1
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Hossain MA. Targeting the RAS upstream and downstream signaling pathway for Cancer treatment. Eur J Pharmacol 2024:176727. [PMID: 38866361 DOI: 10.1016/j.ejphar.2024.176727] [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: 03/08/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/14/2024]
Abstract
Cancer often involves the overactivation of RAS/RAF/MEK/ERK (MAPK) and PI3K-Akt-mTOR pathways due to mutations in genes like RAS, RAF, PTEN, and PIK3CA. Various strategies are employed to address the overactivation of these pathways, among which targeted therapy emerges as a promising approach. Directly targeting specific proteins, leads to encouraging results in cancer treatment. For instance, RTK inhibitors such as imatinib and afatinib selectively target these receptors, hindering ligand binding and reducing signaling initiation. These inhibitors have shown potent efficacy against Non-Small Cell Lung Cancer. Other inhibitors, like lonafarnib targeting Farnesyltransferase and GGTI 2418 targeting geranylgeranyl Transferase, disrupt post-translational modifications of proteins. Additionally, inhibition of proteins like SOS, SH2 domain, and Ras demonstrate promising anti-tumor activity both in vivo and in vitro. Targeting downstream components with RAF inhibitors such as vemurafenib, dabrafenib, and sorafenib, along with MEK inhibitors like trametinib and binimetinib, has shown promising outcomes in treating cancers with BRAF-V600E mutations, including myeloma, colorectal, and thyroid cancers. Furthermore, inhibitors of PI3K (e.g., apitolisib, copanlisib), AKT (e.g., ipatasertib, perifosine), and mTOR (e.g., sirolimus, temsirolimus) exhibit promising efficacy against various cancers such as Invasive Breast Cancer, Lymphoma, Neoplasms, and hematological malignancies. This review offers an overview of small molecule inhibitors targeting specific proteins within the RAS upstream and downstream signaling pathways in cancer.
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Affiliation(s)
- Md Arafat Hossain
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh;.
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2
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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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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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Motta M, Barresi S, Pizzi S, Bifano D, Lopez Marti J, Garrido-Pontnou M, Flex E, Bruselles A, Giovannoni I, Rotundo G, Fragale A, Tirelli V, Vallese S, Ciolfi A, Bisogno G, Alaggio R, Tartaglia M. RAF1 gene fusions are recurrent driver events in infantile fibrosarcoma-like mesenchymal tumors. J Pathol 2024; 263:166-177. [PMID: 38629245 DOI: 10.1002/path.6272] [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: 11/08/2023] [Revised: 12/21/2023] [Accepted: 02/13/2024] [Indexed: 05/12/2024]
Abstract
Infantile fibrosarcomas (IFS) and congenital mesoblastic nephroma (CMN) are rare myofibroblastic tumors of infancy and early childhood commonly harboring the ETV6::NTRK3 gene fusion. IFS/CMN are considered as tumors with an 'intermediate prognosis' as they are locally aggressive, but rarely metastasize, and generally have a favorable outcome. A fraction of IFS/CMN-related neoplasms are negative for the ETV6::NTRK3 gene rearrangement and are characterized by other chimeric proteins promoting MAPK signaling upregulation. In a large proportion of these tumors, which are classified as IFS-like mesenchymal neoplasms, the contributing molecular events remain to be identified. Here, we report three distinct rearrangements involving RAF1 among eight ETV6::NTRK3 gene fusion-negative tumors with an original histological diagnosis of IFS/CMN. The three fusion proteins retain the entire catalytic domain of the kinase. Two chimeric products, GOLGA4::RAF1 and LRRFIP2::RAF1, had previously been reported as driver events in different cancers, whereas the third, CLIP1::RAF1, represents a novel fusion protein. We demonstrate that CLIP1::RAF1 acts as a bona fide oncoprotein promoting cell proliferation and migration through constitutive upregulation of MAPK signaling. We show that the CLIP1::RAF1 hyperactive behavior does not require RAS activation and is mediated by constitutive 14-3-3 protein-independent dimerization of the chimeric protein. As previously reported for the ETV6::NTRK3 fusion protein, CLIP1::RAF1 similarly upregulates PI3K-AKT signaling. Our findings document that RAF1 gene rearrangements represent a recurrent event in ETV6::NTRK3-negative IFS/CMN and provide a rationale for the use of inhibitors directed to suppress MAPK and PI3K-AKT signaling in these cancers. © 2024 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Marialetizia Motta
- Molecular Genetics and Functional Genomics Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Sabina Barresi
- Pathology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Simone Pizzi
- Molecular Genetics and Functional Genomics Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Delfina Bifano
- Pathology Unit, Santobono-Pausilipon Children's Hospital, Naples, Italy
| | - Jennifer Lopez Marti
- Department of Pathology, Hospital Nacional de Pediatria Juan P. Garrahan, Buenos Aires, Argentina
| | | | - Elisabetta Flex
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Alessandro Bruselles
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | | | - Giovannina Rotundo
- Molecular Genetics and Functional Genomics Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Alessandra Fragale
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | | | - Silvia Vallese
- Pathology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Andrea Ciolfi
- Molecular Genetics and Functional Genomics Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Gianni Bisogno
- Pediatric Hematology-Oncology Division, University Hospital, Padova, Italy
| | - Rita Alaggio
- Pathology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Department of Medical and Surgical Sciences and Biotechnologies, Sapienza University, Latina, Italy
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
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5
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Mehrabipour M, Nakhaei-Rad S, Dvorsky R, Lang A, Verhülsdonk P, Ahmadian MR, Piekorz RP. SIRT4 as a novel interactor and candidate suppressor of C-RAF kinase in MAPK signaling. Life Sci Alliance 2024; 7:e202302507. [PMID: 38499327 PMCID: PMC10948936 DOI: 10.26508/lsa.202302507] [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: 12/04/2023] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 03/20/2024] Open
Abstract
Cellular responses leading to development, proliferation, and differentiation depend on RAF/MEK/ERK signaling, which integrates and amplifies signals from various stimuli for downstream cellular responses. C-RAF activation has been reported in many types of tumor cell proliferation and developmental disorders, necessitating the discovery of potential C-RAF protein regulators. Here, we identify a novel and specific protein interaction between C-RAF among the RAF kinase paralogs, and SIRT4 among the mitochondrial sirtuin family members SIRT3, SIRT4, and SIRT5. Structurally, C-RAF binds to SIRT4 through the N-terminal cysteine-rich domain, whereas SIRT4 predominantly requires the C-terminus for full interaction with C-RAF. Interestingly, SIRT4 specifically interacts with C-RAF in a pre-signaling inactive (serine 259-phosphorylated) state. Consistent with this finding, the expression of SIRT4 in HEK293 cells results in an up-regulation of pS259-C-RAF levels and a concomitant reduction in MAPK signaling as evidenced by strongly decreased phospho-ERK signals. Thus, we propose an additional extra-mitochondrial function of SIRT4 as a cytosolic tumor suppressor of C-RAF-MAPK signaling, besides its metabolic tumor suppressor role of glutamate dehydrogenase and glutamate levels in mitochondria.
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Affiliation(s)
- Mehrnaz Mehrabipour
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Saeideh Nakhaei-Rad
- Stem Cell Biology, and Regenerative Medicine Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Radovan Dvorsky
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Alexander Lang
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Patrick Verhülsdonk
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Mohammad R Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Roland P Piekorz
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
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6
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Smith SF, Islam AFMT, Alimukhamedov S, Weiss ET, Charest PG. Molecular determinants of Ras-mTORC2 signaling. J Biol Chem 2024:107423. [PMID: 38815864 DOI: 10.1016/j.jbc.2024.107423] [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: 02/10/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 06/01/2024] Open
Abstract
Recent research has identified the mechanistic Target of Rapamycin Complex 2 (mTORC2) as a conserved direct effector of Ras proteins. While previous studies suggested the involvement of the Switch I (SWI) effector domain of Ras in binding mTORC2 components, the regulation of the Ras-mTORC2 pathway is not entirely understood. In Dictyostelium, mTORC2 is selectively activated by the Ras protein RasC, and the RasC-mTORC2 pathway then mediates chemotaxis to cAMP and cellular aggregation by regulating the actin cytoskeleton and promoting cAMP signal relay. Here, we investigated the role of specific residues in RasC's SWI, C-terminal allosteric domain, and hypervariable region (HVR) related to mTORC2 activation. Interestingly, our results suggest that RasC SWI residue A31, which was previously implicated in RasC-mediated aggregation, regulates RasC's specific activation by the Aimless RasGEF. On the other hand, our investigation identified a crucial role for RasC SWI residue T36, with secondary contributions from E38 and allosteric domain residues. Finally, we found that conserved basic residues and the adjacent prenylation site in the HVR, which are crucial for RasC's membrane localization, are essential for RasC-mTORC2 pathway activation by allowing for both RasC's own cAMP-induced activation and its subsequent activation of mTORC2. Therefore, our findings revealed new determinants of RasC-mTORC2 pathway specificity in Dictyostelium, contributing to a deeper understanding of Ras signaling regulation in eukaryotic cells.
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Affiliation(s)
- Stephen F Smith
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - A F M Tariqul Islam
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA
| | | | - Ethan T Weiss
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - Pascale G Charest
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA; Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA; University of Arizona Cancer Center, Tucson, AZ, USA.
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7
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Ye H, Zhu Y, Kong Y, Wen H, Lu W, Wang D, Tang S, Zhan M, Lu G, Shao C, Wang N, Hao H. Carbene Footprinting Directs Design of Genetically Encoded Proximity-Reactive Protein Binders. Anal Chem 2024; 96:7566-7576. [PMID: 38684118 DOI: 10.1021/acs.analchem.4c00424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Genetically encoding proximal-reactive unnatural amino acids (PrUaas), such as fluorosulfate-l-tyrosine (FSY), into natural proteins of interest (POI) confer the POI with the ability to covalently bind to its interacting proteins (IPs). The PrUaa-incorporated POIs hold promise for blocking undesirable POI-IP interactions. Selecting appropriate PrUaa anchor sites is crucial, but it remains challenging with the current methodology, which heavily relies on crystallography to identify the proximal residues between the POIs and the IPs for the PrUaa anchorage. To address the challenge, here, we propose a footprinting-directed genetically encoded covalent binder (footprinting-GECB) approach. This approach employs carbene footprinting, a structural mass spectrometry (MS) technique that quantifies the extent of labeling of the POI following the addition of its IP, and thus identifies the responsive residues. By genetically encoding PrUaa into these responsive sites, POI variants with covalent bonding ability to its IP can be produced without the need for crystallography. Using the POI-IP model, KRAS/RAF1, we showed that engineering FSY at the footprint-assigned KRAS residue resulted in a KRAS variant that can bind irreversibly to RAF1. Additionally, we inserted FSY at the responsive residue in RAF1 upon footprinting the oncogenic KRASG12D/RAF1, which lacks crystal structure, and generated a covalent binder to KRASG12D. Together, we demonstrated that by adopting carbene footprinting to direct PrUaa anchorage, we can greatly expand the opportunities for designing covalent protein binders for PPIs without relying on crystallography. This holds promise for creating effective PPI inhibitors and supports both fundamental research and biotherapeutics development.
