Raf Kinase Family Research Articles

A fluorescence-based sensor for calibrated measurement of protein kinase stability in live cells.

Oncogenic mutations can destabilize signaling proteins, resulting in increased or unregulated activity. Thus, there is considerable interest in mapping the relationship between mutations and the stability of signaling proteins, to better understand the consequences of oncogenic mutations and potentially inform the development of new therapeutics. Here, we develop a tool to study protein-kinase stability in live mammalian cells and the effects of the HSP90 chaperone system on the stability of these kinases. We determine the expression levels of protein kinases by monitoring the fluorescence of fluorescent proteins fused to those kinases, normalized to that of co-expressed reference fluorescent proteins. We used this tool to study the dependence of Src- and Raf-family kinases on the HSP90 system. We demonstrate that this sensor reports on destabilization induced by oncogenic mutations in these kinases. We also show that Src-homology 2 and Src-homology 3 domains, which are required for autoinhibition of Src-family kinases, stabilize these kinase domains in the cell. Our expression-calibrated sensor enables the facile characterization of the effects of mutations and small-molecule drugs on protein-kinase stability.

Regulation of RAF family kinases: new insights from recent structural and biochemical studies.

The RAF kinases are required for signal transduction through the RAS-RAF-MEK-ERK pathway, and their activity is frequently up-regulated in human cancer and the RASopathy developmental syndromes. Due to their complex activation process, developing drugs that effectively target RAF function has been a challenging endeavor, highlighting the need for a more detailed understanding of RAF regulation. This review will focus on recent structural and biochemical studies that have provided 'snapshots' into the RAF regulatory cycle, revealing structures of the autoinhibited BRAF monomer, active BRAF and CRAF homodimers, as well as HSP90/CDC37 chaperone complexes containing CRAF or BRAFV600E. In addition, we will describe the insights obtained regarding how BRAF transitions between its regulatory states and examine the roles that various BRAF domains and 14-3-3 dimers play in both maintaining BRAF as an autoinhibited monomer and in facilitating its transition to an active dimer. We will also address the function of the HSP90/CDC37 chaperone complex in stabilizing the protein levels of CRAF and certain oncogenic BRAF mutants, and in serving as a platform for RAF dephosphorylation mediated by the PP5 protein phosphatase. Finally, we will discuss the regulatory differences observed between BRAF and CRAF and how these differences impact the function of BRAF and CRAF as drivers of human disease.

Abstract 619: Comprehensive cell line profiling of monomer- and dimer-selective small molecule RAF inhibitors uncovers determinants of cellular responses

Abstract Dysregulation of the Mitogen-Activated Protein Kinase (MAPK) pathway is a frequent event in many cancers. The RAF family of kinases, which includes ARAF, BRAF, and CRAF (RAF1), plays a key role in MAPK signaling. Of the three isoforms, only BRAF is currently targeted by approved RAF inhibitors. These inhibitors were designed to target BRAF-mutant variants that act as oncogenic monomers. However, BRAF-monomer inhibitors can induce activation of wild-type RAF by the formation of dimers, resulting in hyperproliferative lesions of BRAF wild-type cells. Additionally, BRAF-monomer inhibitors do not target RAF-dimers, although this is a potential vulnerability of many MAPK-driven cancers. Novel inhibitors are in development to circumvent these limitations. Further insights into the precise targeting and mechanism of action of RAF inhibitors can help in determining the most promising avenues for drug development. We performed extensive cellular profiling experiments with three approved and five clinical stage inhibitors of RAF to gain more insight into the differences and cellular targeting of these agents. The inhibitors were tested in cell viability assays on a panel of 130 human cancer cell lines from diverse tissue origins. Cell lines were exposed to dose ranges of each inhibitor spanning four logarithmic orders, and viability was determined by measurement of intracellular ATP. Effects of compound on cell viability were related to genomic, transcriptomic, and proteomic status using bioinformatics, with the aim to identify predictive biomarkers for drug response, and to determine selective targeting of MAPK-driven cell lines. Additionally, the primary mechanism of cellular inhibitor activity was determined by relating cell line responses to gene dependency data from large CRISPR knockout screens. Our results showed striking similarity in the overall inhibitory profile of BRAF-monomer inhibitors and the vemurafenib-derivative and paradox breaker plixorafenib, which all selectively targeted BRAF-mutant cell lines. However, whereas vemurafenib increased cell viability in RAS-mutant cell lines at high drug concentrations, this effect was greatly reduced for plixorafenib. Western blot analysis of phosphorylated MEK and ERK levels in RAS-mutant cell lines treated with BRAF-monomer inhibitors confirmed MAPK pathway activation as cause of the increased cell viability. In addition, RAF-dimer inhibitors potently targeted BRAF-mutant cell lines, as well as several KRAS- and NRAS-mutant cell lines. Lastly, correlation analyses of cell line profiling data with CRISPR knockout data revealed the preferential targeting of RAF1-dependent cell lines by the dual RAF/MEK inhibitor avutometinib. The results of our analyses shed light on the intricacies of cellular targeting by RAF inhibitors and provide insights to guide the development of new RAF inhibitors. Citation Format: Jeffrey J. Kooijman, Awan Al Koerdi, Sjoerd B. van der Leeuw, Daphne J. Kluitmans, Esmee van den Bossche, Jelle Dylus, Jeroen A. de Roos, Janneke J. Melis, Nicole Willemsen-Seegers, Guido J. Zaman. Comprehensive cell line profiling of monomer- and dimer-selective small molecule RAF inhibitors uncovers determinants of cellular responses [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 619.

