An investigation of binding interactions of tumor-targeted peptide conjugated polyphenols with the kinase domain of ephrin B4 and B2 receptors
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I. Banerjee | Rachel E. Daso | Saige M. Mitchell | R. M. Heise | Dominic J. Lambo | Molly E. Murray | Molly E Murray
[1] Aiping Lu,et al. ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties , 2021, Nucleic Acids Res..
[2] Mélaine A. Kuenemann,et al. New machine learning and physics-based scoring functions for drug discovery , 2021, Scientific Reports.
[3] I. Provazník,et al. In silico screening and molecular dynamics of phytochemicals from Indian cuisine against SARS-CoV-2 MPro , 2020, Journal of biomolecular structure & dynamics.
[4] Neelam Sharma,et al. AntiCP 2.0: an updated model for predicting anticancer peptides. , 2020, Briefings in bioinformatics.
[5] B. Aderibigbe,et al. Cinnamic Acid Derivatives and Their Biological Efficacy , 2020, International journal of molecular sciences.
[6] R. Gomaa,et al. Quinazoline Based HSP90 Inhibitors: Synthesis, Modeling Study and ADME Calculations Towards Breast Cancer Targeting. , 2020, Bioorganic & medicinal chemistry letters.
[7] V. Shukla,et al. An ayurvedic perspective along with in silico study of the drugs for the management of SARS-CoV-2 , 2020, Journal of Ayurveda and Integrative Medicine.
[8] Keunwan Park,et al. Evolutionary chemical binding similarity approach integrated with 3D-QSAR method for effective virtual screening , 2020, BMC Bioinformatics.
[9] Yan Li,et al. Therapeutic effects of ephrin B receptor 2 inhibitors screened by molecular docking on cutaneous squamous cell carcinoma , 2020, The Journal of dermatological treatment.
[10] Laurent Emmanuel Dardenne,et al. Highly Flexible Ligand Docking: Benchmarking of the DockThor Program on the LEADS-PEP Protein-Peptide Data Set , 2020, J. Chem. Inf. Model..
[11] W. Catalona,et al. EPHB4 inhibition activates ER stress to promote immunogenic cell death of prostate cancer cells , 2019, Cell Death & Disease.
[12] Pedro H M Torres,et al. Key Topics in Molecular Docking for Drug Design , 2019, International journal of molecular sciences.
[13] P. W. Janes,et al. Eph receptor signalling: from catalytic to non-catalytic functions , 2019, Oncogene.
[14] Gergana Gocheva,et al. A Look at Receptor-Ligand Pairs for Active-Targeting Drug Delivery from Crystallographic and Molecular Dynamics Perspectives. , 2019, Molecular pharmaceutics.
[15] Zheng Gao,et al. Assessing the performance of three resveratrol in binding with SIRT1 by molecular dynamics simulation and MM/GBSA methods: the weakest binding of resveratrol 3 to SIRT1 triggers a possibility of dissociation from its binding site , 2019, Journal of Computer-Aided Molecular Design.
[16] Friedrich Rippmann,et al. Avoiding hERG-liability in drug design via synergetic combinations of different (Q)SAR methodologies and data sources: a case study in an industrial setting , 2019, Journal of Cheminformatics.
[17] Eric P. Winer,et al. Breast Cancer Treatment: A Review , 2019, JAMA.
[18] L. Alisaraie,et al. Drug metabolites and their effects on the development of adverse reactions: Revisiting Lipinski’s Rule of Five , 2018, International journal of pharmaceutics.
[19] B. Kuster,et al. NVP‐BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family , 2018, ChemMedChem.
[20] S. Joshi,et al. In silico binding affinity studies of N-9 substituted 6-(4-(4-propoxyphenyl)piperazin-1-yl)-9H-purine derivatives-Target for P70-S6K1 & PI3K-δ kinases , 2018 .
[21] Yanmin Zhang,et al. Targeting receptor tyrosine kinase EphB4 in cancer therapy. , 2017, Seminars in cancer biology.