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Affiliation(s)
- Hui Ye
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang No. 24, Nanjing 210009, Jiangsu, China
| | - Yinxue Zhu
- School of Pharmacy, China Pharmaceutical University, Tongjiaxiang No. 24, Nanjing 210009, Jiangsu, China
| | - Ying Kong
- School of Pharmacy, China Pharmaceutical University, Tongjiaxiang No. 24, Nanjing 210009, Jiangsu, China
| | - Hongtao Wen
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang No. 24, Nanjing 210009, Jiangsu, China
| | - Wenjie Lu
- School of Pharmacy, China Pharmaceutical University, Tongjiaxiang No. 24, Nanjing 210009, Jiangsu, China
| | - Dexiang Wang
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang No. 24, Nanjing 210009, Jiangsu, China
| | - Shuo Tang
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Pharmacy, Nanjing University of Chinese Medicine, No. 138 Xianlin Avenue, Nanjing 210023, Jiangsu, China
| | - Mengru Zhan
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Pharmacy, Nanjing University of Chinese Medicine, No. 138 Xianlin Avenue, Nanjing 210023, Jiangsu, China
| | - Gaoyuan Lu
- School of Pharmacy, China Pharmaceutical University, Tongjiaxiang No. 24, Nanjing 210009, Jiangsu, China
| | - Chang Shao
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang No. 24, Nanjing 210009, Jiangsu, China
| | - Nanxi Wang
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Pharmacy, Nanjing University of Chinese Medicine, No. 138 Xianlin Avenue, Nanjing 210023, Jiangsu, China
| | - Haiping Hao
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang No. 24, Nanjing 210009, Jiangsu, China
- School of Pharmacy, China Pharmaceutical University, Tongjiaxiang No. 24, Nanjing 210009, Jiangsu, China
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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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Adamopoulos C, Papavassiliou KA, Poulikakos PI, Papavassiliou AG. RAF and MEK Inhibitors in Non-Small Cell Lung Cancer. Int J Mol Sci 2024; 25:4633. [PMID: 38731852 PMCID: PMC11083651 DOI: 10.3390/ijms25094633] [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: 02/29/2024] [Revised: 04/17/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
Lung cancer, despite recent advancements in survival rates, represents a significant global health burden. Non-small cell lung cancer (NSCLC), the most prevalent type, is driven largely by activating mutations in Kirsten rat sarcoma viral oncogene homologue (KRAS) and receptor tyrosine kinases (RTKs), and less in v-RAF murine sarcoma viral oncogene homolog B (BRAF) and mitogen-activated protein-kinase kinase (MEK), all key components of the RTK-RAS-mitogen-activated protein kinase (MAPK) pathway. Learning from melanoma, the identification of BRAFV600E substitution in NSCLC provided the rationale for the investigation of RAF and MEK inhibition as a therapeutic strategy. The regulatory approval of two RAF-MEK inhibitor combinations, dabrafenib-trametinib, in 2017, and encorafenib-binimetinib, in 2023, signifies a breakthrough for the management of BRAFV600E-mutant NSCLC patients. However, the almost universal emergence of acquired resistance limits their clinical benefit. New RAF and MEK inhibitors, with distinct biochemical characteristics, are in preclinical and clinical development. In this review, we aim to provide valuable insights into the current state of RAF and MEK inhibition in the management of NSCLC, fostering a deeper understanding of the potential impact on patient outcomes.
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Affiliation(s)
- Christos Adamopoulos
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
- Department of Oncological Sciences, Precision Immunology Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Kostas A. Papavassiliou
- First University Department of Respiratory Medicine, ‘Sotiria’ Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Poulikos I. Poulikakos
- Department of Oncological Sciences, Precision Immunology Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Athanasios G. Papavassiliou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
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10
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Mbonye U, Karn J. The cell biology of HIV-1 latency and rebound. Retrovirology 2024; 21:6. [PMID: 38580979 PMCID: PMC10996279 DOI: 10.1186/s12977-024-00639-w] [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: 04/07/2024] Open
Abstract
Transcriptionally latent forms of replication-competent proviruses, present primarily in a small subset of memory CD4+ T cells, pose the primary barrier to a cure for HIV-1 infection because they are the source of the viral rebound that almost inevitably follows the interruption of antiretroviral therapy. Over the last 30 years, many of the factors essential for initiating HIV-1 transcription have been identified in studies performed using transformed cell lines, such as the Jurkat T-cell model. However, as highlighted in this review, several poorly understood mechanisms still need to be elucidated, including the molecular basis for promoter-proximal pausing of the transcribing complex and the detailed mechanism of the delivery of P-TEFb from 7SK snRNP. Furthermore, the central paradox of HIV-1 transcription remains unsolved: how are the initial rounds of transcription achieved in the absence of Tat? A critical limitation of the transformed cell models is that they do not recapitulate the transitions between active effector cells and quiescent memory T cells. Therefore, investigation of the molecular mechanisms of HIV-1 latency reversal and LRA efficacy in a proper physiological context requires the utilization of primary cell models. Recent mechanistic studies of HIV-1 transcription using latently infected cells recovered from donors and ex vivo cellular models of viral latency have demonstrated that the primary blocks to HIV-1 transcription in memory CD4+ T cells are restrictive epigenetic features at the proviral promoter, the cytoplasmic sequestration of key transcription initiation factors such as NFAT and NF-κB, and the vanishingly low expression of the cellular transcription elongation factor P-TEFb. One of the foremost schemes to eliminate the residual reservoir is to deliberately reactivate latent HIV-1 proviruses to enable clearance of persisting latently infected cells-the "Shock and Kill" strategy. For "Shock and Kill" to become efficient, effective, non-toxic latency-reversing agents (LRAs) must be discovered. Since multiple restrictions limit viral reactivation in primary cells, understanding the T-cell signaling mechanisms that are essential for stimulating P-TEFb biogenesis, initiation factor activation, and reversing the proviral epigenetic restrictions have become a prerequisite for the development of more effective LRAs.
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Affiliation(s)
- Uri Mbonye
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
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11
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Shen C, Yin J, Wang M, Yu Z, Xu X, Zhou Z, Hu Y, Xia C, Hu G. Mutations influence the conformational dynamics of the GDP/KRAS complex. J Biomol Struct Dyn 2024:1-14. [PMID: 38529923 DOI: 10.1080/07391102.2024.2331627] [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: 01/22/2024] [Accepted: 02/20/2024] [Indexed: 03/27/2024]
Abstract
Mutations near allosteric sites can have a significant impact on the function of KRAS. Three specific mutations, K104Q, G12D/K104Q, and G12D/G75A, which are located near allosteric positions, were selected to investigate the molecular mechanisms behind mutation-induced influences on the activity of KRAS. Gaussian accelerated molecular dynamics (GaMD) simulations followed by the principal component analysis (PCA) were performed to improve the sampling of conformational states. The results revealed that these mutations significantly alter the structural flexibility, correlated motions, and dynamic behavior of the switch regions that are essential for KRAS binding to effectors or regulators. Furthermore, the mutations have a significant impact on the hydrogen bonding interactions between GDP and the switch regions, as well as on the electrostatic interactions of magnesium ions (Mg2+) with these regions. Our results verified that these mutations strongly influence the binding of KRAS to its effectors or regulators and allosterically regulate the activity. We believe that this work can provide valuable theoretical insights into a deeper understanding of KRAS function.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Congcong Shen
- Shandong Key Laboratory of Biophysics, Dezhou University, Dezhou, China
| | - Jie Yin
- Qingyun People's Hospital, Dezhou, China
| | - Min Wang
- Qingyun People's Hospital, Dezhou, China
| | - Zhiping Yu
- Shandong Key Laboratory of Biophysics, Dezhou University, Dezhou, China
| | - Xin Xu
- School of Science, Xi'an Polytechnic University, Xi'an, China
| | - Zhongshun Zhou
- School of Science, Xi'an Polytechnic University, Xi'an, China
| | - Yingshi Hu
- Shandong Key Laboratory of Biophysics, Dezhou University, Dezhou, China
| | - Caijuan Xia
- School of Science, Xi'an Polytechnic University, Xi'an, China
| | - Guodong Hu
- Shandong Key Laboratory of Biophysics, Dezhou University, Dezhou, China
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12
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Lee SY, Lee KY. Conditional Cooperativity in RAS Assembly Pathways on Nanodiscs and Altered GTPase Cycling. Angew Chem Int Ed Engl 2024; 63:e202316942. [PMID: 38305637 DOI: 10.1002/anie.202316942] [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: 11/08/2023] [Revised: 01/28/2024] [Accepted: 02/01/2024] [Indexed: 02/03/2024]
Abstract
Self-assemblies (i.e., nanoclusters) of the RAS GTPase on the membrane act as scaffolds that activate downstream RAF kinases and drive MAPK signaling for cell proliferation and tumorigenesis. However, the mechanistic details of nanoclustering remain largely unknown. Here, size-tunable nanodisc platforms and paramagnetic relaxation enhancement (PRE) analyses revealed the structural basis of the cooperative assembly processes of fully processed KRAS, mutated in a quarter of human cancers. The cooperativity is modulated by the mutation and nucleotide states of KRAS and the lipid composition of the membrane. Notably, the oncogenic mutants assemble in nonsequential pathways with two mutually cooperative 'α/α' and 'α/β' interfaces, while α/α dimerization of wild-type KRAS promotes the secondary α/β interaction sequentially. Mutation-based interface engineering was used to selectively trap the oligomeric intermediates of KRAS and probe their favorable interface interactions. Transiently exposed interfaces were available for the assembly. Real-time NMR demonstrated that higher-order oligomers retain higher numbers of active GTP-bound protomers in KRAS GTPase cycling. These data provide a deeper understanding of the nanocluster-enhanced signaling in response to the environment. Furthermore, our methodology is applicable to assemblies of many other membrane GTPases and lipid nanoparticle-based formulations of stable protein oligomers with enhanced cooperativity.
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Affiliation(s)
- Soo-Yeon Lee
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi-Do, South Korea
| | - Ki-Young Lee
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi-Do, South Korea
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13
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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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14
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Hanrahan AJ, Chen Z, Rosen N, Solit DB. BRAF - a tumour-agnostic drug target with lineage-specific dependencies. Nat Rev Clin Oncol 2024; 21:224-247. [PMID: 38278874 DOI: 10.1038/s41571-023-00852-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2023] [Indexed: 01/28/2024]
Abstract
In June 2022, the FDA granted Accelerated Approval to the BRAF inhibitor dabrafenib in combination with the MEK inhibitor trametinib for the treatment of adult and paediatric patients (≥6 years of age) with unresectable or metastatic BRAFV600E-mutant solid tumours, except for BRAFV600E-mutant colorectal cancers. The histology-agnostic approval of dabrafenib plus trametinib marks the culmination of two decades of research into the landscape of BRAF mutations in human cancers, the biochemical mechanisms underlying BRAF-mediated tumorigenesis, and the clinical development of selective RAF and MEK inhibitors. Although the majority of patients with BRAFV600E-mutant tumours derive clinical benefit from BRAF inhibitor-based combinations, resistance to treatment develops in most. In this Review, we describe the biochemical basis for oncogenic BRAF-induced activation of MAPK signalling and pan-cancer and lineage-specific mechanisms of intrinsic, adaptive and acquired resistance to BRAF inhibitors. We also discuss novel RAF inhibitors and drug combinations designed to delay the emergence of treatment resistance and/or expand the population of patients with BRAF-mutant cancers who benefit from molecularly targeted therapies.
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Affiliation(s)
- Aphrothiti J Hanrahan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ziyu Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Physiology, Biophysics & Systems Biology, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA
| | - Neal Rosen
- Molecular Pharmacology Program, Sloan Kettering Institute for Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - David B Solit
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Weill Cornell Medical College, Cornell University, New York, NY, USA.
