1
|
Kugler V, Schwaighofer S, Feichtner A, Enzler F, Fleischmann J, Strich S, Schwarz S, Wilson R, Tschaikner P, Troppmair J, Sexl V, Meier P, Kaserer T, Stefan E. Impact of protein and small molecule interactions on kinase conformations. eLife 2024; 13:RP94755. [PMID: 39088265 PMCID: PMC11293870 DOI: 10.7554/elife.94755] [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: 08/02/2024] Open
Abstract
Protein kinases act as central molecular switches in the control of cellular functions. Alterations in the regulation and function of protein kinases may provoke diseases including cancer. In this study we investigate the conformational states of such disease-associated kinases using the high sensitivity of the kinase conformation (KinCon) reporter system. We first track BRAF kinase activity conformational changes upon melanoma drug binding. Second, we also use the KinCon reporter technology to examine the impact of regulatory protein interactions on LKB1 kinase tumor suppressor functions. Third, we explore the conformational dynamics of RIP kinases in response to TNF pathway activation and small molecule interactions. Finally, we show that CDK4/6 interactions with regulatory proteins alter conformations which remain unaffected in the presence of clinically applied inhibitors. Apart from its predictive value, the KinCon technology helps to identify cellular factors that impact drug efficacies. The understanding of the structural dynamics of full-length protein kinases when interacting with small molecule inhibitors or regulatory proteins is crucial for designing more effective therapeutic strategies.
Collapse
Affiliation(s)
- Valentina Kugler
- Institute for Molecular Biology and Center for Molecular Biosciences Innsbruck (CMBI), University of InnsbruckInnsbruckAustria
- Tyrolean Cancer Research Institute (TKFI)InnsbruckAustria
| | - Selina Schwaighofer
- Institute for Molecular Biology and Center for Molecular Biosciences Innsbruck (CMBI), University of InnsbruckInnsbruckAustria
- Tyrolean Cancer Research Institute (TKFI)InnsbruckAustria
| | - Andreas Feichtner
- Institute for Molecular Biology and Center for Molecular Biosciences Innsbruck (CMBI), University of InnsbruckInnsbruckAustria
- Tyrolean Cancer Research Institute (TKFI)InnsbruckAustria
| | - Florian Enzler
- Daniel Swarovski Research Laboratory, Department of Visceral, Transplant and Thoracic Surgery, Medical University of InnsbruckInnsbruckAustria
| | - Jakob Fleischmann
- Institute for Molecular Biology and Center for Molecular Biosciences Innsbruck (CMBI), University of InnsbruckInnsbruckAustria
- Tyrolean Cancer Research Institute (TKFI)InnsbruckAustria
| | - Sophie Strich
- Institute for Molecular Biology and Center for Molecular Biosciences Innsbruck (CMBI), University of InnsbruckInnsbruckAustria
- Tyrolean Cancer Research Institute (TKFI)InnsbruckAustria
| | - Sarah Schwarz
- Tyrolean Cancer Research Institute (TKFI)InnsbruckAustria
| | - Rebecca Wilson
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer ResearchLondonUnited Kingdom
| | - Philipp Tschaikner
- Tyrolean Cancer Research Institute (TKFI)InnsbruckAustria
- KinCon biolabs GmbHInnsbruckAustria
| | - Jakob Troppmair
- Daniel Swarovski Research Laboratory, Department of Visceral, Transplant and Thoracic Surgery, Medical University of InnsbruckInnsbruckAustria
| | | | - Pascal Meier
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer ResearchLondonUnited Kingdom
| | - Teresa Kaserer
- Institute of Pharmacy/Pharmaceutical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of InnsbruckInnsbruckAustria
| | - Eduard Stefan
- Institute for Molecular Biology and Center for Molecular Biosciences Innsbruck (CMBI), University of InnsbruckInnsbruckAustria
- Tyrolean Cancer Research Institute (TKFI)InnsbruckAustria
- KinCon biolabs GmbHInnsbruckAustria
| |
Collapse
|
2
|
Steffen CL, Manoharan GB, Pavic K, Yeste-Vázquez A, Knuuttila M, Arora N, Zhou Y, Härmä H, Gaigneaux A, Grossmann TN, Abankwa DK. Identification of an H-Ras nanocluster disrupting peptide. Commun Biol 2024; 7:837. [PMID: 38982284 PMCID: PMC11233548 DOI: 10.1038/s42003-024-06523-9] [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: 10/07/2023] [Accepted: 06/28/2024] [Indexed: 07/11/2024] Open
Abstract
Hyperactive Ras signalling is found in most cancers. Ras proteins are only active in membrane nanoclusters, which are therefore potential drug targets. We previously showed that the nanocluster scaffold galectin-1 (Gal1) enhances H-Ras nanoclustering via direct interaction with the Ras binding domain (RBD) of Raf. Here, we establish that the B-Raf preference of Gal1 emerges from the divergence of the Raf RBDs at their proposed Gal1-binding interface. We then identify the L5UR peptide, which disrupts this interaction by binding with low micromolar affinity to the B- and C-Raf-RBDs. Its 23-mer core fragment is sufficient to interfere with H-Ras nanoclustering, modulate Ras-signalling and moderately reduce cell viability. These latter two phenotypic effects may also emerge from the ability of L5UR to broadly engage with several RBD- and RA-domain containing Ras interactors. The L5UR-peptide core fragment is a starting point for the development of more specific reagents against Ras-nanoclustering and -interactors.
Collapse
Affiliation(s)
- Candy Laura Steffen
- Cancer Cell Biology and Drug Discovery group, Department of Life Sciences and Medicine, University of Luxembourg, 4362, Esch-sur-Alzette, Luxembourg
| | - Ganesh Babu Manoharan
- Cancer Cell Biology and Drug Discovery group, Department of Life Sciences and Medicine, University of Luxembourg, 4362, Esch-sur-Alzette, Luxembourg
| | - Karolina Pavic
- Cancer Cell Biology and Drug Discovery group, Department of Life Sciences and Medicine, University of Luxembourg, 4362, Esch-sur-Alzette, Luxembourg
| | - Alejandro Yeste-Vázquez
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), VU University Amsterdam, Amsterdam, The Netherlands
| | - Matias Knuuttila
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Neha Arora
- Department of Integrative Biology and Pharmacology, McGovern Medical School, UT Health, Houston, TX, 77030, USA
| | - Yong Zhou
- Department of Integrative Biology and Pharmacology, McGovern Medical School, UT Health, Houston, TX, 77030, USA
| | - Harri Härmä
- Chemistry of Drug Development, Department of Chemistry, University of Turku, 20500, Turku, Finland
| | - Anthoula Gaigneaux
- Bioinformatics Core, Department of Life Sciences and Medicine, University of Luxembourg, 4367, Esch-sur-Alzette, Luxembourg
| | - Tom N Grossmann
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), VU University Amsterdam, Amsterdam, The Netherlands
| | - Daniel Kwaku Abankwa
- Cancer Cell Biology and Drug Discovery group, Department of Life Sciences and Medicine, University of Luxembourg, 4362, Esch-sur-Alzette, Luxembourg.
