Curriculum Vitae - Istituto Italiano di Tecnologia

Curriculum Vitae
Dr. Giovanni Bottegoni
Computational Medicinal Chemist
th
Born in Ancona, Italy - December 12 1976
Dept. of Drug Discovery and Development
Istituto Italiano di Tecnologia
via Morego n.30
Genova (GE), 16163
ITALY
Work: +39 010 71781522
Mobile: +39 333 8476379
[email protected]
[email protected]
Work Experiences
•
Team Leader
2012 - Present Istituto Italiano Tecnologia, Genoa, GE – ITALY
Within the Computational Chemistry and Structural Biophysics function, I am currently in
charge of planning and coordinating virtual ligand screening and structure-based hit-tolead optimization campaigns on targets of interest in several drug discovery projects.
•
Visiting Scientist
February 2012 – April 2012 The Skaggs School of Pharmacy and Pharmaceutical
Sciences and San Diego Supercomputer Center (SDSU), University of California,
San Diego, CA – USA
At UCSD, I’ve been working on assessing the reliability of the results provided by
several docking paradigms typically employed in hit discovery when applied in
advanced stages of drug development, namely in hit-to-lead and lead optimization
campaigns.
•
Sr Post Doc
2008 - 2012 Istituto Italiano Tecnologia, Genoa, GE - ITALY
In the Computational Medicinal Chemistry group I applied state-of-the-art docking
and MD techniques to molecular targets of interest in the fields of neurodegeneration,
cognitive disorders, and inflammation.
•
Post Doc
2006 - 2008 The Scripps Research Institute, La Jolla, CA - USA
As a post doc in the lab of Professor Ruben Abagyan, I've been developing and
applying advanced ligand docking and VLS protocols. More specifically, I've been
studying the implementation of the receptor flexibility in standard simulations.
Education
•
Doctoral Degree. Graduate school in Medicinal Chemistry
2003 - 2005 University of Bologna, Bologna, BO
Graduate School in Medicinal Chemistry. Research Title: Development of Statistical Tools
to improve Performance of Conformational Sampling and Docking Programs of Interest in
Computational Medicinal Chemistry. Supervisor: Prof. Maurizio Recanatini
•
Master Degree. Pharmaceutical Biotechnology, Faculty of Pharmacy
1995 - 2002 University of Bologna, Bologna, BO
Final Dissertation Title: Study of the 3D structures of Cyclin Dependent Kinase 5 and its
activator Nck5A through the homology modeling technique. Supervisor: Prof. Maurizio
Recanatini. Final Mark: 110/110 cum laude
Professional Skills and Languages
•
Relevant Skills: Molecular Modeling, Drug Design, Virtual Screening, Docking,
Molecular Dynamics, Computational Chemistry, Cluster Analysis, Drug Discovery.
•
Software of relevance in Computational Medicinal Chemistry: ICM, Modeller,
AMBER, NAMD, ACEMD, G09, enhanced sampling tools (PLUMED), Schrodinger
(MCPRO+, LigPrep, MacroModel).
•
OSs and Programming Languages: Linux, MacOS, and Windows; Matlab, Python.
•
Italian (native) and English (fluent)
Peer-Reviewed Publications
Scarpi D., Cirelli D., Matrone C., Castronovo G., Rosini P., Occhiato E.G., Romano F., Bartali L.,
Clemente A.M., Bottegoni G., Cavalli A., De Chiara G., Bonini P., Calissano P., Palamara A.T.,
Garaci E., Torcia M.G., Guarna A., Cozzolino F. Low molecular weight, non-peptidic agonists of
TrkA receptor with NGF-mimetic activity. Cell Death Dis. 2012
Garuti L., Roberti M., Bottegoni G. Polo-Like Kinase Inhibitors. 2012 Curr Med Chem 19 in print
Kacker P., Masetti M., Mangold M., Bottegoni G., Cavalli A. Combining dyad protonation and
active site plasticity in BACE-1 structure-based drug design J Chem Inf Modeling 2012 52 (5) 10791085
Fu J.*, Bottegoni G.*, Sasso O, Bertorelli R, Rocchia W, Masetti M, Guijarro A, Lodola A, Armirotti
A, Garau G, Bandiera T, Reggiani A, Mor M, Cavalli A, Piomelli D. A catalytically silent FAAH-1
variant drives anandamide transport in neurons. Nature Neurosci. 2012 15(1) 64-69 *equal
contribution
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. Synthesis
of Monomeric Derivatives To Probe Memoquin's Bivalent Interactions. 2011 J Med Chem 54(24)
8299-8304
Favia AD., Bottegoni G., Nobeli I., Bisignano P., Cavalli A. SERAPhiC: a Benchmark for in Silico
Fragment-Based Drug Design. 2011 J Chem Inf Model. 51(11) 2882-2896
De Vivo M., Bottegoni G., Berteotti A., Recanatini M., Gervasio F.L., Cavalli A. Cyclin-dependent
kinases: bridging their structure and function through computations. 2011 Future Medicinal
Chemistry 3(12) 1551-1559
Bottegoni G.*, Favia AD.*, Recanatini M., Cavalli A. Polypharmacology: fragment-based