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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15
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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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16
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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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17
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Lee KY. Membrane-Driven Dimerization of the Peripheral Membrane Protein KRAS: Implications for Downstream Signaling. Int J Mol Sci 2024; 25:2530. [PMID: 38473778 DOI: 10.3390/ijms25052530] [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: 12/15/2023] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
Transient homo-dimerization of the RAS GTPase at the plasma membrane has been shown to promote the mitogen-activated protein kinase (MAPK) signaling pathway essential for cell proliferation and oncogenesis. To date, numerous crystallographic studies have focused on the well-defined GTPase domains of RAS isoforms, which lack the disordered C-terminal membrane anchor, thus providing limited structural insight into membrane-bound RAS molecules. Recently, lipid-bilayer nanodisc platforms and paramagnetic relaxation enhancement (PRE) analyses have revealed several distinct structures of the membrane-anchored homodimers of KRAS, an isoform that is most frequently mutated in human cancers. The KRAS dimerization interface is highly plastic and altered by biologically relevant conditions, including oncogenic mutations, the nucleotide states of the protein, and the lipid composition. Notably, PRE-derived structures of KRAS homodimers on the membrane substantially differ in terms of the relative orientation of the protomers at an "α-α" dimer interface comprising two α4-α5 regions. This interface plasticity along with the altered orientations of KRAS on the membrane impact the accessibility of KRAS to downstream effectors and regulatory proteins. Further, nanodisc platforms used to drive KRAS dimerization can be used to screen potential anticancer drugs that target membrane-bound RAS dimers and probe their structural mechanism of action.
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Affiliation(s)
- Ki-Young Lee
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Pocheon-si 11160, Gyeonggi-Do, Republic of Korea
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18
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Whitley MJ, Tran TH, Rigby M, Yi M, Dharmaiah S, Waybright TJ, Ramakrishnan N, Perkins S, Taylor T, Messing S, Esposito D, Nissley DV, McCormick F, Stephen AG, Turbyville T, Cornilescu G, Simanshu DK. Comparative analysis of KRAS4a and KRAS4b splice variants reveals distinctive structural and functional properties. SCIENCE ADVANCES 2024; 10:eadj4137. [PMID: 38354232 DOI: 10.1126/sciadv.adj4137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 01/12/2024] [Indexed: 02/16/2024]
Abstract
KRAS, the most frequently mutated oncogene in human cancer, produces two isoforms, KRAS4a and KRAS4b, through alternative splicing. These isoforms differ in exon 4, which encodes the final 15 residues of the G-domain and hypervariable regions (HVRs), vital for trafficking and membrane localization. While KRAS4b has been extensively studied, KRAS4a has been largely overlooked. Our multidisciplinary study compared the structural and functional characteristics of KRAS4a and KRAS4b, revealing distinct structural properties and thermal stability. Position 151 influences KRAS4a's thermal stability, while position 153 affects binding to RAF1 CRD protein. Nuclear magnetic resonance analysis identified localized structural differences near sequence variations and provided a solution-state conformational ensemble. Notably, KRAS4a exhibits substantial transcript abundance in bile ducts, liver, and stomach, with transcript levels approaching KRAS4b in the colon and rectum. Functional disparities were observed in full-length KRAS variants, highlighting the impact of HVR variations on interaction with trafficking proteins and downstream effectors like RAF and PI3K within cells.
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Affiliation(s)
- Matthew J Whitley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Timothy H Tran
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Megan Rigby
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Ming Yi
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Srisathiyanarayanan Dharmaiah
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Timothy J Waybright
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Nitya Ramakrishnan
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Shelley Perkins
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Troy Taylor
- 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
| | - Dominic Esposito
- 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
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, 1450 3rd Street, San Francisco, CA, USA
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Thomas Turbyville
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Gabriel Cornilescu
- 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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19
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Sharma AK, Pei J, Yang Y, Dyba M, Smith B, Rabara D, Larsen EK, Lightstone FC, Esposito D, Stephen AG, Wang B, Beltran PJ, Wallace E, Nissley DV, McCormick F, Maciag AE. Revealing the mechanism of action of a first-in-class covalent inhibitor of KRASG12C (ON) and other functional properties of oncogenic KRAS by 31P NMR. J Biol Chem 2024; 300:105650. [PMID: 38237681 PMCID: PMC10877953 DOI: 10.1016/j.jbc.2024.105650] [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: 09/18/2023] [Revised: 12/27/2023] [Accepted: 12/29/2023] [Indexed: 02/17/2024] Open
Abstract
Individual oncogenic KRAS mutants confer distinct differences in biochemical properties and signaling for reasons that are not well understood. KRAS activity is closely coupled to protein dynamics and is regulated through two interconverting conformations: state 1 (inactive, effector binding deficient) and state 2 (active, effector binding enabled). Here, we use 31P NMR to delineate the differences in state 1 and state 2 populations present in WT and common KRAS oncogenic mutants (G12C, G12D, G12V, G13D, and Q61L) bound to its natural substrate GTP or a commonly used nonhydrolyzable analog GppNHp (guanosine-5'-[(β,γ)-imido] triphosphate). Our results show that GppNHp-bound proteins exhibit significant state 1 population, whereas GTP-bound KRAS is primarily (90% or more) in state 2 conformation. This observation suggests that the predominance of state 1 shown here and in other studies is related to GppNHp and is most likely nonexistent in cells. We characterize the impact of this differential conformational equilibrium of oncogenic KRAS on RAF1 kinase effector RAS-binding domain and intrinsic hydrolysis. Through a KRAS G12C drug discovery, we have identified a novel small-molecule inhibitor, BBO-8956, which is effective against both GDP- and GTP-bound KRAS G12C. We show that binding of this inhibitor significantly perturbs state 1-state 2 equilibrium and induces an inactive state 1 conformation in GTP-bound KRAS G12C. In the presence of BBO-8956, RAF1-RAS-binding domain is unable to induce a signaling competent state 2 conformation within the ternary complex, demonstrating the mechanism of action for this novel and active-conformation inhibitor.
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Affiliation(s)
- Alok K Sharma
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, Maryland, USA.
| | - Jun Pei
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Yue Yang
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Marcin Dyba
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, Maryland, USA
| | - Brian Smith
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, Maryland, USA
| | - Dana Rabara
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, Maryland, USA
| | - Erik K Larsen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, Maryland, USA
| | - Felice C Lightstone
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Dominic Esposito
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, Maryland, USA
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, Maryland, USA
| | - Bin Wang
- BridgeBio Oncology Therapeutics, BridgeBio Pharma, Inc, Palo Alto, California, USA
| | - Pedro J Beltran
- BridgeBio Oncology Therapeutics, BridgeBio Pharma, Inc, Palo Alto, California, USA
| | - Eli Wallace
- BridgeBio Oncology Therapeutics, BridgeBio Pharma, Inc, Palo Alto, California, USA
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, Maryland, USA
| | - Frank McCormick
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, Maryland, USA; BridgeBio Oncology Therapeutics, BridgeBio Pharma, Inc, Palo Alto, California, USA; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Anna E Maciag
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, Maryland, USA.
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20
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Riaud M, Maxwell J, Soria-Bretones I, Dankner M, Li M, Rose AAN. The role of CRAF in cancer progression: from molecular mechanisms to precision therapies. Nat Rev Cancer 2024; 24:105-122. [PMID: 38195917 DOI: 10.1038/s41568-023-00650-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/27/2023] [Indexed: 01/11/2024]
Abstract
The RAF family of kinases includes key activators of the pro-tumourigenic mitogen-activated protein kinase pathway. Hyperactivation of RAF proteins, particularly BRAF and CRAF, drives tumour progression and drug resistance in many types of cancer. Although BRAF is the most studied RAF protein, partially owing to its high mutation incidence in melanoma, the role of CRAF in tumourigenesis and drug resistance is becoming increasingly clinically relevant. Here, we summarize the main known regulatory mechanisms and gene alterations that contribute to CRAF activity, highlighting the different oncogenic roles of CRAF, and categorize RAF1 (CRAF) mutations according to the effect on kinase activity. Additionally, we emphasize the effect that CRAF alterations may have on drug resistance and how precision therapies could effectively target CRAF-dependent tumours. Here, we discuss preclinical and clinical findings that may lead to improved treatments for all types of oncogenic RAF1 alterations in cancer.
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Affiliation(s)
- Melody Riaud
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada
| | - Jennifer Maxwell
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada
- Division of Experimental Medicine, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Isabel Soria-Bretones
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Matthew Dankner
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada
- Faculty of Medicine, McGill University, Montreal, Quebec, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - Meredith Li
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada
| | - April A N Rose
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada.
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada.
- Division of Experimental Medicine, Faculty of Medicine, McGill University, Montreal, Quebec, Canada.
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21
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Weng C, Faure AJ, Escobedo A, Lehner B. The energetic and allosteric landscape for KRAS inhibition. Nature 2024; 626:643-652. [PMID: 38109937 PMCID: PMC10866706 DOI: 10.1038/s41586-023-06954-0] [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: 12/06/2022] [Accepted: 12/07/2023] [Indexed: 12/20/2023]
Abstract
Thousands of proteins have been validated genetically as therapeutic targets for human diseases1. However, very few have been successfully targeted, and many are considered 'undruggable'. This is particularly true for proteins that function via protein-protein interactions-direct inhibition of binding interfaces is difficult and requires the identification of allosteric sites. However, most proteins have no known allosteric sites, and a comprehensive allosteric map does not exist for any protein. Here we address this shortcoming by charting multiple global atlases of inhibitory allosteric communication in KRAS. We quantified the effects of more than 26,000 mutations on the folding of KRAS and its binding to six interaction partners. Genetic interactions in double mutants enabled us to perform biophysical measurements at scale, inferring more than 22,000 causal free energy changes. These energy landscapes quantify how mutations tune the binding specificity of a signalling protein and map the inhibitory allosteric sites for an important therapeutic target. Allosteric propagation is particularly effective across the central β-sheet of KRAS, and multiple surface pockets are genetically validated as allosterically active, including a distal pocket in the C-terminal lobe of the protein. Allosteric mutations typically inhibit binding to all tested effectors, but they can also change the binding specificity, revealing the regulatory, evolutionary and therapeutic potential to tune pathway activation. Using the approach described here, it should be possible to rapidly and comprehensively identify allosteric target sites in many proteins.
