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Shaban N, Kamashev D, Emelianova A, Buzdin A. Targeted Inhibitors of EGFR: Structure, Biology, Biomarkers, and Clinical Applications. Cells 2023; 13:47. [PMID: 38201251 PMCID: PMC10778338 DOI: 10.3390/cells13010047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Members of the EGFR family of tyrosine kinase receptors are major regulators of cellular proliferation, differentiation, and survival. In humans, abnormal activation of EGFR is associated with the development and progression of many cancer types, which makes it an attractive target for molecular-guided therapy. Two classes of EGFR-targeted cancer therapeutics include monoclonal antibodies (mAbs), which bind to the extracellular domain of EGFR, and tyrosine kinase inhibitors (TKIs), which mostly target the intracellular part of EGFR and inhibit its activity in molecular signaling. While EGFR-specific mAbs and three generations of TKIs have demonstrated clinical efficacy in various settings, molecular evolution of tumors leads to apparent and sometimes inevitable resistance to current therapeutics, which highlights the need for deeper research in this field. Here, we tried to provide a comprehensive and systematic overview of the rationale, molecular mechanisms, and clinical significance of the current EGFR-targeting drugs, highlighting potential candidate molecules in development. We summarized the underlying mechanisms of resistance and available personalized predictive approaches that may lead to improved efficacy of EGFR-targeted therapies. We also discuss recent developments and the use of specific therapeutic strategies, such as multi-targeting agents and combination therapies, for overcoming cancer resistance to EGFR-specific drugs.
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Affiliation(s)
- Nina Shaban
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia; (D.K.); (A.B.)
- Laboratory for Translational Genomic Bioinformatics, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Dmitri Kamashev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia; (D.K.); (A.B.)
- Laboratory for Translational Genomic Bioinformatics, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
- Institute of Personalized Oncology, I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Aleksandra Emelianova
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, Moscow 119991, Russia;
| | - Anton Buzdin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia; (D.K.); (A.B.)
- Laboratory for Translational Genomic Bioinformatics, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
- Institute of Personalized Oncology, I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
- PathoBiology Group, European Organization for Research and Treatment of Cancer (EORTC), 1200 Brussels, Belgium
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Ferreira AS, Lopacinski A, Batista M, Hiraiwa PM, Guimarães BG, Zanchin NIT. A toolkit for recombinant production of seven human EGF family growth factors in active conformation. Sci Rep 2022; 12:5034. [PMID: 35322149 PMCID: PMC8943033 DOI: 10.1038/s41598-022-09060-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/14/2022] [Indexed: 12/17/2022] Open
Abstract
Epidermal growth factors (EGF) play a wide range of roles in embryogenesis, skin development, immune response homeostasis. They are involved in several pathologies as well, including several cancer types, psoriasis, chronic pain and chronic kidney disease. All members share the structural EGF domain, which is responsible for receptor interaction, thereby initiating transduction of signals. EGF growth factors have intense use in fundamental research and high potential for biotechnological applications. However, due to their structural organization with three disulfide bonds, recombinant production of these factors in prokaryotic systems is not straightforward. A significant fraction usually forms inclusion bodies. For the fraction remaining soluble, misfolding and incomplete disulfide bond formation may affect the amount of active factor in solution, which can compromise experimental conclusions and biotechnological applications. In this work, we describe a reliable procedure to produce seven human growth factors of the EGF family in Escherichia coli. Biophysical and stability analyses using limited proteolysis, light scattering, circular dichroism and nanoDSF show that the recombinant factors present folded and stable conformation. Cell proliferation and scratch healing assays confirmed that the recombinant factors are highly active at concentrations as low as 5 ng/ml.
