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Li H, Chai M, Chen Y, Zhou F, Ren X, Xu J, Wang J, Wang Z, Huang W. Discovery of LHF418 as a new potent SOS1 PROTAC degrader. Bioorg Med Chem 2024; 103:117661. [PMID: 38489998 DOI: 10.1016/j.bmc.2024.117661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/17/2024]
Abstract
Son of sevenless homolog 1 (SOS1) plays a pivotal role as a molecular switch in the conversion of GDP-bound inactive KRAS to its active GTP-bound form, making SOS1 a promising therapeutic target for KRAS-driven cancers. While the most advanced SOS1 inhibitor has processed to phase I clinical trial, the exploration of novel SOS1 targeting strategies with distinct modes of action remains required. By employing proteolysis targeting chimera (PROTAC) technology, we obtained a series of new SOS1 degraders. The representative compound LHF418 potently induced SOS1 degradation with a DC50 value of 209.4 nM and a Dmax value of over 80 %. Mechanistic studies have illuminated that compound LHF418 induced the formation of ternary complex involving SOS1-PROTAC-cereblon (CRBN) and triggered SOS1 protein degradation in a CRBN- and proteasome-dependent manner. In addition, compound LHF418 effectively inhibited KRAS-RAF-ERK signalling, leading to the suppression of colony formation in KRAS-driven cancer cells. Overall, compound LHF418 represents a new lead compound in the developing novel and potent therapy for the treatment of KRAS-driven cancers.
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Affiliation(s)
- Huifan Li
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Minxue Chai
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China; Key Laboratory of Functional Molecular Solids, Ministry of Education, Anhui Laboratory of Molecule-Based Materials, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, China
| | - Yihan Chen
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Fengtao Zhou
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, College of Pharmacy, Jinan University, Guangzhou 511400, China
| | - Xiaomei Ren
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jian Xu
- Livzon Research Institute, Livzon Pharmaceutical Group Inc., Zhuhai 519000, China
| | - Jian Wang
- Key Laboratory of Functional Molecular Solids, Ministry of Education, Anhui Laboratory of Molecule-Based Materials, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, China.
| | - Zhen Wang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China; Ningbo Zhongke Creation Center of New Materials, Ningbo 315000, China.
| | - Weixue Huang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China; Ningbo Zhongke Creation Center of New Materials, Ningbo 315000, China.
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2
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Wu J, Li X, Wu C, Wang Y, Zhang J. Current advances and development strategies of targeting son of sevenless 1 (SOS1) in drug discovery. Eur J Med Chem 2024; 268:116282. [PMID: 38430853 DOI: 10.1016/j.ejmech.2024.116282] [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: 01/19/2024] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 03/05/2024]
Abstract
The Son of Sevenless 1 (SOS1) guanine nucleotide exchange factor, prevalent across eukaryotic species, plays a pivotal role in facilitating the attachment of RAS protein to GTP, thereby regulating the activation of intracellular RAS proteins. This regulation is part of a feedback mechanism involving SOS1, which allows both activators and inhibitors of SOS1 to exert control over downstream signaling pathways, demonstrating potential anti-tumor effects. Predominantly, small molecule modulators that target SOS1 focus on a hydrophobic pocket within the CDC25 protein domain. The effectiveness of these modulators largely depends on their ability to interact with specific amino acids, notably Phe890 and Tyr884. This interaction is crucial for influencing the protein-protein interaction (PPI) between RAS and the catalytic domain of SOS1. Currently, most small molecule modulators targeting SOS1 are in the preclinical research phase, with a few advancing to clinical trials. This progression raises safety concerns, making the assurance of drug safety a primary consideration alongside the enhancement of efficacy in the development of SOS1 modulators. This review encapsulates recent advancements in the chemical categorization of SOS1 inhibitors and activators. It delves into the evolution of small molecule modulation targeting SOS1 and offers perspectives on the design of future generations of selective SOS1 small molecule modulators.
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Affiliation(s)
- Jialin Wu
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Xiaoxue Li
- Department of Dermatology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Chengyong Wu
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yuxi Wang
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Jifa Zhang
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
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3
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Yun S, Scott E, Laganowsky A. Biophysical Characterization of RAS-SOS Complexes by Native Mass Spectrometry. Methods Mol Biol 2024; 2797:177-193. [PMID: 38570460 DOI: 10.1007/978-1-0716-3822-4_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
RAS is regulated by specific guanine nucleotide exchange factors, such as Son of Sevenless (SOS), that activates RAS by facilitating the exchange of inactive, GDP-bound RAS with GTP. The catalytic activity of SOS is known to be allosterically modulated by an active, GTP-bound RAS. However, it remains poorly understood how oncogenic RAS mutants interact with SOS and modulate its activity. In this chapter, we describe the application of native mass spectrometry (MS) to monitor the assembly of the catalytic domain of SOS (SOScat) with RAS and cancer-associated mutants. Results from this approach have led to the discovery of different molecular assemblies and distinct conformers of SOScat engaging KRAS. It was also found that KRASG13D exhibits high affinity for SOScat and is a potent allosteric modulator of its SOScat activity. KRASG13D-GTP can allosterically increase the nucleotide exchange rate of KRAS at the active site by more than twofold compared to the wild-type protein. Furthermore, small-molecule RAS•SOS disruptors fail to dissociate KRASG13D•SOScat complexes, underscoring the need for more potent disruptors targeting oncogenic RAS mutants. Taken together, native MS will be instrumental in better understanding the interaction between oncogenic RAS mutants and SOS, which is of crucial importance for development of improved therapeutics.
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Affiliation(s)
- Sangho Yun
- Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Elena Scott
- Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX, USA.
