TEAD proteins are the transcriptional effectors of the Hippo signaling pathway that bind coactivators YAP/TAZ to activate gene expression programs involved in cell survival, proliferation, and drug resistance. TEAD-dependent transcription is elevated in many tumor types through a variety of mechanisms including loss-of-function mutations in Hippo pathway tumor suppressors, and as an adaptive resistance mechanism in response to EGFR TKI and KRAS inhibition. Therefore, targeting the YAP/TAZ-TEAD signaling axis has the potential to provide clinical benefit either as a monotherapy or combination strategy across diverse indications. Here, we characterize the activity of AZ'4331, a TEAD palmitoylation inhibitor which displays anti-tumor efficacy in multiple pre-clinical models of Hippo pathway-dysregulated cancers. Metabolic labeling studies show that TEAD proteins rapidly cycle between apo- and palmitoylated states, and that AZ'4331 inhibits the palmitoylation of TEAD1-4 paralogs. Functionally, AZ'4331 reduces YAP-TEAD binding and TEAD-dependent transcription, leading to reduced cell cycle progression and proliferation in Hippo pathway-altered NCI-H226 cells in vitro. AZ'4331 elicits robust monotherapy activity across mesothelioma and head and neck squamous cell carcinoma xenografts, and significantly enhances the efficacy of osimertinib in EGFR-mutant non-small cell lung cancer in vitro. However, this combination benefit only translates in vivo when osimertinib is administered at doses below clinically relevant levels, suggesting that TEAD inhibition enhances the efficacy of osimertinib in settings where EGFR signaling is incompletely suppressed. Collectively, these findings highlight the promise of TEAD inhibition as a therapeutic strategy for the treatment of Hippo pathway-driven cancers.

Abstract TEAD1-4 are DNA bound transcription factors regulated by the Hippo tumor suppressor pathway that bind the coactivators YAP/TAZ to activate oncogenic gene expression programs involved in cell survival, proliferation, and drug resistance. TEAD-dependent transcription is activated in many tumor types through a variety of mechanisms including LOF Hippo pathway mutations (e.g. NF2, LATS) and YAP/TAZ amplification, and also as an adaptive resistance mechanism, for example in response to EGFR TKI and KRAS inhibition. Here, we report the initial characterization of a novel pan-TEAD inhibitor, AZ4331, which was identified following a structure-guided drug design campaign. AZ4331 disrupts the post-translational palmitoylation of TEAD proteins through covalent binding to a conserved cysteine residue resulting in inhibition of TEAD-dependent transcriptional output. AZ4331 inhibited the proliferation of NF2m NCI-H226 cells (GI50: 92 nM) while having no effect on Hippo-wild type NCI-H2452 (GI50: undetermined). Cell-based metabolic labeling studies demonstrated the ability of AZ4331 to inhibit palmitoylation of all four TEAD paralogs and led to disruption of the YAP/TEAD complex assessed by immunoprecipitation resulting in reduced TEAD transcriptional output as assessed by qPCR. Furthermore, in vivo profiling showed AZ4331 achieved sufficient exposures (plasma free Cmax: 2.7 µM) and robust target engagement as measured through reduction of multiple canonical TEAD target genes (CTGF [IC50: 0.127 µM], ANKRD1, AMOTL2 and CYR61) in Hippo-altered mesothelioma xenograft tumors. This target engagement in turn drove inhibition of tumor proliferation in xenograft models representing common Hippo-alterations. AZ4331 treatment of NF2m NCI-H226 and LATS1/2 loss MSTO-211H mesothelioma xenografts drove 50% and 93% regression of tumors, respectively. While treatment of head and neck squamous cell carcinoma FAT1m FaDu and YAP1amp Detroit562 xenografts lead to 58% tumor growth inhibition and 35% tumor regression, respectively. These findings identify AZ4331 as a potent inhibitor of the TEAD transcription factor family and further validate the inhibition of TEAD in Hippo-altered cancers as a potential therapeutic strategy. Citation Format: Jacob A. Gordon, Jolanta Dubauskaite, Michelle DuPont, Nin Guan, Geoff Holdgate, Scott Mlynarski, Neil Umbreit, Danielle Sanchez, Abhishek Srivastava, Janek Suski, Nancy Su, Ryan Richards, Sabina Cosulich, Corinne Reimer, James Brownell. Discovery of potent and selective pan-TEAD autopalmitoylation inhibitors for the treatment of Hippo-pathway altered cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6589.

