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Comprehensive in Vitro Characterization of the Mechanism of Action of EPI-7386, an Androgen Receptor N-Terminal Domain Inhibitor

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Comprehensive in Vitro Characterization of the Mechanism of Action of EPI-7386, an Androgen Receptor N-Terminal Domain Inhibitor #1209 Comprehensive in vitro characterization of the mechanism of action of EPI-7386, an androgen receptor N-terminal domain inhibitor Nan Hyung Hong1, Shihua Sun2, Peter Virsik1, Alessandra Cesano1, Han-Jie Zhou1, Elahe A. Mostaghel3,4,5, Stephen R. Plymate2,4, Ronan Le Moigne1 1 ESSA Pharma Corp, South San Francisco , CA 2 University of Washington, Division of Gerontology and Geriatric Medicine, Seattle, WA 3 Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA 4 VA Puget Sound Health Care System, Seattle, WA 5 University of Washington, Medical Oncology Division, Seattle, WA Contact: [email protected] Presented at AACR Annual Meeting 2021 Background v As a key driver of prostate cancer, androgen receptor (AR) signaling has been a major target of prostate cancer therapy v All current anti-androgens function through the ligand-binding aniten domain (LBD) of the AR v Anti-androgen resistance mechanisms generally develop at the LBD, due to mutations in the LBD itself and the expression of constitutively active splice variants of AR that lack the LBD v Anitens are small molecules capable of targeting the AR N- terminal domain that can inhibit transcriptional activity of the AR even in the presence of LBD-driven anti-androgen resistance Figure 1. Anitens are first-in-class NTD inhibitors of the androgen receptor. Structure of the androgen receptor (AR) and mechanism of inhibition. The AR comprises three main functional domains: the LBD, involved v EPI-7386 is a new generation of aniten which exhibits high in binding with androgens, the DBD, and the NTD, which orchestrate the potency, low metabolism, on-target specificity transactivation of the receptor. It was previously demonstrated that the first- generation aniten and its stereoisomers specifically bind to the transactivation unit 5 (Tau5) of AR NTD to block essential protein-protein interactions required for the transcriptional activity of AR1-3. 1De Mol et al., ACS Chem Biol, 2016, 2Andersen et al., Cancer Cell, 2010, 3CONFIDENTIALSadar, Cancer Res, 2011 2 EPI-7386 interacts with both AR-FL and AR-V7 AR-FL (+100 nM DHT) in LNCaP cells AR-V7 (-DHT) in LNCaP95 cells A D EPI-7386 B 3 µM EPI-7386 C E 30 µM EPI-7386 F DMSO DMSO 1.5 1.0 1.0 1.0 1.0 0µM 0µM 41°C 39°C /I /I /I /I x x I x CETSA EC x I 0.5 50 I I 0.5 0.5 0.5 CETSA EC50 : 6.4 µM : 4.3 µM 0.0 0.0 0.0 40 44 48 52 -7 -6 -5 -4 40 45 50 55 -9 -8 -7 -6 -5 -4 °C [M] °C [M] Figure 2. Cellular Thermal Shift Assay (CETSA) of AR target engagement by EPI-7386. AR target engagement by EPI-7386 induced a decrease in AR thermal stability. (A-C) AR-FL target engagement in LNCaP cells was determined in the presence of 100 nM DHT and (D-F) AR-V7 in LNCaP95 cells