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Filizola Lab Publications
Jounal Articles | Book Chapters | Abstracts
Journal Articles51. Provasi, D., Bortolato A., Filizola, M. “Exploring Molecular Mechanisms of Ligand Recognition by Opioid Receptors with Metadynamics.” Biochemistry (2009), 48(42):10020-10029. 50. Mobarec, J.C., Sanchez, R., Filizola, M. "Modern Homology Modeling of G-Protein Coupled Receptors: Which Structural Template to Use?" Journal of Medicinal Chemistry (2009), 52 (16), 5207-5216. 49. Filizola, M. "Increasingly accurate dynamic molecular models of G-protein coupled receptor oligomers: Panacea or Pandora's box for novel drug discovery?" Life Sciences (2009) in press. 48. Bortolato, A., Mobarec, J.C., Provasi, D., Filizola, M. "Progress in Elucidating the Structural and Dynamic Character of G-Protein Coupled Receptor Oligomers for Use in Drug Discovery" Current Pharmaceutical Design (2009), 15(35):4017-4025. 47. Blue,R., Kowalska,M.A., Hirsch, J., Murcia, M., Janczak, C., Harrington, A., Jirouskova, M., Li, J., Fuentes, R., Thornton, M.A., Filizola, M., Poncz, M., and Coller, B.S. "Structural and therapeutic insights from the species specificity and in vivo antithrombotic activity of a novel IIb-specific IIb3 antagonist" Blood (2009) 114(1):195-201. 46. Provasi, D., Murcia, M., Coller, B.S., and Filizola, M. “Targeted Molecular Dynamics Reveals Overall Common Conformational Changes Upon Hybrid Domain Swing-Out in beta3 Integrins.” PROTEINS: Structure, Function, and Bioinformatics (2009) 77(2):447-489. 45. Guo,W., Urizar, E., Kralikova,M., Mobarec,J.C., Shi, L., Filizola, M., Javitch, J.A. "Dopamine D2 Receptors Form Higher Order Oligomers at Physiological Expression Levels" The EMBO Journal, (2008), 27(17):2293-304. 44. Mobarec, J.C. & Filizola, M. "Advances in the Development and Application of Computational Methodologies for Structural Modeling of G-Protein Coupled Receptors" Expert Opinion on Drug Discovery (2008) 3:343-355. 43. González-Maeso, J., Ang, R., Yuen, T, Chan, P., Weisstaub, N.V., López-Giménez, J., Zhou, M., Okawa, Y., Callado, L.F., Milligan, G., Gingrich, J.A., Filizola, M., Meana, J.J., Sealfon, S.C. "Identification of a Novel Serotonin/Glutamate Receptor Complex Implicated in Psychosis" Nature (2008) 452:93-7. 42. Taylor, M. Fung, H.K., Rajgaria, R., Filizola, M., Weinstein, H., Floudas, C.A. "Mutations Affecting the Oligomerization Interface of G-Protein Coupled Receptors Revealed by a Novel De-novo Protein Design Framework." Biophysical Journal (2008) 94:2470-81. 41. Murcia, M., Jirouskova, M., Li, J.H., Coller, B.S., Filizola, M. "Functional and computational studies of the LIgand-associated Metal Binding Site (LIMBS) of beta3 integrins" PROTEINS: Structure, Function, and Bioinformatics (2008) 71:1779-1791. 40. Niv, M.Y., Filizola, M. “Influence of Oligomerization on the Dynamics of G-Protein Coupled Receptors as Assessed by Normal Mode Analysis.” PROTEINS: Structure, Function, and Bioinformatics (2008) 71:575-586. 39. Skrabanek, L., Murcia, M., Bouvier, M., Devi, L., George, S.R., Lohse, M.J., Milligan, G., Neubig, R., Palczewski, K., Parmentier, M., Pin, J.P., Vriend, G., Javitch, J.A., Campagne, F., Filizola, M. "Requirements and ontology for a G protein-coupled receptor oligomerization knowledge base." BMC Bioinformatics (2007) 8:177. 