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De Vivo

Dr. Marco De Vivo

Group Leader

 

Professional career

2013- Principal Investigator (Tenure Track since 09/2014), Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia (IIT), Genoa, Italy

2009-2013 Team Leader in computational chemistry and project leader in drug discovery, Istituto Italiano di Tecnologia (IIT), Genoa, Italy

2007-2009 Research Scientist at Rib-X Pharmaceuticals, Inc., New Haven, CT - USA (now Melinta Therapeutics)

2004-2007 Postdoctoral Researcher in the group of Prof. Michael L. Klein, Center for Molecular Modeling, Dept. of Chemistry University of Pennsylvania (UPenn), Philadelphia, PA – USA

2003 Visiting Scientist at the Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH), Zürich, Switzerland.

2001-2002 Visiting Scientist at the International School for Advanced Studies (SISSA), Trieste, Italy.

 

Education

2004 - PhD in Pharmaceutical Sciences, Dept. of Pharmaceutical Sciences, University of Bologna, Italy.

2000 - BA and MSc in Chemistry (Italian Laurea), Dept. of Chemistry, University of Bologna, Italy.

 

Current research

In his research lines, Marco De Vivo pursues his interest in enzymatic catalysis and drug discovery through the application of molecular modeling to study enzymes of pharmaceutical relevance. Toward this end, in his lab they integrate computational and medicinal chemistry to design, synthesize and test novel compounds. Results are fully integrated with structural, biochemical and pharmacological data to characterize function and inhibition of targeted enzymes, and perform structure-based drug discovery of new molecular entities endowed with a desired pharmacological activity.

 

Publications

1. G. Palermo, I. Bauer, P. Campomares, A. Cavalli, A. Armirotti, S. Girotto, U. Roethlisberger, M. De Vivo, “Keys to lipid selection in FAAH catalysis: Structural flexibility, gating residues and multiple binding pockets”, Plos Comp. Biol. 2015, 11(6): e1004231

2. G. Palermo, M. De Vivo, “Computational Chemistry for Drug Discovery” Encyclopedia of Nanotechnology (Springer) – 2015, pp 1-15

3. G. Palermo, A. Cavalli, M. L. Klein, M. Alfonso-Prieto, M. Dal Peraro, M. De Vivo, “Catalytic metal ions and enzymatic processing of DNA and RNA”, Accounts Chem. Res., 2015 Feb 17;48(2):220-8

4. D. Pizzirani, A. Bach, N. Realini, A. Armirotti, L. Mengatto, I. Bauer, S. Girotto, C. Pagliuca, M. De Vivo, M. Summa, A. Ribeiro, D. Piomelli, “Benzoxazolone-Carboxamides: Potent systemically active inhibitors of intracellular Acid Ceramidase”, Angew Chem Int Ed Engl. 2015 Jan 7;54(2):485-9

5. G. Palermo, U. Roethlisberger, A. Cavalli, M. De Vivo, “Computational insights into function and inhibition of FAAH” (Review), Eur. J. Med. Chem., 2015 Feb 16;91:15-26

6. G. Palermo, P. Campomares, A. Cavalli, U. Roethlisberger, M. De Vivo, “Anandamide hydrolysis in FAAH reveals a dual strategy for efficient enzyme-assisted amide bond cleavage via nitrogen inversion”, J. Phys. Chem. B 2015 Jan 22;119(3):789-801.Special Issue, W. L. Jorgensen 65th birthday

7. G. Palermo, P. Campomares, M. Neri, D. Piomelli, A. Cavalli, U. Roethlisberger, M. De Vivo, “Wagging the tail: essential role of substrate flexibility in FAAH catalysis”, J. Chem. Theory Comput., 2013, 9 (2), pp 1202–1213

8. G. Palermo, M. Stenta, A. Cavalli, M. Dal Peraro, M. De Vivo, “Molecular simulations highlight the role of metals in catalysis and inhibition of type II topoisomerase”, J. Chem. Theory Comput., (Letter) 2013, 9 (2), pp 857–862. Cover Article for February 2013, Vol. 9 Num. 2

9. L. Bertolacci, E. Romeo, M. Veronesi, P. Magotti, C. Albani, M. Dionisi, C. Lambruschini, R. Scarpelli, A. Cavalli, M. De Vivo, D. Piomelli, G. Garau, “A binding site for non-steroidal anti-inflammatory drugs in Fatty Acid Amide Hydrolase”, J. Am. Chem. Soc., (Communication) 2013 Jan 9;135(1):22-5