was determined in the absence of DHT. (A, D) Representative Western Blot showing thermostable AR-FL in LNCaP cells (A) or AR-V7 in LNCaP95 (D) following heat shock in the presence (+) or absence (-) of EPI-7386. (B, E) Melt and shift curve of AR-FL in LNCaP cells (B) or AR-V7 in LNCaP95 cells (E) treated with EPI-7386 (blue) at the indicated concentration and DMSO control (black). (C, F) Isothermal (47℃) dose-response curve of AR-FL in LNCaP cells and AR-V7 in LNCaP95 cells. Potency of target engagement (CETSA EC50) was calculated from multiple independent experiments (n≥9). * AR-V7 specific antibody (clone RM7; RevMab) was used to detect AR-V7 in LNCaP95. ** No AR-V7 thermal shift was induced by DHT unlike AR-FL, confirming assay specificity to AR-V7 lacking LBD CONFIDENTIAL 3 EPI-7386 is active in the AR splice variant (ARv567es) expressing cell line A B C CWR AD1 Luc_9-21-20_controlCWR onlyCWR-R1 AD1-AD1 Luc_9-21-20 CWR D567 Luc_6-19-20_controlCWRCWR alone D567-R1 Luc_6-19-20_treatment-D567 CWR-R1-D567 : expressing only AR-FL 6000 6000 : expressing only ARv567es 20000 20000 EPI-7386 : expressing only ARv567es CWR D567 MTT_4-29-20_noR1881_%CWR D567 MTT_4-29-20_w/R1881_%_% 400 Enzalutamide 300 4000 4000 120 120 300 100 100 200 80 80 200 2000 2000 60 60 100 40 40 Viability (%) RL (Firefly/Protein) RL RL (Firefly/Protein) RL RL (Firefly/Protein) RL 100 20 20 0 0 0 0 0 0 5 5 5 5 10 20 10 10 10 10 2.5 2.5 2.5 2.5 1.11 0.37 3.33 1.25 1.25 1.25 1.25 0.123 0.156 0.313 0.625 0.156 0.313 0.625 DMSO 0.156 0.313 0.625 0.156 0.313 0.625 DMSO DMSO DMSO EPI-7386 [µM] Enzalutamide [µM] EPI-7386 [µM] Enzalutamide [µM] 10 uM Enza EPI-7386 [µM] 10 uM EPI-7386 10 nMR1881 10 nMR1881 - R1881 + 1nM R1881 Figure 3. Effect of EPI-7386 against AR splice variant driven transcriptional activity and cell growth. (A,B) AR-driven transcriptional activity was assessed using a probasin promoter (ARR2PB) driven luciferase reporter in CWR-R1-AD1 cells expressing only AR-FL in the presence of 5%FBS (A) or in CWR-R1-D567 cells expressing only AR-V567es under serum free condition (B). (C) Cell viability analysis of CWR-R1-D567 with MTT assay showing relative viable cell % to DMSO control after 72 hr treatment of EPI-7386 or enzalutamide in the absence or presence of R1881. * CWR-R1-D567 cells were derived from the CWR-R1-AD1 cells by TALEN-mediated deletion of AR exons 5-74 4NyquistCONFIDENTIAL et al., PNAS, 2013 4 EPI-7386 inhibits AR genomic binding PROMOTER (0-3 kb) 5`-UTR A + 1nM R1881 B EXON C FKBP5 TMPRSS2 KLK3 CHRNA2 SLC45A3 53.30% INTRON 10 !M 10 !M PROMOTER3`-UTR (0-3 kb) 5`-UTRDOWNSTREAM (0-3 kb) DMSO 1 nM R1881 EPI-7386 Enza DMSO EXONDIST INTERGENIC (525) INTRON [0-327] [0-42] [0-20] [0-131] [0-50] 3`-UTR PROMOTERPROMOTER (0-3 kb) (0-3 kb) DMSO DOWNSTREAM5`-UTR (0-3 kb) 5`-UTR 1nM R1881 DISTEXON INTERGENIC EXON 1nM R1881 (31510) INTRON INTRONPROMOTER3`-UTR (0-3 kb) 3`-UTR5`-UTRDOWNSTREAM (0-3 kb)10μM EPI-7386 10!M EPI-7386 Total=100 DOWNSTREAMEXONDIST INTERGENIC (0-3 kb) (9121) DISTINTRON INTERGENIC R1881 10µM Enza 3`-UTR + DOWNSTREAM (0-3 kb) 10!MEnza Total=100.1 DIST INTERGENIC (10249) Copy of Copy of Copy of Copy of KLK2, FKBP5, TMPRSS2 0 25 50 75 100 E 30 Total=100.1 DMSO R1881 Percentage (%) 20 Total=100 5 uM EPI-7386 5 uM Enza D Total=100 6 % of Target % of Background treatment De novo Motif P-value Best match Sequences with Motif Sequences with Motif G A TTT DMSO CAC 1e-92 66.85% 18.42% FOXA1(Forkhead) 4 TATTTGTCGA 20 A A CTC G GT R1881 G T A AT T 1e-202 19.04% 2.88% GRE/ARE(NR) GG T A ACT C GA A T CG GAGAC C 10 2 R1881 AGA + ATGTAA C 1e-479 70.55% 19.51% FOXA1(Forkhead) C A T GAC T C T T CCA T 0 10 µM EPI-7386 Binding Events Detected per 1000 cells -5 0 5 -5 0 5-5 0 5-5 0 5 R1881 G TTA G T C C + AGT 1e-444 68.70% 19.45% FOXA1(Forkhead) T T G 0 A G CT C C T AA A Distance from center (Kb) 10 µM Enza Untr12 KLK3 KLK2 FKBP5 TMPRSS2 Untr12 KLK3 KLK2 FKBP5 TMPRSS2 6h 24h Figure 4. ChIP-seq analysis of AR genomic distribution. (A-D) Cells were treated with DMSO, R1881, EPI-7386 or enzalutamide(Enza) in the presence of R1881 as indicated for 24 h. (A) Heatmap view of AR ChIP-seq signals around AR peaks (± 5 kb) detected in LNCaP cells with treatments as indicated. (B) Bar chart showing genomic distribution of AR- binding peaks including promoters (withing 3 kb upstream of TSS), 5’ UTRs, exons, introns, 3’UTRs, downstream (within 3 kb downstream of the gene), and intergenic regions. Total peak numbers are also noted. (C) Gene track view of AR ChIP-seq data at FKBP5, TMPRSS2, KLK3, CHRNA2, and SLC45A3 loci, visualized by Integrative Genomics Viewer (IGV). (D) The top enriched motifs present in AR ChIP-seq peaks of each condition identified using Homer. (E) ChIP-qPCR validation in LNCaP cells with AR antibody. Cells were treated with DMSO, 1 nM R1881, EPI-7386, or enzalutamide in the presence of 1nM R1881 for 6 or 24 h. Untr12, primer that binds to gene dessert area in chromosome 12, was used for negative control locus. CONFIDENTIAL 5 EPI-7386 shows superior activity than enzalutamide in the AR-V7 expressing LNCaP95 cells by modulating both AR-FL and AR-V7 driven gene expression +/- R1881 FC3_padj<0.01 A downregulated upregulated 7.5uM Enzalutamide N/A C Z-score -4 2 - R1881 7.5uM EPI-7386 982 959 7.5uM Enzalutamide 97 / 59 NUCB2 LAMC1 GCLC 7.5uM EPI-7386 776 1032 GULP1 + R1881 PFKFB2 HOMER2 AKAP12 0 500 1000 1500 2000 2500 NCOA1 RHOU Number of genes ELL2 HIF1A w/ 1nM R1881 PRKCD KLK3 KLK2 FASN B HOXB13 Withoutno R1881 R1881 With 1nM R1881 C19orf48 CROT Vehicle 5 uM ENZ 5 uM EPI-7386 GNAI1 Vehicle 5 uM ENZ 5 uM EPI-7386 PPAP2A R1881 7.5 uM ENZ 7.5 uM EPI-7386 7.5 uM ENZ 7.5 uM EPI-7386 SLC45A3 FKBP5 60 F2RL1 2.0 45 ATAD 2 30 GUCY1A3 LPAR3 GRIN3A 1.5 18 AD AM7 ETV1 15 CBR4 STEAP2 SNX1 1.0 12 MAPK8 RTN4 9 DOPEY2 MBOAT2 STK39 0.5 6 UBE2E3 PRKD1 3 STEAP1 Relative mRNA expression Relative mRNA Relative mRNA expression Relative mRNA 0.0 0 5 uM EPI-7386 7.5 uM EPI-7386 Vehicle 5 or 7.5 uM enzalutamide KLK3 KLK2 KLK3 KLK2 FKBP5 NKX3-1 FKBP5 NKX3-1 CHRNA2 CHRNA2 TMPRSS2 SLC45A3 TMPRSS2 SLC45A3 Figure 5.
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