Publications & Inventions
ARTICLES
* Indicates when MarcoDV is the only or joint corresponding author
58. E. Donati, V. Genna, and M. De Vivo*
"Recruiting mechanism and functional role of the third metal ion in the enzymatic activity of 5' structure-specific nucleases"
J. Am. Chem. Soc, 2020 (Link)
57. J. Akkarapattiakal Kuriappan, N. Osheroff, and M. De Vivo*
"Smoothed Potential MD Simulations for Dissociation Kinetics of Etoposide to Unravel Isoform Specificity in Targeting Human Topoisomerase II"
J. Chem. Inf. Model. 2019, 59 (9), pp 4007-4017 (Link)
56. S. Vanni, L. Riccardi, G. Palermo, and M. De Vivo*
"Structure and Dynamics of the Acyl Chains in the Membrane Trafficking and Enzymatic Processing of Lipids"
Acc. Chem. Res, 2019, 52 (11), pp 3087 - 3096 (Link)
55. V. Genna, M. Marcia, and M. De Vivo*
"A Transient and Flexible Cation-Pi Interaction Promotes Hydrolysis of Nucleic Acids in DNA and RNA Nucleases"
J. Am. Chem. Soc, 2019, 141 (27), pp 10770-10776 (Link)
54. L. Riccardi, F. De Biasi, M. De Vivo, T. Burgi, F. Rastrelli, and G. Salassa
"The Dynamic Origin of Chirality Transfer between Chiral Surface and Achiral Ligand in Au38 Clusters"
ACS Nano, 2019, 13 (6), pp 7127-7134 (Link)
53. X. Sun, L. Riccardi, F. De Biasi, F. Rastrelli, M. De Vivo,* and F. Mancin*
"Molecular Dynamics Simulation-Directed Rational Design of Nanoreceptors with Targeted Affinity"
Angewandte Chemie, 2019, 58 (23), pp 7702-7707 (Link)
52. S. Franco-Ulloa, L. Riccardi, F. Rimembrana, M. Pini, M. De Vivo*
"NanoModeler: A Webserver for Molecular Simulations and Engineering of Nanoparticles"
J. Chem. Theory Comput., 2019, 15 (3), pp 2022–2032 (Link)
Cover Article
51. V. Genna, E. Donati, M. De Vivo*
"The Catalytic Mechanism of DNA and RNA Polymerases" (Perspective)
ACS Catal., 2018, 8 (12), pp 11103–11118 (Link)
50. M. Hjortness, L. Riccardi, A. Hongdusit, P. Zwart, B. Sankaran, M. De Vivo, J. M. Fox
"Evolutionary Conserved Allosteric Communication in Protein Tyrosine Phosphatases"
Biochemistry, 2018, 57 (45), pp 6443–6451 (Link)
49. M. Hjortness, L. Riccardi, A. Hongdusit, A. Ruppe, M. Zhao, E. Kim, P. Zwart, B. Sankaran, H. Arthanari, M. Sousa, M. De Vivo, J. M. Fox
"Abietane-Type Diterpenoids Inhibit Protein Tyrosine Phosphatases by Stabilizing an Inactive Enzyme Conformation"
Biochemistry, 2018, 57 (40), pp 5886–5896 (Link)
48. L. Riccardi, V. Genna, M. De Vivo*
"Metal-ligand interactions in drug design" (Perspective)
Nature Reviews Chemistry, 2018, 2, 100–112 (Link)
47. A. A Oviatt, J. A Kuriappan, E. Minniti, K. R. Vann, P. Onuorah, A. Minarini, M. De Vivo*, N. Osheroff
"Polyamine-containing etoposide derivatives as poisons of human type II topoisomerases: Differential effects on topoisomerase IIa and IIb"
Bioorg. Med. Chem. Lett., 2018, 28, 2961-2968 (Link)
46. V. Genna, P. Carloni, M. De Vivo*
"A strategically located Arg/Lys residue promotes correct base paring during nucleic acid biosynthesis in polymerases"