approaches and computational methods in the search for novel multitarget drugs. 2011 Drug
Discovery Today in print *equal contribution
Garuti L., Roberti M., Bottegoni G. Non-ATP Competitive Protein Kinase Inhibitor. 2011 Curr Med
Chem 18 2981-2994
Belluti F., Bartolini M., Bottegoni G., Bisi A., Cavalli A., Andrisano V., Rampa A. Benzophenonebased derivatives: A novel series of potent and selective dual inhibitors of acetylcholinesterase and
acetylcholinesterase-induced beta-amyloid aggregation. 2011 Eur J Med Chem 46 1682-1693
Bottegoni G., Rocchia W., Rueda M., Abagyan R., Cavalli A. Systematic Exploitation of Multiple
Receptor Conformations in Virtual Ligand Screening. 2011 Plos One 6(5) e18845
Bottegoni G. Protein-Ligand Docking 2011 Frontiers in Bioscience 17 2289-2306
Garuti L., Roberti M., Bottegoni G. Non-ATP Competitive Protein Kinase Inhibitor. 2010 Curr Med
Chem 17 2804-2821
Rueda M., Bottegoni G., Abagyan R. Recipes for the Selection of Experimental Protein
Conformations for Virtual Screening. 2010 J Chem Inf Modeling 50 186-193
Garuti, L., Roberti M., Bottegoni G. Small Molecules Aurora Kinases Inhibitors. 2009 Curr Med
Chem 16 1949-1963
Rueda, M., Bottegoni G., Abagyan, R. Consistent improvement of cross docking results using
binding site ensembles generated with Elastic Network Normal Modes. 2009 J Chem Inf Modeling
49 716-725
Bottegoni, G., Kufareva, I., Totrov, M., Abagyan, R. Four -dimensional Docking: a fast and
accurate account of receptor flexibility in ligand docking. 2009 J Med Chem 52 397-406
Bottegoni, G., Kufareva, I., Totrov, M., Abagyan, R. A new method for ligand docking to flexible
receptors by dual alanine scanning and refinement (SCARE). 2008 J CAMD 22(5) 311-325
Bottegoni, G., Rocchia, W., Recanatini, M., Cavalli, A. AClAP, Autonomous hierarchical
agglomerative Cluster Analysis based Protocol to partition conformational datasets Bioinformatics
2006 22(14) 58-65
Bottegoni G., Cavalli A., Recanatini M. A comparative study on the application of hierarchicalagglomerative clustering approaches to the outputs of reiterated docking runs. J Chem Inf Model.
2006 45(2) 852-862
De Vivo M., Cavalli A., Bottegoni G., Carloni P., Recanatini M. Role of phosphorylated Thr160 for
the activation of the CDK2/Cyclin A complex. Proteins. 2006 62 89-98.
Recanatini, M.; Cavalli, A.; Bottegoni, G., Computational approaches to the study of dual-site and
peripheral site binding ache inhibitors. Chem Biol Interact 2005, 157-158, 414-415.
Cavalli A., Bottegoni G., Raco C., De Vivo M., Recanatini M. A computational study of the binding
of propidium to the peripheral anionic site of human acetylcholinesterase. J. Med. Chem. 2004 47
3991-3999.
Recanatini M., Bottegoni G., Cavalli A. In Silico Antitarget Screening. Drug Discovery Today:
Technologies 2004 1 209-215.
Book Chapters
Bottegoni G., Rocchia W., Cavalli A. (2012) Application of Conformational Clustering in
Protein-Ligand Docking. In Computer-aided Drug Design, Methods in Molecular Biology,
Baron, R., Ed. Humana Press, 819 p 169-186
Roberti M., Bottegoni G., Recanatini M. (2010) Multiple Ligand Strategy in anticancer drug
discovery. In Multifunctional Drugs: New Chimeras in Medicinal Chemistry, Rapposelli, S., Ed.
Transworld Research Network: Kerala, p 217-242
Recent Congresses, Conferences, and Meetings.
Bottegoni G., Kufareva I., Abagyan R., Cavalli A. (2012) Can Ligand Docking Efficiently
Predict Activity Cliffs? (poster), Nuove Prospettive in Chimica Farmaceutica, April 2012,
Riccione (RN) - Italy
Bottegoni G., (2012) Computational Hit Discovery of a Novel Anandamide Transport Inhibitor
nd
(oral presentation, invited), 2 ICM User Group Meeting, March 2012, San Diego, CA - USA
Bottegoni G., (2012) Computational Hit Discovery of a Novel Anandamide Transport Inhibitor
(oral presentation), ACS National Meeting, March 2012, San Diego, CA - USA
Bottegoni G., (2011) Computational Hit Discovery of a Novel Anandamide Transport Inhibitor
(oral presentation, invited), Computationally-driven Drug Discovery, November 2011, L’Aquila
- Italy
Bottegoni G., (2011) Computational Hit Discovery of a Novel Anandamide Transport Inhibitor
(oral presentation, invited), Innovative Approaches to Computational Drug Discovery, October
2011, CECAM-EPFL, Lausanne - Switzerland
Bottegoni G., Veronesi M., Dalvit C., Cavalli A. (2011) Virtual Ligand Screening Studies on an
Intermediate State of CDK5 (poster), Nuove Prospettive in Chimica Farmaceutica, March
2011, Trieste (TS) - Italy