Covalent Inhibitors Research Articles

Abstract 1925: Wild-type RAS signaling is an essential therapeutic target in RAS-mutated cancers

Abstract Single-agent targeting of RAS-mutated cancers using RAF/MEK/ERK or PI3K/AKT pathway inhibitors is ineffective; blocking one pathway relieves negative feedback control of RTK signaling and hyperactivates parallel effector pathways. While combined MEK and PI3K inhibition is effective in preclinical models, toxicity of this combination prevents its clinical use. Alternative strategies for treating RAS-mutated cancers are essential. Therapeutics directly targeting mutated RAS proteins have the potential to spare normal cellular function thereby lessening overall toxicity. Unfortunately, direct RAS inhibition as a monotherapy does not fully block RAS effector signaling. RAS proteins show differential activation of RAF and PI3K pathways: KRAS potently activates RAF but poorly activates PI3K, whereas HRAS effectively activates PI3K but poorly activates RAF. Further, mutant RAS inhibition relieves negative feedback controls leading to rapid hyperactivation of RTK−WT RAS signaling. A more comprehensive understanding of the interplay between mutant RAS and RTK−WT RAS signaling is essential to developing rational therapeutic approaches to treat RAS-mutated cancers. We found that WT RAS enhanced mutant RAS-driven transformation by activating RAS effectors poorly engaged by mutated RAS. Further, inhibition of RAS effectors activated poorly by mutant RAS synergized with and limited resistance to mutant HRAS and KRAS inhibitors. The mutant HRAS inhibitor tipifarnib blocked PI3K signaling and synergized with MEK inhibitors in HRAS-mutated cancer cell lines; covalent KRASG12C inhibitors blocked MEK signaling and synergized with PI3K inhibitors in KRASG12C- mutated cell lines. Synergy between inhibitors of mutant RAS and RAS effectors was dependent on intact RTK/WT RAS signaling and was lost in both RASless or SOSless MEFs. Dual knock-out of WT RAS isoforms in KRAS- and HRAS-mutated cancer cell lines reduced PI3K signaling in KRAS-mutant cell lines and MAPK signaling in HRAS-mutant cell lines and reduced proliferation, confirming our findings in MEF cells. Overall, our data highlight the critical role of WT RAS isoforms in supporting mutant RAS signaling and should be considered when designing combination therapies in RAS-mutated cancers. Citation Format: Nancy E. Sealover, Bridget Finniff, Jacob Hughes, Hyun Lee, Robert L. Kortum. Wild-type RAS signaling is an essential therapeutic target in RAS-mutated 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 1925.

Abstract 4723: Target engagement sheds light on difference in drug efficacy in breast cancer cell lines

Abstract Breast cancer is a serious disease that affects millions of women worldwide, and 700,000 people succumb to the disease annually. Breast cancers are divided into several functional subgroups based on molecular characteristics and growth pattern: Luminal A and B, HER2 positive (HER2+) and triple negative. The subgroups are important from a clinical perspective as they partially guide treatment strategies. In this study we wanted to investigate the difference in target engagement with four drugs indicated for treatment of different types of breast cancer: Alpelisib, Neratinib, Vinorelbine, and Docetaxel. Five different human breast cancer cell lines were included, representing Luminal A (MCF-7, T-47D), HER2+ (SK-BR-3, BT-474), and triple negative (BT-20). We used CETSA® (CEllular Thermal Shift Assay) coupled to mass spectrometry detection to assess proteome wide changes in protein thermal stability in intact breast cancer cell lines. CETSA is unique as a target engagement detection modality as it allows for target engagement assessment in intact cells with unaltered drug molecules. Also, as biology is intact in live cells it is possible to follow compound induced downstream signaling or phenotypic events that result in changed thermal stability of proteins. In addition to assessing protein thermal stability with CETSA, which is a short treatment of 1 h, we also subjected cells in culture to prolonged drug exposures, ≤72 h, in order to measure viability. This was done to correlate early changes in protein thermal stability to the viability phenotype that manifested later. In general, responses both in protein thermal stability and cell viability was heterogenous among the cell lines. The most homogenous response in viability was observed for the Phosphatidyl Inositol 3’ kinase inhibitor Alpelisib, which reduced viability to 20 - 40% in all cell lines. In contrast, partial resistance was shown to the other drugs by at least one of the cell lines. For Alpelisib, the amount and type of proteins that were thermally shifted correlated with the effect on viability. The covalent HER2 inhibitor Neratinib was most effective in inhibiting viability in HER2+ cells and proteins of the HER2 pathway were thermally shifted in these cells, which was not observed for the other cell lines. Viability of the other cell lines were also affected by Neratinib, but only at higher concentrations. Both microtubule inhibitors induced thermal stabilization of tubulins, but that did not always translate into efficacy in the viability assay. However, sensitive cell lines showed thermal shifts of tubulins at lower concentrations of compound. In oncology drug development it is important that effects on viability are driven by on-target efficacy and not by off-target effects. Here we show the benefit of connecting knowledge of target engagement and phenotypic readouts; what targets are engaged, at which concentrations, and what is the corresponding phenotype. Citation Format: Tomas Friman, Tuomas Tolvanen, Merve Kacal, Victoria Brehmer, Stina Lundgren, Laurence Arnold, Daniel Martinez Molina. Target engagement sheds light on difference in drug efficacy in breast cancer cell lines [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 4723.