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Bhadhadhara K, Jani V, Koulgi S, Sonavane U, Joshi R. Studying early structural changes in SOS1 mediated KRAS activation mechanism. Curr Res Struct Biol 2023; 7:100115. [PMID: 38188543 PMCID: PMC10765296 DOI: 10.1016/j.crstbi.2023.100115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 01/09/2024] Open
Abstract
KRAS activation is known to be modulated by a guanine nucleotide exchange factor (GEF), namely, Son of Sevenless1 (SOS1). SOS1 facilitates the exchange of GDP to GTP thereby leading to activation of KRAS. The binding of GDP/GTP to KRAS at the REM/allosteric site of SOS1 regulates the activation of KRAS at CDC25/catalytic site by facilitating its exchange. Different aspects of the allosteric activation of KRAS through SOS1 are still being explored. To understand the SOS1 mediated activation of KRAS, molecular dynamics simulations for a total of nine SOS1 complexes (KRAS-SOS1-KRAS) were performed. These nine systems comprised different combinations of KRAS-bound nucleotides (GTP/GDP) at REM and CDC25 sites of SOS1. Various conformational and thermodynamic parameters were analyzed for these simulation systems. MMPBSA free energy analysis revealed that binding at CDC25 site of SOS1 was significantly low for GDP-bound KRAS as compared to that of GTP-bound KRAS. It was observed that presence of either GDP/GTP bound KRAS at the REM site of SOS1 affected the activation related changes in the KRAS present at CDC25 site. The conformational changes at the catalytic site of SOS1 resulting from GDP/GTP-bound KRAS at the allosteric changes may hint at KRAS activation through different pathways (slow/fast/rare). The allosteric effect on activation of KRAS at CDC25 site may be due to conformations adopted by switch-I, switch-II, beta2 regions of KRAS at REM site. The effect of structural rearrangements occurring at allosteric KRAS may have led to increased interactions between SOS1 and KRAS at both the sites. The SOS1 residues involved in these important interactions with KRAS at the REM site were R694, S732 and K735. Whereas the ones interacting with KRAS at CDC25 site were S807, W809 and K814. This may suggest the crucial role of these residues in guiding the allosteric activation of KRAS at CDC25 site. The conformational shifts observed in the switch-I, switch-II and alpha3 regions of KRAS at CDC25 site may be attributed to be a part of allosteric activation. The binding affinities, interacting residues and conformational dynamics may provide an insight into development of inhibitors targeting the SOS1 mediated KRAS activation.
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Affiliation(s)
- Kirti Bhadhadhara
- High Performance Computing-Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Innovation Park, Panchawati, Pashan, Pune, 411008, India
| | - Vinod Jani
- High Performance Computing-Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Innovation Park, Panchawati, Pashan, Pune, 411008, India
| | - Shruti Koulgi
- High Performance Computing-Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Innovation Park, Panchawati, Pashan, Pune, 411008, India
| | - Uddhavesh Sonavane
- High Performance Computing-Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Innovation Park, Panchawati, Pashan, Pune, 411008, India
| | - Rajendra Joshi
- High Performance Computing-Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Innovation Park, Panchawati, Pashan, Pune, 411008, India
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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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6
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Yun SD, Scott E, Moghadamchargari Z, Laganowsky A. 2'-Deoxy Guanosine Nucleotides Alter the Biochemical Properties of Ras. Biochemistry 2023; 62:2450-2460. [PMID: 37487239 PMCID: PMC11131413 DOI: 10.1021/acs.biochem.3c00258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Ras proteins in the mitogen-activated protein kinase (MAPK) signaling pathway represent one of the most frequently mutated oncogenes in cancer. Ras binds guanosine nucleotides and cycles between active (GTP) and inactive (GDP) conformations to regulate the MAPK signaling pathway. Guanosine and other nucleotides exist in cells as either 2'-hydroxy or 2'-deoxy forms, and imbalances in the deoxyribonucleotide triphosphate pool have been associated with different diseases, such as diabetes, obesity, and cancer. However, the biochemical properties of Ras bound to dGNP are not well understood. Herein, we use native mass spectrometry to monitor the intrinsic GTPase activity of H-Ras and N-Ras oncogenic mutants, revealing that the rate of 2'-deoxy guanosine triphosphate (dGTP) hydrolysis differs compared to the hydroxylated form, in some cases by seven-fold. Moreover, K-Ras expressed from HEK293 cells exhibited a higher than anticipated abundance of dGNP, despite the low abundance of dGNP in cells. Additionally, the GTPase and dGTPase activity of K-RasG12C was found to be accelerated by 10.2- and 3.8-fold in the presence of small molecule covalent inhibitors, which may open opportunities for the development of Pan-Ras inhibitors. The molecular assemblies formed between H-Ras and N-Ras, including mutant forms, with the catalytic domain of SOS (SOScat) were also investigated. The results show that the different mutants of H-Ras and N-Ras not only engage SOScat differently, but these assemblies are also dependent on the form of guanosine triphosphate bound to Ras. These findings bring to the forefront a new perspective on the nucleotide-dependent biochemical properties of Ras that may have implications for the activation of the MAPK signaling pathway and Ras-driven cancers.
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Affiliation(s)
- Sangho D. Yun
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Elena Scott
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | | | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX 77843
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He H, Chen R, Wang Z, Qing L, Zhang Y, Liu Y, Pan W, Fang H, Zhang S. Design of Orally-bioavailable Tetra-cyclic phthalazine SOS1 inhibitors with high selectivity against EGFR. Bioorg Chem 2023; 136:106536. [PMID: 37054529 DOI: 10.1016/j.bioorg.2023.106536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/28/2023] [Accepted: 04/07/2023] [Indexed: 04/15/2023]
Abstract
KRAS mutations (G12C, G12D, etc.) are implicated in the oncogenesis and progression of many deadliest cancers. Son of sevenless homolog 1 (SOS1) is a crucial regulator of KRAS to modulate KRAS from inactive to active states. We previously discovered tetra-cyclic quinazolines as an improved scaffold for inhibiting SOS1-KRAS interaction. In this work, we report the design of tetra-cyclic phthalazine derivatives for selectively inhibiting SOS1 against EGFR. The lead compound 6c displayed remarkable activity to inhibit the proliferation of KRAS(G12C)-mutant pancreas cells. 6c showed a favorable pharmacokinetic profile in vivo, with a bioavailability of 65.8% and exhibited potent tumor suppression in pancreas tumor xenograft models. These intriguing results suggested that 6c has the potential to be developed as a drug candidate for KRAS-driven tumors.
