool compounds, sulfonamide EPZ031686 and sulfamide EPZ030456, with cellular potency at a level sufficient to probe the in vitro biology of SMYD3 inhibition. EPZ031686 shows good bioavailability following oral dosing in mice making it a suitable tool for potential in vivo target validation studies.

CARM1 is an arginine methyltransferase with diverse histone and non-histone substrates implicated in the regulation of cellular processes including transcriptional co-activation and RNA processing. CARM1 overexpression has been reported in multiple cancer types and has been shown to modulate oncogenic pathways in in vitro studies. Detailed understanding of the mechanism of action of CARM1 in oncogenesis has been limited by a lack of selective tool compounds, particularly for in vivo studies. We describe the identification and characterization of, to our knowledge, the first potent and selective inhibitor of CARM1 that exhibits anti-proliferative effects both in vitro and in vivo and, to our knowledge, the first demonstration of a role for CARM1 in multiple myeloma (MM). EZM2302 (GSK3359088) is an inhibitor of CARM1 enzymatic activity in biochemical assays (IC50 = 6 nM) with broad selectivity against other histone methyltransferases. Treatment of MM cell lines with EZM2302 leads to inhibition of PABP1 and SMB methylation and cell stasis with IC50 values in the nanomolar range. Oral dosing of EZM2302 demonstrates dose-dependent in vivo CARM1 inhibition and anti-tumor activity in an MM xenograft model. EZM2302 is a validated chemical probe suitable for further understanding the biological role CARM1 plays in cancer and other diseases.

A key challenge in the development of precision medicine is defining the phenotypic consequences of pharmacological modulation of specific target macromolecules. To address this issue, a variety of genetic, molecular and chemical tools can be used. All of these approaches can produce misleading results if the specificity of the tools is not well understood and the proper controls are not performed. In this paper we illustrate these general themes by providing detailed studies of small molecule inhibitors of the enzymatic activity of two members of the SMYD branch of the protein lysine methyltransferases, SMYD2 and SMYD3. We show that tool compounds as well as CRISPR/Cas9 fail to reproduce many of the cell proliferation findings associated with SMYD2 and SMYD3 inhibition previously obtained with RNAi based approaches and with early stage chemical probes.

A full account of studies that culminated in the total synthesis of both antipodes and the assignment of its absolute configuration of Saudin, a hypoglycemic natural product. Two approaches are described, the first proceeding though bicyclic lactone intermediates and related second monocyclic esters. The former was obtained via asymmetric Diels–Alder cycloaddition and the latter by an asymmetric annulation protocol. Both approaches employ a Lewis acid promoted Claisen rearrangement, with the successful approach taking advantage of bidentate chelation to control the facial selectivity of the key Claisen rearrangement.

WHSC1 is a histone methyltransferase that is responsible for mono- and dimethylation of lysine 36 on histone H3 and has been implicated as a driver in a variety of hematological and solid tumors. Currently, there is a complete lack of validated chemical matter for this important drug discovery target. Herein we report on the first fully validated WHSC1 inhibitor, PTD2, a norleucine-containing peptide derived from the histone H4 sequence. This peptide exhibits micromolar affinity towards WHSC1 in biochemical and biophysical assays. Furthermore, a crystal structure was solved with the peptide in complex with SAM and the SET domain of WHSC1L1. This inhibitor is an important first step in creating potent, selective WHSC1 tool compounds for the purposes of understanding the complex biology in relation to human disease.

A novel aryl pyrazole series of arginine methyltransferase inhibitors has been identified. Synthesis of analogues within this series yielded the first potent, selective, small molecule PRMT6 inhibitor tool compound, EPZ020411. PRMT6 overexpression has been reported in several cancer types suggesting that inhibition of PRMT6 activity may have therapeutic utility. Identification of EPZ020411 provides the field with the first small molecule tool compound for target validation studies. EPZ020411 shows good bioavailability following subcutaneous dosing in rats making it a suitable tool for in vivo studies.

A unique 11b‐substituted indeno[2,1‐c]quinolin‐6‐one ring system was prepared in good yield and the structure of the product was unequivocally determined by X‐ray crystallography.