Abstract 5902: Targeting MAPK-driven tumors via inhibition of MAP2K4

Abstract MAPK pathway activation is a feature of multiple tumor types. Drugging KRAS and BRAF, the two main oncogenic drivers in the MAPK pathway, has proven successful in the clinic. Inhibition of the downstream effectors, MEK and ERK, can also induce tumor regression. Despite this, many tumors are intrinsically resistant to MAPK pathway inhibitors, or acquire resistance under selective pressure to drug treatment. This creates a need for combination treatments to improve clinical responses. A synthetic lethal (SL) interaction between inhibition of the MAPK pathway and blockade of JNK-JUN signaling has recently been described1. Specifically, data from yeast genetics and CRISPR knockout experiments in human cells have identified MAP2K4 as a potential therapeutic target that could be combined with MAPK inhibitors. To date, however, no potent MAP2K4 inhibitors with in vitro and cellular selectivity against key anti-targets have been reported. Here, we describe the development of potent covalent inhibitors of MAP2K4 kinase activity. Biochemical and cell-based assays show that the compound(s) are selective for MAP2K4 versus anti-targets including MAP2K7 and ERK kinases. The combination of MAP2K4 and MEK/ERK inhibitors was effective in cell lines driven by MAPK signaling. These data provide the rationale for further development of MAP2K4 inhibitors to advance our understanding of this novel drug combination.

Abstract 3938: A novel mouse model reveals potential therapeutic strategies for RIT1-driven lung adenocarcinomas

Abstract Gain-of-function oncogenic mutations in RIT1 have been identified in lung adenocarcinoma and are mutually exclusive with other reported driver mutations, highlighting the role of RIT1 as a cancer driver. RIT1 is a poorly-studied non-classical RAS GTPase and, to date, there are no reported genetically-engineered mouse models of RIT1-driven lung adenocarcinoma. Here, we have generated a conditional knock-in allele within the endogenous mouse Rit1 locus, introducing the most frequent mutation observed in lung adenocarcinomas (RIT1M90I). Upon intranasal administration of adenovirus encoding the Cre recombinase to induce somatic recombination in the mouse lungs, we observed the formation of discrete adenomas. Although Rit1M90I mutation can promote lung tumor initiation in mice, we found that this phenotype is less penetrant than the common KrasG12D mutation. Immunohistochemistry analysis of Rit1M90I and KrasG12D tumors showed expression of typical histological markers associated with lung adenocarcinoma (i.e., TTF1 and SPC), as well as increased levels of Ki67 and pERK expression. Next, to develop potential pharmacological strategies for RIT1-driven lung tumors, we first explored drugs that inhibit the RAS/MAPK pathway and are either FDA-approved or under clinical development. In vitro experiments with cell lines carrying the RIT1M90I mutation demonstrated high sensitivity to SHP2, MEK, RAF, and RAS inhibitors. In vivo, SHP2 and RAS, but not MEK, inhibitors slowed down tumor progression in both cell line and patient-derived xenografts. Our results indicate that, although RAS signaling might be needed for RIT1-dependent growth, these tumors are not sensitive to MAPK inhibition as a monotherapy and, hence, other pathways could contribute to tumor growth. Therefore, we decided to explore whether targeting RIT1 directly, could be a more beneficial strategy for these tumors. In order to inhibit oncogenic RIT1 directly, we have undertaken two complementary approaches. First, because RIT1 mutations were shown to impair its proteolysis, we explored whether restoring RIT1 proteasomal degradation could be a promising strategy. Recently, the development of Proteolysis Targeting Chimeras (PROTAC) has demonstrated that targeted degradation can be used as a pharmacological approach for the treatment of cancer. Therefore, we have tested successfully several proof-of-concept PROTAC approaches that caused degradation of oncogenic RIT1 in different cellular models. Second, we used a chemical biology approach to assess whether covalent inhibitors directed against the closely-related GTPase KRAS could cross-react and bind to oncogenic RIT1. We have identified a molecule that binds RIT1 and we are currently characterizing it in our preclinical models. Overall, our work provides comprehensive insights into the oncogenic role of RIT1 in lung cancer emphasizing its potential as a therapeutic target. Citation Format: Alessandro Mauro Mozzarelli, Antonio Cuevas-Navarro, Anatoly Urisman, Pau Castel. A novel mouse model reveals potential therapeutic strategies for RIT1-driven lung adenocarcinomas [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 3938.