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland.
| |
Collapse
|
3
|
Liu-Smith F, Lin J. Unsupervised Analysis Reveals the Involvement of Key Immune Response Genes and the Matrisome in Resistance to BRAF and MEK Inhibitors in Melanoma. Cancers (Basel) 2024; 16:2313. [PMID: 39001376 PMCID: PMC11240363 DOI: 10.3390/cancers16132313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 06/14/2024] [Accepted: 06/17/2024] [Indexed: 07/16/2024] Open
Abstract
Melanoma tumors exhibit a wide range of heterogeneity in genomics even with shared mutations in the MAPK pathway, including BRAF mutations. Consistently, adaptive drug resistance to BRAF inhibitors and/or BRAF plus MEK inhibitors also exhibits a wide range of heterogeneous responses, which poses an obstacle for discovering common genes and pathways that can be used in clinic for overcoming drug resistance. This study objectively analyzed two sets of previously published tumor genomics data comparing pre-treated melanoma tumors and BRAFi- and/or MEKi-resistant tumors. Heterogeneity in response to BRAFi and BRAFi/MEKi was evident because the pre-treated tumors and resistant tumors did not exhibit a tendency of clustering together. Differentially expressed gene (DEG) analysis revealed eight genes and two related enriched signature gene sets (matrisome and matrisome-associated signature gene sets) shared by both sets of data. The matrisome was closely related to the tumor microenvironment and immune response, and five out of the eight shared genes were also related to immune response. The PLXNC1 gene links the shared gene set and the enriched signature gene sets as it presented in all analysis results. As the PLXNC1 gene was up-regulated in the resistant tumors, we validated the up-regulation of this gene in a laboratory using vemurafenib-resistant cell lines. Given its role in promoting inflammation, this study suggests that resistant tumors exhibit an inflammatory tumor microenvironment. The involvement of the matrisome and the specific set of immune genes identified in this study may provide new opportunities for developing future therapeutic methods.
Collapse
Affiliation(s)
- Feng Liu-Smith
- Department of Preventive Medicine, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38105, USA;
- Department of Dermatology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38105, USA
| | - Jianjian Lin
- Department of Preventive Medicine, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38105, USA;
| |
Collapse
|
4
|
Scardaci R, Berlinska E, Scaparone P, Vietti Michelina S, Garbo E, Novello S, Santamaria D, Ambrogio C. Novel RAF-directed approaches to overcome current clinical limits and block the RAS/RAF node. Mol Oncol 2024; 18:1355-1377. [PMID: 38362705 PMCID: PMC11161739 DOI: 10.1002/1878-0261.13605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 11/30/2023] [Accepted: 01/30/2024] [Indexed: 02/17/2024] Open
Abstract
Mutations in the RAS-RAF-MEK-ERK pathway are frequent alterations in cancer and RASopathies, and while RAS oncogene activation alone affects 19% of all patients and accounts for approximately 3.4 million new cases every year, less frequent alterations in the cascade's downstream effectors are also involved in cancer etiology. RAS proteins initiate the signaling cascade by promoting the dimerization of RAF kinases, which can act as oncoproteins as well: BRAFV600E is the most common oncogenic driver, mutated in the 8% of all malignancies. Research in this field led to the development of drugs that target the BRAFV600-like mutations (Class I), which are now utilized in clinics, but cause paradoxical activation of the pathway and resistance development. Furthermore, they are ineffective against non-BRAFV600E malignancies that dimerize and could be either RTK/RAS independent or dependent (Class II and III, respectively), which are still lacking an effective treatment. This review discusses the recent advances in anti-RAF therapies, including paradox breakers, dimer-inhibitors, immunotherapies, and other novel approaches, critically evaluating their efficacy in overcoming the therapeutic limitations, and their putative role in blocking the RAS pathway.
Collapse
Affiliation(s)
- Rossella Scardaci
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology CenterUniversity of TorinoItaly
| | - Ewa Berlinska
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology CenterUniversity of TorinoItaly
| | - Pietro Scaparone
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology CenterUniversity of TorinoItaly
| | - Sandra Vietti Michelina
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology CenterUniversity of TorinoItaly
| | - Edoardo Garbo
- Department of OncologyUniversity of Torino, San Luigi HospitalOrbassanoItaly
| | - Silvia Novello
- Department of OncologyUniversity of Torino, San Luigi HospitalOrbassanoItaly
| | - David Santamaria
- Centro de Investigación del CáncerCSIC‐Universidad de SalamancaSpain
| | - Chiara Ambrogio
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology CenterUniversity of TorinoItaly
| |
Collapse
|
5
|
Al-Masri C, Trozzi F, Lin SH, Tran O, Sahni N, Patek M, Cichonska A, Ravikumar B, Rahman R. Investigating the conformational landscape of AlphaFold2-predicted protein kinase structures. BIOINFORMATICS ADVANCES 2023; 3:vbad129. [PMID: 37786533 PMCID: PMC10541651 DOI: 10.1093/bioadv/vbad129] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/28/2023] [Accepted: 09/13/2023] [Indexed: 10/04/2023]
Abstract
Summary Protein kinases are a family of signaling proteins, crucial for maintaining cellular homeostasis. When dysregulated, kinases drive the pathogenesis of several diseases, and are thus one of the largest target categories for drug discovery. Kinase activity is tightly controlled by switching through several active and inactive conformations in their catalytic domain. Kinase inhibitors have been designed to engage kinases in specific conformational states, where each conformation presents a unique physico-chemical environment for therapeutic intervention. Thus, modeling kinases across conformations can enable the design of novel and optimally selective kinase drugs. Due to the recent success of AlphaFold2 in accurately predicting the 3D structure of proteins based on sequence, we investigated the conformational landscape of protein kinases as modeled by AlphaFold2. We observed that AlphaFold2 is able to model several kinase conformations across the kinome, however, certain conformations are only observed in specific kinase families. Furthermore, we show that the per residue predicted local distance difference test can capture information describing structural flexibility of kinases. Finally, we evaluated the docking performance of AlphaFold2 kinase structures for enriching known ligands. Taken together, we see an opportunity to leverage AlphaFold2 models for structure-based drug discovery against kinases across several pharmacologically relevant conformational states. Availability and implementation All code used in the analysis is freely available at https://github.com/Harmonic-Discovery/AF2-kinase-conformational-landscape.
