1
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Chen T, Tang X, Wang Z, Feng F, Xu C, Zhao Q, Wu Y, Sun H, Chen Y. Inhibition of Son of Sevenless Homologue 1 (SOS1): Promising therapeutic treatment for KRAS-mutant cancers. Eur J Med Chem 2023; 261:115828. [PMID: 37778239 DOI: 10.1016/j.ejmech.2023.115828] [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: 07/04/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/03/2023]
Abstract
Kristen rat sarcoma (KRAS) is one of the most common oncogenes in human cancers. As a guanine nucleotide exchange factor, Son of Sevenless Homologue 1 (SOS1) represents a potential therapeutic concept for the treatment of KRAS-mutant cancers because of its activation on KRAS and downstream signaling pathways. In this review, we provide a comprehensive overview of the structure, biological function, and regulation of SOS1. We also focus on the recent advances in SOS1 inhibitors and emphasize their binding modes, structure-activity relationships and pharmacological activities. We hope that this publication can provide a comprehensive compendium on the rational design of SOS1 inhibitors.
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Affiliation(s)
- Tingkai Chen
- School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, People's Republic of China
| | - Xu Tang
- School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, People's Republic of China
| | - Zhenqi Wang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, People's Republic of China
| | - Feng Feng
- School of Pharmacy, Nanjing Medical University, 211166, Nanjing, People's Republic of China
| | - Chunlei Xu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, People's Republic of China
| | - Qun Zhao
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, People's Republic of China
| | - Yulan Wu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, People's Republic of China
| | - Haopeng Sun
- School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, People's Republic of China.
| | - Yao Chen
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, People's Republic of China.
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2
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Wu X, Song W, Cheng C, Liu Z, Li X, Cui Y, Gao Y, Li D. Small molecular inhibitors for KRAS-mutant cancers. Front Immunol 2023; 14:1223433. [PMID: 37662925 PMCID: PMC10470052 DOI: 10.3389/fimmu.2023.1223433] [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: 05/16/2023] [Accepted: 07/31/2023] [Indexed: 09/05/2023] Open
Abstract
Three rat sarcoma (RAS) gene isoforms, KRAS, NRAS, and HRAS, constitute the most mutated family of small GTPases in cancer. While the development of targeted immunotherapies has led to a substantial improvement in the overall survival of patients with non-KRAS-mutant cancer, patients with RAS-mutant cancers have an overall poorer prognosis owing to the high aggressiveness of RAS-mutant tumors. KRAS mutations are strongly implicated in lung, pancreatic, and colorectal cancers. However, RAS mutations exhibit diverse patterns of isoforms, substitutions, and positions in different types of cancers. Despite being considered "undruggable", recent advances in the use of allele-specific covalent inhibitors against the most common mutant form of RAS in non-small-cell lung cancer have led to the development of effective pharmacological interventions against RAS-mutant cancer. Sotorasib (AMG510) has been approved by the FDA as a second-line treatment for patients with KRAS-G12C mutant NSCLC who have received at least one prior systemic therapy. Other KRAS inhibitors are on the way to block KRAS-mutant cancers. In this review, we summarize the progress and promise of small-molecule inhibitors in clinical trials, including direct inhibitors of KRAS, pan-RAS inhibitors, inhibitors of RAS effector signaling, and immune checkpoint inhibitors or combinations with RAS inhibitors, to improve the prognosis of tumors with RAS mutations.
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Affiliation(s)
- Xuan Wu
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Wenping Song
- Department of Pharmacy, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
- Henan Engineering Research Center for Tumor Precision Medicine and Comprehensive Evaluation, Henan Cancer Hospital, Zhengzhou, China
- Henan Provincial Key Laboratory of Anticancer Drug Research, Henan Cancer Hospital, Zhengzhou, China
| | - Cheng Cheng
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Ziyang Liu
- Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Xiang Li
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Yu Cui
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Yao Gao
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Ding Li
- Department of Pharmacy, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
- Henan Engineering Research Center for Tumor Precision Medicine and Comprehensive Evaluation, Henan Cancer Hospital, Zhengzhou, China
- Henan Provincial Key Laboratory of Anticancer Drug Research, Henan Cancer Hospital, Zhengzhou, China
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3
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Luo G, Wang B, Hou Q, Wu X. Development of Son of Sevenless Homologue 1 (SOS1) Modulators To Treat Cancers by Regulating RAS Signaling. J Med Chem 2023; 66:4324-4341. [PMID: 36987571 DOI: 10.1021/acs.jmedchem.2c01729] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Son of sevenless homologue 1 (SOS1) protein is universally expressed in cells and plays an important role in the RAS signaling pathway. Specifically, this protein interacts with RAS in response to upstream stimuli to promote guanine nucleotide exchange in RAS and activates the downstream signaling pathways. Thus, targeting SOS1 is a new approach for treating RAS-driven cancers. In this Perspective, we briefly summarize the structural and functional aspects of SOS1 and focus on recent advances in the discovery of activators, inhibitors, and PROTACs that target SOS1. This review aims to provide a timely and updated overview on the strategies for targeting SOS1 in cancer therapy.
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Affiliation(s)
- Guangmei Luo
- Department of Medicinal Chemistry, School of Pharmacy and Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Bingrui Wang
- Department of Medicinal Chemistry, School of Pharmacy and Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Qiangqiang Hou
- Department of Medicinal Chemistry, School of Pharmacy and Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Xiaoxing Wu
- Department of Medicinal Chemistry, School of Pharmacy and Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
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4
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Li A, Li X, Zou J, Zhuo X, Chen S, Chai X, Gai C, Xu W, Zhao Q, Zou Y. SOS1-inspired hydrocarbon-stapled peptide as a pan-Ras inhibitor. Bioorg Chem 2023; 135:106500. [PMID: 37003134 DOI: 10.1016/j.bioorg.2023.106500] [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: 02/24/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 04/03/2023]
Abstract
Blocking the interaction between Ras and Son of Sevenless homolog 1 (SOS1) has been an attractive therapeutic strategy for treating cancers involving oncogenic Ras mutations. K-Ras mutation is the most common in Ras-driven cancers, accounting for 86%, with N-Ras mutation and H-Ras mutation accounting for 11% and 3%, respectively. Here, we report the design and synthesis of a series of hydrocarbon-stapled peptides to mimic the alpha-helix of SOS1 as pan-Ras inhibitors. Among these stapled peptides, SSOSH-5 was identified to maintain a well-constrained alpha-helical structure and bind to H-Ras with high affinity. SSOSH-5 was furthermore validated to bind with Ras similarly to the parent linear peptide through structural modeling analysis. This optimized stapled peptide was proven to be capable of effectively inhibiting the proliferation of pan-Ras-mutated cancer cells and inducing apoptosis in a dose-dependent manner by modulating downstream kinase signaling. Of note, SSOSH-5 exhibited a high capability of crossing cell membranes and strong proteolytic resistance. We demonstrated that the peptide stapling strategy is a feasible approach for developing peptide-based pan-Ras inhibitors. Furthermore, we expect that SSOSH-5 can be further characterized and optimized for the treatment of Ras-driven cancers.
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Affiliation(s)
- Anpeng Li
- School of Pharmacy, Naval Medical University, Shanghai, PR China; 92805 Military Hospital, Qingdao, PR China
| | - Xiang Li
- School of Pharmacy, Naval Medical University, Shanghai, PR China
| | - Jihua Zou
- School of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, PR China
| | - Xiaobin Zhuo
- School of Pharmacy, Naval Medical University, Shanghai, PR China
| | - Shuai Chen
- School of Pharmacy, Naval Medical University, Shanghai, PR China
| | - Xiaoyun Chai
- School of Pharmacy, Naval Medical University, Shanghai, PR China
| | - Conghao Gai
- School of Pharmacy, Naval Medical University, Shanghai, PR China
| | - Weiheng Xu
- School of Pharmacy, Naval Medical University, Shanghai, PR China.
| | - Qingjie Zhao
- School of Pharmacy, Naval Medical University, Shanghai, PR China.
| | - Yan Zou
- School of Pharmacy, Naval Medical University, Shanghai, PR China.
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5
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Wallon L, Khan I, Teng KW, Koide A, Zuberi M, Li J, Ketavarapu G, Traaseth NJ, O’Bryan JP, Koide S. Inhibition of RAS-driven signaling and tumorigenesis with a pan-RAS monobody targeting the Switch I/II pocket. Proc Natl Acad Sci U S A 2022; 119:e2204481119. [PMID: 36252024 PMCID: PMC9618066 DOI: 10.1073/pnas.2204481119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 08/25/2022] [Indexed: 11/18/2022] Open
Abstract
RAS mutants are major therapeutic targets in oncology with few efficacious direct inhibitors available. The identification of a shallow pocket near the Switch II region on RAS has led to the development of small-molecule drugs that target this site and inhibit KRAS(G12C) and KRAS(G12D). To discover other regions on RAS that may be targeted for inhibition, we have employed small synthetic binding proteins termed monobodies that have a strong propensity to bind to functional sites on a target protein. Here, we report a pan-RAS monobody, termed JAM20, that bound to all RAS isoforms with nanomolar affinity and demonstrated limited nucleotide-state specificity. Upon intracellular expression, JAM20 potently inhibited signaling mediated by all RAS isoforms and reduced oncogenic RAS-mediated tumorigenesis in vivo. NMR and mutation analysis determined that JAM20 bound to a pocket between Switch I and II, which is similarly targeted by low-affinity, small-molecule inhibitors, such as BI-2852, whose in vivo efficacy has not been demonstrated. Furthermore, JAM20 directly competed with both the RAF(RBD) and BI-2852. These results provide direct validation of targeting the Switch I/II pocket for inhibiting RAS-driven tumorigenesis. More generally, these results demonstrate the utility of tool biologics as probes for discovering and validating druggable sites on challenging targets.
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Affiliation(s)
- Lauren Wallon
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016
| | - Imran Khan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425
- Ralph H. Johnson VA Medical Center, Charleston, SC 29401
| | - Kai Wen Teng
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016
| | - Akiko Koide
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016
- Department of Medicine, New York University School of Medicine, New York, NY 10016
| | - Mariyam Zuberi
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425
- Ralph H. Johnson VA Medical Center, Charleston, SC 29401
| | - Jianping Li
- Department of Chemistry, New York University, New York, NY 10003
| | - Gayatri Ketavarapu
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016
| | | | - John P. O’Bryan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425
- Ralph H. Johnson VA Medical Center, Charleston, SC 29401
| | - Shohei Koide
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016
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6
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He X, Du K, Wang Y, Fan J, Li M, Ni D, Lu S, Bian X, Liu Y. Autopromotion of K-Ras4B Feedback Activation Through an SOS-Mediated Long-Range Allosteric Effect. Front Mol Biosci 2022; 9:860962. [PMID: 35463958 PMCID: PMC9023742 DOI: 10.3389/fmolb.2022.860962] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/01/2022] [Indexed: 12/14/2022] Open
Abstract
The Ras-specific guanine nucleotide exchange factors Son of Sevenless (SOS) regulates Ras activation by converting inactive GDP-bound to active GTP-bound states. The catalytic activity of Ras is further allosterically regulated by GTP−Ras bound to a distal site through a positive feedback loop. To address the mechanism underlying the long-range allosteric activation of the catalytic K-Ras4B by an additional allosteric GTP–Ras through SOS, we employed molecular dynamics simulation of the K-Ras4BG13D•SOScat complex with and without an allosteric GTP-bound K-Ras4BG13D. We found that the binding of an allosteric GTP−K-Ras4BG13D enhanced the affinity between the catalytic K-Ras4BG13D and SOScat, forming a more stable conformational state. The peeling away of the switch I from the nucleotide binding site facilitated the dissociation of GDP, thereby contributing to the increased nucleotide exchange rate. The community networks further showed stronger edge connection upon allosteric GTP−K-Ras4BG13D binding, which represented an increased interaction between catalytic K-Ras4BG13D and SOScat. Moreover, GTP−K-Ras4BG13D binding transmitted allosteric signaling pathways though the Cdc25 domain of SOS that enhanced the allosteric regulatory from the K-Ras4BG13D allosteric site to the catalytic site. This study may provide an in-depth mechanism for abnormal activation and allosteric regulation of K-Ras4BG13D.
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Affiliation(s)
- Xuan He
- Department of Pharmacy, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Kui Du
- School of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, China
| | - Yuanhao Wang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jigang Fan
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Mingyu Li
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Duan Ni
- The Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia
| | - Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
- *Correspondence: Shaoyong Lu, ; Xiaolan Bian, ; Yaqin Liu,
| | - Xiaolan Bian
- Department of Pharmacy, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
- *Correspondence: Shaoyong Lu, ; Xiaolan Bian, ; Yaqin Liu,
| | - Yaqin Liu
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
- *Correspondence: Shaoyong Lu, ; Xiaolan Bian, ; Yaqin Liu,
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7
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Johnson CW, Seo HS, Terrell EM, Yang MH, KleinJan F, Gebregiworgis T, Gasmi-Seabrook GMC, Geffken EA, Lakhani J, Song K, Bashyal P, Popow O, Paulo JA, Liu A, Mattos C, Marshall CB, Ikura M, Morrison DK, Dhe-Paganon S, Haigis KM. Regulation of GTPase function by autophosphorylation. Mol Cell 2022; 82:950-968.e14. [PMID: 35202574 PMCID: PMC8986090 DOI: 10.1016/j.molcel.2022.02.011] [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: 05/12/2021] [Revised: 11/29/2021] [Accepted: 02/04/2022] [Indexed: 10/19/2022]
Abstract
A unifying feature of the RAS superfamily is a conserved GTPase cycle by which these proteins transition between active and inactive states. We demonstrate that autophosphorylation of some GTPases is an intrinsic regulatory mechanism that reduces nucleotide hydrolysis and enhances nucleotide exchange, altering the on/off switch that forms the basis for their signaling functions. Using X-ray crystallography, nuclear magnetic resonance spectroscopy, binding assays, and molecular dynamics on autophosphorylated mutants of H-RAS and K-RAS, we show that phosphoryl transfer from GTP requires dynamic movement of the switch II region and that autophosphorylation promotes nucleotide exchange by opening the active site and extracting the stabilizing Mg2+. Finally, we demonstrate that autophosphorylated K-RAS exhibits altered effector interactions, including a reduced affinity for RAF proteins in mammalian cells. Thus, autophosphorylation leads to altered active site dynamics and effector interaction properties, creating a pool of GTPases that are functionally distinct from their non-phosphorylated counterparts.