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Affiliation(s)
- Chenchun Weng
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Andre J Faure
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Albert Escobedo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ben Lehner
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- University Pompeu Fabra (UPF), Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
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22
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Xiong D, Qiu Y, Zhao J, Zhou Y, Lee D, Gupta S, Torres M, Lu W, Liang S, Kang JJ, Eng C, Loscalzo J, Cheng F, Yu H. Structurally-informed human interactome reveals proteome-wide perturbations by disease mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.24.538110. [PMID: 37162909 PMCID: PMC10168245 DOI: 10.1101/2023.04.24.538110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Human genome sequencing studies have identified numerous loci associated with complex diseases. However, translating human genetic and genomic findings to disease pathobiology and therapeutic discovery remains a major challenge at multiscale interactome network levels. Here, we present a deep-learning-based ensemble framework, termed PIONEER (Protein-protein InteractiOn iNtErfacE pRediction), that accurately predicts protein binding partner-specific interfaces for all known protein interactions in humans and seven other common model organisms, generating comprehensive structurally-informed protein interactomes. We demonstrate that PIONEER outperforms existing state-of-the-art methods. We further systematically validated PIONEER predictions experimentally through generating 2,395 mutations and testing their impact on 6,754 mutation-interaction pairs, confirming the high quality and validity of PIONEER predictions. We show that disease-associated mutations are enriched in PIONEER-predicted protein-protein interfaces after mapping mutations from ~60,000 germline exomes and ~36,000 somatic genomes. We identify 586 significant protein-protein interactions (PPIs) enriched with PIONEER-predicted interface somatic mutations (termed oncoPPIs) from pan-cancer analysis of ~11,000 tumor whole-exomes across 33 cancer types. We show that PIONEER-predicted oncoPPIs are significantly associated with patient survival and drug responses from both cancer cell lines and patient-derived xenograft mouse models. We identify a landscape of PPI-perturbing tumor alleles upon ubiquitination by E3 ligases, and we experimentally validate the tumorigenic KEAP1-NRF2 interface mutation p.Thr80Lys in non-small cell lung cancer. We show that PIONEER-predicted PPI-perturbing alleles alter protein abundance and correlates with drug responses and patient survival in colon and uterine cancers as demonstrated by proteogenomic data from the National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium. PIONEER, implemented as both a web server platform and a software package, identifies functional consequences of disease-associated alleles and offers a deep learning tool for precision medicine at multiscale interactome network levels.
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Affiliation(s)
- Dapeng Xiong
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Center for Innovative Proteomics, Cornell University, Ithaca, NY 14853, USA
| | - Yunguang Qiu
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Junfei Zhao
- Department of Systems Biology, Herbert Irving Comprehensive Center, Columbia University, New York, NY 10032, USA
| | - Yadi Zhou
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Dongjin Lee
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Shobhita Gupta
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Center for Innovative Proteomics, Cornell University, Ithaca, NY 14853, USA
- Biophysics Program, Cornell University, Ithaca, NY 14853, USA
| | - Mateo Torres
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Center for Innovative Proteomics, Cornell University, Ithaca, NY 14853, USA
| | - Weiqiang Lu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Siqi Liang
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jin Joo Kang
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Center for Innovative Proteomics, Cornell University, Ithaca, NY 14853, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Joseph Loscalzo
- Channing Division of Network Medicine, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Feixiong Cheng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Haiyuan Yu
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Center for Innovative Proteomics, Cornell University, Ithaca, NY 14853, USA
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23
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Zhang JZ, Nguyen WH, Greenwood N, Rose JC, Ong SE, Maly DJ, Baker D. Computationally designed sensors detect endogenous Ras activity and signaling effectors at subcellular resolution. Nat Biotechnol 2024:10.1038/s41587-023-02107-w. [PMID: 38273065 DOI: 10.1038/s41587-023-02107-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024]
Abstract
The utility of genetically encoded biosensors for sensing the activity of signaling proteins has been hampered by a lack of strategies for matching sensor sensitivity to the physiological concentration range of the target. Here we used computational protein design to generate intracellular sensors of Ras activity (LOCKR-based Sensor for Ras activity (Ras-LOCKR-S)) and proximity labelers of the Ras signaling environment (LOCKR-based, Ras activity-dependent Proximity Labeler (Ras-LOCKR-PL)). These tools allow the detection of endogenous Ras activity and labeling of the surrounding environment at subcellular resolution. Using these sensors in human cancer cell lines, we identified Ras-interacting proteins in oncogenic EML4-Alk granules and found that Src-Associated in Mitosis 68-kDa (SAM68) protein specifically enhances Ras activity in the granules. The ability to subcellularly localize endogenous Ras activity should deepen our understanding of Ras function in health and disease and may suggest potential therapeutic strategies.
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Affiliation(s)
- Jason Z Zhang
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
| | - William H Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Nathan Greenwood
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - John C Rose
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Shao-En Ong
- Department of Pharmacology, University of Washington, Seattle, WA, USA
| | - Dustin J Maly
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Department of Chemistry, University of Washington, Seattle, WA, USA.
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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24
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Castelli M, Marchetti F, Osuna S, F. Oliveira AS, Mulholland AJ, Serapian SA, Colombo G. Decrypting Allostery in Membrane-Bound K-Ras4B Using Complementary In Silico Approaches Based on Unbiased Molecular Dynamics Simulations. J Am Chem Soc 2024; 146:901-919. [PMID: 38116743 PMCID: PMC10785808 DOI: 10.1021/jacs.3c11396] [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: 10/13/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/21/2023]
Abstract
Protein functions are dynamically regulated by allostery, which enables conformational communication even between faraway residues, and expresses itself in many forms, akin to different "languages": allosteric control pathways predominating in an unperturbed protein are often unintuitively reshaped whenever biochemical perturbations arise (e.g., mutations). To accurately model allostery, unbiased molecular dynamics (MD) simulations require integration with a reliable method able to, e.g., detect incipient allosteric changes or likely perturbation pathways; this is because allostery can operate at longer time scales than those accessible by plain MD. Such methods are typically applied singularly, but we here argue their joint application─as a "multilingual" approach─could work significantly better. We successfully prove this through unbiased MD simulations (∼100 μs) of the widely studied, allosterically active oncotarget K-Ras4B, solvated and embedded in a phospholipid membrane, from which we decrypt allostery using four showcase "languages": Distance Fluctuation analysis and the Shortest Path Map capture allosteric hotspots at equilibrium; Anisotropic Thermal Diffusion and Dynamical Non-Equilibrium MD simulations assess perturbations upon, respectively, either superheating or hydrolyzing the GTP that oncogenically activates K-Ras4B. Chosen "languages" work synergistically, providing an articulate, mutually coherent, experimentally consistent picture of K-Ras4B allostery, whereby distinct traits emerge at equilibrium and upon GTP cleavage. At equilibrium, combined evidence confirms prominent allosteric communication from the membrane-embedded hypervariable region, through a hub comprising helix α5 and sheet β5, and up to the active site, encompassing allosteric "switches" I and II (marginally), and two proposed pockets. Upon GTP cleavage, allosteric perturbations mostly accumulate on the switches and documented interfaces.
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Affiliation(s)
- Matteo Castelli
- Department
of Chemistry, University of Pavia, viale T. Taramelli 12, 27100 Pavia, Italy
| | - Filippo Marchetti
- Department
of Chemistry, University of Pavia, viale T. Taramelli 12, 27100 Pavia, Italy
- INSTM, via G. Giusti 9, 50121 Florence, Italy
- E4
Computer Engineering, via Martiri delle libertà 66, 42019 Scandiano (RE), Italy
| | - Sílvia Osuna
- Institut
de Química Computacional i Catàlisi (IQCC) and Departament
de Química, Universitat de Girona, Girona, Catalonia E-17071, Spain
- ICREA, Barcelona, Catalonia E-08010, Spain
| | - A. Sofia F. Oliveira
- Centre for
Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Adrian J. Mulholland
- Centre for
Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Stefano A. Serapian
- Department
of Chemistry, University of Pavia, viale T. Taramelli 12, 27100 Pavia, Italy
| | - Giorgio Colombo
- Department
of Chemistry, University of Pavia, viale T. Taramelli 12, 27100 Pavia, Italy
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25
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Nissley DV, Stephen AG, Yi M, McCormick F. Progress in Targeting KRAS Directly. Methods Mol Biol 2024; 2797:1-12. [PMID: 38570448 DOI: 10.1007/978-1-0716-3822-4_1] [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] [Indexed: 04/05/2024]
Abstract
RAS research has entered the world of translational and clinical science. Progress has been based on our appreciation of the role of RAS mutations in different types of cancer and the effects of these mutations on the biochemical, structural, and biophysical properties of the RAS proteins themselves, particularly KRAS, on which most attention has been focused. This knowledge base, while still growing, has enabled creative chemical approaches to targeting KRAS directly. Our understanding of RAS signaling pathways in normal and cancer cells plays an important role for developing RAS inhibitors but also continues to reveal new approaches to targeting RAS through disruption of signaling complexes and downstream pathways.
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Affiliation(s)
- Dwight V Nissley
- 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
| | - Ming Yi
- 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
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26
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Chan AH, Simanshu DK. Crystallographic Studies of KRAS in Complex with Small Molecules and RAS-Binding Proteins. Methods Mol Biol 2024; 2797:47-65. [PMID: 38570452 DOI: 10.1007/978-1-0716-3822-4_5] [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] [Indexed: 04/05/2024]
Abstract
RAS proteins play a vital role in regulating downstream signaling and essential cellular processes, positioning them as key players in normal cellular physiology and disease development. Among the various isoforms of RAS, KRAS stands out as one of the most frequently mutated genes in human cancer. The prevalence of RAS mutations in cancer often involves single amino acid substitutions at codons 12, 13, or 61. These mutations disrupt the RAS protein's inherent ability to transition between its active and inactive states, resulting in a constant activation signal and driving uncontrolled cell growth. Crystallization and structural analysis of KRAS with inhibitors and RAS-binding proteins play a pivotal role in unraveling the structural and mechanistic details of KRAS function, aiding in drug discovery efforts, and advancing our understanding of KRAS-driven diseases. Here, we present our experimental methodology for crystallizing KRAS in the presence of covalent or non-covalent small molecules and proteins acting as effectors or regulators of RAS. We detail the techniques for successful crystallization and the subsequent optimization of crystallization conditions. The resulting crystals and their structures will provide valuable insights into the key interactions between KRAS and its partner proteins or potential inhibitors, offering a foundation for developing targeted therapies that are more potent and selective against KRAS-driven cancers.
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Affiliation(s)
- Albert H Chan
- 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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27
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Tariq M, Ikeya T, Togashi N, Fairall L, Kamei S, Mayooramurugan S, Abbott LR, Hasan A, Bueno-Alejo C, Sukegawa S, Romartinez-Alonso B, Muro Campillo MA, Hudson AJ, Ito Y, Schwabe JW, Dominguez C, Tanaka K. Structural insights into the complex of oncogenic KRas4B G12V and Rgl2, a RalA/B activator. Life Sci Alliance 2024; 7:e202302080. [PMID: 37833074 PMCID: PMC10576006 DOI: 10.26508/lsa.202302080] [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: 04/06/2023] [Revised: 09/28/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
About a quarter of total human cancers carry mutations in Ras isoforms. Accumulating evidence suggests that small GTPases, RalA, and RalB, and their activators, Ral guanine nucleotide exchange factors (RalGEFs), play an essential role in oncogenic Ras-induced signalling. We studied the interaction between human KRas4B and the Ras association (RA) domain of Rgl2 (Rgl2RA), one of the RA-containing RalGEFs. We show that the G12V oncogenic KRas4B mutation changes the interaction kinetics with Rgl2RA The crystal structure of the KRas4BG12V: Rgl2RA complex shows a 2:2 heterotetramer where the switch I and switch II regions of each KRasG12V interact with both Rgl2RA molecules. This structural arrangement is highly similar to the HRasE31K:RALGDSRA crystal structure and is distinct from the well-characterised Ras:Raf complex. Interestingly, the G12V mutation was found at the dimer interface of KRas4BG12V with its partner. Our study reveals a potentially distinct mode of Ras:effector complex formation by RalGEFs and offers a possible mechanistic explanation for how the oncogenic KRas4BG12V hyperactivates the RalA/B pathway.