The synthetic routes of sorafenib and its applications on hepatocellular carcinoma

Cancer stands as the second leading cause of global mortality, with a staggering one in five individuals worldwide facing a cancer diagnosis in their lifetime. Addressing cancer prevention has emerged as a significant issue in the field of public health in the 21st century. Hepatocellular carcinoma (HCC) - the primary liver cancer type - not only ranks as one of the top five most frequent cancers globally, but also distressingly represents the fourth leading cause of cancer-related deaths. Notably, it claims the top spot in cancer-related mortality worldwide. Hepatocellular carcinoma is characterized by its high incidence, swift progression, recurrent nature, proclivity for metastasis, and distressingly high mortality rate. A significant proportion of cases trace a three-step path, hepatitis B infection leading to cirrhosis culminating in hepatocellular carcinoma. Sorafenib, a multi-targeted kinase inhibitor, offers promise in combatting this formidable adversary. It works by inhibiting key targets like vascular endothelial growth factor receptors (VEGFR1, VEGFR2, VEGFR3), platelet-derived growth factor receptor (PDGFR-), and RAF family kinases, which contributes to its healing effects. This article delves into the synthetic pathway of sorafenib, elucidating its impactful role in cancer treatment, and expounds on its advantageous attributes.

Utilizing CD44v6 and V600EBRAF-mutation for in vitro targeted combination therapy of thyroid carcinomas

AimThe aim of this study was to assess the feasibility of targeted therapy of thyroid carcinoma, first exploring potential targets BRAF, EGFR and CD44v6 in patient material through immunohistochemistry and mutation analysis. Materials and methodsA patient cohort (n = 22) consisting of seven papillary (PTC), eight anaplastic (ATC) and seven follicular (FTC) thyroid carcinomas were evaluated. Additionally, eight thyroid carcinoma cells lines were analyzed for CD44v6-expression and sensitivity to the multi-kinase inhibitor sorafenib (Nexavar®), which targets numerous serine/threonine and tyrosine kinases, including the Raf family kinases. Targeted therapy using 131I-AbN44v6, a novel anti-CD44v6 antibody, and/or sorafenib was evaluated in 3D multicellular tumor spheroids. ResultsOf the two cell surface proteins, EGFR and CD44v6, the latter was overexpressed in >80 % of samples, while EGFR-expression levels were moderate at best in only a few samples. BRAF mutations were more common in PTC patient samples than in ATC samples, while FTC samples did not harbor BRAF mutations. CD44v6-expression levels in the thyroid carcinoma cell lines were more heterogenous compared to patient samples, while BRAF mutational status was in line with the original tumor type. Monotherapy in 3D multicellular ATC tumor spheroids with either 131I-AbN44v6 or sorafenib resulted in delayed spheroid growth. The combination of 131I-AbN44v6 and sorafenib was the most potent and resulted in significantly impaired spheroid growth. ConclusionThis “proof of concept” targeted therapy study in the in vitro ATC 3D multicellular tumor spheroids indicated applicability of utilizing CD44v6 for molecular radiotherapy both as a monotherapy and in combination with sorafenib.