Pharmacokinetic and metabolite identification studies were conducted to understand the clearance pathways of EPZ011652 [(2-aminoethyl)(methyl)({3-[4-(propan-2-yloxy)phenyl]-1H-pyrazol-4-yl}methyl)amine], a potent protein arginine N-methyltransferase inhibitor. Metabolic clearance was the major pathway of EPZ011652 elimination in rats with structural elucidation of metabolites via liquid chromatography - mass spectrometry (LC-MSn) accurate mass measurement revealing the formation of a novel aliphatic N-acetylated metabolite (M1) located on the terminal nitrogen of the ethylene-diamine side chain. EPZ015564, a synthetic standard of the N-acetyl product, was prepared and was also generated by human and rat, but not dog hepatocytes. In rat hepatocytes, on incubation with EPZ011652, the concentration of EPZ015564 initially increased before decreasing with incubation time, suggesting that the metabolite is itself a substrate for other metabolizing enzymes, in agreement with the identification of metabolites M2, M3, and M4 in rat bile, all N-acetylated metabolites, undergoing sequential phase I (demethylation, oxidation) or phase II (sulfation) reactions. Reaction phenotyping with recombinant human N-acetyltransferase (NAT) isoforms revealed that both NAT1 and NAT2 are capable of acetylating EPZ011652, although with different catalytic efficiencies. Kinetic profiles of EPZ015564 formation followed classic Michaelis-Menten behavior with apparent Km values of >1000 μM for NAT1 and 165 ± 14.1 µM for NAT2. The in vitro intrinsic clearance for EPZ011652 by NAT2 (110 μL/min/mg) was 500-fold greater than by NAT1. In summary, we report the unusual N-acetylation of an aliphatic amine and discuss the implications for drug discovery and clinical development.

In the course of synthetic studies aimed at the elaboration of highly funtionalized ketone 1, we observed what appeared to be an extremely rare example of the addition of a trialkylborane to a carbonyl group. We were able to confirm the initial spectroscopic structural assignment by X-ray crystallography. Some preliminary mechanistic experiments suggest that the addition occurs directly in the absence of oxygen prior to oxidation of the trialkylborane during workup.

A series of diphenyl ethers was prepared and evaluated for androgen receptor antagonist activity in human androgen receptor binding and cellular functional assays. Analogs with potent in vitro activities were evaluated for topical in vivo efficacy in the Golden Syrian Hamster ear model. Several compounds showed reduction in wax esters in this validated animal model.

The radical decarboxylation–sulfoxide cycloelimination of 2′-pyridylthio esters formed from a series of podocarpic acid derivatives gives Δ4(18) -alkenes in high yield. An exception is the 13-nitro acid (2) which affords a thiohydroxamic ester (28), the relative stability of which is attributed to inhibition of the radical chain reaction by the nitro group. The stereochemistry of the pyridyl sulfide (18) has been confirmed by X-ray crystallography.

The First total synthesis of enantiopure triptoquinone F (6) starting from podocarpic acid (10) is reported, as well as formal syntheses of enantiopure triptoquinones D (4) and E (5). An acid-promoted Fries rearrangement of a benzannulated lactone (14) has been used as a direct, moderately high yielding route for introduction of C11 functionality. Treatment of methyl 12-methoxypodocarpa-8,11,13-trien-19-oate (11) with t-butylhydroperoxide and a catalytic amount of ruthenium(III) chloride gives a mixture (1 : 1) of diastereomeric t-butylcyclohexadienones (26) and (28).

The scope of acid-promoted Fries rearrangements of benzannulated lactones has been examined. The reaction is applicable to seven-membered lactones possessing a sufficiently activated aromatic ring but not to six-membered lactones, and it proceeds in higher yield for diterpenoid lactones than for lower molecular weight lactones. The structures of the 2,6-methano-bridged benzoxocin side products (23), (24), and (25) from rearrangement of the diterpenoid lactone (11) have been assigned.

A short efficient enantioselective synthesis of both (+)- and (−)-saudin, a naturally occurring hypoglycemic diterpene, is described. This synthesis establishes the absolute configuration of natural (−)-saudin for the first time. The key steps include the enantioselective construction of a dimethyl Hagemann's ester by an asymmetric Michael reaction and establishment of the key 1,3 disposed quaternary centers by means of a novel Ti(IV) promoted Claisen rearrangement. The assembly of the polycyclic ketal skeleton was likely under kinetic control proceeding via formation of the C1oxygen−C7 bond through an oxonium ion intermediate in the final stage.