38. Pin, J.-P., Neubig, R., Bouvier, M., Devi, L., Filizola, M., Javitch, J.A., Lohse, M.J., Milligan, G., Palczewski, K., Parmentier, M., Spedding, M. “International Union of Basic and Clinical Pharmacology. LXVII. Recommendations for the Recognition and Nomenclature of G Protein-Coupled Receptor Heteromultimers.” Pharmacological Reviews (2007) 59:5-13. 37. Filizola, M., Wang, S.X., Weinstein, H. “Dynamic Models of G-Protein Coupled Receptors Dimers: Indications of Asymmetry in the Rhodopsin Dimer from Molecular Dynamics Simulations in a POPC Bilayer.” Journal of Computer-Aided Molecular Design (2006) 20(7-8):405-16. 36. Niv, M.Y., Skrabanek, L., Filizola, M., Weinstein, H. “Modeling activated states of GPCRs: the rhodopsin template” Journal of Computer-Aided Molecular Design (2006) 20(7-8):437-48.[pdf] 35. Mezei, M. & Filizola, M. “TRAJELIX: A computational tool for the geometric characterization of protein helices during molecular dynamics simulations.” Journal of Computer-Aided Molecular Design 2006 20: 97-107.[pdf] 34. Guo, W., Shi, L., Filizola, M., Weinstein, H., Javitch, J.A. “Crosstalk in G protein-coupled receptors: changes at the transmembrane homodimer interface determine activation” Proceedings of the National Academy of Science (2005) 102(48):17495-17500.[pdf] 33. Filizola, M., Weinstein, H. “The structure and dynamics of GPCR oligomers: A new focus in models of cell signaling mechanisms and drug design.” Current Opinion in Drug Discovery & Development (2005) 8(5):577-84.[pdf] 32. Filizola M. & Weinstein, H. “The study of G-protein coupled receptor oligomerization with computational modeling and bioinformatics.” FEBS Journal (2005) 272, 2926-2938.[pdf] 31. Filizola, M., Hassan, S.A., Artoni, A., Coller, B.S., Weinstein, H. “Mechanistic insights from a refined three-dimensional model of integrin alphaIIbbeta3” Journal of Biological Chemistry (2004) 279(23), 24624-24630.[pdf] 30. Filizola, M., Olmea, O., Weinstein, H. “Prediction of heterodimerization interfaces of G-protein coupled receptors with a new subtractive correlated mutation method” Protein Engineering (2002) 15, 881-885.[pdf] 29. Filizola, M. and Weinstein, H. “Structural models for dimerization of G-protein coupled receptors: The opioid receptor homodimers” Biopolymers (Peptide Science) (2002) 66, 317-325. (Journal Cover Illustration).[pdf] 28. Filizola, M. & Harris, D.H. “Molecular determinants of recognition and activation at GABAA/benzodiazepine receptors” International Journal of Quantum Chemistry (2002) 88, 56-64.[pdf] 27. Filizola, M. & Perez, J.J. “Assessment of the bioactive conformation of the vasoactive intestinal peptide (VIP) by computational methods” International Journal of Quantum Chemistry (2002) 88, 201-210.[pdf] 26. Filizola, M., Tasso, S.M., Loew, G.H., Villar, H.O., “Global physicochemical properties as activity discriminants for the mGluR1 subtype of metabotropic glutamate receptors” Journal of Computational Chemistry (2001) 22 (16), 2018-2027.[pdf] 25. Filizola, M., Villar, H.O., Loew, G.H. "Differentiation of delta, mu, and kappa opioid receptor agonists based on pharmacophore development and computed physicochemical properties" Journal of Computer Aided Molecular Design (2001) 15(4), 297-307.[pdf] 24. Filizola, M., Villar, H.O., Loew, G.H. "Molecular determinants of non-specific recognition of delta, mu, and kappa opioid receptors" Bioorganic Medicinal Chemistry (2001) 9(1), 69-76.