Cryo-EM structure of a RAS/RAF recruitment complex

RAF-family kinases are activated by recruitment to the plasma membrane by GTP-bound RAS, whereupon they initiate signaling through the MAP kinase cascade. Prior structural studies of KRAS with RAF have focused on the isolated RAS-binding and cysteine-rich domains of RAF (RBD and CRD, respectively), which interact directly with RAS. Here we describe cryo-EM structures of a KRAS bound to intact BRAF in an autoinhibited state with MEK1 and a 14-3-3 dimer. Analysis of this KRAS/BRAF/MEK1/14-3-3 complex reveals KRAS bound to the RAS-binding domain of BRAF, captured in two orientations. Core autoinhibitory interactions in the complex are unperturbed by binding of KRAS and in vitro activation studies confirm that KRAS binding is insufficient to activate BRAF, absent membrane recruitment. These structures illustrate the separability of binding and activation of BRAF by RAS and suggest stabilization of this pre-activation intermediate as an alternative therapeutic strategy to blocking binding of KRAS.

Abstract PR06: Germline RASopathy mutations provide insights into the differential regulation of RAF family kinases

Abstract The RAS-MAPK pathway is a hotspot for somatic mutations in human cancer and for germline mutations in the RASopathy developmental syndromes. Understanding the regulatory mechanisms that govern this pathway is critical for identifying new drug targets and establishing effective therapeutic approaches for RASopathy and cancer patients alike. RASopathies are caused by mutations in many of the same genes as those found in cancer, however RASopathy mutations must be tolerated during development and as a result tend to be distinct those in cancer in terms of their location within the protein or in which family member or isoform they occur. In the case of the RAF kinase, BRAF, oncogenic mutations occur overwhelmingly in the catalytic (CAT) region, whereas RASopathy mutations are also frequently reported in cysteine-rich domain (CRD). The CRD is a zinc-stabilized lipid and protein binding domain in the RAF regulatory (REG) region. Previous studies have shown that the CRD plays roles in RAS activation of RAF by interacting with phosphatidylserine (PS) in the plasma membrane and by bindings directly to RAS GTPases. Conversely, the CRD also plays a role in the autoinhibitory interactions of the REG and CAT domains under quiescent conditions. Indeed, recently published cryo-EM structures of autoinhibited BRAF show the CRD bound to the CAT domain in cis and to the 14-3-3 dimer that stabilizes the REG-CAT interactions in trans. However, the relative importance of these functions and the residues which mediate them are not well understood. Through the characterization of a panel of RASopathy CRD mutations we show that they can be grouped into three distinct classes based on their abilities to relieve autoinhibition and/or enhance PS binding, with relief of autoinhibition being the major factor determining BRAF biological activity and mutational severity in zebrafish developmental studies. Encouragingly, these findings tracked well with RASopathy patient reports, indicating the utility of our approaches as prognostic indicators of RASopathy mutation severity in patients. Further, we found that the CRD is required to maintain BRAF in a non-signaling state and mutations which disrupt this function result in elevated RAS-dependent and RAS-independent BRAF function. Importantly, our studies indicate that stabilizing CRD-mediated autoinhibition may be a viable approach to prevent the aberrant BRAF activation found in many cancers and the RASopathy syndromes. Finally, when we compared the properties of BRAF CRD to those of CRAF, we found that that BRAF CRD is a stronger mediator of both autoinhibition and PS binding. In contrast, my preliminary studies indicate that CRAF CRD may instead play a greater role in direct RAS binding. Moreover, despite its reduced role in autoinhibition, CRAF CRD retains its ability to bind 14-3-3 proteins and we are currently investigating the interplay of 14-3-3, RAS and the CRD in regulating CRAF function. Citation Format: Russell Spencer-Smith, Elizabeth M. Terrell, Christine Insinna, Constance Agamasu, Morgan E. Wagner, Daniel A. Ritt, Jim Stauffer, Andrew G. Stephen, Deborah K. Morrison. Germline RASopathy mutations provide insights into the differential regulation of RAF family kinases [abstract]. In: Proceedings of the AACR Special Conference: Targeting RAS; 2023 Mar 5-8; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Res 2023;21(5_Suppl):Abstract nr PR06.

