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Articles on drug design

    2012

  1. Elena Lorente, Susana Infantes, David Abia, Eilon Barnea, Ilan Beer, Ruth García, Fátima Lasala, Mercedes Jiménez, Carmen Mir, Antonio Morreale, Arie Admon, Daniel López
    A Viral, Transporter Associated with Antigen Processing (TAP)-independent, High Affinity Ligand with Alternative Interactions Endogenously Presented by the Nonclassical Human Leukocyte Antigen E Class I Molecule.
    Journal of Biological Chemistry 287 (42), 34895-34903 [Pubmed]

  2. Javier Klett, Alfonso Núñez-Salgado, Helena G. Dos Santos, Álvaro Cortés-Cabrera, Almudena Perona, Rubén Gil-Redondo, David Abia, Federico Gago, and Antonio Morreale
    MM-ISMSA: an ultra-fast and accurate scoring function for protein-protein docking.
    J. Chem. Theory Comput., 8, 3395-3408 (2012) [Pubmed]

  3. Álvaro Cortés Cabrera, Javier Klett, Helena G. Dos Santos, Almudena Perona, Rubén Gil-Redondo, Sandrea M. Francis, Eva M. Priego, Federico Gago, and Antonio Morreale
    CRDOCK: An Ultrafast Multipurpose Protein−Ligand Docking Tool.
    J. Chem. Inf. Model., 52, 2300-20309 (2012)[Pubmed]

  4. Claire Coderch, Javier Klett, Antonio Morreale, J. Fernando Díaz, and Federico Gago
    Comparative Binding Energy (COMBINE) Analysis Supports a Proposal for the Binding Mode of Epothilones to β-Tubulin.
    Chem. Med. Chem., 7, 836 – 843, 2012 [Pubmed]

  5. Antonio Morreale, Federico Gago.
    COMparative BINding Energy (COMBINE) Analysis as a Structure-Based 3D-QSAR Method.
    Physico-Chemical and Computational Approaches to Drug Discovery. RSC Drug Discovery Series, 23, 244-272 (2012) [Pubmed]

  6. Romero O, Filice M, Rivas Bde L, Carrasco-Lopez C, Klett J, Morreale A, Hermoso JA, Guisan JM, Abian O, Palomo JM.
    Semisynthetic peptide-lipase conjugates for improved biotransformations.
    Chem Commun (Camb). 2012 Sep 18;48(72):9053-5. Epub 2012 [Pubmed]

  7. Álvaro Cortés-Cabrera, Federico Gago, and Antonio Morreale
    A reverse combination of structure-based and ligand-based strategies for virtual screening.
    J. Comput.-Aided Mol. Des., 26, 319–327, 2012 [Pubmed]

  8. Juan Bueren-Calabuig; Ana Negri; Federico; Antonio Morreale; and Federico Gago
    Rationale for the opposite stereochemistry of the major monoadducts and interstrand crosslinks formed by mitomycin C and its decarbamoylated analogue at CpG steps in DNA and the effect of cytosine modification on reactivity.
    Organic & Biomolecular Chemistry, accepted (2011) [Pubmed]

    9. 2011

  9. Gonzalo Pérez-Siles; Enrique Núñez; Antonio Morreale; Esperanza Jiménez; Alejandra Leo-Macías; Guillermo Pita; Francesca Cherubino; Rachele Sangaletti; Elena Bossi; Ángel R. Ortíz; Carmen Aragón and Beatriz López-Corcuera
    An aspartate residue in the external vestibule of glycine transporter 2 (GLYT2) controls cation access and transport coupling.
    Biochemical Journal [Pubmed]

  10. Claire Coderch; Antonio Morreale; and Federico Gago
    Tubulin-based structure-affinity relationships for antimitotic Vinca alkaloids
    Anti-cancer agents in medicinal chemistry, in the press (2011) [Pubmed]