J. Am. Chem. Soc., 2018, 140 (9), pp 3312–3321 (Link)
Cover Article
45. S. Franco-Ulloa, G. La Sala, G.P. Miscione, M. De Vivo*
"Novel Bacterial Topoisomerase Inhibitors Exploit Asp83 and the Intrinsic Flexibility of the DNA Gyrase Binding Site"
Int. J. Mol. Sci. 2018, 19(2), 453 – (Link)
44. J. A. Ortega, L. Riccardi, E. Minniti, M. Borgogno, J. M. Arencibia, M. L. Greco, A. Minarini, C. Sissi, M. De Vivo*
"Pharmacophore hybridization to discover novel Topoisomerase II poisons with promising antiproliferative activity"
J. Med. Chem. 2018, 61 (3), pp 1375–1379 – (Link)
Cover Article
43. V. Genna, M. Colombo, M. De Vivo*, M. Marcia
“Second-shell basic residues expand the two-metal-ion architecture of DNA and RNA processing enzymes”,
Structure (Cell Press), 2018, 26, 40–50 – (Link)
42. E. Minniti, J. A. W. Byl, L. Riccardi, C. Sissi, M. Rosini, M. De Vivo, A. Minarini, N. Osheroff
“Novel xanthone-polyamine conjugates as catalytic inhibitors of human topoisomerase IIa”,
Bioorg. Med. Chem. Lett., 2017, 27, 4687–4693 – (Link)
41. G. La Sala, S. Decherchi, M. De Vivo*, W. Rocchia
“Allosteric communication networks in proteins revealed through pocket crosstalk analysis”,
ACS Central Science, 2017, 3 (9), pp 949–960 – (Link)
• Highlighted in First Reactions ACS Central Science, "Toward Understanding “the Ways” of Allosteric Drugs", by R. Amaro 2017, 3 (9), pp 925–926.
Cover Article
40. L. Riccardi, L. Gabrielli, X. Sun, F. De Biasi, F. Rastrelli, F. Mancin, M. De Vivo*
“Nanoparticle-based receptors mimic protein-ligand recognition”
Chem (Cell Press), 2017, 3, 92-109 (Link)
Cover Article for July 13, 2017
39. J. A. Ortega, J. M. Arencibia, G. La Sala, M. Borgogno, L. Bono, A. Armirotti, S. Girotto, A. Ganesan, M. De Vivo*
“Pharmacophore identification and scaffold exploration to discover novel, potent and chemically stable inhibitors of acid ceramidase in melanoma cells”,
J. Med. Chem. 2017 60 (13), pp 5800–5815 (Link)
38. M. De Vivo* and A. Cavalli
“Recent advances in dynamic docking for drug discovery”,
WIREs Computational Molecular Science, 2017, 7:e1320. (Link)
Cover Article
37. L. Riccardi, J. M Arencibia, L. Bono, A. Armirotti, S. Girotto, M. De Vivo*
"Lid domain plasticity and lipid flexibility modulate enzyme specificity in human monoacylglycerol lipase"
BBA - Molecular and Cell Biology of Lipids, 2017, 1862, 441–451 (Link)
36. G. La Sala, L. Riccardi, R. Gaspari, A. Cavalli, O. Hantschel, M. De Vivo*
"HRD motif as the central hub of the signaling network for activation loop autophosphorylation in Abl kinase"
J. Chem. Theory Comput., 2016, 12 (11), pp 5563–5574 (Link)
Cover Article for November 8, 2016 (Link)
35. V. Genna, P. Vidossich, E. Ippolito, P. Carloni, M. De Vivo*
"A self-activated mechanism for nucleic acid polymerization catalyzed by DNA/RNA polymerases"
J. Am. Chem. Soc., 2016, 138 (44), pp 14592–14598 (Link)
• Highlighted in JACS Spotlights, "Polymerases May Progress with the Help of Hydrogen Bonding", by Deirdre Lockwood (Ph.D.)