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Affiliation(s)
- Mishal Tariq
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Teppei Ikeya
- https://ror.org/00ws30h19 Department of Chemistry, Tokyo Metropolitan University, Hachioji, Japan
| | - Naoyuki Togashi
- https://ror.org/00ws30h19 Department of Chemistry, Tokyo Metropolitan University, Hachioji, Japan
| | - Louise Fairall
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
- https://ror.org/04h699437 Leicester Institute of Structure and Chemical Biology, University of Leicester, Leicester, UK
| | - Shun Kamei
- https://ror.org/00ws30h19 Department of Chemistry, Tokyo Metropolitan University, Hachioji, Japan
| | - Sannojah Mayooramurugan
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Lauren R Abbott
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Anab Hasan
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Carlos Bueno-Alejo
- https://ror.org/04h699437 Leicester Institute of Structure and Chemical Biology, University of Leicester, Leicester, UK
| | - Sakura Sukegawa
- https://ror.org/00ws30h19 Department of Chemistry, Tokyo Metropolitan University, Hachioji, Japan
| | - Beatriz Romartinez-Alonso
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
- https://ror.org/04h699437 Leicester Institute of Structure and Chemical Biology, University of Leicester, Leicester, UK
| | - Miguel Angel Muro Campillo
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Andrew J Hudson
- https://ror.org/04h699437 Leicester Institute of Structure and Chemical Biology, University of Leicester, Leicester, UK
- https://ror.org/04h699437 Department of Chemistry, University of Leicester, Leicester, UK
| | - Yutaka Ito
- https://ror.org/00ws30h19 Department of Chemistry, Tokyo Metropolitan University, Hachioji, Japan
| | - John Wr Schwabe
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
- https://ror.org/04h699437 Leicester Institute of Structure and Chemical Biology, University of Leicester, Leicester, UK
| | - Cyril Dominguez
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
- https://ror.org/04h699437 Leicester Institute of Structure and Chemical Biology, University of Leicester, Leicester, UK
| | - Kayoko Tanaka
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
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28
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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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29
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Wang P, Laster K, Jia X, Dong Z, Liu K. Targeting CRAF kinase in anti-cancer therapy: progress and opportunities. Mol Cancer 2023; 22:208. [PMID: 38111008 PMCID: PMC10726672 DOI: 10.1186/s12943-023-01903-x] [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: 08/31/2023] [Accepted: 11/16/2023] [Indexed: 12/20/2023] Open
Abstract
The RAS/mitogen-activated protein kinase (MAPK) signaling cascade is commonly dysregulated in human malignancies by processes driven by RAS or RAF oncogenes. Among the members of the RAF kinase family, CRAF plays an important role in the RAS-MAPK signaling pathway, as well as in the progression of cancer. Recent research has provided evidence implicating the role of CRAF in the physiological regulation and the resistance to BRAF inhibitors through MAPK-dependent and MAPK-independent mechanisms. Nevertheless, the effectiveness of solely targeting CRAF kinase activity remains controversial. Moreover, the kinase-independent function of CRAF may be essential for lung cancers with KRAS mutations. It is imperative to develop strategies to enhance efficacy and minimize toxicity in tumors driven by RAS or RAF oncogenes. The review investigates CRAF alterations observed in cancers and unravels the distinct roles of CRAF in cancers propelled by diverse oncogenes. This review also seeks to summarize CRAF-interacting proteins and delineate CRAF's regulation across various cancer hallmarks. Additionally, we discuss recent advances in pan-RAF inhibitors and their combination with other therapeutic approaches to improve treatment outcomes and minimize adverse effects in patients with RAF/RAS-mutant tumors. By providing a comprehensive understanding of the multifaceted role of CRAF in cancers and highlighting the latest developments in RAF inhibitor therapies, we endeavor to identify synergistic targets and elucidate resistance pathways, setting the stage for more robust and safer combination strategies for cancer treatment.
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Affiliation(s)
- Penglei Wang
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450000, China
- Tianjian Laboratory for Advanced Biomedical Sciences, Zhengzhou, 450052, Henan, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, China
| | - Kyle Laster
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, China
| | - Xuechao Jia
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450000, China
- Tianjian Laboratory for Advanced Biomedical Sciences, Zhengzhou, 450052, Henan, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, China
| | - Zigang Dong
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450000, China.
- Tianjian Laboratory for Advanced Biomedical Sciences, Zhengzhou, 450052, Henan, China.
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, China.
- Department of Pathophysiology, School of Basic Medical Sciences, China-US (Henan) Hormel Cancer Institute, AMS, College of Medicine, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, Henan, China.
| | - Kangdong Liu
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450000, China.
- Tianjian Laboratory for Advanced Biomedical Sciences, Zhengzhou, 450052, Henan, China.
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, China.
- Department of Pathophysiology, School of Basic Medical Sciences, China-US (Henan) Hormel Cancer Institute, AMS, College of Medicine, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, Henan, China.
- Basic Medicine Sciences Research Center, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China.
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, 450000, Henan, China.
- Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou University, Zhengzhou, 450000, Henan, China.
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30
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Bahar ME, Kim HJ, Kim DR. Targeting the RAS/RAF/MAPK pathway for cancer therapy: from mechanism to clinical studies. Signal Transduct Target Ther 2023; 8:455. [PMID: 38105263 PMCID: PMC10725898 DOI: 10.1038/s41392-023-01705-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/03/2023] [Accepted: 11/12/2023] [Indexed: 12/19/2023] Open
Abstract
Metastatic dissemination of solid tumors, a leading cause of cancer-related mortality, underscores the urgent need for enhanced insights into the molecular and cellular mechanisms underlying metastasis, chemoresistance, and the mechanistic backgrounds of individuals whose cancers are prone to migration. The most prevalent signaling cascade governed by multi-kinase inhibitors is the mitogen-activated protein kinase (MAPK) pathway, encompassing the RAS-RAF-MAPK kinase (MEK)-extracellular signal-related kinase (ERK) pathway. RAF kinase is a primary mediator of the MAPK pathway, responsible for the sequential activation of downstream targets, such as MEK and the transcription factor ERK, which control numerous cellular and physiological processes, including organism development, cell cycle control, cell proliferation and differentiation, cell survival, and death. Defects in this signaling cascade are associated with diseases such as cancer. RAF inhibitors (RAFi) combined with MEK blockers represent an FDA-approved therapeutic strategy for numerous RAF-mutant cancers, including melanoma, non-small cell lung carcinoma, and thyroid cancer. However, the development of therapy resistance by cancer cells remains an important barrier. Autophagy, an intracellular lysosome-dependent catabolic recycling process, plays a critical role in the development of RAFi resistance in cancer. Thus, targeting RAF and autophagy could be novel treatment strategies for RAF-mutant cancers. In this review, we delve deeper into the mechanistic insights surrounding RAF kinase signaling in tumorigenesis and RAFi-resistance. Furthermore, we explore and discuss the ongoing development of next-generation RAF inhibitors with enhanced therapeutic profiles. Additionally, this review sheds light on the functional interplay between RAF-targeted therapies and autophagy in cancer.
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Affiliation(s)
- Md Entaz Bahar
- Department of Biochemistry and Convergence Medical Sciences and Institute of Medical Science, Gyeongsang National University, College of Medicine, Jinju, South Korea
| | - Hyun Joon Kim
- Department of Anatomy and Convergence Medical Sciences and Institute of Medical Science, Gyeongsang National University, College of Medicine, Jinju, South Korea
| | - Deok Ryong Kim
- Department of Biochemistry and Convergence Medical Sciences and Institute of Medical Science, Gyeongsang National University, College of Medicine, Jinju, South Korea.
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31
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Ta L, Tsai BL, Deng W, Sha J, Varuzhanyan G, Tran W, Wohlschlegel JA, Carr-Ascher JR, Witte ON. Wild-type C-Raf gene dosage and dimerization drive prostate cancer metastasis. iScience 2023; 26:108480. [PMID: 38089570 PMCID: PMC10711388 DOI: 10.1016/j.isci.2023.108480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 10/04/2023] [Accepted: 11/15/2023] [Indexed: 02/01/2024] Open
Abstract
Mutated Ras and Raf kinases are well-known to promote cancer metastasis via flux through the Ras/Raf/MEK/ERK (mitogen-activated protein kinase [MAPK]) pathway. A role for non-mutated Raf in metastasis is also emerging, but the key mechanisms remain unclear. Elevated expression of any of the three wild-type Raf family members (C, A, or B) can drive metastasis. We utilized an in vivo model to show that wild-type C-Raf overexpression can promote metastasis of immortalized prostate cells in a gene dosage-dependent manner. Analysis of the transcriptomic and phosphoproteomic landscape indicated that C-Raf-driven metastasis is accompanied by upregulated MAPK signaling. Use of C-Raf mutants demonstrated that the dimerization domain, but not its kinase activity, is essential for metastasis. Endogenous Raf monomer knockouts revealed that C-Raf's ability to form dimers with endogenous Raf molecules is important for promoting metastasis. These data identify wild-type C-Raf heterodimer signaling as a potential target for treating metastatic disease.
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Affiliation(s)
- Lisa Ta
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles; Los Angeles, CA 90095, USA
| | - Brandon L. Tsai
- Department of Human Genetics, University of California, Los Angeles; Los Angeles, CA 90095, USA
| | - Weixian Deng
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA 90095, USA
| | - Jihui Sha
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA 90095, USA
| | - Grigor Varuzhanyan
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles; Los Angeles, CA 90095, USA
| | - Wendy Tran
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles; Los Angeles, CA 90095, USA
| | - James A. Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA 90095, USA
| | - Janai R. Carr-Ascher
- Department of Internal Medicine, Division of Hematology/Oncology, University of California, Davis, Sacramento, CA 95817, USA
- Department of Orthopedic Surgery, University of California, Davis; Sacramento, CA 95817, USA
| | - Owen N. Witte
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles; Los Angeles, CA 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles; Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles; Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles; Los Angeles, CA 90095, USA
- Parker Institute for Cancer Immunotherapy, University of California, Los Angeles; Los Angeles, CA 90095, USA
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32
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Vasta JD, Michaud A, Zimprich CA, Beck MT, Swiatnicki MR, Zegzouti H, Thomas MR, Wilkinson J, Crapster JA, Robers MB. Protomer selectivity of type II RAF inhibitors within the RAS/RAF complex. Cell Chem Biol 2023; 30:1354-1365.e6. [PMID: 37643616 DOI: 10.1016/j.chembiol.2023.07.019] [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: 02/08/2023] [Revised: 05/12/2023] [Accepted: 07/31/2023] [Indexed: 08/31/2023]
Abstract
RAF dimer inhibitors offer therapeutic potential in RAF- and RAS-driven cancers. The utility of such drugs is predicated on their capacity to occupy both RAF protomers in the RAS-RAF signaling complex. Here we describe a method to conditionally quantify drug-target occupancy at selected RAF protomers within an active RAS-RAF complex in cells. RAF target engagement can be measured in the presence or absence of any mutant KRAS allele, enabling the high-affinity state of RAF dimer inhibitors to be quantified in the cellular milieu. The intracellular protomer selectivity of clinical-stage type II RAF inhibitors revealed that ARAF protomer engagement, but not engagement of BRAF or CRAF, is commensurate with inhibition of MAPK signaling in various mutant RAS cell lines. Our results support a fundamental role for ARAF in mutant RAS signaling and reveal poor ARAF protomer vulnerability for a cohort of RAF inhibitors undergoing clinical evaluation.