Collapse
Affiliation(s)
- Carmen Al-Masri
- Harmonic Discovery Inc., New York, NY 10013, United States
- Department of Physics and Astronomy, University of California Irvine, Irvine, CA 92697, United States
| | | | - Shu-Hang Lin
- Harmonic Discovery Inc., New York, NY 10013, United States
- Department of Chemical Engineering, University of Michigan Ann Arbor, Ann Arbor, MI 48109, United States
| | - Oanh Tran
- Harmonic Discovery Inc., New York, NY 10013, United States
- Department of Chemistry, University of California Irvine, Irvine, CA 92697, United States
| | - Navriti Sahni
- Harmonic Discovery Inc., New York, NY 10013, United States
| | - Marcel Patek
- Harmonic Discovery Inc., New York, NY 10013, United States
| | - Anna Cichonska
- Harmonic Discovery Inc., New York, NY 10013, United States
| | | | - Rayees Rahman
- Harmonic Discovery Inc., New York, NY 10013, United States
| |
Collapse
|
6
|
Lauinger M, Christen D, Klar RFU, Roubaty C, Heilig CE, Stumpe M, Knox JJ, Radulovich N, Tamblyn L, Xie IY, Horak P, Forschner A, Bitzer M, Wittel UA, Boerries M, Ball CR, Heining C, Glimm H, Fröhlich M, Hübschmann D, Gallinger S, Fritsch R, Fröhling S, O'Kane GM, Dengjel J, Brummer T. BRAF Δβ3-αC in-frame deletion mutants differ in their dimerization propensity, HSP90 dependence, and druggability. SCIENCE ADVANCES 2023; 9:eade7486. [PMID: 37656784 DOI: 10.1126/sciadv.ade7486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 08/02/2023] [Indexed: 09/03/2023]
Abstract
In-frame BRAF exon 12 deletions are increasingly identified in various tumor types. The resultant BRAFΔβ3-αC oncoproteins usually lack five amino acids in the β3-αC helix linker and sometimes contain de novo insertions. The dimerization status of BRAFΔβ3-αC oncoproteins, their precise pathomechanism, and their direct druggability by RAF inhibitors (RAFi) has been under debate. Here, we functionally characterize BRAFΔLNVTAP>F and two novel mutants, BRAFdelinsFS and BRAFΔLNVT>F, and compare them with other BRAFΔβ3-αC oncoproteins. We show that BRAFΔβ3-αC oncoproteins not only form stable homodimers and large multiprotein complexes but also require dimerization. Nevertheless, details matter as aromatic amino acids at the deletion junction of some BRAFΔβ3-αC oncoproteins, e.g., BRAFΔLNVTAP>F, increase their stability and dimerization propensity while conferring resistance to monomer-favoring RAFi such as dabrafenib or HSP 90/CDC37 inhibition. In contrast, dimer-favoring inhibitors such as naporafenib inhibit all BRAFΔβ3-αC mutants in cell lines and patient-derived organoids, suggesting that tumors driven by such oncoproteins are vulnerable to these compounds.
Collapse
Affiliation(s)
- Manuel Lauinger
- Institute of Molecular Medicine, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Daniel Christen
- Institute of Molecular Medicine, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), partner site Freiburg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Rhena F U Klar
- Institute of Molecular Medicine, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), partner site Freiburg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Freeze-O Organoid Bank, University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of Internal Medicine I (Hematology, Oncology, and Stem Cell Transplantation), University Hospital of Freiburg, Freiburg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Carole Roubaty
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Christoph E Heilig
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Michael Stumpe
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Jennifer J Knox
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Nikolina Radulovich
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Laura Tamblyn
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Irene Y Xie
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Peter Horak
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Andrea Forschner
- Department of Dermatology, University Hospital of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University, Tübingen, Germany
| | - Michael Bitzer
- German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University, Tübingen, Germany
- Center for Personalized Medicine Tübingen, Eberhard Karls University, Tübingen, Germany
- Department of Internal Medicine I, Eberhard-Karls University, Tübingen, Germany
| | - Uwe A Wittel
- Department of General and Visceral Surgery, University of Freiburg Medical Center, Faculty of Medicine, 79106 Freiburg, Germany
| | - Melanie Boerries
- German Cancer Consortium (DKTK), partner site Freiburg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Comprehensive Cancer Center Freiburg (CCCF), Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Claudia R Ball
- Department for Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- Technische Universität Dresden, Faculty of Biology, Technische Universität Dresden, Dresden, Germany
| | - Christoph Heining
- Department for Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
| | - Hanno Glimm
- Department for Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- Translational Functional Cancer Genomics, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martina Fröhlich
- Computational Oncology Group, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Hübschmann
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Computational Oncology Group, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Pattern Recognition and Digital Medicine Group, Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
| | - Steven Gallinger
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ralph Fritsch
- Department of Internal Medicine I (Hematology, Oncology, and Stem Cell Transplantation), University Hospital of Freiburg, Freiburg, Germany
- Department of Medical Oncology and Haematology, University Hospital of Zurich, Zurich, Switzerland
| | - Stefan Fröhling
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Grainne M O'Kane
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jörn Dengjel
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Tilman Brummer
- Institute of Molecular Medicine, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- German Cancer Consortium (DKTK), partner site Freiburg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Freeze-O Organoid Bank, University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Comprehensive Cancer Center Freiburg (CCCF), Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Center for Biological Signalling Studies BIOSS, University of Freiburg, 79104 Freiburg, Germany
| |
Collapse
|
7
|
Kugler V, Lieb A, Guerin N, Donald BR, Stefan E, Kaserer T. Disruptor: Computational identification of oncogenic mutants disrupting protein-protein and protein-DNA interactions. Commun Biol 2023; 6:720. [PMID: 37443295 PMCID: PMC10344873 DOI: 10.1038/s42003-023-05089-2] [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: 04/03/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
We report an Osprey-based computational protocol to prospectively identify oncogenic mutations that act via disruption of molecular interactions. It is applicable to analyse both protein-protein and protein-DNA interfaces and it is validated on a dataset of clinically relevant mutations. In addition, it is used to predict previously uncharacterised patient mutations in CDK6 and p16 genes, which are experimentally confirmed to impair complex formation.
Collapse
Affiliation(s)
- Valentina Kugler
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - Andreas Lieb
- Institute of Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Nathan Guerin
- Department of Computer Science, Duke University, Durham, NC, USA
| | - Bruce R Donald
- Department of Computer Science, Duke University, Durham, NC, USA
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
- Department of Chemistry, Duke University, Durham, NC, USA
- Department of Mathematics, Duke University, Durham, NC, USA
| | - Eduard Stefan
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, 6020, Innsbruck, Austria
- Institute of Molecular Biology, University of Innsbruck, Innsbruck, Austria
| | - Teresa Kaserer
- Institute of Pharmacy/Pharmaceutical Chemistry, University of Innsbruck, Innsbruck, Austria.
| |
Collapse
|
8
|
Rohrer L, Spohr C, Beha C, Griffin R, Braun S, Halbach S, Brummer T. Analysis of RAS and drug induced homo- and heterodimerization of RAF and KSR1 proteins in living cells using split Nanoluc luciferase. Cell Commun Signal 2023; 21:136. [PMID: 37316874 DOI: 10.1186/s12964-023-01146-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 04/27/2023] [Indexed: 06/16/2023] Open
Abstract
The dimerization of RAF kinases represents a key event in their activation cycle and in RAS/ERK pathway activation. Genetic, biochemical and structural approaches provided key insights into this process defining RAF signaling output and the clinical efficacy of RAF inhibitors (RAFi). However, methods reporting the dynamics of RAF dimerization in living cells and in real time are still in their infancy. Recently, split luciferase systems have been developed for the detection of protein-protein-interactions (PPIs), incl. proof-of-concept studies demonstrating the heterodimerization of the BRAF and RAF1 isoforms. Due to their small size, the Nanoluc luciferase moieties LgBiT and SmBiT, which reconstitute a light emitting holoenzyme upon fusion partner promoted interaction, appear as well-suited to study RAF dimerization. Here, we provide an extensive analysis of the suitability of the Nanoluc system to study the homo- and heterodimerization of BRAF, RAF1 and the related KSR1 pseudokinase. We show that KRASG12V promotes the homo- and heterodimerization of BRAF, while considerable KSR1 homo- and KSR1/BRAF heterodimerization already occurs in the absence of this active GTPase and requires a salt bridge between the CC-SAM domain of KSR1 and the BRAF-specific region. We demonstrate that loss-of-function mutations impairing key steps of the RAF activation cycle can be used as calibrators to gauge the dynamics of heterodimerization. This approach identified the RAS-binding domains and the C-terminal 14-3-3 binding motifs as particularly critical for the reconstitution of RAF mediated LgBiT/SmBiT reconstitution, while the dimer interface was less important for dimerization but essential for downstream signaling. We show for the first time that BRAFV600E, the most common BRAF oncoprotein whose dimerization status is controversially portrayed in the literature, forms homodimers in living cells more efficiently than its wildtype counterpart. Of note, Nanoluc activity reconstituted by BRAFV600E homodimers is highly sensitive to the paradox-breaking RAFi PLX8394, indicating a dynamic and specific PPI. We report the effects of eleven ERK pathway inhibitors on RAF dimerization, incl. third-generation compounds that are less-defined in terms of their dimer promoting abilities. We identify Naporafenib as a potent and long-lasting dimerizer and show that the split Nanoluc approach discriminates between type I, I1/2 and II RAFi. Video Abstract.
