Ligand-, structure- and pharmacophore-based molecular fingerprints: a case study on adenosine A1, A2A, A2B, and A3 receptor antagonists
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Hugo Gutiérrez-de-Terán | Raimund Mannhold | Francesco Sirci | Laura Goracci | David Rodríguez | Jacqueline van Muijlwijk-Koezen | R. Mannhold | D. Rodríguez | H. Gutiérrez‐de‐Terán | L. Goracci | F. Sirci | J. V. Muijlwijk-Koezen | Laura Goracci
[1] Martin Grosell,et al. Biochimica et Biophysica Acta (BBA)/Biomembranes: Preface , 2003 .
[2] David Rodríguez,et al. Molecular dynamics simulations reveal insights into key structural elements of adenosine receptors. , 2011, Biochemistry.
[3] B. Fredholm,et al. International Union of Pharmacology. XXV. Nomenclature and classification of adenosine receptors. , 2001, Pharmacological reviews.
[4] Kenneth A Jacobson,et al. Modeling the adenosine receptors: comparison of the binding domains of A2A agonists and antagonists. , 2003, Journal of medicinal chemistry.
[5] J. Ballesteros,et al. [19] Integrated methods for the construction of three-dimensional models and computational probing of structure-function relations in G protein-coupled receptors , 1995 .
[6] P Willett,et al. Development and validation of a genetic algorithm for flexible docking. , 1997, Journal of molecular biology.
[7] J. Linden,et al. Molecular cloning and characterization of the human A3 adenosine receptor. , 1993, Proceedings of the National Academy of Sciences of the United States of America.
[8] Bartosz Trzaskowski,et al. Predicted 3D structures for adenosine receptors bound to ligands: comparison to the crystal structure. , 2010, Journal of structural biology.
[9] H. Adam. ADVANCES IN PHARMACOLOGY , 1951 .
[10] T. Blundell,et al. Comparative protein modelling by satisfaction of spatial restraints. , 1993, Journal of molecular biology.
[11] R. Stevens,et al. Structure of an Agonist-Bound Human A2A Adenosine Receptor , 2011, Science.
[12] R. Stevens,et al. The 2.6 Angstrom Crystal Structure of a Human A2A Adenosine Receptor Bound to an Antagonist , 2008, Science.
[13] K. Jacobson,et al. Pharmacology of purine and pyrimidine receptors. Preface. , 2011, Advances in Pharmacology.
[14] J. Thornton,et al. PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .
[15] R. Fisher. THE USE OF MULTIPLE MEASUREMENTS IN TAXONOMIC PROBLEMS , 1936 .
[16] David Rogers,et al. Extended-Connectivity Fingerprints , 2010, J. Chem. Inf. Model..
[17] Ruben Abagyan,et al. Structure based prediction of subtype-selectivity for adenosine receptor antagonists , 2011, Neuropharmacology.
[18] Xiaofen Li,et al. Selective, high affinity A(2B) adenosine receptor antagonists: N-1 monosubstituted 8-(pyrazol-4-yl)xanthines. , 2008, Bioorganic & medicinal chemistry letters.
[19] Jack Snoeyink,et al. Nucleic Acids Research Advance Access published April 22, 2007 MolProbity: all-atom contacts and structure validation for proteins and nucleic acids , 2007 .
[20] R. Stevens,et al. Trapping small caffeine in a large GPCR pocket. , 2011, Structure.
[21] G. Cruciani,et al. Hydrogen bonding interactions of covalently bonded fluorine atoms: from crystallographic data to a new angular function in the GRID force field. , 2004, Journal of medicinal chemistry.
[22] K. Varani,et al. Adenosine receptors in health and disease. , 2011, Advances in pharmacology.
[23] Tudor I. Oprea,et al. Chemography: the Art of Navigating in Chemical Space , 2000 .
[24] Jonas Boström,et al. Assessing the performance of OMEGA with respect to retrieving bioactive conformations. , 2003, Journal of molecular graphics & modelling.
[25] M. Loza,et al. 1,3-Dialkyl-8-(hetero)aryl-9-OH-9-deazaxanthines as potent A2B adenosine receptor antagonists: design, synthesis, structure-affinity and structure-selectivity relationships. , 2008, Bioorganic & medicinal chemistry.
[26] Barbara Cacciari,et al. Synthesis, biological activity, and molecular modeling investigation of new pyrazolo[4,3-e]-1,2,4-triazolo[1,5-c]pyrimidine derivatives as human A(3) adenosine receptor antagonists. , 2002, Journal of medicinal chemistry.
[27] X. García‐Mera,et al. Pyrimidine derivatives as potent and selective A3 adenosine receptor antagonists. , 2011, Journal of medicinal chemistry.
[28] Thomas Stützle,et al. Empirical Scoring Functions for Advanced Protein-Ligand Docking with PLANTS , 2009, J. Chem. Inf. Model..