Abstract 6501: Development and characterization of covalent inhibitors of the RAS-PIK3CA interaction

Abstract RAS proteins are membrane bound GTPases that when hyperactivated, act as oncogenes through activation of the MAPK & PI3K pathways. Each of these pathways has oncogenic potential, as exemplified by the high frequency of BRAF mutations in melanoma and PIK3CA and PTEN mutations in breast and gynecological cancers. Simultaneous activation of these pathways, as occurs in RAS driven cancers, generates aggressive cancers that present a significant clinical challenge. KRAS, the most commonly mutated RAS isoform, is also the most frequently mutated oncogene in cancer. While treatment options have improved for a subset of these patients due to the accelerated approval of KRAS-G12C inhibitors, the rapid development of resistance highlights the continued need for effective treatments. In RAS driven cell and animal models, dual inhibition of the MAPK &PI3K pathways has shown superior efficacy relative to targeting the individual pathways, however dose limiting toxicities in humans have prevented this combination strategy from finding clinical success. While physiological activation of the MAPK pathway is RAS dependent, the interaction between RAS and the catalytic subunit of PI3Kα, PIK3CA, serves as an amplifier but not a primary activator of this pathway. This interaction is particularly important in cancerous cells as it serves to amplify basal PI3K activity and support tumor progression. Conversely, in healthy cells, RAS independent activation of PI3K by upstream signaling factors is sufficient for maintaining physiological homeostasis. Unfortunately, traditional strategies of targeting the PI3K pathway have been unable to capitalize on this therapeutic opportunity as they do not discriminate between RAS dependent and RAS independent signaling. This leads to on-target dose-limiting toxicities, most commonly hyperglycemia and rash. We have discovered small molecules that disrupt the RAS:PIK3CA interaction through covalent ligation of C242, in the RAS binding domain, adjacent to the RAS binding interface. Using a Nanobit system to measure the RAS:PIK3CA interaction and signaling assays in “RAS active” cells, we have optimized molecules that disrupt the RAS:PIK3CA interaction and inhibit RAS mediated activation of PIK3CA. These molecules show robust inhibition of PIK3CA signaling, and tumor growth inhibition in cancer models, but unlike PIK3CA active site inhibitors, they do not impact glucose handling. Profound efficacy is seen when these RAS:PIK3CA inhibitors are used in combination with an agent targeting the MAPK pathway or with a therapy directly targeting mutant KRAS. Finally, we found that ligation of C242 on PIK3CA blocks HER2/3 driven activation of PI3Kα in a RAS independent manner. Overall, our data supports the clinical investigation of these molecules, particularly in combination with rationally chosen therapies where they may provide a tolerable and efficacious means of blocking the PI3K pathway. Citation Format: Joseph Klebba, Junko Tamiya, Jinwei Wang, Hui Miao, Kelsey Lamb, Aaron Snead, Antonio Esparza-Oros, Richard Lin, Chanyu Yue, Stephanie Grabow, Steffen Bernard, Yongsheng Liu, Benjamin Horning, Melissa Hoffman, Marie Pariollaud, Taylor Wyrick, Holly Parker, John Sigler, Martha Pastuszka, David Weinstein, Todd Kinsella, Matt Patricelli. Development and characterization of covalent inhibitors of the RAS-PIK3CA interaction [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 6501.

Abstract 1940: Identifying resistant mechanisms to direct KRAS inhibitors in NSCLC

Abstract Mutations in the KRAS oncogenic driver gene are frequently found in malignancies such as pancreatic, colorectal, and lung cancers. The replacement of the amino acid glycine at position 12 (e.g., G12C, G12D, G12V) is a frequent mutation that traps the protein in an active state and promotes uncontrolled cell proliferation. KRAS was regarded as "undruggable" for many years due to insufficient drug-binding pockets on the protein's surface. Recent breakthroughs, however, have resulted in the development of covalent inhibitors capable of selectively targeting the KRAS G12C mutation, like Sotorasib (AMG510) and Adagrasib (MRTX849) which are approved by the FDA due to their encouraging effects in clinical trials. The identification of selective inhibitors of other oncogenic KRAS alleles, such as the noncovalent KRAS-G12D inhibitor, MRTX1133, and a pan-KRAS-inhibitor drug (BI2865) is also a promising next step in the treatment of KRAS-dependent malignancies. While these inhibitors have shown initial success, their use frequently leads to resistance, the mechanisms of which largely remain unknown. To fill this essential research gap, we are employing our pre-clinical syngeneic mouse models and KRAS mutant allele-specific cell lines to investigate the underlying molecular processes of acquired resistance to direct KRAS allele-specific inhibitors. Using these murine syngeneic cell lines and human NSCLC cell lines, we have generated a panel of cell lines with acquired resistance to these direct KRAS inhibitors. To elucidate the molecular underpinnings of acquired resistance to direct KRAS inhibitors, we performed proteomic profiling of the sensitive and resistant cells by RPPA analysis. Among the several proteins whose expressions were altered in the KRAS-inhibitor-resistant cells, we identified the YAP/TEAD1 pathway that was commonly upregulated in the cells resistant to MRTX849 (G12Ci) or MRTX1133 (G12Di). We also observed significant re-sensitization of the resistant cells to the specific KRAS inhibitors upon genetic or pharmacological inhibition of TEAD using siRNA or a TEAD-inhibitor, in vitro. Tumors from syngeneic mice that were implanted with KRAS inhibitor-resistant cells or their sensitive versions and treated with the specific KRAS inhibitors for 3-4 weeks, also exhibited increased nuclear YAP1 localization in the resistant tumors. We are currently performing in vitro and in vivo studies to understand the therapeutic efficacy of a TEAD inhibitor in combination with KRASi (MRTX849 or MRTX1133) to either reverse or prevent resistance to these direct KRAS inhibitors. We are also trying to identify alterations in the tumor immune microenvironment upon combination therapy targeting KRAS and TEAD. Successful completion of this research will help address the urgent need to understand ways to overcome resistance to KRAS inhibitors and increase their clinical efficacy. Citation Format: Samrat T. Kundu, David H. Peng, B. Leticia Rodriguez, Eileen L. McCarthy, Don L. Gibbons. Identifying resistant mechanisms to direct KRAS inhibitors in NSCLC [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 1940.