Analysis of the ERK Pathway Cysteinome for Targeted Covalent Inhibition of RAF and MEK Kinases

The ERK pathway is one of the most important signaling cascades involved in tumorigenesis. So far, eight noncovalent inhibitors of RAF and MEK kinases in the ERK pathway have been approved by the FDA for the treatment of cancers; however, their efficacies are limited due to various resistance mechanisms. There is an urgent need to develop novel targeted covalent inhibitors. Here we report a systematic study of the covalent ligandabilities of the ERK pathway kinases (ARAF, BRAF, CRAF, KSR1, KSR2, MEK1, MEK2, ERK1, and ERK2) using constant pH molecular dynamics titration and pocket analysis. Our data revealed that the hinge GK (gate keeper)+3 cysteine in RAF family kinases (ARAF, BRAF, CRAF, KSR1, and KSR2) and the back loop cysteine in MEK1 and MEK2 are reactive and ligandable. Structure analysis suggests that the type II inhibitors belvarafenib and GW5074 may be used as scaffolds for designing pan-RAF or CRAF-selective covalent inhibitors directed at the GK+3 cysteine, while the type III inhibitor cobimetinib may be modified to label the back loop cysteine in MEK1/2. The reactivities and ligandabilities of the remote cysteine in MEK1/2 and the DFG-1 cysteine in MEK1/2 and ERK1/2 are also discussed. Our work provides a starting point for medicinal chemists to design novel covalent inhibitors of the ERK pathway kinases. The computational protocol is general and can be applied to the systematic evaluation of covalent ligandabilities of the human cysteinome.

Structure and RAF family kinase isoform selectivity of type II RAF inhibitors tovorafenib and naporafenib

Upon activation by RAS, RAF family kinases initiate signaling through the MAP kinase cascade to control cell growth, proliferation, and differentiation. Among RAF isoforms (ARAF, BRAF, and CRAF), oncogenic mutations are by far most frequent in BRAF. The BRAFV600E mutation drives more than half of all malignant melanoma and is also found in many other cancers. Selective inhibitors of BRAFV600E (vemurafenib, dabrafenib, encorafenib) are used clinically for these indications, but they are not effective inhibitors in the context of oncogenic RAS, which drives dimerization and activation of RAF, nor for malignancies driven by aberrantly dimerized truncation/fusion variants of BRAF. By contrast, a number of "type II" RAF inhibitors have been developed as potent inhibitors of RAF dimers. Here, we compare potency of type II inhibitors tovorafenib (TAK-580) and naporafenib (LHX254) in biochemical assays against the three RAF isoforms and describe crystal structures of both compounds in complex with BRAF. We find that tovorafenib and naporafenib are most potent against CRAF but markedly less potent against ARAF. Crystal structures of both compounds with BRAFV600E or WT BRAF reveal the details of their molecular interactions, including the expected type II-binding mode, with full occupancy of both subunits of the BRAF dimer. Our findings have important clinical ramifications. Type II RAF inhibitors are generally regarded as pan-RAF inhibitors, but our studies of these two agents, together with recent work with type II inhibitors belvarafenib and naporafenib, indicate that relative sparing of ARAF may be a property of multiple drugs of this class.

Abstract 2438: Determining the role of non-mutated C-Raf kinase in metastatic disease