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Affiliation(s)
- Huan He
- School of Pharmaceutical Sciences, Guizhou University, Guiyang 550025, PR China; Key Laboratory of Coal Conversion and New Carbon Materials of Hubei Province, College of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, PR China; Wuhan Yuxiang Pharmaceutical Technology Co., Ltd., Wuhan 430200, PR China
| | - Ruiqi Chen
- Key Laboratory of Coal Conversion and New Carbon Materials of Hubei Province, College of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, PR China
| | - Ziwei Wang
- Key Laboratory of Coal Conversion and New Carbon Materials of Hubei Province, College of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, PR China
| | - Luolong Qing
- Key Laboratory of Coal Conversion and New Carbon Materials of Hubei Province, College of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, PR China
| | - Yu Zhang
- Key Laboratory of Coal Conversion and New Carbon Materials of Hubei Province, College of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, PR China
| | - Yi Liu
- Key Laboratory of Coal Conversion and New Carbon Materials of Hubei Province, College of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, PR China; School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, PR China; Hubei Key Laboratory of Radiation Chemistry and Functional Materials, Hubei University of Science and Technology, Xianning 437100, PR China
| | - Weidong Pan
- School of Pharmaceutical Sciences, Guizhou University, Guiyang 550025, PR China.
| | - Huaxiang Fang
- Key Laboratory of Coal Conversion and New Carbon Materials of Hubei Province, College of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, PR China.
| | - Silong Zhang
- School of Pharmaceutical Sciences, Guizhou University, Guiyang 550025, PR China; Key Laboratory of Coal Conversion and New Carbon Materials of Hubei Province, College of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, PR China; Wuhan Yuxiang Pharmaceutical Technology Co., Ltd., Wuhan 430200, PR China.
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8
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Pal S. Impact of Hydrogen‐Bond Surrogate Model on Helix Stabilization and Development of Protein‐Protein Interaction Inhibitors. ChemistrySelect 2023. [DOI: 10.1002/slct.202204207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Affiliation(s)
- Sunit Pal
- Chemical Genomics Centre of the Max Planck Society Max Planck Institute of Molecular Physiology Otto-Hahn-Str. 11 44227 Dortmund Germany
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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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Pua LJW, Mai CW, Chung FFL, Khoo ASB, Leong CO, Lim WM, Hii LW. Functional Roles of JNK and p38 MAPK Signaling in Nasopharyngeal Carcinoma. Int J Mol Sci 2022; 23:ijms23031108. [PMID: 35163030 PMCID: PMC8834850 DOI: 10.3390/ijms23031108] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/11/2022] [Accepted: 01/11/2022] [Indexed: 02/05/2023] Open
Abstract
c-Jun N-terminal kinase (JNK) and p38 mitogen-activated protein kinase (MAPK) family members integrate signals that affect proliferation, differentiation, survival, and migration in a cell context- and cell type-specific way. JNK and p38 MAPK activities are found upregulated in nasopharyngeal carcinoma (NPC). Studies have shown that activation of JNK and p38 MAPK signaling can promote NPC oncogenesis by mechanisms within the cancer cells and interactions with the tumor microenvironment. They regulate multiple transcription activities and contribute to tumor-promoting processes, ranging from cell proliferation to apoptosis, inflammation, metastasis, and angiogenesis. Current literature suggests that JNK and p38 MAPK activation may exert pro-tumorigenic functions in NPC, though the underlying mechanisms are not well documented and have yet to be fully explored. Here, we aim to provide a narrative review of JNK and p38 MAPK pathways in human cancers with a primary focus on NPC. We also discuss the potential therapeutic agents that could be used to target JNK and p38 MAPK signaling in NPC, along with perspectives for future works. We aim to inspire future studies further delineating JNK and p38 MAPK signaling in NPC oncogenesis which might offer important insights for better strategies in diagnosis, prognosis, and treatment decision-making in NPC patients.
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Affiliation(s)
- Lesley Jia Wei Pua
- School of Postgraduate Studies, International Medical University, Bukit Jalil, Kuala Lumpur 57000, Malaysia; (L.J.W.P.); (C.-O.L.)
- Center for Cancer and Stem Cell Research, Development and Innovation (IRDI), Institute for Research, International Medical University, Bukit Jalil, Kuala Lumpur 57000, Malaysia; (C.-W.M.); (A.S.-B.K.)
| | - Chun-Wai Mai
- Center for Cancer and Stem Cell Research, Development and Innovation (IRDI), Institute for Research, International Medical University, Bukit Jalil, Kuala Lumpur 57000, Malaysia; (C.-W.M.); (A.S.-B.K.)
| | - Felicia Fei-Lei Chung
- Department of Medical Sciences, School of Medical and Life Sciences, Sunway University, Bandar Sunway 47500, Malaysia;
| | - Alan Soo-Beng Khoo
- Center for Cancer and Stem Cell Research, Development and Innovation (IRDI), Institute for Research, International Medical University, Bukit Jalil, Kuala Lumpur 57000, Malaysia; (C.-W.M.); (A.S.-B.K.)
| | - Chee-Onn Leong
- School of Postgraduate Studies, International Medical University, Bukit Jalil, Kuala Lumpur 57000, Malaysia; (L.J.W.P.); (C.-O.L.)
- Center for Cancer and Stem Cell Research, Development and Innovation (IRDI), Institute for Research, International Medical University, Bukit Jalil, Kuala Lumpur 57000, Malaysia; (C.-W.M.); (A.S.-B.K.)
- AGTC Genomics, Bukit Jalil, Kuala Lumpur 57000, Malaysia
| | - Wei-Meng Lim
- Center for Cancer and Stem Cell Research, Development and Innovation (IRDI), Institute for Research, International Medical University, Bukit Jalil, Kuala Lumpur 57000, Malaysia; (C.-W.M.); (A.S.-B.K.)