Collapse
Affiliation(s)
- Lino Rohrer
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Corinna Spohr
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Carina Beha
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Ricarda Griffin
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Sandra Braun
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Sebastian Halbach
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Tilman Brummer
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany.
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany.
- Comprehensive Cancer Center Freiburg (CCCF), Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, 79106, Germany.
- Center for Biological Signalling Studies BIOSS, University of Freiburg, Freiburg, 79104, Germany.
| |
Collapse
|
9
|
Fleischmann J, Schwaighofer S, De Falco L, Enzler F, Feichtner A, Kugler V, Tschaikner P, Huber RG, Stefan E. Tracking and blocking interdependencies of cellular BRAF-MEK oncokinase activities. PNAS NEXUS 2023; 2:pgad185. [PMID: 37325027 PMCID: PMC10267685 DOI: 10.1093/pnasnexus/pgad185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 05/22/2023] [Indexed: 06/17/2023]
Abstract
The selective targeting of mutated kinases in cancer therapies has the potential to improve therapeutic success and thereby the survival of patients. In the case of melanoma, the constitutively active MAPK pathway is targeted by a combinatorial inhibition of BRAF and MEK activities. These MAPK pathway players may display patient-specific differences in the onco-kinase mutation spectrum, which needs to be considered for the design of more efficient personalized therapies. Here, we extend a bioluminescence-based kinase conformation biosensor (KinCon) to allow for live-cell tracking of interconnected kinase activity states. First, we show that common MEK1 patient mutations promote a structural rearrangement of the kinase to an opened and active conformation. This effect was reversible by the binding of MEK inhibitors to mutated MEK1, as shown in biosensor assays and molecular dynamics simulations. Second, we implement a novel application of the KinCon technology for tracking the simultaneous, vertical targeting of the two functionally linked kinases BRAF and MEK1. Thus, we demonstrate that, in the presence of constitutively active BRAF-V600E, specific inhibitors of both kinases are efficient in driving MEK1 into a closed, inactive conformation state. We compare current melanoma treatments and show that combinations of BRAFi and MEKi display a more pronounced structural change of the drug sensor than the respective single agents, thereby identifying synergistic effects among these drug combinations. In summary, we depict the extension of the KinCon biosensor technology to systematically validate, anticipate, and personalize tailored drug arrangements using a multiplexed setup.
Collapse
Affiliation(s)
- Jakob Fleischmann
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, Innsbruck 6020, Austria
| | - Selina Schwaighofer
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, Innsbruck 6020, Austria
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, Innsbruck 6020, Austria
| | - Louis De Falco
- Bioinformatics Institute (BII), Agency for Science Technology and Research (A*STAR), 30 Biopolis Street, Matrix #07-01, Singapore 138671, Singapore
| | - Florian Enzler
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, Innsbruck 6020, Austria
| | - Andreas Feichtner
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, Innsbruck 6020, Austria
| | - Valentina Kugler
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, Innsbruck 6020, Austria
| | - Philipp Tschaikner
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, Innsbruck 6020, Austria
- Institute of Molecular Biology, University of Innsbruck, Technikerstrasse 25, Innsbruck 6020, Austria
| | - Roland G Huber
- Bioinformatics Institute (BII), Agency for Science Technology and Research (A*STAR), 30 Biopolis Street, Matrix #07-01, Singapore 138671, Singapore
| | - Eduard Stefan
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, Innsbruck 6020, Austria
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, Innsbruck 6020, Austria
- Institute of Molecular Biology, University of Innsbruck, Technikerstrasse 25, Innsbruck 6020, Austria
| |
Collapse
|
10
|
Torres-Quesada O, Strich S, Stefan E. Kinase perturbations redirect mitochondrial function in cancer. BIOENERGETICS COMMUNICATIONS 2022; 2022:17. [PMID: 37081928 PMCID: PMC7614455 DOI: 10.26124/bec:2022-0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Protein kinases take the center stage in numerous signaling pathways by phosphorylating compartmentalized protein substrates for controlling cell proliferation, cell cycle and metabolism. Kinase dysfunctions have been linked to numerous human diseases such as cancer. This has led to the development of kinase inhibitors which aim to target oncogenic kinase activities. The specificity of the cancer blockers depends on the range of targeted kinases. Therefore, the question arises of how cell-type-specific off-target effects impair the specificities of cancer drugs. Blockade of kinase activities has been shown to converge on the energetic organelle, the mitochondria. In this review, we highlight examples of selected major kinases that impact mitochondrial signaling. Further, we discuss pharmacological strategies to target kinase activities linked to cancer progression and redirecting mitochondrial function. Finally, we propose that cell-based recordings of mitochondrial bioenergetic states might predict off-target or identify specific on-target effects of kinase inhibitors.
Collapse
Affiliation(s)
- Omar Torres-Quesada
- Tyrolean Cancer Research Institute, Innrain 66, 6020 Innsbruck, Austria
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
- Corresponding authors: ;
| | - Sophie Strich
- Tyrolean Cancer Research Institute, Innrain 66, 6020 Innsbruck, Austria
| | - Eduard Stefan
- Tyrolean Cancer Research Institute, Innrain 66, 6020 Innsbruck, Austria
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
- Corresponding authors: ;
| |
Collapse
|
11
|
Guerin N, Feichtner A, Stefan E, Kaserer T, Donald BR. Resistor: An algorithm for predicting resistance mutations via Pareto optimization over multistate protein design and mutational signatures. Cell Syst 2022; 13:830-843.e3. [PMID: 36265469 PMCID: PMC9589925 DOI: 10.1016/j.cels.2022.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/29/2022] [Accepted: 09/13/2022] [Indexed: 01/26/2023]
Abstract
Resistance to pharmacological treatments is a major public health challenge. Here, we introduce Resistor-a structure- and sequence-based algorithm that prospectively predicts resistance mutations for drug design. Resistor computes the Pareto frontier of four resistance-causing criteria: the change in binding affinity (ΔKa) of the (1) drug and (2) endogenous ligand upon a protein's mutation; (3) the probability a mutation will occur based on empirically derived mutational signatures; and (4) the cardinality of mutations comprising a hotspot. For validation, we applied Resistor to EGFR and BRAF kinase inhibitors treating lung adenocarcinoma and melanoma. Resistor correctly identified eight clinically significant EGFR resistance mutations, including the erlotinib and gefitinib "gatekeeper" T790M mutation and five known osimertinib resistance mutations. Furthermore, Resistor predictions are consistent with BRAF inhibitor sensitivity data from both retrospective and prospective experiments using KinCon biosensors. Resistor is available in the open-source protein design software OSPREY.
