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Bonsor DA, Simanshu DK. RAS and SHOC2 Roles in RAF Activation and Therapeutic Considerations. ANNUAL REVIEW OF CANCER BIOLOGY 2024; 8:97-113. [PMID: 38882927 PMCID: PMC11178279 DOI: 10.1146/annurev-cancerbio-062822-030450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Mutations in RAS proteins play a pivotal role in the development of human cancers, driving persistent RAF activation and deregulating the Mitogen-Activated Protein Kinase (MAPK) signaling pathway. While progress has been made in targeting specific oncogenic RAS proteins, effective drug-based therapies for the majority of RAS mutations remain limited. Recent investigations on RAS-RAF complexes and the SHOC2-MRAS-PP1C holoenzyme complex have provided crucial insights into the structural and functional aspects of RAF activation within the MAPK signaling pathway. Moreover, these studies have also unveiled new blueprints for developing inhibitors allowing us to think beyond the current RAS and MEK inhibitors. In this review, we explore the roles of RAS and SHOC2 in activating RAF and discuss potential therapeutic strategies to target these proteins. A comprehensive understanding of the molecular interactions involved in RAF activation and their therapeutic implications holds the potential to drive innovative approaches in combating RAS/RAF-driven cancers.
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Affiliation(s)
- Daniel A Bonsor
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
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2
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Paul JW, Muratcioğlu S, Kuriyan J. A fluorescence-based sensor for calibrated measurement of protein kinase stability in live cells. Protein Sci 2024; 33:e5023. [PMID: 38801214 PMCID: PMC11129626 DOI: 10.1002/pro.5023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/22/2024] [Accepted: 05/02/2024] [Indexed: 05/29/2024]
Abstract
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.
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Affiliation(s)
- Joseph W. Paul
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
- California Institute for Quantitative Bioscience (QB3)University of CaliforniaBerkeleyCaliforniaUSA
| | - Serena Muratcioğlu
- Department of BiochemistryVanderbilt University School of MedicineNashvilleTennesseeUSA
| | - John Kuriyan
- Department of BiochemistryVanderbilt University School of MedicineNashvilleTennesseeUSA
- Department of ChemistryVanderbilt UniversityNashvilleTennesseeUSA
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3
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Liu NF, Enomoto M, Marshall CB, Ikura M. Reconstitution and characterization of BRAF in complex with 14-3-3 and KRAS4B on nanodiscs. Protein Sci 2024; 33:e5016. [PMID: 38747381 PMCID: PMC11094772 DOI: 10.1002/pro.5016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 04/17/2024] [Accepted: 04/25/2024] [Indexed: 05/19/2024]
Abstract
RAF kinases are key components of the RAS-MAPK signaling pathway, which drives cell growth and is frequently overactivated in cancer. Upstream signaling activates the small GTPase RAS, which recruits RAF to the cell membrane, driving a transition of the latter from an auto-inhibited monomeric conformation to an active dimer. Despite recent progress, mechanistic details underlying RAF activation remain unclear, particularly the role of RAS and the membrane in mediating this conformational rearrangement of RAF together with 14-3-3 to permit RAF kinase domain dimerization. Here, we reconstituted an active complex of dimeric BRAF, a 14-3-3 dimer and two KRAS4B on a nanodisc bilayer and verified that its assembly is GTP-dependent. Biolayer interferometry (BLI) was used to compare the binding affinities of monomeric versus dimeric full-length BRAF:14-3-3 complexes for KRAS4B-conjugated nanodiscs (RAS-ND) and to investigate the effects of membrane lipid composition and spatial density of KRAS4B on binding. 1,2-Dioleoyl-sn-glycero-3-phospho-L-serine (DOPS) and higher KRAS4B density enhanced the interaction of BRAF:14-3-3 with RAS-ND to different degrees depending on BRAF oligomeric state. We utilized our reconstituted system to dissect the effects of KRAS4B and the membrane on the kinase activity of monomeric and dimeric BRAF:14-3-3 complexes, finding that KRAS4B or nanodiscs alone were insufficient to stimulate activity, whereas RAS-ND increased activity of both states of BRAF. The reconstituted assembly of full-length BRAF with 14-3-3 and KRAS on a cell-free, defined lipid bilayer offers a more holistic biophysical perspective to probe regulation of this multimeric signaling complex at the membrane surface.
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Affiliation(s)
- Ningdi F. Liu
- Princess Margaret Cancer CentreUniversity Health NetworkTorontoOntarioCanada
- Department of Medical BiophysicsUniversity of TorontoTorontoOntarioCanada
| | - Masahiro Enomoto
- Princess Margaret Cancer CentreUniversity Health NetworkTorontoOntarioCanada
| | | | - Mitsuhiko Ikura
- Princess Margaret Cancer CentreUniversity Health NetworkTorontoOntarioCanada
- Department of Medical BiophysicsUniversity of TorontoTorontoOntarioCanada
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4
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Scardaci R, Berlinska E, Scaparone P, Vietti Michelina S, Garbo E, Novello S, Santamaria D, Ambrogio C. Novel RAF-directed approaches to overcome current clinical limits and block the RAS/RAF node. Mol Oncol 2024; 18:1355-1377. [PMID: 38362705 PMCID: PMC11161739 DOI: 10.1002/1878-0261.13605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 11/30/2023] [Accepted: 01/30/2024] [Indexed: 02/17/2024] Open
Abstract
Mutations in the RAS-RAF-MEK-ERK pathway are frequent alterations in cancer and RASopathies, and while RAS oncogene activation alone affects 19% of all patients and accounts for approximately 3.4 million new cases every year, less frequent alterations in the cascade's downstream effectors are also involved in cancer etiology. RAS proteins initiate the signaling cascade by promoting the dimerization of RAF kinases, which can act as oncoproteins as well: BRAFV600E is the most common oncogenic driver, mutated in the 8% of all malignancies. Research in this field led to the development of drugs that target the BRAFV600-like mutations (Class I), which are now utilized in clinics, but cause paradoxical activation of the pathway and resistance development. Furthermore, they are ineffective against non-BRAFV600E malignancies that dimerize and could be either RTK/RAS independent or dependent (Class II and III, respectively), which are still lacking an effective treatment. This review discusses the recent advances in anti-RAF therapies, including paradox breakers, dimer-inhibitors, immunotherapies, and other novel approaches, critically evaluating their efficacy in overcoming the therapeutic limitations, and their putative role in blocking the RAS pathway.
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Affiliation(s)
- Rossella Scardaci
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology CenterUniversity of TorinoItaly
| | - Ewa Berlinska
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology CenterUniversity of TorinoItaly
| | - Pietro Scaparone
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology CenterUniversity of TorinoItaly
| | - Sandra Vietti Michelina
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology CenterUniversity of TorinoItaly
| | - Edoardo Garbo
- Department of OncologyUniversity of Torino, San Luigi HospitalOrbassanoItaly
| | - Silvia Novello
- Department of OncologyUniversity of Torino, San Luigi HospitalOrbassanoItaly
| | - David Santamaria
- Centro de Investigación del CáncerCSIC‐Universidad de SalamancaSpain
| | - Chiara Ambrogio
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology CenterUniversity of TorinoItaly
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5
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Sigaud R, Brummer T, Kocher D, Milde T, Selt F. MOST wanted: navigating the MAPK-OIS-SASP-tumor microenvironment axis in primary pediatric low-grade glioma and preclinical models. Childs Nerv Syst 2024:10.1007/s00381-024-06463-z. [PMID: 38789691 DOI: 10.1007/s00381-024-06463-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024]
Abstract
Understanding the molecular and cellular mechanisms driving pediatric low-grade glioma (pLGG)-the most prevalent brain tumor in children-is essential for the identification and evaluation of novel effective treatments. This review explores the intricate relationship between the mitogen-activated protein kinase (MAPK) pathway, oncogene-induced senescence (OIS), the senescence-associated secretory phenotype (SASP), and the tumor microenvironment (TME), integrating these elements into a unified framework termed the MAPK/OIS/SASP/TME (MOST) axis. This integrated approach seeks to deepen our understanding of pLGG and improve therapeutic interventions by examining the MOST axis' critical influence on tumor biology and response to treatment. In this review, we assess the axis' capacity to integrate various biological processes, highlighting new targets for pLGG treatment, and the need for characterized in vitro and in vivo preclinical models recapitulating pLGG's complexity to test targets. The review underscores the need for a comprehensive strategy in pLGG research, positioning the MOST axis as a pivotal approach in understanding pLGG. This comprehensive framework will open promising avenues for patient care and guide future research towards inventive treatment options.
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Affiliation(s)
- Romain Sigaud
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany.
- National Center for Tumor Diseases (NCT), Heidelberg, Germany.
| | - Tilman Brummer
- Institute, of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Centre for Biological Signaling Studies BIOSS, University of Freiburg and German Consortium for Translational Cancer Research (DKTK), Freiburg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniela Kocher
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Till Milde
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Florian Selt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany.
- National Center for Tumor Diseases (NCT), Heidelberg, Germany.
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany.
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6
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Vickery HR, Virta JM, Konstantinidou M, Arkin MR. Development of a NanoBRET assay for evaluation of 14-3-3σ molecular glues. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024:100165. [PMID: 38797286 DOI: 10.1016/j.slasd.2024.100165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 05/08/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024]
Abstract
We report the development of a 384-well formatted NanoBRET assay to characterize molecular glues of 14-3-3/client interactions in living cells. The seven isoforms of 14-3-3 are dimeric hub proteins with diverse roles including transcription factor regulation and signal transduction. 14-3-3 interacts with hundreds of client proteins to regulate their function and is therefore an ideal therapeutic target when client selectivity can be achieved. We have developed the NanoBRET system for three 14-3-3σ client proteins CRAF, TAZ, and estrogen receptor α (ERα), which represent three specific binding modes. We have measured stabilization of 14-3-3σ/client complexes by molecular glues with EC50 values between 100 nM and 1 μM in cells, which align with the EC50 values calculated by fluorescence anisotropy in vitro. Developing this NanoBRET system for the hub protein 14-3-3σ allows for a streamlined approach, bypassing multiple optimization steps in the assay development process for other 14-3-3σ clients. The NanoBRET system allows for an assessment of PPI stabilization in a more physiologically relevant, cell-based environment using full-length proteins. The method is applicable to diverse protein-protein interactions (PPIs) and offers a robust platform to explore libraries of compounds for both PPI stabilizers and inhibitors.
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Affiliation(s)
- Holly R Vickery
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco 94158, United States
| | - Johanna M Virta
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco 94158, United States
| | - Markella Konstantinidou
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco 94158, United States
| | - Michelle R Arkin
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco 94158, United States.
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7
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Rasmussen DM, Semonis MM, Greene JT, Muretta JM, Thompson AR, Toledo Ramos S, Thomas DD, Pomerantz WCK, Freedman TS, Levinson NM. Allosteric coupling asymmetry mediates paradoxical activation of BRAF by type II inhibitors. eLife 2024; 13:RP95481. [PMID: 38742856 PMCID: PMC11093583 DOI: 10.7554/elife.95481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024] Open
Abstract
The type II class of RAF inhibitors currently in clinical trials paradoxically activate BRAF at subsaturating concentrations. Activation is mediated by induction of BRAF dimers, but why activation rather than inhibition occurs remains unclear. Using biophysical methods tracking BRAF dimerization and conformation, we built an allosteric model of inhibitor-induced dimerization that resolves the allosteric contributions of inhibitor binding to the two active sites of the dimer, revealing key differences between type I and type II RAF inhibitors. For type II inhibitors the allosteric coupling between inhibitor binding and BRAF dimerization is distributed asymmetrically across the two dimer binding sites, with binding to the first site dominating the allostery. This asymmetry results in efficient and selective induction of dimers with one inhibited and one catalytically active subunit. Our allosteric models quantitatively account for paradoxical activation data measured for 11 RAF inhibitors. Unlike type II inhibitors, type I inhibitors lack allosteric asymmetry and do not activate BRAF homodimers. Finally, NMR data reveal that BRAF homodimers are dynamically asymmetric with only one of the subunits locked in the active αC-in state. This provides a structural mechanism for how binding of only a single αC-in inhibitor molecule can induce potent BRAF dimerization and activation.