- School of Pharmacy, International Medical University, Bukit Jalil, Kuala Lumpur 57000, Malaysia
- Correspondence: (W.-M.L.); (L.-W.H.)
| | - Ling-Wei Hii
- Center for Cancer and Stem Cell Research, Development and Innovation (IRDI), Institute for Research, International Medical University, Bukit Jalil, Kuala Lumpur 57000, Malaysia; (C.-W.M.); (A.S.-B.K.)
- School of Pharmacy, International Medical University, Bukit Jalil, Kuala Lumpur 57000, Malaysia
- Correspondence: (W.-M.L.); (L.-W.H.)
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11
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Han CW, Jeong MS, Jang SB. Understand KRAS and the Quest for Anti-Cancer Drugs. Cells 2021; 10:cells10040842. [PMID: 33917906 PMCID: PMC8068306 DOI: 10.3390/cells10040842] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/06/2021] [Accepted: 04/06/2021] [Indexed: 12/30/2022] Open
Abstract
The KRAS oncogene is mutated in approximately ~30% of human cancers, and the targeting of KRAS has long been highlighted in many studies. Nevertheless, attempts to target KRAS directly have been ineffective. This review provides an overview of the structure of KRAS and its characteristic signaling pathways. Additionally, we examine the problems associated with currently available KRAS inhibitors and discuss promising avenues for drug development.
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Affiliation(s)
- Chang Woo Han
- Institute of Systems Biology, Pusan National University, Jangjeon-dong, Geumjeong-gu, Busan 46241, Korea;
| | - Mi Suk Jeong
- Institute for Plastic Information and Energy Materials and Sustainable Utilization of Photovoltaic Energy Research Center, Pusan National University, Jangjeon-dong, Geumjeong-gu, Busan 46241, Korea
- Correspondence: (M.S.J.); (S.B.J.); Tel.: +82-51-510-2523 (M.S.J. & S.B.J.)
| | - Se Bok Jang
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Jangjeon-dong, Geumjeong-gu, Busan 46241, Korea
- Correspondence: (M.S.J.); (S.B.J.); Tel.: +82-51-510-2523 (M.S.J. & S.B.J.)
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12
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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: 16] [Impact Index Per Article: 5.3] [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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13
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Ramharter J, Kessler D, Ettmayer P, Hofmann MH, Gerstberger T, Gmachl M, Wunberg T, Kofink C, Sanderson M, Arnhof H, Bader G, Rumpel K, Zöphel A, Schnitzer R, Böttcher J, O'Connell JC, Mendes RL, Richard D, Pototschnig N, Weiner I, Hela W, Hauer K, Haering D, Lamarre L, Wolkerstorfer B, Salamon C, Werni P, Munico-Martinez S, Meyer R, Kennedy MD, Kraut N, McConnell DB. One Atom Makes All the Difference: Getting a Foot in the Door between SOS1 and KRAS. J Med Chem 2021; 64:6569-6580. [PMID: 33719426 DOI: 10.1021/acs.jmedchem.0c01949] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
KRAS, the most common oncogenic driver in human cancers, is controlled and signals primarily through protein-protein interactions (PPIs). The interaction between KRAS and SOS1, crucial for the activation of KRAS, is a typical, challenging PPI with a large contact surface area and high affinity. Here, we report that the addition of only one atom placed between Y884SOS1 and A73KRAS is sufficient to convert SOS1 activators into SOS1 inhibitors. We also disclose the discovery of BI-3406. Combination with the upstream EGFR inhibitor afatinib shows in vivo efficacy against KRASG13D mutant colorectal tumor cells, demonstrating the utility of BI-3406 to probe SOS1 biology. These findings challenge the dogma that large molecules are required to disrupt challenging PPIs. Instead, a "foot in the door" approach, whereby single atoms or small functional groups placed between key PPI interactions, can lead to potent inhibitors even for challenging PPIs such as SOS1-KRAS.
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Affiliation(s)
- Juergen Ramharter
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Dirk Kessler
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Peter Ettmayer
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Marco H Hofmann
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Thomas Gerstberger
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Michael Gmachl
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Tobias Wunberg
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Christiane Kofink
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Michael Sanderson
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Heribert Arnhof
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Gerd Bader
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Klaus Rumpel
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Andreas Zöphel
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Renate Schnitzer
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Jark Böttcher
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Jonathan C O'Connell
- Forma Therapeutics, 500 Arsenal Street, Suite 100, Watertown, Massachusetts 02472, United States
| | - Rachel L Mendes
- Forma Therapeutics, 500 Arsenal Street, Suite 100, Watertown, Massachusetts 02472, United States
| | - David Richard
- Forma Therapeutics, 500 Arsenal Street, Suite 100, Watertown, Massachusetts 02472, United States
| | - Nikolai Pototschnig
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Irene Weiner
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Wolfgang Hela
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Katja Hauer
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Daniela Haering
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Lyne Lamarre
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Bernhard Wolkerstorfer
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Christian Salamon
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Patrick Werni
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Silvia Munico-Martinez
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Reiner Meyer
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Matthew D Kennedy
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Norbert Kraut
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Darryl B McConnell
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
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14
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Lin MM. Circuit Reduction of Heterogeneous Nonequilibrium Systems. PHYSICAL REVIEW LETTERS 2020; 125:218101. [PMID: 33274997 DOI: 10.1103/physrevlett.125.218101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/19/2020] [Accepted: 10/09/2020] [Indexed: 06/12/2023]
Abstract
Predicting the behavior of heterogeneous nonequilibrium systems is currently analytically intractable. Consequently, complex biological systems have resisted unifying principles. Here, I introduce a mapping from dynamical systems to battery-resistor circuits. I show that in these transformed variables (i) arbitrary numbers of heterogeneous dynamical transitions can be reduced to a Thevenin equivalent resistor which is invariant to driving from equilibrium, (ii) resistors (together with the external driving sources) are sufficient to describe system behavior, and (iii) the resistor's directional symmetry leads to universal theorems of nonequilibrium behavior. This mapping is used to derive two general steady-state relations. First, for any cyclic process, the maximum amplification of any state is tightly bounded by the total dissipation of all states; experimental data are used to show that the master signal protein Ras achieves this bound. Second, for any process, the response of any reaction due to driving any other reaction is identical to the reciprocal response rescaled by the ratio of the corresponding Thevenin resistors. This result generalizes Onsager's reciprocal relation to the strongly driven regime and makes a testable prediction about how systems should be designed or evolved to maximize response. These analytic results represent a new perspective applicable to biological complexity and suggest that this mapping provides the natural variables to study heterogeneous nonequilibrium systems.