10. A.D. Favia, D. Habrant, R. Scarpelli, M. Migliore, C. Albani, S. M. Bertozzi, M. Dionisi, G. Tarozzo, D. Piomelli, A. Cavalli, M. De Vivo, “Identification and characterization of carprofen as a multitarget fatty acid amide hydrolase/Cyclooxygenase inhibitor”, J. Med. Chem., 2012, 55 (20), pp 8807–8826

11. S. V. C. Vummaleti, D. Branduardi, M. Masetti, M. De Vivo, R. Motterlini, A. Cavalli, “Theoretical Insights into the Mechanism of Carbon Monoxide (CO) Release from CO-Releasing Molecules”, Chemistry: A European Journal, 2012, Vol. 18, Issue 30, 9267-9275.

12. A. Lodola, D. Branduardi, M. De Vivo, L. Capoferri, M. Mor, D. Piomelli, A. Cavalli, ”A catalytic mechanism for cysteine N-terminal nucleophile hydrolases, as revealed by free energy simulations”, Plos One, 2012, 7(2), e32397

13. G. Palermo, D. Branduardi, M. Masetti, A. Lodola, M. Mor, D. Piomelli, A. Cavalli, M. De Vivo, “Covalent inhibitors of fatty acid amide hydrolase: A rationale for the activity of piperidine and piperazine aryl ureas”, J. Med. Chem., 2011, 54 (19), 6612–6623

14. M. De Vivo, G. Bottegoni, A. Berteotti, M. Recanatini, F.L. Gervasio, A. Cavalli, “Cyclin-dependent Kinases: Bridging their Structure and Function through Computations”, Future Medicinal Chemistry, Sep;3(12):1551-9, 2011 (Review)

15. D. Branduardi, M. De Vivo, N. Rega, V. Barone, A. Cavalli, “Methyl phosphate dianion hydrolysis in solution characterized by path collective variables coupled with DFT-based enhanced sampling simulations”, J. Chem. Theory Comput., 2011, 7, 539-543 (Letter)

16. M. De Vivo, “Bridging Quantum Mechanics and Structure-Based Drug Design”, Front Biosci. 2011, Jan 1; 16: 1619-1633. (Review)

17. M. H. Ho, M. De Vivo, M. Dal Peraro, M. L. Klein, “Understanding the Effect of Magnesium Ion Concentration on the Catalytic Activity of Ribonuclease H through Computation: Does a Third Metal Binding Site Modulate Endonuclease Activity?”
J. Am. Chem. Soc., 2010, 132, 13702-13712.

18. M. H. Ho, M. De Vivo, M. Dal Peraro, M. L. Klein, “Unraveling the Catalytic Pathway of Metalloenzyme Farnesyltransferase through QM/MM Computation”, J. Chem. Theory Comput., 2009, 5, 1657-1666.

19. M. De Vivo*, M. Dal Peraro, M. L. Klein, “Phosphodiester Cleavage in Ribonuclease H occurs via an Associative Two-Metal-Aided Catalytic Mechanism”, J. Am. Chem. Soc., 2008 130(33),10955-62. Highlighted in JACS select 2008, 130 (50),16824–16827.

20. M. De Vivo, A. Cavalli, P. Carloni, M. Recanatini, “Computational Study of the Phosphoryl Transfer Catalyzed by a Cyclin-Dependent Kinase”, Chemistry: A European Journal, 2007 13(30), 8437-44.

21. M. De Vivo*, B. Ensing, M. Dal Peraro, G. A. Gomez, D. W. Christianson, M. L. Klein, “Proton Shuttles and Phosphatase Activity in Soluble Epoxide Hydrolase”, J. Am. Chem. Soc., 2007, 129(2), 387-394.

22. M. Dal Peraro, K. Spiegel, G. Lamoureux, M. De Vivo, W. F. DeGrado, M. L. Klein, “Modeling the Charge Distribution at Metal Sites in Proteins for Molecular Dynamics Simulations”, J. Struct. Biol., 2007, 157(3), 444-453.

23. B. Ensing, M. De Vivo, Z. Liu, P. Moore, M. L. Klein, “Metadynamics as a Tool for Exploring Free Energy Landscape of Chemical Reactions”, Accounts Chem. Res., 2006, 39, 73.

24. M. De Vivo, A. Cavalli, G. Bottegoni, P. Carloni, M. Recanatini, “Role of Phosphorylated Thr160 for the Activation of the CDK2/Cyclin A Complex”, Proteins, 2006, 62, 89-98.

