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Mathpal S, Joshi T, Sharma P, Maiti P, Nand M, Pande V, Chandra S. In silico screening of chalcone derivatives as promising EGFR-TK inhibitors for the clinical treatment of cancer. 3 Biotech 2024; 14:18. [PMID: 38130684 PMCID: PMC10730483 DOI: 10.1007/s13205-023-03858-8] [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: 06/14/2023] [Accepted: 11/18/2023] [Indexed: 12/23/2023] Open
Abstract
Epidermal growth factor receptor (EGFR) promotes tumorigenic characteristics and activates cancer-associated signaling pathways such as Wnt/-catenin, transforming growth factor (TGF-β), and phosphoinositide-3-kinase (PI3K). Several inhibitors have been reported to suppress the activity of EGFR and are being used in cancer treatment. However, patients in the malignant stage of cancer show resistance to those inhibitors, opening a wide space for research to discover novel inhibitors. Therefore, we carried out machine learning and virtual screening to discover novel inhibitors with high affinity against EGFR-TK. Initially, a library of 2640 chalcones were screened out using a machine-learning model developed based on the random forest algorithm, exhibiting high sensitivity and a Receiver Operating Characteristic curve (ROC area) of 0.99. Furthermore, out of the initial 2640 screened compounds, 412 compounds exhibiting potential activity are subjected to evaluation for drug-likeness properties through different filters: Blood-brain barrier penetration, Lipinski's rule, CMC-50 like rule, Veber rule, and Ghose filter, alongside Cell Line Cytotoxicity Prediction. A total of 30 compounds that successfully pass through all these filters are selected for molecular docking. Of these, 6 compounds display substantial binding affinity and closer interaction with the conserved catalytic residues of the target EGFR-TK compared to the reference molecule (erlotinib). Furthermore, molecular dynamics simulation studies were conducted on four compounds (CID-375861, CID-375862, CID-23636403, and CID-259166) to confirm the stability of the docked complexes over a 100 ns simulation trajectory. Additionally, the binding free energy calculations by MMPBSA reveal that these four chalcone compounds exhibit strong affinity towards the EGFR-TK enzyme, with binding free energies of - 65.421 kJ/mol, - 94.266 kJ/mol, - 80.044 kJ/mol, and - 79.734 kJ/mol, respectively. The findings from this investigation highlight a set of promising chalcone compounds that have the potential to be developed into effective drugs for the treatment of various cancers. Further research and development on these compounds could pave the way for novel therapeutic interventions. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03858-8.
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Affiliation(s)
- Shalini Mathpal
- Department of Biotechnology, Bhimtal Campus, Kumaun University, Bhimtal, Uttarakhand 263136 India
| | - Tushar Joshi
- Department of Biotechnology, Bhimtal Campus, Kumaun University, Bhimtal, Uttarakhand 263136 India
| | - Priyanka Sharma
- Department of Botany, D.S.B Campus, Kumaun University, Nainital, Uttarakhand India
| | - Priyanka Maiti
- Centre for Environmental Assessment and Climate Change, G.B. Pant, National Institute of Himalayan Environment (GBP-NIHE), Kosi-Katarmal, Almora, Uttarakhand 263643 India
| | - Mahesha Nand
- ENVIS Centre on Himalayan Ecology, G.B. Pant National Institute of Himalayan Environment (GBP-NIHE), Kosi-Katarmal, Almora, Uttarakhand 263643 India
| | - Veena Pande
- Department of Biotechnology, Bhimtal Campus, Kumaun University, Bhimtal, Uttarakhand 263136 India
| | - Subhash Chandra
- Computational Biology and Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand 263601 India
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2
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Fotie J, Matherne CM, Mather JB, Wroblewski JE, Johnson K, Boudreaux LG, Perez AA. The Fundamental Role of Oxime and Oxime Ether Moieties in Improving the Physicochemical and Anticancer Properties of Structurally Diverse Scaffolds. Int J Mol Sci 2023; 24:16854. [PMID: 38069175 PMCID: PMC10705934 DOI: 10.3390/ijms242316854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
The present review explores the critical role of oxime and oxime ether moieties in enhancing the physicochemical and anticancer properties of structurally diverse molecular frameworks. Specific examples are carefully selected to illustrate the distinct contributions of these functional groups to general strategies for molecular design, modulation of biological activities, computational modeling, and structure-activity relationship studies. An extensive literature search was conducted across three databases, including PubMed, Google Scholar, and Scifinder, enabling us to create one of the most comprehensive overviews of how oximes and oxime ethers impact antitumor activities within a wide range of structural frameworks. This search focused on various combinations of keywords or their synonyms, related to the anticancer activity of oximes and oxime ethers, structure-activity relationships, mechanism of action, as well as molecular dynamics and docking studies. Each article was evaluated based on its scientific merit and the depth of the study, resulting in 268 cited references and more than 336 illustrative chemical structures carefully selected to support this analysis. As many previous reviews focus on one subclass of this extensive family of compounds, this report represents one of the rare and fully comprehensive assessments of the anticancer potential of this group of molecules across diverse molecular scaffolds.
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Affiliation(s)
- Jean Fotie
- Department of Chemistry and Physics, Southeastern Louisiana University, SLU 10878, Hammond, LA 70402-0878, USA; (C.M.M.); (J.B.M.); (J.E.W.); (K.J.); (L.G.B.); (A.A.P.)
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3
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Komkov AV, Sukhanova AА, Menchikov LG, Zavarzin IV. о-Aminopyrimidine Aldehydes and Ketones: Synthesis and use as Precursors to Fused Pyrimidines. Chem Heterocycl Compd (N Y) 2022. [DOI: 10.1007/s10593-022-03141-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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4
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Tan L, Zhang J, Wang Y, Wang X, Wang Y, Zhang Z, Shuai W, Wang G, Chen J, Wang C, Ouyang L, Li W. Development of Dual Inhibitors Targeting Epidermal Growth Factor Receptor in Cancer Therapy. J Med Chem 2022; 65:5149-5183. [PMID: 35311289 DOI: 10.1021/acs.jmedchem.1c01714] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Epidermal growth factor receptor (EGFR) is of great significance in mediating cell signaling transduction and tumor behaviors. Currently, third-generation inhibitors of EGFR, especially osimertinib, are at the clinical frontier for the treatment of EGFR-mutant non-small-cell lung cancer (NSCLC). Regrettably, the rapidly developing drug resistance caused by EGFR mutations and the compensatory mechanism have largely limited their clinical efficacy. Given the synergistic effect between EGFR and other compensatory targets during tumorigenesis and tumor development, EGFR dual-target inhibitors are promising for their reduced risk of drug resistance, higher efficacy, lower dosage, and fewer adverse events than those of single-target inhibitors. Hence, we present the synergistic mechanism underlying the role of EGFR dual-target inhibitors against drug resistance, their structure-activity relationships, and their therapeutic potential. Most importantly, we emphasize the optimal target combinations and design strategies for EGFR dual-target inhibitors and provide some perspectives on new challenges and future directions in this field.