Abstract 1938: WEE1 inhibition prevents and overcomes resistance to KRAS inhibitors in lung cancer by enhancing MCL1-mediated apoptosis

Abstract Background: While novel covalent inhibitors of KRAS G12C have been approved in non-small-cell lung cancer (NSCLC), their efficacies are known to be limited. To enhance the therapeutic potential of KRAS inhibitors, combination strategies need to be developed. In this study, we conducted a large-scale screening to identify novel combination partners that induced synergistic efficacy with KRAS inhibitors. Additionally, mechanistic analyses were conducted to clarify the synergistic effects in combination and their role in conferring resistance to KRAS inhibitors. Methods: To identify novel combination partners of KRAS inhibitors, we conducted high-throughput screening (HTS) using a chemical library composed of 1,400 kinase inhibitors. Sotorasib was used as a KRAS inhibitor. Anti-proliferative and apoptotic effects in vitro were assessed by ATP-based cell viability assay, and caspase 3/7 assay and/or Annexin V assay, respectively. Protein expression levels were assessed by immunoblotting. In vivo studies were performed using a H358 xenograft nude mouse model and a patient-derived xenograft model (PDX). PDX samples were provided by the National Cancer Center J-PDX library, Japan. Results: HTS identified the WEE1 inhibitor AZD1775, a G2/M checkpoint abrogator in clinical-stage development, as a promising combination partner of KRAS inhibitors in KRAS G12C mutant NSCLC. Synergistic effects of KRAS and WEE1 inhibitors were confirmed across multiple KRAS G12C mutant NSCLC cell lines, independently of their co-occurring oncogenic mutation profiles. The combination treatment enhanced apoptotic cell death, being upregulated pro-apoptotic protein BIM, while downregulated anti-apoptotic protein MCL1. In vivo efficacy studies in combination with sotorasib and AZD1775 also demonstrated remarkable tumor regression and durable response in both CDX and PDX models. We also generated sotorasib-resistant H23 (H23-SR) cells, confirming upregulation of both WEE1 and MCL1 in the resistant cells. Ectopic overexpression of WEE1 in H23, on the contrary, conferred resistance to sotorasib. Furthermore, WEE1 inhibition re-sensitized H23-SR cells to KRAS inhibitors. Conclusion: Our results suggest that the WEE1-MCL1 axis plays an important role in both the initial therapeutic efficacy and the acquired resistance to KRAS inhibitors. These findings could pave the way for a novel therapeutic strategy for KRAS G12C mutant NSCLC. Citation Format: Gaku Yamamoto, Kosuke Tanaka, Ryo Kamata, Takehiro Nakao, Shunta Mori, Jie Liu, Susumu S. Kobayashi, Akihiro Ohashi. WEE1 inhibition prevents and overcomes resistance to KRAS inhibitors in lung cancer by enhancing MCL1-mediated apoptosis [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 1938.

Abstract 1215: DIRAS3 inhibits oncogenic RAS signaling and RAS-dependent cell growth driven by prevalent KRAS hot spot mutations

Abstract RAS mutations are found in 30% of human cancers and are characterized by hotspot mutations at codons G12, G13, and Q61. This results in constitutively activated RAS proteins. Despite recent advances in drug design and the emergence of covalent inhibitors, effectively targeting mutant RAS remains challenging. Our group previously identified the tumor suppressor protein DIRAS3, which directly binds Ras and inhibits its function by disrupting KRAS dimers/nanoclusters and blocking effector activation. DIRAS3 expression reduced cancer cell growth in pancreatic and ovarian cancers. To determine whether DIRAS3 plays a definitive role in inhibiting mutant KRAS, we comprehensively characterized DIRAS3's RAS-inhibitory effects using RASless mouse embryo fibroblast (MEF) cells as a model system lacking endogenous RAS isoforms. We ectopically expressed various KRAS mutations in these cells and then examined DIRAS3's effect on each KRAS mutant clone. We analyzed downstream RAS signaling, colony formation, cell viability, and toxicity. Our results showed that DIRAS3 significantly inhibited RAS-dependent colony formation in KRAS mutant (G12C, G12D, G12V, G13D, G12R, Q61R, Q61L) but not wild-type KRAS clones. However, when we added epidermal growth factor (EGF) to the medium, DIRAS3 expression inhibited wild-type KRAS activity, decreasing colony formation. This suggests that DIRAS3 selectively affects the active, GTP-bound form of KRAS and downstream signaling. Additionally, DIRAS3 expression decreased Erk1/2 phosphorylation in MEF cells with mutant KRAS, but not in the cells with a BRAFV600E mutation. This indicates that DIRAS3 specifically inhibits the KRAS-mediated MEK/ERK signaling, cell proliferation, and cytotoxicity. Moreover, to determine the critical region for DIRAS3's RAS-inhibitory function, we compared wild-type DIRAS3 and deletions (ΔNTE, ΔCTE, ΔNCTE). Our results showed both termini are required to effectively suppress clonogenic growth, emphasizing the requirement for DIRAS3 to anchor to the plasma membrane and interact with the RAS dimer interface to inhibit RAS-dependent tumor growth. In conclusion, our findings underscore the potent and specific inhibitory effects of DIRAS3 on RAS-driven oncogenesis, positioning it as a promising pan-RAS inhibitor for RAS-mutant cancers. Citation Format: Gamze Bildik, Junchen Liu, Weiqun Mao, Hailing Yang, John F. Hancock, Robert C. Bast, Zhen Lu. DIRAS3 inhibits oncogenic RAS signaling and RAS-dependent cell growth driven by prevalent KRAS hot spot mutations [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 1215.