[pdf] 23. Filizola, M., Harris, D.H., Loew, G.H. "Development of a 3D pharmacophore for non-specific ligand recognition of alpha1, alpha2, alpha3, alpha5, and alpha6 containing GABAA/benzodiazepine receptors" Bioorganic Medicinal Chemistry (2000) 8 (7), 1799-1807.[pdf] 22. Filizola, M. & Loew, G.H. "Probing the role of protein environment in Compound I formation of Chloroperoxidase (CPO)" Journal of American Chemical Society (2000) 122, 3599-3605.[pdf] 21. Corcho, F., Filizola, M., Perez, J.J. "Evaluation of the iterative simulated annealing technique in conformational search of peptides" Chemical Physics Letters (2000) 319, 65-70.[pdf] 20. Filizola, M., Harris, D.L., Loew, G.H. "Benzodiazepine-induced hyperphagia: Development and assessment of a 3D pharmacophore by computational methods" Journal of Biomolecular Structure & Dynamics (2000) 17 (5): 769-778. (Journal Cover Illustration).[pdf] 19. Filizola, M. & Loew, G.H. "Role of protein environment in horseradish peroxidase Compound I formation: Molecular dynamics simulations of horseradish peroxidase-HOOH complex" Journal of American Chemical Society (2000) 122 (1): 18-25.[pdf] 18. Perez, J.J., Filizola, M., Corcho, F., "Docking of peptide T onto the D1 domain of CD4 receptor" Journal of Biomolecular Structure & Dynamics (2000) 17 (4): 1-9.[pdf] 17. Filizola, M., Laakkonen, L., Loew, G.H. "3D modeling, ligand binding and activation studies of the cloned mouse delta, mu, and kappa opioid receptors" Protein Engineering (1999) 12 (11): 927-942.[pdf] 16. Filizola, M., Cartení-Farina, M., Perez, J.J. "Molecular modeling study of the differential ligand-receptor interaction at the delta, mu, and kappa opioid receptors" Journal of Computer Aided Molecular Design (1999) 13:397-407.[pdf] 15. Corcho, F.J., Filizola, M., Perez, J.J. "Assessment of the bioactive conformation of the farnesyltransferase protein binding recognition motif by computational methods" Journal of Biomolecular Structure & Dynamics (1999) 16: 1043-1052.[pdf] 14. Filizola, M., Cartení-Farina, M., Perez, J.J. "Modeling of the 3D structure of rhodopsin using a de novo approach to build G-protein coupled receptors" Journal of Physical Chemistry (1999) 103: 2520-2527.[pdf] 13. Filizola, M., Llorens, O., Cartenì-Farina, M., Perez, J.J. "New insights into the conformational requirements of B2 bradykinin antagonism" Bioorganic Medicinal Chemistry (1998) 6: 1491-1500.[pdf] 12. Filizola, M., Perez, J.J., Cartení-Farina, M. "Bundle: A program for building the transmembrane domains of G-protein coupled receptors" Journal of Computer Aided Molecular Design (1998) 12:111-118.[pdf] 11. Perez, J.J., Filizola, M., Cartení-Farina, M. "A general procedure for building the transmembrane domains of G-protein coupled receptors" Journal of Mathematical Chemistry (1998) 23: 229-238.[pdf] 10. Filizola, M., Centeno, N.B., Cartení-Farina, M. Perez, J.J., "Conformational analysis of the highly potent Bradykinin antagonist Hoe-140 by means of two different computational methods" Journal of Biomolecular Structure & Dynamics (1998), 15 (4): 639-652.[pdf] 9. Llorens, O., Filizola, M., Spisani, S., Marastoni, M., Herranz, C., Perez, J.J "Amygdalin binds to the CD4 receptor as suggested from molecular modeling studies" Bioorganic Medicinal Chemistry Letters (1998), 8: 781-786.