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Affiliation(s)
- Lun Tan
- Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China.,Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China.,Precision Medicine Key Laboratory of Sichuan Province and Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
| | - Jifa Zhang
- Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China.,Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China.,Precision Medicine Key Laboratory of Sichuan Province and Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
| | - Yuxi Wang
- Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China.,Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China.,Precision Medicine Key Laboratory of Sichuan Province and Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
| | - Xiye Wang
- Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
| | - Yanyan Wang
- Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
| | - Zhixiong Zhang
- Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
| | - Wen Shuai
- Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China.,Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China.,Precision Medicine Key Laboratory of Sichuan Province and Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
| | - Guan Wang
- Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
| | - Juncheng Chen
- Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China.,Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China.,Precision Medicine Key Laboratory of Sichuan Province and Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
| | - Chengdi Wang
- Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China.,Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
| | - Liang Ouyang
- Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China.,Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China.,Precision Medicine Key Laboratory of Sichuan Province and Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China.,Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China.,Precision Medicine Key Laboratory of Sichuan Province and Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
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5
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Reckoning apigenin and kaempferol as a potential multi-targeted inhibitor of EGFR/HER2-MEK pathway of metastatic colorectal cancer identified using rigorous computational workflow. Mol Divers 2022; 26:3337-3356. [PMID: 35147860 DOI: 10.1007/s11030-022-10396-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 01/22/2022] [Indexed: 11/27/2022]
Abstract
In the past two decades, the treatment of metastatic colorectal cancer (mCRC) has been revolutionized as multiple cytotoxic, biological, and targeted drugs are being approved. Unfortunately, tumors treated with single targeted agents or therapeutics usually develop resistance. According to pathway-oriented screens, mCRC cells evade EGFR inhibition by HER2 amplification and/or activating Kras-MEK downstream signaling. Therefore, treating mCRC patients with dual EGFR/HER2 inhibitors, MEK inhibitors, or the combination of the two drugs envisaged to prevent the resistance development which eventually improves the overall survival rate. In the present study, we aimed to screen potential phytochemical lead compounds that could multi-target EGFR, HER2, and MEK1 (Mitogen-activated protein kinase kinase) using a computer-aided drug design approach that includes molecular docking, endpoint binding free energy calculation using MM-GBSA, ADMET, and molecular dynamics (MD) simulations. Docking studies revealed that, unlike all other ligands, apigenin and kaempferol exhibit the highest docking score against all three targets. Details of ADMET analysis, MM/GBSA, and MD simulations helped us to conclusively determine apigenin and kaempferol as potentially an inhibitor of EGFR, HER2, and MEK1 apigenin and kaempferol against mCRC at a systemic level. Additionally, both apigenin and kaempferol elicited antiangiogenic properties in a dose-dependent manner. Collectively, these findings provide the rationale for drug development aimed at preventing CRC rather than intercepting resistance.
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6
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Bashant MM, Mitchell SM, Hart LR, Lebedenko CG, Banerjee IA. In silico studies of interactions of peptide-conjugated cholesterol metabolites and betulinic acid with EGFR, LDR, and N-terminal fragment of CCKA receptors. J Mol Model 2021; 28:16. [PMID: 34961887 DOI: 10.1007/s00894-021-05007-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 12/14/2021] [Indexed: 11/25/2022]
Abstract
In this work, we designed three new ligands by conjugating cholesterol metabolites 3-hydroxy-5-cholestenoic acid (3-HC) and 3-oxo-4-cholestenoic acid (3-OC) and the natural tri-terpenoid betulinic acid with the tumor-targeting peptide YHWYGYTPQNVI. Molecular interactions with the unconjugated peptide and the conjugates were examined with three receptors that are commonly overexpressed in pancreatic adenocarcinoma cells using ligand docking and molecular dynamics. This study demonstrated the utility of the designed conjugates as a valuable scaffold for potentially targeting EGFR and LDLR receptors. Our results indicate that the conjugates showed strong binding affinities and formation of stable complexes with EGFR, while the unconjugated peptide, BT-peptide conjugate, an 3-HC-peptide conjugate showed the formation of fairly stable complexes with LDLR receptor. For EGFR, two receptor kinase domains were explored. Interactions with the N-terminal domain of CCKA-R were relatively weaker. For LDLR, binding occurred in the beta-propeller region. For the N-terminal fragment of CCKA-R, the conjugates induced significant conformational changes in the receptor. The molecular dynamic simulations for 100 ns demonstrate that BT-peptide conjugates and the unconjugated peptide had the highest binding and formed the most stable complexes with EGFR. RMSD and trajectory analyses indicate that these molecules transit to a dynamically stable configuration in most cases within 60 ns. NMA analysis indicated that amongst the conjugates that showed relatively higher interactions with the respective receptors, the highest potential for deformability was seen for the N-terminal-47 amino acid region of the CCKA-R receptor with and the lowest for the LDLR-receptor. Thus, the newly designed compounds may be evaluated in the future toward developing drug delivery materials for targeting tumor cells overexpressing LDLR or EGFR.
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Affiliation(s)
- Madeline M Bashant
- Department of Chemistry, Fordham University, 441 East Fordham Road, Bronx, NY, 10458, USA
| | - Saige M Mitchell
- Department of Chemistry, Fordham University, 441 East Fordham Road, Bronx, NY, 10458, USA
| | - Lucy R Hart
- Department of Chemistry, Fordham University, 441 East Fordham Road, Bronx, NY, 10458, USA
| | - Charlotta G Lebedenko
- Department of Chemistry, Fordham University, 441 East Fordham Road, Bronx, NY, 10458, USA
| | - Ipsita A Banerjee
- Department of Chemistry, Fordham University, 441 East Fordham Road, Bronx, NY, 10458, USA.