Collapse
Affiliation(s)
- Nathan Guerin
- Department of Computer Science, Duke University, Durham, NC 27708, USA
| | - Andreas Feichtner
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, 6020 Tyrol, Austria
| | - Eduard Stefan
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, 6020 Tyrol, Austria; Tyrolean Cancer Research Institute, Innsbruck, 6020 Tyrol, Austria
| | - Teresa Kaserer
- Institute of Pharmacy/Pharmaceutical Chemistry, University of Innsbruck, Innsbruck, 6020 Tyrol, Austria.
| | - Bruce R Donald
- Department of Computer Science, Duke University, Durham, NC 27708, USA; Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA; Department of Chemistry, Duke University, Durham, NC 27708, USA; Department of Mathematics, Duke University, Durham, NC 27708, USA.
| |
Collapse
|
12
|
Torres-Quesada O, Doerrier C, Strich S, Gnaiger E, Stefan E. Physiological Cell Culture Media Tune Mitochondrial Bioenergetics and Drug Sensitivity in Cancer Cell Models. Cancers (Basel) 2022; 14:cancers14163917. [PMID: 36010911 PMCID: PMC9405899 DOI: 10.3390/cancers14163917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/04/2022] [Accepted: 08/11/2022] [Indexed: 12/03/2022] Open
Abstract
Simple Summary Cell biologists trust in standard media for analyzing cellular functions and for the specification of target-oriented drug efficacies in cell culture settings. Here, we present a general applicable workflow for the constant monitoring of bioenergetic states of cells grown in 2D cell models to accompany tailored drug discovery efforts. Using in-depth high-resolution respirometry analyses (HRR) of mitochondrial function, we unveiled that the human-plasma-like media (HPLM) altered cellular energetic states. In a systematic HRR setup for drug profiling experiments, we revealed an unexpected side effect of an FDA-approved cancer drug on mitochondrial function, exclusively in HPLM. Thus, we believe that both the recordings of bioenergetic states and the use of more physiological media would improve and reshape cell-based drug discovery ventures. Abstract Two-dimensional cell cultures are established models in research for studying and perturbing cell-type specific functions. However, many limitations apply to the cell growth in a monolayer using standard cell culture media. Although they have been used for decades, their formulations do not mimic the composition of the human cell environment. In this study, we analyzed the impact of a newly formulated human plasma-like media (HPLM) on cell proliferation, mitochondrial bioenergetics, and alterations of drug efficacies using three distinct cancer cell lines. Using high-resolution respirometry, we observed that cells grown in HPLM displayed significantly altered mitochondrial bioenergetic profiles, particularly related to mitochondrial density and mild uncoupling of respiration. Furthermore, in contrast to standard media, the growth of cells in HPLM unveiled mitochondrial dysfunction upon exposure to the FDA-approved kinase inhibitor sunitinib. This seemingly context-dependent side effect of this drug highlights that the selection of the cell culture medium influences the assessment of cancer drug sensitivities. Thus, we suggest to prioritize media with a more physiological composition for analyzing bioenergetic profiles and to take it into account for assigning drug efficacies in the cell culture model of choice.
Collapse
Affiliation(s)
- Omar Torres-Quesada
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, 6020 Innsbruck, Austria
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
- Correspondence: (O.T.-Q.); (E.S.)
| | | | - Sophie Strich
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, 6020 Innsbruck, Austria
| | - Erich Gnaiger
- Oroboros Instruments, Schoepfstrasse 18, 6020 Innsbruck, Austria
| | - Eduard Stefan
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, 6020 Innsbruck, Austria
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
- Correspondence: (O.T.-Q.); (E.S.)
| |
Collapse
|
13
|
Feichtner A, Kugler V, Schwaighofer S, Nuener T, Fleischmann J, Stefan E. Tracking mutation and drug-driven alterations of oncokinase conformations. MEMO 2022; 15:137-142. [PMID: 35677701 PMCID: PMC7612828 DOI: 10.1007/s12254-021-00790-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Numerous kinases act as central nodes of cellular signaling networks. As such, many of these enzymes function as molecular switches for coordinating spatiotemporal signal transmission. Typically, it is the compartmentalized phosphorylation of protein substrates which relays the transient input signal to determine decisive physiological cell responses. Genomic alterations affect kinase abundance and/or their activities which contribute to the malignant transformation, progression, and metastasis of human cancers. Thus, major drug discovery efforts have been made to identify lead molecules targeting clinically relevant oncokinases. The concept of personalized medicine aims to apply the therapeutic agent with the highest efficacy towards a patient-specific mutation. Here, we discuss the implementation of a cell-based reporter system which may foster the decision-making process to identify the most promising lead-molecules. We present a modular kinase conformation (KinCon) biosensor platform for live-cell analyses of kinase activity states. This biosensor facilitates the recording of kinase activity conformations of the wild-type and the respective mutated kinase upon lead molecule exposure. We reflect proof-of-principle studies demonstrating how this technology has been extended to profile drug properties of the full-length kinases BRAF and MEK1 in intact cells. Further, we pinpoint how this technology may open new avenues for systematic and patient-tailored drug discovery efforts. Overall, this precision-medicineoriented biosensor concept aims to determine kinase inhibitor specificity and anticipate their drug efficacies.
Collapse
Affiliation(s)
- Andreas Feichtner
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Valentina Kugler
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Selina Schwaighofer
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Thomas Nuener
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Jakob Fleischmann
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Eduard Stefan
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria; Tyrolean Cancer Research Institute, Innrain 66, 6020 Innsbruck, Austria
| |
Collapse
|
14
|
Classical RAS proteins are not essential for paradoxical ERK activation induced by RAF inhibitors. Proc Natl Acad Sci U S A 2022; 119:2113491119. [PMID: 35091470 PMCID: PMC8812530 DOI: 10.1073/pnas.2113491119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2021] [Indexed: 11/21/2022] Open
Abstract
RAF inhibitors unexpectedly induce ERK activation in normal and oncogenic RAS tumor cells, making them unsuitable for treating RAS-driven cancers. The precise mechanism of this paradox is not fully understood but is believed to be RAS dependent. In this study, we discovered that classical RAS proteins are not essential for RAF inhibitor-induced ERK activation in H/N/KRAS-less mouse embryonic fibroblasts. We further showed that the MRAS/SHOC2 complex is required for the classical RAS-independent paradoxical ERK activation. Our findings provide new insights into the mechanism of paradoxical ERK activation by RAF inhibitors, and they have important therapeutic implications for developing effective RAF inhibitors. RAF inhibitors unexpectedly induce ERK signaling in normal and tumor cells with elevated RAS activity. Paradoxical activation is believed to be RAS dependent. In this study, we showed that LY3009120, a pan-RAF inhibitor, can unexpectedly cause paradoxical ERK activation in KRASG12C-dependent lung cancer cell lines, when KRAS is inhibited by ARS1620, a KRASG12C inhibitor. Using H/N/KRAS-less mouse embryonic fibroblasts, we discovered that classical RAS proteins are not essential for RAF inhibitor-induced paradoxical ERK signaling. In their absence, RAF inhibitors can induce ERK phosphorylation, ERK target gene transcription, and cell proliferation. We further showed that the MRAS/SHOC2 complex is required for this process. This study highlights the complexity of the allosteric RAF regulation by RAF inhibitors, and the importance of other RAS-related proteins in this process.