Bfl-1 is overexpressed in both hematological and solid tumors; therefore, inhibitors of Bfl-1 are highly desirable. A DNA-encoded chemical library (DEL) screen against Bfl-1 identified the first known reversible covalent small-molecule ligand for Bfl-1. The binding was validated through biophysical and biochemical techniques, which confirmed the reversible covalent mechanism of action and pointed to binding through Cys55. This represented the first identification of a cyano-acrylamide reversible covalent compound from a DEL screen and highlights further opportunities for covalent drug discovery through DEL screening. A 10-fold improvement in potency was achieved through a systematic SAR exploration of the hit. The more potent analogue compound 13 was successfully cocrystallized in Bfl-1, revealing the binding mode and providing further evidence of a covalent interaction with Cys55.

Covalent hit identification is a viable approach to identify chemical starting points against difficult-to-drug targets. While most researchers screen libraries of <2k electrophilic fragments, focusing on lead-like compounds can be advantageous in terms of finding hits with improved affinity and with a better chance of identifying cryptic pockets. However, due to the increased molecular complexity, larger numbers of compounds (>10k) are desirable to ensure adequate coverage of chemical space. Herein, the approach taken to build a library of 12k covalent lead-like compounds is reported, utilizing legacy compounds, robust library chemistry, and acquisitions. The lead-like covalent library was screened against the antiapoptotic protein Bfl-1, and six promising hits that displaced the BIM peptide from the PPI interface were identified. Intriguingly, X-ray crystallography of lead-like compound 8 showed that it binds to a previously unobserved conformation of the Bfl-1 protein and is an ideal starting point for the optimization of Bfl-1 inhibitors.

Bfl-1, a member of the Bcl-2 family of proteins, plays a crucial role in apoptosis regulation and has been implicated in cancer cell survival and resistance to venetoclax therapy. Due to the unique cysteine residue in the BH3 binding site, the development of covalent inhibitors targeting Bfl-1 represents a promising strategy for cancer treatment. Herein, the optimization of a covalent cellular tool from a lead-like hit using structure based design is described. Informed by a reversible X-ray fragment screen, the strategy to establish interactions with a key glutamic acid residue (Glu78) and optimize binding in a cryptic pocket led to a 1000-fold improvement in biochemical potency without increasing reactivity of the warhead. Compound (R,R,S)-26 has a k(inact)/K-I of 4600 M-1 s(-1), shows <1 mu M caspase activation in a cellular assay and cellular target engagement, and has good physicochemical properties and a promising in vivo profile.

BFL1, a member of the antiapoptotic BCL2 family, has been relatively understudied compared to its counterparts despite evidence of its overexpression in various hematological malignancies. Across two articles, we describe the development of BFL1 in vivo tools. The first article describes the hit identification from a covalent fragment library and the subsequent evolution from the hit to compound 6.22 This work reports the structure-based optimization of compound 6 into a series of BFL1 inhibitors selective over the other BCL2 family members, with low nanomolar cellular activity when combined with AZD5991, exemplified by compound 20. Compound 20 demonstrated a cell death phenotype in SUDHL1 and OCILY10 cell lines and in the in vivo study, BFL1 stabilization and cleaved caspase 3 activation were observed in a dose-dependent manner. In addition, the enzymatic turnover studies with the BFL1 protein showed that compound 20 stabilized the protein, extending the half-life to 10.8 h.

Transient exposure to AZD4573 induces apoptosis upon depletion of Mcl-1.

List of antibodies (S1), PK/PD/efficacy model parameters (S2), putative cancer-associated genes (S3), and transcripts modulated by AZD4573 (S4).

Intermittent dosing of AZD4573 drives regression of hematological tumor xenografts as predicted by a PK/PD/efficacy model.

Identification of highly selective and potent CDK9 inhibitor, AZD4573.

List of proteins modulated by AZD4573 (S5), genes rapidly modulated by AZD4573 (S6), and AZD4573 cancer cell line pharmacology (S7).

AZD4573 induces rapid cell death across a diverse panel of hematological cancer cell lines.

Material, methods, supplementary references, and list of supplementary tables.