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Tao Y, Zhao J, Yin J, Zhou Z, Li H, Zang J, Wang T, Wang Y, Guo C, Zhu F, Dai S, Wang F, Zhao H, Mao H, Liu F, Zhang L, Wang Q. Hepatocyte TIPE2 is a fasting-induced Raf-1 inactivator that drives hepatic gluconeogenesis to maintain glucose homeostasis. Metabolism 2023; 148:155690. [PMID: 37717724 DOI: 10.1016/j.metabol.2023.155690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 08/21/2023] [Accepted: 09/13/2023] [Indexed: 09/19/2023]
Abstract
BACKGROUND The liver regulates metabolic balance during fasting-feeding cycle. Hepatic adaptation to fasting is precisely modulated on multiple levels. Tumor necrosis factor-α-induced protein 8-like 2 (TIPE2) is a negative regulator of immunity that reduces several liver pathologies, but its physiological roles in hepatic metabolism are largely unknown. METHODS TIPE2 expression was examined in mouse liver during fasting-feeding cycle. TIPE2-knockout mice, liver-specific TIPE2-knockout mice, liver-specific TIPE2-overexpressed mice were examined for fasting blood glucose and pyruvate tolerance test. Primary hepatocytes or liver tissues from these mice were evaluated for glucose production, lipid accumulation, gene expression and regulatory pathways. TIPE2 interaction with Raf-1 and TIPE2 transcription regulated by PPAR-α were examined using gene overexpression or knockdown, co-immunoprecipitation, western blot, luciferase reporter assay and DNA-protein binding assay. RESULTS TIPE2 expression was upregulated in fasted mouse liver and starved hepatocytes, which was positively correlated with gluconeogenic genes. Liver-specific TIPE2 deficiency impaired blood glucose homeostasis and gluconeogenic capacity in mice upon fasting, while liver-specific TIPE2 overexpression elevated fasting blood glucose and hepatic gluconeogenesis in mice. In primary hepatocytes upon starvation, TIPE2 interacted with Raf-1 to accelerate its ubiquitination and degradation, resulting in ERK deactivation and FOXO1 maintenance to sustain gluconeogenesis. During prolonged fasting, hepatic TIPE2 deficiency caused aberrant activation of ERK-mTORC1 axis that increased hepatic lipid accumulation via lipogenesis. In hepatocytes upon starvation, PPAR-α bound with TIPE2 promoter and triggered its transcriptional expression. CONCLUSIONS Hepatocyte TIPE2 is a PPAR-α-induced Raf-1 inactivator that sustains hepatic gluconeogenesis and prevents excessive hepatic lipid accumulation, playing beneficial roles in hepatocyte adaptation to fasting.
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Affiliation(s)
- Yan Tao
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Jingyuan Zhao
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Jilong Yin
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Zixin Zhou
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Huijie Li
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Jinhao Zang
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Tianci Wang
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Yalin Wang
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Chun Guo
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Faliang Zhu
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Shen Dai
- Department of Physiology and Pathology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Fuwu Wang
- Key Laboratory for Experimental Teratology of Ministry of Education, Shandong Key Laboratory of Mental Disorders, Department of Histology and Embryology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Hui Zhao
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250033, China
| | - Haiting Mao
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250033, China
| | - Fengming Liu
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Lining Zhang
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Qun Wang
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China.
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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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35
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Bonsor DA, Simanshu DK. Structural insights into the role of SHOC2-MRAS-PP1C complex in RAF activation. FEBS J 2023; 290:4852-4863. [PMID: 37074066 PMCID: PMC10584989 DOI: 10.1111/febs.16800] [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: 02/17/2023] [Revised: 04/07/2023] [Accepted: 04/18/2023] [Indexed: 04/20/2023]
Abstract
RAF activation is a key step for signalling through the mitogen-activated protein kinase (MAPK) pathway. The SHOC2 protein, along with MRAS and PP1C, forms a high affinity, heterotrimeric holoenzyme that activates RAF kinases by dephosphorylating a specific phosphoserine. Recently, our research, along with that of three other teams, has uncovered valuable structural and functional insights into the SHOC2-MRAS-PP1C (SMP) holoenzyme complex. In this structural snapshot, we review SMP complex assembly, the dependency on the bound-nucleotide state of MRAS, the substitution of MRAS by the canonical RAS proteins and the roles of SHOC2 and MRAS on PP1C activity and specificity. Furthermore, we discuss the effect of several RASopathy mutations identified within the SMP complex and explore potential therapeutic approaches for targeting the SMP complex in RAS/RAF-driven cancers and RASopathies.
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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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36
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Johnson CW, Fetics SK, Davis KP, Rodrigues JA, Mattos C. Allosteric site variants affect GTP hydrolysis on Ras. Protein Sci 2023; 32:e4767. [PMID: 37615343 PMCID: PMC10510474 DOI: 10.1002/pro.4767] [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: 04/21/2023] [Revised: 08/03/2023] [Accepted: 08/21/2023] [Indexed: 08/25/2023]
Abstract
RAS GTPases are proto-oncoproteins that regulate cell growth, proliferation, and differentiation in response to extracellular signals. The signaling functions of RAS, and other small GTPases, are dependent on their ability to cycle between GDP-bound and GTP-bound states. Structural analyses suggest that GTP hydrolysis catalyzed by HRAS can be regulated by an allosteric site located between helices 3, 4, and loop 7. Here we explore the relationship between intrinsic GTP hydrolysis on HRAS and the position of helix 3 and loop 7 through manipulation of the allosteric site, showing that the two sites are functionally connected. We generated several hydrophobic mutations in the allosteric site of HRAS to promote shifts in helix 3 relative to helix 4. By combining crystallography and enzymology to study these mutants, we show that closure of the allosteric site correlates with increased hydrolysis of GTP on HRAS in solution. Interestingly, binding to the RAS binding domain of RAF kinase (RAF-RBD) inhibits GTP hydrolysis in the mutants. This behavior may be representative of a cluster of mutations found in human tumors, which potentially cooperate with RAF complex formation to stabilize the GTP-bound state of RAS.
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Affiliation(s)
- Christian W. Johnson
- Department of Chemistry and Chemical BiologyNortheastern UniversityBostonMassachusettsUSA
| | - Susan K. Fetics
- Department of Molecular and Structural BiochemistryNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Kathleen P. Davis
- Department of Molecular and Structural BiochemistryNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Jose A. Rodrigues
- Department of Chemistry and Chemical BiologyNortheastern UniversityBostonMassachusettsUSA
| | - Carla Mattos
- Department of Chemistry and Chemical BiologyNortheastern UniversityBostonMassachusettsUSA
- Department of Molecular and Structural BiochemistryNorth Carolina State UniversityRaleighNorth CarolinaUSA
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37
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Hansen AL, Xiang X, Yuan C, Bruschweiler-Li L, Brüschweiler R. Excited-state observation of active K-Ras reveals differential structural dynamics of wild-type versus oncogenic G12D and G12C mutants. Nat Struct Mol Biol 2023; 30:1446-1455. [PMID: 37640864 PMCID: PMC10584678 DOI: 10.1038/s41594-023-01070-z] [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: 05/17/2023] [Accepted: 07/17/2023] [Indexed: 08/31/2023]
Abstract
Despite the prominent role of the K-Ras protein in many different types of human cancer, major gaps in atomic-level information severely limit our understanding of its functions in health and disease. Here, we report the quantitative backbone structural dynamics of K-Ras by solution nuclear magnetic resonance spectroscopy of the active state of wild-type K-Ras bound to guanosine triphosphate (GTP) nucleotide and two of its oncogenic P-loop mutants, G12D and G12C, using a new nanoparticle-assisted spin relaxation method, relaxation dispersion and chemical exchange saturation transfer experiments covering the entire range of timescales from picoseconds to milliseconds. Our combined experiments allow detection and analysis of the functionally critical Switch I and Switch II regions, which have previously remained largely unobservable by X-ray crystallography and nuclear magnetic resonance spectroscopy. Our data reveal cooperative transitions of K-Ras·GTP to a highly dynamic excited state that closely resembles the partially disordered K-Ras·GDP state. These results advance our understanding of differential GTPase activities and signaling properties of the wild type versus mutants and may thus guide new strategies for the development of therapeutics.
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Affiliation(s)
- Alexandar L Hansen
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH, USA
| | - Xinyao Xiang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Chunhua Yuan
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH, USA
| | - Lei Bruschweiler-Li
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH, USA.
| | - Rafael Brüschweiler
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH, USA.
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA.
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA.
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38
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Chen PY, Huang BJ, Harris M, Boone C, Wang W, Carias H, Mesiona B, Mavrici D, Kohler AC, Bollag G, Zhang C, Zhang Y, Shannon K. Structural and functional analyses of a germline KRAS T50I mutation provide insights into Raf activation. JCI Insight 2023; 8:e168445. [PMID: 37681415 PMCID: PMC10544224 DOI: 10.1172/jci.insight.168445] [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: 01/04/2023] [Accepted: 08/02/2023] [Indexed: 09/09/2023] Open
Abstract
A T50I substitution in the K-Ras interswitch domain causes Noonan syndrome and emerged as a third-site mutation that restored the in vivo transforming activity and constitutive MAPK pathway activation by an attenuated KrasG12D,E37G oncogene in a mouse leukemia model. Biochemical and crystallographic data suggested that K-RasT50I increases MAPK signal output through a non-GTPase mechanism, potentially by promoting asymmetric Ras:Ras interactions between T50 and E162. We generated a "switchable" system in which K-Ras mutant proteins expressed at physiologic levels supplant the fms like tyrosine kinase 3 (FLT3) dependency of MOLM-13 leukemia cells lacking endogenous KRAS and used this system to interrogate single or compound G12D, T50I, D154Q, and E162L mutations. These studies support a key role for the asymmetric lateral assembly of K-Ras in a plasma membrane-distal orientation that promotes the formation of active Ras:Raf complexes in a membrane-proximal conformation. Disease-causing mutations such as T50I are a valuable starting point for illuminating normal Ras function, elucidating mechanisms of disease, and identifying potential therapeutic opportunities for Rasopathy disorders and cancer.