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Affiliation(s)
- Damien M Rasmussen
- Department of Pharmacology, University of MinnesotaMinneapolisUnited States
- Department of Biochemistry, Molecular Biology, and Biophysics, University of MinnesotaMinneapolisUnited States
| | - Manny M Semonis
- Department of Pharmacology, University of MinnesotaMinneapolisUnited States
| | - Joseph T Greene
- Department of Pharmacology, University of MinnesotaMinneapolisUnited States
| | - Joseph M Muretta
- Department of Biochemistry, Molecular Biology, and Biophysics, University of MinnesotaMinneapolisUnited States
| | - Andrew R Thompson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of MinnesotaMinneapolisUnited States
| | | | - David D Thomas
- Department of Biochemistry, Molecular Biology, and Biophysics, University of MinnesotaMinneapolisUnited States
| | | | - Tanya S Freedman
- Department of Pharmacology, University of MinnesotaMinneapolisUnited States
- Center for Immunology, University of MinnesotaMinneapolisUnited States
- Masonic Cancer Center, University of MinnesotaMinneapolisUnited States
| | - Nicholas M Levinson
- Department of Pharmacology, University of MinnesotaMinneapolisUnited States
- Masonic Cancer Center, University of MinnesotaMinneapolisUnited States
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8
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Zhong G, Zhao Y, Zhuang D, Chung WK, Shen Y. PreMode predicts mode-of-action of missense variants by deep graph representation learning of protein sequence and structural context. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.20.581321. [PMID: 38746140 PMCID: PMC11092447 DOI: 10.1101/2024.02.20.581321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Accurate prediction of the functional impact of missense variants is important for disease gene discovery, clinical genetic diagnostics, therapeutic strategies, and protein engineering. Previous efforts have focused on predicting a binary pathogenicity classification, but the functional impact of missense variants is multi-dimensional. Pathogenic missense variants in the same gene may act through different modes of action (i.e., gain/loss-of-function) by affecting different aspects of protein function. They may result in distinct clinical conditions that require different treatments. We developed a new method, PreMode, to perform gene-specific mode-of-action predictions. PreMode models effects of coding sequence variants using SE(3)-equivariant graph neural networks on protein sequences and structures. Using the largest-to-date set of missense variants with known modes of action, we showed that PreMode reached state-of-the-art performance in multiple types of mode-of-action predictions by efficient transfer-learning. Additionally, PreMode's prediction of G/LoF variants in a kinase is consistent with inactive-active conformation transition energy changes. Finally, we show that PreMode enables efficient study design of deep mutational scans and optimization in protein engineering.
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9
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Piercey O, Tie J, Hollande F, Wong HL, Mariadason J, Desai J. BRAF V600E-Mutant Metastatic Colorectal Cancer: Current Evidence, Future Directions, and Research Priorities. Clin Colorectal Cancer 2024:S1533-0028(24)00030-6. [PMID: 38816264 DOI: 10.1016/j.clcc.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 04/24/2024] [Indexed: 06/01/2024]
Abstract
BRAFV600E-mutant metastatic colorectal cancer represents a distinct molecular phenotype known for its aggressive biological behavior, resistance to standard therapies, and poor survival rates. Improved understanding of the biology of the BRAF oncogene has led to the development of targeted therapies that have paved the way for a paradigm shift in managing this disease. However, despite significant recent advancements, responses to targeted therapies are short-lived, and several challenges remain. In this review, we discuss how progress in treating BRAFV600E-mutant metastatic colorectal cancer has been made through a better understanding of its unique biological and clinical features. We provide an overview of the evidence to support current treatment approaches and discuss critical areas of need and future research strategies that hold the potential to refine clinical practice further. We also discuss some challenging aspects of managing this disease, particularly the complexity of acquired resistance mechanisms that develop under the selective pressure of targeted therapies and rational strategies being investigated to overcome them.
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Affiliation(s)
- Oliver Piercey
- Peter MacCallum Cancer Centre, Melbourne, Australia; Centre for Cancer Research, The University of Melbourne, Melbourne, Australia; Department of Clinical Pathology, The University of Melbourne, Australia.
| | - Jeanne Tie
- Peter MacCallum Cancer Centre, Melbourne, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia; Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Frederic Hollande
- Centre for Cancer Research, The University of Melbourne, Melbourne, Australia; Department of Clinical Pathology, The University of Melbourne, Australia
| | - Hui-Li Wong
- Peter MacCallum Cancer Centre, Melbourne, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia; Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - John Mariadason
- Olivia Newton John Cancer Wellness and Research Centre, Heidelberg, Australia; School of Medicine, La Trobe University, Melbourne, Australia
| | - Jayesh Desai
- Peter MacCallum Cancer Centre, Melbourne, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
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10
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Konstantinidou M, Arkin MR. Molecular glues for protein-protein interactions: Progressing toward a new dream. Cell Chem Biol 2024:S2451-9456(24)00130-2. [PMID: 38701786 DOI: 10.1016/j.chembiol.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/08/2024] [Accepted: 04/08/2024] [Indexed: 05/05/2024]
Abstract
The modulation of protein-protein interactions with small molecules is one of the most rapidly developing areas in drug discovery. In this review, we discuss advances over the past decade (2014-2023) focusing on molecular glues (MGs)-monovalent small molecules that induce proximity, either by stabilizing native interactions or by inducing neomorphic interactions. We include both serendipitous and rational discoveries and describe the different approaches that were used to identify them. We classify the compounds in three main categories: degradative MGs, non-degradative MGs or PPI stabilizers, and MGs that induce self-association. Diverse, illustrative examples with structural data are described in detail, emphasizing the elements of molecular recognition and cooperative binding at the interface that are fundamental for a MG mechanism of action.
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Affiliation(s)
- Markella Konstantinidou
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michelle R Arkin
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, San Francisco, CA 94143, USA.
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11
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Aya F, Lanuza-Gracia P, González-Pérez A, Bonnal S, Mancini E, López-Bigas N, Arance A, Valcárcel J. Genomic deletions explain the generation of alternative BRAF isoforms conferring resistance to MAPK inhibitors in melanoma. Cell Rep 2024; 43:114048. [PMID: 38614086 DOI: 10.1016/j.celrep.2024.114048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 02/06/2024] [Accepted: 03/19/2024] [Indexed: 04/15/2024] Open
Abstract
Resistance to MAPK inhibitors (MAPKi), the main cause of relapse in BRAF-mutant melanoma, is associated with the production of alternative BRAF mRNA isoforms (altBRAFs) in up to 30% of patients receiving BRAF inhibitor monotherapy. These altBRAFs have been described as being generated by alternative pre-mRNA splicing, and splicing modulation has been proposed as a therapeutic strategy to overcome resistance. In contrast, we report that altBRAFs are generated through genomic deletions. Using different in vitro models of altBRAF-mediated melanoma resistance, we demonstrate the production of altBRAFs exclusively from the BRAF V600E allele, correlating with corresponding genomic deletions. Genomic deletions are also detected in tumor samples from melanoma and breast cancer patients expressing altBRAFs. Along with the identification of altBRAFs in BRAF wild-type and in MAPKi-naive melanoma samples, our results represent a major shift in our understanding of mechanisms leading to the generation of BRAF transcripts variants associated with resistance in melanoma.
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Affiliation(s)
- Francisco Aya
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Medical Oncology Department, Hospital Clinic, Barcelona, Spain; Institut de Investigacions Biomedicas August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Pablo Lanuza-Gracia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Abel González-Pérez
- Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Sophie Bonnal
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Estefania Mancini
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Nuria López-Bigas
- Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Ana Arance
- Medical Oncology Department, Hospital Clinic, Barcelona, Spain; Institut de Investigacions Biomedicas August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Juan Valcárcel
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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12
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Dedden D, Nitsche J, Schneider EV, Thomsen M, Schwarz D, Leuthner B, Grädler U. Cryo-EM Structures of CRAF 2/14-3-3 2 and CRAF 2/14-3-3 2/MEK1 2 Complexes. J Mol Biol 2024; 436:168483. [PMID: 38331211 DOI: 10.1016/j.jmb.2024.168483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/22/2023] [Accepted: 02/02/2024] [Indexed: 02/10/2024]
Abstract
RAF protein kinases are essential effectors in the MAPK pathway and are important cancer drug targets. Structural understanding of RAF activation is so far based on cryo-electron microscopy (cryo-EM) and X-ray structures of BRAF in different conformational states as inactive or active complexes with KRAS, 14-3-3 and MEK1. In this study, we have solved the first cryo-EM structures of CRAF2/14-3-32 at 3.4 Å resolution and CRAF2/14-3-32/MEK12 at 4.2 Å resolution using CRAF kinase domain expressed as constitutively active Y340D/Y341D mutant in insect cells. The overall architecture of our CRAF2/14-3-32 and CRAF2/14-3-32/MEK12 cryo-EM structures is highly similar to corresponding BRAF structures in complex with 14-3-3 or 14-3-3/MEK1 and represent the activated dimeric RAF conformation. Our CRAF cryo-EM structures provide additional insights into structural understanding of the activated CRAF2/14-3-32/MEK12 complex.
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Affiliation(s)
- Dirk Dedden
- Proteros biostructures GmbH, Bunsenstraße 7a, D-82152 Planegg-Martinsried, Germany
| | - Julius Nitsche
- Proteros biostructures GmbH, Bunsenstraße 7a, D-82152 Planegg-Martinsried, Germany
| | | | - Maren Thomsen
- Proteros biostructures GmbH, Bunsenstraße 7a, D-82152 Planegg-Martinsried, Germany
| | - Daniel Schwarz
- The Healthcare Business of Merck KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Birgitta Leuthner
- The Healthcare Business of Merck KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Ulrich Grädler
- The Healthcare Business of Merck KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany.
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13
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Marsiglia WM, Chow A, Khan ZM, He L, Dar AC. Live-cell target engagement of allosteric MEKi on MEK-RAF/KSR-14-3-3 complexes. Nat Chem Biol 2024; 20:373-381. [PMID: 37919548 PMCID: PMC10948974 DOI: 10.1038/s41589-023-01454-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 09/19/2023] [Indexed: 11/04/2023]
Abstract
The RAS-mitogen-activated protein kinase (MAPK) pathway includes KSR, RAF, MEK and the phospho-regulatory sensor 14-3-3. Specific assemblies among these components drive various diseases and likely dictate efficacy for numerous targeted therapies, including allosteric MEK inhibitors (MEKi). However, directly measuring drug interactions on physiological RAS-MAPK complexes in live cells has been inherently challenging to query and therefore remains poorly understood. Here we present a series of NanoBRET-based assays to quantify direct target engagement of MEKi on MEK1 and higher-order MEK1-bound complexes with ARAF, BRAF, CRAF, KSR1 and KSR2 in the presence and absence of 14-3-3 in living cells. We find distinct MEKi preferences among these complexes that can be compiled to generate inhibitor binding profiles. Further, these assays can report on the influence of the pathogenic BRAF-V600E mutant on MEKi binding. Taken together, these approaches can be used as a platform to screen for compounds intended to target specific complexes in the RAS-MAPK cascade.
