Scientific Background

Scientific Background
  • Huecas, S. Marcelo F , Perona A, B. Ruiz-Ávila L, Morreale A,  Cañada, FJ,  Jimenez-Barbero,J, and Andreu JM (2015). "Beyond a Fluorescent Probe: Inhibition of Cell Division Protein FtsZ by mant-GTP Elucidated by NMR and Biochemical Approaches" ACS Chem. Biol., 2015, 10 (10), pp 2382–2392
  • Borroto A, Abia D and Alarcon B (2014). "Crammed signaling motifs in the T-cell receptor." Immunology Letters 161(1): 113-117.
  • Fulde M, Bernardo-Garcia N, Rohde M, Nachtigall N, Frank R, Preissner KT, Klett J, Morreale A, Chhatwal GS, Hermoso JA and Bergmann S (2014). "Pneumococcal phosphoglycerate kinase interacts with plasminogen and its tissue activator." Thrombosis and Haemostasis 111(3): 401-416.
  • Klett J, Cortes-Cabrera A, Gil-Redondo R, Gago F and Morreale A (2014). "ALFA: Automatic Ligand Flexibility Assignment." Journal of Chemical Information and Modeling 54(1): 314-323.
  • Willemen HLDM, Campos PM, Lucas E, Morreale A, Gil-Redondo R, Agut J, Gonzalez FV, Ramos P, Heijnen C, Mayor F, Jr., Kavelaars A and Murga C (2014). "A novel p38 MAPK docking-groove-targeted compound is a potent inhibitor of inflammatory hyperalgesia." Biochemical Journal 459: 427-439.
  • Alvarez-Navarro C, Cragnolini JJ, Dos Santos HG, Barnea E, Admon A, Morreale A and Lopez de Castro JA (2013). "Novel HLA-B27-restricted Epitopes from Chlamydia trachomatis Generated upon Endogenous Processing of Bacterial Proteins Suggest a Role of Molecular Mimicry in Reactive Arthritis." Journal of Biological Chemistry 288(36): 25810-25825.
  • Coderch C, Tang Y, Klett J, Zhang S-E, Ma Y-T, Wang S, Matesanz R, Pera B, Canales A, Jimenez-Barbero J, Morreale A, Fernando Diaz J, Fang W-S and Gago F (2013). "A structure-based design of new C2- and C13-substituted taxanes: tubulin binding affinities and extended quantitative structure-activity relationships using comparative binding energy (COMBINE) analysis." Organic & Biomolecular Chemistry 11(18): 3046-3056.
  • Cortes-Cabrera A, Morris GM, Finn PW, Morreale A and Gago F (2013). "Comparison of ultra-fast 2D and 3D ligand and target descriptors for side effect prediction and network analysis in polypharmacology." British Journal of Pharmacology 170(3): 557-567.
  • Dos Santos HG, Abia D, Janowski R, Mortuza G, Bertero MG, Boutin M, Guarin N, Mendez-Giraldez R, Nunez A, Pedrero JG, Redondo P, Sanz M, Speroni S, Teichert F, Bruix M, Carazo JM, Gonzalez C, Reina J, Valpuesta JM, Vernos I, Zabala JC, Montoya G, Coll M, Bastolla U and Serrano L (2013). "Structure and Non-Structure of Centrosomal Proteins." Plos One 8(5).
  • Gallego-Villar L, Perez-Cerda C, Perez B, Abia D, Ugarte M, Richard E and Desviat LR (2013). "Functional characterization of novel genotypes and cellular oxidative stress studies in propionic acidemia." Journal of Inherited Metabolic Disease 36(5): 731-740.
  • Marcelo F, Huecas S, Ruiz-Avila LB, Canada FJ, Perona A, Poveda A, Martin-Santamaria S, Morreale A, Jimenez-Barbero J and Andreu JM (2013). "Interactions of Bacterial Cell Division Protein FtsZ with C8-Substituted Guanine Nucleotide Inhibitors. A Combined NMR, Biochemical and Molecular Modeling Perspective." Journal of the American Chemical Society 135(44): 16418-16428.
  • Matamoros T, Barrioluengo V, Abia D and Menendez-Arias L (2013). "Major Groove Binding Track Residues of the Connection Subdomain of Human Immunodeficiency Virus Type 1 Reverse Transcriptase Enhance cDNA Synthesis at High Temperatures." Biochemistry 52(51): 9318-9328.