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Affiliation(s)
- Milo M Lin
- Green Center for Molecular, Computational, and Systems Biology, Department of Biophysics, Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, Texas 75235, USA
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15
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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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16
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Hussain J, Chhabria D, Kirubakaran S. Design, synthesis and biological evaluation of new Myo-inositol derivatives as potential RAS inhibitors. Bioorg Med Chem Lett 2020; 30:127290. [PMID: 32631512 DOI: 10.1016/j.bmcl.2020.127290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/23/2020] [Accepted: 05/25/2020] [Indexed: 02/07/2023]
Abstract
Ras is a small family of GTPases that control numerous cellular functions like cell proliferation, growth, survival, gene expression, and is closely engaged in cancer pathogenesis. The ras-targeted methodology entails a holy grail in oncology. Nevertheless, there are no specific molecules reported targeting the same, although it is a known oncogene for more than three decades. In this study, we have designed and synthesized new phosphate derivatives of Myo-inositol to inhibit the oncogenic KRAS pathway in breast cancer cells, which has been validated by cellular and theoretical studies. The synthesized compound 1b (C2-O-phosphate derivative of Myo-inositol 1,3,5-orthobenzoate) inhibited the downstream signaling pathway of oncogenic KRAS, RAF/MEK/ERK. Furthermore, we also found that this compound induced necrosis/apoptosis and causes cell cycle arrest. This class of molecules may work as a potential inhibitor of breast cancer caused by a mutation in KRAS and its downstream proteins. Though the efficacy of the molecules is in the micromolar scale, they have not been explored previously for RAS inhibition. Impressive preliminary results are presented in this article which could be further explored for its detailed biological studies to get better candidates as RAS inhibitors.
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Affiliation(s)
- Javeena Hussain
- Discipline of Chemistry, IIT Gandhinagar, Palaj, Gandhinagar 382355, India
| | - Dimple Chhabria
- Discipline of Chemistry, IIT Gandhinagar, Palaj, Gandhinagar 382355, India
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17
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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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18
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Guo Y, Zhu J, Wang X, Li R, Jiang K, Chen S, Fan J, Xue L, Hao D. Orai1 Promotes Osteosarcoma Metastasis by Activating the Ras-Rac1-WAVE2 Signaling Pathway. Med Sci Monit 2019; 25:9227-9236. [PMID: 31796725 PMCID: PMC6909920 DOI: 10.12659/msm.919594] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background The purpose of this study was to investigate whether Orai1 plays a role in the metastasis of osteosarcoma. Material/Methods The expression of Orai1 was silenced by small interfering RNAs against Orai1 (Orai1 siRNA) in osteosarcoma MG-63 cells. Various experiments were carried out to detect the changes in migration, invasion, and adhesion ability of these osteosarcoma cells. Furthermore, the activity of Rac1, Wave2, and Ras was detected using Western blot analysis. Moreover, the Rac1 and Ras inhibitors were used to confirm whether the Ras-Rac1-WAVE2 signaling pathway was involved in osteosarcoma metastasis promoted by Orai1. Results We found that the migration, invasion, and adhesion ability of MG-63 cells were significantly reduced after silencing Orai1 expression (p<0.05). Moreover, the activity of the Rac1-WAVE2 signaling pathway was significantly inhibited after silencing of Orai1 expression (p<0.05). After the Rac1 inhibitor was added, Orai1 siRNA could not further inhibit migration, invasion, and adhesion of the osteosarcoma cells. Further experiments showed that Ras activity was significantly inhibited after silencing Orai1 expression (p<0.05). Moreover, Orai1 siRNA did not further inhibit the activity of the Rac1-WAVE2 signaling pathway nor did it further inhibit the migration, invasion, and adhesion ability of osteosarcoma cells following the addition of Ras inhibitors. Conclusions Orai1 activates the Ras-Rac1-WAVE2 signaling pathway to promote metastasis of osteosarcoma. Abnormal expression or function of Orai1 may be an important cause of osteosarcoma metastasis.
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Affiliation(s)
- Yunshan Guo
- Department of Spinal Surgery, Hong Hui Hospital, Xi'an Jiao Tong University, Xi'an, Shaanxi, China (mainland)
| | - Jinwen Zhu
- Department of Spinal Surgery, Hong Hui Hospital, Xi'an Jiao Tong University, Xi'an, Shaanxi, China (mainland)
| | - Xiaodong Wang
- Department of Spinal Surgery, Hong Hui Hospital, Xi'an Jiao Tong University, Xi'an, Shaanxi, China (mainland)
| | - Ruoyu Li
- Department of Spinal Surgery, Hong Hui Hospital, Xi'an Jiao Tong University, Xi'an, Shaanxi, China (mainland)
| | - Kuo Jiang
- Department of Spinal Surgery, Hong Hui Hospital, Xi'an Jiao Tong University, Xi'an, Shaanxi, China (mainland)
| | - Shi Chen
- Department of Emergency Medicine, Hong Hui Hospital, Xi'an Jiao Tong University, Xi'an, Shaanxi, China (mainland)
| | - Jinzhu Fan
- Department of Orthopedics, Hong Hui Hospital, Xi'an Jiao Tong University, Xi'an, Shaanxi, China (mainland)
| | - Liujie Xue
- Department of Spinal Surgery, Hong Hui Hospital, Xi'an Jiao Tong University, Xi'an, Shaanxi, China (mainland)
| | - Dingjun Hao
- Department of Spinal Surgery, Hong Hui Hospital, Xi'an Jiao Tong University, Xi'an, Shaanxi, China (mainland)
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19
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Braicu C, Buse M, Busuioc C, Drula R, Gulei D, Raduly L, Rusu A, Irimie A, Atanasov AG, Slaby O, Ionescu C, Berindan-Neagoe I. A Comprehensive Review on MAPK: A Promising Therapeutic Target in Cancer. Cancers (Basel) 2019; 11:cancers11101618. [PMID: 31652660 PMCID: PMC6827047 DOI: 10.3390/cancers11101618] [Citation(s) in RCA: 467] [Impact Index Per Article: 93.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/13/2019] [Accepted: 10/16/2019] [Indexed: 02/07/2023] Open
Abstract
The mitogen-activated protein kinase (MAPK) pathway is an important bridge in the switch from extracellular signals to intracellular responses. Alterations of signaling cascades are found in various diseases, including cancer, as a result of genetic and epigenetic changes. Numerous studies focused on both the homeostatic and the pathologic conduct of MAPK signaling; however, there is still much to be deciphered in terms of regulation and action models in both preclinical and clinical research. MAPK has implications in the response to cancer therapy, particularly the activation of the compensatory pathways in response to experimental MAPK inhibition. The present paper discusses new insights into MAPK as a complex cell signaling pathway with roles in the sustenance of cellular normal conduit, response to cancer therapy, and activation of compensatory pathways. Unfortunately, most MAPK inhibitors trigger resistance due to the activation of compensatory feed-back loops in tumor cells and tumor microenvironment components. Therefore, novel combinatorial therapies have to be implemented for cancer management in order to restrict the possibility of alternative pathway activation, as a perspective for developing novel therapies based on integration in translational studies.