Abstract 6585: Combination RASG12C(ON) and RASMULTI(ON) inhibition overcomes resistance and prolongs durability in preclinical models of mutant KRASG12C-driven cancers

Abstract Inhibitors of the GDP-bound state of mutant KRASG12C protein (KRASG12C(OFF)), e.g., adagrasib and sotorasib, have shown clinical activity in patients with KRASG12C-driven NSCLC, CRC and PDAC. However, most patients exhibit progression on monotherapy treatment in months, underlining the need for combination therapeutic approaches that improve the durability of the anti-tumor activity seen with KRASG12C inhibitors. RMC-6291 is a mutant-selective covalent inhibitor of the GTP-bound RAS(ON) form of RASG12C, while RMC-6236 is a non-covalent RASMULTI(ON) inhibitor of both mutant and wild-type variants of canonical RAS isoforms. In models harboring diverse alterations driving resistance mechanisms to KRASG12C(OFF) inhibitors – including reactivation of KRASG12C and wild-type RAS by increased RTK signaling, acquired secondary oncogenic RAS mutations, and KRAS amplification – both RMC-6291 and RMC-6236 exhibited superior anti-cancer activity as single agents when compared to KRASG12C(OFF) inhibitors. Thus, we hypothesized that a combination of RMC-6291 and RMC-6236 could address a broad spectrum of observed clinically relevant resistance mechanisms to KRASG12C(OFF) inhibitors that reactivate RAS signaling via mutant and wild-type RAS isoforms and compromise the depth and durability of anti-tumor response. In a mouse clinical trial with KRASG12C xenograft models, daily oral administration of RMC-6291 induced objective responses in 18 out of 25 NSCLC PDX and CDX models as assessed by mRECIST. In a subpanel of 7 NSCLC models that are relatively refractory to KRASG12C(OFF) inhibitor monotherapy, RMC-6236 alone somewhat prolonged the durability of response, while the combination of RMC-6291 with RMC-6236 improved the depth of response and significantly extended the durability thereof. In contrast to NSCLC, in models of KRASG12C CRC tumors a more heterogeneous response to RMC-6291 monotherapy was observed with objective responses in 4 out of 15 CRC models. The addition of RMC-6236 to RMC-6291 substantially improved the depth and duration of anti-tumor response in the resistant models to KRASG12C inhibitor alone. The combination of RMC-6291 with RMC-6236 at preclinical target doses did not affect the systemic or tumor exposures of each compound and was well tolerated in tumor-bearing immune-deficient animals. Both investigational agents RMC-6236 and RMC-6291 have shown promising anti-tumor activity as monotherapies in preclinical models and, more recently, showed preliminary clinical activity in patients with RAS-driven tumors at exposures that were well tolerated. The addition of RMC-6236 to RMC-6291 shows combinatorial activity in preclinical models that are relatively less responsive to either inhibitor alone. A clinical trial combining RMC-6291 with RMC-6236 in patients with mutant KRASG12C tumors is currently enrolling. Citation Format: Xing Wei, Matthew Holderfield, Yu Chi Yang, Kyle Seamon, Jay Dinglasan, Nilufar Montazar, Bianca Lee, Shurui Cai, Lick Lai, Ida Aronchik, Stephanie Chang, Zhican Wang, Pete Wildes, Jacqueline A. Smith, Jingjing Jiang, Mallika Singh. Combination RASG12C(ON) and RASMULTI(ON) inhibition overcomes resistance and prolongs durability in preclinical models of mutant KRASG12C-driven 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 6585.

Abstract 1973: Discovery of the first-in-class SHP1 covalent inhibitor for cancer immunotherapy