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Affiliation(s)
- William M Marsiglia
- Department of Oncological Sciences, The Tisch Cancer Institute, Mount Sinai Center for Therapeutic Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Pharmacological Sciences, The Tisch Cancer Institute, Mount Sinai Center for Therapeutic Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Pharmacology and Toxicology, The University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Arthur Chow
- Department of Oncological Sciences, The Tisch Cancer Institute, Mount Sinai Center for Therapeutic Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pharmacological Sciences, The Tisch Cancer Institute, Mount Sinai Center for Therapeutic Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Program in Chemical Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zaigham M Khan
- Department of Oncological Sciences, The Tisch Cancer Institute, Mount Sinai Center for Therapeutic Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pharmacological Sciences, The Tisch Cancer Institute, Mount Sinai Center for Therapeutic Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Liu He
- Department of Oncological Sciences, The Tisch Cancer Institute, Mount Sinai Center for Therapeutic Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pharmacological Sciences, The Tisch Cancer Institute, Mount Sinai Center for Therapeutic Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Program in Chemical Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arvin C Dar
- Department of Oncological Sciences, The Tisch Cancer Institute, Mount Sinai Center for Therapeutic Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Pharmacological Sciences, The Tisch Cancer Institute, Mount Sinai Center for Therapeutic Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Program in Chemical Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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14
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Shrestha R, Carpenter TS, Van QN, Agamasu C, Tonelli M, Aydin F, Chen D, Gulten G, Glosli JN, López CA, Oppelstrup T, Neale C, Gnanakaran S, Gillette WK, Ingólfsson HI, Lightstone FC, Stephen AG, Streitz FH, Nissley DV, Turbyville TJ. Membrane lipids drive formation of KRAS4b-RAF1 RBDCRD nanoclusters on the membrane. Commun Biol 2024; 7:242. [PMID: 38418613 PMCID: PMC10902389 DOI: 10.1038/s42003-024-05916-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 02/14/2024] [Indexed: 03/02/2024] Open
Abstract
The oncogene RAS, extensively studied for decades, presents persistent gaps in understanding, hindering the development of effective therapeutic strategies due to a lack of precise details on how RAS initiates MAPK signaling with RAF effector proteins at the plasma membrane. Recent advances in X-ray crystallography, cryo-EM, and super-resolution fluorescence microscopy offer structural and spatial insights, yet the molecular mechanisms involving protein-protein and protein-lipid interactions in RAS-mediated signaling require further characterization. This study utilizes single-molecule experimental techniques, nuclear magnetic resonance spectroscopy, and the computational Machine-Learned Modeling Infrastructure (MuMMI) to examine KRAS4b and RAF1 on a biologically relevant lipid bilayer. MuMMI captures long-timescale events while preserving detailed atomic descriptions, providing testable models for experimental validation. Both in vitro and computational studies reveal that RBDCRD binding alters KRAS lateral diffusion on the lipid bilayer, increasing cluster size and decreasing diffusion. RAS and membrane binding cause hydrophobic residues in the CRD region to penetrate the bilayer, stabilizing complexes through β-strand elongation. These cooperative interactions among lipids, KRAS4b, and RAF1 are proposed as essential for forming nanoclusters, potentially a critical step in MAP kinase signal activation.
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Affiliation(s)
- Rebika Shrestha
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD, 21701, USA
| | - Timothy S Carpenter
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Que N Van
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD, 21701, USA
| | - Constance Agamasu
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD, 21701, USA
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Fikret Aydin
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - De Chen
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD, 21701, USA
| | - Gulcin Gulten
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD, 21701, USA
| | - James N Glosli
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Cesar A López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Tomas Oppelstrup
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Chris Neale
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Sandrasegaram Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - William K Gillette
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD, 21701, USA
| | - Helgi I Ingólfsson
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Felice C Lightstone
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Andrew G Stephen
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD, 21701, USA
| | - Frederick H Streitz
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Dwight V Nissley
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD, 21701, USA
| | - Thomas J Turbyville
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD, 21701, USA.
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15
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Maisonneuve P, Sahmi M, Bergeron-Labrecque F, Ma XI, Queguiner J, Arseneault G, Lefrançois M, Kurinov I, Fronzes R, Sicheri F, Therrien M. The CNK-HYP scaffolding complex promotes RAF activation by enhancing KSR-MEK interaction. Nat Struct Mol Biol 2024:10.1038/s41594-024-01233-6. [PMID: 38388830 DOI: 10.1038/s41594-024-01233-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 01/29/2024] [Indexed: 02/24/2024]
Abstract
The RAS-MAPK pathway regulates cell proliferation, differentiation and survival, and its dysregulation is associated with cancer development. The pathway minimally comprises the small GTPase RAS and the kinases RAF, MEK and ERK. Activation of RAF by RAS is notoriously intricate and remains only partially understood. There are three RAF isoforms in mammals (ARAF, BRAF and CRAF) and two related pseudokinases (KSR1 and KSR2). RAS-mediated activation of RAF depends on an allosteric mechanism driven by the dimerization of its kinase domain. Recent work on human RAFs showed that MEK binding to KSR1 promotes KSR1-BRAF heterodimerization, which leads to the phosphorylation of free MEK molecules by BRAF. Similar findings were made with the single Drosophila RAF homolog. Here we show that the fly scaffold proteins CNK and HYP stabilize the KSR-MEK interaction, which in turn enhances RAF-KSR heterodimerization and RAF activation. The cryogenic electron microscopy structure of the minimal KSR-MEK-CNK-HYP complex reveals a ring-like arrangement of the CNK-HYP complex allowing CNK to simultaneously engage KSR and MEK, thus stabilizing the binary interaction. Together, these results illuminate how CNK contributes to RAF activation by stimulating the allosteric function of KSR and highlight the diversity of mechanisms impacting RAF dimerization as well as the regulatory potential of the KSR-MEK interaction.
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Affiliation(s)
- Pierre Maisonneuve
- Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, F-33600, Pessac, France.
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.
| | - Malha Sahmi
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Montréal, Quebec, Canada
| | - Fanny Bergeron-Labrecque
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Montréal, Quebec, Canada
| | - Xianjie Iris Ma
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Juliette Queguiner
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Montréal, Quebec, Canada
| | - Geneviève Arseneault
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Montréal, Quebec, Canada
| | - Martin Lefrançois
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Montréal, Quebec, Canada
| | - Igor Kurinov
- Department of Chemistry and Chemical Biology, Cornell University, NE-CAT, Argonne, IL, USA
| | - Rémi Fronzes
- Institut Européen de Chimie et Biologie, Université de Bordeaux-CNRS (UMR 5234), Pessac, France
| | - Frank Sicheri
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.
- Departments of Molecular Genetics and Biochemistry, University of Toronto, Toronto, Ontario, Canada.
| | - Marc Therrien
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Montréal, Quebec, Canada.
- Département de pathologie et biologie cellulaire, Université de Montréal, Montréal, Quebec, Canada.
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16
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Deng L, Yang Y, Huang J. [Progress of BRAF Gene Alteration in Non-small Cell Lung Cancer]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2024; 27:73-80. [PMID: 38296628 PMCID: PMC10895288 DOI: 10.3779/j.issn.1009-3419.2024.101.01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Indexed: 02/02/2024]
Abstract
V-Raf murine sarcoma viral oncogene homolog B (BRAF) alteration is one of the most essential driver genes of non-small cell lung cancer (NSCLC). BRAF encodes serine/threonine protein kinases, and its mutations typically lead to protein compositional activation, thereby activating the mitogen-activated protein kinase kinase (MEK) signaling pathway. A promising new approach for the treatment of mutated BRAF and/or downstream MEK may provide customized treatment opportunities for BRAF driven NSCLC patients. However, combination therapy is necessary to overcome the difficulties such as short duration of benefit, poor therapeutic effect of non-V600 BRAF mutations and susceptibility to drug resistance. This article reviewed the progress in structural characteristics, related signaling pathways, mutation types of BRAF gene, and the clinical pathological relationship between BRAF mutations and NSCLC, as well as the therapy, in order to provide more evidences for clinical doctors to make treatment decisions.
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Affiliation(s)
- Libian Deng
- Department of Pathology, The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang 524002, China
| | - Yaxian Yang
- Guangzhou Huayin Health Medical Group Co., Ltd, Guangzhou 510700, China
| | - Jian Huang
- Department of Pathological Diagnosis and Research Center, The Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China
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17
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Trebino TE, Markusic B, Nan H, Banerjee S, Wang Z. Unveiling the domain-specific and RAS isoform-specific details of BRAF kinase regulation. eLife 2023; 12:RP88836. [PMID: 38150000 PMCID: PMC10752582 DOI: 10.7554/elife.88836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023] Open
Abstract
BRAF is a key member in the MAPK signaling pathway essential for cell growth, proliferation, and differentiation. Mutant BRAF is often the underlying cause of various types of cancer and mutant RAS, the upstream regulator of BRAF, is a driver of up to one-third of all cancers. BRAF interacts with RAS and undergoes a conformational change from an inactive, autoinhibited monomer to an active dimer, which propagates downstream signaling. Because of BRAF's complex regulation mechanism, the exact order and magnitude of its activation steps have yet to be confirmed experimentally. By studying the inter- and intramolecular interactions of BRAF, we unveil the domain-specific and isoform-specific details of BRAF regulation through pulldown assays, open surface plasmon resonance (OpenSPR), and hydrogen-deuterium exchange mass spectrometry (HDX-MS). We demonstrate that the BRAF specific region (BSR) and cysteine rich domain (CRD) play a crucial role in regulating the activation of BRAF in a RAS isoform-specific manner. Moreover, we quantified the binding affinities between BRAF N-terminal and kinase domains (KD) to reveal their individual roles in autoinhibition. Our findings also indicate that oncogenic BRAF-KDD594G mutant has a lower affinity for the N-terminal domains, implicating that pathogenic BRAF acts through decreased propensity for autoinhibition. Collectively, our study provides valuable insight into the activation mechanism of BRAF kinase to guide the development of new therapeutic strategies for cancer treatment.
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Affiliation(s)
| | - Borna Markusic
- Rowan UniversityGlassboroUnited States
- Max Planck Institute of BiophysicsFrankfurt am MainGermany
| | - Haihan Nan
- Rowan UniversityGlassboroUnited States
- School of Laboratory Medicine and Life Science, Wenzhou Medical UniversityWenzhouChina
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18
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Paul JW, Muratcioğlu S, Kuriyan J. A Fluorescence-Based Sensor for Calibrated Measurement of Protein Kinase Stability in Live Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570636. [PMID: 38106090 PMCID: PMC10723428 DOI: 10.1101/2023.12.07.570636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
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 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 monitor the fluorescence of kinases fused to a fluorescent protein relative to that of a co-expressed reference fluorescent protein. 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 (SH2) and Src-homology 3 (SH3) 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.
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Affiliation(s)
- Joseph W. Paul
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720 USA
- California Institute for Quantitative Bioscience (QB3), University of California, Berkeley, CA, 94720 USA
| | - Serena Muratcioğlu
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232 USA
| | - John Kuriyan
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232 USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37240 USA
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19
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Cabrera-Montes J, Aguirre DT, Viñas-López J, Lorente-Herraiz L, Recio-Poveda L, Albiñana V, Pérez-Pérez J, Botella LM, Cuesta AM. Mutation in Chek2 triggers von Hippel-Lindau hemangioblastoma growth. Acta Neurochir (Wien) 2023; 165:4241-4251. [PMID: 37843608 PMCID: PMC10739370 DOI: 10.1007/s00701-023-05825-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/05/2023] [Indexed: 10/17/2023]
Abstract
PURPOSE Von Hippel-Lindau (VHL) is a rare inherited disease mainly characterized by the growth of tumours, predominantly hemangioblastomas (Hbs) in the CNS and retina, and renal carcinomas. The natural history of VHL disease is variable, differing in the age of onset and its penetrance, even among relatives. Unfortunately, sometimes VHL shows more severe than average: the onset starts in adolescence, and surgeries are required almost every year. In these cases, the factor that triggers the appearance and growth of Hbs usually remains unknown, although additional mutations are suspected. METHODS We present the case of a VHL patient whose first surgery was at 13 years of age. Then, along his next 8 years, he has undergone 5 surgeries for resection of 10 CNS Hbs. To clarify this severe VHL condition, DNA from a CNS Hb and white blood cells (WBC) was sequenced using next-generation sequencing technology. RESULTS Massive DNA sequencing of the WBC (germ line) revealed a pathogenic mutation in CHEK2 and the complete loss of a VHL allele (both tumour suppressors). Moreover, in the tumour sample, several mutations, in BRAF1 and PTPN11 were found. Familiar segregation studies showed that CHEK2 mutation was in the maternal lineage, while VHL was inherited by paternal lineage. CONCLUSIONS Finally, clinical history correlated to the different genotypes in the family, concluding that the severity of these VHL manifestations are due to both, VHL-and-CHEK2 mutations. This case report aims to notice the importance of deeper genetic analyses, in inherited rare diseases, to uncover non-expected mutations.