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Affiliation(s)
- Arthur Schveitzer Ferreira
- Laboratory of Structural Biology and Protein Engineering, Carlos Chagas Institute, FIOCRUZ Paraná, Curitiba, PR, Brazil
- Cellular and Molecular Biology Graduate Program, Federal University of Paraná, Curitiba, PR, Brazil
| | - Amanda Lopacinski
- Laboratory of Structural Biology and Protein Engineering, Carlos Chagas Institute, FIOCRUZ Paraná, Curitiba, PR, Brazil
- Cellular and Molecular Biology Graduate Program, Federal University of Paraná, Curitiba, PR, Brazil
| | - Michel Batista
- Mass Spectrometry Facility RPT02H, Carlos Chagas Institute, FIOCRUZ Paraná, Curitiba, PR, Brazil
| | - Priscila Mazzocchi Hiraiwa
- Laboratory of Structural Biology and Protein Engineering, Carlos Chagas Institute, FIOCRUZ Paraná, Curitiba, PR, Brazil
| | - Beatriz Gomes Guimarães
- Laboratory of Structural Biology and Protein Engineering, Carlos Chagas Institute, FIOCRUZ Paraná, Curitiba, PR, Brazil
| | - Nilson Ivo Tonin Zanchin
- Laboratory of Structural Biology and Protein Engineering, Carlos Chagas Institute, FIOCRUZ Paraná, Curitiba, PR, Brazil.
- Cellular and Molecular Biology Graduate Program, Federal University of Paraná, Curitiba, PR, Brazil.
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3
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Epiregulin as an Alternative Ligand for Leptin Receptor Alleviates Glucose Intolerance without Change in Obesity. Cells 2022; 11:cells11030425. [PMID: 35159237 PMCID: PMC8834548 DOI: 10.3390/cells11030425] [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: 12/21/2021] [Revised: 01/18/2022] [Accepted: 01/22/2022] [Indexed: 11/16/2022] Open
Abstract
The leptin receptor (LepR) acts as a signaling nexus for the regulation of glucose uptake and obesity, among other metabolic responses. The functional role of LepR under leptin-deficient conditions remains unclear. This study reports that epiregulin (EREG) governed glucose uptake in vitro and in vivo in Lepob mice by activating LepR under leptin-deficient conditions. Single and long-term treatment with EREG effectively rescued glucose intolerance in comparative insulin and EREG tolerance tests in Lepob mice. The immunoprecipitation study revealed binding between EREG and LepR in adipose tissue of Lepob mice. EREG/LepR regulated glucose uptake without changes in obesity in Lepob mice via mechanisms, including ERK activation and translocation of GLUT4 to the cell surface. EREG-dependent glucose uptake was abolished in Leprdb mice which supports a key role of LepR in this process. In contrast, inhibition of the canonical epidermal growth factor receptor (EGFR) pathway implicated in other EREG responses, increased glucose uptake. Our data provide a basis for understanding glycemic responses of EREG that are dependent on LepR unlike functions mediated by EGFR, including leptin secretion, thermogenesis, pain, growth, and other responses. The computational analysis identified a conserved amino acid sequence, supporting an evolutionary role of EREG as an alternative LepR ligand.