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Affiliation(s)
- Christian W Johnson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Hyuk-Soo Seo
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Elizabeth M Terrell
- Laboratory of Cell and Developmental Signaling, NCI-Frederick, Frederick, MD 21702, USA
| | - Moon-Hee Yang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Fenneke KleinJan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Teklab Gebregiworgis
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | | | - Ezekiel A Geffken
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jimit Lakhani
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kijun Song
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Puspalata Bashyal
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Olesja Popow
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Andrea Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | | | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Deborah K Morrison
- Laboratory of Cell and Developmental Signaling, NCI-Frederick, Frederick, MD 21702, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Kevin M Haigis
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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8
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Zhou C, Fan Z, Zhou Z, Li Y, Cui R, Liu C, Zhou G, Diao X, Jiang H, Zheng M, Zhang S, Xu T. Discovery of the First-in-Class Agonist-Based SOS1 PROTACs Effective in Human Cancer Cells Harboring Various KRAS Mutations. J Med Chem 2022; 65:3923-3942. [PMID: 35230841 DOI: 10.1021/acs.jmedchem.1c01774] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Regulating SOS1 functions may result in targeted pan-KRAS therapies. Small-molecule SOS1 inhibitors showed promising anticancer potential, and the most advanced inhibitor BI 1701963 is currently under phase I clinical studies. SOS1 agonists provide new opportunities to treat cancer; however, the underlying mechanisms still warrant investigation. We here report the discovery of the first SOS1 PROTACs designed uniquely by connecting a VHL ligand to the reported SOS1 agonist, ensuring that the observed inhibitory activity results from degraders. The best compound 9d induced SOS1 degradation in various KRAS-driven cancer cells and displayed superior antiproliferation activity compared to the agonist itself. Tumor xenograft study clearly showed the promising antitumor potency of 9d against human lung cancer. This study provides good evidence of using agonists to design SOS1 PROTACs and demonstrates that targeted SOS1 degradation represents an effective therapeutic strategy for overcoming KRAS-driven cancers.
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Affiliation(s)
- Chuan Zhou
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Zisheng Fan
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China.,Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Zehui Zhou
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yupeng Li
- Masonic Cancer Center & Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Rongrong Cui
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China.,Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Chaoyi Liu
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Guizhen Zhou
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China.,Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Xingxing Diao
- Shanghai Center for Drug Metabolism and Pharmacokinetics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Hualiang Jiang
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China.,Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Mingyue Zheng
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China.,Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Sulin Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Tianfeng Xu
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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9
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The Q61H mutation decouples KRAS from upstream regulation and renders cancer cells resistant to SHP2 inhibitors. Nat Commun 2021; 12:6274. [PMID: 34725361 PMCID: PMC8560773 DOI: 10.1038/s41467-021-26526-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 09/23/2021] [Indexed: 12/31/2022] Open
Abstract
Cancer cells bearing distinct KRAS mutations exhibit variable sensitivity to SHP2 inhibitors (SHP2i). Here we show that cells harboring KRAS Q61H are uniquely resistant to SHP2i, and investigate the underlying mechanisms using biophysics, molecular dynamics, and cell-based approaches. Q61H mutation impairs intrinsic and GAP-mediated GTP hydrolysis, and impedes activation by SOS1, but does not alter tyrosyl phosphorylation. Wild-type and Q61H-mutant KRAS are both phosphorylated by Src on Tyr32 and Tyr64 and dephosphorylated by SHP2, however, SHP2i does not reduce ERK phosphorylation in KRAS Q61H cells. Phosphorylation of wild-type and Gly12-mutant KRAS, which are associated with sensitivity to SHP2i, confers resistance to regulation by GAP and GEF activities and impairs binding to RAF, whereas the near-complete GAP/GEF-resistance of KRAS Q61H remains unaltered, and high-affinity RAF interaction is retained. SHP2 can stimulate KRAS signaling by modulating GEF/GAP activities and dephosphorylating KRAS, processes that fail to regulate signaling of the Q61H mutant. SHP2 promotes RAS-driven MAPK signalling, but it is unclear why cancer cells with distinct KRAS mutations exhibit differential sensitivity to SHP2 inhibition. Here the authors show that KRAS Q61H is decoupled from SHP2- mediated upstream regulation, thus Q61H pancreatic cancer cells maintain MAPK signalling and are refractory to SHP2 inhibitors.
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10
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Fowlkes JL, Thrailkill KM, Bunn RC. RASopathies: The musculoskeletal consequences and their etiology and pathogenesis. Bone 2021; 152:116060. [PMID: 34144233 PMCID: PMC8316423 DOI: 10.1016/j.bone.2021.116060] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/07/2021] [Accepted: 06/10/2021] [Indexed: 01/07/2023]
Abstract
The RASopathies comprise an ever-growing number of clinical syndromes resulting from germline mutations in components of the RAS/MAPK signaling pathway. While multiple organs and tissues may be affected by these mutations, this review will focus on how these mutations specifically impact the musculoskeletal system. Herein, we review the genetics and musculoskeletal phenotypes of these syndromes in humans. We discuss how mutations in the RASopathy syndromes have been studied in translational mouse models. Finally, we discuss how signaling molecules within the RAS/MAPK pathway are involved in normal and abnormal bone biology in the context of osteoblasts, osteoclasts and chondrocytes.
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Affiliation(s)
- John L Fowlkes
- University of Kentucky Barnstable Brown Diabetes Center, Department of Pediatrics, University of Kentucky College of Medicine, Lexington, KY 40536, United States of America.
| | - Kathryn M Thrailkill
- University of Kentucky Barnstable Brown Diabetes Center, Department of Pediatrics, University of Kentucky College of Medicine, Lexington, KY 40536, United States of America
| | - R Clay Bunn
- University of Kentucky Barnstable Brown Diabetes Center, Department of Pediatrics, University of Kentucky College of Medicine, Lexington, KY 40536, United States of America
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11
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A Rational Design of α-Helix-Shaped Peptides Employing the Hydrogen-Bond Surrogate Approach: A Modulation Strategy for Ras-RasGRF1 Interaction in Neuropsychiatric Disorders. Pharmaceuticals (Basel) 2021; 14:ph14111099. [PMID: 34832880 PMCID: PMC8623491 DOI: 10.3390/ph14111099] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 01/09/2023] Open
Abstract
In the last two decades, abnormal Ras (rat sarcoma protein)-ERK (extracellular signal-regulated kinase) signalling in the brain has been involved in a variety of neuropsychiatric disorders, including drug addiction, certain forms of intellectual disability, and autism spectrum disorder. Modulation of membrane-receptor-mediated Ras activation has been proposed as a potential target mechanism to attenuate ERK signalling in the brain. Previously, we showed that a cell penetrating peptide, RB3, was able to inhibit downstream signalling by preventing RasGRF1 (Ras guanine nucleotide-releasing factor 1), a neuronal specific GDP/GTP exchange factor, to bind Ras proteins, both in brain slices and in vivo, with an IC50 value in the micromolar range. The aim of this work was to mutate and improve this peptide through computer-aided techniques to increase its inhibitory activity against RasGRF1. The designed peptides were built based on the RB3 peptide structure corresponding to the α-helix of RasGRF1 responsible for Ras binding. For this purpose, the hydrogen-bond surrogate (HBS) approach was exploited to maintain the helical conformation of the designed peptides. Finally, residue scanning, MD simulations, and MM-GBSA calculations were used to identify 18 most promising α-helix-shaped peptides that will be assayed to check their potential activity against Ras-RasGRF1 and prevent downstream molecular events implicated in brain disorders.
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12
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Thompson SK, Buckl A, Dossetter AG, Griffen E, Gill A. Small molecule Son of Sevenless 1 (SOS1) inhibitors: a review of the patent literature. Expert Opin Ther Pat 2021; 31:1189-1204. [PMID: 34253125 DOI: 10.1080/13543776.2021.1952984] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Up to 30% of all human cancers are driven by the overactivation of RAS signaling. Son of Sevenless 1 (SOS1) is a central node in RAS signaling pathways and modulation of SOS1-mediated RAS activation represents a unique opportunity for treating RAS-addicted cancers. Several recent publications and patent documents have demonstrated the ability of small molecules to affect the activation of RAS by SOS1 and have shown their potential for the treatment of cancers driven by RAS mutants.Areas covered: Documents focusing on both small-molecule inhibitors and activators of the SOS1:RAS interaction and their potential use as cancer therapeutics are covered. A total of 10 documents from 4 applicants are evaluated with discussion focusing on structural modifications of these compounds as well as relevant preclinical data.Expert opinion: The last decade has seen a significant increase in research and disclosures in the development of small-molecule SOS1 inhibitors. Considering the promising data that have been disclosed, interest in this area of research will likely remain strong for the foreseeable future. With the first SOS1 inhibitor currently in phase I clinical trials, the outcome of these trials will likely influence future development of SOS1 inhibitors for treatment of RAS-driven cancers.
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Affiliation(s)
- Severin K Thompson
- Department of Discovery Chemistry, Revolution Medicines Inc., Redwood City, CA, USA
| | - Andreas Buckl
- Department of Discovery Chemistry, Revolution Medicines Inc., Redwood City, CA, USA
| | | | - Ed Griffen
- Medchemica Limited, Biohub, Mereside, Cheshire, UK
| | - Adrian Gill
- Department of Discovery Chemistry, Revolution Medicines Inc., Redwood City, CA, USA
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13
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Chen J, Wang L, Wang W, Sun H, Pang L, Bao H. Conformational transformation of switch domains in GDP/K-Ras induced by G13 mutants: An investigation through Gaussian accelerated molecular dynamics simulations and principal component analysis. Comput Biol Med 2021; 135:104639. [PMID: 34247129 DOI: 10.1016/j.compbiomed.2021.104639] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/05/2021] [Accepted: 07/05/2021] [Indexed: 10/20/2022]
Abstract
Mutations in K-Ras are involved in a large number of all human cancers, thus, K-Ras is regarded as a promising target for anticancer drug design. Understanding the target roles of K-Ras is important for providing insights on the molecular mechanism underlying the conformational transformation of the switch domains in K-Ras due to mutations. In this study, multiple replica Gaussian accelerated molecular (MR-GaMD) simulations and principal component analysis (PCA) were applied to probe the effect of G13A, G13D and G13I mutations on conformational transformations of the switch domains in GDP-associated K-Ras. The results suggest that G13A, G13D and G13I enhance the structural flexibility of the switch domains, change the correlated motion modes of the switch domains and strengthen the total motion strength of K-Ras compared with the wild-type (WT) K-Ras. Free energy landscape analyses not only show that the switch domains of the GDP-bound inactive K-Ras mainly exist as a closed state but also indicate that mutations evidently alter the free energy profile of K-Ras and affect the conformational transformation of the switch domains between the closed and open states. Analyses of hydrophobic interaction contacts and hydrogen bonding interactions show that the mutations scarcely change the interaction network of GDP with K-Ras and only disturb the interaction of GDP with the switch (SW1). In summary, two newly introduced mutations, G13A and G13I, play similar adjustment roles in the conformational transformations of two switch domains to G13D and are possibly utilized to tune the activity of K-Ras and the binding of guanine nucleotide exchange factors.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan, 250357, China.
| | - Lifei Wang
- School of Science, Shandong Jiaotong University, Jinan, 250357, China
| | - Wei Wang
- School of Science, Shandong Jiaotong University, Jinan, 250357, China
| | - Haibo Sun
- School of Science, Shandong Jiaotong University, Jinan, 250357, China
| | - Laixue Pang
- School of Science, Shandong Jiaotong University, Jinan, 250357, China
| | - Huayin Bao
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China.
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14
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Kessler D, Gerlach D, Kraut N, McConnell DB. Targeting Son of Sevenless 1: The pacemaker of KRAS. Curr Opin Chem Biol 2021; 62:109-118. [PMID: 33848766 DOI: 10.1016/j.cbpa.2021.02.014] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 02/23/2021] [Accepted: 02/27/2021] [Indexed: 12/12/2022]
Abstract
Son of Sevenless (SOS) is a guanine nucleotide exchange factor that activates the important cell signaling switch KRAS. SOS acts as a pacemaker for KRAS, the beating heart of cancer, by catalyzing the "beating" from the KRAS(off) to the KRAS(on) conformation. Activating mutations in SOS1 are common in Noonan syndrome and oncogenic alterations in KRAS drive 1 in seven human cancers. Promising clinical efficacy has been observed for selective KRASG12C inhibitors, but the vast majority of oncogenic KRAS alterations remain undrugged. The discovery of a druggable pocket on SOS1 has led to potent SOS1 inhibitors such as BI-3406. SOS1 inhibition leads to antiproliferative effects against all major KRAS mutants. The first SOS1 inhibitor has entered clinical trials for KRAS-mutated cancers. In this review, we provide an overview of SOS1 function, its association with cancer and RASopathies, known SOS1 activators and inhibitors, and a future perspective is provided.