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7
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Eissa AAM, Aljamal KFM, Ibrahim HS, Abdelrasheed Allam H. Design and synthesis of novel pyridopyrimidine derivatives with anchoring non-coplanar aromatic extensions of EGFR inhibitory activity. Bioorg Chem 2021; 116:105318. [PMID: 34488123 DOI: 10.1016/j.bioorg.2021.105318] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/25/2021] [Accepted: 08/29/2021] [Indexed: 01/06/2023]
Abstract
The present study describes the synthesis of three series of 4-substituted pyridopyrimidin derivatives 4a-h, 5a-d. 6a-d, starting from 2-amino-6-(4-methoxyphenyl)-4-(4-(substituted) phenyl)nicotinonitrile 2a-d via the reaction with N,N-dimethyl-N-' substituted phenyl formimidamide to obtain 4a-h or with either phenyl isothiocyanate 1:1 and 1:2 to obtain 5a-d, 6a-d respectively. The synthesized compounds were evaluated for their effectiveness as EGFR inhibitors against Gefitinib. Six compounds; 4b,g,h, 5c and 6a,d prompted significantly higher EGFR inhibitory activity relative to that of Gefitinib. While two compounds 4d and 4f showed IC50 values non-significantly different from that of the reference drug. Furthermore, compounds 4a, 4 h, 6a and 6d were chosen to be assessed in vitro for their cytotoxicity against two EGFR-overexpressing cell lines; two human cancer cell lines namely: MCF7 and MDA-MB-361. Moreover, cell cycle analysis and apoptotic assay was applied for compound 4b that showed most potent inhibitory activity on EGFR, and the highest cytotoxicity against MCF7 and MDA-MB-361, where cell cycle arrest was achieved at pre G and S phases with increased apoptosis. Additionally, a molecular docking study was achieved to inspect the interaction of this compound with the active site of EGFR-TK.
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Affiliation(s)
- Amal A M Eissa
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo 11562, Egypt
| | - Kholoud F M Aljamal
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo 11562, Egypt
| | - Hany S Ibrahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo 11829, Egypt.
| | - Heba Abdelrasheed Allam
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo 11562, Egypt.
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8
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Haddad Y, Remes M, Adam V, Heger Z. Toward structure-based drug design against the epidermal growth factor receptor (EGFR). Drug Discov Today 2020; 26:289-295. [PMID: 33075469 PMCID: PMC7567673 DOI: 10.1016/j.drudis.2020.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/25/2020] [Accepted: 10/12/2020] [Indexed: 01/23/2023]
Abstract
Structural variations in EGFR should not be ignored in structure-based drug design. Main variations involve inward and outward folding of C-helix in the kinase N-lobe. Origins of variations are mutations and drug R-groups but not the drug core. Comparative modeling, fitting and clustering are imperative steps in EGFR drug design. Alternatively, volume and shape of binding site can be used to filter ligands against structures.
Most of the available crystal structures of epidermal growth factor receptor (EGFR) kinase domain, bound to drug inhibitors, originated from ligand-based drug design studies. Here, we used variations in 110 crystal structures to assemble eight distinct families highlighting the C-helix orientation in the N-lobe of the EGFR kinase domain. The families shared similar mutational profiles and similarity in the ligand R-groups (chemical composition, geometry, and charge) facing the C-helix, mutation sites, and DFG domain. For structure-based drug design, we recommend a systematic decision-making process for choice of template, guided by appropriate pairwise fitting and clustering before the molecular docking step. Alternatively, the binding site shape/volume can be used to filter and select the compound libraries.
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Affiliation(s)
- Yazan Haddad
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, 612 00 Brno, Czech Republic
| | - Marek Remes
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, 612 00 Brno, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, 612 00 Brno, Czech Republic
| | - Zbynek Heger
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, 612 00 Brno, Czech Republic.
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Pathak P, Naumovich V, Grishina M, Potemkin V. The study of EGFR-ligand complex electron property relationship with biological activity. J Biomol Struct Dyn 2020; 40:375-388. [PMID: 32897174 DOI: 10.1080/07391102.2020.1813629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The present investigation grounded on estimation of electron properties of the structures of EGFR proteins-ligand complexes using our laboratory-developed methodology AlteQ approach, which describes the molecular electron density of the complex in space for a certain point in three-dimensional coordinates. Briefly, the system embodies molecular electron density as a sum of Slater's type atomic increments of the molecular system. Further, using this methodology, we calculated different electron characteristics of selected EGFR protein-ligand complexes and established the relationship between different electron properties with their experimental pharmacological activity value (pIC50). The study suggested that EGFR inhibitory activity has higher correlation with intermolecular contacts of H with pi-system of aromatic ring between protein and ligands. Therefore, this created model has impact to identify and design potential ligands against EGFR in anticancer drug discovery.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Prateek Pathak
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Vladislav Naumovich
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Maria Grishina
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Vladimir Potemkin
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
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Introducing a pyrazolopyrimidine as a multi-tyrosine kinase inhibitor, using multi-QSAR and docking methods. Mol Divers 2020; 25:949-965. [PMID: 32297121 DOI: 10.1007/s11030-020-10080-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 03/29/2020] [Indexed: 12/16/2022]
Abstract
In cancer disease, which is one of the problems of today's human societies, the expression of some tyrosine kinase receptors that are effective in the growth and proliferation of cancerous cells rises. Therefore, it is essential to develop and propose new drugs to target the receptors. Performing modeling calculations such as QSAR and docking makes the drug discovery process more efficient. Thus, backpropagation artificial neural network was used for multidimensional quantitative structure-activity relationship (QSAR) to identify essential features of pyrazolopyrimidine moiety, responsible for anticancer activity. The statistical parameters of the model show that multi-QSAR has sufficient validity and accuracy. According to the QSAR modeling, among 26 compounds, the interaction of eight candidates with EGFR, FGFR4, PDGFRA, and VEGFR2 was analyzed by docking modeling. The results showed that 1u compound binds to proteins in a more appropriate area (except FGFR4) with acceptable energy. The results of docking for VEGFR2 binding showed that 1u binds to the active site and binding site of receptor, and it was in the interaction with ten residues in the sites. Although the binding site of 1u molecule in the FGFR4 was not suitable, the binding free energy was excellent (- 9.22 kcal mol-1), which was less than those two anticancer drugs of gefitinib and regorafenib. Furthermore, the values of binding free energy were - 8.69, - 9.64, and - 9.19 kcal mol-1 for EGFR, PDGFRA, and VEGFR2, respectively. Therefore, this study introduces 1u as an anticancer agent that can inhibit the tyrosine kinase receptors.