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Mitchell R, Mikolajczak M, Kersten C, Fleetwood-Walker S. ErbB1-dependent signalling and vesicular trafficking in primary afferent nociceptors associated with hypersensitivity in neuropathic pain. Neurobiol Dis 2020; 142:104961. [DOI: 10.1016/j.nbd.2020.104961] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/26/2020] [Accepted: 06/08/2020] [Indexed: 02/06/2023] Open
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Role of Epidermal Growth Factor Receptor (EGFR) and Its Ligands in Kidney Inflammation and Damage. Mediators Inflamm 2018; 2018:8739473. [PMID: 30670929 PMCID: PMC6323488 DOI: 10.1155/2018/8739473] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 10/29/2018] [Accepted: 11/07/2018] [Indexed: 12/29/2022] Open
Abstract
Chronic kidney disease (CKD) is characterized by persistent inflammation and progressive fibrosis, ultimately leading to end-stage renal disease. Although many studies have investigated the factors involved in the progressive deterioration of renal function, current therapeutic strategies only delay disease progression, leaving an unmet need for effective therapeutic interventions that target the cause behind the inflammatory process and could slow down or reverse the development and progression of CKD. Epidermal growth factor receptor (EGFR) (ERBB1), a membrane tyrosine kinase receptor expressed in the kidney, is activated after renal damage, and preclinical studies have evidenced its potential as a therapeutic target in CKD therapy. To date, seven official EGFR ligands have been described, including epidermal growth factor (EGF) (canonical ligand), transforming growth factor-α, heparin-binding epidermal growth factor, amphiregulin, betacellulin, epiregulin, and epigen. Recently, the connective tissue growth factor (CTGF/CCN2) has been described as a novel EGFR ligand. The direct activation of EGFR by its ligands can exert different cellular responses, depending on the specific ligand, tissue, and pathological condition. Among all EGFR ligands, CTGF/CCN2 is of special relevance in CKD. This growth factor, by binding to EGFR and downstream signaling pathway activation, regulates renal inflammation, cell growth, and fibrosis. EGFR can also be “transactivated” by extracellular stimuli, including several key factors involved in renal disease, such as angiotensin II, transforming growth factor beta (TGFB), and other cytokines, including members of the tumor necrosis factor superfamily, showing another important mechanism involved in renal pathology. The aim of this review is to summarize the contribution of EGFR pathway activation in experimental kidney damage, with special attention to the regulation of the inflammatory response and the role of some EGFR ligands in this process. Better insights in EGFR signaling in renal disease could improve our current knowledge of renal pathology contributing to therapeutic strategies for CKD development and progression.
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Cao XW, Yang XZ, Du X, Fu LY, Zhang TZ, Shan HW, Zhao J, Wang FJ. Structure optimisation to improve the delivery efficiency and cell selectivity of a tumour-targeting cell-penetrating peptide. J Drug Target 2018; 26:777-792. [PMID: 29303375 DOI: 10.1080/1061186x.2018.1424858] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cell-penetrating peptide (CPP) is used for the delivery of biomacromolecules across the cell membrane and is limited in cancer therapy due to the lack of cell selectivity. Epidermal growth factor receptor (EGFR) has been widely used in clinical targeted therapy for tumours. Here, we reported a novel tumour targeting cell-penetrating peptide (TCPP), EHB (ELBD-C6H) with 20-fold and 3000-fold greater transmembrane ability and tumour cell selectivity than our previously reported S3-HBD and classic CPP TAT, respectively. In this new TCPP, a specific alpha helix structure was inserted into a repeated amino acid (AA) sequence formed by tandem multiple selected key AA residues of vaccinia growth factor (VGF), and this sequence was then fused to a tailored heparin binding domain sequence (C6H) derived from heparin-binding epidermal growth factor-like growth factor to intensify its targeting delivery ability. EHB could carry anticancer proteins such as MAP30 (Momordica Antiviral Protein 30 kDa) into EGFR-overexpressing cancer cell and inhibit cell growth, but it had a greatly reduced interaction with normal cells. These results indicated that EHB, as a novel efficient TCPP for the selective delivery of drug molecules into cancer cells, would help to improve the efficacy and safety of anti-tumour drugs.