Abstract Many aggressive epithelial cancers do not carry targetable driver mutations (Mendiratta et al. 2021, NCI-MATCH Clinical trial NCT02465060). Commonly altered signaling pathways highlight the propensity for tumors to depend on such pathways for growth and survival where genomic alterations may not be required for pathway activation. The Raf family kinases are crucial mediators of the Ras/Raf/MEK/ERK (MAPK) cascade, which has been shown to be upregulated in a subset of metastatic cancers and are mutated in many epithelial cancers. A recent study suggests non-mutated C-Raf can drive metastasis to the lungs, bone, and various other tissues (Faltermeir et al. 2016). Though the mechanism of C-Raf driven metastasis is likely through MAPK activation, C-Raf has been demonstrated to possess MAPK independent roles that may also contribute to this phenotype. In this study, we explored various C-Raf functions as drivers of metastasis in an intracardiac mouse model system. Using a series of Raf knock-out cell lines and mutants targeting functional residues in C-Raf, we demonstrated that C-Raf dimerization is necessary to drive metastasis. We further showed that the metastasis-promoting activity of C-Raf is dependent on co-expression of its family member, B-Raf, for an accelerated metastatic phenotype. However, overexpression of a kinase-dead C-Raf mutant was still able to produce metastases albeit with lower efficiency, suggesting C-Raf possesses non-kinase dependent functions that also contributed to metastasis. Together, these results point to the importance of Raf non-canonical roles in oncogenic processes that may be unappreciated in metastatic disease. Citation Format: Lisa H. Ta, Janai R. Carr-Ascher, Weixian Deng, Brandon L. Tsai, Wendy Tran, Donny Gun, Donghui Cheng, Jihui Sha, Yeonjoo Hwang, John W. Phillips, Matthew B. Obusan, Nathanael J. Bangayan, Miyako Noguchi, Zhiyuan Mao, Chia-Chun Chen, Liang Wang, Grigor Varuzhanyan, John D. Gordon, James W. Wohlschlegel, Owen N. Witte. Determining the role of non-mutated C-Raf kinase in metastatic disease [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2438.

Abstract 2677: JZP815, a potent and selective pan-RAF inhibitor, demonstrates efficacy in RAF and RAS mutant tumor pre-clinical models

Abstract Activation of the mitogen-activated protein kinase (MAPK) pathway by oncogenic mutations in RAS and RAF is a frequent driver of human cancer. Targeting specific components of the pathway is a precise and rational route to deliver benefits to cancer patients with high unmet therapeutic needs. The RAF kinase proteins (ARAF, BRAF, CRAF) are core pathway components which mediate MAPK signaling. Mutations in these critical signaling proteins leads to constitutive activation of the MAPK pathway and tumor growth. Using state of the art screening methodologies and medicinal chemistry we discovered and developed a next generation pan-RAF kinase inhibitor, JZP815, which potently inhibits wild-type and mutant RAF kinases in cell-free and cell-based assays. JZP815 is a selective RAF kinase inhibitor that suppresses all 3 RAF kinase family members at low-to-sub nanomolar potencies in cell-free assays. Moreover, in tumor cells JZP815 does not induce significant paradoxical pathway activation, observed with approved 1st generation BRAF-selective inhibitors, while demonstrating equivalent potencies for MAPK pathway inhibition driven by either mutant RAF monomers or RAS-induced RAF dimers in tumor cells. JZP815 significantly inhibited tumor growth as a single agent in multiple mouse xenograft solid tumor models harboring RAS and/or BRAF mutations. Furthermore, JZP815’s favorable pharmacokinetic profile sustained on-target pathway pharmacodynamic responses in a predictable dose and time dependent manner. JZP815 demonstrated enhanced activity when combined with inhibitors of other MAPK pathway components in both class 2 and class 3 mutant BRAF patient-derived tumor cells ex vivo, and KRAS mutant NSCLC and CRC xenografts in vivo. In summary, JZP815 is a potent and selective pan-RAF inhibitor that is orally bioavailable in multiple preclinical species with a well-behaved safety profile and pharmacokinetic properties predicted to provide drug exposure required for target engagement in humans, and therefore suitable for advancing into first-in-human trials. Citation Format: Robert Hauptschein, Simon Woodcock, Andrew Belfield, Helen Mason, Dorottya Keppel, Svetlana Markova, Kyuri Kim, Shane Roller, Caroline Phillips, Clifford D. Jones, Robin C. Humphreys. JZP815, a potent and selective pan-RAF inhibitor, demonstrates efficacy in RAF and RAS mutant tumor pre-clinical models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2677.

Pharmacokinetic Exposures Associated With Oral Administration of Sorafenib in Dogs With Spontaneous Tumors.