  • Singh PK, Ramachandran G, Ramos-Ruiz R, Peiro-Pastor R, Abia D, Wu LJ and Meijer WJJ (2013). "Mobility of the Native Bacillus subtilis Conjugative Plasmid pLS20 Is Regulated by Intercellular Signaling." Plos Genetics 9(10).
  • Bueren-Calabuig JA, Negri A, Morreale A and Gago F (2012). "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 (vol 10, pg 1543, 2012)." Organic & Biomolecular Chemistry 10(48): 9750-9750.
  • Bueren-Calabuig JA, Negri A, Morreale A and Gago F (2012). "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 10(8): 1543-1552.
  • Coderch C, Klett J, Morreale A, Fernando Diaz J and Gago F (2012). "Comparative Binding Energy (COMBINE) Analysis Supports a Proposal for the Binding Mode of Epothilones to beta-Tubulin." Chemmedchem 7(5): 836-843.
  • Coderch C, Morreale A and Gago F (2012). "Tubulin-based Structure-affinity Relationships for Antimitotic Vinca Alkaloids." Anti-Cancer Agents in Medicinal Chemistry 12(3): 219-225.
  • Cortes Cabrera A, Klett J, Dos Santos HG, Perona A, Gil-Redondo R, Francis SM, Priego EM, Gago F and Morreale A (2012). "CRDOCK: an ultrafast multipurpose protein-ligand docking tool." Journal of chemical information and modeling 52(8): 2300-2309.
  • Cortes-Cabrera A, Gago F and Morreale A (2012). "A reverse combination of structure-based and ligand-based strategies for virtual screening." Journal of Computer-Aided Molecular Design 26(3): 319-327.
  • Cortes-Cabrera A, Morreale A, Gago F and Abad-Zapatero C (2012). "AtlasCBS: a web server to map and explore chemico-biological space." Journal of Computer-Aided Molecular Design 26(9): 995-1003.
  • Klett J, Nunez-Salgado A, Dos Santos HG, Cortes-Cabrera A, Perona A, Gil-Redondo R, Abia D, Gago F and Morreale A (2012). "MM-ISMSA: An Ultrafast and Accurate Scoring Function for Protein- Protein Docking." Journal of Chemical Theory and Computation 8(9): 3395-3408.
  • Lopez-Tarifa P, Sanchez-Sanz G, Alkorta I, Elguero J, Sanz D, Perona A and Claramunt RM (2012). "The tautomeric structures of 3(5),3 '(5 ')-azopyrazole (E)-1,2-di(1H-pyrazol-3(5)-yl)diazene) : The combined use of NMR and electronic spectroscopies with DFT calculations." Journal of Molecular Structure 1015: 138-146.
  • Lorente E, Infantes S, Abia D, Barnea E, Beer I, Garcia R, Lasala F, Jimenez M, Mir C, Morreale A, Admon A and Lopez D (2012). "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.
  • Perez-Siles G, Nunez E, Morreale A, Jimenez E, Leo-Macias A, Pita G, Cherubino F, Sangaletti R, Bossi E, Ortiz AR, Aragon C and Lopez-Corcuera B (2012). "An aspartate residue in the external vestibule of GLYT2 (glycine transporter 2) controls cation access and transport coupling." Biochemical Journal 442: 323-334.
  • Romero O, Filice M, de las Rivas B, Carrasco-Lopez C, Klett J, Morreale A, Hermoso JA, Guisan JM, Abian O and Palomo JM (2012). "Semisynthetic peptide-lipase conjugates for improved biotransformations." Chemical Communications 48(72): 9053-9055.
  • Ruiz FM, Francis SM, Tintore M, Ferreira R, Gil-Redondo R, Morreale A, Ortiz AR, Eritja R and Fabrega C (2012). "Receptor-Based Virtual Screening and Biological Characterization of Human Apurinic/Apyrimidinic Endonuclease (Ape1) Inhibitors." Chemmedchem 7(12): 2168-2178.
  • Camargo H, Nusspaumer G, Abia D, Briceno V, Remacha M and Ballesta JPG (2011). "The amino terminal end determines the stability and assembling capacity of eukaryotic ribosomal stalk proteins P1 and P2." Nucleic Acids Research 39(9): 3735-3743.
  • Cortes Cabrera A, Gil-Redondo R, Perona A, Gago F and Morreale A (2011). "VSDMIP 1.5: an automated structure- and ligand-based virtual screening platform with a PyMOL graphical user interface." Journal of Computer-Aided Molecular Design 25(9): 813-824.