  11. Álvaro Cortés-Cabrera; Rubén Gil-Redondo; Almudena Perona A; Federico Gago; and Antonio Morreale
    VSDMIP 1.5: an automated structure- and ligand-based virtual screening platform with a PyMOL graphical user interface
    J. Comput.-Aided Mol. Design, 25, 813-824 (2011) [Pubmed]

  12. Gonzalo Pérez-Siles; Antonio Morreale; Alejandra Leo-Macías; Guillermo Pita; Ángel R. Ortíz; Carmen Aragón; Beatriz López-Corcuera
    Molecular basis of the differential interaction with lithium of glycinetransporters GLYT1 and GLYT2
    J. Neurochem., 118, 195-204 (2011) [Pubmed]

  13. Emna Maalej; Fakher Chabchoub; Abdelouahid Samadi; Cristóbal de los Ríos; Almudena Perona; Antonio Morreale; José Marco-Contelles
    Synthesis, biological assessment and molecular modeling of 14-aryl-10,11,12,14-tetrahydro-9H-benzo[5,6]chromeno[2,3-b]quinolin-13-amines
    Bioorg. Med. Chem. Lett., 21, 2384-2388 (2011) [Pubmed]

    14. 2010

  14. Schaffner-Barbero C; Gil-Redondo R; Ruiz-Avila LB; Huecas S; Läppchen T; den Blaauwen T; Diaz JF; Morreale A; Andreu JM.
    Insights into Nucleotide Recognition by Cell Division Protein FtsZ from a mant-GTP Competition Assay and Molecular Dynamics.
    Biochemistry. 2010 Dec 14;49(49):10458-10472. [Pubmed]

  15. Scheper J; Guerra-Rebollo M; Sanclimens G; Moure A; Masip I; González-Ruiz D; Rubio N; Crosas B; Meca-Cortés O; Loukili N; Plans V; Morreale A; Blanco J; Ortiz AR; Messeguer A; Thomson TM.
    Protein-protein interaction antagonists as novel inhibitors of non-canonical polyubiquitylation.
    PLoS One. 2010 Jun 30;5(6):e11403. [Pubmed]

  16. Pino-Angeles A; Morreale A; Negri A; Sánchez-Jiménez F; Moya-García AA.
    Substrate uptake and protein stability relationship in mammalian histidine decarboxylase.
    Proteins. 2010;78:154-61. [Pubmed]

  17. Gil-Redondo R; Klett J; Gago F; Morreale A.
    gCOMBINE: A graphical user interface to perform structure-based comparative binding energy (COMBINE) analysis on a set of ligand-receptor complexes.
    Proteins. 2010 Jan;78(1):162-72. [Pubmed]

    18. 2009

  18. Moya-García, A.A.; Pino-Angeles, A.; Gil-Redondo, R.; Morreale, A. and Sanchez-Jimenez, F.
    Structural features of mammalian histidine decarboxylase reveal the basis for specific inhibition.
    Br J Pharmacol, 157, 4-13. [Pubmed] [PDF]

  19. Maria Rodriguez-Mateos; David Abia; Juan J. Garcia-Gomez; Antonio Morreale; Jesus de la Cruz; Cruz Santos; Miguel Remacha; Juan P. G. Ballesta
    The amino terminal domain from Mrt4 protein can functionally replace the RNA binding domain of the ribosomal P0 protein.
    Nucleic Acids Research Advance Access. April 3, 2009 [Pubmed] [PDF]

  20. Gil-Redondo, R.; Estrada, J.; Morreale, A.; Herranz, F.; Sancho, J.; Ortiz, A. R.
    VDSMIP: virtual screening data management on an integrated platform.
    J Comput Aided Mol Des. 2009, 23: 171-184 [Pubmed] [PDF]

    21. 2008

  21. Ruiz, F.; Gil-Redondo, R.; Morreale, A.; Ortiz, A.R.; Fabrega, C.; Bravo, J.
    Structure-Based Discovery of novel non-nucleosidic DNA Alkyltransferase inhibitors: virtual screening and in vitro and in vivo activities.
    J Chem Inf Model 2008, 48:844-854 [Pubmed] [PDF]