Collapse
|
15
|
Baffi TR, Lordén G, Wozniak JM, Feichtner A, Yeung W, Kornev AP, King CC, Del Rio JC, Limaye AJ, Bogomolovas J, Gould CM, Chen J, Kennedy EJ, Kannan N, Gonzalez DJ, Stefan E, Taylor SS, Newton AC. mTORC2 controls the activity of PKC and Akt by phosphorylating a conserved TOR interaction motif. Sci Signal 2021; 14:eabe4509. [PMID: 33850054 PMCID: PMC8208635 DOI: 10.1126/scisignal.abe4509] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The complex mTORC2 is accepted to be the kinase that controls the phosphorylation of the hydrophobic motif, a key regulatory switch for AGC kinases, although whether mTOR directly phosphorylates this motif remains controversial. Here, we identified an mTOR-mediated phosphorylation site that we termed the TOR interaction motif (TIM; F-x3-F-pT), which controls the phosphorylation of the hydrophobic motif of PKC and Akt and the activity of these kinases. The TIM is invariant in mTORC2-dependent AGC kinases, is evolutionarily conserved, and coevolved with mTORC2 components. Mutation of this motif in Akt1 and PKCβII abolished cellular kinase activity by impairing activation loop and hydrophobic motif phosphorylation. mTORC2 directly phosphorylated the PKC TIM in vitro, and this phosphorylation event was detected in mouse brain. Overexpression of PDK1 in mTORC2-deficient cells rescued hydrophobic motif phosphorylation of PKC and Akt by a mechanism dependent on their intrinsic catalytic activity, revealing that mTORC2 facilitates the PDK1 phosphorylation step, which, in turn, enables autophosphorylation. Structural analysis revealed that PKC homodimerization is driven by a TIM-containing helix, and biophysical proximity assays showed that newly synthesized, unphosphorylated PKC dimerizes in cells. Furthermore, disruption of the dimer interface by stapled peptides promoted hydrophobic motif phosphorylation. Our data support a model in which mTORC2 relieves nascent PKC dimerization through TIM phosphorylation, recruiting PDK1 to phosphorylate the activation loop and triggering intramolecular hydrophobic motif autophosphorylation. Identification of TIM phosphorylation and its role in the regulation of PKC provides the basis for AGC kinase regulation by mTORC2.
Collapse
Affiliation(s)
- Timothy R Baffi
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
- Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Gema Lordén
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
| | - Jacob M Wozniak
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
- Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, USA
| | - Andreas Feichtner
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck A-6020, Austria
| | - Wayland Yeung
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Alexandr P Kornev
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
| | - Charles C King
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
| | - Jason C Del Rio
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
- Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Ameya J Limaye
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA
| | - Julius Bogomolovas
- Department of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Christine M Gould
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
- Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Ju Chen
- Department of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Eileen J Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - David J Gonzalez
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, USA
| | - Eduard Stefan
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck A-6020, Austria
| | - Susan S Taylor
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
| | - Alexandra C Newton
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
16
|
Allosteric Kinase Inhibitors Reshape MEK1 Kinase Activity Conformations in Cells and In Silico. Biomolecules 2021; 11:biom11040518. [PMID: 33808483 PMCID: PMC8065916 DOI: 10.3390/biom11040518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/26/2021] [Accepted: 03/27/2021] [Indexed: 01/26/2023] Open
Abstract
Mutations at different stages of the mitogen-activated protein kinase (MAPK) signaling pathway lead to aberrant activation of the involved protein kinase entities. These oncogenic modifications alter signal propagation which converge on the gatekeeper kinases MEK1/2, transmitting the input signal to ERK1/2. Thus, targeted MEK inhibition causes qualitative alterations of carcinogenic MAPK signals. Phosphorylation of the MEK1 activation loop at the positions S218 and S222 by RAF kinases triggers the conformational alignment of MEK's catalytic pocket to enable ATP-binding and substrate phosphorylation. We have extended a kinase conformation (KinCon) biosensor platform to record MEK1 activity dynamics. In addition to MEK phosphorylation by BRAF, the integration of the phosphorylation-mimetic mutations S218D/S222D triggered opening of the kinase. Structural rearrangement may involve the flexibility of the N terminal MEK1 A-helix. Application of the allosterically acting MEK inhibitors (MEKi) trametinib, cobimentinib, refametinib, and selumetinib converted activated MEK1 KinCon reporters back into a more closed inactive conformation. We confirmed MEK1 KinCon activity dynamics upon drug engagement using the patient-derived melanoma cell line A2058, which harbors the V600E hotspot BRAF mutation. In order to confirm biosensor dynamics, we simulated structure dynamics of MEK1 kinase in the presence and absence of mutations and/or MEKi binding. We observed increased dynamics for the S218D/S222D double mutant particularly in the region of the distal A-helix and alpha-C helix. These data underline that MEK1 KinCon biosensors have the potential to be subjected to MEKi efficacy validations in an intact cell setting.
Collapse
|
17
|
Siddiqui FA, Parkkola H, Vukic V, Oetken-Lindholm C, Jaiswal A, Kiriazis A, Pavic K, Aittokallio T, Salminen TA, Abankwa D. Novel Small Molecule Hsp90/Cdc37 Interface Inhibitors Indirectly Target K-Ras-Signaling. Cancers (Basel) 2021; 13:927. [PMID: 33672199 PMCID: PMC7927014 DOI: 10.3390/cancers13040927] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/12/2021] [Accepted: 02/17/2021] [Indexed: 12/23/2022] Open
Abstract
The ATP-competitive inhibitors of Hsp90 have been tested predominantly in kinase addicted cancers; however, they have had limited success. A mechanistic connection between Hsp90 and oncogenic K-Ras is not known. Here, we show that K-Ras selectivity is enabled by the loss of the K-Ras membrane nanocluster modulator galectin-3 downstream of the Hsp90 client HIF-1α. This mechanism suggests a higher drug sensitivity in the context of KRAS mutant, HIF-1α-high and/or Gal3-high cancer cells, such as those found, in particular, in pancreatic adenocarcinoma. The low toxicity of conglobatin further indicates a beneficial on-target toxicity profile for Hsp90/Cdc37 interface inhibitors. We therefore computationally screened >7 M compounds, and identified four novel small molecules with activities of 4 μM-44 μM in vitro. All of the compounds were K-Ras selective, and potently decreased the Hsp90 client protein levels without inducing the heat shock response. Moreover, they all inhibited the 2D proliferation of breast, pancreatic, and lung cancer cell lines. The most active compounds from each scaffold, furthermore, significantly blocked 3D spheroids and the growth of K-Ras-dependent microtumors. We foresee new opportunities for improved Hsp90/Cdc37 interface inhibitors in cancer and other aging-associated diseases.
Collapse
Affiliation(s)
- Farid Ahmad Siddiqui
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; (F.A.S.); (H.P.); (V.V.); (C.O.-L.); (A.K.)
| | - Hanna Parkkola
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; (F.A.S.); (H.P.); (V.V.); (C.O.-L.); (A.K.)
| | - Vladimir Vukic
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; (F.A.S.); (H.P.); (V.V.); (C.O.-L.); (A.K.)