  • Isabel Vega A, Perez-Cerda C, Abia D, Gamez A, Briones P, Artuch R, Desviat LR, Ugarte M and Perez B (2011). "Expression analysis revealing destabilizing mutations in phosphomannomutase 2 deficiency (PMM2-CDG)." Journal of Inherited Metabolic Disease 34(4): 929-939.
  • Maalej E, Chabchoub F, Samadi A, de los Rios C, Perona A, Morreale A and Marco-Contelles J (2011). "Synthesis, biological assessment and molecular modeling of 14-aryl-10,11,12,14-tetrahydro-9H-benzo 5,6 chromeno 2,3-b quinolin-13-a mines." Bioorganic & Medicinal Chemistry Letters 21(8): 2384-2388.
  • Perez-Siles G, Morreale A, Leo-Macias A, Pita G, Ortiz AR, Aragon C and Lopez-Corcuera B (2011). "Molecular basis of the differential interaction with lithium of glycine transporters GLYT1 and GLYT2." Journal of Neurochemistry 118(2): 195-204.
  • Abia D, Bastolla U, Chacon P, Fabrega C, Gago F, Morreale A and Tramontano A (2010). "ANGEL RAMIREZ ORTIZ (1966-2008) IN MEMORIAM." Proteins-Structure Function and Bioinformatics 78(1): III-VIII.
  • Arechaga I, Swamy M, Abia D, Schamel WA, Alarcon B and Maria Valpuesta J (2010). "Structural characterization of the TCR complex by electron microscopy." International Immunology 22(11): 897-903.
  • Bermudo R, Abia D, Benitez D, Carrio A, Vilella R, Ortiz AR, Thomson TM and Fernandez PL (2010). Discovery of genomic alterations through coregulation analysis of closely linked genes: a frequent gain in 17q25.3 in prostate cancer. Toward Personalized Medicine for Cancer. D. Braaten. 1210: 17-24.
  • Gil-Redondo R, Klett J, Gago F and Morreale A (2010). "gCOMBINE: A graphical user interface to perform structure-based comparative binding energy (COMBINE) analysis on a set of ligand-receptor complexes." Proteins-Structure Function and Bioinformatics 78(1): 162-172.
  • Jorge-Finnigan A, Aguado C, Sanchez-Alcudia R, Abia D, Richard E, Merinero B, Gamez A, Banerjee R, Desviat LR, Ugarte M and Perez B (2010). "Functional and Structural Analysis of Five Mutations Identified in Methylmalonic Aciduria cblB Type." Human Mutation 31(9): 1033-1042.
  • Martin V, Abia D, Domingo E and Grande-Perez A (2010). "An interfering activity against lymphocytic choriomeningitis virus replication associated with enhanced mutagenesis." Journal of General Virology 91: 990-1003.
  • Pascual-Garcia A, Abia D, Mendez R, Nido GS and Bastolla U (2010). "Quantifying the evolutionary divergence of protein structures: The role of function change and function conservation." Proteins-Structure Function and Bioinformatics 78(1): 181-196.
  • Sanz D, Perona A, Claramunt RM, Pinilla E, Rosario Torres M and Elguero J (2010). "Protonation effects on the chemical shifts of Schiff bases derived from 3-hydroxypyridin-4-carboxaldehyde." Arkivoc: 102-113.
  • Schaffner-Barbero C, Gil-Redondo R, Ruiz-Avila LB, Huecas S, Lappchen T, den Blaauwen T, Fernando Diaz J, Morreale A and Andreu JM (2010). "Insights into Nucleotide Recognition by Cell Division Protein FtsZ from a mant-GTP Competition Assay and Molecular Dynamics." Biochemistry 49(49): 10458-10472.
  • Scheper J, Guerra-Rebollo M, Sanclimens G, Moure A, Masip I, Gonzalez-Ruiz D, Rubio N, Crosas B, Meca-Cortes O, Loukili N, Plans V, Morreale A, Blanco J, Ortiz AR, Messeguer A and Thomson TM (2010). "Protein-Protein Interaction Antagonists as Novel Inhibitors of Non-Canonical Polyubiquitylation." Plos One 5(6).
  • Gil-Redondo R, Estrada J, Morreale A, Herranz F, Sancho J and Ortiz AR (2009). "VSDMIP: virtual screening data management on an integrated platform." Journal of Computer-Aided Molecular Design 23(3): 171-184.