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Affiliation(s)
- Jorge Cabrera-Montes
- Department of Neurosurgery, Sanitary Investigation Institute - Fundación Jiménez Diaz (IIS-FJD), Fundación Jiménez Díaz University Hospital, Madrid, Spain
| | - Daniel T Aguirre
- Department of Neurosurgery, Sanitary Investigation Institute - Fundación Jiménez Diaz (IIS-FJD), Fundación Jiménez Díaz University Hospital, Madrid, Spain
| | | | - Laura Lorente-Herraiz
- Department of Molecular Biomedicine, Center for Biological Research Margarita Salas, CIB-CSIC, Madrid, Spain
- Rare Diseases Networking Biomedical Research Centre (CIBERER), Unit, 707, Madrid, Spain
| | - Lucía Recio-Poveda
- Department of Molecular Biomedicine, Center for Biological Research Margarita Salas, CIB-CSIC, Madrid, Spain
- Rare Diseases Networking Biomedical Research Centre (CIBERER), Unit, 707, Madrid, Spain
| | - Virginia Albiñana
- Department of Molecular Biomedicine, Center for Biological Research Margarita Salas, CIB-CSIC, Madrid, Spain
- Rare Diseases Networking Biomedical Research Centre (CIBERER), Unit, 707, Madrid, Spain
| | | | - Luisa M Botella
- Department of Molecular Biomedicine, Center for Biological Research Margarita Salas, CIB-CSIC, Madrid, Spain.
- Rare Diseases Networking Biomedical Research Centre (CIBERER), Unit, 707, Madrid, Spain.
| | - Angel M Cuesta
- Rare Diseases Networking Biomedical Research Centre (CIBERER), Unit, 707, Madrid, Spain.
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Complutense University of Madrid, Madrid, Spain.
- Health Research Institute of the Clínico San Carlos Hospital (IdISSC), Madrid, Spain.
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20
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Rasmussen DM, Semonis MM, Greene JT, Muretta JM, Thompson AR, Ramos ST, Thomas DD, Pomerantz WC, Freedman TS, Levinson NM. Allosteric coupling asymmetry mediates paradoxical activation of BRAF by type II inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.18.536450. [PMID: 37131649 PMCID: PMC10153139 DOI: 10.1101/2023.04.18.536450] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The type II class of RAF inhibitors currently in clinical trials paradoxically activate BRAF at subsaturating concentrations. Activation is mediated by induction of BRAF dimers, but why activation rather than inhibition occurs remains unclear. Using biophysical methods tracking BRAF dimerization and conformation we built an allosteric model of inhibitor-induced dimerization that resolves the allosteric contributions of inhibitor binding to the two active sites of the dimer, revealing key differences between type I and type II RAF inhibitors. For type II inhibitors the allosteric coupling between inhibitor binding and BRAF dimerization is distributed asymmetrically across the two dimer binding sites, with binding to the first site dominating the allostery. This asymmetry results in efficient and selective induction of dimers with one inhibited and one catalytically active subunit. Our allosteric models quantitatively account for paradoxical activation data measured for 11 RAF inhibitors. Unlike type II inhibitors, type I inhibitors lack allosteric asymmetry and do not activate BRAF homodimers. Finally, NMR data reveal that BRAF homodimers are dynamically asymmetric with only one of the subunits locked in the active αC-in state. This provides a structural mechanism for how binding of only a single αC-in inhibitor molecule can induce potent BRAF dimerization and activation.
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Affiliation(s)
- Damien M. Rasmussen
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, 55455
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455
| | - Manny M. Semonis
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, 55455
| | - Joseph T. Greene
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, 55455
| | - Joseph M. Muretta
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455
| | - Andrew R. Thompson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455
| | | | - David D. Thomas
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455
| | | | - Tanya S. Freedman
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, 55455
- Center for Immunology, University of Minnesota, Minneapolis, MN, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455
| | - Nicholas M. Levinson
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455
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21
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Martin-Vega A, Cobb MH. Navigating the ERK1/2 MAPK Cascade. Biomolecules 2023; 13:1555. [PMID: 37892237 PMCID: PMC10605237 DOI: 10.3390/biom13101555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
The RAS-ERK pathway is a fundamental signaling cascade crucial for many biological processes including proliferation, cell cycle control, growth, and survival; common across all cell types. Notably, ERK1/2 are implicated in specific processes in a context-dependent manner as in stem cells and pancreatic β-cells. Alterations in the different components of this cascade result in dysregulation of the effector kinases ERK1/2 which communicate with hundreds of substrates. Aberrant activation of the pathway contributes to a range of disorders, including cancer. This review provides an overview of the structure, activation, regulation, and mutational frequency of the different tiers of the cascade; with a particular focus on ERK1/2. We highlight the importance of scaffold proteins that contribute to kinase localization and coordinate interaction dynamics of the kinases with substrates, activators, and inhibitors. Additionally, we explore innovative therapeutic approaches emphasizing promising avenues in this field.
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Affiliation(s)
- Ana Martin-Vega
- Department of Pharmacology, UT Southwestern Medical Center, 6001 Forest Park Rd., Dallas, TX 75390, USA;
| | - Melanie H. Cobb
- Department of Pharmacology, UT Southwestern Medical Center, 6001 Forest Park Rd., Dallas, TX 75390, USA;
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, 6001 Forest Park Rd., Dallas, TX 75390, USA
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22
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Mendiratta G, Stites E. Theoretical analysis reveals a role for RAF conformational autoinhibition in paradoxical activation. eLife 2023; 12:e82739. [PMID: 37823369 PMCID: PMC10627510 DOI: 10.7554/elife.82739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/10/2023] [Indexed: 10/13/2023] Open
Abstract
RAF kinase inhibitors can, under certain conditions, increase RAF kinase signaling. This process, which is commonly referred to as 'paradoxical activation' (PA), is incompletely understood. We use mathematical and computational modeling to investigate PA and derive rigorous analytical expressions that illuminate the underlying mechanism of this complex phenomenon. We find that conformational autoinhibition modulation by a RAF inhibitor could be sufficient to create PA. We find that experimental RAF inhibitor drug dose-response data that characterize PA across different types of RAF inhibitors are best explained by a model that includes RAF inhibitor modulation of three properties: conformational autoinhibition, dimer affinity, and drug binding within the dimer (i.e., negative cooperativity). Overall, this work establishes conformational autoinhibition as a robust mechanism for RAF inhibitor-driven PA based solely on equilibrium dynamics of canonical interactions that comprise RAF signaling and inhibition.
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Affiliation(s)
- Gaurav Mendiratta
- Integrative Biology Laboratory, Salk Institute for Biological StudiesLa JollaUnited States
| | - Edward Stites
- Department of Laboratory Medicine, Yale UniversityNew HavenUnited States
- Yale Cancer Center, Yale School of MedicineNew HavenUnited States
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23
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Polo-Cuadrado E, López-Cuellar L, Acosta-Quiroga K, Rojas-Peña C, Brito I, Cisterna J, Trilleras J, Alderete JB, Duarte Y, Gutiérrez M. Comprehensive analysis of crystal structure, spectroscopic properties, quantum chemical insights, and molecular docking studies of two pyrazolopyridine compounds: potential anticancer agents. RSC Adv 2023; 13:30118-30128. [PMID: 37849708 PMCID: PMC10578360 DOI: 10.1039/d3ra04874h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/24/2023] [Indexed: 10/19/2023] Open
Abstract
In this study, two pyrazolo[3,4-b]pyridine derivatives (4a and 4b) were grown using a slow evaporation solution growth technique and characterized by FT-IR, HRMS, 1H/13C NMR spectroscopy, and X-ray crystallography. The 4a and 4b structures crystallized in monoclinic and triclinic systems with space groups P21/n and P1̄, respectively. Theoretical calculations were performed at the DFT/B3LYP level for the optimized geometries. The results were in excellent agreement with the experimental data (spectroscopic and XRD). This investigation encompasses molecular modeling studies including Hirshfeld surface analysis, energy framework calculations, and frontier molecular orbital analysis. Intermolecular interactions within the crystal structures of the compounds were explored through Hirshfeld surface analysis, which revealed the notable presence of hydrogen bonding and hydrophobic interactions. This insight provides valuable information on the structural stability and potential solubility characteristics of these compounds. The research was extended to docking analysis with eight distinct kinases (BRAF, HER2, CSF1R, MEK2, PDGFRA, JAK, AKT1, and AKT2). The results of this analysis demonstrate that both 4a and 4b interact effectively with the kinase-binding sites through a combination of hydrophobic interactions and hydrogen bonding. Compound 4a had the best affinity for proteins; this is related to the fact that the compound is not rigid and has a small size, allowing it to sit well at any binding site. This study contributes to the advancement of kinase inhibitor research and offers potential avenues for the development of new therapeutic agents for cancer treatment.
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Affiliation(s)
- Efraín Polo-Cuadrado
- Laboratorio Síntesis Orgánica y Actividad Biológica (LSO-Act-Bio), Instituto de Química de Recursos Naturales, Universidad de Talca Casilla 747 Talca 3460000 Chile
| | - Lorena López-Cuellar
- Laboratorio Síntesis Orgánica y Actividad Biológica (LSO-Act-Bio), Instituto de Química de Recursos Naturales, Universidad de Talca Casilla 747 Talca 3460000 Chile
- Universidad de la Amazonia, Programa de Química Cl. 17 Diagonal 17 con, Cra. 3F Florencia 180001 Colombia
| | - Karen Acosta-Quiroga
- Doctorado en Química, Departamento de Química Inorgánica y Analítica, Universidad de Chile Santiago Chile
| | - Cristian Rojas-Peña
- Doctorado en Química, Departamento de Química Inorgánica y Analítica, Universidad de Chile Santiago Chile
| | - Iván Brito
- Departamento de Química, Facultad de Ciencias Básicas, Universidad de Antofagasta Avenida. Universidad de Antofagasta, Campus Coloso Antofagasta 02800 Chile
| | - Jonathan Cisterna
- Departamento de Química, Facultad de Ciencias, Universidad Católica del Norte Sede Casa Central, Av. Angamos 0610 Antofagasta Chile
| | - Jorge Trilleras
- Grupo de Investigación en Compuestos Heterocíclicos, Universidad del Atlántico Puerto Colombia 081007 Colombia
| | - Joel B Alderete
- Instituto de Química de Recursos Naturales (IQRN), Universidad de Talca Avenida Lircay S/N, Casilla 747 Talca Chile
| | - Yorley Duarte
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad, Andrés Bello Av. Republica 330 Santiago 8370146 Chile
- Interdisciplinary Centre for Neuroscience of Valparaíso, Facultad de Ciencias, Universidad de Valparaíso Valparaíso 2381850 Chile
| | - Margarita Gutiérrez
- Laboratorio Síntesis Orgánica y Actividad Biológica (LSO-Act-Bio), Instituto de Química de Recursos Naturales, Universidad de Talca Casilla 747 Talca 3460000 Chile
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24
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Yu A, Nguyen DH, Nguyen TJ, Wang Z. A novel phosphorylation site involved in dissociating RAF kinase from the scaffolding protein 14-3-3 and disrupting RAF dimerization. J Biol Chem 2023; 299:105188. [PMID: 37625591 PMCID: PMC10520314 DOI: 10.1016/j.jbc.2023.105188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 08/01/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Rapidly accelerated fibrosarcoma (ARAF, BRAF, CRAF) kinase is central to the MAPK pathway (RAS-RAF-MEK-ERK). Inactive RAF kinase is believed to be monomeric, autoinhibited, and cytosolic, while activated RAF is recruited to the membrane via RAS-GTP, leading to the relief of autoinhibition, phosphorylation of key regulatory sites, and dimerization of RAF protomers. Although it is well known that active and inactive BRAF have differential phosphorylation sites that play a crucial role in regulating BRAF, key details are still missing. In this study, we report the characterization of a novel phosphorylation site, BRAFS732 (equivalent in CRAFS624), located in proximity to the C-terminus binding motif for the 14-3-3 scaffolding protein. At the C terminus, 14-3-3 binds to BRAFpS729 (CRAFpS621) and enhances RAF dimerization. We conducted mutational analysis of BRAFS732A/E and CRAFS624A/E and revealed that the phosphomimetic S→E mutant decreases 14-3-3 association and RAF dimerization. In normal cell signaling, dimerized RAF phosphorylates MEK1/2, which is observed in the phospho-deficient S→A mutant. Our results suggest that phosphorylation and dephosphorylation of this site fine-tune the association of 14-3-3 and RAF dimerization, ultimately impacting MEK phosphorylation. We further characterized the BRAF homodimer and BRAF:CRAF heterodimer and identified a correlation between phosphorylation of this site with drug sensitivity. Our work reveals a novel negative regulatory role for phosphorylation of BRAFS732 and CRAFS624 in decreasing 14-3-3 association, dimerization, and MEK phosphorylation. These findings provide insight into the regulation of the MAPK pathway and may have implications for cancers driven by mutations in the pathway.