- Faculty of Technology, University of Novi Sad, 21000 Novi Sad, Serbia
| | - Christina Oetken-Lindholm
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; (F.A.S.); (H.P.); (V.V.); (C.O.-L.); (A.K.)
| | - Alok Jaiswal
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014 Helsinki, Finland; (A.J.); (T.A.)
| | - Alexandros Kiriazis
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; (F.A.S.); (H.P.); (V.V.); (C.O.-L.); (A.K.)
| | - Karolina Pavic
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg;
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014 Helsinki, Finland; (A.J.); (T.A.)
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, N-0310 Oslo, Norway
- Centre for Biostatistics and Epidemiology (OCBE), Faculty of Medicine, University of Oslo, N-0372 Oslo, Norway
| | - Tiina A. Salminen
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
| | - Daniel Abankwa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; (F.A.S.); (H.P.); (V.V.); (C.O.-L.); (A.K.)
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg;
| |
Collapse
|
18
|
Tschaikner PM, Regele D, Röck R, Salvenmoser W, Meyer D, Bouvier M, Geley S, Stefan E, Aanstad P. Feedback control of the Gpr161-G αs-PKA axis contributes to basal Hedgehog repression in zebrafish. Development 2021; 148:dev.192443. [PMID: 33531430 DOI: 10.1242/dev.192443] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 01/14/2021] [Indexed: 01/26/2023]
Abstract
Hedgehog (Hh) ligands act as morphogens to direct patterning and proliferation during embryonic development. Protein kinase A (PKA) is a central negative regulator of Hh signalling, and in the absence of Hh ligands, PKA activity prevents inappropriate expression of Hh target genes. The orphan G-protein-coupled receptor Gpr161 contributes to the basal Hh repression machinery by activating PKA. Gpr161 acts as an A-kinase-anchoring protein, and is itself phosphorylated by PKA, but the functional significance of PKA phosphorylation of Gpr161 in the context of Hh signalling remains unknown. Here, we show that loss of Gpr161 in zebrafish leads to constitutive activation of medium and low, but not maximal, levels of Hh target gene expression. Furthermore, we find that PKA phosphorylation-deficient forms of Gpr161, which we show directly couple to Gαs, display an increased sensitivity to Shh, resulting in excess high-level Hh signalling. Our results suggest that PKA feedback-mediated phosphorylation of Gpr161 may provide a mechanism for fine-tuning Gpr161 ciliary localisation and PKA activity.
Collapse
Affiliation(s)
- Philipp M Tschaikner
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Innsbruck 6020, Austria.,Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck 6020, Austria
| | - Dominik Regele
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Innsbruck 6020, Austria
| | - Ruth Röck
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck 6020, Austria
| | - Willi Salvenmoser
- Institute of Zoology and Center of Molecular Bioscience Innsbruck, University of Innsbruck, Innsbruck 6020, Austria
| | - Dirk Meyer
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Innsbruck 6020, Austria
| | - Michel Bouvier
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Stephan Geley
- Division of Molecular Pathophysiology, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Eduard Stefan
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck 6020, Austria
| | - Pia Aanstad
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Innsbruck 6020, Austria
| |
Collapse
|
19
|
Alabi S, Jaime-Figueroa S, Yao Z, Gao Y, Hines J, Samarasinghe KTG, Vogt L, Rosen N, Crews CM. Mutant-selective degradation by BRAF-targeting PROTACs. Nat Commun 2021; 12:920. [PMID: 33568647 PMCID: PMC7876048 DOI: 10.1038/s41467-021-21159-7] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 01/14/2021] [Indexed: 12/26/2022] Open
Abstract
Over 300 BRAF missense mutations have been identified in patients, yet currently approved drugs target V600 mutants alone. Moreover, acquired resistance inevitably emerges, primarily due to RAF lesions that prevent inhibition of BRAF V600 with current treatments. Therefore, there is a need for new therapies that target other mechanisms of activated BRAF. In this study, we use the Proteolysis Targeting Chimera (PROTAC) technology, which promotes ubiquitination and degradation of neo-substrates, to address the limitations of BRAF inhibitor-based therapies. Using vemurafenib-based PROTACs, we achieve low nanomolar degradation of all classes of BRAF mutants, but spare degradation of WT RAF family members. Our lead PROTAC outperforms vemurafenib in inhibiting cancer cell growth and shows in vivo efficacy in a Class 2 BRAF xenograft model. Mechanistic studies reveal that BRAFWT is spared due to weak ternary complex formation in cells owing to its quiescent inactivated conformation, and activation of BRAFWT sensitizes it to degradation. This study highlights the degree of selectivity achievable with degradation-based approaches by targeting mutant BRAF-driven cancers while sparing BRAFWT, providing an anti-tumor drug modality that expands the therapeutic window. Hundreds of BRAF mutations have been identified in patients with cancer but currently approved drugs only target BRAF V600 mutants. Here, the authors develop a vemurafenib-based PROTAC that induces degradation of all classes of BRAF mutants without affecting wild-type RAF proteins.
Collapse
Affiliation(s)
| | - Saul Jaime-Figueroa
- Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA
| | - Zhan Yao
- Program in Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yijun Gao
- Program in Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John Hines
- Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA
| | | | - Lea Vogt
- Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA
| | - Neal Rosen
- Program in Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Craig M Crews
- Department of Pharmacology, New Haven, CT, USA. .,Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA. .,Department of Chemistry, Yale University, New Haven, CT, USA.
| |
Collapse
|
20
|
Mutation-oriented profiling of autoinhibitory kinase conformations predicts RAF inhibitor efficacies. Proc Natl Acad Sci U S A 2020; 117:31105-31113. [PMID: 33229534 PMCID: PMC7733820 DOI: 10.1073/pnas.2012150117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Kinase-targeted therapies have the potential to improve the survival of patients with cancer. However, the cancer-specific spectrum of kinase alterations exhibits distinct functional properties and requires mutation-oriented drug treatments. Besides post-translational modifications and diverse intermolecular interactions of kinases, it is the distinct disease mutation which reshapes full-length kinase conformations, affecting their activity. Oncokinase mutation profiles differ between cancer types, as it was shown for BRAF in melanoma and non-small-cell lung cancers. Here, we present the target-oriented application of a kinase conformation (KinCon) reporter platform for live-cell measurements of autoinhibitory kinase activity states. The bioluminescence-based KinCon biosensor allows the tracking of conformation dynamics of full-length kinases in intact cells and real time. We show that the most frequent BRAF cancer mutations affect kinase conformations and thus the engagement and efficacy of V600E-specific BRAF inhibitors (BRAFi). We illustrate that the patient mutation harboring KinCon reporters display differences in the effectiveness of the three clinically approved BRAFi vemurafenib, encorafenib, and dabrafenib and the preclinical paradox breaker PLX8394. We confirmed KinCon-based drug efficacy predictions for BRAF mutations other than V600E in proliferation assays using patient-derived lung cancer cell lines and by analyzing downstream kinase signaling. The systematic implementation of such conformation reporters will allow to accelerate the decision process for the mutation-oriented RAF-kinase cancer therapy. Moreover, we illustrate that the presented kinase reporter concept can be extended to other kinases which harbor patient mutations. Overall, KinCon profiling provides additional mechanistic insights into full-length kinase functions by reporting protein-protein interaction (PPI)-dependent, mutation-specific, and drug-driven changes of kinase activity conformations.