  • Land EJ, Perona A, Ramsden CA and Riley PA (2009). "Dopamine quinone chemistry: a study of the influence of amide, amidine and guanidine substituents -NH-CX-Y on the mode of reaction." Organic & Biomolecular Chemistry 7(5): 944-950.
  • Martinez-Martin N, Risueno RM, Morreale A, Zaldivar I, Fernandez-Arenas E, Herranz F, Ortiz AR and Alarcon B (2009). "Cooperativity Between T Cell Receptor Complexes Revealed by Conformational Mutants of CD3 epsilon." Science Signaling 2(83).
  • Moya-Garcia AA, Pino-Angeles A, Gil-Redondo R, Morreale A and Sanchez-Jimenez F (2009). "Structural features of mammalian histidine decarboxylase reveal the basis for specific inhibition." British Journal of Pharmacology 157(1): 4-13.
  • Pascual-Garcia A, Abia D, Ortiz AR and Bastolla U (2009). "Cross-Over between Discrete and Continuous Protein Structure Space: Insights into Automatic Classification and Networks of Protein Structures." Plos Computational Biology 5(3).
  • Priego E-M, Aguado L, Thibaut HJ, Luisa Jimeno M, Morreale A, Gago F, Camarasa M-J, Neyts J and Perez-Perez M-J (2009). "REQUIREMENTS AT THE PURINE MOIETY FOR THE INHIBITORY ACTIVITY OF 9-ARYLPURINES AGAINST COXSACKIE VIRUS B3 (CVB3) REPLICATION." Drugs of the Future 34: 135-135.
  • Rodriguez-Mateos M, Abia D, Garcia-Gomez JJ, Morreale A, de la Cruz J, Santos C, Remacha M and Ballesta JPG (2009). "The amino terminal domain from Mrt4 protein can functionally replace the RNA binding domain of the ribosomal P0 protein." Nucleic Acids Research 37(11): 3514-3521.
  • Rosa Lopez-Huertas M, Callejas S, Abia D, Dopazo A, Alcami J and Coiras M (2009). "Modifications in host cell structure and functions mediated by Tat intracellular expression are greatly dependent on the second exon." Retrovirology 6.
  • Bermudo R, Abia D, Ferrer B, Nayach I, Benguria A, Zaballos A, del Rey J, Miro R, Campo E, Martinez-A C, Ortiz AR, Fernandez PL and Thomson TM (2008). "Co-regulation analysis of closely linked genes identifies a highly recurrent gain on chromosome 17q25.3 in prostate cancer." Bmc Cancer 8.
  • Bermudo R, Abia D, Ferrer B, Nayach T, Benguria A, Zaballos A, Campo E, Ortiz AR, Thomson TM and Fernandez PL (2008). "Linear Discriminant Analysis of transcriptomic data reveals a 7-gene signature diagnostic of prostate cancer." Virchows Archiv 452: S44-S44.
  • Inforzato A, Rivieccio V, Morreale AP, Bastone A, Salustri A, Scarchilli L, Verdoliva A, Vincenti S, Gallo G, Chiapparino C, Pacello L, Nucera E, Serlupi-Crescenzi O, Day AJ, Bottazzi B, Mantovani A, De Santis R and Salvatori G (2008). "Structural characterization of PTX3 disulfide bond network and its multimeric status in cumulus matrix organization." Journal of Biological Chemistry 283(15): 10147-10161.
  • Perona A, Sanz D, Claramunt RM and Elguero J (2008). "NMR studies of novel Schiff bases derived from L-alpha-amino methyl esters and 3-hydroxypyridin-4-carboxaldehyde." Magnetic Resonance in Chemistry 46(10): 930-938.
  • Ruiz FM, Gil-Redondo R, Morreale A, Ortiz AR, Fabrega C and Bravo J (2008). "Structure-based discovery of novel non-nucleosidic DNA alkyltransferase inhibitors: Virtual screening and in vitro and in vivo activities." Journal of Chemical Information and Modeling 48(4): 844-854.
  • Garcia-Marcos A, Morreale A, Guarinos E, Briones E, Remacha M, Ortiz AR and Ballesta JPG (2007). "In vivo assembling of bacterial ribosomal protein L11 into yeast ribosomes makes the particles sensitive to the prokaryotic specific antibiotic thiostrepton." Nucleic Acids Research 35(21): 7109-7117.
  • Morreale A, Gil-Redondo R and Ortiz AR (2007). "A new implicit solvent model for protein-ligand docking." Proteins-Structure Function and Bioinformatics 67(3): 606-616.