[22] Olivier Michielin,et al. SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules , 2017, Scientific Reports.
[23] X. Zhang,et al. Ferulic acid exerts antitumor activity and inhibits metastasis in breast cancer cells by regulating epithelial to mesenchymal transition. , 2016, Oncology reports.
[24] Janez Konc,et al. Computational Drug Repositioning by Target Hopping: A Use Case in Chagas Disease. , 2016, Current pharmaceutical design.
[25] F. Jin,et al. Gallic acid induces apoptosis and enhances the anticancer effects of cisplatin in human small cell lung cancer H446 cell line via the ROS-dependent mitochondrial apoptotic pathway. , 2016, Oncology reports.
[26] Yacine Benguerba,et al. Dehydration of natural gas using choline chloride based deep eutectic solvents: COSMO-RS prediction , 2016 .
[27] S. Zahler,et al. Three stories on Eph kinase inhibitors: From in silico discovery to in vivo validation. , 2016, European journal of medicinal chemistry.
[28] B. Lesyng,et al. Cinnamic Acid Derivatives as Inhibitors of Oncogenic Protein Kinases--Structure, Mechanisms and Biomedical Effects. , 2016, Current medicinal chemistry.
[29] Y. Gilad,et al. Synthesis, biological studies and molecular dynamics of new anticancer RGD-based peptide conjugates for targeted drug delivery. , 2016, Bioorganic & medicinal chemistry.
[30] Jie Huang,et al. Erythropoietin Stimulates Tumor Growth via EphB4. , 2015, Cancer cell.
[31] Hwangseo Park,et al. Computational prediction of octanol-water partition coefficient based on the extended solvent-contact model. , 2015, Journal of molecular graphics & modelling.
[32] Mohammad Imran Siddiqi,et al. Identification of Novel Inhibitors of Mycobacterium tuberculosis PknG Using Pharmacophore Based Virtual Screening, Docking, Molecular Dynamics Simulation, and Their Biological Evaluation , 2015, J. Chem. Inf. Model..
[33] Xiaoxiong Zeng,et al. Polymer nanoparticles composed with gallic acid grafted chitosan and bioactive peptides combined antioxidant, anticancer activities and improved delivery property for labile polyphenols , 2015 .
[34] Botao Fa,et al. Pi-pi Stacking Mediated Cooperative Mechanism for Human Cytochrome P450 3A4 , 2015, Molecules.
[35] Yang Zhang,et al. I-TASSER server: new development for protein structure and function predictions , 2015, Nucleic Acids Res..
[36] Michael Schroeder,et al. PLIP: fully automated protein–ligand interaction profiler , 2015, Nucleic Acids Res..
[37] S. Genheden,et al. The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities , 2015, Expert opinion on drug discovery.
[38] Lakshmi Ptv,et al. ACPP: A Web Server for Prediction and Design of Anti-cancer Peptides , 2015, International Journal of Peptide Research and Therapeutics.
[39] T. Nakagawa,et al. Multitargeting strategy using lenvatinib and golvatinib: Maximizing anti-angiogenesis activity in a preclinical cancer model , 2015, Cancer science.
[40] Yang Zhang,et al. The I-TASSER Suite: protein structure and function prediction , 2014, Nature Methods.
[41] Helio J. C. Barbosa,et al. A dynamic niching genetic algorithm strategy for docking highly flexible ligands , 2014, Inf. Sci..
[42] J. Guzman,et al. Natural Cinnamic Acids, Synthetic Derivatives and Hybrids with Antimicrobial Activity , 2014, Molecules.
[43] Olivier Michielin,et al. iLOGP: A Simple, Robust, and Efficient Description of n-Octanol/Water Partition Coefficient for Drug Design Using the GB/SA Approach , 2014, J. Chem. Inf. Model..
[44] R. Nussinov,et al. Promiscuous and specific recognition among ephrins and Eph receptors. , 2014, Biochimica et biophysica acta.