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11
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QSAR study of human epidermal growth factor receptor (EGFR) inhibitors: conformation-independent models. Med Chem Res 2019. [DOI: 10.1007/s00044-019-02437-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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12
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Milik SN, Lasheen DS, Serya RA, Abouzid KA. How to train your inhibitor: Design strategies to overcome resistance to Epidermal Growth Factor Receptor inhibitors. Eur J Med Chem 2017; 142:131-151. [DOI: 10.1016/j.ejmech.2017.07.023] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/11/2017] [Accepted: 07/14/2017] [Indexed: 01/05/2023]
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13
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Duchowicz PR, Fioressi SE, Castro E, Wróbel K, Ibezim NE, Bacelo DE. Conformation-Independent QSAR Study on Human Epidermal Growth Factor Receptor-2 (HER2) Inhibitors. ChemistrySelect 2017. [DOI: 10.1002/slct.201700436] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Pablo R. Duchowicz
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas INIFTA (CCT La Plata-CONICET, UNLP); Diag. 113 y 64, Sucursal 4, C.C. 16 1900 La Plata Argentina
| | - Silvina E. Fioressi
- Departamento de Química; Facultad de Ciencias Exactas y Naturales; Universidad de Belgrano, Villanueva 1324 CP 1426; Buenos Aires Argentina
| | - Eduardo Castro
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas INIFTA (CCT La Plata-CONICET, UNLP); Diag. 113 y 64, Sucursal 4, C.C. 16 1900 La Plata Argentina
| | | | - Nnenna E. Ibezim
- Department of Computer Education; University of Nigeria; Nsukka Nigeria
| | - Daniel E. Bacelo
- Departamento de Química; Facultad de Ciencias Exactas y Naturales; Universidad de Belgrano, Villanueva 1324 CP 1426; Buenos Aires Argentina
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14
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Qu D, Yan A, Zhang JS. SAR and QSAR study on the bioactivities of human epidermal growth factor receptor-2 (HER2) inhibitors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2017; 28:111-132. [PMID: 28235391 DOI: 10.1080/1062936x.2017.1284898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 01/16/2017] [Indexed: 06/06/2023]
Abstract
In this paper, structure-activity relationship (SAR, classification) and quantitative structure-activity relationship (QSAR) models have been established to predict the bioactivity of human epidermal growth factor receptor-2 (HER2) inhibitors. For the SAR study, we established six SAR (or classification) models to distinguish highly and weakly active HER2 inhibitors. The dataset contained 868 HER2 inhibitors, which was split into a training set including 580 inhibitors and a test set including 288 inhibitors by a Kohonen's self-organizing map (SOM), or a random method. The SAR models were performed using support vector machine (SVM), random forest (RF) and multilayer perceptron (MLP) methods. Among the six models, SVM models obtained superior results compared with other models. The prediction accuracy of the best model (model 1A) was 90.27% and the Matthews correlation coefficient (MCC) was 0.80 on the test set. For the QSAR study, we chose 286 HER2 inhibitors to establish six quantitative prediction models using MLR, SVM and MLP methods. The correlation coefficient (r) of the best model (model 4B) was 0.92 on the test set. The descriptors analysis showed that HAccN, lone pair electronegativity and π electronegativity were closely related to the bioactivity of HER2 inhibitors.
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Affiliation(s)
- D Qu
- a State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology , Beijing , P.R. China
| | - A Yan
- a State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology , Beijing , P.R. China
| | - J S Zhang
- b The High School Affiliated to Renmin University of China , Beijing , P.R. China
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15
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Mahajan P, Suri N, Mehra R, Gupta M, Kumar A, Singh SK, Nargotra A. Discovery of novel small molecule EGFR inhibitory leads by structure and ligand-based virtual screening. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1728-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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16
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17
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Allen WJ, Balius TE, Mukherjee S, Brozell SR, Moustakas DT, Lang PT, Case DA, Kuntz ID, Rizzo RC. DOCK 6: Impact of new features and current docking performance. J Comput Chem 2015; 36:1132-56. [PMID: 25914306 DOI: 10.1002/jcc.23905] [Citation(s) in RCA: 449] [Impact Index Per Article: 49.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 03/01/2015] [Accepted: 03/07/2015] [Indexed: 12/11/2022]
Abstract
This manuscript presents the latest algorithmic and methodological developments to the structure-based design program DOCK 6.7 focused on an updated internal energy function, new anchor selection control, enhanced minimization options, a footprint similarity scoring function, a symmetry-corrected root-mean-square deviation algorithm, a database filter, and docking forensic tools. An important strategy during development involved use of three orthogonal metrics for assessment and validation: pose reproduction over a large database of 1043 protein-ligand complexes (SB2012 test set), cross-docking to 24 drug-target protein families, and database enrichment using large active and decoy datasets (Directory of Useful Decoys [DUD]-E test set) for five important proteins including HIV protease and IGF-1R. Relative to earlier versions, a key outcome of the work is a significant increase in pose reproduction success in going from DOCK 4.0.2 (51.4%) → 5.4 (65.2%) → 6.7 (73.3%) as a result of significant decreases in failure arising from both sampling 24.1% → 13.6% → 9.1% and scoring 24.4% → 21.1% → 17.5%. Companion cross-docking and enrichment studies with the new version highlight other strengths and remaining areas for improvement, especially for systems containing metal ions. The source code for DOCK 6.7 is available for download and free for academic users at http://dock.compbio.ucsf.edu/.
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Affiliation(s)
- William J Allen
- Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, New York, 11794
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18
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Li Y, Li X, Dong Z. Statistical analysis of EGFR structures' performance in virtual screening. J Comput Aided Mol Des 2015; 29:1045-55. [PMID: 26476847 DOI: 10.1007/s10822-015-9877-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 10/14/2015] [Indexed: 12/11/2022]
Abstract
In this work the ability of EGFR structures to distinguish true inhibitors from decoys in docking and MM-PBSA is assessed by statistical procedures. The docking performance depends critically on the receptor conformation and bound state. The enrichment of known inhibitors is well correlated with the difference between EGFR structures rather than the bound-ligand property. The optimal structures for virtual screening can be selected based purely on the complex information. And the mixed combination of distinct EGFR conformations is recommended for ensemble docking. In MM-PBSA, a variety of EGFR structures have identically good performance in the scoring and ranking of known inhibitors, indicating that the choice of the receptor structure has little effect on the screening.
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Affiliation(s)
- Yan Li
- The Hormel Institute, University of Minnesota, Austin, MN, 55912, USA.
| | - Xiang Li
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Zigang Dong
- The Hormel Institute, University of Minnesota, Austin, MN, 55912, USA.
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Discovery of a series of novel phenylpiperazine derivatives as EGFR TK inhibitors. Sci Rep 2015; 5:13934. [PMID: 26349898 PMCID: PMC4563558 DOI: 10.1038/srep13934] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 08/07/2015] [Indexed: 11/08/2022] Open
Abstract
Human epidermal growth factor receptor (EGFR) is an important drug target that plays a fundamental role in signal transduction pathways in oncology. We report herein the discovery of a novel class of phenylpiperazine derivatives with improved potency toward EGFR. The biological activity of compound 3p as inhibitor of EGFR was further investigated both in vitro and in vivo. Notably, compound 3p exhibited an IC50 in the nanomolar range in A549 cell cultures and induced a cessation of tumor growth with no toxicity, as determined by loss of body weight and death of treated mice. Compoutational docking studies also showed that compound 3p has interaction with EGFR key residues in the active site.