Abstract Cancer immunotherapy refers to the approach leveraging patients’ immune system against tumor, which has gained tremendous progress hallmarked by immune checkpoint blockade and adoptive cell therapies. However, contemporary strategies suffer from limited responses, adverse side effects, and low tissue penetration due to utilization of macromolecules, calling for more efficacious and safer alternative strategies. SHP1 is a protein tyrosine phosphatase (PTP) primarily expressed in hematopoietic cells and has been shown to negatively regulate immune responses in T cells and natural killer (NK) cells, and SHP1 deletion in these cells has shown to promote their anti-tumor functions. Recent studies also demonstrated that inducible SHP1 knockout inhibited tumor growth in vivo through immune activation. Although presented as an attractive target, no high-quality small molecule inhibitors have been reported for SHP1 due to its undruggable nature. Through high-throughput screening and extensive medicinal chemistry, we have acquired the first-in-class SHP1 covalent inhibitor M029, which shows >25-fold selectivity against SHP2, its closest analogues and >60-fold selectivity against other PTPs and cysteine-based proteins. Further proteomics studies reveal that M029 is superiorly selective for SHP1 in cellulo. Additionally, M029 is stable in 100-fold excessive glutathione with a half-life of >35 hours and non-toxic up to 100 µM to healthy cells, such high stability was also reflected by its oral bioavailability with a F% of 10%. M029 treatment significantly activated T cell receptor signaling in T cells and NK cells killing effects in vitro. Furthermore, oral dosage of M029 significantly delayed tumor progression in mice bearing MC38 tumors through enhanced T cell and NK cell infiltration and activation and prolonging of T cell exhaustion. To validate that the compound acted through immune activation, we dosed the mice with anti-CD8+ or anti-NK1.1 during M029 treatment, both of which abolished the compound efficacy, corroborating with its mechanism of action. Meanwhile, to assess the compound safety, we dosed the mice up to 100 mg/kg for 8 days, where no significant body weight change or cytokine storm were observed. Collectively, we have developed the first SHP1 covalent inhibitor with high selectivity and strong anti-tumor efficacy. This study is the first characterization of pharmacological SHP1 inhibition as cancer immunotherapy and solidified its potential as an immunotherapeutic target. The development of M029 will also enlighten drug discovery strategies against SHP1 or other undruggable PTPs. Citation Format: Zihan Qu, Frederick Nguele Meke, Zheng Zhang, Yunpeng Bai, Aaron D. Krabill, Christine S. Muli, Brenson A. Jassim, Jiajun Dong, Jinyue Li, Nguyen Yuyen, Andy W. Tao, Darci T. Trader, Zhong-Yin Zhang. Discovery of the first-in-class SHP1 covalent inhibitor for cancer immunotherapy [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 1973.

Abstract 384: SLC7A11 modulates sensitivity to the first-in-class mitochondrial peroxiredoxin 3 inhibitor thiostrepton (RSO-021) via a ferroptosis independent pathway

Abstract Mitochondrial peroxiredoxin 3 (PRX3) has been identified as an actionable cancer vulnerability that is currently being investigated in the first-in-human phase 1 clinical trial, MITOPE (NCT05278975). RSO-021 (thiostrepton or TS) is a redox-active drug that inhibits PRX3’s peroxidase activity via covalent adduction of its active site peroxidatic and resolving cysteine residues, forming an irreversible crosslink across the protein dimer. Covalent inhibition of PRX3 results in tumor cell death due to a diminished ability to remove high levels of mitochondrial reactive oxygen species (ROS) in cancer cells. To better understand the mechanism underpinning sensitivity and resistance, TS-tolerant human mesothelioma cell lines were generated under constant TS pressure and subjected to a drug-screen comprising chemotherapeutic agents, metabolic inhibitors, ROS modulating agents and ferroptosis-inducing compounds, to identify synergistic interactions compared with TS- sensitive cell lines. Erastin, an SLC7A11 inhibitor exhibited the greatest synergy when combined with TS, potentiated PRX3 covalent crosslinking and cellular ROS levels. Synergy with TS was enhanced by cystine depletion and could be phenocopied by siRNA knockdown of SLC7A11. SLC7A11 was up-regulated in TS-tolerant cells and resistance could be overcome with erastin. TS-tolerant cell lines have significantly reduced glutathione levels and slowed proliferation. Ferroptosis inhibitors ferrostatin-1 and liproxstatin-1 did not inhibit TS or TS in combination with erastin. In summary, SLC7A11 up-regulation confers tolerance to TS through a mechanism involving a cysteine-dependent modulation of the redox state independent of canonical ferroptosis, that can be overcome by the addition of an SLC7A11 inhibitor. The correlation between SLC7A11 with response to TS in a 33-patient primary mesothelioma explant co-clinical trial, and patients enrolled into the MITOPE phase 1/2 trial will be presented. Citation Format: Terri Messier, Victoria Gibson, Aleksandra Bzura, Joanna Dzialo, Charlotte Poile, Stephanie Stead, Alexis Saaman, George N. Naumov, Dean A. Fennell, Brian Cunniff. SLC7A11 modulates sensitivity to the first-in-class mitochondrial peroxiredoxin 3 inhibitor thiostrepton (RSO-021) via a ferroptosis independent pathway [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 384.

Discovery of a Covalent Inhibitor Selectively Targeting the Autophosphorylation Site of c-Src Kinase.

Nonreceptor tyrosine kinase c-Src plays a crucial role in cell signaling and contributes to tumor progression. However, the development of selective c-Src inhibitors turns out to be challenging. In our previous study, we performed posttranslational modification-inspired drug design (PTMI-DD) to provide a plausible way for designing selective kinase inhibitors. In this study, after identifying a unique pocket comprising a less conserved cysteine and an autophosphorylation site in c-Src as well as a promiscuous covalent inhibitor, chemical optimization was performed to obtain (R)-LW-Srci-8 with nearly 75-fold improved potency (IC50 = 35.83 ± 7.21 nM). Crystallographic studies revealed the critical C-F···C═O interactions that may contribute to tight binding. The kinact and Ki values validated the improved binding affinity and decreased warhead reactivity of (R)-LW-Srci-8 for c-Src. Notably, in vitro tyrosine kinase profiling and cellular activity-based protein profiling (ABPP) cooperatively indicated a specific inhibition of c-Src by (R)-LW-Srci-8. Intriguingly, (R)-LW-Srci-8 preferentially binds to inactive c-Src with unphosphorylated Y419 both in vitro and in cells, subsequently disrupting the autophosphorylation. Collectively, our study demonstrated the feasibility of developing selective kinase inhibitors by cotargeting a nucleophilic residue and a posttranslational modification site and providing a chemical probe for c-Src functional studies.