[pdf] 8. Filizola, M., Rosell, G., Guerrero, A., Perez, J.J., "Conformational requirements for inhibition of the pheromone catabolism in Spodoptera littoralis" QSAR (1998) 17: 205-210.[pdf] 7. Llorens, O., Centeno, N.B., Filizola, M., Spisani, S., Marastoni, M., Calafell, M., Herranz, C., Perez, J.J. "A proposed bioactive form of peptide T and the design of peptidomimetics" Letters in Peptide Science (1998), 5:179–182.[pdf] 6. Filizola, M., Perez, J.J., Palomer, A., Mauleón, D., "Comparative molecular modeling study of the three dimensional structures of prostaglandin endoperoxide H2 synthase 1 and 2 (COX-1 and COX-2)" Journal of Molecular Graphics (1997), 15: 290-300.[pdf] 5. Filizola, M., Cartení-Farina, M., Perez, J.J. "Conformational study of vasoactive intestinal peptide (VIP) by computational methods", Journal of Peptide Research (1997), 50: 55-64.[pdf] 4. Filizola, M., Centeno, N., Perez, J. J. "Computational study of the conformational domains of peptideT" Journal of Peptide Science, (1997), 3: 85-92.[pdf] 3. Saviano, M., Rossi, F., Filizola, M., Di Blasio, B., Pedone, C."[Aib5,6-D-Ala8]cyclolinopeptide A grown from a benzene/acetonitrile mixture" Acta Crystallographica Sect.C (1995) C51, Part4: 663-666.[pdf] 2. Saviano, M., Rossi, F., Filizola, M., Isernia, C., Di Blasio, B., Benedetti, E., Pedone, C., Siemion, Z., Pedyczak, A. "Bioactive peptides: conformational studies of [Tyr4]cyclolinopeptide A" Biopolymers (1995), 36: 453-460.[pdf] 1. Zanotti, G., Rossi, F., Saviano, M., Tancredi, T., Saviano, G., Maione, A., Filizola, M., Di Blasio, B., Pedone, C. "A potent cyclolinopeptide A analogue: solid state and solution conformation of cyclo[Pro-Phe-Phe-Ala-Glu(otBu)]2" Journal of American Chemical Society (1995), 117: 8651-8658.[pdf] Jounal Articles | Book Chapters | Abstracts Book Chapters2. Filizola, M., Guo, W., Javitch, J.A., Weinstein, H. "Oligomerization domains of G-protein Coupled Receptors: Insights into the structural basis of GPCR association". In: Contemporary Clinical Neuroscience: The G Protein-Coupled Receptor Handbook, Ed: L.A. Devi, Humana Press Inc., Totowa, NJ, (2005) Chapter 11, pp. 243-265.[pdf] 1. Filizola, M., Visiers, I., Skrabanek, L., Campagne, F. and Weinstein H. “Functional mechanisms of GPCRs in a structural context.” In Molecular Neuropharmacology: Strategies and Methods, Eds., A. Schousboe and H. Bräuner-Osborne, Humana Press Inc., Totowa, NJ, (2003) Chapter 13, pp.235-266.[pdf] Jounal Articles | Book Chapters | Abstracts Abstracts26. Bortolato, A., Aburi, M., Urizar, E., Javitch, J.A., Filizola, M. “Modern Molecular Models and Simulations of Opioid Receptor Dimers.” Biophys. J. 2009 Volume 96, Issue 3, Pages 677a-677a 17. Murcia, M., Jiroušková, M., Li, J., Coller, B. S., Filizola, M. “Equilibrium and Non-Equilibrium Molecular Dynamics Simulations Provide Potential Mechanisms for the Loss of Ligand Binding to αIIbβ3 Mutants Affecting the Ligand-Induced Metal Binding Site (LIMBS)” Poster Presentation. BLOOD 108 (11): 512A-512A 1805 Part 1 NOV 16 2006. 16. Jirouskova, M., Murcia, M., Li, J.H., Coller, B.S., Filizola, M. “Functional and computational analysis of the role of the adjacent to metal ion-dependent adhesion site (ADMIDAS) of integrin alphaIIbbeta 3” Talk BLOOD 108 (11): 46A-47A 143 Part 1 NOV 16 2006. 