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Affiliation(s)
- Dirk Kessler
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120, Vienna, Austria
| | - Daniel Gerlach
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120, Vienna, Austria
| | - Norbert Kraut
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120, Vienna, Austria
| | - Darryl B McConnell
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120, Vienna, Austria.
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15
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Molecular assemblies of the catalytic domain of SOS with KRas and oncogenic mutants. Proc Natl Acad Sci U S A 2021; 118:2022403118. [PMID: 33723061 DOI: 10.1073/pnas.2022403118] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Ras is regulated by a specific guanine nucleotide exchange factor Son of Sevenless (SOS), which facilitates the exchange of inactive, GDP-bound Ras with GTP. The catalytic activity of SOS is also allosterically modulated by an active Ras (Ras-GTP). However, it remains poorly understood how oncogenic Ras mutants interact with SOS and modulate its activity. Here, native ion mobility-mass spectrometry is employed to monitor the assembly of the catalytic domain of SOS (SOScat) with KRas and three cancer-associated mutants (G12C, G13D, and Q61H), leading to the discovery of different molecular assemblies and distinct conformers of SOScat engaging KRas. We also find KRasG13D exhibits high affinity for SOScat and is a potent allosteric modulator of its activity. A structure of the KRasG13D•SOScat complex was determined using cryogenic electron microscopy providing insight into the enhanced affinity of the mutant protein. In addition, we find that KRasG13D-GTP can allosterically increase the nucleotide exchange rate of KRas at the active site more than twofold compared to KRas-GTP. Furthermore, small-molecule Ras•SOS disruptors fail to dissociate KRasG13D•SOScat complexes, underscoring the need for more potent disruptors. Taken together, a better understanding of the interaction between oncogenic Ras mutants and SOS will provide avenues for improved therapeutic interventions.
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16
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Chen J, Zhang S, Wang W, Pang L, Zhang Q, Liu X. Mutation-Induced Impacts on the Switch Transformations of the GDP- and GTP-Bound K-Ras: Insights from Multiple Replica Gaussian Accelerated Molecular Dynamics and Free Energy Analysis. J Chem Inf Model 2021; 61:1954-1969. [PMID: 33739090 DOI: 10.1021/acs.jcim.0c01470] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mutations yield significant effect on the structural flexibility of two switch domains, SW1 and SW2, in K-Ras, which is considered as an important target of anticancer drug design. To unveil a molecular mechanism with regard to mutation-mediated tuning on the activity of K-Ras, multiple replica Gaussian accelerated molecular dynamics (MR-GaMD) simulations followed by analysis of free energy landscapes (FELs) are performed on the GDP- and GTP-bound wild-type (WT), G12V, and D33E K-Ras. The results suggest that G12V and D33E not only evidently change the flexibility of SW1 and SW2 but also greatly affect correlated motions of SW1 and SW2 separately relative to the P-loop and SW1, which exerts a certain tuning on the activity of K-Ras. The information stemming from the analyses of FELs reveals that the conformations of SW1 and SW2 are in high disorders in the GDP- and GTP-associated WT and mutated K-Ras, possibly producing significant effect on binding of guanine nucleotide exchange factors or effectors to K-Ras. The interaction networks of GDP and GTP with K-Ras are identified and the results uncover that the instability in hydrogen-bonding interactions of SW1 with GDP and GTP is mostly responsible for conformational disorder of SW1 and SW2 as well as tunes the activity of oncogenic K-Ras.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Shaolong Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China
| | - Wei Wang
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Laixue Pang
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Qinggang Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China
| | - Xinguo Liu
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China
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17
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Inaba H, Miao Q, Nakata T. Optogenetic control of small GTPases reveals RhoA mediates intracellular calcium signaling. J Biol Chem 2021; 296:100290. [PMID: 33453281 PMCID: PMC7949103 DOI: 10.1016/j.jbc.2021.100290] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 01/06/2021] [Accepted: 01/11/2021] [Indexed: 01/05/2023] Open
Abstract
Rho/Ras family small GTPases are known to regulate numerous cellular processes, including cytoskeletal reorganization, cell proliferation, and cell differentiation. These processes are also controlled by Ca2+, and consequently, cross talk between these signals is considered likely. However, systematic quantitative evaluation has not yet been reported. To fill this gap, we constructed optogenetic tools to control the activity of small GTPases (RhoA, Rac1, Cdc42, Ras, Rap, and Ral) using an improved light-inducible dimer system (iLID). We characterized these optogenetic tools with genetically encoded red fluorescence intensity-based small GTPase biosensors and confirmed these optogenetic tools’ specificities. Using these optogenetic tools, we investigated calcium mobilization immediately after small GTPase activation. Unexpectedly, we found that a transient intracellular calcium elevation was specifically induced by RhoA activation in RPE1 and HeLa cells. RhoA activation also induced transient intracellular calcium elevation in MDCK and HEK293T cells, suggesting that generally RhoA induces calcium signaling. Interestingly, the molecular mechanisms linking RhoA activation to calcium increases were shown to be different among the different cell types: In RPE1 and HeLa cells, RhoA activated phospholipase C epsilon (PLCε) at the plasma membrane, which in turn induced Ca2+ release from the endoplasmic reticulum (ER). The RhoA–PLCε axis induced calcium-dependent nuclear factor of activated T cells nuclear translocation, suggesting that it does activate intracellular calcium signaling. Conversely, in MDCK and HEK293T cells, RhoA–ROCK–myosin II axis induced the calcium transients. These data suggest universal coordination of RhoA and calcium signaling in cellular processes, such as cellular contraction and gene expression.
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Affiliation(s)
- Hironori Inaba
- Department of Cell Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan; The Center for Brain Integration Research (CBIR), Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Qianqian Miao
- Department of Cell Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan; The Center for Brain Integration Research (CBIR), Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Takao Nakata
- Department of Cell Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan; The Center for Brain Integration Research (CBIR), Tokyo Medical and Dental University (TMDU), Tokyo, Japan.
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18
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Baltanás FC, Zarich N, Rojas-Cabañeros JM, Santos E. SOS GEFs in health and disease. Biochim Biophys Acta Rev Cancer 2020; 1874:188445. [PMID: 33035641 DOI: 10.1016/j.bbcan.2020.188445] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/01/2020] [Accepted: 10/01/2020] [Indexed: 12/11/2022]
Abstract
SOS1 and SOS2 are the most universal and widely expressed family of guanine exchange factors (GEFs) capable or activating RAS or RAC1 proteins in metazoan cells. SOS proteins contain a sequence of modular domains that are responsible for different intramolecular and intermolecular interactions modulating mechanisms of self-inhibition, allosteric activation and intracellular homeostasis. Despite their homology, analyses of SOS1/2-KO mice demonstrate functional prevalence of SOS1 over SOS2 in cellular processes including proliferation, migration, inflammation or maintenance of intracellular redox homeostasis, although some functional redundancy cannot be excluded, particularly at the organismal level. Specific SOS1 gain-of-function mutations have been identified in inherited RASopathies and various sporadic human cancers. SOS1 depletion reduces tumorigenesis mediated by RAS or RAC1 in mouse models and is associated with increased intracellular oxidative stress and mitochondrial dysfunction. Since WT RAS is essential for development of RAS-mutant tumors, the SOS GEFs may be considered as relevant biomarkers or therapy targets in RAS-dependent cancers. Inhibitors blocking SOS expression, intrinsic GEF activity, or productive SOS protein-protein interactions with cellular regulators and/or RAS/RAC targets have been recently developed and shown preclinical and clinical effectiveness blocking aberrant RAS signaling in RAS-driven and RTK-driven tumors.
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Affiliation(s)
- Fernando C Baltanás
- Centro de Investigación del Cáncer - IBMCC (CSIC-USAL) and CIBERONC, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Natasha Zarich
- Unidad Funcional de Investigación de Enfermedades Crónicas (UFIEC) and CIBERONC, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain
| | - Jose M Rojas-Cabañeros
- Unidad Funcional de Investigación de Enfermedades Crónicas (UFIEC) and CIBERONC, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain
| | - Eugenio Santos
- Centro de Investigación del Cáncer - IBMCC (CSIC-USAL) and CIBERONC, Universidad de Salamanca, 37007 Salamanca, Spain.
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Yin G, Zhang J, Nair V, Truong V, Chaia A, Petela J, Harrison J, Gorfe AA, Campbell SL. KRAS Ubiquitination at Lysine 104 Retains Exchange Factor Regulation by Dynamically Modulating the Conformation of the Interface. iScience 2020; 23:101448. [PMID: 32882514 PMCID: PMC7479270 DOI: 10.1016/j.isci.2020.101448] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/13/2020] [Accepted: 08/06/2020] [Indexed: 12/13/2022] Open
Abstract
RAS proteins function as highly regulated molecular switches that control cellular growth. In addition to regulatory proteins, RAS undergoes a number of posttranslational modifications (PTMs) that regulate its activity. Lysine 104, a hot spot for multiple PTMs, is a highly conserved residue that forms key interactions that stabilize the RAS helix-2(H2)/helix-3(H3) interface. Mutation at 104 attenuates interaction with guanine nucleotide exchange factors (GEFs), whereas ubiquitination at lysine 104 retains GEF regulation. To elucidate how ubiquitination modulates RAS function, we generated monoubiquitinated KRAS at 104 using chemical biology approaches and conducted biochemical, NMR, and computational analyses. We find that ubiquitination promotes a new dynamic interaction network and alters RAS conformational dynamics to retain GEF function. These findings reveal a mechanism by which ubiquitination can regulate protein function.
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Affiliation(s)
- Guowei Yin
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China
| | - Jerry Zhang
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Vinay Nair
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
- MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Vinh Truong
- Department of Chemistry, University of the Pacific, Stockton, CA, USA
| | - Angelo Chaia
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Johnny Petela
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Joseph Harrison
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Chemistry, University of the Pacific, Stockton, CA, USA
| | - Alemayehu A. Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
- MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Sharon L. Campbell
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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20
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Buday L, Vas V. Novel regulation of Ras proteins by direct tyrosine phosphorylation and dephosphorylation. Cancer Metastasis Rev 2020; 39:1067-1073. [PMID: 32936431 PMCID: PMC7680326 DOI: 10.1007/s10555-020-09918-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 06/19/2020] [Indexed: 12/01/2022]
Abstract
Somatic mutations in the RAS genes are frequent in human tumors, especially in pancreatic, colorectal, and non-small-cell lung cancers. Such mutations generally decrease the ability of Ras to hydrolyze GTP, maintaining the protein in a constitutively active GTP-bound form that drives uncontrolled cell proliferation. Efforts to develop drugs that target Ras oncoproteins have been unsuccessful. Recent emerging data suggest that Ras regulation is more complex than the scientific community has believed for decades. In this review, we summarize advances in the "textbook" view of Ras activation. We also discuss a novel type of Ras regulation that involves direct phosphorylation and dephosphorylation of Ras tyrosine residues. The discovery that pharmacological inhibition of the tyrosine phosphoprotein phosphatase SHP2 maintains mutant Ras in an inactive state suggests that SHP2 could be a novel drug target for the treatment of Ras-driven human cancers.
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Affiliation(s)
- László Buday
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, 1117, Hungary.
- Department of Medical Chemistry, Semmelweis University Medical School, Budapest, 1094, Hungary.
| | - Virág Vas
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, 1117, Hungary
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21
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Cowan JR, Salyer L, Wright NT, Kinnamon DD, Amaya P, Jordan E, Bamshad MJ, Nickerson DA, Hershberger RE. SOS1 Gain-of-Function Variants in Dilated Cardiomyopathy. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2020; 13:e002892. [PMID: 32603605 DOI: 10.1161/circgen.119.002892] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Dilated cardiomyopathy (DCM) is a genetically heterogeneous cardiac disease characterized by progressive ventricular enlargement and reduced systolic function. Here, we report genetic and functional analyses implicating the rat sarcoma signaling protein, SOS1 (Son of sevenless homolog 1), in DCM pathogenesis. METHODS Exome sequencing was performed on 412 probands and family members from our DCM cohort, identifying several SOS1 variants with potential disease involvement. As several lines of evidence have implicated dysregulated rat sarcoma signaling in the pathogenesis of DCM, we assessed functional impact of each variant on the activation of ERK (extracellular signal-regulated kinase), AKT (protein kinase B), and JNK (c-Jun N-terminal kinase) pathways. Relative expression levels were determined by Western blot in HEK293T cells transfected with variant or wild-type human SOS1 expression constructs. RESULTS A rare SOS1 variant [c.571G>A, p.(Glu191Lys)] was found to segregate alongside an A-band TTN truncating variant in a pedigree with aggressive, early-onset DCM. Reduced disease severity in the absence of the SOS1 variant suggested its potential involvement as a genetic risk factor for DCM in this family. Exome sequencing identified 5 additional SOS1 variants with potential disease involvement in 4 other families [c.1820T>C, p.(Ile607Thr); c.2156G>C, p.(Gly719Ala); c.2230A>G, p.(Arg744Gly); c.2728G>C, p.(Asp910His); c.3601C>T, p.(Arg1201Trp)]. Impacted amino acids occupied a number of functional domains relevant to SOS1 activity, including the N-terminal histone fold, as well as the C-terminal REM (rat sarcoma exchange motif), CDC25 (cell division cycle 25), and PR (proline-rich) tail domains. Increased phosphorylated ERK expression relative to wild-type levels was seen for all 6 SOS1 variants, paralleling known disease-relevant SOS1 signaling profiles. CONCLUSIONS These data support gain-of-function variation in SOS1 as a contributing factor to isolated DCM.