A novel nonsteroidal androgen receptor antagonist, (R)-4-(1-benzyl-4,4-dimethyl-2-oxopyrrolidin-3-yloxy)-2-(trifluoromethyl)benzonitrile (1), for the topical control of sebum production is reported. This compound, which is potent, selective, and efficacious in the clinically validated golden Syrian hamster ear animal model, was designed to be delivered to the pilosebaceous unit, the site of action, preferentially by the follicular route.

A thyroid hormone receptor beta subtype-selective thyromimetic 5 was found to be efficacious in both mouse and monkey hair growth models after topical applications. It penetrates the skin according to the test in human cadaver skin mounted onto Franz diffusion chambers. The serum drug level of 5 is below the limit of quantification during tests in the bald stump-tailed macaques (Macaca arctoides). It is tested negative in the 3T3 neutral red uptake (NRU) phototoxicity test, indicating a low risk for causing photo-irritation. It is also rapidly metabolized according to the PK data, thus the systemic exposure is limited.

The first examples of thioether-substituted benzonitriles as potential soft-drug androgen receptor antagonists are reported. A number of 4-(alkylthio)- and of 4-(arylthio)-benzonitrile analogs were evaluated in human androgen receptor binding and cellular functional assays. Analogs with potent in vitro binding and cellular activities were evaluated for topical in vivo efficacy in the Golden Syrian hamster ear model. Analogs from both the 4-(alkylthio)- and of 4-(arylthio)-benzonitrile series showed moderate reduction of wax esters in vivo.

A practical Buchwald-Hartwig amination of 2-bromopyridines with volatile amines is developed in sealed tubes. The method provides an expedient entry to a variety of secondary and tertiary aminopyridines that are otherwise not readily synthesized.

SMYD3 (Set and Mynd Domain containing 3) is a lysine methyltransferase overexpressed in several cancer types including breast, prostrate, pancreatic, and lung, and this overexpression is associated with poor clinical prognosis. Genetic knockdown of SMYD3 by shRNA has been shown to decrease proliferation in a range of cancer cell lines suggesting that inhibition of SMYD3 may have therapeutic utility. In this presentation we describe the discovery and optimization of a novel series of oxindole sulfonamides and sulfamides with SMYD3 inhibitory activity. One of these compounds, EPZ030456, has a SMYD3 biochemical IC50 of 4 nM and is active in cells with an IC50 of 48 nM in a trimethyl MAP3K2 (MEKK2) in-cell western (ICW) assay. The crystal structure of this compound was solved with SMYD3 and the nucleotide substrate, S-adenosylmethionine and shows the oxindole portion of the molecule extends into the SMYD3 lysine binding channel. EPZ030456 shows < 30% inhibition at a 10 uM screening concentration against 17 histone methyltransferase targets tested, including SMYD2. Further optimization within the series resulted in EPZ031686 which has similar potency to EPZ030456 with a biochemical IC50 of 3 nM and an ICW IC50 of 36 nM and in addition exhibits good bioavailability following oral dosing in mice. Hence, EPZ031686 is a suitable tool to study the role of SMYD3 in cancer and other therapeutic areas, using both in vitro and in vivo models. Citation Format: Lorna H. Mitchell, Paula A. Boriack-Sjodin, Sherri Smith, Michael Thomenius, Nathalie Rioux, Michael Munchhof, James E. Mills, Christine Klaus, Jennifer Totman, Thomas V. Riera, Alejandra Raimondi, Suzanne L. Jacques, Megan Foley, Nigel J. Waters, Kevin W. Kuntz, Tim J. Wigle, Margaret Porter Scott, Robert A. Copeland, Jesse J. Smith, Richard Chesworth. Identification of a novel potent selective SMYD3 inhibitor with oral bioavailability. [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 C85.