    22. 2007

  22. García Marcos, A.; Morreale, A.; Guarinos, E.; Briones, E.; Remacha, M.; Ortiz, A.R.; P.G.Ballesta.
    In vivo assembling of bacterial ribosomal protein L11 into yeast ribosomes makes the particles sensitive to the prokaryotic specific antibiotic thriostrepton.
    Nucleic Acid Research [Pubmed] [PDF]

  23. Morreale, A.; Gil-Redondo, R.; Ortiz, A.R.
    A new implicit solvent model for protein-ligand docking.
    Proteins 2007 May, 67: 606-16. [Pubmed] [PDF] [Material suplementario]

    24. 2006

  24. Arias-Pérez, M.S.; Cosme, A.; Gálvez, E.; Morreale, A.; Sanz-Aparicio, J.; Fonseca, I.
    Structural study of () ethyl 3-acyloxy-1-azabicyclo [2.2.2.] octane-3-carboxylates by H, C NMR spectroscopy, X-ray crystallography and DFT calculations.
    Journal of Mol Structure 2006, 789: 71-80.[PDF]

  25. Talavera, D.; Morreale, A.; Meyer, T.; Hospital, A.; Ferrer-Costa, C.; Gelpi, J.Ll.; La Cruz, X. de; Soliva, R.; Luque, F. J.; Orozco, M.
    A fast method for the determintation of fractional contributions to solvation in proteins.
    Protein Sci. 2006 Nov; 15(11): 2525-33. [Pubmed] [PDF]

  26. Murcia, M.; Morreale, A.; Ortiz, A.R.
    Comparative Binding Energy Analysis Considering Multiple Receptors: A Step toward 3D-QSAR Models for Multiple Targets.
    J.Med.Chem. 2006 Oct 19; 49 (21): 6241-53. [Pubmed] [PDF] [Material suplementario]

  27. Ortiz, A.R.; Gómez-Puertas, P.; Leo-Macías, A.; L&oacutepez-Romero, P.; Lopez-Viñas, E.; Morreale, A.; Murcia, M.; Wang, K.
    Computational approaches to model ligand selectivity in drug design.
    Curr Top Med Chem. 2006; 6(1):41-55. [Pubmed] [PDF]

    28. 2004

  28. Wang, K.; Murcia, M.; Constans, P.; Pérez, C.; Ortiz, A.R.
    Gaussian mapping of chemical fragments in ligand binding sites.
    J Comput Aided Mol Des (2004) 18, 101-18. [Pubmed] [PDF]

  29. Murcia, M.; Ortiz, AR.
    Virtual screening with flexible docking and COMBINE-based models. Application to a series of factor Xa inhibitors.
    J Med Chem (2004) 47, 805-20. [Pubmed] [PDF]

    30. 2003

  30. Sanchez-Carbayo, M.; Socci, ND.; Lozano, JJ.; Li, W.; Charytonowicz, E.; Belbin, TJ.; Prystowsky, MB.; Ortiz, A.R.; Childs, G. ; Cordon-Cardo, C.
    Gene discovery in bladder cancer progression using cDNA microarrays.
    Am J Pathol (2003) 163, 505-16. [Pubmed] [PDF]

    31. 2001

  31. Pérez, C.; Ortiz, A.R. Evaluation of docking functions for protein-ligand docking.
    J Med Chem (2001) 44, 3768-85. [Pubmed] [PDF]

  32. Kmunícek, J.; Luengo, S.; Gago, F.; Ortiz, A.R.; Wade, RC.; Damborský, J.
    Comparative binding energy analysis of the substrate specificity of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10.
    Biochemistry (2001) 40, 8905-17. [Pubmed] [PDF]

    33. 1998

  33. Pérez, C.; Pastor, M.; Ortiz, AR.; Gago, F.
    Comparative binding energy analysis of HIV-1 protease inhibitors: incorporation of solvent effects and validation as a powerful tool in receptor-based drug design.
    J Med Chem (1998) 41, 836-52. [Pubmed] [PDF]