25. M. De Vivo*, B. Ensing, M. L. Klein, “Computational Study of Phosphatase Activity in Soluble Epoxyde Hydrolase: High Efficiency through a Water Bridge Mediated Proton Shuttle”, J. Am. Chem. Soc., 2005, 127(32), 11226-11227. (Communication)

26. A. Bottoni, G.P. Miscione, M. De Vivo, “A Theoretical DFT Investigation of the Lysozyme Mechanism. Computational Evidence for a Covalent Intermediate Pathway” Proteins, 2005, 59, 118-130.

27. A. Cavalli, G. Bottegoni, C. Raco, M. De Vivo, M. Recanatini, “A Computational Study of the Binding of Propidium to the Peripheral Anionic Site of Human Acetylcholinesterase”, J. Med. Chem., 2004, 47, 3991-3999.

28. E. G. Occhiato, A. Ferrali, G. Menchi, A. Guarna, G. Danza, A. Comerci, R. Mancina, M. Serio, G. Garotta, A. Cavalli, M. De Vivo, M. Recanatini, “Synthesis, Biological Activity, and Three-Dimensional Quantitative Structure-Activity Relationship Model for a Series of Benzo[c]quinolizin-3-ones, Nonsteroidal Inhibitors of Human Steroid 5alpha-Reductase 1”, J. Med. Chem., 2004, 47, 3546-3560.

29. A. Cavalli^, M. De Vivo^, M. Recanatini (^Co-first author), “Density Functional Study of the Enzymatic Reaction Catalyzed by a Cyclin-Dependent Kinase”, Chem. Comm., 2003, 1308-1309.

30. F. Bernardi, A. Bottoni, M. De Vivo, M. Garavelli, G. Keserü, G. Náray-Szabó, “A Hypothetical Mechanism for HIV-1 Integrase Catalytic Action: DFT Modeling of a Bio-mimetic Environment”, Chem. Phys. Lett., 2002, 362, 1-7.

 

Book chapters

1. M. Cascella, M. Dal Peraro, M. De Vivo, “Computational chemistry strategies tackling function and inhibition of pharmaceutically relevant targets” in Volume 1 of the eBooks series entitled, “Frontiers in Computational Chemistry” by Zaheer ul Haq and Jeffry D. Madura Pp. 290-343 (54) (2015)

2. A. Lodola and M. De Vivo, “The increasing role of QM/MM in drug discovery” in “Structural and mechanistic enzymology: Bringing together experiments and computing”, Edited by Christo Z. Christov and Tatyana Karabencheva-Christova, Elsevier. (2012)

 

Patents and Inventions

• Joint inventor of 3 patents from IIT:

1.Patent application number IT MI2014A000863, "Benzoxazolone derivatives as Acid Ceramidase inhibitors, and their use as medicaments", Piomelli D., Pagliuca C., Pizzirani D., Bach A., Realini N., De Vivo M.
2.PCT (2014), WO 2014/023643 A1, “Multitarget FAAH and COX inhibitors and therapeutical uses thereof”, De Vivo M., Scarpelli R., Cavalli A., Migliore M., Piomelli D., Habrant D., Favia A.D.
3.PCT Int. Appl. (2012), No. PCT/EP2012/061662, “Carprofen derivatives as inhibitors of FAAH and/or COXs”, De Vivo M., Scarpelli R., Cavalli A., Favia A.D., Habrant D., Piomelli D.

• Joint inventor of 3 patents from Rib-x Pharmaceuticals “Antimicrobial compounds and methods of making and using the same”:

4.PCT (2011), WO 2011047323, Duffy E., Bhattacharjee A., O’Dowd H., De Vivo M., Du Y., Sinishtaj S., Tang Y., Wimberly B.
5.PCT (2011), WO 2011047320, Duffy E., Bhattacharjee A., O’Dowd H., Chen S., De Vivo M.,Lou R., Wimberly B.
6.PCT (2011), WO 2011047319, Duffy E., Bhattacharjee A., O’Dowd H., De Vivo M., Kanyo Z., Martinow J., Paik I., Scheideman M., Sinishtaj S., Wimberly B., Wu Y.

 

Addresses

Laboratory of Molecular Modeling and Drug Discovery
Italian Institute of Technology (IIT)
Via Morego 30
16163 Genova
Italy
IAS-5 / INM-9
Computational Biomedicine
Forschungszentrum Jülich
Wilhelm-Johnen-Straße
52428 Jülich

Contact

Phone: +39 010 71781577
email: Marco.DeVivo@iit.it

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