[45] J. Brennecke,et al. Excess enthalpy of monoethanolamine + ionic liquid mixtures: how good are COSMO-RS predictions? , 2014, The journal of physical chemistry. B.
[46] T. Attwood,et al. Completing the structural family portrait of the human EphB tyrosine kinase domains , 2014, Protein science : a publication of the Protein Society.
[47] A. Andres,et al. Overexpression of EphB4 in the mammary epithelium shifts the differentiation pathway of progenitor cells and promotes branching activity and vascularization , 2014, Development, growth & differentiation.
[48] Stefano Mariani,et al. Surface plasmon resonance applications in clinical analysis , 2014, Analytical and Bioanalytical Chemistry.
[49] G. Batist,et al. Role of the EphB2 receptor in autophagy, apoptosis and invasion in human breast cancer cells. , 2014, Experimental cell research.
[50] M. Incerti,et al. Target Hopping as a Useful Tool for the Identification of Novel EphA2 Protein–Protein Antagonists , 2014, ChemMedChem.
[51] A. Misra,et al. Epidermal growth factor receptor targeting in cancer: a review of trends and strategies. , 2013, Biomaterials.
[52] A. Iafrate,et al. The EphB4 Receptor Tyrosine Kinase Promotes Lung Cancer Growth: A Potential Novel Therapeutic Target , 2013, PloS one.
[53] Sagar H. Barage,et al. Molecular Dynamics Simulation and Molecular Docking Studies of Angiotensin Converting Enzyme with Inhibitor Lisinopril and Amyloid Beta Peptide , 2013, The Protein Journal.
[54] C. Jeong,et al. Antiangiogenic Effects of P‐Coumaric Acid in Human Endothelial Cells , 2013, Phytotherapy research : PTR.
[55] Wei Zhu,et al. Bioavailability and pharmacokinetics of genistein: mechanistic studies on its ADME. , 2012, Anti-cancer agents in medicinal chemistry.
[56] Bianca Villavicencio,et al. Recent Progress of Molecular Docking Simulations Applied to Development of Drugs , 2012 .
[57] R. Noberini,et al. Inhibition of Eph receptor-ephrin ligand interaction by tea polyphenols. , 2012, Pharmacological research.
[58] Jianxing Song,et al. Protein dynamics at Eph receptor-ligand interfaces as revealed by crystallography, NMR and MD simulations , 2012, BMC biophysics.
[59] L. Flammini,et al. Polyphenol rich botanicals used as food supplements interfere with EphA2-ephrinA1 system. , 2011, Pharmacological Research.
[60] Huijun Sun,et al. Molecular modeling study of checkpoint kinase 1 inhibitors by multiple docking strategies and prime/MM–GBSA calculation , 2011, J. Comput. Chem..
[61] D. Cross,et al. Inhibitors of the tyrosine kinase EphB4. Part 4: Discovery and optimization of a benzylic alcohol series. , 2011, Bioorganic & medicinal chemistry letters.
[62] P. De,et al. Cinnamic acid derivatives as anticancer agents-a review. , 2011, Current medicinal chemistry.
[63] M. Incerti,et al. Lithocholic Acid Is an Eph-ephrin Ligand Interfering with Eph-kinase Activation , 2011, PloS one.
[64] S. Karthikeyan,et al. Inhibitory effect of caffeic acid on cancer cell proliferation by oxidative mechanism in human HT-1080 fibrosarcoma cell line , 2011, Molecular and Cellular Biochemistry.
[65] S. Mittal,et al. Emerging strategies for EphA2 receptor targeting for cancer therapeutics , 2011, Expert opinion on therapeutic targets.
[66] S. Borstnar,et al. Triple negative breast cancer – prognostic factors and survival , 2010, Radiology and oncology.
[67] Bert L. de Groot,et al. Ligand docking and binding site analysis with PyMOL and Autodock/Vina , 2010, J. Comput. Aided Mol. Des..