    34. 1997

  34. Checa, A.; Ortiz, AR.; de Pascual-Teresa, B.; Gago, F.
    Assessment of solvation effects on calculated binding affinity differences: trypsin inhibition by flavonoids as a model system for congeneric series.
    J Med Chem (1997) 40, 4136-45 [Pubmed] [PDF]

  35. Ortiz, AR.; Pastor, M.; Palomer, A.; Cruciani, G.; Gago, F.; Wade, RC.
    Reliability of comparative molecular field analysis models: effects of data scaling and variable selection using a set of human synovial fluid phospholipase A2 inhibitors.
    J Med Chem (1997) 40, 1136-48. [Pubmed] [PDF]

  36. Gallego, J.; Ortiz, AR.; de Pascual-Teresa, B.; Gago, F.
    Structure-affinity relationships for the binding of actinomycin D to DNA.
    J Comput Aided Mol Des (1997) 11, 114-28. [Pubmed] [PDF]

    37. 1996

  37. Magrans,J.O; Ortiz, A.R.; Molins, A.; Lebouille, P.H.P.; Sanchez-Quesada, J.; Pons, M.; Gago, F.; de Mendoza, J.
    A designed non-peptidic receptor that mimics the phosphocoline binding site of the McPC603 antibody.
    Angew.Chem.Int.Ed.Eng. (1996) 35, 2712-1715.[Pubmed] [PDF]

  38. de Pascual-Teresa, B.; Gallego, J.; Ortiz, AR.; Gago, F.
    Molecular dynamics simulations of the bis-intercalated complexes of ditercalinium and Flexi-Di with the hexanucleotide d(GCGCGC)2: theoretical analysis of the interaction and rationale for the sequence binding specificity.
    J Med Chem (1996) 39, 4810-24: [Pubmed] [PDF]

    39. 1995

  39. Ortiz, AR.; Pisabarro, MT.; Gago, F.; Wade, RC.
    Prediction of drug binding affinities by comparative binding energy analysis.
    J Med Chem (1995) 38, 2681-91. [Pubmed] [PDF]

    40. 1994

  40. Pisabarro, MT.; Ortiz, AR.; Palomer, A.; Cabré, F.; García, L.; Wade, RC.; Gago, F.; Mauleón, D.; Carganico, G.
    Rational modification of human synovial fluid phospholipase A2 inhibitors.
    J Med Chem (1994) 37, 337-41. [Pubmed] [PDF]

    41. 1993

  41. Ortiz, AR.; Pisabarro, MT.; Gago, F.
    Molecular model of the interaction of bee venom phospholipase A2 with manoalide.
    J Med Chem (1993) 36, 1866-79. [Pubmed] [PDF]

  42. Gallego, J.; Ortiz, AR.; Gago, F.
    A molecular dynamics study of the bis-intercalation complexes of echinomycin with d(ACGT)2 and d(TCGA)2: rationale for sequence-specific Hoogsteen base pairing.
    J Med Chem (1993) 36, 1548-61. [Pubmed] [PDF]

  43. Minguez, J.M.; Gandasegui, T.; Vaquero, J.J.; Alvarez-Builla, J.; Garcia-Navio, J.L; Gago, F.; Ortiz, A.R.; Gomez-Sal, P.; Torres, R.; Rodrigo, M.
    New 3-(2'-benzimidazolyl) imidazo [1,2-a] pyridinium mesomeric betaines. Synthesis and structure.
    J. Org. Chem. (1993) 58, 6030-6037.[Pubmed] [PDF]

    44. 1992

  44. Ortiz, AR.; Pisabarro, MT.; Gallego, J.; Gago, F.
    Implications of a consensus recognition site for phosphatidylcholine separate from the active site in cobra venom phospholipases A2.
    Biochemistry (1992) 31, 2887-96. [Pubmed] [PDF]

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