Receptor-guided 3D-QSAR studies, molecular dynamics simulation and free energy calculations of Btk kinase inhibitors
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Seung Joo Cho | Hee-Young Kang | Anand Balupuri | Pavithra K. Balasubramanian | P. K. Balasubramanian | A. Balupuri | S. Cho | Hee-Young Kang
[1] Seung Joo Cho,et al. 3D QSAR modeling study on 7-aminofuro [2,3-c] pyridine derivatives as TAK1 inhibitors using CoMFA and COMSIA , 2014, Medicinal Chemistry Research.
[2] Ruisheng Zhang,et al. Receptor- and ligand-based 3D-QSAR study for a series of non-nucleoside HIV-1 reverse transcriptase inhibitors. , 2009, Bioorganic & medicinal chemistry.
[3] I. Weissman,et al. Posttranscriptional regulation of Bruton's tyrosine kinase expression in antigen receptor-stimulated splenic B cells. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[4] D J Rawlings,et al. In situ detection of activated Bruton's tyrosine kinase in the Ig signaling complex by phosphopeptide-specific monoclonal antibodies. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[5] A. Sali,et al. Comparative protein structure modeling of genes and genomes. , 2000, Annual review of biophysics and biomolecular structure.
[6] Chang-Guo Zhan,et al. Combined 3D-QSAR Modeling and Molecular Docking Study on Indolinone Derivatives as Inhibitors of 3-Phosphoinositide-Dependent Protein Kinase-1 , 2008, J. Chem. Inf. Model..
[7] H. Kubinyi. Comparative Molecular Field Analysis (CoMFA) , 2002 .
[8] W. L. Jorgensen,et al. Comparison of simple potential functions for simulating liquid water , 1983 .
[9] J. Cohen,et al. Mechanisms of Lymphocyte Activation and Immune Regulation V , 1994, Advances in Experimental Medicine and Biology.
[10] Berk Hess,et al. P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation. , 2008, Journal of chemical theory and computation.
[11] Paola Gramatica,et al. Real External Predictivity of QSAR Models. Part 2. New Intercomparable Thresholds for Different Validation Criteria and the Need for Scatter Plot Inspection , 2012, J. Chem. Inf. Model..
[12] D. Vetrie,et al. The gene involved in X-linked agammaglobulinaemia is a member of the src family of protein-tyrosine kinases , 1993, Nature.
[13] Fatih M. Uckun,et al. Bruton’s Tyrosine Kinase as an Inhibitor of the Fas/CD95 Death-inducing Signaling Complex* , 1999, The Journal of Biological Chemistry.
[14] O. Witte,et al. X-linked agammaglobulinemia and Bruton's tyrosine kinase. , 1994, Advances in experimental medicine and biology.
[15] Junmei Wang,et al. Development and testing of a general amber force field , 2004, J. Comput. Chem..
[16] Yan Wang,et al. Discovery of a series of 2,5-diaminopyrimidine covalent irreversible inhibitors of Bruton's tyrosine kinase with in vivo antitumor activity. , 2014, Journal of medicinal chemistry.
[17] G. Klebe,et al. Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity. , 1994, Journal of medicinal chemistry.
[18] L. Silvian,et al. Structures of human Bruton's tyrosine kinase in active and inactive conformations suggest a mechanism of activation for TEC family kinases , 2010, Protein science : a publication of the Protein Society.
[19] Kunal Roy,et al. Some case studies on application of “rm2” metrics for judging quality of quantitative structure–activity relationship predictions: Emphasis on scaling of response data , 2013, J. Comput. Chem..
[20] Christine Kinnon,et al. Pillars Article: The Gene Involved in X-linked Agammaglobulinaemia Is a Member of the Src Family of Protein-Tyrosine Kinases. Nature. 1993. 361: 226–233 , 2012 .
[21] David S. Goodsell,et al. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function , 1998, J. Comput. Chem..
[22] Ornella Parolini,et al. Deficient expression of a B cell cytoplasmic tyrosine kinase in human X-linked agammaglobulinemia , 1993, Cell.
[23] David S. Goodsell,et al. A semiempirical free energy force field with charge‐based desolvation , 2007, J. Comput. Chem..
[24] F. Uckun,et al. Bruton's tyrosine kinase (BTK) as a dual-function regulator of apoptosis. , 1998, Biochemical pharmacology.
[25] Zheng Yang,et al. Design and synthesis of carbazole carboxamides as promising inhibitors of Bruton's tyrosine kinase (BTK) and Janus kinase 2 (JAK2). , 2015, Bioorganic & medicinal chemistry letters.
[26] H. Berendsen,et al. Molecular dynamics with coupling to an external bath , 1984 .
[27] Paola Gramatica,et al. Real External Predictivity of QSAR Models: How To Evaluate It? Comparison of Different Validation Criteria and Proposal of Using the Concordance Correlation Coefficient , 2011, J. Chem. Inf. Model..
[28] Narayanan Eswar,et al. Protein structure modeling with MODELLER. , 2008, Methods in molecular biology.
[29] Mauno Vihinen,et al. Bruton’s tyrosine kinase (Btk): function, regulation, and transformation with special emphasis on the PH domain , 2009, Immunological reviews.