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Affiliation(s)
- Pan-Yu Chen
- Department of Pediatrics, UCSF, San Francisco, California, USA
| | | | - Max Harris
- Department of Pediatrics, UCSF, San Francisco, California, USA
| | | | - Weijie Wang
- Department of Pediatrics, UCSF, San Francisco, California, USA
| | - Heidi Carias
- Plexxikon Inc., South San Francisco, California, USA
| | - Brian Mesiona
- Plexxikon Inc., South San Francisco, California, USA
| | | | | | - Gideon Bollag
- Plexxikon Inc., South San Francisco, California, USA
| | - Chao Zhang
- Plexxikon Inc., South San Francisco, California, USA
| | - Ying Zhang
- Plexxikon Inc., South San Francisco, California, USA
| | - Kevin Shannon
- Department of Pediatrics, UCSF, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
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39
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Özgü E, Aydin E, Adibi A, Tokat ÜM, Tutar O, Hu J, Demiray I, Kurzrock R, Demiray M. Exceptional Response to MEK Inhibition in a Patient With RAF1-Mutant Myxofibrosarcoma: Case Report and Mechanistic Overview. JCO Precis Oncol 2023; 7:e2300299. [PMID: 38127827 PMCID: PMC10752463 DOI: 10.1200/po.23.00299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/25/2023] [Accepted: 10/11/2023] [Indexed: 12/23/2023] Open
Abstract
Complete response to Trametinib in a heavily-pretreated sarcoma: RAF1 as a predictor of MEKi Response
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Affiliation(s)
- Eylül Özgü
- Medicana International Atasehir Hospital, Demiray Precision Oncology Center, Istanbul, Turkey
| | - Esranur Aydin
- Medicana International Atasehir Hospital, Demiray Precision Oncology Center, Istanbul, Turkey
| | - Ashkan Adibi
- Medicana International Atasehir Hospital, Demiray Precision Oncology Center, Istanbul, Turkey
- Istanbul University, Institute of Oncology, Department of Basic Oncology, Division of Cancer Genetics, Istanbul, Turkey
| | - Ünal Metin Tokat
- Medicana International Atasehir Hospital, Demiray Precision Oncology Center, Istanbul, Turkey
| | - Onur Tutar
- İstanbul University-Cerrahpaşa, Cerrahpaşa Faculty of Medicine, Department of Internal Medicine, Istanbul, Turkey
| | - Jiancheng Hu
- Division of Cellular and Molecular Research, Singapore, Singapore
- Cancer and Stem Cell Program, Duke-NUS Medical School, Singapore, Singapore
| | - Irem Demiray
- Koc University, Department of Molecular Biology and Genetics, Istanbul, Turkey
| | - Razelle Kurzrock
- Medical College of Wisconsin, Milwaukee, WI
- WIN Consortium, Paris, France
| | - Mutlu Demiray
- Medicana International Atasehir Hospital, Demiray Precision Oncology Center, Istanbul, Turkey
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40
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Schulze CJ, Seamon KJ, Zhao Y, Yang YC, Cregg J, Kim D, Tomlinson A, Choy TJ, Wang Z, Sang B, Pourfarjam Y, Lucas J, Cuevas-Navarro A, Santos CA, Vides A, Li C, Marquez A, Zhong M, Vemulapalli V, Weller C, Gould A, Whalen DM, Salvador A, Milin A, Saldajeno-Concar M, Dinglasan N, Chen A, Evans J, Knox JE, Koltun ES, Singh M, Nichols R, Wildes D, Gill AL, Smith JAM, Lito P. Chemical remodeling of a cellular chaperone to target the active state of mutant KRAS. Science 2023; 381:794-799. [PMID: 37590355 PMCID: PMC10474815 DOI: 10.1126/science.adg9652] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 06/28/2023] [Indexed: 08/19/2023]
Abstract
The discovery of small-molecule inhibitors requires suitable binding pockets on protein surfaces. Proteins that lack this feature are considered undruggable and require innovative strategies for therapeutic targeting. KRAS is the most frequently activated oncogene in cancer, and the active state of mutant KRAS is such a recalcitrant target. We designed a natural product-inspired small molecule that remodels the surface of cyclophilin A (CYPA) to create a neomorphic interface with high affinity and selectivity for the active state of KRASG12C (in which glycine-12 is mutated to cysteine). The resulting CYPA:drug:KRASG12C tricomplex inactivated oncogenic signaling and led to tumor regressions in multiple human cancer models. This inhibitory strategy can be used to target additional KRAS mutants and other undruggable cancer drivers. Tricomplex inhibitors that selectively target active KRASG12C or multiple RAS mutants are in clinical trials now (NCT05462717 and NCT05379985).
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Affiliation(s)
| | - Kyle J. Seamon
- Department of Biology, Revolution Medicines, Inc., Redwood City, CA, 94063
| | - Yulei Zhao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer, New York, NY, 10065
| | - Yu C. Yang
- Department of Biology, Revolution Medicines, Inc., Redwood City, CA, 94063
| | - Jim Cregg
- Department of Discovery Chemistry, Revolution Medicines, Inc., Redwood City, CA, 94063
| | - Dongsung Kim
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer, New York, NY, 10065
| | - Aidan Tomlinson
- Department of Discovery Chemistry, Revolution Medicines, Inc., Redwood City, CA, 94063
| | - Tiffany J. Choy
- Department of Biology, Revolution Medicines, Inc., Redwood City, CA, 94063
| | - Zhican Wang
- Department of Non-clinical Development and Clinical Pharmacology, Revolution Medicines, Inc., Redwood City, CA, 94063
| | - Ben Sang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer, New York, NY, 10065
| | - Yasin Pourfarjam
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer, New York, NY, 10065
| | - Jessica Lucas
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer, New York, NY, 10065
| | - Antonio Cuevas-Navarro
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer, New York, NY, 10065
| | - Carlos Ayala Santos
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer, New York, NY, 10065
| | - Alberto Vides
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer, New York, NY, 10065
| | - Chuanchuan Li
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer, New York, NY, 10065
| | - Abby Marquez
- Department of Discovery Chemistry, Revolution Medicines, Inc., Redwood City, CA, 94063
| | - Mengqi Zhong
- Department of Discovery Chemistry, Revolution Medicines, Inc., Redwood City, CA, 94063
| | | | - Caroline Weller
- Department of Biology, Revolution Medicines, Inc., Redwood City, CA, 94063
| | - Andrea Gould
- Department of Biology, Revolution Medicines, Inc., Redwood City, CA, 94063
| | - Daniel M. Whalen
- Department of Discovery Chemistry, Revolution Medicines, Inc., Redwood City, CA, 94063
| | - Anthony Salvador
- Department of Discovery Chemistry, Revolution Medicines, Inc., Redwood City, CA, 94063
| | - Anthony Milin
- Department of Discovery Chemistry, Revolution Medicines, Inc., Redwood City, CA, 94063
| | - Mae Saldajeno-Concar
- Department of Discovery Chemistry, Revolution Medicines, Inc., Redwood City, CA, 94063
| | - Nuntana Dinglasan
- Department of Biology, Revolution Medicines, Inc., Redwood City, CA, 94063
| | - Anqi Chen
- Department of Discovery Chemistry, Revolution Medicines, Inc., Redwood City, CA, 94063
| | - Jim Evans
- Department of Biology, Revolution Medicines, Inc., Redwood City, CA, 94063
| | - John E. Knox
- Department of Discovery Chemistry, Revolution Medicines, Inc., Redwood City, CA, 94063
| | - Elena S. Koltun
- Department of Discovery Chemistry, Revolution Medicines, Inc., Redwood City, CA, 94063
| | - Mallika Singh
- Department of Biology, Revolution Medicines, Inc., Redwood City, CA, 94063
| | - Robert Nichols
- Department of Biology, Revolution Medicines, Inc., Redwood City, CA, 94063
| | - David Wildes
- Department of Biology, Revolution Medicines, Inc., Redwood City, CA, 94063
| | - Adrian L. Gill
- Department of Discovery Chemistry, Revolution Medicines, Inc., Redwood City, CA, 94063
| | | | - Piro Lito
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer, New York, NY, 10065
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065
- Department of Medicine, Weill Cornell Medical College, New York, NY, 10065
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41
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Chen X, An Y, Tan M, Xie D, Liu L, Xu B. Biological functions and research progress of eIF4E. Front Oncol 2023; 13:1076855. [PMID: 37601696 PMCID: PMC10435865 DOI: 10.3389/fonc.2023.1076855] [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: 11/04/2022] [Accepted: 01/30/2023] [Indexed: 08/22/2023] Open
Abstract
The eukaryotic translation initiation factor eIF4E can specifically bind to the cap structure of an mRNA 5' end, mainly regulating translation initiation and preferentially enhancing the translation of carcinogenesis related mRNAs. The expression of eIF4E is closely related to a variety of malignant tumors. In tumor cells, eIF4E activity is abnormally increased, which stimulates cell growth, metastasis and translation of related proteins. The main factors affecting eIF4E activity include intranuclear regulation, phosphorylation of 4EBPs, and phosphorylation and sumoylation of eIF4E. In this review, we summarize the biological functions and the research progress of eIF4E, the main influencing factors of eIF4E activity, and the recent progress of drugs targeting eIF4E, in the hope of providing new insights for the treatment of multiple malignancies and development of targeted drugs.
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Affiliation(s)
- Xiaocong Chen
- Department of Clinical Medicine, Fenyang College of Shanxi Medical University, Fenyang, China
| | - Yang An
- Department of Clinical Medicine, Fenyang College of Shanxi Medical University, Fenyang, China
| | - Mengsi Tan
- Department of Clinical Medicine, Fenyang College of Shanxi Medical University, Fenyang, China
| | - Dongrui Xie
- Department of Clinical Medicine, Fenyang College of Shanxi Medical University, Fenyang, China
| | - Ling Liu
- Department of Medical Laboratory Science, Fenyang College of Shanxi Medical University, Fenyang, China
- Key Laboratory of Lvliang for Clinical Molecular Diagnostics, Fenyang, China
- Department of Clinical Laboratory, Fenyang Hospital of Shanxi Province, Fenyang, China
| | - Benjin Xu
- Department of Medical Laboratory Science, Fenyang College of Shanxi Medical University, Fenyang, China
- Key Laboratory of Lvliang for Clinical Molecular Diagnostics, Fenyang, China
- Department of Clinical Laboratory, Fenyang Hospital of Shanxi Province, Fenyang, China
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42
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Ahmad M, Movileanu L. Multiplexed imaging for probing RAS-RAF interactions in living cells. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184173. [PMID: 37211322 PMCID: PMC10330472 DOI: 10.1016/j.bbamem.2023.184173] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/18/2023] [Accepted: 05/08/2023] [Indexed: 05/23/2023]
Abstract
GTP-bound RAS interacts with its protein effectors in response to extracellular stimuli, leading to chemical inputs for downstream pathways. Significant progress has been made in measuring these reversible protein-protein interactions (PPIs) in various cell-free environments. Yet, acquiring high sensitivity in heterogeneous solutions remains challenging. Here, using an intermolecular fluorescence resonance energy transfer (FRET) biosensing approach, we develop a method to visualize and localize HRAS-CRAF interactions in living cells. We demonstrate that the EGFR activation and the HRAS-CRAF complex formation can be concurrently probed in a single cell. This biosensing strategy discriminates EGF-stimulated HRAS-CRAF interactions at the cell and organelle membranes. In addition, we provide quantitative FRET measurements for assessing these transient PPIs in a cell-free environment. Finally, we prove the utility of this approach by showing that an EGFR-binding compound is a potent inhibitor of HRAS-CRAF interactions. The outcomes of this work form a fundamental basis for further explorations of the spatiotemporal dynamics of various signaling networks.
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Affiliation(s)
- Mohammad Ahmad
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA; Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, NY 13244, USA; The BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA.
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43
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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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44
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Cuevas-Navarro A, Wagner M, Van R, Swain M, Mo S, Columbus J, Allison MR, Cheng A, Messing S, Turbyville TJ, Simanshu DK, Sale MJ, McCormick F, Stephen AG, Castel P. RAS-dependent RAF-MAPK hyperactivation by pathogenic RIT1 is a therapeutic target in Noonan syndrome-associated cardiac hypertrophy. SCIENCE ADVANCES 2023; 9:eadf4766. [PMID: 37450595 PMCID: PMC10348673 DOI: 10.1126/sciadv.adf4766] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 06/14/2023] [Indexed: 07/18/2023]
Abstract
RIT1 is a RAS guanosine triphosphatase (GTPase) that regulates different aspects of signal transduction and is mutated in lung cancer, leukemia, and in the germline of individuals with Noonan syndrome. Pathogenic RIT1 proteins promote mitogen-activated protein kinase (MAPK) hyperactivation; however, this mechanism remains poorly understood. Here, we show that RAF kinases are direct effectors of membrane-bound mutant RIT1 necessary for MAPK activation. We identify critical residues in RIT1 that facilitate interaction with membrane lipids and show that these are necessary for association with RAF kinases and MAPK activation. Although mutant RIT1 binds to RAF kinases directly, it fails to activate MAPK signaling in the absence of classical RAS proteins. Consistent with aberrant RAF/MAPK activation as a driver of disease, we show that pathway inhibition alleviates cardiac hypertrophy in a mouse model of RIT1 mutant Noonan syndrome. These data shed light on the function of pathogenic RIT1 and identify avenues for therapeutic intervention.