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Affiliation(s)
- Alison Yu
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, New Jersey, USA
| | - Duc Huy Nguyen
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, New Jersey, USA
| | - Thomas Joseph Nguyen
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, New Jersey, USA
| | - Zhihong Wang
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, New Jersey, USA.
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25
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Trebino T, Markusic B, Nan H, Banerjee S, Wang Z. Unveiling the Domain-Specific and RAS Isoform-Specific Details of BRAF Regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.538112. [PMID: 37163002 PMCID: PMC10168249 DOI: 10.1101/2023.04.24.538112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
BRAF is a key member in the MAPK signaling pathway essential for cell growth, proliferation, and differentiation. Dysregulation or mutation of BRAF is often the underlying cause of various types of cancer. RAS, a small GTPase protein that acts upstream of BRAF, has been identified as a driver of up to one-third of all cancers. When BRAF interacts with RAS via the RAS binding domain (RBD) and membrane recruitment, BRAF undergoes a conformational change from an inactive, autoinhibited monomer to an active dimer and subsequently phosphorylates MEK to propagate the signal. Despite the central role of BRAF in cellular signaling, the exact order and magnitude of its activation steps has yet to be confirmed experimentally. By studying the inter- and intramolecular interactions of BRAF, we unveil the domain-specific and isoform-specific details of BRAF regulation. We employed pulldown assays, open surface plasmon resonance (OpenSPR), and hydrogen-deuterium exchange mass spectrometry (HDX-MS) to investigate the roles of the regulatory regions in BRAF activation and autoinhibition. Our results demonstrate that the BRAF specific region (BSR) and cysteine rich domain (CRD) play a crucial role in regulating the activity of BRAF. Moreover, we quantified the autoinhibitory binding affinities between the N-terminal domains and the kinase domain (KD) of BRAF and revealed the individual roles of the BRAF regulatory domains. Additionally, our findings provide evidence that the BSR negatively regulates BRAF activation in a RAS isoform-specific manner. Our findings also indicate that oncogenic BRAF-KDD594G mutant has a lower affinity for the regulatory domains, implicating that pathogenic BRAF acts through decreased propensity for autoinhibition. Collectively, our study provides valuable insights into the activation mechanism of BRAF kinase and may help to guide the development of new therapeutic strategies for cancer treatment.
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Affiliation(s)
- Tarah Trebino
- Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, USA
| | - Borna Markusic
- Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, USA
- Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Haihan Nan
- Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, USA
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Shrhea Banerjee
- Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, USA
| | - Zhihong Wang
- Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, USA
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26
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Lauinger M, Christen D, Klar RFU, Roubaty C, Heilig CE, Stumpe M, Knox JJ, Radulovich N, Tamblyn L, Xie IY, Horak P, Forschner A, Bitzer M, Wittel UA, Boerries M, Ball CR, Heining C, Glimm H, Fröhlich M, Hübschmann D, Gallinger S, Fritsch R, Fröhling S, O'Kane GM, Dengjel J, Brummer T. BRAF Δβ3-αC in-frame deletion mutants differ in their dimerization propensity, HSP90 dependence, and druggability. SCIENCE ADVANCES 2023; 9:eade7486. [PMID: 37656784 DOI: 10.1126/sciadv.ade7486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 08/02/2023] [Indexed: 09/03/2023]
Abstract
In-frame BRAF exon 12 deletions are increasingly identified in various tumor types. The resultant BRAFΔβ3-αC oncoproteins usually lack five amino acids in the β3-αC helix linker and sometimes contain de novo insertions. The dimerization status of BRAFΔβ3-αC oncoproteins, their precise pathomechanism, and their direct druggability by RAF inhibitors (RAFi) has been under debate. Here, we functionally characterize BRAFΔLNVTAP>F and two novel mutants, BRAFdelinsFS and BRAFΔLNVT>F, and compare them with other BRAFΔβ3-αC oncoproteins. We show that BRAFΔβ3-αC oncoproteins not only form stable homodimers and large multiprotein complexes but also require dimerization. Nevertheless, details matter as aromatic amino acids at the deletion junction of some BRAFΔβ3-αC oncoproteins, e.g., BRAFΔLNVTAP>F, increase their stability and dimerization propensity while conferring resistance to monomer-favoring RAFi such as dabrafenib or HSP 90/CDC37 inhibition. In contrast, dimer-favoring inhibitors such as naporafenib inhibit all BRAFΔβ3-αC mutants in cell lines and patient-derived organoids, suggesting that tumors driven by such oncoproteins are vulnerable to these compounds.
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Affiliation(s)
- Manuel Lauinger
- Institute of Molecular Medicine, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Daniel Christen
- Institute of Molecular Medicine, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), partner site Freiburg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Rhena F U Klar
- Institute of Molecular Medicine, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), partner site Freiburg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Freeze-O Organoid Bank, University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of Internal Medicine I (Hematology, Oncology, and Stem Cell Transplantation), University Hospital of Freiburg, Freiburg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Carole Roubaty
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Christoph E Heilig
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Michael Stumpe
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Jennifer J Knox
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Nikolina Radulovich
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Laura Tamblyn
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Irene Y Xie
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Peter Horak
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Andrea Forschner
- Department of Dermatology, University Hospital of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University, Tübingen, Germany
| | - Michael Bitzer
- German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University, Tübingen, Germany
- Center for Personalized Medicine Tübingen, Eberhard Karls University, Tübingen, Germany
- Department of Internal Medicine I, Eberhard-Karls University, Tübingen, Germany
| | - Uwe A Wittel
- Department of General and Visceral Surgery, University of Freiburg Medical Center, Faculty of Medicine, 79106 Freiburg, Germany
| | - Melanie Boerries
- German Cancer Consortium (DKTK), partner site Freiburg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Comprehensive Cancer Center Freiburg (CCCF), Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Claudia R Ball
- Department for Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- Technische Universität Dresden, Faculty of Biology, Technische Universität Dresden, Dresden, Germany
| | - Christoph Heining
- Department for Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
| | - Hanno Glimm
- Department for Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- Translational Functional Cancer Genomics, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martina Fröhlich
- Computational Oncology Group, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Hübschmann
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Computational Oncology Group, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Pattern Recognition and Digital Medicine Group, Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
| | - Steven Gallinger
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ralph Fritsch
- Department of Internal Medicine I (Hematology, Oncology, and Stem Cell Transplantation), University Hospital of Freiburg, Freiburg, Germany
- Department of Medical Oncology and Haematology, University Hospital of Zurich, Zurich, Switzerland
| | - Stefan Fröhling
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Grainne M O'Kane
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jörn Dengjel
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Tilman Brummer
- Institute of Molecular Medicine, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- German Cancer Consortium (DKTK), partner site Freiburg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Freeze-O Organoid Bank, University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Comprehensive Cancer Center Freiburg (CCCF), Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Center for Biological Signalling Studies BIOSS, University of Freiburg, 79104 Freiburg, Germany
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27
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Townley R, Deniaud A, Stacy KS, Torres CSR, Cheraghi F, Wicker NB, de la Cova CC. The E3/E4 ubiquitin ligase UFD-2 suppresses normal and oncogenic signaling mediated by a Raf ortholog in Caenorhabditis elegans. Sci Signal 2023; 16:eabq4355. [PMID: 37643243 PMCID: PMC10656100 DOI: 10.1126/scisignal.abq4355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 08/10/2023] [Indexed: 08/31/2023]
Abstract
Signaling by the kinase cascade composed of Raf, MEK, and ERK is critical for animal development and is often inappropriately activated in human malignancies. We sought to identify factors that control signaling mediated by the Caenorhabditis elegans Raf ortholog LIN-45. A genetic screen showed that the degradation of LIN-45 required the E3/E4 ubiquitin ligase UFD-2. Both UFD-2 and its partner, the ATP-dependent segregase CDC-48, were required for the developmental regulation of LIN-45 protein abundance. We showed that UFD-2 acted in the same pathway as the E3 ubiquitin ligase SCFSEL-10 to decrease LIN-45 abundance in cells in which Raf-MEK-ERK signaling was most highly active. UFD-2 also reduced the protein abundance of activated LIN-45 carrying a mutation equivalent to the cancer-associated BRAF(V600E) variant. Our structure-function studies showed that the disruption of LIN-45 domains that mediate protein-protein interactions, including the conserved cysteine-rich domain and 14-3-3 binding motifs, were required for UFD-2-independent degradation of LIN-45. We propose a model in which UFD-2 and CDC-48 act downstream of SCFSEL-10 to remove LIN-45 from its protein interaction partners and facilitate proteasomal targeting and degradation. These findings imply that UFD-2 and CDC-48 may be important for Raf degradation during normal and oncogenic Ras and MAPK signaling in mammalian cells.
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Affiliation(s)
- Robert Townley
- Department of Biological Sciences, University of Wisconsin-Milwaukee; Milwaukee, Wisconsin, 53201 USA
| | - Augustin Deniaud
- Department of Biological Sciences, University of Wisconsin-Milwaukee; Milwaukee, Wisconsin, 53201 USA
| | - Kennedy S. Stacy
- Department of Biological Sciences, University of Wisconsin-Milwaukee; Milwaukee, Wisconsin, 53201 USA
| | | | - Fatemeh Cheraghi
- Department of Biological Sciences, University of Wisconsin-Milwaukee; Milwaukee, Wisconsin, 53201 USA
| | - Nicole B. Wicker
- Department of Biological Sciences, University of Wisconsin-Milwaukee; Milwaukee, Wisconsin, 53201 USA
| | - Claire C. de la Cova
- Department of Biological Sciences, University of Wisconsin-Milwaukee; Milwaukee, Wisconsin, 53201 USA
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28
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Singh A, Sonawane P, Kumar A, Singh H, Naumovich V, Pathak P, Grishina M, Khalilullah H, Jaremko M, Emwas AH, Verma A, Kumar P. Challenges and Opportunities in the Crusade of BRAF Inhibitors: From 2002 to 2022. ACS OMEGA 2023; 8:27819-27844. [PMID: 37576670 PMCID: PMC10413849 DOI: 10.1021/acsomega.3c00332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 02/27/2023] [Indexed: 08/15/2023]
Abstract
Serine/threonine-protein kinase B-Raf (BRAF; RAF = rapidly accelerated fibrosarcoma) plays an important role in the mitogen-activated protein kinase (MAPK) signaling cascade. Somatic mutations in the BRAF gene were first discovered in 2002 by Davies et al., which was a major breakthrough in cancer research. Subsequently, three different classes of BRAF mutants have been discovered. This class includes class I monomeric mutants (BRAFV600), class II BRAF homodimer mutants (non-V600), and class III BRAF heterodimers (non-V600). Cancers caused by these include melanoma, thyroid cancer, ovarian cancer, colorectal cancer, nonsmall cell lung cancer, and others. In this study, we have highlighted the major binding pockets in BRAF protein, their active and inactive conformations with inhibitors, and BRAF dimerization and its importance in paradoxical activation and BRAF mutation. We have discussed the first-, second-, and third-generation drugs approved by the Food and Drug Administration and drugs under clinical trials with all four different binding approaches with DFG-IN/OUT and αC-IN/OUT for BRAF protein. We have investigated particular aspects and difficulties with all three generations of inhibitors. Finally, this study has also covered recent developments in synthetic BRAF inhibitors (from their discovery in 2002 to 2022), their unique properties, and importance in inhibiting BRAF mutants.