[29] Paolo Benedetti,et al. FLAP: GRID Molecular Interaction Fields in Virtual Screening. Validation using the DUD Data Set , 2010, J. Chem. Inf. Model..
[30] K. Klotz,et al. Improving Potency, Selectivity, and Water Solubility of Adenosine A1 Receptor Antagonists: Xanthines Modified at Position 3 and Related Pyrimido[1,2,3‐cd]purinediones , 2006, ChemMedChem.
[31] Feixiong Cheng,et al. Insights into binding modes of adenosine A(2B) antagonists with ligand-based and receptor-based methods. , 2010, European journal of medicinal chemistry.
[32] Nathan Robertson,et al. Article pubs.acs.org/jmc Identification of Novel Adenosine A 2A Receptor Antagonists by Virtual Screening , 2022 .
[33] A. Ivanov,et al. Molecular modeling and molecular dynamics simulation of the human A2B adenosine receptor. The study of the possible binding modes of the A2B receptor antagonists. , 2005, Journal of Medicinal Chemistry.
[34] Hui Li,et al. Molecular docking study of A3 adenosine receptor antagonists and pharmacophore-based drug design , 2009, Neurochemistry International.
[35] J. H. Stapleton. Wiley Series in Probability and Statistics , 2007 .
[36] Kenneth A Jacobson,et al. Recent developments in adenosine receptor ligands and their potential as novel drugs. , 2011, Biochimica et biophysica acta.
[37] G Burnstock,et al. Receptors for purines and pyrimidines. , 1998, Pharmacological reviews.
[38] H. L. Morgan. The Generation of a Unique Machine Description for Chemical Structures-A Technique Developed at Chemical Abstracts Service. , 1965 .
[39] Peter Ertl,et al. Evolution of the physicochemical properties of marketed drugs: can history foretell the future? , 2011, Drug discovery today.
[40] V. Jaakola,et al. Structural features of adenosine receptors: from crystal to function. , 2011, Biochimica et biophysica acta.
[41] M. Congreve,et al. Structure of the adenosine A(2A) receptor in complex with ZM241385 and the xanthines XAC and caffeine. , 2011, Structure.
[42] S. Iwata,et al. G protein-coupled receptor inactivation by an allosteric inverse-agonist antibody , 2011, Nature.
[43] Jonathan S. Mason,et al. Discovery of 1,2,4-Triazine Derivatives as Adenosine A2A Antagonists using Structure Based Drug Design , 2012, Journal of medicinal chemistry.
[44] E. Novellino,et al. 2-(Benzimidazol-2-yl)quinoxalines: a novel class of selective antagonists at human A(1) and A(3) adenosine receptors designed by 3D database searching. , 2005, Journal of medicinal chemistry.
[45] Kenneth A. Jacobson,et al. Structural Determinants of A3 Adenosine Receptor Activation: Nucleoside Ligands at the Agonist/Antagonist Boundary , 2002 .
[46] Jean-Paul Chilès,et al. Wiley Series in Probability and Statistics , 2012 .
[47] G. Stiles,et al. Molecular cloning and characterization of an adenosine receptor: the A3 adenosine receptor. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[48] Thomas Stützle,et al. An ant colony optimization approach to flexible protein–ligand docking , 2007, Swarm Intelligence.
[49] A. IJzerman,et al. 2,6-disubstituted and 2,6,8-trisubstituted purines as adenosine receptor antagonists. , 2006, Journal of Medicinal Chemistry.
[50] Loriano Storchi,et al. New and Original pKa Prediction Method Using Grid Molecular Interaction Fields , 2007, J. Chem. Inf. Model..
[51] J. Wess,et al. Site-directed Mutagenesis Identifies Residues Involved in Ligand Recognition in the Human A2a Adenosine Receptor (*) , 1995, The Journal of Biological Chemistry.
[52] James E. J. Mills,et al. High-Throughput Virtual Screening of Proteins Using GRID Molecular Interaction Fields , 2010, J. Chem. Inf. Model..
[53] M Pastor,et al. VolSurf: a new tool for the pharmacokinetic optimization of lead compounds. , 2000, European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences.
[54] J. Thompson,et al. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. , 1997, Nucleic acids research.
[55] S. Moro,et al. 2-Phenylpyrazolo[4,3-d]pyrimidin-7-one as a new scaffold to obtain potent and selective human A3 adenosine receptor antagonists: new insights into the receptor-antagonist recognition. , 2009, Journal of medicinal chemistry.
[56] Brian D. Hudson,et al. Parameter Based Methods for Compound Selection from Chemical Databases , 1996 .
[57] Feixiong Cheng,et al. Pharmacophore modeling of human adenosine receptor A2A antagonists , 2010, Journal of molecular modeling.
[58] J. H. Burn,et al. ADVANCES IN PHARMACOLOGY , 1957 .