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Affiliation(s)
- Antonio Cuevas-Navarro
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Morgan Wagner
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Richard Van
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Monalisa Swain
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Stephanie Mo
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - John Columbus
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Madeline R. Allison
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alice Cheng
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Simon Messing
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Thomas J. Turbyville
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Dhirendra K. Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Matthew J. Sale
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Frank McCormick
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Andrew G. Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Pau Castel
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
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45
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Chao FA, Chan AH, Dharmaiah S, Schwieters CD, Tran TH, Taylor T, Ramakrishnan N, Esposito D, Nissley DV, McCormick F, Simanshu DK, Cornilescu G. Reduced dynamic complexity allows structure elucidation of an excited state of KRAS G13D. Commun Biol 2023; 6:594. [PMID: 37268708 DOI: 10.1038/s42003-023-04960-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 05/19/2023] [Indexed: 06/04/2023] Open
Abstract
Localized dynamics of RAS, including regions distal to the nucleotide-binding site, is of high interest for elucidating the mechanisms by which RAS proteins interact with effectors and regulators and for designing inhibitors. Among several oncogenic mutants, methyl relaxation dispersion experiments reveal highly synchronized conformational dynamics in the active (GMPPNP-bound) KRASG13D, which suggests an exchange between two conformational states in solution. Methyl and 31P NMR spectra of active KRASG13D in solution confirm a two-state ensemble interconverting on the millisecond timescale, with a major Pγ atom peak corresponding to the dominant State 1 conformation and a secondary peak indicating an intermediate state different from the known State 2 conformation recognized by RAS effectors. High-resolution crystal structures of active KRASG13D and KRASG13D-RAF1 RBD complex provide snapshots of the State 1 and 2 conformations, respectively. We use residual dipolar couplings to solve and cross-validate the structure of the intermediate state of active KRASG13D, showing a conformation distinct from those of States 1 and 2 outside the known flexible switch regions. The dynamic coupling between the conformational exchange in the effector lobe and the breathing motion in the allosteric lobe is further validated by a secondary mutation in the allosteric lobe, which affects the conformational population equilibrium.
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Affiliation(s)
- Fa-An Chao
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, 21701, USA.
| | - Albert H Chan
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, 21701, USA
| | - Srisathiyanarayanan Dharmaiah
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, 21701, USA
| | - Charles D Schwieters
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Building 12A, 20892-5624, Bethesda, MD, USA
| | - Timothy H Tran
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, 21701, USA
| | - Troy Taylor
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, 21701, USA
| | - Nitya Ramakrishnan
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, 21701, USA
| | - Dominic Esposito
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, 21701, USA
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, 21701, USA
| | - Frank McCormick
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, 21701, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1450 3rd Street, San Francisco, CA, 94158, USA
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, 21701, USA.
| | - Gabriel Cornilescu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, 21701, USA.
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46
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Simanshu DK, Philips MR, Hancock JF. Consensus on the RAS dimerization hypothesis: Strong evidence for lipid-mediated clustering but not for G-domain-mediated interactions. Mol Cell 2023; 83:1210-1215. [PMID: 36990093 PMCID: PMC10150945 DOI: 10.1016/j.molcel.2023.03.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/24/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023]
Abstract
One of the open questions in RAS biology is the existence of RAS dimers and their role in RAF dimerization and activation. The idea of RAS dimers arose from the discovery that RAF kinases function as obligate dimers, which generated the hypothesis that RAF dimer formation might be nucleated by G-domain-mediated RAS dimerization. Here, we review the evidence for RAS dimerization and describe a recent discussion among RAS researchers that led to a consensus that the clustering of two or more RAS proteins is not due to the stable association of G-domains but, instead, is a consequence of RAS C-terminal membrane anchors and the membrane phospholipids with which they interact.
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Affiliation(s)
- Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
| | - Mark R Philips
- Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA.
| | - John F Hancock
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA.
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47
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Shi S, Zheng L, Ren Y, Wang Z. Impacts of Mutations in the P-Loop on Conformational Alterations of KRAS Investigated with Gaussian Accelerated Molecular Dynamics Simulations. Molecules 2023; 28:molecules28072886. [PMID: 37049650 PMCID: PMC10095679 DOI: 10.3390/molecules28072886] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/19/2023] [Accepted: 03/20/2023] [Indexed: 04/14/2023] Open
Abstract
G12 mutations heavily affect conformational transformation and activity of KRAS. In this study, Gaussian accelerated molecular dynamics (GaMD) simulations were performed on the GDP-bound wild-type (WT), G12A, G12D, and G12R KRAS to probe mutation-mediated impacts on conformational alterations of KRAS. The results indicate that three G12 mutations obviously affect the structural flexibility and internal dynamics of the switch domains. The analyses of the free energy landscapes (FELs) suggest that three G12 mutations induce more conformational states of KRAS and lead to more disordered switch domains. The principal component analysis shows that three G12 mutations change concerted motions and dynamics behavior of the switch domains. The switch domains mostly overlap with the binding region of KRAS to its effectors. Thus, the high disorder states and concerted motion changes of the switch domains induced by G12 mutations affect the activity of KRAS. The analysis of interaction network of GDP with KRAS signifies that the instability in the interactions of GDP and magnesium ion with the switch domain SW1 drives the high disordered state of the switch domains. This work is expected to provide theoretical aids for understanding the function of KRAS.
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Affiliation(s)
- Shuhua Shi
- School of Science, Shandong Jianzhu University, Jinan 250101, China
| | - Linqi Zheng
- School of Science, Shandong Jianzhu University, Jinan 250101, China
| | - Yonglian Ren
- School of Science, Shandong Jianzhu University, Jinan 250101, China
| | - Ziyu Wang
- School of Science, Shandong Jianzhu University, Jinan 250101, China
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
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48
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Leini R, Pantsar T. In Silico Evaluation of the Thr58-Associated Conserved Water with KRAS Switch-II Pocket Binders. J Chem Inf Model 2023; 63:1490-1505. [PMID: 36854010 PMCID: PMC10015465 DOI: 10.1021/acs.jcim.2c01479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
The KRAS switch-II pocket (SII-P) has proven to be one of the most successful tools for targeting KRAS with small molecules to date. This has been demonstrated with several KRAS(G12C)-targeting covalent inhibitors, already resulting in two FDA-approved drugs. Several earlier-stage compounds have also been reported to engage KRAS SII-P with other position 12 mutants, including G12D, G12S, and G12R. A highly conserved water molecule exists in the KRAS SII-P, linking Thr58 of switch-II and Gly10 of β1 sheet. This conserved water is also present in the cocrystal structures of most of the disclosed small-molecule inhibitors but is only displaced by a handful of SII-P binders. Here, we evaluated the conserved water molecule energetics by the WaterMap for the SII-P binders with publicly disclosed structures and studied the water behavior in the presence of selected inhibitors by microsecond timescale molecular dynamics (MD) simulations using two water models (total simulation time of 120 μs). Our data revealed the high-energy nature of this hydration site when coexisting with an SII-P binder and that there is a preference for a single isolated hydration site in this location within the most advanced compounds. Furthermore, water displacement was only achieved with a few disclosed compounds and was suboptimal, as for instance a cyanomethyl group as a water displacer appears to introduce repulsion with the native conformation of Thr58. These results suggested that this conserved water should be considered more central when designing new inhibitors, especially in the design of noncovalent inhibitors targeting the SII-P.
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Affiliation(s)
- Renne Leini
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Yliopistonranta 1C, 70210 Kuopio, Finland
| | - Tatu Pantsar
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Yliopistonranta 1C, 70210 Kuopio, Finland
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49
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Narayan B, Kiel C, Buchete NV. Classification of GTP-dependent K-Ras4B active and inactive conformational states. J Chem Phys 2023; 158:091104. [PMID: 36889947 DOI: 10.1063/5.0139181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
Classifying reliably active and inactive molecular conformations of wildtype (WT) and mutated oncogenic proteins is a key, ongoing challenge in molecular cancer studies. Here, we probe the GTP-bound K-Ras4B conformational dynamics using long-time atomistic molecular dynamics (MD) simulations. We extract and analyze the detailed underlying free energy landscape of WT K-Ras4B. We use two key reaction coordinates, labeled d1 and d2 (i.e., distances coordinating the Pβ atom of the GTP ligand with two key residues, T35 and G60), shown to correlate closely with activities of WT and mutated K-Ras4B. However, our new K-Ras4B conformational kinetics study reveals a more complex network of equilibrium Markovian states. We show that a new reaction coordinate is required to account for the orientation of acidic K-Ras4B sidechains such as D38 with respect to the interface with binding effector RAF1 and rationalize the activation/inactivation propensities and the corresponding molecular binding mechanisms. We use this understanding to unveil how a relatively conservative mutation (i.e., D33E, in the switch I region) can lead to significantly different activation propensities compared with WT K-Ras4B. Our study sheds new light on the ability of residues near the K-Ras4B-RAF1 interface to modulate the network of salt bridges at the binding interface with the RAF1 downstream effector and, thus, to influence the underlying GTP-dependent activation/inactivation mechanism. Altogether, our hybrid MD-docking modeling approach enables the development of new in silico methods for quantitative assessment of activation propensity changes (e.g., due to mutations or local binding environment). It also unveils the underlying molecular mechanisms and facilitates the rational design of new cancer drugs.
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Affiliation(s)
- Brajesh Narayan
- School of Physics, University College Dublin, Belfield, Dublin 4, Ireland
| | - Christina Kiel
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
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50
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Dynamic regulation of RAS and RAS signaling. Biochem J 2023; 480:1-23. [PMID: 36607281 PMCID: PMC9988006 DOI: 10.1042/bcj20220234] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/16/2022] [Accepted: 12/23/2022] [Indexed: 01/07/2023]
Abstract
RAS proteins regulate most aspects of cellular physiology. They are mutated in 30% of human cancers and 4% of developmental disorders termed Rasopathies. They cycle between active GTP-bound and inactive GDP-bound states. When active, they can interact with a wide range of effectors that control fundamental biochemical and biological processes. Emerging evidence suggests that RAS proteins are not simple on/off switches but sophisticated information processing devices that compute cell fate decisions by integrating external and internal cues. A critical component of this compute function is the dynamic regulation of RAS activation and downstream signaling that allows RAS to produce a rich and nuanced spectrum of biological outputs. We discuss recent findings how the dynamics of RAS and its downstream signaling is regulated. Starting from the structural and biochemical properties of wild-type and mutant RAS proteins and their activation cycle, we examine higher molecular assemblies, effector interactions and downstream signaling outputs, all under the aspect of dynamic regulation. We also consider how computational and mathematical modeling approaches contribute to analyze and understand the pleiotropic functions of RAS in health and disease.
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