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Affiliation(s)
- Jason R Cowan
- Dorothy M. Davis Heart and Lung Research Institute (J.R.C., L.S., D.D.K., P.A., E.J., R.E.H.), Department of Internal Medicine, The Ohio State University College of Medicine, Columbus.,Division of Human Genetics (J.R.C., L.S., D.D.K., P.A., E.J., R.E.H.), Department of Internal Medicine, The Ohio State University College of Medicine, Columbus
| | - Lorien Salyer
- Dorothy M. Davis Heart and Lung Research Institute (J.R.C., L.S., D.D.K., P.A., E.J., R.E.H.), Department of Internal Medicine, The Ohio State University College of Medicine, Columbus.,Division of Human Genetics (J.R.C., L.S., D.D.K., P.A., E.J., R.E.H.), Department of Internal Medicine, The Ohio State University College of Medicine, Columbus
| | - Nathan T Wright
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA (N.T.W.)
| | - Daniel D Kinnamon
- Dorothy M. Davis Heart and Lung Research Institute (J.R.C., L.S., D.D.K., P.A., E.J., R.E.H.), Department of Internal Medicine, The Ohio State University College of Medicine, Columbus.,Division of Human Genetics (J.R.C., L.S., D.D.K., P.A., E.J., R.E.H.), Department of Internal Medicine, The Ohio State University College of Medicine, Columbus
| | - Pedro Amaya
- Dorothy M. Davis Heart and Lung Research Institute (J.R.C., L.S., D.D.K., P.A., E.J., R.E.H.), Department of Internal Medicine, The Ohio State University College of Medicine, Columbus.,Division of Human Genetics (J.R.C., L.S., D.D.K., P.A., E.J., R.E.H.), Department of Internal Medicine, The Ohio State University College of Medicine, Columbus
| | - Elizabeth Jordan
- Dorothy M. Davis Heart and Lung Research Institute (J.R.C., L.S., D.D.K., P.A., E.J., R.E.H.), Department of Internal Medicine, The Ohio State University College of Medicine, Columbus.,Division of Human Genetics (J.R.C., L.S., D.D.K., P.A., E.J., R.E.H.), Department of Internal Medicine, The Ohio State University College of Medicine, Columbus
| | - Michael J Bamshad
- Department of Pediatrics (M.J.B.), University of Washington, Seattle
| | | | - Ray E Hershberger
- Dorothy M. Davis Heart and Lung Research Institute (J.R.C., L.S., D.D.K., P.A., E.J., R.E.H.), Department of Internal Medicine, The Ohio State University College of Medicine, Columbus.,Division of Human Genetics (J.R.C., L.S., D.D.K., P.A., E.J., R.E.H.), Department of Internal Medicine, The Ohio State University College of Medicine, Columbus.,Division of Cardiovascular Medicine (R.E.H.), Department of Internal Medicine, The Ohio State University College of Medicine, Columbus
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22
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Bera AK, Lu J, Wales TE, Gondi S, Gurbani D, Nelson A, Engen JR, Westover KD. Structural basis of the atypical activation mechanism of KRAS V14I. J Biol Chem 2019; 294:13964-13972. [PMID: 31341022 PMCID: PMC6755796 DOI: 10.1074/jbc.ra119.009131] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/18/2019] [Indexed: 01/20/2023] Open
Abstract
RAS regulation and signaling are largely accomplished by direct protein-protein interactions, making RAS protein dynamics a critical determinant of RAS function. Here, we report a crystal structure of GDP-bound KRASV14I, a mutated KRAS variant associated with the developmental RASopathy disorder Noonan syndrome (NS), at 1.5-1.6 Å resolution. The structure is notable for revealing a marked extension of switch 1 away from the G-domain and nucleotide-binding site of the KRAS protein. We found that this extension is associated with a loss of the magnesium ion and a tilt in the position of the guanine base because of the additional carbon introduced by the isoleucine substitution. Hydrogen-deuterium exchange MS analysis confirmed that this conformation occurs in solution, but also disclosed a difference in kinetics when compared with KRASA146T, another RAS mutant that displays a nearly identical conformation in previously reported crystal structures. This conformational change contributed to a high rate of guanine nucleotide-exchange factor (GEF)-dependent and -independent nucleotide exchange and to an increase in affinity for SOS Ras/Rac GEF 1 (SOS1), which appears to be the major mode of activation for this RAS variant. These results highlight a mechanistic connection between KRASA146T and KRASV14I that may have implications for the regulation of these variants and for the development of therapeutic strategies to manage KRAS variant-associated disorders.
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Affiliation(s)
- Asim K Bera
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390
| | - Jia Lu
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Masachusetts 02115
| | - Sudershan Gondi
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390
| | - Deepak Gurbani
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390
| | - Andrew Nelson
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Masachusetts 02115
| | - Kenneth D Westover
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390
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23
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Khaled M, Gorfe A, Sayyed-Ahmad A. Conformational and Dynamical Effects of Tyr32 Phosphorylation in K-Ras: Molecular Dynamics Simulation and Markov State Models Analysis. J Phys Chem B 2019; 123:7667-7675. [PMID: 31419909 PMCID: PMC7020251 DOI: 10.1021/acs.jpcb.9b05768] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Phosphorylation of tyrosine 32 in K-Ras has been shown to influence function by disrupting the GTPase cycle. To shed light on the underlying mechanism and atomic basis of this process, we carried out a comparative investigation of the oncogenic G12D K-Ras mutant and its phosphorylated variant (pTyr32) using all-atom molecular dynamics simulations and Markov state models. We show that, despite sharing a number of common features, G12D and pTyr32-G12D K-Ras exhibit some distinct conformational states and fluctuations. In addition to notable differences in conformation and dynamics of residues surrounding the GTP binding site, nonlocal changes were observed at a number of loops. Switch I is more flexible in pTyr32-G12D K-Ras while switch II is more flexible in G12D K-Ras. We also used time-lagged independent component analysis and k-means clustering to identify five metastable states for each system. We utilized transition path theory to calculate the transition probabilities for each state to build a Markov state model for each system. These models and other close inspections suggest that the phosphorylation of Tyr32 strongly affects protein dynamics and the active site conformation, especially with regards to the canonical switch conformations and dynamics.
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Affiliation(s)
- Mohammed Khaled
- Department of Physics, Birzeit University, PO Box 14, Birzeit, Palestine
| | - Alemayehu Gorfe
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, Texas 77030, United States
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24
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Kessler D, Gmachl M, Mantoulidis A, Martin LJ, Zoephel A, Mayer M, Gollner A, Covini D, Fischer S, Gerstberger T, Gmaschitz T, Goodwin C, Greb P, Häring D, Hela W, Hoffmann J, Karolyi-Oezguer J, Knesl P, Kornigg S, Koegl M, Kousek R, Lamarre L, Moser F, Munico-Martinez S, Peinsipp C, Phan J, Rinnenthal J, Sai J, Salamon C, Scherbantin Y, Schipany K, Schnitzer R, Schrenk A, Sharps B, Siszler G, Sun Q, Waterson A, Wolkerstorfer B, Zeeb M, Pearson M, Fesik SW, McConnell DB. Drugging an undruggable pocket on KRAS. Proc Natl Acad Sci U S A 2019; 116:15823-15829. [PMID: 31332011 PMCID: PMC6689897 DOI: 10.1073/pnas.1904529116] [Citation(s) in RCA: 239] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The 3 human RAS genes, KRAS, NRAS, and HRAS, encode 4 different RAS proteins which belong to the protein family of small GTPases that function as binary molecular switches involved in cell signaling. Activating mutations in RAS are among the most common oncogenic drivers in human cancers, with KRAS being the most frequently mutated oncogene. Although KRAS is an excellent drug discovery target for many cancers, and despite decades of research, no therapeutic agent directly targeting RAS has been clinically approved. Using structure-based drug design, we have discovered BI-2852 (1), a KRAS inhibitor that binds with nanomolar affinity to a pocket, thus far perceived to be "undruggable," between switch I and II on RAS; 1 is mechanistically distinct from covalent KRASG12C inhibitors because it binds to a different pocket present in both the active and inactive forms of KRAS. In doing so, it blocks all GEF, GAP, and effector interactions with KRAS, leading to inhibition of downstream signaling and an antiproliferative effect in the low micromolar range in KRAS mutant cells. These findings clearly demonstrate that this so-called switch I/II pocket is indeed druggable and provide the scientific community with a chemical probe that simultaneously targets the active and inactive forms of KRAS.
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Affiliation(s)
- Dirk Kessler
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Michael Gmachl
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Andreas Mantoulidis
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Laetitia J Martin
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Andreas Zoephel
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Moriz Mayer
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Andreas Gollner
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - David Covini
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Silke Fischer
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Thomas Gerstberger
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Teresa Gmaschitz
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Craig Goodwin
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37235
| | - Peter Greb
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Daniela Häring
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Wolfgang Hela
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Johann Hoffmann
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Jale Karolyi-Oezguer
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Petr Knesl
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Stefan Kornigg
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Manfred Koegl
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Roland Kousek
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Lyne Lamarre
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Franziska Moser
- Discovery Research, Boehringer Ingelheim Pharma GmbH & Co KG, D-88397 Biberach an der Riss, Germany
| | - Silvia Munico-Martinez
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Christoph Peinsipp
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Jason Phan
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37235
| | - Jörg Rinnenthal
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Jiqing Sai
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37235
| | - Christian Salamon
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Yvonne Scherbantin
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Katharina Schipany
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Renate Schnitzer
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Andreas Schrenk
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Bernadette Sharps
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Gabriella Siszler
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Qi Sun
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37235
| | - Alex Waterson
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37235
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235
| | - Bernhard Wolkerstorfer
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Markus Zeeb
- Discovery Research, Boehringer Ingelheim Pharma GmbH & Co KG, D-88397 Biberach an der Riss, Germany
| | - Mark Pearson
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Stephen W Fesik
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37235
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37235
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235
| | - Darryl B McConnell
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria;
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25
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Agnew HD, Coppock MB, Idso MN, Lai BT, Liang J, McCarthy-Torrens AM, Warren CM, Heath JR. Protein-Catalyzed Capture Agents. Chem Rev 2019; 119:9950-9970. [PMID: 30838853 DOI: 10.1021/acs.chemrev.8b00660] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein-catalyzed capture agents (PCCs) are synthetic and modular peptide-based affinity agents that are developed through the use of single-generation in situ click chemistry screens against large peptide libraries. In such screens, the target protein, or a synthetic epitope fragment of that protein, provides a template for selectively promoting the noncopper catalyzed azide-alkyne dipolar cycloaddition click reaction between either a library peptide and a known ligand or a library peptide and the synthetic epitope. The development of epitope-targeted PCCs was motivated by the desire to fully generalize pioneering work from the Sharpless and Finn groups in which in situ click screens were used to develop potent, divalent enzymatic inhibitors. In fact, a large degree of generality has now been achieved. Various PCCs have demonstrated utility for selective protein detection, as allosteric or direct inhibitors, as modulators of protein folding, and as tools for in vivo tumor imaging. We provide a historical context for PCCs and place them within the broader scope of biological and synthetic aptamers. The development of PCCs is presented as (i) Generation I PCCs, which are branched ligands engineered through an iterative, nonepitope-targeted process, and (ii) Generation II PCCs, which are typically developed from macrocyclic peptide libraries and are precisely epitope-targeted. We provide statistical comparisons of Generation II PCCs relative to monoclonal antibodies in which the protein target is the same. Finally, we discuss current challenges and future opportunities of PCCs.
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Affiliation(s)
- Heather D Agnew
- Indi Molecular, Inc. , 6162 Bristol Parkway , Culver City , California 90230 , United States
| | - Matthew B Coppock
- Sensors and Electron Devices Directorate , U.S. Army Research Laboratory , Adelphi , Maryland 20783 , United States
| | - Matthew N Idso
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109-5234 , United States
| | - Bert T Lai
- Indi Molecular, Inc. , 6162 Bristol Parkway , Culver City , California 90230 , United States
| | - JingXin Liang
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109-5234 , United States
| | - Amy M McCarthy-Torrens
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109-5234 , United States
| | - Carmen M Warren
- Indi Molecular, Inc. , 6162 Bristol Parkway , Culver City , California 90230 , United States
| | - James R Heath
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109-5234 , United States
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26
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Bandaru P, Kondo Y, Kuriyan J. The Interdependent Activation of Son-of-Sevenless and Ras. Cold Spring Harb Perspect Med 2019; 9:cshperspect.a031534. [PMID: 29610148 DOI: 10.1101/cshperspect.a031534] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The guanine-nucleotide exchange factor (GEF) Son-of-Sevenless (SOS) plays a critical role in metazoan signaling by converting Ras•GDP (guanosine diphosphate) to Ras•GTP (guanosine triphosphate) in response to tyrosine kinase activation. Structural studies have shown that SOS differs from other Ras-specific GEFs in that SOS is itself activated by Ras•GTP binding to an allosteric site, distal to the site of nucleotide exchange. The activation of SOS involves membrane recruitment and conformational changes, triggered by lipid binding, that open the allosteric binding site for Ras•GTP. This is in contrast to other Ras-specific GEFs, which are activated by second messengers that more directly affect the active site. Allosteric Ras•GTP binding stabilizes SOS at the membrane, where it can turn over other Ras molecules processively, leading to an ultrasensitive response that is distinct from that of other Ras-specific GEFs.