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20
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Liu W, Ning JF, Meng QW, Hu J, Zhao YB, Liu C, Cai L. Navigating into the binding pockets of the HER family protein kinases: discovery of novel EGFR inhibitor as antitumor agent. DRUG DESIGN DEVELOPMENT AND THERAPY 2015; 9:3837-51. [PMID: 26229444 PMCID: PMC4517520 DOI: 10.2147/dddt.s85357] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The epidermal growth factor receptor (EGFR) family has been validated as a successful antitumor drug target for decades. Known EGFR inhibitors were exposed to distinct drug resistance against the various EGFR mutants within non-small-cell lung cancer (NSCLC), particularly the T790M mutation. Although so far a number of studies have been reported on the development of third-generation EGFR inhibitors for overcoming the resistance issue, the design procedure largely depends on the intuition of medicinal chemists. Here we retrospectively make a detailed analysis of the 42 EGFR family protein crystal complexes deposited in the Protein Data Bank (PDB). Based on the analysis of inhibitor binding modes in the kinase catalytic cleft, we identified a potent EGFR inhibitor (compound A-10) against drug-resistant EGFR through fragment-based drug design. This compound showed at least 30-fold more potency against EGFR T790M than the two control molecules erlotinib and gefitinib in vitro. Moreover, it could exhibit potent HER2 inhibitory activities as well as tumor growth inhibitory activity. Molecular docking studies revealed a structural basis for the increased potency and mutant selectivity of this compound. Compound A-10 may be selected as a promising candidate in further preclinical studies. In addition, our findings could provide a powerful strategy to identify novel selective kinase inhibitors on the basis of detailed kinase–ligand interaction space in the PDB.
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Affiliation(s)
- Wei Liu
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, People's Republic of China
| | - Jin-Feng Ning
- The Thoracic Surgery Department, Harbin Medical University Cancer Hospital, Harbin, People's Republic of China
| | - Qing-Wei Meng
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, People's Republic of China
| | - Jing Hu
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, People's Republic of China
| | - Yan-Bin Zhao
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, People's Republic of China
| | - Chao Liu
- General Surgery Department, Mudanjiang Guanliju Central Hospital, Mishan, Heilongjiang Province, People's Republic of China
| | - Li Cai
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, People's Republic of China
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Piegholdt S, Pallauf K, Esatbeyoglu T, Speck N, Reiss K, Ruddigkeit L, Stocker A, Huebbe P, Rimbach G. Biochanin A and prunetin improve epithelial barrier function in intestinal CaCo-2 cells via downregulation of ERK, NF-κB, and tyrosine phosphorylation. Free Radic Biol Med 2014; 70:255-64. [PMID: 24631489 DOI: 10.1016/j.freeradbiomed.2014.02.025] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2013] [Revised: 02/14/2014] [Accepted: 02/25/2014] [Indexed: 01/10/2023]
Abstract
The single-layered gut epithelium represents the primary line of defense against environmental stressors; thereby monolayer integrity and tightness are essentially required to maintain gut health and function. To date only a few plant-derived phytochemicals have been described as affecting intestinal barrier function. We investigated the impact of 28 secondary plant compounds on the barrier function of intestinal epithelial CaCo-2/TC-7 cells via transepithelial electrical resistance (TEER) measurements. Apart from genistein, the compounds that had the biggest effect in the TEER measurements were biochanin A and prunetin. These isoflavones improved barrier tightness by 36 and 60%, respectively, compared to the untreated control. Furthermore, both isoflavones significantly attenuated TNFα-dependent barrier disruption, thereby maintaining a high barrier resistance comparable to nonstressed cells. In docking analyses exploring the putative interaction with the tyrosine kinase EGFR, these novel modulators of barrier tightness showed very similar values compared to the known tyrosine kinase inhibitor genistein. Both biochanin A and prunetin were also identified as potent reducers of NF-κB and ERK activation, zonula occludens 1 tyrosine phosphorylation, and metalloproteinase-mediated shedding activity, which may account for the barrier-improving ability of these isoflavones.
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Affiliation(s)
- Stefanie Piegholdt
- Institute of Human Nutrition and Food Science, Christian-Albrechts-University Kiel, D-24118 Kiel, Germany
| | - Kathrin Pallauf
- Institute of Human Nutrition and Food Science, Christian-Albrechts-University Kiel, D-24118 Kiel, Germany
| | - Tuba Esatbeyoglu
- Institute of Human Nutrition and Food Science, Christian-Albrechts-University Kiel, D-24118 Kiel, Germany
| | - Nancy Speck
- Department of Dermatology and Allergology, University Hospital Schleswig-Holstein, Campus Kiel, D-24105 Kiel, Germany
| | - Karina Reiss
- Department of Dermatology and Allergology, University Hospital Schleswig-Holstein, Campus Kiel, D-24105 Kiel, Germany
| | - Lars Ruddigkeit
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
| | - Achim Stocker
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
| | - Patricia Huebbe
- Institute of Human Nutrition and Food Science, Christian-Albrechts-University Kiel, D-24118 Kiel, Germany
| | - Gerald Rimbach
- Institute of Human Nutrition and Food Science, Christian-Albrechts-University Kiel, D-24118 Kiel, Germany.
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22
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Tang C, Liang Y, Bai S, He H, Chen Y, Yang G, Fu L. Synthesis and antiproliferative evaluation of novel tetrahydrobenzo[4′,5′]thieno[3′,2′:5,6]pyrido[4,3-d]pyrimidine derivatives. RSC Adv 2014. [DOI: 10.1039/c4ra03535f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A series of tetrahydrobenzo[4′,5′]thienophene[3′,2′:5,6]pyrido[4,3-d]pyrimidine-4-(3H)-one derivatives were synthesized and evaluated for their antiproliferative activities.