[59] Massimo Baroni,et al. Virtual screening for novel openers of pancreatic K(ATP) channels. , 2007, Journal of medicinal chemistry.
[60] Jing Wei,et al. 3D-Pharmacophore Models for Selective A2A and A2B Adenosine Receptor Antagonists , 2007, J. Chem. Inf. Model..
[61] J. A. Grant,et al. A fast method of molecular shape comparison: A simple application of a Gaussian description of molecular shape , 1996, J. Comput. Chem..
[62] A. Sali,et al. Modeling of loops in protein structures , 2000, Protein science : a publication of the Protein Society.
[63] G. Giannaccini,et al. Study on affinity profile toward native human and bovine adenosine receptors of a series of 1,8-naphthyridine derivatives. , 2004, Journal of medicinal chemistry.
[64] C. Müller,et al. 2-Amino-5-benzoyl-4-phenylthiazoles: Development of potent and selective adenosine A1 receptor antagonists. , 2010, Bioorganic & medicinal chemistry.
[65] T. Tuccinardi,et al. Molecular modeling of adenosine receptors: new results and trends , 2008, Medicinal research reviews.
[66] J. Gasteiger,et al. Neural networks as data mining tools in drug design , 2003 .
[67] K. Varani,et al. Design, synthesis, and biological evaluation of new 8-heterocyclic xanthine derivatives as highly potent and selective human A2B adenosine receptor antagonists. , 2004, Journal of medicinal chemistry.
[68] Chun Wei Yap,et al. Pharmacophore elucidation for a new series of 2-aryl-pyrazolo-triazolo-pyrimidines as potent human A3 adenosine receptor antagonists. , 2011, Bioorganic & medicinal chemistry letters.
[69] Gabriele Cruciani,et al. A Common Reference Framework for Analyzing/Comparing Proteins and Ligands. Fingerprints for Ligands And Proteins (FLAP): Theory and Application , 2007, J. Chem. Inf. Model..
[70] P. Carrupt,et al. Molecular fields in quantitative structure–permeation relationships: the VolSurf approach , 2000 .
[71] B. Fredholm,et al. International Union of Basic and Clinical Pharmacology. LXXXI. Nomenclature and Classification of Adenosine Receptors—An Update , 2011, Pharmacological Reviews.
[72] K. Jacobson,et al. Derivatives of the triazoloquinazoline adenosine antagonist (CGS15943) are selective for the human A3 receptor subtype. , 1996, Journal of medicinal chemistry.
[73] Stefano Sabatini,et al. Discovery of novel inhibitors of the NorA multidrug transporter of Staphylococcus aureus. , 2011, Journal of medicinal chemistry.
[74] Dimitar Hristozov,et al. Exploring Potency and Selectivity Receptor Antagonist Profiles Using a Multilabel Classification Approach: The Human Adenosine Receptors as a Key Study , 2009, J. Chem. Inf. Model..
[75] K. Varani,et al. Recent developments in the field of A2A and A3 adenosine receptor antagonists. , 2003, European journal of medicinal chemistry.
[76] M. Trincavelli,et al. Synthesis and 3D QSAR of new pyrazolo[3,4-b]pyridines: potent and selective inhibitors of A1 adenosine receptors. , 2005, Journal of medicinal chemistry.
[77] B. Fredholm. Physiological and pathophysiological roles of adenosine , 2011 .
[78] Stefano Costanzi,et al. Ligand and structure-based methodologies for the prediction of the activity of G protein-coupled receptor ligands , 2009, J. Comput. Aided Mol. Des..
[79] K. Jacobson,et al. Identification by Site-directed Mutagenesis of Residues Involved in Ligand Recognition and Activation of the Human A3 Adenosine Receptor* , 2002, The Journal of Biological Chemistry.
[80] Thomas Borrmann,et al. 1-alkyl-8-(piperazine-1-sulfonyl)phenylxanthines: development and characterization of adenosine A2B receptor antagonists and a new radioligand with subnanomolar affinity and subtype specificity. , 2009, Journal of medicinal chemistry.
[81] J. Díaz,et al. Synthesis of N-pyrimidinyl-2-phenoxyacetamides as adenosine A2A receptor antagonists. , 2008, Bioorganic & medicinal chemistry letters.
[82] C. Masimirembwa,et al. Structural analysis of CYP2C9 and CYP2C5 and an evaluation of commonly used molecular modeling techniques. , 2004, Drug metabolism and disposition: the biological fate of chemicals.
[83] K. Jacobson,et al. Neoceptor concept based on molecular complementarity in GPCRs: a mutant adenosine A(3) receptor with selectively enhanced affinity for amine-modified nucleosides. , 2001, Journal of medicinal chemistry.
[84] Dov Barak,et al. Evaluation of homology modeling of G-protein-coupled receptors in light of the A(2A) adenosine receptor crystallographic structure. , 2009, Journal of medicinal chemistry.