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Affiliation(s)
- Pradeep Bandaru
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, Howard Hughes Medical Institute, University of California, Berkeley, California 94720
| | - Yasushi Kondo
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, Howard Hughes Medical Institute, University of California, Berkeley, California 94720
| | - John Kuriyan
- Departments of Molecular and Cell Biology and of Chemistry, California Institute for Quantitative Biosciences, Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Howard Hughes Medical Institute, University of California, Berkeley, California 94720
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27
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Kano Y, Gebregiworgis T, Marshall CB, Radulovich N, Poon BPK, St-Germain J, Cook JD, Valencia-Sama I, Grant BMM, Herrera SG, Miao J, Raught B, Irwin MS, Lee JE, Yeh JJ, Zhang ZY, Tsao MS, Ikura M, Ohh M. Tyrosyl phosphorylation of KRAS stalls GTPase cycle via alteration of switch I and II conformation. Nat Commun 2019; 10:224. [PMID: 30644389 PMCID: PMC6333830 DOI: 10.1038/s41467-018-08115-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 12/17/2018] [Indexed: 12/27/2022] Open
Abstract
Deregulation of the RAS GTPase cycle due to mutations in the three RAS genes is commonly associated with cancer development. Protein tyrosine phosphatase SHP2 promotes RAF-to-MAPK signaling pathway and is an essential factor in RAS-driven oncogenesis. Despite the emergence of SHP2 inhibitors for the treatment of cancers harbouring mutant KRAS, the mechanism underlying SHP2 activation of KRAS signaling remains unclear. Here we report tyrosyl-phosphorylation of endogenous RAS and demonstrate that KRAS phosphorylation via Src on Tyr32 and Tyr64 alters the conformation of switch I and II regions, which stalls multiple steps of the GTPase cycle and impairs binding to effectors. In contrast, SHP2 dephosphorylates KRAS, a process that is required to maintain dynamic canonical KRAS GTPase cycle. Notably, Src- and SHP2-mediated regulation of KRAS activity extends to oncogenic KRAS and the inhibition of SHP2 disrupts the phosphorylation cycle, shifting the equilibrium of the GTPase cycle towards the stalled ‘dark state’. Deregulation of the RAS GTPase cycle due to mutations in RAS genes is commonly associated with cancer development. Here authors use NMR and mass spectrometry to shows that KRAS phosphorylation via Src alters the conformation of switch I and II regions and thereby impacts the GTPase cycle.
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Affiliation(s)
- Yoshihito Kano
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada.,Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada
| | - Teklab Gebregiworgis
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Christopher B Marshall
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Nikolina Radulovich
- Princess Margaret Cancer Centre, University Health Network and Department of Pathology, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Betty P K Poon
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada
| | - Jonathan St-Germain
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Jonathan D Cook
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada
| | - Ivette Valencia-Sama
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada.,Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, 686 Bay Street, Toronto, ON, 5G OA4, Canada
| | - Benjamin M M Grant
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Silvia Gabriela Herrera
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jinmin Miao
- Department of Medicinal Chemistry and Molecular Pharmacology, Center for Cancer Research and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, IN, 47907, USA
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Meredith S Irwin
- Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, 686 Bay Street, Toronto, ON, 5G OA4, Canada
| | - Jeffrey E Lee
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada
| | - Jen Jen Yeh
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA.,Department of Surgery, University of North Carolina, Chapel Hill, NC, 27599, USA.,Department of Pharmacology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Zhong-Yin Zhang
- Department of Medicinal Chemistry and Molecular Pharmacology, Center for Cancer Research and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, IN, 47907, USA
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network and Department of Pathology, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Michael Ohh
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada. .,Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada.
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28
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Cai D, Choi PS, Gelbard M, Meyerson M. Identification and Characterization of Oncogenic SOS1 Mutations in Lung Adenocarcinoma. Mol Cancer Res 2019; 17:1002-1012. [PMID: 30635434 DOI: 10.1158/1541-7786.mcr-18-0316] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 04/18/2018] [Accepted: 01/04/2019] [Indexed: 12/27/2022]
Abstract
Lung adenocarcinomas are characterized by mutations in the receptor tyrosine kinase (RTK)/Ras/Raf pathway, with up to 75% of cases containing mutations in known driver genes. However, the driver alterations in the remaining cases are yet to be determined. Recent exome sequencing analysis has identified SOS1, encoding a guanine nucleotide exchange factor, as significantly mutated in lung adenocarcinomas lacking canonical oncogenic RTK/Ras/Raf pathway mutations. Here, we demonstrate that ectopic expression of lung adenocarcinoma-derived mutants of SOS1 induces anchorage-independent cell growth in vitro and tumor formation in vivo. Biochemical experiments suggest that these mutations lead to overactivation of the Ras pathway, which can be suppressed by mutations that disrupt either the Ras-GEF or putative Rac-GEF activity of SOS1. Transcriptional profiling reveals that the expression of mutant SOS1 leads to the upregulation of MYC target genes and genes associated with Ras transformation. Furthermore, we demonstrate that an AML cancer cell line harboring a lung adenocarcinoma-associated mutant SOS1 is dependent on SOS1 for survival and is also sensitive to MEK inhibition. Our work provides experimental evidence for the role of SOS1 as an oncogene and suggests a possible therapeutic strategy to target SOS1-mutated cancers. IMPLICATIONS: This study demonstrates that SOS1 mutations found in lung adenocarcinoma are oncogenic and that MEK inhibition may be a therapeutic avenue for the treatment of SOS1-mutant cancers.
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Affiliation(s)
- Diana Cai
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Program in Genetics and Genomics, Harvard University, Boston, Massachusetts
| | - Peter S Choi
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Maya Gelbard
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Matthew Meyerson
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts. .,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
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29
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Sheffels E, Sealover NE, Wang C, Kim DH, Vazirani IA, Lee E, M Terrell E, Morrison DK, Luo J, Kortum RL. Oncogenic RAS isoforms show a hierarchical requirement for the guanine nucleotide exchange factor SOS2 to mediate cell transformation. Sci Signal 2018; 11:11/546/eaar8371. [PMID: 30181243 DOI: 10.1126/scisignal.aar8371] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
About a third of tumors have activating mutations in HRAS, NRAS, or KRAS, genes encoding guanosine triphosphatases (GTPases) of the RAS family. In these tumors, wild-type RAS cooperates with mutant RAS to promote downstream effector activation and cell proliferation and transformation, suggesting that upstream activators of wild-type RAS are important modulators of mutant RAS-driven oncogenesis. The guanine nucleotide exchange factor (GEF) SOS1 mediates KRAS-driven proliferation, but little is understood about the role of SOS2. We found that RAS family members have a hierarchical requirement for the expression and activity of SOS2 to drive cellular transformation. In mouse embryonic fibroblasts (MEFs), SOS2 critically mediated mutant KRAS-driven, but not HRAS-driven, transformation. Sos2 deletion reduced epidermal growth factor (EGF)-dependent activation of wild-type HRAS and phosphorylation of the kinase AKT in cells expressing mutant RAS isoforms. Assays using pharmacological inhibitors revealed a hierarchical requirement for signaling by phosphoinositide 3-kinase (PI3K) in promoting RAS-driven cellular transformation that mirrored the requirement for SOS2. KRAS-driven transformation required the GEF activity of SOS2 and was restored in Sos2-/- MEFs by expression of constitutively activated PI3K. Finally, CRISPR/Cas9-mediated deletion of SOS2 reduced EGF-stimulated AKT phosphorylation and synergized with MEK inhibition to revert the transformed phenotype of human KRAS mutant pancreatic and lung tumor cells. These results indicate that SOS2-dependent PI3K signaling mediates mutant KRAS-driven transformation, revealing therapeutic targets in KRAS-driven cancers. Our data also reveal the importance of three-dimensional culture systems in investigating the mediators of mutant KRAS.
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Affiliation(s)
- Erin Sheffels
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Nancy E Sealover
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Chenyue Wang
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Do Hyung Kim
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Isabella A Vazirani
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Elizabeth Lee
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Elizabeth M Terrell
- Laboratory of Cell and Developmental Signaling, National Cancer Institute (NCI)-Frederick, Frederick, MD 21702, USA
| | - Deborah K Morrison
- Laboratory of Cell and Developmental Signaling, National Cancer Institute (NCI)-Frederick, Frederick, MD 21702, USA
| | - Ji Luo
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert L Kortum
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA.
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30
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Liao TJ, Jang H, Fushman D, Nussinov R. Allosteric KRas4B Can Modulate SOS1 Fast and Slow Ras Activation Cycles. Biophys J 2018; 115:629-641. [PMID: 30097175 PMCID: PMC6103739 DOI: 10.1016/j.bpj.2018.07.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 07/18/2018] [Accepted: 07/19/2018] [Indexed: 01/08/2023] Open
Abstract
Membrane-anchored Ras family proteins are activated by guanine nucleotide exchange factors such as SOS1. The CDC25 domain of SOS1 catalyzes GDP-to-GTP exchange, thereby activating Ras. Here, we aim to decipher the activation mechanism of KRas4B, a significantly mutated oncogene. We perform large-scale molecular dynamics simulations on 12 SOS1 systems, scrutinizing each step in two possible KRas4B activation cycles, fast and slow. To activate KRas4B at the CDC25 catalytic site, the allosteric site in the Ras exchanger motif (REM) domain of SOS1 needs to recruit a (nucleotide-bound) KRas4B molecule. Our simulations indicate that KRas4B-GTP interacts with the REM allosteric site more strongly than with the CDC25 catalytic site, consistent with its allosteric role in the GDP-to-GTP exchange. In the fast cycle, the allosteric KRas4B-GTP induces conformational change at the catalytic site. The conformational change facilitates loading KRas4B-GDP at the catalytic site and opening the KRas4B nucleotide-binding site for GDP release and GTP binding. GTP binding reduces the affinity of KRas4B-GTP to the CDC25 catalytic site, resulting in its release. By contrast, in the slow cycle, KRas4B-GDP binds at the allosteric REM site. The limited, altered conformational change that it induces prevents the exact alignments of switch I and II of KRas4B. The increasing binding strength at both binding sites due to interactions of regions other than switch I and II retards GDP release from the catalytic KRas4B, thus KRas4B activation. The accelerated activation cycle supports a positive feedback loop with allosteric signals communicating between the two Ras molecules and is the predominant, native function of SOS. SOS1 activation details may help drug discovery to inhibit Ras activation.
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Affiliation(s)
- Tsung-Jen Liao
- Cancer and Inflammation Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland; Biophysics Program
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland
| | - David Fushman
- Biophysics Program; Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
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31
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McCarthy AM, Kim J, Museth AK, Henning RK, Heath JE, Winson E, Oh JJ, Liang J, Hong S, Heath JR. Allosteric Inhibitor of KRas Identified Using a Barcoded Assay Microchip Platform. Anal Chem 2018; 90:8824-8830. [PMID: 29979578 DOI: 10.1021/acs.analchem.8b00706] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Protein catalyzed capture agents (PCCs) are synthetic antibody surrogates that can target a wide variety of biologically relevant proteins. As a step toward developing a high-throughput PCC pipeline, we report on the preparation of a barcoded rapid assay platform for the analysis of hits from PCC library screens. The platform is constructed by first surface patterning a micrometer scale barcode composed of orthogonal ssDNA strands onto a glass slide. The slide is then partitioned into microwells, each of which contains multiple copies of the full barcode. Biotinylated candidate PCCs from a click screen are assembled onto the barcode stripes using a complementary ssDNA-encoded cysteine-modified streptavidin library. This platform was employed to evaluate candidate PCC ligands identified from an epitope targeted in situ click screen against the two conserved allosteric switch regions of the Kirsten rat sarcoma (KRas) protein. A single microchip was utilized for the simultaneous evaluation of 15 PCC candidate fractions under more than a dozen different assay conditions. The platform also permitted more than a 10-fold savings in time and a more than 100-fold reduction in biological and chemical reagents relative to traditional multiwell plate assays. The best ligand was shown to exhibit an in vitro inhibition constant (IC50) of ∼24 μM.