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Affiliation(s)
- Xue-Wei Cao
- a State Key Laboratory of Bioreactor Engineering , East China University of Science and Technology , Shanghai , PR China
| | - Xu-Zhong Yang
- b Zhejiang Reachall Pharmaceutical Co. Ltd , Zhejiang , PR China
| | - Xuan Du
- a State Key Laboratory of Bioreactor Engineering , East China University of Science and Technology , Shanghai , PR China
| | - Long-Yun Fu
- b Zhejiang Reachall Pharmaceutical Co. Ltd , Zhejiang , PR China
| | - Tao-Zhu Zhang
- b Zhejiang Reachall Pharmaceutical Co. Ltd , Zhejiang , PR China
| | - Han-Wen Shan
- b Zhejiang Reachall Pharmaceutical Co. Ltd , Zhejiang , PR China
| | - Jian Zhao
- a State Key Laboratory of Bioreactor Engineering , East China University of Science and Technology , Shanghai , PR China
| | - Fu-Jun Wang
- b Zhejiang Reachall Pharmaceutical Co. Ltd , Zhejiang , PR China.,c Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine , Shanghai , PR China
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Sudhakar DR, P. K, Subbarao N. Docking and molecular dynamics simulation study of EGFR1 with EGF-like peptides to understand molecular interactions. MOLECULAR BIOSYSTEMS 2016; 12:1987-95. [DOI: 10.1039/c6mb00032k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Epidermal growth factor receptors (EGFRs) are oncogenes, which regulate the expression of genes in various pathways, allowing cells to grow and divide.
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Affiliation(s)
- D. Raja Sudhakar
- School of Computational and Integrative Sciences
- Jawaharlal Nehru University
- New Delhi-110067
- India
| | - Kalaiarasan P.
- National Centre of Applied Human Genetics
- School of Life Sciences
- Jawaharlal Nehru University
- New Delhi
- India
| | - Naidu Subbarao
- School of Computational and Integrative Sciences
- Jawaharlal Nehru University
- New Delhi-110067
- India
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Kado Y, Mizohata E, Nagatoishi S, Iijima M, Shinoda K, Miyafusa T, Nakayama T, Yoshizumi T, Sugiyama A, Kawamura T, Lee YH, Matsumura H, Doi H, Fujitani H, Kodama T, Shibasaki Y, Tsumoto K, Inoue T. Epiregulin Recognition Mechanisms by Anti-epiregulin Antibody 9E5: STRUCTURAL, FUNCTIONAL, AND MOLECULAR DYNAMICS SIMULATION ANALYSES. J Biol Chem 2015; 291:2319-30. [PMID: 26627827 DOI: 10.1074/jbc.m115.656009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Indexed: 11/06/2022] Open
Abstract
Epiregulin (EPR) is a ligand of the epidermal growth factor (EGF) family that upon binding to its epidermal growth factor receptor (EGFR) stimulates proliferative signaling, especially in colon cancer cells. Here, we describe the three-dimensional structure of the EPR antibody (the 9E5(Fab) fragment) in the presence and absence of EPR. Among the six complementarity-determining regions (CDRs), CDR1-3 in the light chain and CDR2 in the heavy chain predominantly recognize EPR. In particular, CDR3 in the heavy chain dramatically moves with cis-trans isomerization of Pro(103). A molecular dynamics simulation and mutational analyses revealed that Arg(40) in EPR is a key residue for the specific binding of 9E5 IgG. From isothermal titration calorimetry analysis, the dissociation constant was determined to be 6.5 nm. Surface plasmon resonance analysis revealed that the dissociation rate of 9E5 IgG is extremely slow. The superimposed structure of 9E5(Fab)·EPR on the known complex structure of EGF·EGFR showed that the 9E5(Fab) paratope overlaps with Domains I and III on the EGFR, which reveals that the 9E5(Fab)·EPR complex could not bind to the EGFR. The 9E5 antibody will also be useful in medicine as a neutralizing antibody specific for colon cancer.