J. Am. Chem. Soc., 2016, 138 (44), pp 14507–14508
Cover Article for November 9, 2016 (Link)
34. M. Pavlin, G. Rossetti, M. De Vivo, P. Carloni
“Carnosine and Homocarnosine Degration Mechanisms by the Human Carnosinase Enzyme CN1: Insights from Multiscale Simulations”
Biochemistry, 2016 – 55 (19), pp 2772–2784 (Link)
33. 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 (Link)
Cover Article for April 7 issue (Link)
32. 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), pp 4035–4061 (Link)
Perspective on the special issue "Computational Methods for Drug Discovery and Design"
F1000 Prime Recommended (two recommendations) (Link)
31. G. Palermo, A.D. Favia, M. Convertino, M. De Vivo*
"The Molecular Basis for Dual Fatty Acid Amide Hydrolase (FAAH)/Cyclooxygenase (COX) Inhibition"
ChemMedChem, 2016, Volume 11, Issue 12, Pages 1252–1258 (Link)
30. 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 (Link)
Cover Article (Back cover, October 2015)
29. 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 Comput Biol, 2015, 11(6): e1004231 (Link)
Cover Article for June 2015 (Link)
28. 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 (Link)
27. 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 (Link)
Special Issue: Prof. W.L. Jorgensen Festschrift
26. 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 (Link)
25. G. Palermo, U. Roethlisberger, A. Cavalli, M. De Vivo*
“Computational insights into function and inhibition of Fatty Acid Amide Hydrolase”
Eur. J. Med. Chem., 2015, Feb 16;91:15-26 (Review) (Link)
24. 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 (Link)
23. 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., 2013, 9 (2), pp 857–862 (Letter) (Link)
Cover Article - February 2013, Vol. 9 Number 2
22. 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., 2013, Jan 9;135(1):22-5 (Communication) (Link)
21. 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 (Link)
20. 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 (Link)
19. 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 (Link)
18. 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), pp 6612–6623 (Link)
17. 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, 2011 Sep;3(12):1551-9 (Review) (Link)
16. D. Branduardi, M. De Vivo, N. Rega, V. Barone, A. Cavalli
"Methylphosphate 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) (Link)
15. M. De Vivo*
"Bridging Quantum Mechanics and Structure-Based Drug Design"
Front Biosci., 2011, Jan 1; 16: 1619-1633. (Review) (Link)
14. 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. (Link)
13. 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. (Link)
12. 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. (Link)
• Highlighted in JACS select 2008, 130 (50),16824–16827.
11. 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. (Link)
1o. 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. (Link)
9. 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. (Link)
8. 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. (Link)
7. 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. (Link)
6. 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) (Link)
5. 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. (Link)
F1000 Prime Recommended (by Prof. A. Warshel) (Link)
4. 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. (Link)
3. 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. (Link)
2. 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. (Link)
1. 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. (Link)
_________________________________________________________
BOOK CHAPTERS
5. M. De Vivo*, M. Masetti, G. Rossetti
“Molecular modelling and simulations applied to challenging drug discovery targets”
in “Computational Tools for Chemical Biology”, Royal Society of Chemistry, 2017 (Link)
Edited: Sonsoles Martín-Santamaría - Invited contribution
4. J. Dreyer, G. Brancato, E. Ippoliti, V. Genna, M. De Vivo, P. Carloni, U. Rothlisberger
“First Principle Methods in Biology: From Continuum Models to Hybrid Ab Initio Quantum Mechanics/Molecular Mechanics”
in "Simulating Enzyme Reactivity" - Published by The Royal Society of Chemistry, 2017 (Link)
Edited by Iñaki Tuñón and Vicente Moliner - Invited contribution
3. G. Palermo, M. De Vivo*
“Computational Chemistry for Drug Discovery"
Encyclopedia of Nanotechnology, Springer – 2015, pp 1-15 (Link) - Invited contribution
2. M. Cascella, M. Dal Peraro, M. De Vivo*
“Computational chemistry strategies tackling function and inhibition of pharmaceutically relevant targets”
Pp. 290-343 (54) in Volume 1 of the eBooks series entitled
“Frontiers in Computational Chemistry” by Bentham Science Publishers – 2015 (Link) - Invited contribution
1. 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 (Link) - Invited contribution
_________________________________________________________
BOOK REVIEW
"Enzyme Technologies: Pluripotent Players in Discovering Therapeutic Agents."