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Affiliation(s)
- Amy M McCarthy
- The Arthur Amos Noyes Laboratory of Chemical Physics, Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , California 91125 , United States
| | - Jungwoo Kim
- The Arthur Amos Noyes Laboratory of Chemical Physics, Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , California 91125 , United States
| | - A Katrine Museth
- The Arthur Amos Noyes Laboratory of Chemical Physics, Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , California 91125 , United States
| | - Ryan K Henning
- The Arthur Amos Noyes Laboratory of Chemical Physics, Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , California 91125 , United States
| | - John E Heath
- The Arthur Amos Noyes Laboratory of Chemical Physics, Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , California 91125 , United States
| | - Emma Winson
- The Arthur Amos Noyes Laboratory of Chemical Physics, Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , California 91125 , United States
| | - Joseph J Oh
- The Arthur Amos Noyes Laboratory of Chemical Physics, Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , California 91125 , United States
| | - Jingxin Liang
- The Institute for Systems Biology , 401 N. Terry Avenue , Seattle , Washington 98109 , United States
| | - Sunga Hong
- The Institute for Systems Biology , 401 N. Terry Avenue , Seattle , Washington 98109 , United States
| | - James R Heath
- The Arthur Amos Noyes Laboratory of Chemical Physics, Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , California 91125 , United States.,The Institute for Systems Biology , 401 N. Terry Avenue , Seattle , Washington 98109 , United States
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32
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Mott HR, Owen D. Bioblockades join the assault on small G protein signalling. Semin Cancer Biol 2018; 54:149-161. [PMID: 29307570 DOI: 10.1016/j.semcancer.2018.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 01/04/2018] [Indexed: 01/06/2023]
Abstract
Inhibition of Ras signalling has been a goal almost since its central role in cell signalling and its deregulation in disease were discovered. Early attempts at inhibiting its post-translational modification using peptidomimetics were successful in cell culture but failed spectacularly in clinical trials, making industry wary of targeting this critical oncoprotein. Small molecule inhibition of the protein-protein interactions involving Ras has also been difficult due to the nature of the interaction interface. Recent improvements in design, synthesis and selection of stabilised peptides, peptidomimetics and macrocycles have suggested that these biologics may represent a new hope in Ras inhibition. Here we review the various ways in which Ras has been targeted with these molecules. We also describe work on related small G proteins of the Ras superfamily, since many of the principles may be applicable to Ras, and these also provide inhibition of pathways downstream of Ras.
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Affiliation(s)
- Helen R Mott
- Department of Biochemistry, 80, Tennis Court Road, Cambridge CB2 1GA, UK.
| | - Darerca Owen
- Department of Biochemistry, 80, Tennis Court Road, Cambridge CB2 1GA, UK.
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33
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Gentile DR, Rathinaswamy MK, Jenkins ML, Moss SM, Siempelkamp BD, Renslo AR, Burke JE, Shokat KM. Ras Binder Induces a Modified Switch-II Pocket in GTP and GDP States. Cell Chem Biol 2017; 24:1455-1466.e14. [PMID: 29033317 PMCID: PMC5915340 DOI: 10.1016/j.chembiol.2017.08.025] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Revised: 07/31/2017] [Accepted: 08/30/2017] [Indexed: 12/31/2022]
Abstract
Covalent inhibitors of K-Ras(G12C) have been reported that exclusively recognize the GDP state. Here, we utilize disulfide tethering of a non-natural cysteine (K-Ras(M72C)) to identify a new switch-II pocket (S-IIP) binding ligand (2C07) that engages the active GTP state. Co-crystal structures of 2C07 bound to H-Ras(M72C) reveal binding in a cryptic groove we term S-IIG. In the GppNHp state, 2C07 binding to a modified S-IIP pushes switch I away from the nucleotide, breaking the network of polar contacts essential for adopting the canonical GTP state. Biochemical studies show that 2C07 alters nucleotide preference and inhibits SOS binding and catalyzed nucleotide exchange. 2C07 was converted to irreversible covalent analogs, which target both nucleotide states, inhibit PI3K activation in vitro, and function as occupancy probes to detect reversible engagement in competition assays. Targeting both nucleotide states opens the possibility of inhibiting oncogenic mutants of Ras, which exist predominantly in the GTP state in cells.
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Affiliation(s)
- Daniel R Gentile
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | - Manoj K Rathinaswamy
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Meredith L Jenkins
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Steven M Moss
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | - Braden D Siempelkamp
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Adam R Renslo
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada.
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA.
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34
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Ivanova AA, Caspary T, Seyfried NT, Duong DM, West AB, Liu Z, Kahn RA. Biochemical characterization of purified mammalian ARL13B protein indicates that it is an atypical GTPase and ARL3 guanine nucleotide exchange factor (GEF). J Biol Chem 2017; 292:11091-11108. [PMID: 28487361 PMCID: PMC5491791 DOI: 10.1074/jbc.m117.784025] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 05/02/2017] [Indexed: 12/11/2022] Open
Abstract
Primary cilia play central roles in signaling during metazoan development. Several key regulators of ciliogenesis and ciliary signaling are mutated in humans, resulting in a number of ciliopathies, including Joubert syndrome (JS). ARL13B is a ciliary GTPase with at least three missense mutations identified in JS patients. ARL13B is a member of the ADP ribosylation factor family of regulatory GTPases, but is atypical in having a non-homologous, C-terminal domain of ∼20 kDa and at least one key residue difference in the consensus GTP-binding motifs. For these reasons, and to establish a solid biochemical basis on which to begin to model its actions in cells and animals, we developed preparations of purified, recombinant, murine Arl13b protein. We report results from assays for solution-based nucleotide binding, intrinsic and GTPase-activating protein-stimulated GTPase, and ARL3 guanine nucleotide exchange factor activities. Biochemical analyses of three human missense mutations found in JS and of two consensus GTPase motifs reinforce the atypical properties of this regulatory GTPase. We also discovered that murine Arl13b is a substrate for casein kinase 2, a contaminant in our preparation from human embryonic kidney cells. This activity, and the ability of casein kinase 2 to use GTP as a phosphate donor, may be a source of differences between our data and previously published results. These results provide a solid framework for further research into ARL13B on which to develop models for the actions of this clinically important cell regulator.
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Affiliation(s)
| | - Tamara Caspary
- Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322 and
| | | | | | - Andrew B West
- the Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Zhiyong Liu
- the Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, Birmingham, Alabama 35294
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35
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Sayyed-Ahmad A, Prakash P, Gorfe AA. Distinct dynamics and interaction patterns in H- and K-Ras oncogenic P-loop mutants. Proteins 2017; 85:1618-1632. [PMID: 28498561 DOI: 10.1002/prot.25317] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 04/27/2017] [Accepted: 05/05/2017] [Indexed: 12/31/2022]
Abstract
Despite years of study, the structural or dynamical basis for the differential reactivity and oncogenicity of Ras isoforms and mutants remains unclear. In this study, we investigated the effects of amino acid variations on the structure and dynamics of wild type and oncogenic mutants G12D, G12V, and G13D of H- and K-Ras proteins. Based on data from µs-scale molecular dynamics simulations, we show that the overall structure of the proteins remains similar but there are important differences in dynamics and interaction networks. We identified differences in residue interaction patterns around the canonical switch and distal loop regions, and persistent sodium ion binding near the GTP particularly in the G13D mutants. Our results also suggest that different Ras variants have distinct local structural features and interactions with the GTP, variations that have the potential to affect GTP release and hydrolysis. Furthermore, we found that H-Ras proteins and particularly the G12V and G13D variants are significantly more flexible than their K-Ras counterparts. Finally, while most of the simulated proteins sampled the effector-interacting state 2 conformational state, G12V and G13D H-Ras adopted an open switch state 1 conformation that is defective in effector interaction. These differences have implications for Ras GTPase activity, effector or exchange factor binding, dimerization and membrane interaction. Proteins 2017; 85:1618-1632. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Abdallah Sayyed-Ahmad
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas, 77030
| | - Priyanka Prakash
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas, 77030
| | - Alemayehu A Gorfe
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas, 77030
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36
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37
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Mechanism of SOS PR-domain autoinhibition revealed by single-molecule assays on native protein from lysate. Nat Commun 2017; 8:15061. [PMID: 28452363 PMCID: PMC5414354 DOI: 10.1038/ncomms15061] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 02/23/2017] [Indexed: 12/16/2022] Open
Abstract
The guanine nucleotide exchange factor (GEF) Son of Sevenless (SOS) plays a critical role in signal transduction by activating Ras. Here we introduce a single-molecule assay in which individual SOS molecules are captured from raw cell lysate using Ras-functionalized supported membrane microarrays. This enables characterization of the full-length SOS protein, which has not previously been studied in reconstitution due to difficulties in purification. Our measurements on the full-length protein reveal a distinct role of the C-terminal proline-rich (PR) domain to obstruct the engagement of allosteric Ras independently of the well-known N-terminal domain autoinhibition. This inhibitory role of the PR domain limits Grb2-independent recruitment of SOS to the membrane through binding of Ras·GTP in the SOS allosteric binding site. More generally, this assay strategy enables characterization of the functional behaviour of GEFs with single-molecule precision but without the need for purification.
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38
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Yin G, Kistler S, George SD, Kuhlmann N, Garvey L, Huynh M, Bagni RK, Lammers M, Der CJ, Campbell SL. A KRAS GTPase K104Q Mutant Retains Downstream Signaling by Offsetting Defects in Regulation. J Biol Chem 2017; 292:4446-4456. [PMID: 28154176 DOI: 10.1074/jbc.m116.762435] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 01/27/2017] [Indexed: 11/06/2022] Open
Abstract
The KRAS GTPase plays a critical role in the control of cellular growth. The activity of KRAS is regulated by guanine nucleotide exchange factors (GEFs), GTPase-activating proteins (GAPs), and also post-translational modification. Lysine 104 in KRAS can be modified by ubiquitylation and acetylation, but the role of this residue in intrinsic KRAS function has not been well characterized. We find that lysine 104 is important for GEF recognition, because mutations at this position impaired GEF-mediated nucleotide exchange. Because the KRAS K104Q mutant has recently been employed as an acetylation mimetic, we conducted a series of studies to evaluate its in vitro and cell-based properties. Herein, we found that KRAS K104Q exhibited defects in both GEF-mediated exchange and GAP-mediated GTP hydrolysis, consistent with NMR-detected structural perturbations in localized regions of KRAS important for recognition of these regulatory proteins. Despite the partial defect in both GEF and GAP regulation, KRAS K104Q did not alter steady-state GTP-bound levels or the ability of the oncogenic KRAS G12V mutant to cause morphologic transformation of NIH 3T3 mouse fibroblasts and of WT KRAS to rescue the growth defect of mouse embryonic fibroblasts deficient in all Ras genes. We conclude that the KRAS K104Q mutant retains both WT and mutant KRAS function, probably due to offsetting defects in recognition of factors that up-regulate (GEF) and down-regulate (GAP) RAS activity.
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Affiliation(s)
- Guowei Yin
- From the Department of Biochemistry and Biophysics
| | - Samantha Kistler
- From the Department of Biochemistry and Biophysics.,Department of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy
| | - Samuel D George
- Department of Pharmacology, and.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27699
| | - Nora Kuhlmann
- the Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), Joseph-Stelzmann-Strasse 26, University of Cologne, 50931 Cologne, Germany, and
| | - Leslie Garvey
- the NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Minh Huynh
- From the Department of Biochemistry and Biophysics.,Department of Pharmacology, and.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27699
| | - Rachel K Bagni
- the NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Michael Lammers
- the Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), Joseph-Stelzmann-Strasse 26, University of Cologne, 50931 Cologne, Germany, and
| | - Channing J Der
- Department of Pharmacology, and.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27699
| | - Sharon L Campbell
- From the Department of Biochemistry and Biophysics, .,Department of Pharmacology, and.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27699
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39
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One-way membrane trafficking of SOS in receptor-triggered Ras activation. Nat Struct Mol Biol 2016; 23:838-46. [PMID: 27501536 PMCID: PMC5016256 DOI: 10.1038/nsmb.3275] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 07/08/2016] [Indexed: 02/07/2023]
Abstract
SOS is a key activator of the small GTPase Ras. In cells, SOS-Ras signaling is thought to be initiated predominantly by membrane-recruitment of SOS via the adaptor Grb2 and balanced by rapidly reversible Grb2:SOS binding kinetics. However, SOS has multiple protein and lipid interactions that provide linkage to the membrane. In reconstituted membrane experiments, these Grb2-independent interactions are sufficient to retain SOS on the membrane for many minutes, during which a single SOS molecule can processively activate thousands of Ras molecules. These observations raise questions concerning how receptors maintain control of SOS in cells and how membrane-recruited SOS is ultimately released. We addressed these questions in quantitative reconstituted SOS-deficient chicken B cell signaling systems combined with single molecule measurements in supported membranes. These studies reveal an essentially one-way trafficking process in which membrane-recruited SOS remains trapped on the membrane and continuously activates Ras until it is actively removed via endocytosis.
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40
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Lu S, Jang H, Muratcioglu S, Gursoy A, Keskin O, Nussinov R, Zhang J. Ras Conformational Ensembles, Allostery, and Signaling. Chem Rev 2016; 116:6607-65. [PMID: 26815308 DOI: 10.1021/acs.chemrev.5b00542] [Citation(s) in RCA: 253] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Ras proteins are classical members of small GTPases that function as molecular switches by alternating between inactive GDP-bound and active GTP-bound states. Ras activation is regulated by guanine nucleotide exchange factors that catalyze the exchange of GDP by GTP, and inactivation is terminated by GTPase-activating proteins that accelerate the intrinsic GTP hydrolysis rate by orders of magnitude. In this review, we focus on data that have accumulated over the past few years pertaining to the conformational ensembles and the allosteric regulation of Ras proteins and their interpretation from our conformational landscape standpoint. The Ras ensemble embodies all states, including the ligand-bound conformations, the activated (or inactivated) allosteric modulated states, post-translationally modified states, mutational states, transition states, and nonfunctional states serving as a reservoir for emerging functions. The ensemble is shifted by distinct mutational events, cofactors, post-translational modifications, and different membrane compositions. A better understanding of Ras biology can contribute to therapeutic strategies.