Collapse
|
21
|
Targeting KRAS mutant cancers by preventing signaling transduction in the MAPK pathway. Eur J Med Chem 2020; 211:113006. [PMID: 33228976 DOI: 10.1016/j.ejmech.2020.113006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/05/2020] [Accepted: 11/06/2020] [Indexed: 01/06/2023]
Abstract
KRAS genes are the most commonly mutated oncogenes in cancer. Unfortunately, effective therapeutic strategies for targeting KRAS mutant cancers have proven to be difficult to obtain. A key reason for this setback is due to the lack of success direct KRAS mutant inhibitors have received. Researchers have turned their efforts away from targeting the KRAS nucleotide-binding site directly and towards targeting other areas of the MAPK signaling pathway to block KRAS function. Researchers found that inhibiting enzymes and protein-protein interactions involved in the MAPK signaling pathway inhibit the activation of KRAS mutant therefore can lead to a potential therapeutic for KRAS mutated cancers. Throughout the past two decades, various indirect inhibitors have been designed and tested. EGFR and MEK inhibitors have presented with less success; however, significant advances have been made when targeting the plasma membrane localization process and the allosteric site of KRAS mutant. Farnesyltransferase and allosteric inhibitors have both advanced to human clinical trials. This comprehensive review presents the most recent developments of direct and indirect KRAS mutant inhibitors. This review summarizes published data on the inhibitory and anti-cancer activity of compounds that target KRAS activation as well as highlights the most promising strategies for targeting KRAS mutant cancers.
Collapse
|
22
|
Abankwa D, Gorfe AA. Mechanisms of Ras Membrane Organization and Signaling: Ras Rocks Again. Biomolecules 2020; 10:E1522. [PMID: 33172116 PMCID: PMC7694788 DOI: 10.3390/biom10111522] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/03/2020] [Accepted: 11/04/2020] [Indexed: 12/17/2022] Open
Abstract
Ras is the most frequently mutated oncogene and recent drug development efforts have spurred significant new research interest. Here we review progress toward understanding how Ras functions in nanoscale, proteo-lipid signaling complexes on the plasma membrane, called nanoclusters. We discuss how G-domain reorientation is plausibly linked to Ras-nanoclustering and -dimerization. We then look at how these mechanistic features could cooperate in the engagement and activation of RAF by Ras. Moreover, we show how this structural information can be integrated with microscopy data that provide nanoscale resolution in cell biological experiments. Synthesizing the available data, we propose to distinguish between two types of Ras nanoclusters, an active, immobile RAF-dependent type and an inactive/neutral membrane anchor-dependent. We conclude that it is possible that Ras reorientation enables dynamic Ras dimerization while the whole Ras/RAF complex transits into an active state. These transient di/oligomer interfaces of Ras may be amenable to pharmacological intervention. We close by highlighting a number of open questions including whether all effectors form active nanoclusters and whether there is an isoform specific composition of Ras nanocluster.
Collapse
Affiliation(s)
- Daniel Abankwa
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette 4362, Luxembourg
| | - Alemayehu A. Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, TX 77030, USA
| |
Collapse
|
23
|
Kanat O, Ertas H, Caner B. Contemporary treatment approaches for metastatic colorectal cancer driven by BRAF V600 mutations. World J Gastrointest Oncol 2020; 12:1080-1090. [PMID: 33133378 PMCID: PMC7579731 DOI: 10.4251/wjgo.v12.i10.1080] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/07/2020] [Accepted: 09/22/2020] [Indexed: 02/05/2023] Open
Abstract
The treatment of metastatic colorectal cancer (mCRC) harboring BRAF V600 mutations is challenging. These tumors are often refractory to standard treatment. Therefore, the patients may exhibit rapid clinical deterioration, depriving them of the chance to receive salvage therapy. In newly diagnosed patients with good performance status, the administration of an intensive chemotherapy regimen like FOLFOXIRI (5-fluorouracil, leucovorin, oxaliplatin, and irinotecan) along with the antiangiogenic agent bevacizumab can modify this aggressive behavior of the disease and improve patient clinical outcomes. The recently published results of the BEACON (Binimetinib, Encorafenib, and Cetuximab Combined to Treat BRAF-Mutant Colorectal Cancer) study demonstrated that a combination therapy consisting of BRAF, epidermal growth factor receptor, and mitogen-activated protein kinase kinase inhibitors could be a useful second-or third-line alternative. This review summarizes the current treatment strategies for BRAF-mutant mCRC.
Collapse
Affiliation(s)
- Ozkan Kanat
- Department of Medical Oncology, Acıbadem Bursa Hospital, Bursa 16059, Turkey
| | - Hulya Ertas
- Department of Medical Oncology, Bursa City Hospital, Bursa 16059, Turkey
| | - Burcu Caner
- Department of Medical Oncoloy, Balıkesir Ataturk City Hospital, Bursa 16059, Turkey
| |
Collapse
|
24
|
Enzler F, Tschaikner P, Schneider R, Stefan E. KinCon: Cell-based recording of full-length kinase conformations. IUBMB Life 2020; 72:1168-1174. [PMID: 32027084 PMCID: PMC7318358 DOI: 10.1002/iub.2241] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 01/16/2020] [Indexed: 01/26/2023]
Abstract
The spectrum of kinase alterations displays distinct functional characteristics and requires kinase mutation-oriented strategies for therapeutic interference. Besides phosphotransferase activity, protein abundance, and intermolecular interactions, particular patient-mutations promote pathological kinase conformations. Despite major advances in identifying lead molecules targeting clinically relevant oncokinase functions, still many kinases are neglected and not part of drug discovery efforts. One explanation is attributed to challenges in tracking kinase activities. Chemical probes are needed to functionally annotate kinase functions, whose activities may not always depend on catalyzing phospho-transfer. Such non-catalytic kinase functions are related to transitions of full-length kinase conformations. Recent findings underline that cell-based reporter systems can be adapted to record conformation changes of kinases. Here, we discuss the possible applications of an extendable kinase conformation (KinCon) reporter toolbox for live-cell recording of kinase states. KinCon is a genetically encoded bioluminescence-based biosensor platform, which can be subjected for measurements of conformation dynamics of mutated kinases upon small molecule inhibitor exposure. We hypothesize that such biosensors can be utilized to delineate the molecular modus operandi for kinase and pseudokinase regulation. This should pave the path for full-length kinase-targeted drug discovery efforts aiming to identify single and combinatory kinase inhibitor therapies with increased specificity and efficacy.
Collapse
Affiliation(s)
- Florian Enzler
- Institute of Biochemistry and Center for Molecular Biosciences, University of InnsbruckInnsbruckAustria
| | - Philipp Tschaikner
- Institute of Biochemistry and Center for Molecular Biosciences, University of InnsbruckInnsbruckAustria
| | - Rainer Schneider
- Institute of Biochemistry and Center for Molecular Biosciences, University of InnsbruckInnsbruckAustria
| | - Eduard Stefan
- Institute of Biochemistry and Center for Molecular Biosciences, University of InnsbruckInnsbruckAustria
| |
Collapse
|