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Affiliation(s)
- Cornelia Braicu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Mihail Buse
- MEDFUTURE-Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Constantin Busuioc
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Rares Drula
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Diana Gulei
- MEDFUTURE-Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Lajos Raduly
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | | | - Alexandru Irimie
- Department of Surgery, The Oncology Institute "Prof. Dr. Ion Chiricuta", 40015 Cluj-Napoca, Romania.
- Department of Surgical Oncology and Gynecological Oncology, Iuliu Hatieganu University of Medicine and Pharmacy, 40015 Cluj-Napoca, Romania.
| | - Atanas G Atanasov
- Department of Pharmacognosy, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria.
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzebiec, 05-552 Magdalenka, Poland.
- Institute of Neurobiology, Bulgarian Academy of Sciences, 23 Acad. G. Bonchev str., 1113 Sofia, Bulgaria.
| | - Ondrej Slaby
- Central European Institute of Technology, Masaryk University, 601 77 Brno, Czech Republic.
- Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, 601 77 Brno, Czech Republic.
| | - Calin Ionescu
- th Surgical Department, Municipal Hospital, 400139, Cluj-Napoca, Romania.
- Department of Surgery, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
- MEDFUTURE-Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
- Department of Functional Genomics and Experimental Pathology, The Oncology Institute Prof. Dr. Ion Chiricuta, Republicii 34 Street, 400015 Cluj-Napoca, Romania.
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20
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Donohue E, Khorsand S, Mercado G, Varney KM, Wilder PT, Yu W, MacKerell AD, Alexander P, Van QN, Moree B, Stephen AG, Weber DJ, Salafsky J, McCormick F. Second harmonic generation detection of Ras conformational changes and discovery of a small molecule binder. Proc Natl Acad Sci U S A 2019; 116:17290-17297. [PMID: 31399543 PMCID: PMC6717309 DOI: 10.1073/pnas.1905516116] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Second harmonic generation (SHG) is an emergent biophysical method that sensitively measures real-time conformational change of biomolecules in the presence of biological ligands and small molecules. This study describes the successful implementation of SHG as a primary screening platform to identify fragment ligands to oncogenic Kirsten rat sarcoma (KRas). KRas is the most frequently mutated driver of pancreatic, colon, and lung cancers; however, there are few well-characterized small molecule ligands due to a lack of deep binding pockets. Using SHG, we identified a fragment binder to KRasG12D and used 1H 15N transverse relaxation optimized spectroscopy (TROSY) heteronuclear single-quantum coherence (HSQC) NMR to characterize its binding site as a pocket adjacent to the switch 2 region. The unique sensitivity of SHG furthered our study by revealing distinct conformations induced by our hit fragment compared with 4,6-dichloro-2-methyl-3-aminoethyl-indole (DCAI), a Ras ligand previously described to bind the same pocket. This study highlights SHG as a high-throughput screening platform that reveals structural insights in addition to ligand binding.
