Projects
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SERAPhiC
(Selected Fragment Protein Complexes)
presented at the EFMC-ISMC 2010, XXIst Symposium on Medicinal Chemistry 2010 (Brussels)
presented at the Fragment Based Lead Discovery Conference 2010
(Philadelphia)
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Current projects: New generation of 3D-QSA(P)R based on quantum-mechanical descriptors. Design of dual COXs/FAAH inhibitors. Design of GSK-3beta inhibitors for Alzheimer's disease. Protein clustering by means of potential maps comparison. High quality dataset for fragment-based drug design (SeRAPhiC)
General research interests: Protein-Ligand interactions (MM simulations), molecular dynamics simulation, enhanced sampling methods, comparative modeling, chemoinformatics and computational structural biology.
Old projects: Drug design of Acetyl and Butirryl Cholinesterases inhibitors as potential anti Alzheimer agents. 3D theoretical model of the human Aromatase enzyme (PDB accession code 1TQA) and design of potential inhibitors as anti breast cancer agents (docking simulations and 3D-QSAR approaches). Docking studies on members of the Short Chain Dehydrogenase/Reductase (SDR) family. Docking studies and chemical profiling of members of the human cytosolic Sulfotranferases (hSULTs) family. 11-beta-HSD type 1 protein, metadynamics study: Effects of single-point mutations on the protein capabilities. Characterisation of SDRs with unknown functions.
Other Publications
Favia AD, Masetti M, Recanatini M, Cavalli A. Substrate Binding Process and Mechanistic Functioning of Type 1 11b-Hydroxysteroid Dehydrogenase from Enhanced Sampling Methods. PLoS one. In press (WEB_LINK)
Favia AD, Bottegoni G, Nobeli I, Bisignano P, Cavalli A. SERAPhiC: a Benchmark for in Silico Fragment-Based Drug Design. J Chem Inf Model. In press (WEB_LINK)
Bicego M, Favia AD, Bisignano P, Cavalli A, Murino V. An innovative protocol for comparing protein binding sites via atomic grids maps. KDIR 2011 proceedings. Accepted
Bottegoni G, Favia AD, Recanatini M, Cavalli A. The role of fragment-based and computational methods in polypharmacology. Drug Discov Today. In press (WEB_LINK)
Stefanachi A, Favia AD, Nicolotti O, Leonetti F, Pisani L, Catto M, Zimmer C, Hartmann RW, Carotti A. Design, Synthesis, and Biological Evaluation of Imidazolyl Derivatives of 4,7-Disubstituted Coumarins as Aromatase Inhibitors Selective over 17-α-Hydroxylase/C17-20 Lyase. J Med Chem. 2011;54(6):1613-25. (WEB_LINK)
Favia AD, Nobeli I. Using chemical structure to infer biological function. In Computational Approaches in Cheminformatics and Bioinformatics (Bender, A. & Rajarshi, G., eds.). Wiley. In press. Book Chapter (WEB_LINK)
Favia AD. Theoretical and computational approaches to ligand-based drug discovery. Front Biosci. 2011;1(16):1276-1290. (WEB_LINK)
Kahraman A, Morris RJ, Laskowski RA, Favia AD, Thornton JM. On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins. Proteins. 2009;78:1120-1136. (WEB_LINK)
Nobeli I, Favia AD, Thornton JM. Protein promiscuity and its implications for biotechnology. Nat Biotechnol. 2009;27(2):157-167. (WEB_LINK)
El-Hawari Y, Favia AD, Pilka ES, Kisiela M, Oppermann U, Martin HJ, Maser E. Analysis of the substrate-binding site of human carbonyl reductases CBR1 and CBR3 by site-directed mutagenesis. Chem Biol Interact. 2009;178(1-3):234-41. (WEB_LINK)
Persson B, Kallberg Y, Bray JE, Bruford E, Dellaporta SL, Favia AD, Duarte RG, Jörnvall H, Kavanagh KL, Kedishvili N, Kisiela M, Maser E, Mindnich R, Orchard S, Penning TM, Thornton JM, Adamski J, Oppermann U. The SDR (short-chain dehydrogenase/reductase and related enzymes) nomenclature initiative. Chem Biol Interact. 2009;178(1-3):94-98. (WEB_LINK)
Blum A, Favia AD, Maser E. 11beta-Hydroxysteroid dehydrogenase type 1 inhibitors with oleanan and ursan scaffolds. Mol Cell Endocrinol. 2009;301(1-2):132-6. (WEB_LINK)
Thornton JM, Favia AD, Nobeli I, Furnham N. The evolution of specificity in large protein families. Febs Journal. 2008;275:23-23. (WEB_LINK)
Favia AD, Nobeli I, Glaser F, Thornton JM. Molecular docking for substrate identification: the short-chain dehydrogenases/reductases. J Mol Biol. 2008;375(3):855-874. (WEB_LINK)
Catto M, Nicolotti O, Leonetti F, Carotti A, Favia AD, Soto-Otero R, Mendez-Alvarez E, Carotti A. Structural insights into monoamine oxidase inhibitory potency and selectivity of 7-substituted coumarins from ligand- and target-based approaches. J Med Chem. 2006;49(16):4912-4925. (WEB_LINK)
Favia AD, Cavalli A, Masetti M, Carotti A, Recanatini M. Three-dimensional model of the human aromatase enzyme and density functional parameterization of the iron-containing protoporphyrin IX for a molecular dynamics study of heme-cysteinato cytochromes. Proteins. 2006;62(4):1074-1087. (WEB_LINK)
Leonetti F, Favia A, Rao A, Aliano R, Paluszcak A, Hartmann RW, Carotti A. Design, synthesis, and 3D QSAR of novel potent and selective aromatase inhibitors. J Med Chem. 2004;47(27):6792-6803. (WEB_LINK)