Abstract Purpose: Targeting Bcl-2 family members upregulated in multiple cancers has emerged as an important area of cancer therapeutics. While venetoclax, a Bcl-2–selective inhibitor, has had success in the clinic, another family member, Bcl-xL, has also emerged as an important target and as a mechanism of resistance. Therefore, we developed a dual Bcl-2/Bcl-xL inhibitor that broadens the therapeutic activity while minimizing Bcl-xL–mediated thrombocytopenia. Experimental Design: We used structure-based chemistry to design a small-molecule inhibitor of Bcl-2 and Bcl-xL and assessed the activity against in vitro cell lines, patient samples, and in vivo models. We applied pharmacokinetic/pharmacodynamic (PK/PD) modeling to integrate our understanding of on-target activity of the dual inhibitor in tumors and platelets across dose levels and over time. Results: We discovered AZD4320, which has nanomolar affinity for Bcl-2 and Bcl-xL, and mechanistically drives cell death through the mitochondrial apoptotic pathway. AZD4320 demonstrates activity in both Bcl-2– and Bcl-xL–dependent hematologic cancer cell lines and enhanced activity in acute myeloid leukemia (AML) patient samples compared with the Bcl-2–selective agent venetoclax. A single intravenous bolus dose of AZD4320 induces tumor regression with transient thrombocytopenia, which recovers in less than a week, suggesting a clinical weekly schedule would enable targeting of Bcl-2/Bcl-xL–dependent tumors without incurring dose-limiting thrombocytopenia. AZD4320 demonstrates monotherapy activity in patient-derived AML and venetoclax-resistant xenograft models. Conclusions: AZD4320 is a potent molecule with manageable thrombocytopenia risk to explore the utility of a dual Bcl-2/Bcl-xL inhibitor across a broad range of tumor types with dysregulation of Bcl-2 prosurvival proteins.

4 Abstract : 61 Purpose : Cyclin-dependent kinase 9 (CDK9) is a transcriptional regulator and potential 62 therapeutic target for many cancers. Multiple non-selective CDK9 inhibitors have 63 progressed clinically but were limited by a narrow therapeutic window. This work 64 describes a novel, potent, and highly selective CDK9 inhibitor, AZD4573. 65 Experimental Design : The anti-tumor activity of AZD4573 was determined across broad 66 cancer cell line panels in vitro as well as cell line- and patient-derived xenograft models 67 in vivo . Multiple approaches, including integrated transcriptomic and proteomic 68 analyses, loss-of-function pathway interrogation, and pharmacological comparisons, 69 were employed to further understand the major mechanism driving AZD4573 activity 70 and to establish an exposure/effect relationship. 71 Results : AZD4573 is a highly selective and potent CDK9 inhibitor. It demonstrated rapid 72 induction of apoptosis and subsequent cell death broadly across hematological cancer 73 models in vitro , and Mcl-1 depletion in a dose- and time-dependent manner was 74 identified as a major mechanism through which AZD4573 induces cell death in tumor 75 cells. This pharmacodynamic response was also observed in vivo , which led to 76 regressions in both subcutaneous tumor xenografts and disseminated models at 77 tolerated doses both as monotherapy or in combination with venetoclax. This 78 understanding of the mechanism, exposure, and anti-tumor activity of AZD4573 79 facilitated development of a robust PK/PD/efficacy model used to inform the clinical trial 80 design. 81 Conclusions : Selective targeting of CDK9 enables the indirect inhibition of Mcl-1, 82 providing a therapeutic option for Mcl-1-dependent diseases. Accordingly, AZD4573 is cell This work describes the mechanism of action and preclinical activity of the novel and highly selective CDK9 inhibitor, AZD4573. An agnostic approach utilizing integrated transcriptomic and proteomic analyses revealed MCL1 as one of the top oncogenes most significantly and robustly down-regulated at the mRNA and protein level upon acute AZD4573 treatment. Subsequent pharmacological studies further supported an Mcl-1-mediated mechanism, including derivation of a PK/PD/efficacy model linking CDK9 inhibition, Mcl-1 depletion, and induction of apoptosis in response to AZD4573. preclinical

Over the last ten years, targeted covalent inhibition has become a key discipline within medicinal chemistry research, most notably in the development of oncology therapeutics. One area where this approach is under-represented, however, is in targeting protein-protein interactions. This is primarily because these hydrophobic interfaces lack appropriately located cysteine residues to allow for standard conjugate addition chemistry. Herein, we report our development of the first covalent inhibitors of the antiapoptotic protein B-cell lymphoma extra-large (Bcl-xL), utilizing a sulfonyl fluoride (SF) warhead to selectively covalently modify tyrosine 101 of the BH3 domain-binding groove. These compounds display time-dependent inhibition in a biochemical assay and are cellularly active (U266B1). In addition, compound 7 was further elaborated to generate a chemical-biology probe molecule, which may find utility in understanding the intricacies of Bcl-xL biology.