Targeting KRAS mutations in pancreatic cancer: opportunities for future strategies.

Targeting the RAS pathway remains the holy grail of precision oncology. In the case of pancreatic ductal adenocarcinomas (PDAC), 90-92% harbor mutations in the oncogene KRAS, triggering canonical MAPK signaling. The smooth structure of the altered KRAS protein without a binding pocket and its affinity for GTP have, in the past, hampered drug development. The emergence of KRASG12C covalent inhibitors has provided renewed enthusiasm for targeting KRAS. The numerous pathways implicated in RAS activation do, however, lead to the development of early resistance. In addition, the dense stromal niche and immunosuppressive microenvironment dictated by oncogenic KRAS can influence treatment responses, highlighting the need for a combination-based approach. Given that mutations in KRAS occur early in PDAC tumorigenesis, an understanding of its pleiotropic effects is key to progress in this disease. Herein, we review current perspectives on targeting KRAS with a focus on PDAC.

Dimethyl fumarate covalently modifies Cys673 of NLRP3 to exert anti-inflammatory effects

The NLRP3 inflammasome plays a pivotal role in various chronic inflammation-driven human diseases. However, no drugs specifically targeting NLRP3 inflammasome have been approved by the Food and Drug Administration (FDA) of the United States. In our current study, we showed that dimethyl fumarate (DMF) efficiently suppressed the activation of the NLRP3 inflammasome induced by multiple agonists and covalently modified Cys673 of NLRP3, thereby impeding the interaction between NLRP3 and NEK7. The inhibitory effect of DMF was nullified by anaplerosis of the Cys673 mutant (but not the wild-type) NLRP3 in Nlrp3-/- THP-1 cells. Invivo experiments, DMF demonstrated protective effects in the dextran sodium sulfate (DSS)-induced ulcerative colitis of WT mice, but not in Nlrp3-/- mice. In summary, our study identified DMF as a direct covalent inhibitor of NLRP3 and a potential candidate for the treatment of NLRP3 inflammasome-mediated diseases.

Molecular Insights into the Impact of Mutations on the Binding Affinity of Targeted Covalent Inhibitors of BTK.

Targeted covalent inhibitors (TCIs) have witnessed a significant resurgence in recent years, particularly in the kinase drug discovery field for treating diverse clinical indications. The inhibition of Bruton's tyrosine kinase (BTK) for treating B-cell cancers is a classic example where TCIs such as ibrutinib have had breakthroughs in targeted therapy. However, selectivity remains challenging, and the emergence of resistance mutations is a critical concern for clinical efficacy. Computational methods that can accurately predict the impact of mutations on inhibitor binding affinity could prove helpful in informing targeted approaches─providing insights into drug resistance mechanisms. In addition, such systems could help guide the systematic evaluation and impact of mutations in disease models for optimal experimental design. Here, we have employed in silico physics-based methods to understand the effects of mutations on the binding affinity and conformational dynamics of select TCIs of BTK. The TCIs studied include ibrutinib, acalabrutinib, and zanubrutinib─all of which are FDA-approved drugs for treating multiple forms of leukemia and lymphoma. Our results offer useful molecular insights into the structural determinants, thermodynamics, and conformational energies that impact ligand binding for this biological target of clinical relevance.

Matching-Adjusted Indirect Comparison of Brexucabtagene Autoleucel (ZUMA-2) and Pirtobrutinib (BRUIN) in Patients with Relapsed/Refractory Mantle Cell Lymphoma Previously Treated with a Covalent Bruton Tyrosine KinaseInhibitor.

Patients with relapsed/refractory (R/R) mantle cell lymphoma (MCL) often require multiple lines of treatment and have a poor prognosis, particularly after failing covalent Bruton tyrosine kinase inhibitor (cBTKi) therapy. Newer treatments such as brexucabtagene autoleucel (brexu-cel, chimeric antigen receptor Tcell therapy) and pirtobrutinib (non-covalent BTKi) show promise in improving outcomes. Without direct comparative evidence, an unanchored matching-adjusted indirect comparison was conducted to estimate the relative treatment effects of brexu-cel and pirtobrutinib for post-cBTKi R/R MCL. Using logistic propensity score models, individual patient-level data from ZUMA-2 brexu-cel-infused population (N = 68) were weighted to match pre-specified clinically relevant prognostic factors based on study-level data from the BRUIN cBTKi pre-treated cohort (N = 90). The base-case model incorporated the five most pertinent factors reported in ≥ 50% of both trial populations: morphology, MCL International Prognostic Index, number of prior lines of therapy, disease stage, and prior autologous stem cell transplant. A sensitivity analysis additionally incorporated TP53 mutation and Ki-67 proliferation. Relative treatment effects were expressed as odds ratios (ORs) or hazard ratios (HRs) with 95% confidence intervals (CIs). In the base-case model, brexu-cel was associated with higher rates of objective response (OR 10.39 [95%CI 2.81-38.46]) and complete response (OR 10.11 [95%CI 4.26-24.00]), and improved progression-free survival (HR0.44 [95%CI 0.25-0.75]), compared to pirtobrutinib. Overall survival and duration of response favored brexu-cel over pirtobrutinib but the differences crossed the bounds for statistical significance. Findings were consistent across the adjusted and unadjusted analyses. Findings suggest that brexu-cel may offer clinically and statistically significant benefits regarding objective response, complete response, and progression-free survival compared to pirtobrutinib among patients with R/R MCL after prior cBTKi therapy. Given the short follow-up and high degree of censoring in BRUIN, an analysis incorporating updated BRUIN data may provide more definitive overall survival results.