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Affiliation(s)
- Ankit
Kumar Singh
- Department
of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda 151401, India
| | - Pankaj Sonawane
- Department
of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda 151401, India
| | - Adarsh Kumar
- Department
of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda 151401, India
| | - Harshwardhan Singh
- Department
of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda 151401, India
| | - Vladislav Naumovich
- Laboratory
of Computational Modeling of Drugs, Higher Medical and Biological
School, South Ural State University, Chelyabinsk 454008, Russia
| | - Prateek Pathak
- Laboratory
of Computational Modeling of Drugs, Higher Medical and Biological
School, South Ural State University, Chelyabinsk 454008, Russia
| | - Maria Grishina
- Laboratory
of Computational Modeling of Drugs, Higher Medical and Biological
School, South Ural State University, Chelyabinsk 454008, Russia
| | - Habibullah Khalilullah
- Department
of Pharmaceutical Chemistry and Pharmacognosy, Unaizah College of
Pharmacy, Qassim University, Unayzah 51911, Saudi Arabia
| | - Mariusz Jaremko
- Smart-Health
Initiative and Red Sea Research Center, Division of Biological and
Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Abdul-Hamid Emwas
- Core
Laboratories, King Abdullah University of
Science and Technology, Thuwal 23955-6900, Saudi
Arabia
| | - Amita Verma
- Bioorganic
and Medicinal Chemistry Research Laboratory, Department of Pharmaceutical
Sciences, Sam Higginbottom University of
Agriculture, Technology and Sciences, Prayagraj 211007, India
| | - Pradeep Kumar
- Department
of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda 151401, India
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29
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Park E, Rawson S, Schmoker A, Kim BW, Oh S, Song K, Jeon H, Eck MJ. Cryo-EM structure of a RAS/RAF recruitment complex. Nat Commun 2023; 14:4580. [PMID: 37516774 PMCID: PMC10387098 DOI: 10.1038/s41467-023-40299-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 07/19/2023] [Indexed: 07/31/2023] Open
Abstract
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.
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Affiliation(s)
- Eunyoung Park
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Pfizer R&D Center, 3200 Walnut St, Boulder, CO, 80301, USA
| | - Shaun Rawson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Anna Schmoker
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Byeong-Won Kim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- New Drug Development Center, Osong Medical Innovation Foundation, Cheongju, Chungbuk, 28160, Republic of Korea
| | - Sehee Oh
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Kangkang Song
- Department of Biochemistry & Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation St, Worcester, MA, 01605, USA
| | - Hyesung Jeon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
| | - Michael J Eck
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
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30
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Chessel A, De Crozé N, Molina MD, Taberner L, Dru P, Martin L, Lepage T. RAS-independent ERK activation by constitutively active KSR3 in non-chordate metazoa. Nat Commun 2023; 14:3970. [PMID: 37407549 DOI: 10.1038/s41467-023-39606-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 06/21/2023] [Indexed: 07/07/2023] Open
Abstract
During early development of the sea urchin embryo, activation of ERK signalling in mesodermal precursors is not triggered by extracellular RTK ligands but by a cell-autonomous, RAS-independent mechanism that was not understood. We discovered that in these cells, ERK signalling is activated through the transcriptional activation of a gene encoding a protein related to Kinase Suppressor of Ras, that we named KSR3. KSR3 belongs to a family of catalytically inactive allosteric activators of RAF. Phylogenetic analysis revealed that genes encoding kinase defective KSR3 proteins are present in most non-chordate metazoa but have been lost in flies and nematodes. We show that the structure of KSR3 factors resembles that of several oncogenic human RAF mutants and that KSR3 from echinoderms, cnidarians and hemichordates activate ERK signalling independently of RAS when overexpressed in cultured cells. Finally, we used the sequence of KSR3 factors to identify activating mutations of human B-RAF. These findings reveal key functions for this family of factors as activators of RAF in RAS-independent ERK signalling in invertebrates. They have implications on the evolution of the ERK signalling pathway and suggest a mechanism for its co-option in the course of evolution.
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Affiliation(s)
- Aline Chessel
- Institut de Biologie Valrose CNRS, Université Côte d'Azur, Nice, France
| | - Noémie De Crozé
- Institut de Biologie Valrose CNRS, Université Côte d'Azur, Nice, France
| | - Maria Dolores Molina
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
| | - Laura Taberner
- Institut de Biologie Valrose CNRS, Université Côte d'Azur, Nice, France
| | - Philippe Dru
- CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Institut de la Mer de Villefranche, 181 Chemin du Lazaret, 06230, Villefranche-sur-Mer, France
| | - Luc Martin
- Institut de Biologie Valrose CNRS, Université Côte d'Azur, Nice, France
| | - Thierry Lepage
- Institut de Biologie Valrose CNRS, Université Côte d'Azur, Nice, France.
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31
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Rohrer L, Spohr C, Beha C, Griffin R, Braun S, Halbach S, Brummer T. Analysis of RAS and drug induced homo- and heterodimerization of RAF and KSR1 proteins in living cells using split Nanoluc luciferase. Cell Commun Signal 2023; 21:136. [PMID: 37316874 DOI: 10.1186/s12964-023-01146-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 04/27/2023] [Indexed: 06/16/2023] Open
Abstract
The dimerization of RAF kinases represents a key event in their activation cycle and in RAS/ERK pathway activation. Genetic, biochemical and structural approaches provided key insights into this process defining RAF signaling output and the clinical efficacy of RAF inhibitors (RAFi). However, methods reporting the dynamics of RAF dimerization in living cells and in real time are still in their infancy. Recently, split luciferase systems have been developed for the detection of protein-protein-interactions (PPIs), incl. proof-of-concept studies demonstrating the heterodimerization of the BRAF and RAF1 isoforms. Due to their small size, the Nanoluc luciferase moieties LgBiT and SmBiT, which reconstitute a light emitting holoenzyme upon fusion partner promoted interaction, appear as well-suited to study RAF dimerization. Here, we provide an extensive analysis of the suitability of the Nanoluc system to study the homo- and heterodimerization of BRAF, RAF1 and the related KSR1 pseudokinase. We show that KRASG12V promotes the homo- and heterodimerization of BRAF, while considerable KSR1 homo- and KSR1/BRAF heterodimerization already occurs in the absence of this active GTPase and requires a salt bridge between the CC-SAM domain of KSR1 and the BRAF-specific region. We demonstrate that loss-of-function mutations impairing key steps of the RAF activation cycle can be used as calibrators to gauge the dynamics of heterodimerization. This approach identified the RAS-binding domains and the C-terminal 14-3-3 binding motifs as particularly critical for the reconstitution of RAF mediated LgBiT/SmBiT reconstitution, while the dimer interface was less important for dimerization but essential for downstream signaling. We show for the first time that BRAFV600E, the most common BRAF oncoprotein whose dimerization status is controversially portrayed in the literature, forms homodimers in living cells more efficiently than its wildtype counterpart. Of note, Nanoluc activity reconstituted by BRAFV600E homodimers is highly sensitive to the paradox-breaking RAFi PLX8394, indicating a dynamic and specific PPI. We report the effects of eleven ERK pathway inhibitors on RAF dimerization, incl. third-generation compounds that are less-defined in terms of their dimer promoting abilities. We identify Naporafenib as a potent and long-lasting dimerizer and show that the split Nanoluc approach discriminates between type I, I1/2 and II RAFi. Video Abstract.
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Affiliation(s)
- Lino Rohrer
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Corinna Spohr
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Carina Beha
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Ricarda Griffin
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Sandra Braun
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Sebastian Halbach
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Tilman Brummer
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany.
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany.
- Comprehensive Cancer Center Freiburg (CCCF), Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, 79106, Germany.
- Center for Biological Signalling Studies BIOSS, University of Freiburg, Freiburg, 79104, Germany.
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Tkacik E, Li K, Gonzalez-Del Pino G, Ha BH, Vinals J, Park E, Beyett TS, Eck MJ. Structure and RAF family kinase isoform selectivity of type II RAF inhibitors tovorafenib and naporafenib. J Biol Chem 2023; 299:104634. [PMID: 36963492 PMCID: PMC10149214 DOI: 10.1016/j.jbc.2023.104634] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/17/2023] [Accepted: 03/18/2023] [Indexed: 03/26/2023] Open
Abstract
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.
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Affiliation(s)
- Emre Tkacik
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Kunhua Li
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Gonzalo Gonzalez-Del Pino
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Byung Hak Ha
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Javier Vinals
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Eunyoung Park
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Tyler S Beyett
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael J Eck
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.
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Chiang DC, Teh AH, Yap BK. Identification of peptide binding sequence of TRIM25 on 14-3-3σ by bioinformatics and biophysical techniques. J Biomol Struct Dyn 2023; 41:13260-13270. [PMID: 36724456 DOI: 10.1080/07391102.2023.2172458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/19/2023] [Indexed: 02/03/2023]
Abstract
14-3-3σ protein is one of the seven isoforms from the highly conserved eukaryotic 14-3-3 protein family. Downregulation of 14-3-3σ expression has been observed in various tumors. TRIM25 is responsible for the proteolytic degradation of 14-3-3σ, in which abrogation of TRIM25 suppressed tumor growth through 14-3-3σ upregulation. However, to date, the exact 14-3-3σ interacting residues of TRIM25 have yet to be resolved. Thus, this study attempts to identify the peptide binding sequence of TRIM25 on 14-3-3σ via both bioinformatics and biophysical techniques. Multiple sequence alignment of the CC domain of TRIM25 revealed five potential peptide binding sequences (Peptide 1-5). Nuclear magnetic resonance (NMR) assay (1H CPMG) identified Peptide 1 as an important sequence for binding to 14-3-3σ. Competition NMR assay suggested that Peptide 1 binds to the amphipathic pocket of 14-3-3σ with an estimated KD of 116.4 µM by isothermal titration calorimetry. Further in silico docking and molecular dynamics simulations studies proposed that Peptide 1 is likely to interact with Lys49, Arg56, Arg129, and Tyr130 residues at the amphipathic pocket of 14-3-3σ. These results suggest that Peptide 1 may serve as a biological probe or a template to design inhibitors of TRIM25-14-3-3σ interaction as a potentially novel class of anticancer agents.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- De Chen Chiang
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, USM, Penang, Malaysia
| | - Aik-Hong Teh
- Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia
| | - Beow Keat Yap
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, USM, Penang, Malaysia
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34
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Scalia P, Williams SJ, Fujita-Yamaguchi Y, Giordano A. Cell cycle control by the insulin-like growth factor signal: at the crossroad between cell growth and mitotic regulation. Cell Cycle 2023; 22:1-37. [PMID: 36005738 PMCID: PMC9769454 DOI: 10.1080/15384101.2022.2108117] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
In proliferating cells and tissues a number of checkpoints (G1/S and G2/M) preceding cell division (M-phase) require the signal provided by growth factors present in serum. IGFs (I and II) have been demonstrated to constitute key intrinsic components of the peptidic active fraction of mammalian serum. In vivo genetic ablation studies have shown that the cellular signal triggered by the IGFs through their cellular receptors represents a non-replaceable requirement for cell growth and cell cycle progression. Retroactive and current evaluation of published literature sheds light on the intracellular circuitry activated by these factors providing us with a better picture of the pleiotropic mechanistic actions by which IGFs regulate both cell size and mitogenesis under developmental growth as well as in malignant proliferation. The present work aims to summarize the cumulative knowledge learned from the IGF ligands/receptors and their intracellular signaling transducers towards control of cell size and cell-cycle with particular focus to their actionable circuits in human cancer. Furthermore, we bring novel perspectives on key functional discriminants of the IGF growth-mitogenic pathway allowing re-evaluation on some of its signal components based upon established evidences.