PRMT6 is a nuclear-localized arginine methyl transferase (RMT) capable of adding omega-N(G)-monomethylarginine and asymmetric omega-N(G),N(G)-dimethylarginine derivatives to histone and other protein substrates containing a GAR motif. PRMT6 can methylate both histone and non-histone substrates and is the only RMT known to methylate the H3R2 mark. This mark can act in opposition to the activating H3K4me3 mark, effectively acting as a transcriptional repressor. PRMT6 overexpression has been reported in several cancer types including melanoma and bladder, lung, and prostate carcinoma suggesting that inhibition of PRMT6 activity might have therapeutic utility. However, until now no small molecule PRMT6 inhibitor has been available to carry out in vitro and in vivo studies. Here we report identification of an aryl pyrazole as the first small molecule PRMT6 inhibitor. This tool compound has an IC50 of 10nM in a PRMT6 biochemical assay and the binding mode has been elucidated through crystallography. The compound inhibited methylation of H3R2 in a dose dependent manner in an engineered model in which PRMT6 was transiently expressed in the A375 cell line. The tool compound showed a half-life (t½) of 8.54 ± 1.43 h after a 1 mg/kg intravenous administration to rats and bioavailability of 65.6 ± 4.3% for a 5 mg/kg subcutaneous dose, enabling its use in further in vitro and in vivo target validation. Citation Format: Allison Drew, Lorna Mitchell, Nathalie Rioux, Kerren Swinger, Scott Ribich, Suzanne Jacques-O'hagan, Trupti Lingaraj, Tim Wigle, Tom Riera, Richard Chesworth, Jesse Smith. Identification of the first small molecule PRMT6 inhibitor tool compound. [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 5376. doi:10.1158/1538-7445.AM2015-5376

High-throughput screening has identified a novel class of inhibitors of the checkpoint kinase Wee1, which have potential for use in cancer chemotherapy. These inhibitors are based on a 4-phenylpyrrolo[3,4-c]carbazole-1,3(2H,6H)-dione template and have been shown by X-ray crystallography to bind at the ATP site of the enzyme. An extensive study of the effects of substitution around this template has been carried out, which has identified substituents which lead to improvements in potency and selectivity for Wee1. While retention of the maleimide ring and pendant 4-phenyl group is necessary for potency, replacement of the carbazole nitrogen by oxygen is well tolerated and results in improved Wee1 selectivity against the related checkpoint kinase Chk1. Wee1 potency and selectivity are also enhanced by the incorporation of lipophilic functionality at the 2'-position of the 4-phenyl ring, and Wee1 selectivity against Chk1 is favored by C3-C5 alkyl substitution of the carbazole nitrogen. These studies provide a basis for the design of active analogues of the pyrrolocarbazole lead with improved physical properties.

A unique 11b‐substituted indeno[2,1‐c]quinolin‐6‐one ring system was prepared in good yield and the structure of the product was unequivocally determined by X‐ray crystallography.

During preparation of a series of diphenyl ethers it was observed that displacement of an activated aryl fluoride with ortho-hydroxyacetophenone afforded a product that was C-arylated adjacent to the ketone. Evidence suggested this product was formed by Smiles rearrangement of an O-arylated intermediate.

A short efficient enantioselective synthesis of both (+)- and (-)-saudin, a naturally occurring hypoglycemic diterpene, is described. This synthesis establishes the absolute configuration of natural (-)-saudin for the first time. The key steps include the enantioselective construction of a dimethyl Hagemann's ester by an asymmetric Michael reaction and establishment of the key 1,3 disposed quaternary centers by means of a novel Ti(IV) promoted Claisen rearrangement. The assembly of the polycyclic ketal skeleton was likely under kinetic control proceeding via formation of the C1oxygen-C7 bond through an oxonium ion intermediate in the final stage.

The First total synthesis of enantiopure triptoquinone F (6) starting from podocarpic acid (10) is reported, as well as formal syntheses of enantiopure triptoquinones D (4) and E (5). An acid-promoted Fries rearrangement of a benzannulated lactone (14) has been used as a direct, moderately high yielding route for introduction of C11 functionality. Treatment of methyl 12-methoxypodocarpa-8,11,13-trien-19-oate (11) with t-butylhydroperoxide and a catalytic amount of ruthenium(III) chloride gives a mixture (1 : 1) of diastereomeric t-butylcyclohexadienones (26) and (28).

The radical decarboxylation–sulfoxide cycloelimination of 2′-pyridylthio esters formed from a series of podocarpic acid derivatives gives Δ4(18) -alkenes in high yield. An exception is the 13-nitro acid (2) which affords a thiohydroxamic ester (28), the relative stability of which is attributed to inhibition of the radical chain reaction by the nitro group. The stereochemistry of the pyridyl sulfide (18) has been confirmed by X-ray crystallography.