Covalent Fragment Screening and Optimization Identifies the Chloroacetohydrazide Scaffold as Inhibitors for Ubiquitin C-terminal Hydrolase L1.

Dysregulation of the ubiquitin-proteasome systems is a hallmark of various disease states including neurodegenerative diseases and cancer. Ubiquitin C-terminal hydrolase L1 (UCHL1), a deubiquitinating enzyme, is expressed primarily in the central nervous system under normal physiological conditions, however, is considered an oncogene in various cancers, including melanoma, lung, breast, and lymphoma. Thus, UCHL1 inhibitors could serve as a viable treatment strategy against these aggressive cancers. Herein, we describe a covalent fragment screen that identified the chloroacetohydrazide scaffold as a covalent UCHL1 inhibitor. Subsequent optimization provided an improved fragment with single-digit micromolar potency against UCHL1 and selectivity over the closely related UCHL3. The molecule demonstrated efficacy in cellular assays of metastasis. Additionally, we report a ligand-bound crystal structure of the most potent molecule in complex with UCHL1, providing insight into the binding mode and information for future optimization.

Mechanism-Based Macrocyclic Inhibitors of Serine Proteases.

Protease inhibitor drug discovery is challenged by the lack of cellular and oral permeability, selectivity, metabolic stability, and rapid clearance of peptides. Here, we describe the rational design, synthesis, and evaluation of peptidomimetic side-chain-cyclized macrocycles which we converted into covalent serine protease inhibitors with the addition of an electrophilic ketone warhead. We have identified potent and selective inhibitors of TMPRSS2, matriptase, hepsin, and HGFA and demonstrated their improved protease selectivity, metabolic stability, and pharmacokinetic (PK) properties. We obtained an X-ray crystal structure of phenyl ether-cyclized tripeptide VD4162 (8b) bound to matriptase, revealing an unexpected binding conformation. Cyclic biphenyl ether VD5123 (11) displayed the best PK properties in mice with a half-life of 4.5 h and compound exposure beyond 24 h. These new cyclic tripeptide scaffolds can be used as easily modifiable templates providing a new strategy to overcoming the obstacles presented by linear acyclic peptides in protease inhibitor drug discovery.

Design and synthesis of highly selective Janus kinase 3 covalent inhibitors for the treatment of rheumatoid arthritis.

Selective inhibition of Janus kinase 3 (JAK3) is a promising strategy for the treatment of autoimmune diseases. Based on the discovery of a hydrophobic pocket unutilized between the lead compound RB1 and the JAK3 protein, a series of covalent JAK3 inhibitors were prepared by introducing various aromatic fragments to RB1. Among them, J1b (JAK3 IC50 = 7.2 nM, other JAKs IC50 > 1000 nM) stood out because of its low toxicity (MTD > 2 g/kg) and superior anti-inflammatory activity in Institute of Cancer Research mice. Moreover, the acceptable bioavailability (F% = 31.69%) ensured that J1b displayed excellent immune regulation in collagen-induced arthritis mice, whose joints in the high-dose group were almost recovered toa normal state. Given its clear kinase selectivity (Bmx IC50 = 539.9 nM, other Cys909 kinases IC50 > 1000 nM), J1b was nominated as a highly selective JAK3 covalent inhibitor, which could be used to safely treat arthritis and other autoimmune diseases.

Strain-release alkylation of Asp12 enables mutant selective targeting of K-Ras-G12D.

K-Ras is the most commonly mutated oncogene in human cancer. The recently approved non-small cell lung cancer drugs sotorasib and adagrasib covalently capture an acquired cysteine in K-Ras-G12C mutation and lock it in a signaling-incompetent state. However, covalent inhibition of G12D, the most frequent K-Ras mutation particularly prevalent in pancreatic ductal adenocarcinoma, has remained elusive due to the lack of aspartate-targeting chemistry. Here we present a set of malolactone-based electrophiles that exploit ring strain to crosslink K-Ras-G12D at the mutant aspartate to form stable covalent complexes. Structural insights from X-ray crystallography and exploitation of the stereoelectronic requirements for attack of the electrophile allowed development of a substituted malolactone that resisted attack by aqueous buffer but rapidly crosslinked with the aspartate-12 of K-Ras in both GDP and GTP state. The GTP-state targeting allowed effective suppression of downstream signaling, and selective inhibition of K-Ras-G12D-driven cancer cell proliferation in vitro and xenograft growth in mice.