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Affiliation(s)
- Pierluigi Scalia
- ISOPROG-Somatolink EPFP Research Network, Philadelphia, PA, USA, Caltanissetta, Italy,CST, Biology, Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, PA, United states,CONTACT Pierluigi Scalia ISOPROG-Somatolink EPFP Research Network, Philadelphia, PA9102, USA
| | - Stephen J Williams
- ISOPROG-Somatolink EPFP Research Network, Philadelphia, PA, USA, Caltanissetta, Italy,CST, Biology, Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, PA, United states
| | - Yoko Fujita-Yamaguchi
- Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Antonio Giordano
- ISOPROG-Somatolink EPFP Research Network, Philadelphia, PA, USA, Caltanissetta, Italy,School of Medical Biotechnology, University of Siena, Italy
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35
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Gunderwala A, Cope N, Wang Z. Mechanism and inhibition of BRAF kinase. Curr Opin Chem Biol 2022; 71:102205. [PMID: 36067564 PMCID: PMC10396080 DOI: 10.1016/j.cbpa.2022.102205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/29/2022] [Accepted: 07/30/2022] [Indexed: 01/27/2023]
Abstract
The role of BRAF in tumor initiation has been established, however, the precise mechanism of autoinhibition has only been illustrated recently by several structural studies. These structures uncovered the basis by which the regulatory domains engage in regulating the activity of BRAF kinase domain, which lead to a more complete picture of the regulation cycle of RAF kinases. Small molecule BRAF inhibitors developed specifically to target BRAFV600E have proven effective at inhibiting the most dominant BRAF mutant in melanomas, but are less potent against other BRAF mutants in RAS-driven diseases due to paradoxical activation of the MAPK pathway. A variety of new generation inhibitors that do not show paradoxical activation have been developed. Alternatively, efforts have begun to develop inhibitors targeting the dimer interface of BRAF. A deeper understanding of BRAF regulation together with more diverse BRAF inhibitors will be beneficial for drug development in RAF or RASdriven cancers.
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Affiliation(s)
- Amber Gunderwala
- Department of Chemistry & Biochemistry, College of Science and Mathematics, Rowan University, Glassboro, NJ, USA
| | - Nicholas Cope
- Department of Chemistry & Biochemistry, College of Science and Mathematics, Rowan University, Glassboro, NJ, USA
| | - Zhihong Wang
- Department of Chemistry & Biochemistry, College of Science and Mathematics, Rowan University, Glassboro, NJ, USA.
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36
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Oberoi J, Guiu XA, Outwin EA, Schellenberger P, Roumeliotis TI, Choudhary JS, Pearl LH. HSP90-CDC37-PP5 forms a structural platform for kinase dephosphorylation. Nat Commun 2022; 13:7343. [PMID: 36446791 PMCID: PMC9709061 DOI: 10.1038/s41467-022-35143-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/18/2022] [Indexed: 12/02/2022] Open
Abstract
Activation of client protein kinases by the HSP90 molecular chaperone system is affected by phosphorylation at multiple sites on HSP90, the kinase-specific co-chaperone CDC37, and the kinase client itself. Removal of regulatory phosphorylation from client kinases and their release from the HSP90-CDC37 system depends on the Ser/Thr phosphatase PP5, which associates with HSP90 via its N-terminal TPR domain. Here, we present the cryoEM structure of the oncogenic protein kinase client BRAFV600E bound to HSP90-CDC37, showing how the V600E mutation favours BRAF association with HSP90-CDC37. Structures of HSP90-CDC37-BRAFV600E complexes with PP5 in autoinhibited and activated conformations, together with proteomic analysis of its phosphatase activity on BRAFV600E and CRAF, reveal how PP5 is activated by recruitment to HSP90 complexes. PP5 comprehensively dephosphorylates client proteins, removing interaction sites for regulatory partners such as 14-3-3 proteins and thus performing a 'factory reset' of the kinase prior to release.
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Affiliation(s)
- Jasmeen Oberoi
- grid.12082.390000 0004 1936 7590Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ UK
| | - Xavi Aran Guiu
- grid.12082.390000 0004 1936 7590Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ UK
| | - Emily A. Outwin
- grid.12082.390000 0004 1936 7590Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ UK
| | - Pascale Schellenberger
- grid.12082.390000 0004 1936 7590Electron Microscopy Imaging centre, School of Life Sciences, University of Sussex, Falmer, BN1 9QG UK
| | - Theodoros I. Roumeliotis
- grid.18886.3fInstitute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB UK
| | - Jyoti S. Choudhary
- grid.18886.3fInstitute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB UK
| | - Laurence H. Pearl
- grid.12082.390000 0004 1936 7590Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ UK ,grid.18886.3fInstitute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB UK
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37
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Spencer-Smith R, Terrell EM, Insinna C, Agamasu C, Wagner ME, Ritt DA, Stauffer J, Stephen AG, Morrison DK. RASopathy mutations provide functional insight into the BRAF cysteine-rich domain and reveal the importance of autoinhibition in BRAF regulation. Mol Cell 2022; 82:4262-4276.e5. [PMID: 36347258 PMCID: PMC9677513 DOI: 10.1016/j.molcel.2022.10.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 07/16/2022] [Accepted: 10/14/2022] [Indexed: 11/09/2022]
Abstract
BRAF is frequently mutated in human cancer and the RASopathy syndromes, with RASopathy mutations often observed in the cysteine-rich domain (CRD). Although the CRD participates in phosphatidylserine (PS) binding, the RAS-RAF interaction, and RAF autoinhibition, the impact of these activities on RAF function in normal and disease states is not well characterized. Here, we analyze a panel of CRD mutations and show that they increase BRAF activity by relieving autoinhibition and/or enhancing PS binding, with relief of autoinhibition being the major factor determining mutation severity. Further, we show that CRD-mediated autoinhibition prevents the constitutive plasma membrane localization of BRAF that causes increased RAS-dependent and RAS-independent function. Comparison of the BRAF- and CRAF-CRDs also indicates that the BRAF-CRD is a stronger mediator of autoinhibition and PS binding, and given the increased catalytic activity of BRAF, our studies reveal a more critical role for CRD-mediated autoinhibition in BRAF regulation.
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Affiliation(s)
- Russell Spencer-Smith
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702 USA
| | - Elizabeth M Terrell
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702 USA
| | - Christine Insinna
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702 USA
| | - Constance Agamasu
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702 USA
| | - Morgan E Wagner
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702 USA
| | - Daniel A Ritt
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702 USA
| | - Jim Stauffer
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702 USA
| | - Andrew G Stephen
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702 USA
| | - Deborah K Morrison
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702 USA.
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38
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Dar AC, Brady DC. RASopathy mutations open new insights into the mechanism of BRAF activation. Mol Cell 2022; 82:4192-4193. [PMID: 36400004 PMCID: PMC9867872 DOI: 10.1016/j.molcel.2022.10.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 10/30/2022] [Accepted: 10/30/2022] [Indexed: 11/19/2022]
Abstract
Spencer-Smith et al. (2022)1 investigate multiple functions of the BRAF cysteine-rich domain (CRD), finding distinct classes of RASopathy-associated BRAF mutations and unique features among RAF paralogs that may contribute to the spectrum of mutations observed in disease.
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Affiliation(s)
- Arvin C Dar
- Department of Oncological Sciences, The Tisch Cancer Institute, Mount Sinai Centre for Therapeutic Discovery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pharmaceutical Sciences, The Tisch Cancer Institute, Mount Sinai Centre for Therapeutic Discovery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Donita C Brady
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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39
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Ngo VA, Garcia AE. Millisecond molecular dynamics simulations of KRas-dimer formation and interfaces. Biophys J 2022; 121:3730-3744. [PMID: 35462078 PMCID: PMC9617078 DOI: 10.1016/j.bpj.2022.04.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/28/2022] [Accepted: 04/19/2022] [Indexed: 11/02/2022] Open
Abstract
Ras dimers have been proposed as building blocks for initiating the extracellular signal-regulated kinase (ERK)/mitogen-activated protein kinase (MAPK) cellular signaling pathway. To better examine the structure of possible dimer interfaces, the dynamics of Ras dimerization, and its potential signaling consequences, we performed molecular dynamics simulations totaling 1 ms of sampling, using an all-atom model of two full-length, farnesylated, guanosine triphosphate (GTP)-bound, wild-type KRas4b proteins diffusing on 29%POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine)-mixed POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) membranes. Our simulations unveil an ensemble of thermodynamically weak KRas dimers spanning multiple conformations. The most stable conformations, having the largest interface areas, involve helix α2 and a hypervariable region (HVR). Among the dimer conformations, we found that the HVR of each KRas has frequent interactions with various parts of the dimer, thus potentially mediating the dimerization. Some dimer configurations have one KRas G-domain elevated above the lipid bilayer surface by residing on top of the other G-domain, thus likely contributing to the recruitment of cytosolic Raf kinases in the context of a stably formed multi-protein complex. We identified a variant of the α4-α5 KRas-dimer interface that is similar to the interfaces obtained with fluorescence resonance energy transfer (FRET) data of HRas on lipid bilayers. Interestingly, we found two arginine fingers, R68 and R149, that directly interact with the beta-phosphate of the GTP bound in KRas, in a manner similar to what is observed in a crystal structure of GAP-HRas complex, which can facilitate the GTP hydrolysis via the arginine finger of GTPase-activating protein (GAP).
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Affiliation(s)
- Van A Ngo
- Advanced Computing for Life Sciences and Engineering Group, Science Engagement Section, National Center for Computational Sciences, Oak Ridge National Lab, Oak Ridge, Tennessee; Center for Nonlinear Studies (CNLS), Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Angel E Garcia
- Center for Nonlinear Studies (CNLS), Los Alamos National Laboratory, Los Alamos, New Mexico.
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40
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Bonsor DA, Alexander P, Snead K, Hartig N, Drew M, Messing S, Finci LI, Nissley DV, McCormick F, Esposito D, Rodriguez-Viciana P, Stephen AG, Simanshu DK. Structure of the SHOC2-MRAS-PP1C complex provides insights into RAF activation and Noonan syndrome. Nat Struct Mol Biol 2022; 29:966-977. [PMID: 36175670 PMCID: PMC10365013 DOI: 10.1038/s41594-022-00841-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 08/12/2022] [Indexed: 11/08/2022]
Abstract
SHOC2 acts as a strong synthetic lethal interactor with MEK inhibitors in multiple KRAS cancer cell lines. SHOC2 forms a heterotrimeric complex with MRAS and PP1C that is essential for regulating RAF and MAPK-pathway activation by dephosphorylating a specific phosphoserine on RAF kinases. Here we present the high-resolution crystal structure of the SHOC2-MRAS-PP1C (SMP) complex and apo-SHOC2. Our structures reveal that SHOC2, MRAS, and PP1C form a stable ternary complex in which all three proteins synergistically interact with each other. Our results show that dephosphorylation of RAF substrates by PP1C is enhanced upon interacting with SHOC2 and MRAS. The SMP complex forms only when MRAS is in an active state and is dependent on SHOC2 functioning as a scaffolding protein in the complex by bringing PP1C and MRAS together. Our results provide structural insights into the role of the SMP complex in RAF activation and how mutations found in Noonan syndrome enhance complex formation, and reveal new avenues for therapeutic interventions.
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Affiliation(s)
- Daniel A Bonsor
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Patrick Alexander
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kelly Snead
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Nicole Hartig
- UCL Cancer Institute, University College London, London, UK
| | - Matthew Drew
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Simon Messing
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Lorenzo I Finci
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Frank McCormick
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- University of California, San Francisco Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Dominic Esposito
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
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García-Alonso S, Mesa P, Ovejero LDLP, Aizpurua G, Lechuga CG, Zarzuela E, Santiveri CM, Sanclemente M, Muñoz J, Musteanu M, Campos-Olivas R, Martínez-Torrecuadrada J, Barbacid M, Montoya G. Structure of the RAF1-HSP90-CDC37 complex reveals the basis of RAF1 regulation. Mol Cell 2022; 82:3438-3452.e8. [PMID: 36055235 DOI: 10.1016/j.molcel.2022.08.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/21/2022] [Accepted: 08/08/2022] [Indexed: 10/14/2022]
Abstract
RAF kinases are RAS-activated enzymes that initiate signaling through the MAPK cascade to control cellular proliferation, differentiation, and survival. Here, we describe the structure of the full-length RAF1 protein in complex with HSP90 and CDC37 obtained by cryoelectron microscopy. The reconstruction reveals a RAF1 kinase with an unfolded N-lobe separated from its C-lobe. The hydrophobic core of the N-lobe is trapped in the HSP90 dimer, while CDC37 wraps around the chaperone and interacts with the N- and C-lobes of the kinase. The structure indicates how CDC37 can discriminate between the different members of the RAF family. Our structural analysis also reveals that the folded RAF1 assembles with 14-3-3 dimers, suggesting that after folding RAF1 follows a similar activation as B-RAF. Finally, disruption of the interaction between CDC37 and the DFG segment of RAF1 unveils potential vulnerabilities in attempting the pharmacological degradation of RAF1 for therapeutic purposes.