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Affiliation(s)
- Chu Tang
- Laboratory for Natural Product Chemistry
- College of Pharmacy
- South Central University for Nationalities
- Wuhan 430074, P. R. China
| | - Yongju Liang
- State Key Laboratory of Oncology in South China
- Cancer Center, Sun Yat-sen University
- Guangzhou 510060, P. R. China
| | - Shun Bai
- College of Chemistry and Material Sciences
- South Central University for Nationalities
- Wuhan 430074, P. R. China
| | - Hongwu He
- College of Chemistry
- Central China Normal University
- Wuhan 430079, P. R. China
| | - Yu Chen
- College of Chemistry and Material Sciences
- South Central University for Nationalities
- Wuhan 430074, P. R. China
| | - Guangzhong Yang
- Laboratory for Natural Product Chemistry
- College of Pharmacy
- South Central University for Nationalities
- Wuhan 430074, P. R. China
| | - Liwu Fu
- State Key Laboratory of Oncology in South China
- Cancer Center, Sun Yat-sen University
- Guangzhou 510060, P. R. China
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Naulin PA, Alveal NA, Barrera NP. Toward atomic force microscopy and mass spectrometry to visualize and identify lipid rafts in plasmodesmata. FRONTIERS IN PLANT SCIENCE 2014; 5:234. [PMID: 24910637 PMCID: PMC4038920 DOI: 10.3389/fpls.2014.00234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Accepted: 05/11/2014] [Indexed: 05/08/2023]
Abstract
Plant cell-to-cell communication is mediated by nanopores called plasmodesmata (PDs) which are complex structures comprising plasma membrane (PM), highly packed endoplasmic reticulum and numerous membrane proteins. Although recent advances on proteomics have led to insights into mechanisms of transport, there is still an inadequate characterization of the lipidic composition of the PM where membrane proteins are inserted. It has been postulated that PDs could be formed by lipid rafts, however no structural evidence has shown to visualize and analyse their lipid components. In this perspective article, we discuss proposed experiments to characterize lipid rafts and proteins in the PDs. By using atomic force microscopy (AFM) and mass spectrometry (MS) of purified PD vesicles it is possible to determine the presence of lipid rafts, specific bound proteins and the lipidomic profile of the PD under physiological conditions and after changing transport permeability. In addition, MS can determine the stoichiometry of intact membrane proteins inserted in lipid rafts. This will give novel insights into the role of membrane proteins and lipid rafts on the PD structure.
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Affiliation(s)
| | | | - Nelson P. Barrera
- *Correspondence: Nelson P. Barrera, Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Alameda 340, Santiago 8331150, Chile e-mail:
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24
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Chang YS, Wang BC, Yang LL. Pharmacophore Modeling of Tyrosine Kinase Inhibitors: 4-Anilinoquinazoline Derivatives. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.201000127] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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25
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Elassar AZA, Alsughayer A, Sagheer FA. Convenient Synthesis and Antibacterial Activity of Tricyclic Azine Derivatives. JOURNAL OF CHEMICAL RESEARCH 2013. [DOI: 10.3184/174751913x13640546938841] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
1,4-Phenylenediamine reacted readily with 2 mol of ethyl acetoacetate to give diethyl ( 2Z,2′Z)-3,3′-[(1,4-phenylene)-bisimino]dibut-2-enoate, which reacted with dimethylformamide dimethylacetal, activated methylene nitriles, ylidenemalononitriles and phenyl and benzoyl isothiocyanate to give, respectively, a 4,7-phenanthroline-2,9-dicarb-oxylate-1,10-diol, and tricyclic bispyridine and bispyrimidine derivatives. Two compounds showed strong antibacterial activity against several microorganisms, while six others showed high to moderate activity.
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Affiliation(s)
- Abdel-Zaher A. Elassar
- Chemistry Department, Faculty of Science, Kuwait University, PO Box 5969-Safat-13060, Kuwait
- Chemistry Department, Faculty of Science, Helwan University, Helwan, Cairo, Egypt
| | - Abdulhakeem Alsughayer
- Pharmaceutical Science Department, College of Health Science, The Public Authority for Applied Education and Training, Kuwait
| | - Fakhreia Al Sagheer
- Chemistry Department, Faculty of Science, Kuwait University, PO Box 5969-Safat-13060, Kuwait
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26
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Li S, Sun X, Zhao H, Tang Y, Lan M. Discovery of novel EGFR tyrosine kinase inhibitors by structure-based virtual screening. Bioorg Med Chem Lett 2012; 22:4004-9. [DOI: 10.1016/j.bmcl.2012.04.092] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 04/07/2012] [Accepted: 04/19/2012] [Indexed: 01/08/2023]
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27
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Long A, Zhao H, Huang X. Structural basis for the interaction between casein kinase 1 delta and a potent and selective inhibitor. J Med Chem 2012; 55:956-60. [PMID: 22168824 DOI: 10.1021/jm201387s] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Casein kinase 1 delta (CK1δ) and its closest homologue CK1ε are key regulators of diverse cellular growth and survival processes such as Wnt signaling, DNA repair, and circadian rhythms. We report three crystal structures of the kinase domain of human CK1δ, one apo and two complexed with a potent and selective CK1δ/ε inhibitor PF670462 in two different crystal forms. These structures provide a molecular basis for the strong and specific inhibitor interactions and suggest clues for further development of CK1δ/ε inhibitors.
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Affiliation(s)
- Alexander Long
- Department of Molecular Structure, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States
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28
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Li S, Guo C, Zhao H, Tang Y, Lan M. Synthesis and biological evaluation of 4-[3-chloro-4-(3-fluorobenzyloxy)anilino]-6-(3-substituted-phenoxy)pyrimidines as dual EGFR/ErbB-2 kinase inhibitors. Bioorg Med Chem 2012; 20:877-85. [DOI: 10.1016/j.bmc.2011.11.056] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2011] [Revised: 11/25/2011] [Accepted: 11/25/2011] [Indexed: 10/14/2022]
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29
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Yang SC, Chang SS, Chen CYC. Identifying HER2 inhibitors from natural products database. PLoS One 2011; 6:e28793. [PMID: 22174899 PMCID: PMC3236219 DOI: 10.1371/journal.pone.0028793] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 11/15/2011] [Indexed: 01/09/2023] Open
Abstract
The relationship between abnormal HER2 expression and cancer is important in cancer therapeutics. Formation and spread of cancer cells may be restricted by inhibiting HER2. We conducted ligand-based and structure-based studies to assess the potency of natural compounds as potential HER2 inhibitors. Multiple linear regression (MLR) and support vector machine (SVM) models were constructed to predict biological activities of natural compounds, and molecular dynamics (MD) was used to assess their stability with HER2 under a dynamic environment. Predicted bioactivities of the natural compounds ranged from 6.014–9.077 using MLR (r2 = 0.7954) and 5.122–6.950 using SVM (r2 = 0.8620). Both models were in agreement and suggest bioactivity based on candidate structure. Conformation changes caused by MD favored the formation of stabilizing H-bonds. All candidates had higher stability than Lapinatib, which may be due to the number and spatial distribution of additional H-bonds and hydrophobic interactions. Amino acids Lys724 and Lys736 are critical for binding in HER2, and Thr798, Cys805, and Asp808 are also important for increased stability. Candidates may block the entrance to the ATP binding site located within the inner regions and prevent downstream activation of HER2. Our multidirectional approach indicates that the natural compounds have good ligand efficacy in addition to stable binding affinities to HER2, and should be potent candidates of HER2 inhibitors. With regard to drug design, designing HER2 inhibitors with carboxyl or carbonyl groups available for H-bond formation with Lys724 and Lys736, and benzene groups for hydrophobic contact with Cys805 may improve protein-ligand stability.