Sorafenib is a multi-kinase small molecule inhibitor that targets serine/threonine and tyrosine kinases including the RAF kinase family, VEGFR-2, and PDGFR. The aim of this study was to evaluate the systemic pharmacokinetics of a previously defined tolerable oral dose of sorafenib in tumor-bearing dogs. Six client-owned dogs with a cytologic or histologic diagnosis of cancer were enrolled in this open-label, tolerability study. Dogs were administered sorafenib at an intended dose of 3 mg/kg and serum samples were obtained for analysis of sorafenib serum concentrations at 0, 1, 2, 6, 12, 24, 48, 72, 96, and 168 h post-drug administration. Median time to peak serum sorafenib concentration occurred at 4 h (range 2–12 h) resulting in an average serum concentration of 54.9 ± 33.5 ng/mL (118.2 ± 72.1 nM). Mean sorafenib levels declined by over 70% relative to peak serum concentrations by 24 h in all dogs, suggesting the value of at least twice daily administration. Doses of 3 mg/kg were well-tolerated and no patients in the study experienced adverse events that were attributable to sorafenib. Future trials in dogs with cancer are recommended at this dosing schedule to assess the effect of sorafenib administration on anti-tumor efficacy signals and relevant pharmacodynamic target modulation in vivo.

Integrated computational approach for in silico design of new purinyl pyridine derivatives as B-Raf kinase inhibitors

B-Raf is one among the most frequently mutating proto-oncogene which is associated with the serine/threonine Raf kinase family involved in the RAS-RAF-MEK-ERK pathway, which is the most deregulated pathway in human cancers. Mutant B-Raf V600E got an excellent scope for investigation in cancer as a potential therapeutic target. Formerly B-RafV600E is considered the molecular target for numerous antitumor compounds like purinyl pyridine and pyrimidine derivatives. In the current research work using molecular docking approach of Schrodinger Glide 5.6 version, ligand docking, pharmacophore-based virtual screening, binding free energy calculations of a series of 2-amino purinyl pyridine and pyrimidine derivatives were modeled, their docking values were predicted, that were considered to be potent against B-Raf V600E. A five-point hypothesis accompanied by a hydrogen bond acceptor(A), two hydrogen bond donors(D), and two aromatic rings (R) was built with a justifiable R2 value of 0.91 and a Q2 value of 0.64. Then by using Asinex Elite Synergy database, virtual screening was performed, and identified several potential hits. Subsequently, the molecules which had interactions with the target B-Raf kinase were determined by subjecting the obtained hits for SP and XP docking processes. Finally, for the top leads obtained, binding free energies were accomplished. About 16 new purinyl pyridine molecules were also designed. Almost nine molecules manifested crucial ligand interactions and binding free energies. At the outset, this research paved the way for us in spotting new molecules with B-Raf inhibitory activity, which can further be explored to design molecules with enhanced pharmacokinetic profiles.

Silencing ARAF Suppresses the Malignant Phenotypes of Gallbladder Cancer Cells.

ARAF is a member of the RAF kinase family that is necessary for mitogen-activated protein kinase (MAPK) activation in various malignancies, including lung, colorectal, pancreatic, and breast cancers. As the most common biliary tract tumor, gallbladder cancer (GBC) seriously harms human health while the function of ARAF in GBC remains elusive. Here, we found that ARAF expression was upregulated in gallbladder cancer tissues. In vitro, ARAF silencing mediated by RNA interference effectively inhibited cell proliferation, colony formation, migration, and invasion of GBC cells. Moreover, knocking down ARAF suppressed tumor growth in vivo. Our results indicated that ARAF functions as an oncogene in GBC and, thus, could be a potential therapeutic target for GBC.

Functional characterization of a PROTAC directed against BRAF mutant V600E.

The RAF family kinases function in the RAS-ERK pathway to transmit signals from activated RAS to the downstream kinases MEK and ERK. This pathway regulates cell proliferation, differentiation and survival, enabling mutations in RAS and RAF to act as potent drivers of human cancers. Drugs targeting the prevalent oncogenic mutant BRAF(V600E) have shown great efficacy in the clinic, but long-term effectiveness is limited by resistance mechanisms that often exploit the dimerization-dependent process by which RAF kinases are activated. Here, we investigated a proteolysis-targeting chimera (PROTAC) approach to BRAF inhibition. The most effective PROTAC, termed P4B, displayed superior specificity and inhibitory properties relative to non-PROTAC controls in BRAF(V600E) cell lines. In addition, P4B displayed utility in cell lines harboring alternative BRAF mutations that impart resistance to conventional BRAF inhibitors. This work provides a proof of concept for a substitute to conventional chemical inhibition to therapeutically constrain oncogenic BRAF.