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Affiliation(s)
- Elizabeth Donohue
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94158
- Biodesy, Inc., South San Francisco, CA 94080
| | - Sina Khorsand
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94158
- Biodesy, Inc., South San Francisco, CA 94080
| | | | - Kristen M Varney
- Center for Biomolecular Therapeutics, School of Medicine, University of Maryland, Baltimore, MD 21201
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, MD 21201
| | - Paul T Wilder
- Center for Biomolecular Therapeutics, School of Medicine, University of Maryland, Baltimore, MD 21201
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, MD 21201
| | - Wenbo Yu
- Center for Biomolecular Therapeutics, School of Medicine, University of Maryland, Baltimore, MD 21201
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201
| | - Alexander D MacKerell
- Center for Biomolecular Therapeutics, School of Medicine, University of Maryland, Baltimore, MD 21201
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, MD 21201
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201
| | - Patrick Alexander
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Que N Van
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Ben Moree
- Biodesy, Inc., South San Francisco, CA 94080
| | - Andrew G Stephen
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - David J Weber
- Center for Biomolecular Therapeutics, School of Medicine, University of Maryland, Baltimore, MD 21201
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, MD 21201
| | - Joshua Salafsky
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Frank McCormick
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94158;
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
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21
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Chen X, Yao H, Wang H, Mao Y, Liu D, Long D. Extending the Lifetime of Native GTP‐Bound Ras for Site‐Resolved NMR Measurements: Quantifying the Allosteric Dynamics. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201812902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Xiaomin Chen
- Hefei National Laboratory for Physical Sciences at the Microscale & School of Life SciencesUniversity of Science and Technology of China 443 Huangshan Street Hefei Anhui 230027 China
| | - Haijie Yao
- Hefei National Laboratory for Physical Sciences at the Microscale & School of Life SciencesUniversity of Science and Technology of China 443 Huangshan Street Hefei Anhui 230027 China
| | - Hui Wang
- Hefei National Laboratory for Physical Sciences at the Microscale & School of Life SciencesUniversity of Science and Technology of China 443 Huangshan Street Hefei Anhui 230027 China
| | - Yunyun Mao
- Hefei National Laboratory for Physical Sciences at the Microscale & School of Life SciencesUniversity of Science and Technology of China 443 Huangshan Street Hefei Anhui 230027 China
| | - Dan Liu
- Hefei National Laboratory for Physical Sciences at the Microscale & School of Life SciencesUniversity of Science and Technology of China 443 Huangshan Street Hefei Anhui 230027 China
| | - Dong Long
- Hefei National Laboratory for Physical Sciences at the Microscale & School of Life SciencesUniversity of Science and Technology of China 443 Huangshan Street Hefei Anhui 230027 China
- Department of ChemistryUniversity of Science and Technology of China Hefei Anhui China
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22
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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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23
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Chen X, Yao H, Wang H, Mao Y, Liu D, Long D. Extending the Lifetime of Native GTP-Bound Ras for Site-Resolved NMR Measurements: Quantifying the Allosteric Dynamics. Angew Chem Int Ed Engl 2019; 58:2730-2733. [PMID: 30681242 DOI: 10.1002/anie.201812902] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Indexed: 12/18/2022]
Abstract
Characterization of native GTP-bound Ras is important for an appreciation of its cellular signaling and for the design of inhibitors, which however has been depressed by its intrinsic instability. Herein, an effective approach for extending the lifetime of Ras⋅GTP samples by exploiting the active role of Son of Sevenless (Sos) is demonstrated that sustains the activated state of Ras. This approach, combined with a postprocessing method that suppresses residual Ras⋅GDP signals, is applied to the site-resolved NMR measurement of the allosteric dynamics of Ras⋅GTP. The observed network of concerted motions well covers the recently identified allosteric inhibitor-binding pockets, but the motions are more confined than those of Ras⋅GppNHp, advocating the use of native GTP for development of allosteric inhibitors. The Sos-based approach is anticipated to generally facilitate experiments on active Ras when native GTP is preferred.
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Affiliation(s)
- Xiaomin Chen
- Hefei National Laboratory for Physical Sciences at the Microscale & School of Life Sciences, University of Science and Technology of China, 443 Huangshan Street, Hefei, Anhui, 230027, China
| | - Haijie Yao
- Hefei National Laboratory for Physical Sciences at the Microscale & School of Life Sciences, University of Science and Technology of China, 443 Huangshan Street, Hefei, Anhui, 230027, China
| | - Hui Wang
- Hefei National Laboratory for Physical Sciences at the Microscale & School of Life Sciences, University of Science and Technology of China, 443 Huangshan Street, Hefei, Anhui, 230027, China
| | - Yunyun Mao
- Hefei National Laboratory for Physical Sciences at the Microscale & School of Life Sciences, University of Science and Technology of China, 443 Huangshan Street, Hefei, Anhui, 230027, China
| | - Dan Liu
- Hefei National Laboratory for Physical Sciences at the Microscale & School of Life Sciences, University of Science and Technology of China, 443 Huangshan Street, Hefei, Anhui, 230027, China
| | - Dong Long
- Hefei National Laboratory for Physical Sciences at the Microscale & School of Life Sciences, University of Science and Technology of China, 443 Huangshan Street, Hefei, Anhui, 230027, China.,Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, China
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24
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Autoinhibition in Ras effectors Raf, PI3Kα, and RASSF5: a comprehensive review underscoring the challenges in pharmacological intervention. Biophys Rev 2018; 10:1263-1282. [PMID: 30269291 PMCID: PMC6233353 DOI: 10.1007/s12551-018-0461-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 09/17/2018] [Indexed: 02/06/2023] Open
Abstract
Autoinhibition is an effective mechanism that guards proteins against spurious activation. Despite its ubiquity, the distinct organizations of the autoinhibited states and their release mechanisms differ. Signaling is most responsive to the cell environment only if a small shift in the equilibrium is required to switch the system from an inactive (occluded) to an active (exposed) state. Ras signaling follows this paradigm. This underscores the challenge in pharmacological intervention to exploit and enhance autoinhibited states. Here, we review autoinhibition and release mechanisms at the membrane focusing on three representative Ras effectors, Raf protein kinase, PI3Kα lipid kinase, and NORE1A (RASSF5) tumor suppressor, and point to the ramifications to drug discovery. We further touch on Ras upstream and downstream signaling, Ras activation, and the Ras superfamily in this light, altogether providing a broad outlook of the principles and complexities of autoinhibition.
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25
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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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26
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Xie C, Li Y, Li LL, Fan XX, Wang YW, Wei CL, Liu L, Leung ELH, Yao XJ. Identification of a New Potent Inhibitor Targeting KRAS in Non-small Cell Lung Cancer Cells. Front Pharmacol 2017; 8:823. [PMID: 29184501 PMCID: PMC5694459 DOI: 10.3389/fphar.2017.00823] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/30/2017] [Indexed: 12/23/2022] Open
Abstract
KRAS (v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog) is an oncogenic driver with mutations in 30% of non-small cell lung cancer (NSCLC). However, there is no effective clinical drug even though it has been identified as an oncogene for 30 years. In this study, we identified a small molecule inhibitor compound 0375-0604 targeting KRAS by using molecular docking based virtual screening approach. Compound 0375-0604 had a good binding affinity to KRAS in vitro and exhibited cytotoxicity in oncogenic KRAS expressing NSCLC cell lines. Further mechanism study showed that compound 0375-0604 can block the formation of the complex of guanosine triphosphate (GTP) and KRAS in vitro. In addition, compound 0375-0604 inhibited KRAS downstream signaling pathway RAF/MEK/ERK and RAF/PI3K/AKT. Finally, we also found that this compound can inhibit the cell growth through G2/M cell cycle arrest and induce apoptosis on the NSCLC cell lines harboring KRAS mutation. Therefore, compound 0375-0604 may be considered as a potential KRAS inhibitor for treatment of NSCLC carrying KRAS oncogene.