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Affiliation(s)
- Sara García-Alonso
- Experimental Oncology Group, Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid 28029, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Pablo Mesa
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Laura de la Puente Ovejero
- Experimental Oncology Group, Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid 28029, Spain
| | - Gonzalo Aizpurua
- Experimental Oncology Group, Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid 28029, Spain
| | - Carmen G Lechuga
- Experimental Oncology Group, Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid 28029, Spain
| | - Eduardo Zarzuela
- Proteomics Unit, Biotechnology Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid 28029, Spain
| | - Clara M Santiveri
- Spectroscopy and NMR Unit, Structural Biology Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid 28029, Spain
| | - Manuel Sanclemente
- Experimental Oncology Group, Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid 28029, Spain
| | - Javier Muñoz
- Proteomics Unit, Biotechnology Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid 28029, Spain
| | - Mónica Musteanu
- Department Section of Biochemistry and Molecular Biology, Complutense University of Madrid, Madrid 28040, Spain
| | - Ramón Campos-Olivas
- Spectroscopy and NMR Unit, Structural Biology Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid 28029, Spain
| | - Jorge Martínez-Torrecuadrada
- Crystallography and Protein Engineering Unit, Structural Biology Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid 28029, Spain
| | - Mariano Barbacid
- Experimental Oncology Group, Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid 28029, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain.
| | - Guillermo Montoya
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark.
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Qu J, Shen Q, Li Y, Kalyani FS, Liu L, Zhou J, Zhou J. Clinical Characteristics, Co-Mutations, and Treatment Outcomes in Advanced Non-Small-Cell Lung Cancer Patients With the BRAF-V600E Mutation. Front Oncol 2022; 12:911303. [PMID: 35814395 PMCID: PMC9257040 DOI: 10.3389/fonc.2022.911303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 05/24/2022] [Indexed: 02/05/2023] Open
Abstract
BackgroundLimited treatment outcome data is available for advanced non-small cell lung cancer (NSCLC) patients with BRAF V600E mutations. In this multicenter study, we describe therapeutic options and survival outcomes for patients with mutated BRAF V600E.MethodThis was a retrospective study in which BRAF V600E-mutated advanced NSCLC patients were retrospectively recruited between January 2015 and December 2021 and had their clinical characteristics, co-mutations, and treatment efficacy assessed.ResultsFifty-three patients with BRAF V600E-mutant advanced NSCLC were included in the study, of which 64.2% were non-smokers, and the BRAF V600E mutation was more prevalent in men (52.8%). In addition, 96.2% of the patients had adenocarcinoma, and most (96.2%) received first-line therapy (23.5% anti-BRAF), with a progression-free survival (PFS) and overall survival (OS) of 10.0 [95% confidence interval (CI): 1.5–36.0 months] and 24.0 months [95% CI: 3.0–53.0 months], respectively. Twenty-three patients (43.4%) received second-line treatment (39.1% anti-BRAF), and PFS and OS were 5.0 [95% CI: 1.0–21.0 months] and 13.0 months [95% CI: 1.5–26.0 months], respectively. BRAF and MEK-targeted therapy (dabrafenib plus trametinib) produced longer PFS compared with that of chemotherapy with or without bevacizumab as a first-line (NA vs. 4.0 months, P = 0.025) or second-line therapy (6.0 vs. 4.6 months, P = 0.017). NSCLC patients harboring driver oncogene mutations such as BRAF V600E, EGFR, or ALK should be treated using targeted therapies. Concurrent TP53 mutations were the most common, affecting 11.3% (n = 6) of the patients, followed by EGFR 19 Del (n = 5). Patients with concurrent mutations had shorter PFS (9.0 vs. 10.0 months, P = 0.875) and OS (14.0 vs. 15.0 months, P = 0.555) than those without these mutations.ConclusionThese results suggest that combined BRAF- and MEK-targeted therapy is effective in BRAF V600E-mutated advanced NSCLC patients. Dabrafenib and trametinib re-challenge is also an option for patients with BRAF V600E-mutated NSCLC.
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Affiliation(s)
- Jingjing Qu
- Department of Respiratory Disease, Thoracic Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- The Clinical Research Center for Respiratory Diseases of Zhejiang Province, Hangzhou, China
| | - Qian Shen
- Department of Respiratory Disease, Thoracic Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- The Clinical Research Center for Respiratory Diseases of Zhejiang Province, Hangzhou, China
| | - Yuping Li
- Department of Respiratory Disease, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Farhin Shaheed Kalyani
- Department of Respiratory Disease, Thoracic Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Li Liu
- Lung Cancer and Gastroenterology Department, Hunan Cancer Hospital, Affiliated Tumor Hospital of Xiangya Medical School of Central South University, Changsha, China
- *Correspondence: Jianya Zhou, ; Li Liu,
| | - Jianya Zhou
- Department of Respiratory Disease, Thoracic Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- The Clinical Research Center for Respiratory Diseases of Zhejiang Province, Hangzhou, China
- *Correspondence: Jianya Zhou, ; Li Liu,
| | - Jianying Zhou
- Department of Respiratory Disease, Thoracic Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- The Clinical Research Center for Respiratory Diseases of Zhejiang Province, Hangzhou, China
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43
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Murphy BM, Terrell EM, Chirasani VR, Weiss TJ, Lew RE, Holderbaum AM, Dhakal A, Posada V, Fort M, Bodnar MS, Carey LM, Chen M, Burd CJ, Coppola V, Morrison DK, Campbell SL, Burd CE. Enhanced BRAF engagement by NRAS mutants capable of promoting melanoma initiation. Nat Commun 2022; 13:3153. [PMID: 35672316 PMCID: PMC9174180 DOI: 10.1038/s41467-022-30881-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 05/24/2022] [Indexed: 01/07/2023] Open
Abstract
A distinct profile of NRAS mutants is observed in each tumor type. It is unclear whether these profiles are determined by mutagenic events or functional differences between NRAS oncoproteins. Here, we establish functional hallmarks of NRAS mutants enriched in human melanoma. We generate eight conditional, knock-in mouse models and show that rare melanoma mutants (NRAS G12D, G13D, G13R, Q61H, and Q61P) are poor drivers of spontaneous melanoma formation, whereas common melanoma mutants (NRAS Q61R, Q61K, or Q61L) induce rapid tumor onset with high penetrance. Molecular dynamics simulations, combined with cell-based protein-protein interaction studies, reveal that melanomagenic NRAS mutants form intramolecular contacts that enhance BRAF binding affinity, BRAF-CRAF heterodimer formation, and MAPK > ERK signaling. Along with the allelic series of conditional mouse models we describe, these results establish a mechanistic basis for the enrichment of specific NRAS mutants in human melanoma.
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Affiliation(s)
- Brandon M Murphy
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Elizabeth M Terrell
- Laboratory of Cell and Developmental Signaling, National Cancer Institute-Frederick, Frederick, MD, 21702, USA
| | - Venkat R Chirasani
- Department of Biochemistry & Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Tirzah J Weiss
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Rachel E Lew
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, 43210, USA
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Andrea M Holderbaum
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, 43210, USA
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Aastha Dhakal
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Valentina Posada
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Marie Fort
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Michael S Bodnar
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, 43210, USA
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Leiah M Carey
- Department of Biochemistry & Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Min Chen
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, 43210, USA
- Genetically Engineered Mouse Modeling Core, The Ohio State University, Columbus, OH, 43210, USA
| | - Craig J Burd
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Vincenzo Coppola
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, 43210, USA
- Genetically Engineered Mouse Modeling Core, The Ohio State University, Columbus, OH, 43210, USA
| | - Deborah K Morrison
- Laboratory of Cell and Developmental Signaling, National Cancer Institute-Frederick, Frederick, MD, 21702, USA
| | - Sharon L Campbell
- Department of Biochemistry & Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Christin E Burd
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, 43210, USA.
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA.
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Abstract
B-Raf is a protein kinase participating to the regulation of many biological processes in cells. Several studies have demonstrated that this protein is frequently upregulated in human cancers, especially when it bears activating mutations. In the last years, few ATP-competitive inhibitors of B-Raf have been marketed for the treatment of melanoma and are currently under clinical evaluation on a variety of other types of cancer. Although the introduction of drugs targeting B-Raf has provided significant advances in cancer treatment, responses to ATP-competitive inhibitors remain limited, mainly due to selectivity issues, side effects, narrow therapeutic windows, and the insurgence of drug resistance. Impressive research efforts have been made so far towards the identification of novel ATP-competitive modulators with improved efficacy against cancers driven by mutant Raf monomers and dimers, some of them showing good promises. However, several limitations could still be envisioned for these compounds, according to literature data. Besides, increased attentions have arisen around approaches based on the design of allosteric modulators, polypharmacology, proteolysis targeting chimeras (PROTACs) and drug repurposing for the targeting of B-Raf proteins. The design of compounds acting through such innovative mechanisms is rather challenging. However, valuable therapeutic opportunities can be envisioned on these drugs, as they act through innovative mechanisms in which limitations typically observed for approved ATP-competitive B-Raf inhibitors are less prone to emerge. In this article, current approaches adopted for the design of non-ATP competitive inhibitors targeting B-Raf are described, discussing also on the possibilities, ligands acting through such innovative mechanisms could provide for the obtainment of more effective therapies.
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Affiliation(s)
- Luca Pinzi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
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45
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Simanshu DK, Morrison DK. A Structure is Worth a Thousand Words: New Insights for RAS and RAF Regulation. Cancer Discov 2022; 12:899-912. [PMID: 35046094 PMCID: PMC8983508 DOI: 10.1158/2159-8290.cd-21-1494] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022]
Abstract
The RAS GTPases are frequently mutated in human cancer, with KRAS being the predominant tumor driver. For many years, it has been known that the structure and function of RAS are integrally linked, as structural changes induced by GTP binding or mutational events determine the ability of RAS to interact with regulators and effectors. Recently, a wealth of information has emerged from structures of specific KRAS mutants and from structures of multiprotein complexes containing RAS and/or RAF, an essential effector of RAS. These structures provide key insights regarding RAS and RAF regulation as well as promising new strategies for therapeutic intervention. SIGNIFICANCE The RAS GTPases are major drivers of tumorigenesis, and for RAS proteins to exert their full oncogenic potential, they must interact with the RAF kinases to initiate ERK cascade signaling. Although binding to RAS is typically a prerequisite for RAF to become an activated kinase, determining the molecular mechanisms by which this interaction results in RAF activation has been a challenging task. A major advance in understanding this process and RAF regulation has come from recent structural studies of various RAS and RAF multiprotein signaling complexes, revealing new avenues for drug discovery.
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Affiliation(s)
- Dhirendra K. Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Deborah K. Morrison
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland
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Brady DC, Hmeljak J, Dar AC. Understanding and drugging RAS: 40 years to break the tip of the iceberg. Dis Model Mech 2022; 15:274631. [PMID: 35244677 PMCID: PMC8905715 DOI: 10.1242/dmm.049519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Several cancers and rare genetic diseases are caused by dysregulation in the RAS signaling pathway. RAS proteins serve as molecular switches that regulate pathways involved in cellular growth, differentiation and survival. These pathways have been an intense area of investigation for four decades, since the initial identification of somatic RAS mutations linked to human cancers. In the past few years, inhibitors against several RAS effectors, as well as direct inhibitors of the K-RAS mutant G12C, have been developed. This Special Issue in DMM includes original Research articles on RAS-driven cancers and RASopathies. The articles provide insights into mechanisms and biomarkers, and evaluate therapeutic targets. Several articles also present new disease models, whereas others describe technologies or approaches to evaluate the function of RAS in vivo. The collection also includes a series of Review articles on RAS biology and translational aspects of defining and treating RAS-driven diseases. In this Editorial, we summarize this collection and discuss the potential impact of the articles within this evolving area of research. We also identify areas of growth and possible future developments. Summary: This Editorial introduces DMM’s new Special Issue on the RAS pathway. The Guest Editors reflect on the impact of the featured articles on the landscape of the RAS field.
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Affiliation(s)
- Donita C Brady
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Julija Hmeljak
- The Company of Biologists, Bidder Building, Station Road, Histon, Cambridge CB24 9LF, UK
| | - Arvin C Dar
- Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, Center for Therapeutic Discovery, Mount Sinai, New York, NY 10029-5674, USA
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