Edited by Hsiu-Chiung Yang, Wu-Kuang Yeh, James R. McCarthy (Wiley)
Dr. Marco De Vivo
ChemMedChem
Volume 10, Issue 8, page 1443, August 2015 (Link) - Invited contribution
58. E. Donati, V. Genna, and M. De Vivo*
"Recruiting mechanism and functional role of the third metal ion in the enzymatic activity of 5' structure-specific nucleases"
J. Am. Chem. Soc, 2020 (Link)
57. J. Akkarapattiakal Kuriappan, N. Osheroff, and M. De Vivo*
"Smoothed Potential MD Simulations for Dissociation Kinetics of Etoposide to Unravel Isoform Specificity in Targeting Human Topoisomerase II"
J. Chem. Inf. Model. 2019, 59 (9), pp 4007-4017 (Link)
56. S. Vanni, L. Riccardi, G. Palermo, and M. De Vivo*
"Structure and Dynamics of the Acyl Chains in the Membrane Trafficking and Enzymatic Processing of Lipids"
Acc. Chem. Res, 2019, 52 (11), pp 3087 - 3096 (Link)
55. V. Genna, M. Marcia, and M. De Vivo*
"A Transient and Flexible Cation-Pi Interaction Promotes Hydrolysis of Nucleic Acids in DNA and RNA Nucleases"
J. Am. Chem. Soc, 2019, 141 (27), pp 10770-10776 (Link)
54. L. Riccardi, F. De Biasi, M. De Vivo, T. Burgi, F. Rastrelli, and G. Salassa
"The Dynamic Origin of Chirality Transfer between Chiral Surface and Achiral Ligand in Au38 Clusters"
ACS Nano, 2019, 13 (6), pp 7127-7134 (Link)
53. X. Sun, L. Riccardi, F. De Biasi, F. Rastrelli, M. De Vivo,* and F. Mancin*
"Molecular Dynamics Simulation-Directed Rational Design of Nanoreceptors with Targeted Affinity"
Angewandte Chemie, 2019, 58 (23), pp 7702-7707 (Link)
52. S. Franco-Ulloa, L. Riccardi, F. Rimembrana, M. Pini, M. De Vivo*
"NanoModeler: A Webserver for Molecular Simulations and Engineering of Nanoparticles"
J. Chem. Theory Comput., 2019, 15 (3), pp 2022–2032 (Link)
Cover Article
51. V. Genna, E. Donati, M. De Vivo*
"The Catalytic Mechanism of DNA and RNA Polymerases" (Perspective)
ACS Catal., 2018, 8 (12), pp 11103–11118 (Link)
50. M. Hjortness, L. Riccardi, A. Hongdusit, P. Zwart, B. Sankaran, M. De Vivo, J. M. Fox
"Evolutionary Conserved Allosteric Communication in Protein Tyrosine Phosphatases"
Biochemistry, 2018, 57 (45), pp 6443–6451 (Link)
49. M. Hjortness, L. Riccardi, A. Hongdusit, A. Ruppe, M. Zhao, E. Kim, P. Zwart, B. Sankaran, H. Arthanari, M. Sousa, M. De Vivo, J. M. Fox
"Abietane-Type Diterpenoids Inhibit Protein Tyrosine Phosphatases by Stabilizing an Inactive Enzyme Conformation"
Biochemistry, 2018, 57 (40), pp 5886–5896 (Link)
48. L. Riccardi, V. Genna, M. De Vivo*
"Metal-ligand interactions in drug design" (Perspective)
Nature Reviews Chemistry, 2018, 2, 100–112 (Link)
47. A. A Oviatt, J. A Kuriappan, E. Minniti, K. R. Vann, P. Onuorah, A. Minarini, M. De Vivo*, N. Osheroff
"Polyamine-containing etoposide derivatives as poisons of human type II topoisomerases: Differential effects on topoisomerase IIa and IIb"
Bioorg. Med. Chem. Lett., 2018, 28, 2961-2968 (Link)
46. V. Genna, P. Carloni, M. De Vivo*
"A strategically located Arg/Lys residue promotes correct base paring during nucleic acid biosynthesis in polymerases"
J. Am. Chem. Soc., 2018, 140 (9), pp 3312–3321 (Link)
Cover Article
45. S. Franco-Ulloa, G. La Sala, G.P. Miscione, M. De Vivo*
"Novel Bacterial Topoisomerase Inhibitors Exploit Asp83 and the Intrinsic Flexibility of the DNA Gyrase Binding Site"
Int. J. Mol. Sci. 2018, 19(2), 453 – (Link)
44. J. A. Ortega, L. Riccardi, E. Minniti, M. Borgogno, J. M. Arencibia, M. L. Greco, A. Minarini, C. Sissi, M. De Vivo*
"Pharmacophore hybridization to discover novel Topoisomerase II poisons with promising antiproliferative activity"
J. Med. Chem. 2018, 61 (3), pp 1375–1379 – (Link)
Cover Article
43. V. Genna, M. Colombo, M. De Vivo*, M. Marcia
“Second-shell basic residues expand the two-metal-ion architecture of DNA and RNA processing enzymes”,
Structure (Cell Press), 2018, 26, 40–50 – (Link)
42. E. Minniti, J. A. W. Byl, L. Riccardi, C. Sissi, M. Rosini, M. De Vivo, A. Minarini, N. Osheroff
“Novel xanthone-polyamine conjugates as catalytic inhibitors of human topoisomerase IIa”,
Bioorg. Med. Chem. Lett., 2017, 27, 4687–4693 – (Link)
41. G. La Sala, S. Decherchi, M. De Vivo*, W. Rocchia
“Allosteric communication networks in proteins revealed through pocket crosstalk analysis”,
ACS Central Science, 2017, 3 (9), pp 949–960 – (Link)
• Highlighted in First Reactions ACS Central Science, "Toward Understanding “the Ways” of Allosteric Drugs", by R. Amaro 2017, 3 (9), pp 925–926.