  • Perona A, Sanz D, Claramunt RM, Pinilla E, Torres MR and Elguero J (2007). "Acid assisted proton transfer in 4- (4-R-phenylimino)methyl pyridin-3-ols: NMR spectroscopy in solution and solid state, X-ray and UV studies and DFT calculations." Journal of Physical Organic Chemistry 20(8): 610-623.
  • Martin V, Perales C, Abia D, Ortiz AR, Domingo E and Briones C (2006). "Microarray-based identification of antigenic variants of foot-and-mouth disease virus: a bioinformatics quality assessment." Bmc Genomics 7.
  • Murcia M, Morreale A and Ortiz AR (2006). "Comparative binding energy analysis considering multiple receptors: A step toward 3D-QSAR models for multiple targets." Journal of Medicinal Chemistry 49(21): 6241-6253.
  • Ortiz AR, Gomez-Puertas P, Leo-Macias A, Lopez-Romero P, Lopez-Vinas E, Morreale A, Murcia M and Wang K (2006). "Computational approaches to model ligand selectivity in drug design." Current Topics in Medicinal Chemistry 6(1): 41-55.
  • Perona A, Sanz D, Claramunt RM and Elguero J (2006). "Syntheses and structural studies of Schiff bases involving hydrogen bonds." Molecules 11(6): 453-463.
  • Sanz D, Perona A, Claramunt RM, Pinilla E, Torres MR and Elguero J (2006). "Solid-state and solution structural studies of 4-{ C(E) -1H-Azol-1-ylimino)methyl}pyridin-3-ols." Helvetica Chimica Acta 89(7): 1290-1303.
  • Talavera D, Morreale A, Meyer T, Hospital A, Ferrer-Costa C, Gelpi JL, De la Cruz X, Soliva R, Luque FJ and Orozco M (2006). "A fast method for the determination of fractional contributions to solvation in proteins." Protein Science 15(11): 2525-2533.
  • Crespo A, Marti MA, Kalko SG, Morreale A, Orozco M, Gelpi JL, Luque FJ and Estrin DA (2005). "Theoretical study of the truncated hemoglobin HbN: Exploring the molecular basis of the NO detoxification mechanism." Journal of the American Chemical Society 127(12): 4433-4444.
  • Dolker N, Morreale A and Maseras F (2005). "Computational study on the difference between the Co-C bond dissociation energy in methylcobalamin and adenosylcobalamin." Journal of Biological Inorganic Chemistry 10(5): 509-517.
  • Land EJ, Perona A, Ramsden CA and Riley PA (2005). "Oxidation of N-substituted dopamine derivatives: irreversible formation of a spirocyclic product." Organic & Biomolecular Chemistry 3(13): 2387-2388.
  • Lozano JJ, Soler M, Bermudo R, Abia D, Fernandez PL, Thomson TM and Ortiz AR (2005). "Dual activation of pathways regulated by steroid receptors and peptide growth factors in primary prostate cancer revealed by Factor Analysis of microarray data." Bmc Genomics 6.
  • Morreale A, de la Cruz X, Meyer T, Gelpi JL, Luque FJ and Orozco M (2005). "Partition of protein solvation into group contributions from molecular dynamics simulations." Proteins-Structure Function and Bioinformatics 58(1): 101-109.
  • Gonzalez-Guzman M, Abia D, Salinas J, Serrano R and Rodriguez PL (2004). "Two new alleles of the abscisic aldehyde oxidase 3 gene reveal its role in abscisic acid biosynthesis in seeds." Plant Physiology 135(1): 325-333.
  • Marco JL, de los Rios C, Garcia AG, Villarroya M, Carreiras MC, Martins C, Eleuterio A, Morreale A, Orozco M and Luque FJ (2004). "Synthesis, biological evaluation and molecular modelling of diversely functionalized heterocyclic derivatives as inhibitors of acetylcholinesterase/butyrylcholinesterase and modulators of Ca2+ channels and nicotinic receptors." Bioorganic & Medicinal Chemistry 12(9): 2199-2218.
  • Morreale A, de la Cruz X, Meyer T, Gelpi JL, Luque FJ and Orozco M (2004). "Linear response theory: An alternative to PB and GB methods for the analysis of molecular dynamics trajectories?" Proteins-Structure Function and Bioinformatics 57(3): 458-467.
  • Morreale A, Gelpi JL, Luque FJ and Orozco M (2003). "Continuum and discrete calculation of fractional contributions to solvation free energy." Journal of Computational Chemistry 24(13): 1610-1623.