Abstract IA17: Molecular mechanisms that regulate Raf kinase signaling

Abstract Raf kinases are essential for normal Ras pathway signaling, and activating mutations in components of this pathway are associated with a variety of human cancers as well as a group of related developmental disorders known collectively as the RASopathies. Of the core pathway components, the mechanisms that modulate the Raf family kinases are by far the most complex, involving changes in subcellular localization, protein interactions, and phosphorylation/dephosphorylation events. In addition, like numerous other protein kinases, the Raf kinases can form dimers. Functional studies investigating the importance of Raf dimerization have revealed that Raf dimer formation is required for normal Ras-dependent Raf activation and for the biologic activity of many disease-associated Raf mutants. At the meeting, I will present recent work examining the regulatory differences among Raf family members and will discuss how these differences contribute to Raf-mediated disease signaling. I will also present studies investigating the effect that various therapeutic agents have on Raf regulatory interactions and will describe new approaches to disrupt Ras-Raf-MEK-ERK pathway signaling. Citation Format: Deborah Morrison. Molecular mechanisms that regulate Raf kinase signaling [abstract]. In: Proceedings of the AACR Special Conference on Targeting RAS-Driven Cancers; 2018 Dec 9-12; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(5_Suppl):Abstract nr IA17.

Abstract A31: Germline RASopathy mutations provide functional insights into the Raf cysteine-rich domain (CRD)

Abstract The three-member RAF kinase family (A-, B- and C-Raf) are direct Ras effectors and key mediators of the proproliferative MAPK pathway. Somatic driver mutations in the B-Raf kinase domain occur frequently in melanoma and cancers of the thyroid and large intestine. These are predominantly the V600E mutation, which allows B-Raf to signal constitutively as a monomer. Germline mutations in B-Raf also occur and are present in ~67% of the childhood developmental RASopathy-cardiofaciocutaneous (CFC) syndrome. Interestingly, many of these CFC mutations cluster around the cysteine-rich domain (CRD) in the B-Raf regulatory region. CRDs are zinc stabilized structures with two flexible loops that are shown to bind phosphatidylserine (PS), DAG and pro-oncogenic phorbol esters in several PKC family members. Although the B-Raf CRD has not been well characterized, prior studies examining the C-Raf CRD show that it binds to PS through its first flexible loop but does not bind DAG or phorbol esters, likely due to its truncated second loop, which is found in all Raf members. In addition to PS binding, C-Raf CRD may also interact directly with Ras, suggesting a second Ras binding site outside of its Ras binding domain (RBD). Interestingly, B-Raf RASopathy mutations occur in both CRD loops and commonly introduce a positively charged residue suited to interacting with negatively charged lipids in the plasma membrane (PM). Of note, Q257R, which is the most common mutation in CFC, maps to the truncated second loop. Our in-cell studies with full-length B-Raf have shown that RASopathy mutations in both loops enhance biologic activity, PM localization and Ras interaction. However, the biologic activity of loop 1 mutations requires an intact RBD, which is not the case for the loop 2 mutant, Q257R. These data suggest that the Q257R mutant either has increased binding to Ras or allows B-Raf to signal independently of Ras. To further investigate these findings, we are examining differences in localization, Ras interaction and lipid binding using the isolated CRDs of C-Raf, B-Raf and the B-Raf RASopathy mutants. As may be predicted, the RASopathy mutations increased membrane localization over WT B-Raf, with Q257R being the most PM localized. Somewhat surprisingly, expression of the wild-type B-Raf CRD in cells showed greatly enhanced PM localization compared to that of wild-type C-Raf, suggesting functional differences between their CRDs, which we are currently investigating. Citation Format: Russell Spencer-Smith, Elizabeth M. Terrell, Constance Agamasu, Daniel A. Ritt, Alyson K. Freeman, Andrew G. Stephen, Deborah K. Morrison. Germline RASopathy mutations provide functional insights into the Raf cysteine-rich domain (CRD) [abstract]. In: Proceedings of the AACR Special Conference on Targeting RAS-Driven Cancers; 2018 Dec 9-12; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(5_Suppl):Abstract nr A31.