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Affiliation(s)
- Chun Xie
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, China
| | - Ying Li
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, China
| | - Lan-Lan Li
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
| | - Xing-Xing Fan
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, China
| | - Yu-Wei Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, China
| | - Chun-Li Wei
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, China
| | - Liang Liu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, China
| | - Elaine Lai-Han Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, China
| | - Xiao-Jun Yao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, China.,State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
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27
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Müller MP, Jeganathan S, Heidrich A, Campos J, Goody RS. Nucleotide based covalent inhibitors of KRas can only be efficient in vivo if they bind reversibly with GTP-like affinity. Sci Rep 2017. [PMID: 28623374 PMCID: PMC5473928 DOI: 10.1038/s41598-017-03973-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Simple reversible competitive inhibition of nucleotide binding of GTP to Ras family GTPases has long been recognized as an unlikely approach to manipulating the activity of such proteins for experimental or therapeutic purposes. This is due to the high affinity of GTP to GTPases coupled with high cellular GTP concentrations, but also to problems of specificity for the highly conserved binding sites in GTPases. A recent approach suggested that these problems might be overcome by using GDP derivatives that can undergo a covalent reaction with disease specific mutants, in particular addressing inhibition of KRasG12C using GDP equipped with an electrophilic group at the β-phosphate. We show here that a major drawback to this approach is a loss of reversible affinity of such β-modified derivatives for Ras of at least 104 compared to GTP and GDP. With the help of a thorough kinetic characterization, we show that this leads to covalent reaction times that are too slow to make the compounds attractive for intracellular use, but that generation of a hypothetical reactive GDP derivative that retains the high reversible affinity of GDP/GTP to Ras might be a viable alternative.
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Affiliation(s)
- Matthias P Müller
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany. .,Faculty of Chemistry and Chemical Biology, Dortmund University of Technology, Otto-Hahn-Straße 4a, 44227, Dortmund, Germany.
| | - Sadasivam Jeganathan
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Angelika Heidrich
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Jeremy Campos
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Roger S Goody
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany.
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28
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Singh R. Central role of PI3K-SYK interaction in fibrinogen-induced lamellipodia and filopodia formation in platelets. FEBS Open Bio 2016; 6:1285-1296. [PMID: 28255536 PMCID: PMC5324771 DOI: 10.1002/2211-5463.12149] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 10/05/2016] [Accepted: 10/18/2016] [Indexed: 12/27/2022] Open
Abstract
The WAVE complex‐1, a complex of WAVE, Abi1, NAP1, PIR121, HSPC300, RacGTP and Arp2/3 proteins, and WASP complex‐1, a complex of WASP, Cdc42, PIP2, and Arp2/3 proteins, are involved in lamellipodia and filopodia formation, respectively. It is known that the two complexes have opposite dynamics. Furthermore, Rac has two guanine nucleotide exchange factors, Vav and Sos, whose role in activating Rac is not well understood. In this work, by the construction of signaling network, analysis, and mathematical modeling, I show that Sos generates a pulse of WAVE complex‐1, decreasing the response time of WAVE complex‐1 formation upon the stimulation of platelets by fibrinogen. Furthermore, I also show that the dynamics of WAVE and WASP complexes depends on PI3K–SYK interaction. In the absence of this interaction, the WAVE complex‐1 does not form and the WASP complex‐1 remains at the initial, sustained level. Thus, I show the significance of the two protein/protein complexes: Sos and PI3K–SYK interaction, in fibrinogen‐induced lamellipodia and filopodia formation in platelets.
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Affiliation(s)
- Raghvendra Singh
- Department of Chemical Engineering Indian Institute of Technology Kanpur India
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29
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Vo U, Vajpai N, Embrey KJ, Golovanov AP. Dynamic studies of H-Ras•GTPγS interactions with nucleotide exchange factor Sos reveal a transient ternary complex formation in solution. Sci Rep 2016; 6:29706. [PMID: 27412770 PMCID: PMC4944212 DOI: 10.1038/srep29706] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 06/21/2016] [Indexed: 11/26/2022] Open
Abstract
The cycling between GDP- and GTP- bound forms of the Ras protein is partly regulated by the binding of Sos. The structural/dynamic behavior of the complex formed between activated Sos and Ras at the point of the functional cycle where the nucleotide exchange is completed has not been described to date. Here we show that solution NMR spectra of H-Ras∙GTPγS mixed with a functional fragment of Sos (SosCat) at a 2:1 ratio are consistent with the formation of a rather dynamic assembly. H-Ras∙GTPγS binding was in fast exchange on the NMR timescale and retained a significant degree of molecular tumbling independent of SosCat, while SosCat also tumbled largely independently of H-Ras. Estimates of apparent molecular weight from both NMR data and SEC-MALS revealed that, at most, only one H-Ras∙GTPγS molecule appears stably bound to Sos. The weak transient interaction between Sos and the second H-Ras∙GTPγS may provide a necessary mechanism for complex dissociation upon the completion of the native GDP → GTP exchange reaction, but also explains measurable GTP → GTP exchange activity of Sos routinely observed in in vitro assays that use fluorescently-labelled analogs of GTP. Overall, the data presents the first dynamic snapshot of Ras functional cycle as controlled by Sos.
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Affiliation(s)
- Uybach Vo
- Manchester Institute of Biotechnology and Faculty of Life Sciences, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Navratna Vajpai
- AstraZeneca, Discovery Sciences, Mereside, Alderley Park, Cheshire, SK10 4TF, UK
| | - Kevin J Embrey
- AstraZeneca, Discovery Sciences, Mereside, Alderley Park, Cheshire, SK10 4TF, UK
| | - Alexander P Golovanov
- Manchester Institute of Biotechnology and Faculty of Life Sciences, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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30
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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: 259] [Impact Index Per Article: 32.4] [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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