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Affiliation(s)
- Yuji Kado
- From the Division of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-Oka, Suita, Osaka 565-0871, Japan, Interdisciplinary Program for Biomedical Sciences, Institute for Academic Initiatives, Osaka University, 1-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Eiichi Mizohata
- From the Division of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-Oka, Suita, Osaka 565-0871, Japan
| | - Satoru Nagatoishi
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku Tokyo 108-8639, Japan, and
| | - Mariko Iijima
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Number 34 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Keiko Shinoda
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Number 34 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Takamitsu Miyafusa
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku Tokyo 108-8639, Japan, and
| | - Taisuke Nakayama
- From the Division of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-Oka, Suita, Osaka 565-0871, Japan
| | - Takuma Yoshizumi
- From the Division of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-Oka, Suita, Osaka 565-0871, Japan
| | - Akira Sugiyama
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Number 34 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Takeshi Kawamura
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Number 34 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Young-Hun Lee
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Number 34 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Hiroyoshi Matsumura
- From the Division of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-Oka, Suita, Osaka 565-0871, Japan
| | - Hirofumi Doi
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Number 34 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Hideaki Fujitani
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Number 34 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Tatsuhiko Kodama
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Number 34 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Yoshikazu Shibasaki
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Number 34 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Kouhei Tsumoto
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku Tokyo 108-8639, Japan, and
| | - Tsuyoshi Inoue
- From the Division of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-Oka, Suita, Osaka 565-0871, Japan,
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Ceresa BP, Peterson JL. Cell and molecular biology of epidermal growth factor receptor. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 313:145-78. [PMID: 25376492 DOI: 10.1016/b978-0-12-800177-6.00005-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The epidermal growth factor receptor (EGFR) has been one of the most intensely studied cell surface receptors due to its well-established roles in developmental biology, tissue homeostasis, and cancer biology. The EGFR has been critical for creating paradigms for numerous aspects of cell biology, such as ligand binding, signal transduction, and membrane trafficking. Despite this history of discovery, there is a continual stream of evidence that only the surface has been scratched. New ways of receptor regulation continue to be identified, each of which is a potential molecular target for manipulating EGFR signaling and the resultant changes in cell and tissue biology. This chapter is an update on EGFR-mediated signaling, and describes some recent developments in the regulation of receptor biology.
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Affiliation(s)
- Brian P Ceresa
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, USA
| | - Joanne L Peterson
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, USA
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Engin HB, Guney E, Keskin O, Oliva B, Gursoy A. Integrating structure to protein-protein interaction networks that drive metastasis to brain and lung in breast cancer. PLoS One 2013; 8:e81035. [PMID: 24278371 PMCID: PMC3838352 DOI: 10.1371/journal.pone.0081035] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 10/05/2013] [Indexed: 11/18/2022] Open
Abstract
Blocking specific protein interactions can lead to human diseases. Accordingly, protein interactions and the structural knowledge on interacting surfaces of proteins (interfaces) have an important role in predicting the genotype-phenotype relationship. We have built the phenotype specific sub-networks of protein-protein interactions (PPIs) involving the relevant genes responsible for lung and brain metastasis from primary tumor in breast cancer. First, we selected the PPIs most relevant to metastasis causing genes (seed genes), by using the "guilt-by-association" principle. Then, we modeled structures of the interactions whose complex forms are not available in Protein Databank (PDB). Finally, we mapped mutations to interface structures (real and modeled), in order to spot the interactions that might be manipulated by these mutations. Functional analyses performed on these sub-networks revealed the potential relationship between immune system-infectious diseases and lung metastasis progression, but this connection was not observed significantly in the brain metastasis. Besides, structural analyses showed that some PPI interfaces in both metastasis sub-networks are originating from microbial proteins, which in turn were mostly related with cell adhesion. Cell adhesion is a key mechanism in metastasis, therefore these PPIs may be involved in similar molecular pathways that are shared by infectious disease and metastasis. Finally, by mapping the mutations and amino acid variations on the interface regions of the proteins in the metastasis sub-networks we found evidence for some mutations to be involved in the mechanisms differentiating the type of the metastasis.