Architecture of autoinhibited and active BRAF-MEK1-14-3-3 complexes.

RAF family kinases are RAS-activated switches that initiate signaling through the MAP kinase cascade to control cellular proliferation, differentiation and survival1–3. RAF activity is tightly regulated, and inappropriate activation is a frequent cause of cancer4–6. At present, the structural basis for RAF regulation is poorly understood. Here we describe autoinhibited and active state structures of full-length BRAF in complexes with MEK1 and a 14-3-3 dimer, determined using cryo electron microscopy (cryo-EM). A 4.1Å resolution cryo-EM reconstruction reveals an inactive BRAF/MEK1 complex restrained in a cradle formed by the 14-3-3 dimer, which binds the phosphorylated S365 and S729 sites that flank the BRAF kinase domain. The BRAF cysteine-rich domain (CRD) occupies a central position that stabilizes this assembly, but the adjacent RAS-binding domain (RBD) is poorly ordered and peripheral. The 14-3-3 cradle maintains autoinhibition by sequestering the membrane-binding CRD and blocking dimerization of the BRAF kinase domain. In the active state, these inhibitory interactions are released and a single 14-3-3 dimer rearranges to bridge the C-terminal pS729 binding sites of two BRAFs, driving formation of an active, back-to-back BRAF dimer. Our structural snapshots provide a foundation for understanding normal RAF regulation and its mutational disruption in cancer and developmental syndromes.

Characterize Disease-related Mutants of RAF Family Kinases by Using a Set of Practical and Feasible Methods

Characterize Disease-related Mutants of RAF Family Kinases by Using a Set of Practical and Feasible Methods

Abstract 1305: Identification of signal transduction kinases inhibited by pan-RAF inhibitor belvarafenib using FRET imaging technique

Abstract The mitogen-activated protein kinase (MAPK) pathway plays an important role for the survival and proliferation of tumor cells. For example, the activation of the MAPK pathway due to mutations in BRAF, NRAS and KRAS kinases is known to be the causes of various solid tumors and hematologic malignancies. Accordingly, there is a strong need for effective therapeutic drugs for treating cancers caused by genetic mutation of BRAF, NRAS or KRAS. Belvarafenib (HM95573 or GDC5573), currently in Phase 1 clinical trials, is a selective and orally bioavailable pan-RAF kinase inhibitor. When biochemically assayed for hundreds of kinases, Belvarafenib showed selectivity toward RAF family kinases, including strong inhibition activities for BRAF WT, BRAF mutants and CRAF. Previously, we reported that Belvarafenib strongly inhibits the growth of cancer cell lines with BRAF, NRAS or KRAS mutations and also shows excellent anticancer efficacy in animal models using the corresponding cancer cells. In this study, employing fluorescence resonance energy transfer (FRET) imaging, we examined which protein kinases involved in signal transduction are regulated by Belvarafenib and investigated the mechanism of action for the regulation in typical cancer cells harboring BRAF, NRAS or KRAS mutations such as A375 (melamona), SK-MEL-30 (Kwmelamona), HCT116 (CRC), and Calu-6 (NSCLC). Among the various protein kinases that can be involved in signal transduction, we identified with time-lapse FRET imaging that the phosphorylation of ERK, AKT and S6K are inhibited after the treatment of Belvarafenib in the above cancer cells of BRAF, NRAS or KRAS mutations. Of note, BRAF mutant selective inhibitors, Vemurafenib and Dabrafenib were not active in cancer cells of NRAS or KRAS mutations. These results correlate with the in vitro and in vivo anticancer activity in cancer cells of BRAF, NRAS or KRAS mutations. In conclusion, unlike Vemurafenib and Dabrafenib, the pan-RAF inhibitor Belvarafenib could be effective for treating the cancer caused by NRAS or KRAS mutations, as well as BRAF mutations. Citation Format: Dong-Jun Bae, Sang-Yeob Kim, JooYun Byun, InHwan Bae, YoungGil Ahn, YoungHoon Kim, Kwee Hyun Suh. Identification of signal transduction kinases inhibited by pan-RAF inhibitor belvarafenib using FRET imaging technique [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1305.