Abstract Purpose: Cyclin-dependent kinase 9 (CDK9) is a transcriptional regulator and potential therapeutic target for many cancers. Multiple nonselective CDK9 inhibitors have progressed clinically but were limited by a narrow therapeutic window. This work describes a novel, potent, and highly selective CDK9 inhibitor, AZD4573. Experimental Design: The antitumor activity of AZD4573 was determined across broad cancer cell line panels in vitro as well as cell line- and patient-derived xenograft models in vivo. Multiple approaches, including integrated transcriptomic and proteomic analyses, loss-of-function pathway interrogation, and pharmacologic comparisons, were employed to further understand the major mechanism driving AZD4573 activity and to establish an exposure/effect relationship. Results: AZD4573 is a highly selective and potent CDK9 inhibitor. It demonstrated rapid induction of apoptosis and subsequent cell death broadly across hematologic cancer models in vitro, and MCL-1 depletion in a dose- and time-dependent manner was identified as a major mechanism through which AZD4573 induces cell death in tumor cells. This pharmacodynamic (PD) response was also observed in vivo, which led to regressions in both subcutaneous tumor xenografts and disseminated models at tolerated doses both as monotherapy or in combination with venetoclax. This understanding of the mechanism, exposure, and antitumor activity of AZD4573 facilitated development of a robust pharmacokinetic/PD/efficacy model used to inform the clinical trial design. Conclusions: Selective targeting of CDK9 enables the indirect inhibition of MCL-1, providing a therapeutic option for MCL-1–dependent diseases. Accordingly, AZD4573 is currently being evaluated in a phase I clinical trial for patients with hematologic malignancies (clinicaltrials.gov identifier: NCT03263637). See related commentary by Alcon et al., p. 761

Cyclin‐dependent kinase (CDK) 12 knockdown via siRNA decreases the transcription of DNA‐damage‐response genes and sensitizes BRCA wild‐type cells to poly(ADP‐ribose) polymerase (PARP) inhibition. To recapitulate this effect with a small molecule, we sought a potent, selective CDK12 inhibitor. Crystal structures and modeling informed hybridization between dinaciclib and SR‐3029, resulting in lead compound 5 [(S)‐2‐(1‐(6‐(((6,7‐difluoro‐1H‐benzo[d]imidazol‐2‐yl)methyl)amino)‐9‐ethyl‐9H‐purin‐2‐yl)piperidin‐2‐yl)ethan‐1‐ol]. Further structure‐guided optimization delivered a series of selective CDK12 inhibitors, including compound 7 [(S)‐2‐(1‐(6‐(((6,7‐difluoro‐1H‐benzo[d]imidazol‐2‐yl)methyl)amino)‐9‐isopropyl‐9H‐purin‐2‐yl)piperidin‐2‐yl)ethan‐1‐ol]. Profiling of this compound across CDK9, 7, 2, and 1 at high ATP concentration, single‐point kinase panel screening against 352 targets at 0.1 μm, and proteomics via kinase affinity matrix technology demonstrated the selectivity. This series of compounds inhibits phosphorylation of Ser2 on the C‐terminal repeat domain of RNA polymerase II, consistent with CDK12 inhibition. These selective compounds were also acutely toxic to OV90 as well as THP1 cells.

Mcl-1 is a member of the Bcl-2 family of proteins that promotes cell survival by preventing induction of apoptosis in many cancers. High expression of Mcl-1 causes tumorigenesis and resistance to anticancer therapies highlighting the potential of Mcl-1 inhibitors as anticancer drugs. Here, we describe AZD5991, a rationally designed macrocyclic molecule with high selectivity and affinity for Mcl-1 currently in clinical development. Our studies demonstrate that AZD5991 binds directly to Mcl-1 and induces rapid apoptosis in cancer cells, most notably myeloma and acute myeloid leukemia, by activating the Bak-dependent mitochondrial apoptotic pathway. AZD5991 shows potent antitumor activity in vivo with complete tumor regression in several models of multiple myeloma and acute myeloid leukemia after a single tolerated dose as monotherapy or in combination with bortezomib or venetoclax. Based on these promising data, a Phase I clinical trial has been launched for evaluation of AZD5991 in patients with hematological malignancies (NCT03218683).