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Affiliation(s)
- Shaoyong Lu
- Department of Pathophysiology, Shanghai Universities E-Institute for Chemical Biology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine , Shanghai, 200025, China.,Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, National Cancer Institute , Frederick, Maryland 21702, United States
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, National Cancer Institute , Frederick, Maryland 21702, United States
| | | | | | | | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, National Cancer Institute , Frederick, Maryland 21702, United States.,Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Sackler Institute of Molecular Medicine, Tel Aviv University , Tel Aviv 69978, Israel
| | - Jian Zhang
- Department of Pathophysiology, Shanghai Universities E-Institute for Chemical Biology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine , Shanghai, 200025, China
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41
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Nakamura Y, Hibino K, Yanagida T, Sako Y. Switching of the positive feedback for RAS activation by a concerted function of SOS membrane association domains. Biophys Physicobiol 2016; 13:1-11. [PMID: 27924253 PMCID: PMC5042160 DOI: 10.2142/biophysico.13.0_1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 12/11/2015] [Indexed: 01/12/2023] Open
Abstract
Son of sevenless (SOS) is a guanine nucleotide exchange factor that regulates cell behavior by activating the small GTPase RAS. Recent in vitro studies have suggested that an interaction between SOS and the GTP-bound active form of RAS generates a positive feedback loop that propagates RAS activation. However, it remains unclear how the multiple domains of SOS contribute to the regulation of the feedback loop in living cells. Here, we observed single molecules of SOS in living cells to analyze the kinetics and dynamics of SOS behavior. The results indicate that the histone fold and Grb2-binding domains of SOS concertedly produce an intermediate state of SOS on the cell surface. The fraction of the intermediated state was reduced in positive feedback mutants, suggesting that the feedback loop functions during the intermediate state. Translocation of RAF, recognizing the active form of RAS, to the cell surface was almost abolished in the positive feedback mutants. Thus, the concerted functions of multiple membrane-associating domains of SOS governed the positive feedback loop, which is crucial for cell fate decision regulated by RAS.
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Affiliation(s)
- Yuki Nakamura
- Cellular Informatics Laboratory, RIKEN, Wako, Saitama 351-0198, Japan; Nanobiology Laboratories, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kayo Hibino
- Laboratory for Cell Signaling Dynamics, RIKEN QBiC, Suita, Osaka 565-0874, Japan
| | - Toshio Yanagida
- Nanobiology Laboratories, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yasushi Sako
- Cellular Informatics Laboratory, RIKEN, Wako, Saitama 351-0198, Japan; Nanobiology Laboratories, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
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42
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Lito P, Solomon M, Li LS, Hansen R, Rosen N. Allele-specific inhibitors inactivate mutant KRAS G12C by a trapping mechanism. Science 2016; 351:604-8. [PMID: 26841430 DOI: 10.1126/science.aad6204] [Citation(s) in RCA: 445] [Impact Index Per Article: 55.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/06/2016] [Indexed: 12/12/2022]
Abstract
It is thought that KRAS oncoproteins are constitutively active because their guanosine triphosphatase (GTPase) activity is disabled. Consequently, drugs targeting the inactive or guanosine 5'-diphosphate-bound conformation are not expected to be effective. We describe a mechanism that enables such drugs to inhibit KRAS(G12C) signaling and cancer cell growth. Inhibition requires intact GTPase activity and occurs because drug-bound KRAS(G12C) is insusceptible to nucleotide exchange factors and thus trapped in its inactive state. Indeed, mutants completely lacking GTPase activity and those promoting exchange reduced the potency of the drug. Suppressing nucleotide exchange activity downstream of various tyrosine kinases enhanced KRAS(G12C) inhibition, whereas its potentiation had the opposite effect. These findings reveal that KRAS(G12C) undergoes nucleotide cycling in cancer cells and provide a basis for developing effective therapies to treat KRAS(G12C)-driven cancers.
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Affiliation(s)
- Piro Lito
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Martha Solomon
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Neal Rosen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA. Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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43
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Vo U, Vajpai N, Flavell L, Bobby R, Breeze AL, Embrey KJ, Golovanov AP. Monitoring Ras Interactions with the Nucleotide Exchange Factor Son of Sevenless (Sos) Using Site-specific NMR Reporter Signals and Intrinsic Fluorescence. J Biol Chem 2015; 291:1703-1718. [PMID: 26565026 PMCID: PMC4722452 DOI: 10.1074/jbc.m115.691238] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Indexed: 01/07/2023] Open
Abstract
The activity of Ras is controlled by the interconversion between GTP- and GDP-bound forms partly regulated by the binding of the guanine nucleotide exchange factor Son of Sevenless (Sos). The details of Sos binding, leading to nucleotide exchange and subsequent dissociation of the complex, are not completely understood. Here, we used uniformly 15N-labeled Ras as well as [13C]methyl-Met,Ile-labeled Sos for observing site-specific details of Ras-Sos interactions in solution. Binding of various forms of Ras (loaded with GDP and mimics of GTP or nucleotide-free) at the allosteric and catalytic sites of Sos was comprehensively characterized by monitoring signal perturbations in the NMR spectra. The overall affinity of binding between these protein variants as well as their selected functional mutants was also investigated using intrinsic fluorescence. The data support a positive feedback activation of Sos by Ras·GTP with Ras·GTP binding as a substrate for the catalytic site of activated Sos more weakly than Ras·GDP, suggesting that Sos should actively promote unidirectional GDP → GTP exchange on Ras in preference of passive homonucleotide exchange. Ras·GDP weakly binds to the catalytic but not to the allosteric site of Sos. This confirms that Ras·GDP cannot properly activate Sos at the allosteric site. The novel site-specific assay described may be useful for design of drugs aimed at perturbing Ras-Sos interactions.
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Affiliation(s)
- Uybach Vo
- From the Manchester Institute of Biotechnology and Faculty of Life Sciences, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom and
| | - Navratna Vajpai
- Discovery Sciences, AstraZeneca, Mereside, Alderley Park, Cheshire SK10 4TF, United Kingdom
| | - Liz Flavell
- Discovery Sciences, AstraZeneca, Mereside, Alderley Park, Cheshire SK10 4TF, United Kingdom
| | - Romel Bobby
- Discovery Sciences, AstraZeneca, Mereside, Alderley Park, Cheshire SK10 4TF, United Kingdom
| | - Alexander L Breeze
- Discovery Sciences, AstraZeneca, Mereside, Alderley Park, Cheshire SK10 4TF, United Kingdom
| | - Kevin J Embrey
- Discovery Sciences, AstraZeneca, Mereside, Alderley Park, Cheshire SK10 4TF, United Kingdom.
| | - Alexander P Golovanov
- From the Manchester Institute of Biotechnology and Faculty of Life Sciences, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom and.
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44
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Kapoor A, Travesset A. Differential dynamics of RAS isoforms in GDP- and GTP-bound states. Proteins 2015; 83:1091-106. [PMID: 25846136 DOI: 10.1002/prot.24805] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 03/12/2015] [Accepted: 03/20/2015] [Indexed: 11/10/2022]
Abstract
RAS subfamily proteins regulates cell growth promoting signaling processes by cycling between active (GTP-bound) and inactive (GDP-bound) states. Different RAS isoforms, though structurally similar, exhibit functional specificity and are associated with different types of cancers and developmental disorders. Understanding the dynamical differences between the isoforms is crucial for the design of inhibitors that can selectively target a particular malfunctioning isoform. In this study, we provide a comprehensive comparison of the dynamics of all the three RAS isoforms (HRAS, KRAS, and NRAS) using extensive molecular dynamics simulations in both the GDP- (total of 3.06 μs) and GTP-bound (total of 2.4 μs) states. We observed significant differences in the dynamics of the isoforms, which rather interestingly, varied depending on the type of the nucleotide bound and the simulation temperature. Both SwitchI (Residues 25-40) and SwitchII (Residues 59-75) differ significantly in their flexibility in the three isoforms. Furthermore, Principal Component Analysis showed that there are differences in the conformational space sampled by the GTP-bound RAS isoforms. We also identified a previously unreported pocket, which opens transiently during MD simulations, and can be targeted to regulate nucleotide exchange reaction or possibly interfere with membrane localization. Further, we present the first simulation study showing GDP destabilization in the wild-type RAS protein. The destabilization of GDP/GTP occurred only in 1/50 simulations, emphasizing the need of guanine nucleotide exchange factors (GEFs) to accelerate such an extremely unfavorable process. This observation along with the other results presented in this article further support our previously hypothesized mechanism of GEF-assisted nucleotide exchange.
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Affiliation(s)
- Abhijeet Kapoor
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa, 50011
| | - Alex Travesset
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa, 50011
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45
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Evelyn CR, Biesiada J, Duan X, Tang H, Shang X, Papoian R, Seibel WL, Nelson S, Meller J, Zheng Y. Combined rational design and a high throughput screening platform for identifying chemical inhibitors of a Ras-activating enzyme. J Biol Chem 2015; 290:12879-98. [PMID: 25825487 DOI: 10.1074/jbc.m114.634493] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Indexed: 11/06/2022] Open
Abstract
The Ras family small GTPases regulate multiple cellular processes, including cell growth, survival, movement, and gene expression, and are intimately involved in cancer pathogenesis. Activation of these small GTPases is catalyzed by a special class of enzymes, termed guanine nucleotide exchange factors (GEFs). Herein, we developed a small molecule screening platform for identifying lead hits targeting a Ras GEF enzyme, SOS1. We employed an ensemble structure-based virtual screening approach in combination with a multiple tier high throughput experimental screen utilizing two complementary fluorescent guanine nucleotide exchange assays to identify small molecule inhibitors of GEF catalytic activity toward Ras. From a library of 350,000 compounds, we selected a set of 418 candidate compounds predicted to disrupt the GEF-Ras interaction, of which dual wavelength GDP dissociation and GTP-loading experimental screening identified two chemically distinct small molecule inhibitors. Subsequent biochemical validations indicate that they are capable of dose-dependently inhibiting GEF catalytic activity, binding to SOS1 with micromolar affinity, and disrupting GEF-Ras interaction. Mutagenesis studies in conjunction with structure-activity relationship studies mapped both compounds to different sites in the catalytic pocket, and both inhibited Ras signaling in cells. The unique screening platform established here for targeting Ras GEF enzymes could be broadly useful for identifying lead inhibitors for a variety of small GTPase-activating GEF reactions.
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Affiliation(s)
- Chris R Evelyn
- From the Division of Experimental Hematology and Cancer Biology
| | | | - Xin Duan
- From the Division of Experimental Hematology and Cancer Biology
| | - Hong Tang
- Division of Immunobiology, and the Drug Discovery Center and
| | - Xun Shang
- From the Division of Experimental Hematology and Cancer Biology
| | - Ruben Papoian
- the Drug Discovery Center and Departments of Neurology and
| | - William L Seibel
- the Drug Discovery Center and Division of Oncology, Children's Hospital Research Foundation, Cincinnati, Ohio 45229 and
| | | | - Jaroslaw Meller
- Division of Biomedical Informatics, Environmental Health, University of Cincinnati, Cincinnati, Ohio 45267
| | - Yi Zheng
- From the Division of Experimental Hematology and Cancer Biology,
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46
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Evelyn CR, Duan X, Biesiada J, Seibel WL, Meller J, Zheng Y. Rational design of small molecule inhibitors targeting the Ras GEF, SOS1. ACTA ACUST UNITED AC 2014; 21:1618-28. [PMID: 25455859 DOI: 10.1016/j.chembiol.2014.09.018] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 09/02/2014] [Accepted: 09/05/2014] [Indexed: 01/21/2023]
Abstract
Ras GTPases regulate intracellular signaling involved in cell proliferation. Elevated Ras signaling activity has been associated with human cancers. Ras activation is catalyzed by guanine nucleotide exchange factors (GEFs), of which SOS1 is a major member that transduces receptor tyrosine kinase signaling to Ras. We have developed a rational approach coupling virtual screening with experimental screening in identifying small-molecule inhibitors targeting the catalytic site of SOS1 and SOS1-regulated Ras activity. A lead inhibitor, NSC-658497, was found to bind to SOS1, competitively suppress SOS1-Ras interaction, and dose-dependently inhibit SOS1 GEF activity. Mutagenesis and structure-activity relationship studies map the NSC-658497 site of action to the SOS1 catalytic site, and define the chemical moieties in the inhibitor essential for the activity. NSC-658497 showed dose-dependent efficacy in inhibiting Ras, downstream signaling activities, and associated cell proliferation. These studies establish a proof of principle for rational design of small-molecule inhibitors targeting Ras GEF enzymatic activity.
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Affiliation(s)
- Chris R Evelyn
- Division of Experimental Hematology and Cancer Biology, Children's Hospital Research Foundation, Cincinnati, OH 45229, USA
| | - Xin Duan
- Division of Experimental Hematology and Cancer Biology, Children's Hospital Research Foundation, Cincinnati, OH 45229, USA
| | - Jacek Biesiada
- Division of Biomedical Informatics, Children's Hospital Research Foundation, Cincinnati, OH 45229, USA
| | - William L Seibel
- Division of Oncology, Children's Hospital Research Foundation, Cincinnati, OH 45229, USA
| | - Jaroslaw Meller
- Division of Biomedical Informatics, Children's Hospital Research Foundation, Cincinnati, OH 45229, USA; Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Yi Zheng
- Division of Experimental Hematology and Cancer Biology, Children's Hospital Research Foundation, Cincinnati, OH 45229, USA.