[68] Santhosh K. P. Kumar,et al. Novel EphB4 monoclonal antibodies modulate angiogenesis and inhibit tumor growth. , 2010, The American journal of pathology.
[69] R. Sharan,et al. I-TASSER: a unified platform for automated protein structure and function prediction , 2010, Nature Protocols.
[70] M. Breccia,et al. Nilotinib: a second-generation tyrosine kinase inhibitor for chronic myeloid leukemia. , 2010, Leukemia research.
[71] T. Nakagawa,et al. E7050: A dual c‐Met and VEGFR‐2 tyrosine kinase inhibitor promotes tumor regression and prolongs survival in mouse xenograft models , 2010, Cancer science.
[72] S. Goueli,et al. ADP-Glo: A Bioluminescent and homogeneous ADP monitoring assay for kinases. , 2009, Assay and drug development technologies.
[73] A. Caflisch,et al. Structure-based optimization of potent and selective inhibitors of the tyrosine kinase erythropoietin producing human hepatocellular carcinoma receptor B4 (EphB4). , 2009, Journal of medicinal chemistry.
[74] Bingding Huang,et al. MetaPocket: a meta approach to improve protein ligand binding site prediction. , 2009, Omics : a journal of integrative biology.
[75] Sirlester A. Parker,et al. Structural recognition of an optimized substrate for the ephrin family of receptor tyrosine kinases , 2009, The FEBS journal.
[76] Nathanael S Gray,et al. Discovery and structural analysis of Eph receptor tyrosine kinase inhibitors. , 2009, Bioorganic & medicinal chemistry letters.
[77] A. Olson,et al. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading , 2009, J. Comput. Chem..
[78] Xiangrong Song,et al. Preparation and characterization of folate conjugated N-trimethyl chitosan nanoparticles as protein carrier targeting folate receptor: in vitro studies , 2009, Journal of drug targeting.
[79] A. Caflisch,et al. Structure‐based tailoring of compound libraries for high‐throughput screening: Discovery of novel EphB4 kinase inhibitors , 2008, Proteins.
[80] T. Pawson,et al. Effects of dasatinib on EphA2 receptor tyrosine kinase activity and downstream signalling in pancreatic cancer , 2008, British Journal of Cancer.
[81] Jon Read,et al. Inhibitors of the tyrosine kinase EphB4. Part 1: Structure-based design and optimization of a series of 2,4-bis-anilinopyrimidines. , 2008, Bioorganic & medicinal chemistry letters.
[82] J. D. Stuart,et al. Design and effective synthesis of novel templates, 3,7-diphenyl-4-amino-thieno and furo-[3,2-c]pyridines as protein kinase inhibitors and in vitro evaluation targeting angiogenetic kinases. , 2007, Bioorganic & medicinal chemistry letters.
[83] M. Deavers,et al. The receptor tyrosine kinase EphB4 is overexpressed in ovarian cancer, provides survival signals and predicts poor outcome , 2007, British Journal of Cancer.
[84] A. Chakrabarty,et al. Cupredoxin-cancer interrelationship: azurin binding with EphB2, interference in EphB2 tyrosine phosphorylation, and inhibition of cancer growth. , 2007, Biochemistry.
[85] Tingjun Hou,et al. ADME Evaluation in Drug Discovery, 6. Can Oral Bioavailability in Humans Be Effectively Predicted by Simple Molecular Property-Based Rules? , 2007, J. Chem. Inf. Model..
[86] Peter J McCormick,et al. EphB2 and EphB4 receptors forward signaling promotes SDF-1-induced endothelial cell chemotaxis and branching remodeling. , 2006, Blood.
[87] Santhosh K. P. Kumar,et al. Receptor tyrosine kinase EphB4 is a survival factor in breast cancer. , 2006, The American journal of pathology.
[88] Andrew I Su,et al. An efficient rapid system for profiling the cellular activities of molecular libraries. , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[89] P. Kuhn,et al. Structure and thermodynamic characterization of the EphB4/Ephrin-B2 antagonist peptide complex reveals the determinants for receptor specificity. , 2006, Structure.