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Affiliation(s)
- H. Billur Engin
- Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, Istanbul, Turkey
| | - Emre Guney
- Structural Bioinformatics Group (GRIB), Universitat Pompeu Fabra
| | - Ozlem Keskin
- Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, Istanbul, Turkey
| | - Baldo Oliva
- Structural Bioinformatics Group (GRIB), Universitat Pompeu Fabra
| | - Attila Gursoy
- Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, Istanbul, Turkey
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Sanders JM, Wampole ME, Thakur ML, Wickstrom E. Molecular determinants of epidermal growth factor binding: a molecular dynamics study. PLoS One 2013; 8:e54136. [PMID: 23382875 PMCID: PMC3554757 DOI: 10.1371/journal.pone.0054136] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 12/10/2012] [Indexed: 12/22/2022] Open
Abstract
The epidermal growth factor receptor (EGFR) is a member of the receptor tyrosine kinase family that plays a role in multiple cellular processes. Activation of EGFR requires binding of a ligand on the extracellular domain to promote conformational changes leading to dimerization and transphosphorylation of intracellular kinase domains. Seven ligands are known to bind EGFR with affinities ranging from sub-nanomolar to near micromolar dissociation constants. In the case of EGFR, distinct conformational states assumed upon binding a ligand is thought to be a determining factor in activation of a downstream signaling network. Previous biochemical studies suggest the existence of both low affinity and high affinity EGFR ligands. While these studies have identified functional effects of ligand binding, high-resolution structural data are lacking. To gain a better understanding of the molecular basis of EGFR binding affinities, we docked each EGFR ligand to the putative active state extracellular domain dimer and 25.0 ns molecular dynamics simulations were performed. MM-PBSA/GBSA are efficient computational approaches to approximate free energies of protein-protein interactions and decompose the free energy at the amino acid level. We applied these methods to the last 6.0 ns of each ligand-receptor simulation. MM-PBSA calculations were able to successfully rank all seven of the EGFR ligands based on the two affinity classes: EGF>HB-EGF>TGF-α>BTC>EPR>EPG>AR. Results from energy decomposition identified several interactions that are common among binding ligands. These findings reveal that while several residues are conserved among the EGFR ligand family, no single set of residues determines the affinity class. Instead we found heterogeneous sets of interactions that were driven primarily by electrostatic and Van der Waals forces. These results not only illustrate the complexity of EGFR dynamics but also pave the way for structure-based design of therapeutics targeting EGF ligands or the receptor itself.
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Affiliation(s)
- Jeffrey M. Sanders
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Matthew E. Wampole
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Mathew L. Thakur
- Department of Radiology, Thomas Jefferson Medical College, Philadelphia, Pennsylvania, United States of America
- Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Eric Wickstrom
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
- Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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van der Woning SP, Venselaar H, van Rotterdam W, Jacobs-Oomen S, van Leeuwen JEM, van Zoelen EJJ. Role of the C-terminal linear region of EGF-like growth factors in ErbB specificity. Growth Factors 2009; 27:163-72. [PMID: 19384683 DOI: 10.1080/08977190902891010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The epidermal growth factor (EGF)-like growth factors bind their ErbB receptors in a highly selective manner. Recently, we have shown that the sequence YYDLL in the C-terminal linear region is compatible with binding to all ligand-binding ErbB receptors. In the present study, we show that introduction of the YYDLL sequence into the ErbB1 specific ligands EGF and transforming growth factor-alpha (TGFalpha) broadened their receptor specificity towards ErbB4. Upon introduction of the YYDLL sequence into epiregulin, which by itself binds ErbB1 and ErbB4 but not ErbB3, its binding specificity was broadened to ErbB3, concomitant with enhanced affinity for ErbB4. Introduction of the YYDLL sequence into NRG1beta resulted in a 10-fold increase in affinity for ErbB3, without affecting its receptor specificity. Remarkably, the strongly enhanced affinity for ErbB3 negatively influenced their mitogenic activity towards cells coexpressing ErbB2 and ErbB3. These observations are discussed in terms of the optimised ErbB affinity, selectivity and mitogenic potential that have taken place during evolution.