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Affiliation(s)
- Shun-Chieh Yang
- Laboratory of Computational and Systems Biology, China Medical University, Taichung, Taiwan
| | - Su-Sen Chang
- Laboratory of Computational and Systems Biology, China Medical University, Taichung, Taiwan
| | - Calvin Yu-Chian Chen
- Laboratory of Computational and Systems Biology, China Medical University, Taichung, Taiwan
- Department of Bioinformatics, Asia University, Taichung, Taiwan
- China Medical University Beigang Hospital, Yunlin, Taiwan
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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30
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Sawatdichaikul O, Hannongbua S, Sangma C, Wolschann P, Choowongkomon K. In silico screening of epidermal growth factor receptor (EGFR) in the tyrosine kinase domain through a medicinal plant compound database. J Mol Model 2011; 18:1241-54. [PMID: 21713415 DOI: 10.1007/s00894-011-1135-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Accepted: 05/23/2011] [Indexed: 01/26/2023]
Abstract
The unregulated epidermal growth factor receptor tyrosine kinase (ErbB1-TK or EGFR-TK) protein is involved in the proliferation of more than 50% of all cancer types. The reduction of EGFR-TK activity by small or medium-sized molecules has been proven to be an effective treatment for cancer. There is a widespread belief that Chinese medicinal herbs are active against several diseases, including various types of cancer. In this study, 29,960 compounds from the Chemiebase medicinal compound database were virtually screened against the EGFR-TK using AutoDock4.0, GOLD and GLIDE (XP). The results revealed eight potential hits: CAS nos. 104096-45-9, 112649-21-5, 113866-89-0, 142608-98-8, 142608-99-9, 144761-33-1, 155233-17-3 and 80510-05-0. These compounds have been reported to show anticancer activities in the literature. With the help of SiMMap and MOE interaction analysis, the protein-ligand interaction patterns between the functional groups of these compounds and the binding pocket residues were analyzed. Hydrogen bonding and hydrophobic forces are the main components of the interactions of these hits, similar to those observed for the known inhibitors erlotinib, gefitinib and AEE. The physicochemical filter indicates that compounds CAS nos. 104096-45-9 and 144761-33-1 are likely to be potential leads in the drug discovery process.
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Chancellor DR, Davies KE, De Moor O, Dorgan CR, Johnson PD, Lambert AG, Lawrence D, Lecci C, Maillol C, Middleton PJ, Nugent G, Poignant SD, Potter AC, Price PD, Pye RJ, Storer R, Tinsley JM, van Well R, Vickers R, Vile J, Wilkes FJ, Wilson FX, Wren SP, Wynne GM. Discovery of 2-arylbenzoxazoles as upregulators of utrophin production for the treatment of Duchenne muscular dystrophy. J Med Chem 2011; 54:3241-50. [PMID: 21456623 DOI: 10.1021/jm200135z] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A series of novel 2-arylbenzoxazoles that upregulate the production of utrophin in murine H2K cells, as assessed using a luciferase reporter linked assay, have been identified. This compound class appears to hold considerable promise as a potential treatment for Duchenne muscular dystrophy. Following the delineation of structure-activity relationships in the series, a number of potent upregulators were identified, and preliminary ADME evaluation is described. These studies have resulted in the identification of 1, a compound that has been progressed to clinical trials.
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Affiliation(s)
- Daniel R Chancellor
- Summit plc , 91 Milton Park, Abingdon, Oxfordshire, OX14 4RY, United Kingdom
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32
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Suzuki N, Shiota T, Watanabe F, Haga N, Murashi T, Ohara T, Matsuo K, Oomori N, Yari H, Dohi K, Inoue M, Iguchi M, Sentou J, Wada T. Synthesis and evaluation of novel pyrimidine-based dual EGFR/Her-2 inhibitors. Bioorg Med Chem Lett 2011; 21:1601-6. [DOI: 10.1016/j.bmcl.2011.01.119] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 01/25/2011] [Accepted: 01/26/2011] [Indexed: 11/26/2022]
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33
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Huang S, Li R, LaMontagne KR, Greenberger LM, Connolly PJ. 4-Aminopyrimidine-5-carbaldehyde oximes as potent VEGFR-2 inhibitors. Part II. Bioorg Med Chem Lett 2011; 21:1815-8. [DOI: 10.1016/j.bmcl.2011.01.053] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 01/11/2011] [Accepted: 01/13/2011] [Indexed: 01/08/2023]
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34
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Mirza A, Mustafa M, Talevich E, Kannan N. Co-conserved features associated with cis regulation of ErbB tyrosine kinases. PLoS One 2010; 5:e14310. [PMID: 21179209 PMCID: PMC3001462 DOI: 10.1371/journal.pone.0014310] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Accepted: 11/08/2010] [Indexed: 11/18/2022] Open
Abstract
Background The epidermal growth factor receptor kinases, or ErbB kinases, belong to a large sub-group of receptor tyrosine kinases (RTKs), which share a conserved catalytic core. The catalytic core of ErbB kinases have functionally diverged from other RTKs in that they are activated by a unique allosteric mechanism that involves specific interactions between the kinase core and the flanking Juxtamembrane (JM) and COOH-terminal tail (C-terminal tail). Although extensive studies on ErbB and related tyrosine kinases have provided important insights into the structural basis for ErbB kinase functional divergence, the sequence features that contribute to the unique regulation of ErbB kinases have not been systematically explored. Methodology/Principal Findings In this study, we use a Bayesian approach to identify the selective sequence constraints that most distinguish ErbB kinases from other receptor tyrosine kinases. We find that strong ErbB kinase-specific constraints are imposed on residues that tether the JM and C-terminal tail to key functional regions of the kinase core. A conserved RIxKExE motif in the JM-kinase linker region and a glutamine in the inter-lobe linker are identified as two of the most distinguishing features of the ErbB family. While the RIxKExE motif tethers the C-terminal tail to the N-lobe of the kinase domain, the glutamine tethers the C-terminal tail to hinge regions critical for inter-lobe movement. Comparison of the active and inactive crystal structures of ErbB kinases indicates that the identified residues are conformationally malleable and can potentially contribute to the cis regulation of the kinase core by the JM and C-terminal tail. ErbB3, and EGFR orthologs in sponges and parasitic worms, diverge from some of the canonical ErbB features, providing insights into sub-family and lineage-specific functional specialization. Conclusion/Significance Our analysis pinpoints key residues for mutational analysis, and provides new clues to cancer mutations that alter the canonical modes of ErbB kinase regulation.