[90] Sean Ekins,et al. Computational prediction of human drug metabolism , 2005, Expert opinion on drug metabolism & toxicology.
[91] Noritaka Tokui,et al. Designing scaffolds of peptides for phage display libraries. , 2005, Journal of bioscience and bioengineering.
[92] Elena B Pasquale,et al. EphB Receptor-binding Peptides Identified by Phage Display Enable Design of an Antagonist with Ephrin-like Affinity* , 2005, Journal of Biological Chemistry.
[93] Y. Martin,et al. A bioavailability score. , 2005, Journal of medicinal chemistry.
[94] A. Middelberg,et al. Estimating the potential refolding yield of recombinant proteins expressed as inclusion bodies , 2004, Biotechnology and bioengineering.
[95] Paul Polakis,et al. EphB2 as a Therapeutic Antibody Drug Target for the Treatment of Colorectal Cancer , 2004, Cancer Research.
[96] W. Guida,et al. Docking studies and model development of tea polyphenol proteasome inhibitors: Applications to rational drug design , 2003, Proteins.
[97] K. Kullander,et al. Mechanisms and functions of eph and ephrin signalling , 2002, Nature Reviews Molecular Cell Biology.
[98] Jin Chen,et al. The ephrins and Eph receptors in angiogenesis. , 2002, Cytokine & growth factor reviews.
[99] T. Pawson,et al. Structural Basis for Autoinhibition of the EphB2 Receptor Tyrosine Kinase by the Unphosphorylated Juxtamembrane Region , 2001, Cell.
[100] John Hodgson,et al. ADMET—turning chemicals into drugs , 2001, Nature Biotechnology.
[101] E. Offord,et al. Comparison of the antioxidant activity of commonly consumed polyphenolic beverages (coffee, cocoa, and tea) prepared per cup serving. , 2001, Journal of agricultural and food chemistry.
[102] J. Sühnel,et al. C-h⋯π-interactions in proteins , 2001 .
[103] A. Goldberg,et al. Why Does Threonine, and Not Serine, Function as the Active Site Nucleophile in Proteasomes?* , 2000, The Journal of Biological Chemistry.
[104] Y. Tanigawara. Role of P-glycoprotein in drug disposition. , 2000, Therapeutic drug monitoring.
[105] T. Lybrand,et al. Streptavidin-biotin binding energetics. , 1999, Biomolecular engineering.
[106] A. Andres,et al. Cell-type specific and estrogen dependent expression of the receptor tyrosine kinase EphB4 and its ligand ephrin-B2 during mammary gland morphogenesis. , 1998, Journal of cell science.
[107] Y. Imai,et al. Point mutations at threonine-301 modify substrate specificity of rabbit liver microsomal cytochromes P-450 (laurate (ω-1)-hydroxylase and testosterone 16α-hydroxylase) , 1989 .
[108] R. Doolittle,et al. A simple method for displaying the hydropathic character of a protein. , 1982, Journal of molecular biology.
[109] A. Jemal,et al. Breast cancer statistics, 2013 , 2014, CA: a cancer journal for clinicians.
[110] Ting Zhou,et al. Kinase selectivity potential for inhibitors targeting the ATP binding site: a network analysis , 2010, Bioinform..
[111] Yong Zhou,et al. Roll: a new algorithm for the detection of protein pockets and cavities with a rolling probe sphere , 2010, Bioinform..
[112] Mindy I. Davis,et al. A quantitative analysis of kinase inhibitor selectivity , 2008, Nature Biotechnology.
[113] B. Hirst,et al. The ABCs of drug transport in intestine and liver: efflux proteins limiting drug absorption and bioavailability. , 2004, European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences.
[114] A. Andres,et al. Altered mammary epithelial development, pattern formation and involution in transgenic mice expressing the EphB4 receptor tyrosine kinase. , 2002, Journal of cell science.
[115] C. Chuong,et al. Article type Software , 2007 .