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Abstract
Five highly homologous epidermal growth factor receptor ligands were studied by mass spectral analysis, hydrogen/deuterium (H/D) exchange via attenuated total reflectance Fourier transform-infrared spectroscopy, and two-dimensional correlation analysis. These studies were performed to determine the order of events during the exchange process, the extent of H/D exchange, and associated kinetics of exchange for a comparative analysis of these ligands. Furthermore, the secondary structure composition of amphiregulin (AR) and heparin-binding-epidermal growth factor (HB-EGF) was determined. All ligands were found to have similar contributions of 3(10)-helix and random coil with varying contributions of beta-sheets and beta-turns. The extent of exchange was 40%, 65%, 55%, 65%, and 98% for EGF, transforming growth factor-alpha (TGF-alpha), AR, HB-EGF, and epiregulin (ER), respectively. The rate constants were determined and classified as fast, intermediate, and slow: for EGF the 0.20 min(-1) (Tyr), 0.09 min(-1) (Arg, beta-turns), and 1.88 x 10(-3) min(-1) (beta-sheets and 3(10)-helix); and for TGF-alpha 0.91 min(-1) (Tyr), 0.27 min(-1) (Arg, beta-turns), and 1.41 x 10(-4) min(-1) (beta-sheets). The time constants for AR 0.47 min(-1) (Tyr), 0.04 min(-1) (Arg), and 1.00 x 10(-4) min(-1) (buried 3(10)-helix, beta-turns, and beta-sheets); for HB-EGF 0.89 min(-1) (Tyr), 0.14 min(-1) (Arg and 3(10)-helix), and 1.00 x 10(-3) min(-1) (buried 3(10)-helix, beta-sheets, and beta-turns); and for epiregulin 0.16 min(-1) (Tyr), 0.03 min(-1) (Arg), and 1.00 x 10(-4) min(-1) (3(10)-helix and beta-sheets). These results provide essential information toward understanding secondary structure, H/D exchange kinetics, and solvation of these epidermal growth factor receptor ligands in their unbound state.
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McClelland CM, Gullick WJ. Proteomic identification of secreted proteins as surrogate markers for signal transduction inhibitor activity. Br J Cancer 2007; 96:284-9. [PMID: 17211472 PMCID: PMC2360009 DOI: 10.1038/sj.bjc.6603544] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Epidermal growth factor receptor is a potential target for cancer treatment and new small-molecule tyrosine kinase inhibitor drugs have been designed to inhibit its activity. In this work we identify potential surrogate markers of drug activity using a proteomic analysis. Two-dimensional electrophoresis was optimised to compare expression patterns of proteins secreted from the cancer cell lines A431 and A549 treated with Gefitinib (Iressa) vs untreated or vehicle-only-treated samples. Upregulated or downregulated proteins were detected using Phoretix 2D image analysis software. Several proteins were then identified using matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry. In one case, upregulation of Protein Disulphide Isomerase in response to Gefitinib was confirmed by Western blot analysis, and the response was shown to be concentration dependent. The identification of surrogate markers may be of use for the evaluation of new drugs, in preclinical models, in clinical trials and in the therapy of individual patients to give optimal biological drug doses.
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Affiliation(s)
- C M McClelland
- Cancer Biology Laboratory, Department of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - W J Gullick
- Cancer Biology Laboratory, Department of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
- E-mail:
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15
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Patel RD, Kim DJ, Peters JM, Perdew GH. The aryl hydrocarbon receptor directly regulates expression of the potent mitogen epiregulin. Toxicol Sci 2005; 89:75-82. [PMID: 16192470 DOI: 10.1093/toxsci/kfi344] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is known to cause a large number of adverse effects, mediated largely by its binding to the aryl-hydrocarbon receptor (AhR) and subsequent modulation of gene expression. It is thought that AhR mediates these effects through the untimely and disproportionate expression of specific genes. However, the exact mechanism, or the genes involved, through which TCDD leads to these effects is still unknown. This study reports the discovery of a novel target gene, epiregulin, which is regulated by TCDD-activated AhR. Epiregulin is a growth regulator which belongs to the epidermal growth factor (EGF) family. Using real time quantitative PCR (qPCR), it was established that TCDD upregulates epiregulin gene expression. The promoter region of epiregulin has a dioxin responsive element (DRE) 56 nucleotides upstream of the transcription start site, along with three potential Sp1 binding sites. Chromatin immunoprecipitation (ChIP) assays with an anti-AhR antibody showed promoter occupancy upon TCDD treatment. Luciferase reporter assays using a vector harboring the first 125 base pairs of the epiregulin rat promoter revealed an increase in signal on TCDD treatment, which was lost upon mutation of the DRE. Epiregulin and TCDD treatment mediated a dose-dependent increase in primary mouse keratinocyte growth. These results demonstrate that AhR directly increases epiregulin expression, which could play an important role in TCDD mediated tumor promotion observed in rodent models.