15. Murcia, M., Coller, B.S., Filizola, M. “Allosteric transition pathway between inactive and active states of integrin alphallbbeta3 as simulated by targeted molecular dynamics” Poster Presentation. BIOPHYS. J. : 379A-379A Suppl. S JAN 2007. 14. Niv, M.Y., Filizola, M. “Dynamic models of G-protein coupled receptor oligomers: Insights from normal mode analysis.” Poster Presentation. BIOPHYS. J. : 379A-379A Suppl. S JAN 2007. 13. Fowler, J.C., Filizola, M., Weinstein, H., Javitch, J.A., Mailman, R.B. “Stereochemical effects on functional selectivity at the dopamine D2L receptor” Poster Presentation. ACTA PHARMACOLOGICA SINICA 27: 408-408 Suppl. 1 JUL 2006. 12. Filizola, M. “Computational studies of G-protein coupled receptor oligomers” ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 231: - 287-COMP MAR 26 2006. 11. Fowler, J.C., Filizola, M., Weinstein, H., Javitch, J.A., Mailman, R.B. ”Transmembrane five effects on functional gelectivity at the dopamine D21, receptor” Poster Presentation. FASEB JOURNAL 20 (4): A246-A246 Part 1 MAR 6 2006. 10. Filizola, M., Basdevant, N., Weinstein, H. “On the specificity of RGS proteins in regulating G protein-mediated receptor signal transduction pathways.” Poster Presentation. BIOPHYS. J. 90: Suppl. S JAN 2006. 9. Fowler, J.C., Filizola, M., Weinstein, H., Javitch, J.A., Nichols, D.E., Mailman, R.B. “Receptor-ligand interactions related to dopamine D2L, receptor functional selectivity. Poster Presentation. FASEB J. 19 (4): A530-A530 Part 1 Suppl. S MAR 4 2005. 8. Wang, S.X., Filizola, M., Ceruso, M., Weinstein, H. “Rhodopsin dimers: Molecular dynamics simulations using discrete representations of the membrane and water environment.” Poster Presentation. BIOPHYS. J. 88 (1): 81A-81A Part 2 Suppl. S JAN 2005. 7. Filizola M., Hassan SA, French DL, Coller BS, Weinstein H “A refined model of integrin alphaIIbbeta3 using a cognate template and a new method for identifying accurate loop conformations in proteins” Poster Presentation. BIOPHYS. J. 84 (2): 459A-459A Part 2 Suppl. S FEB 2003. 6. Filizola M., Guo W., Javitch JA, Weinstein H “Dimerization in G-protein coupled receptors: Correlation analysis and electron density maps of rhodopsin from different species suggest subtype-specific interfaces” Poster Presentation. BIOPHYS. J. 84 (2): 269A-270A Part 2 Suppl. S FEB 2003. 5. Watts SW, Filizola M, Galligan JJ, Weinstein H, Fink GD “Potential functional interaction of the ETA and ETB receptors” Poster Presentation. HYPERTENSION 40 (3): 26 SEP 2002. 4. Filizola M, Olmea O, Weinstein H “Using correlated mutation analysis to predict the heterodimerization interface of GPCRs” Poster Presentation. BIOPHYS. J. 82 (1): 2307 Part 2 JAN 2002. 3. Filizola M, Villar H, Loew G “A new generation of 3D models of delta, mu and kappa opioid receptors”. Poster Presentation. BIOPHYS. J. 80 (1): 205 Part 2 JAN 2001. 2. Filizola M, Loew GH “Role of protein environment in horseradish peroxidase and chloroperoxidase compound I information” Poster Presentation. BIOPHYS. J. 78 (1): 1677Pos Part 2 JAN 2000. 1. Laakkonen L, Filizola M, Loew G “Construction, assessment and characterization of ligand-receptor complexes in models of opioid receptors” Poster Presentation. BIOPHYS. J. 76 (1): A15-A15 Part 2 JAN 1999. |
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