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47
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Kapoor A, Travesset A. Mechanism of the exchange reaction in HRAS from multiscale modeling. PLoS One 2014; 9:e108846. [PMID: 25272152 PMCID: PMC4182752 DOI: 10.1371/journal.pone.0108846] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 08/28/2014] [Indexed: 11/28/2022] Open
Abstract
HRAS regulates cell growth promoting signaling processes by cycling between active (GTP-bound) and inactive (GDP-bound) states. Understanding the transition mechanism is central for the design of small molecules to inhibit the formation of RAS-driven tumors. Using a multiscale approach involving coarse-grained (CG) simulations, all-atom classical molecular dynamics (CMD; total of 3.02 µs), and steered molecular dynamics (SMD) in combination with Principal Component Analysis (PCA), we identified the structural features that determine the nucleotide (GDP) exchange reaction. We show that weakening the coupling between the SwitchI (residues 25–40) and SwitchII (residues 59–75) accelerates the opening of SwitchI; however, an open conformation of SwitchI is unstable in the absence of guanine nucleotide exchange factors (GEFs) and rises up towards the bound nucleotide to close the nucleotide pocket. Both I21 and Y32, play a crucial role in SwitchI transition. We show that an open SwitchI conformation is not necessary for GDP destabilization but is required for GDP/Mg escape from the HRAS. Further, we present the first simulation study showing displacement of GDP/Mg away from the nucleotide pocket. Both SwitchI and SwitchII, delays the escape of displaced GDP/Mg in the absence of GEF. Based on these results, a model for the mechanism of GEF in accelerating the exchange process is hypothesized.
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Affiliation(s)
- Abhijeet Kapoor
- Physics and Astronomy, Iowa State University, Ames, Iowa, United States of America
- * E-mail:
| | - Alex Travesset
- Physics and Astronomy, Iowa State University, Ames, Iowa, United States of America
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48
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Flex E, Jaiswal M, Pantaleoni F, Martinelli S, Strullu M, Fansa EK, Caye A, De Luca A, Lepri F, Dvorsky R, Pannone L, Paolacci S, Zhang SC, Fodale V, Bocchinfuso G, Rossi C, Burkitt-Wright EMM, Farrotti A, Stellacci E, Cecchetti S, Ferese R, Bottero L, Castro S, Fenneteau O, Brethon B, Sanchez M, Roberts AE, Yntema HG, Van Der Burgt I, Cianci P, Bondeson ML, Cristina Digilio M, Zampino G, Kerr B, Aoki Y, Loh ML, Palleschi A, Di Schiavi E, Carè A, Selicorni A, Dallapiccola B, Cirstea IC, Stella L, Zenker M, Gelb BD, Cavé H, Ahmadian MR, Tartaglia M. Activating mutations in RRAS underlie a phenotype within the RASopathy spectrum and contribute to leukaemogenesis. Hum Mol Genet 2014; 23:4315-27. [PMID: 24705357 PMCID: PMC4103678 DOI: 10.1093/hmg/ddu148] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 03/04/2014] [Indexed: 12/29/2022] Open
Abstract
RASopathies, a family of disorders characterized by cardiac defects, defective growth, facial dysmorphism, variable cognitive deficits and predisposition to certain malignancies, are caused by constitutional dysregulation of RAS signalling predominantly through the RAF/MEK/ERK (MAPK) cascade. We report on two germline mutations (p.Gly39dup and p.Val55Met) in RRAS, a gene encoding a small monomeric GTPase controlling cell adhesion, spreading and migration, underlying a rare (2 subjects among 504 individuals analysed) and variable phenotype with features partially overlapping Noonan syndrome, the most common RASopathy. We also identified somatic RRAS mutations (p.Gly39dup and p.Gln87Leu) in 2 of 110 cases of non-syndromic juvenile myelomonocytic leukaemia, a childhood myeloproliferative/myelodysplastic disease caused by upregulated RAS signalling, defining an atypical form of this haematological disorder rapidly progressing to acute myeloid leukaemia. Two of the three identified mutations affected known oncogenic hotspots of RAS genes and conferred variably enhanced RRAS function and stimulus-dependent MAPK activation. Expression of an RRAS mutant homolog in Caenorhabditis elegans enhanced RAS signalling and engendered protruding vulva, a phenotype previously linked to the RASopathy-causing SHOC2(S2G) mutant. Overall, these findings provide evidence of a functional link between RRAS and MAPK signalling and reveal an unpredicted role of enhanced RRAS function in human disease.
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Affiliation(s)
- Elisabetta Flex
- Dipartimento di Ematologia, Oncologia e Medicina Molecolare and
| | - Mamta Jaiswal
- Institut für Biochemie und Molekularbiologie II, Medizinische Fakultät der Heinrich-Heine Universitat, Düsseldorf 40225, Germany
| | | | | | - Marion Strullu
- Genetics Department, INSERM UMR_S940, Institut Universitaire D'Hématologie (IUH), Université Paris-Diderot Sorbonne-Paris-Cité, Paris 75010, France
| | - Eyad K Fansa
- Institut für Biochemie und Molekularbiologie II, Medizinische Fakultät der Heinrich-Heine Universitat, Düsseldorf 40225, Germany
| | - Aurélie Caye
- Genetics Department, INSERM UMR_S940, Institut Universitaire D'Hématologie (IUH), Université Paris-Diderot Sorbonne-Paris-Cité, Paris 75010, France
| | - Alessandro De Luca
- Laboratorio Mendel, Istituto di Ricovero e Cura a Carattere Scientifico-Casa Sollievo Della Sofferenza, Rome 00198, Italy
| | | | - Radovan Dvorsky
- Institut für Biochemie und Molekularbiologie II, Medizinische Fakultät der Heinrich-Heine Universitat, Düsseldorf 40225, Germany
| | - Luca Pannone
- Dipartimento di Ematologia, Oncologia e Medicina Molecolare and
| | | | - Si-Cai Zhang
- Institut für Biochemie und Molekularbiologie II, Medizinische Fakultät der Heinrich-Heine Universitat, Düsseldorf 40225, Germany
| | | | - Gianfranco Bocchinfuso
- Dipartimento di Scienze e Tecnologie Chimiche, Università 'Tor Vergata', Rome 00133, Italy
| | - Cesare Rossi
- UO Genetica Medica, Policlinico S.Orsola-Malpighi, Bologna 40138, Italy
| | - Emma M M Burkitt-Wright
- Genetic Medicine, Academic Health Science Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester M13 9WL, UK
| | - Andrea Farrotti
- Dipartimento di Scienze e Tecnologie Chimiche, Università 'Tor Vergata', Rome 00133, Italy
| | | | - Serena Cecchetti
- Dipartimento di Biologia Cellulare e Neuroscienze, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Rosangela Ferese
- Laboratorio Mendel, Istituto di Ricovero e Cura a Carattere Scientifico-Casa Sollievo Della Sofferenza, Rome 00198, Italy
| | | | - Silvana Castro
- Istituto di Genetica e Biofisica 'A. Buzzati Traverso', Consiglio Nazionale Delle Ricerche, Naples 80131, Italy
| | | | - Benoît Brethon
- Pediatric Hematology Department, Robert Debré Hospital, Paris 75019, France
| | - Massimo Sanchez
- Dipartimento di Biologia Cellulare e Neuroscienze, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Amy E Roberts
- Department of Cardiology and Division of Genetics, and Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Helger G Yntema
- Department of Human Genetics, Radboud University Medical Centre, and Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen 6500, The Netherlands
| | - Ineke Van Der Burgt
- Department of Human Genetics, Radboud University Medical Centre, and Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen 6500, The Netherlands
| | - Paola Cianci
- Genetica Clinica Pediatrica, Clinica Pediatrica Università Milano Bicocca, Fondazione MBBM, A.O. S. Gerardo, Monza 20900, Italy
| | - Marie-Louise Bondeson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75237, Sweden
| | | | - Giuseppe Zampino
- Istituto di Clinica Pediatrica, Università Cattolica del Sacro Cuore, Rome 00168, Italy
| | - Bronwyn Kerr
- Genetic Medicine, Academic Health Science Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester M13 9WL, UK
| | - Yoko Aoki
- Department of Medical Genetics, Tohoku University School of Medicine, Sendai 980-8574, Japan
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital, University of California School of Medicine, and the Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, 94143, USA
| | - Antonio Palleschi
- Dipartimento di Scienze e Tecnologie Chimiche, Università 'Tor Vergata', Rome 00133, Italy
| | - Elia Di Schiavi
- Istituto di Genetica e Biofisica 'A. Buzzati Traverso', Consiglio Nazionale Delle Ricerche, Naples 80131, Italy
| | - Alessandra Carè
- Dipartimento di Ematologia, Oncologia e Medicina Molecolare and
| | - Angelo Selicorni
- Genetica Clinica Pediatrica, Clinica Pediatrica Università Milano Bicocca, Fondazione MBBM, A.O. S. Gerardo, Monza 20900, Italy
| | | | - Ion C Cirstea
- Institut für Biochemie und Molekularbiologie II, Medizinische Fakultät der Heinrich-Heine Universitat, Düsseldorf 40225, Germany, Leibniz Institute for Age Research, Jena 07745, Germany
| | - Lorenzo Stella
- Dipartimento di Scienze e Tecnologie Chimiche, Università 'Tor Vergata', Rome 00133, Italy
| | - Martin Zenker
- Institute of Human Genetics, University Hospital of Magdeburg, Otto-von-Guericke-University, Magdeburg 39120, Germany
| | - Bruce D Gelb
- Department of Pediatrics and Department of Genetics and Department of Genomic Sciences, Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hélène Cavé
- Genetics Department, INSERM UMR_S940, Institut Universitaire D'Hématologie (IUH), Université Paris-Diderot Sorbonne-Paris-Cité, Paris 75010, France
| | - Mohammad R Ahmadian
- Institut für Biochemie und Molekularbiologie II, Medizinische Fakultät der Heinrich-Heine Universitat, Düsseldorf 40225, Germany
| | - Marco Tartaglia
- Dipartimento di Ematologia, Oncologia e Medicina Molecolare and
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49
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Approach for targeting Ras with small molecules that activate SOS-mediated nucleotide exchange. Proc Natl Acad Sci U S A 2014; 111:3401-6. [PMID: 24550516 DOI: 10.1073/pnas.1315798111] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Aberrant activation of the small GTPase Ras by oncogenic mutation or constitutively active upstream receptor tyrosine kinases results in the deregulation of cellular signals governing growth and survival in ∼30% of all human cancers. However, the discovery of potent inhibitors of Ras has been difficult to achieve. Here, we report the identification of small molecules that bind to a unique pocket on the Ras:Son of Sevenless (SOS):Ras complex, increase the rate of SOS-catalyzed nucleotide exchange in vitro, and modulate Ras signaling pathways in cells. X-ray crystallography of Ras:SOS:Ras in complex with these molecules reveals that the compounds bind in a hydrophobic pocket in the CDC25 domain of SOS adjacent to the Switch II region of Ras. The structure-activity relationships exhibited by these compounds can be rationalized on the basis of multiple X-ray cocrystal structures. Mutational analyses confirmed the functional relevance of this binding site and showed it to be essential for compound activity. These molecules increase Ras-GTP levels and disrupt MAPK and PI3K signaling in cells at low micromolar concentrations. These small molecules represent tools to study the acute activation of Ras and highlight a pocket on SOS that may be exploited to modulate Ras signaling.
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50
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H-Ras forms dimers on membrane surfaces via a protein-protein interface. Proc Natl Acad Sci U S A 2014; 111:2996-3001. [PMID: 24516166 DOI: 10.1073/pnas.1321155111] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The lipid-anchored small GTPase Ras is an important signaling node in mammalian cells. A number of observations suggest that Ras is laterally organized within the cell membrane, and this may play a regulatory role in its activation. Lipid anchors composed of palmitoyl and farnesyl moieties in H-, N-, and K-Ras are widely suspected to be responsible for guiding protein organization in membranes. Here, we report that H-Ras forms a dimer on membrane surfaces through a protein-protein binding interface. A Y64A point mutation in the switch II region, known to prevent Son of sevenless and PI3K effector interactions, abolishes dimer formation. This suggests that the switch II region, near the nucleotide binding cleft, is either part of, or allosterically coupled to, the dimer interface. By tethering H-Ras to bilayers via a membrane-miscible lipid tail, we show that dimer formation is mediated by protein interactions and does not require lipid anchor clustering. We quantitatively characterize H-Ras dimerization in supported membranes using a combination of fluorescence correlation spectroscopy, photon counting histogram analysis, time-resolved fluorescence anisotropy, single-molecule tracking, and step photobleaching analysis. The 2D dimerization Kd is measured to be ∼1 × 10(3) molecules/µm(2), and no higher-order oligomers were observed. Dimerization only occurs on the membrane surface; H-Ras is strictly monomeric at comparable densities in solution. Analysis of a number of H-Ras constructs, including key changes to the lipidation pattern of the hypervariable region, suggest that dimerization is a general property of native H-Ras on membrane surfaces.
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