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MESH Headings
- Animals
- Animals, Newborn
- Cell Line, Transformed
- Cell Line, Tumor
- Cell Proliferation/drug effects
- Cell Transformation, Viral
- Chromatin Immunoprecipitation/methods
- Dose-Response Relationship, Drug
- Epidermal Growth Factor/genetics
- Epidermal Growth Factor/metabolism
- Epiregulin
- Hepatocytes/drug effects
- Hepatocytes/metabolism
- Keratinocytes/drug effects
- Keratinocytes/metabolism
- Mice
- Mice, Inbred C57BL
- Mitogens/genetics
- Mitogens/metabolism
- NIH 3T3 Cells/drug effects
- NIH 3T3 Cells/metabolism
- Polychlorinated Dibenzodioxins/pharmacology
- RNA, Messenger/metabolism
- Receptors, Aryl Hydrocarbon/immunology
- Receptors, Aryl Hydrocarbon/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Transcription, Genetic/drug effects
- Up-Regulation
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Affiliation(s)
- Rushang D Patel
- Graduate Program in Molecular Medicine, The Huck Institutes of the Life Sciences, Department of Veterinary Science and The Center for Molecular Toxicology and Carcinogenesis, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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16
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Alewood D, Nielsen K, Alewood PF, Craik DJ, Andrews P, Nerrie M, White S, Domagala T, Walker F, Rothacker J, Burgess AW, Nice EC. The role of disulfide bonds in the structure and function of murine epidermal growth factor (mEGF). Growth Factors 2005; 23:97-110. [PMID: 16019431 DOI: 10.1080/08977190500096061] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
A systematic study using solid phase peptide synthesis has been undertaken to examine the role of the disulfide bonds in the structure and function of mEGF. A combination of one, two and three native disulfide pair analogues of an active truncated (4-48) form of mEGF have been synthesised by replacing specific cysteine residues with isosteric a-amino-n-butyric acid (Abu). Oxidation of the peptides was performed using either conventional aerobic oxidation at basic pH, in DMSO under acidic conditions or via selective disulfide formation using orthogonal protection of the cysteine pairs. The contribution of individual, or pairs of, disulfide bonds to EGF structure was evaluated by CD and (1)H-NMR spectroscopy. The mitogenic activity of each analogue was determined using Balb/c 3T3 mouse fibroblastsAs we have reported previously (Barnham et al. 1998), the disulfide bond between residues 6 and 20 can be removed with significant retention of biological activity (EC50 20-50 nM). The overall structure of this analogue was similar to that of native mEGF, indicating that the loss of the 6-20 disulfide bridge did not affect the global fold of the molecule. We now show that removal of any other disulfide bond, either singly or in pairs, results in a major disruption of the tertiary structure, and a large loss of activity (EC50>900 nM). Remarkably, the linear analogue appears to have greater activity (EC50 580 nM) than most one and two disulfide bond analogues although it does not have a definable tertiary structure.
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Affiliation(s)
- Dianne Alewood
- The Institute for Molecular Bioscience, The University of Queensland, Australia
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