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Affiliation(s)
- Amar Mirza
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
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Abele E, Abele R, Golomba L, Višņevska J, Beresneva T, Rubina K, Lukevics E. Oximes of six-membered heterocyclic compounds with two and three heteroatoms. II.* Reactions and biological activity (review). Chem Heterocycl Compd (N Y) 2010. [DOI: 10.1007/s10593-010-0602-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kwon SJ, Kim MI, Ku B, Coulombel L, Kim JH, Shawky JH, Linhardt RJ, Dordick JS. Unnatural polyketide analogues selectively target the HER signaling pathway in human breast cancer cells. Chembiochem 2010; 11:573-80. [PMID: 20058253 DOI: 10.1002/cbic.200900674] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Receptor tyrosine kinases are critical targets for the regulation of cell survival. Cancer patients with abnormal receptor tyrosine kinases (RTK) tend to have more aggressive disease with poor clinical outcomes. As a result, human epidermal growth factor receptor kinases, such as EGFR (HER1), HER2, and HER3, represent important therapeutic targets. Several plant polyphenols including the type III polyketide synthase products (genistein, curcumin, resveratrol, and epigallocatechin-3-galate) possess chemopreventive activity, primarily as a result of RTK inhibition. However, only a small fraction of the polyphenolic structural universe has been evaluated. Along these lines, we have developed an in vitro route to the synthesis and subsequent screening of unnatural polyketide analogues with N-acetylcysteamine (SNAc) starter substrates and malonyl-coenzyme A (CoA) and methylmalonyl-CoA as extender substrates. The resulting polyketide analogues possessed a similar structural polyketide backbone (aromatic-2-pyrone) with variable side chains. Screening chalcone synthase (CHS) reaction products against BT-474 cells resulted in identification of several trifluoromethylcinnamoyl-based polyketides that showed strong suppression of the HER2-associated PI3K/AKT signaling pathway, yet did not inhibit the growth of nontransformed MCF-10A breast cells (IC(50)>100 microM). Specifically, 4-trifluoromethylcinnamoyl pyrone (compound 2 e) was highly potent (IC(50)<200 nM) among the test compounds toward proliferation of several breast cancer cell lines. This breadth of activity likely stems from the ability of compound 2 e to inhibit the phosphorylation of HER1, HER2, and HER3. Therefore, these polyketide analogues might prove to be useful drug candidates for potential breast cancer therapy.
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Affiliation(s)
- Seok Joon Kwon
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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Morphy R. Selectively nonselective kinase inhibition: striking the right balance. J Med Chem 2010; 53:1413-37. [PMID: 20166671 DOI: 10.1021/jm901132v] [Citation(s) in RCA: 206] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Richard Morphy
- Medicinal Chemistry Department, Schering-Plough, Newhouse, Lanarkshire, ML1 5SH, UK.
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Kolpak J, Connolly PJ, Lobanov VS, Agrafiotis DK. Enhanced SAR Maps: Expanding the Data Rendering Capabilities of a Popular Medicinal Chemistry Tool. J Chem Inf Model 2009; 49:2221-30. [DOI: 10.1021/ci900264n] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jeremy Kolpak
- Johnson & Johnson Pharmaceutical Research & Development, L.L.C., 665 Stockton Drive, Exton, Pennsylvania 19341
| | - Peter J. Connolly
- Johnson & Johnson Pharmaceutical Research & Development, L.L.C., 665 Stockton Drive, Exton, Pennsylvania 19341
| | - Victor S. Lobanov
- Johnson & Johnson Pharmaceutical Research & Development, L.L.C., 665 Stockton Drive, Exton, Pennsylvania 19341
| | - Dimitris K. Agrafiotis
- Johnson & Johnson Pharmaceutical Research & Development, L.L.C., 665 Stockton Drive, Exton, Pennsylvania 19341
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Jura N, Endres NF, Engel K, Deindl S, Das R, Lamers MH, Wemmer DE, Zhang X, Kuriyan J. Mechanism for activation of the EGF receptor catalytic domain by the juxtamembrane segment. Cell 2009; 137:1293-307. [PMID: 19563760 DOI: 10.1016/j.cell.2009.04.025] [Citation(s) in RCA: 451] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2008] [Revised: 03/09/2009] [Accepted: 04/02/2009] [Indexed: 11/30/2022]
Abstract
Signaling by the epidermal growth factor receptor requires an allosteric interaction between the kinase domains of two receptors, whereby one activates the other. We show that the intracellular juxtamembrane segment of the receptor, known to potentiate kinase activity, is able to dimerize the kinase domains. The C-terminal half of the juxtamembrane segment latches the activated kinase domain to the activator, and the N-terminal half of this segment further potentiates dimerization, most likely by forming an antiparallel helical dimer that engages the transmembrane helices of the activated receptor. Our data are consistent with a mechanism in which the extracellular domains block the intrinsic ability of the transmembrane and cytoplasmic domains to dimerize and activate, with ligand binding releasing this block. The formation of the activating juxtamembrane latch is prevented by the C-terminal tails in a structure of an inactive kinase domain dimer, suggesting how alternative dimers can prevent ligand-independent activation.
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Affiliation(s)
- Natalia Jura
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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Hughes TV, Xu G, Wetter SK, Connolly PJ, Emanuel SL, Karnachi P, Pollack SR, Pandey N, Adams M, Moreno-Mazza S, Middleton SA, Greenberger LM. A novel 5-[1,3,4-oxadiazol-2-yl]-N-aryl-4,6-pyrimidine diamine having dual EGFR/HER2 kinase activity: Design, synthesis, and biological activity. Bioorg Med Chem Lett 2008; 18:4896-9. [DOI: 10.1016/j.bmcl.2008.07.057] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2008] [Revised: 07/10/2008] [Accepted: 07/14/2008] [Indexed: 11/28/2022]
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4-Amino-6-arylamino-pyrimidine-5-carbaldehyde hydrazones as potent ErbB-2/EGFR dual kinase inhibitors. Bioorg Med Chem Lett 2008; 18:4615-9. [PMID: 18653333 DOI: 10.1016/j.bmcl.2008.07.020] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2008] [Revised: 07/07/2008] [Accepted: 07/08/2008] [Indexed: 11/20/2022]
Abstract
Members of a novel class of 4-amino-6-arylamino-pyrimidine-5-carbaldehyde hydrazones were identified as potent dual ErbB-2/EGFR kinase inhibitors using concept-guided design approach. These compounds inhibited the growth of ErbB-2 over-expressing human tumor cell lines (BT474, N87, and SK-BR-3) in vitro. Compound 15 emerged as a key lead and showed significant ability to inhibit growth factor-induced receptor phosphorylation in SK-BR-3 cells (IC(50)=54 nM) and cellular proliferation in vitro (IC(50)=14, 58, and 58 nM for BT474, N87, and SK-BR-3 respectively). The X-ray co-crystal structure of EGFR with a close analog (17) was determined and validated our design rationale.
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