Molecular and Statistical Biophysics Group

2011 Licensed Ph.D:

• Docking Ligands on Protein Surfaces: The Case Study of Prion Protein.
  Kranjc A, Bongarzone S, Rosetti G, Biarnés X, Cavalli A, Bolognesi M, Roberti M, Legname G, Carloni P.
  Journal of Chemical Theory and Computation 2009/5:2565-73.
• Complementary medicinal chemistry-driven strategies toward new antitrypanosomal and antileishmanial lead drug candidates.
  Cavalli A, Lizzi F, Bongarzone S, Belluti F, Piazzi L, Bolognesi ML.
  Fems Immunology And Medical Microbiology 2010/58:51-60.
• Synthesis and evaluation of a library of 2,5-bisdiamino-benzoquinone derivatives as probes to modulate protein-protein interactions in prions.
  Tran HNA, Bongarzone S, Carloni P, Legname G, Bolognesi ML.
  Bioorganic & Medicinal Chemistry Letters 2010/20:1866-68.
• Discovery of a class of diketopiperazines as antiprion compounds.
  Bolognesi ML, Tran, HNA, Staderini M, Monaco A, López-Cobeñas A, Bongarzone S, Biarnés X, López-Alvarado P, Cabezas N, Caramelli M, Carloni P, Menéndez JC, Legname G.
  ChemMedChem 2010/5:1324-1334.
• Parallel synthesis, evaluation, and preliminary structure activity relationship of 2,5-diamino-1,4-benzoquinones as a novel class of bivalent anti-prion compounds.
  Bongarzone S, Tran HNA, Cavalli A, Roberti M, Carloni P, Legname G, Bolognesi ML.
  Journal of Medicinal Chemistry 2010/53.
• Molecular Motion in Drug Design: the coming age of the metadynamics method.
  Biarnés X, Bongarzone S, Vargiu AV, Ruggerone P, Carloni P.
  Journal of Computer-Aided Molecular Design 2011/25:395-402.
• The concept of privileged structures in rational design: focus on acridine and quinoline scaffolfds in neurodegenerative and protozoan diseases.
  Bongarzone S, Bolognesi ML.
  Expert Opinion on Drug Discovery 2011/6:251-68.
• Hybrid Lipoic Acid Derivatives to Attack Prion Disease on Multiple Fronts.
  Bongarzone S, Tran HNA, Cavalli A, Roberti M, Rosini M, Carloni P, Legname G, Bolognesi ML.
  ChemMedChem 2011/6:601-05.
   

• Molecular field theory with atomistic modeling for the curvature elasticity of nematic liquid crystals.
  Cestari M., Bosco A. and Ferrarini A.
  J. Chem. Phys. 2009/131(5), 054104.
• Hybridization in Nanostructured DNA Monolayers Probed by AFM: Theory versus Experiment.
  Bosco A., Bano F., Parisse P., Casalis L., De Simone A. and Micheletti C.
  Nanoscale 2011, accepted.
   

• A small focused chemical library of 2-aminoimidazole derivatives as BACE-1 inhibitors: structure-based design, microwave-assisted synthesis and biological evaluation.
  Chiriano G, De Simone A, Mancini F, Perez DI, Cavalli A, Bolognesi ML, Legname G, Martinez A, Andrisano V, Carloni P, Roberti M.
  Eur J Med Chem 2012/48:206-13.
• Synthesis of monomeric derivatives to probe memoquin’s bivalent interactions
  Bolognesi ML, Chiriano G, Bartolini M, Mancini F, Bottegoni G, Maestri V, Czvitkovich S, Windisch M, Cavalli A, Minarini A, Rosini M, Tumiatti V, Andrisano V, Melchiorre C.
  J Med Chem 2011/54(24):8299-304.
• Sequential virtual screening approach to the identification of small organic molecules as potential BACE-1 inhibitors.
  Chiriano G, Sartini A, Mancini F, Andrisano V, Bolognesi ML, Roberti M, Recanatini M, Carloni P, Cavalli A.
  Chem Biol Drug Des 2011/77(4):268-71.
   

• Conformational ensemble of Huntingtin N-term in aqueous solution explored by atomistic simulations.
  Rossetti G., Cossio P., Laio A. and Carloni P.
  FEBS Letters, Vol. 585, Issue 19, Pages 3086-3089. October 2011.
• Which similarity measure is better for analyzing protein structures in a molecular dynamics trajectory?
  Cossio P., Laio A. and Pietrucci F.
  Physical Chemistry Chemical Physics, 2011/13(22):10421-25.
• Exploring the universe of protein structures beyond the Protein Data Bank.
  Cossio P., Trovato A., Pietrucci F., Seno F., Maritan A. and Laio A.
  PLOS Computational Biology, Vol. 6 , Issue 11, e1000957, November 2010.
• Optimizing the Performance of Bias-Exchange Metadynamics: Folding a 48-Residue LysM Domain Using a Coarse-Grained Model.
  Cossio P., Marinelli F., Pietrucci F. and Laio A.
  Journal of Physical Chemistry B, 2010/114:3259-65.