[30] Ben M. Webb,et al. Comparative Protein Structure Modeling Using Modeller , 2006, Current protocols in bioinformatics.
[31] D J Rawlings,et al. Regulation of Btk function by a major autophosphorylation site within the SH3 domain. , 1996, Immunity.
[32] A. Sali,et al. Modeling of loops in protein structures , 2000, Protein science : a publication of the Protein Society.
[33] Adrian Wiestner,et al. Targeting B-Cell receptor signaling for anticancer therapy: the Bruton's tyrosine kinase inhibitor ibrutinib induces impressive responses in B-cell malignancies. , 2013, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.
[34] D J Rawlings,et al. Phosphorylation of two regulatory tyrosine residues in the activation of Bruton's tyrosine kinase via alternative receptors. , 1997, Proceedings of the National Academy of Sciences of the United States of America.
[35] J. Kinet,et al. Activation of BTK by a Phosphorylation Mechanism Initiated by SRC Family Kinases , 1996, Science.
[36] Seung Joo Cho,et al. Structural insights into the ligand-binding hot spots of APEX1: an in silico analysis , 2015, Medicinal Chemistry Research.
[37] Seung Joo Cho,et al. Molecular modeling studies on series of Btk inhibitors using docking, structure-based 3D-QSAR and molecular dynamics simulation: a combined approach , 2016, Archives of pharmacal research.
[38] T. Darden,et al. A smooth particle mesh Ewald method , 1995 .
[39] W. Paul,et al. Colocalization of X-linked agammaglobulinemia and X-linked immunodeficiency genes. , 1993, Science.
[40] Peter M. Kasson,et al. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit , 2013, Bioinform..
[41] A. Sali,et al. Statistical potential for assessment and prediction of protein structures , 2006, Protein science : a publication of the Protein Society.
[42] O. Witte,et al. Bruton's Tyrosine Kinase is a Key Regulator in B‐Cell Development , 1994, Immunological reviews.
[43] Wei Huang,et al. Synthesis and biological evaluation of novel 7-substituted 3-(4-phenoxyphenyl)thieno[3,2-c]pyridin-4-amines as potent Bruton's tyrosine kinase (BTK) inhibitors. , 2015, Bioorganic & medicinal chemistry.
[44] Wei Huang,et al. Discovery of thieno[3,2-c]pyridin-4-amines as novel Bruton's tyrosine kinase (BTK) inhibitors. , 2015, Bioorganic & medicinal chemistry.
[45] H. Ochs,et al. Rapid tyrosine phosphorylation and activation of Bruton's tyrosine/Tec kinases in platelets induced by collagen binding or CD32 cross-linking. , 2000, Blood.
[46] D. Bentley,et al. The gene involved in X-linked agammaglobulinaemia is a member of the src family of protein-tyrosine kinases , 1993, Nature.
[47] Wim F Vranken,et al. ACPYPE - AnteChamber PYthon Parser interfacE , 2012, BMC Research Notes.
[48] V. Hornak,et al. Comparison of multiple Amber force fields and development of improved protein backbone parameters , 2006, Proteins.
[49] Seung Joo Cho,et al. Molecular Modeling Studies of Trisubstituted Thiazoles as Cdc7 Kinase Inhibitors through 3D-QSAR and Molecular Docking Simulation , 2015 .
[50] F. Uckun,et al. Rational Design and Synthesis of a Novel Anti-leukemic Agent Targeting Bruton′s Tyrosine Kinase (BTK), LFM-A13 [α-Cyano-β-Hydroxy-β-Methyl-N-(2,5-Dibromophenyl)Propenamide]* , 1999, The Journal of Biological Chemistry.
[51] Ding Li,et al. 3D-QSAR studies of azaoxoisoaporphine, oxoaporphine, and oxoisoaporphine derivatives as anti-AChE and anti-AD agents by the CoMFA method. , 2013, Journal of molecular graphics & modelling.
[52] R. Cramer,et al. Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. , 1988, Journal of the American Chemical Society.
[53] T. Kurosaki,et al. Molecular mechanisms in B cell antigen receptor signaling. , 1997, Current opinion in immunology.
[54] Rajendra Kumar,et al. g_mmpbsa - A GROMACS Tool for High-Throughput MM-PBSA Calculations , 2014, J. Chem. Inf. Model..
[55] Seung Joo Cho,et al. Large variation in electrostatic contours upon addition of steric parameters and the effect of charge calculation schemes in CoMFA on mutagenicity of MX analogues , 2012 .
[56] A. Sali,et al. Statistical potentials for fold assessment , 2009 .
[57] Seung Joo Cho,et al. In silico study of 1-(4-Phenylpiperazin-1-yl)-2-(1H-pyrazol-1-yl) ethanones derivatives as CCR1 antagonist: homology modeling, docking and 3D-QSAR approach. , 2014, Bioorganic & medicinal chemistry letters.
[58] Ben M. Webb,et al. Comparative Protein Structure Modeling Using MODELLER , 2016, Current protocols in bioinformatics.
[59] F. Uckun,et al. Crystal Structure of Bruton's Tyrosine Kinase Domain Suggests a Novel Pathway for Activation and Provides Insights into the Molecular Basis of X-linked Agammaglobulinemia* , 2001, The Journal of Biological Chemistry.