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De Vivo

Dr. Marco De Vivo

Group Leader

 

Professional career

2013- Principal Investigator (Tenure Track since 09/2014).
Research Director of the 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.

 

Research interest and activities

In my research lines, I pursue my interest in enzymatic catalysis and drug discovery. Thus, the Lab is focused on the study of catalysis and inhibition of pharmaceutically relevant enzymes. This is performed through the development and application of computational methods, which are fully combined with medicinal chemistry and molecular biology to design, synthesize and test novel compounds. Then, results are 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 the desired pharmacological activity.

Enzymatic catalysis and inhibition is studied by means of classical molecular dynamics simulations coupled with first-principles-based computational methods (e.g., QM/MM simulations) and enhanced sampling techniques for free energy calculations. This multiscale computational approach allows performing computational enzymology for neuroscience and cancer. Then, this detailed knowledge on the target of interest is used to perform docking, virtual screening, de novo small molecules computational design and in silico ADMET evaluation for structure-based drug design of potent enzyme inhibitors. Promising compounds are either purchased or synthesized in the Lab, and assayed to identify and optimize novel small molecules able to inhibit the enzymatic function of interest. The goal is to understand general principles that govern catalysis and use this information to design potent inhibitors as a promising starting point for drug discovery programs.


HOW TO WORK WITH ME AT FZJ:

Motivated and talented students interested in my research lines are always welcome to contact me, and send me their CV and motivation letter. We will explore the available opportunities.

In particular, please, consider the following opportunity:

Excellent candidates can apply for postdoctoral and PhD student positions to work with me at the IAS-5 / INM-9 Computational Biomedicine, Forschungszentrum (FZJ) Jülich, Germany.

If interested and competitive, I will be glad to explore together the possibility to apply for a Humboldt Research Fellowship and join my group as a postdoc at the FZJ.


Selected publications

V. Genna, P. Vidossich, E. Ippoliti, P. Carloni, M. De Vivo
"A self-activated mechanism for nucleic acid polymerization catalyzed by DNA/RNA polymerases"
J. Am. Chem. Soc., 2016 – available online.

V. Genna, R. Gaspari, M. Dal Peraro, M. De Vivo
"Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-η"
Nucleic Acids Res., 2016, 44 (6). 2827-2836
Cover Article - April 7 issue

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, 119(3), 789-801
Special Issue: Prof. W.L. Jorgensen Festschrift

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, 48(2), 220-8

M. De Vivo, M. Masetti, G. Bottegoni, A. Cavalli
"Role of Molecular Dynamics and Related Methods in Drug Discovery"
J. Med. Chem., 2016, 59 (9), 4035–4061.

G. Palermo, E. Minniti, M. L. Greco, L. Riccardi, E. Simoni, M. Convertino, C. Marchetti, M. Rosini, C. Sissi, A. Minarini, M. De Vivo
"An optimized polyamine moiety boosts potency of human type II topoisomerase poisons as quantified by comparative analysis centered on the clinical candidate F14512"
Chem. Comm., 2015, 51, 14310-14313.
Cover Article (Back cover) - October 2015.

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.
Cover Article - June 2015.

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 - February 2013.

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

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.

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.

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.

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)


De VivoComputational enzymology and drug discovery in neuroscience

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

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