Cover Article
40. L. Riccardi, L. Gabrielli, X. Sun, F. De Biasi, F. Rastrelli, F. Mancin, M. De Vivo*
“Nanoparticle-based receptors mimic protein-ligand recognition”
Chem (Cell Press), 2017, 3, 92-109 (Link)
Cover Article for July 13, 2017
39. J. A. Ortega, J. M. Arencibia, G. La Sala, M. Borgogno, L. Bono, A. Armirotti, S. Girotto, A. Ganesan, M. De Vivo*
“Pharmacophore identification and scaffold exploration to discover novel, potent and chemically stable inhibitors of acid ceramidase in melanoma cells”,
J. Med. Chem. 2017 60 (13), pp 5800–5815 (Link)
38. M. De Vivo* and A. Cavalli
“Recent advances in dynamic docking for drug discovery”,
WIREs Computational Molecular Science, 2017, 7:e1320. (Link)
Cover Article
37. L. Riccardi, J. M Arencibia, L. Bono, A. Armirotti, S. Girotto, M. De Vivo*
"Lid domain plasticity and lipid flexibility modulate enzyme specificity in human monoacylglycerol lipase"
BBA - Molecular and Cell Biology of Lipids, 2017, 1862, 441–451 (Link)
36. G. La Sala, L. Riccardi, R. Gaspari, A. Cavalli, O. Hantschel, M. De Vivo*
"HRD motif as the central hub of the signaling network for activation loop autophosphorylation in Abl kinase"
J. Chem. Theory Comput., 2016, 12 (11), pp 5563–5574 (Link)
Cover Article for November 8, 2016 (Link)
35. V. Genna, P. Vidossich, E. Ippolito, P. Carloni, M. De Vivo*
"A self-activated mechanism for nucleic acid polymerization catalyzed by DNA/RNA polymerases"
J. Am. Chem. Soc., 2016, 138 (44), pp 14592–14598 (Link)
• Highlighted in JACS Spotlights, "Polymerases May Progress with the Help of Hydrogen Bonding", by Deirdre Lockwood (Ph.D.)
J. Am. Chem. Soc., 2016, 138 (44), pp 14507–14508
Cover Article for November 9, 2016 (Link)
34. M. Pavlin, G. Rossetti, M. De Vivo, P. Carloni
“Carnosine and Homocarnosine Degration Mechanisms by the Human Carnosinase Enzyme CN1: Insights from Multiscale Simulations”
Biochemistry, 2016 – 55 (19), pp 2772–2784 (Link)
33. 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 (Link)
Cover Article for April 7 issue (Link)
32. 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), pp 4035–4061 (Link)
Perspective on the special issue "Computational Methods for Drug Discovery and Design"
F1000 Prime Recommended (two recommendations) (Link)
31. G. Palermo, A.D. Favia, M. Convertino, M. De Vivo*
"The Molecular Basis for Dual Fatty Acid Amide Hydrolase (FAAH)/Cyclooxygenase (COX) Inhibition"
ChemMedChem, 2016, Volume 11, Issue 12, Pages 1252–1258 (Link)
30. 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 (Link)
Cover Article (Back cover, October 2015)
29. 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 Comput Biol, 2015, 11(6): e1004231 (Link)
Cover Article for June 2015 (Link)
28. 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 (Link)
27. 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 (Link)
Special Issue: Prof. W.L. Jorgensen Festschrift
26. 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 (Link)
25. G. Palermo, U. Roethlisberger, A. Cavalli, M. De Vivo*
“Computational insights into function and inhibition of Fatty Acid Amide Hydrolase”
Eur. J. Med. Chem., 2015, Feb 16;91:15-26 (Review) (Link)
24. 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 (Link)
23. 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., 2013, 9 (2), pp 857–862 (Letter) (Link)
Cover Article - February 2013, Vol. 9 Number 2
22. 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., 2013, Jan 9;135(1):22-5 (Communication) (Link)
21. 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 (Link)
20. 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 (Link)
19. 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 (Link)
18. 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), pp 6612–6623 (Link)
17. 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, 2011 Sep;3(12):1551-9 (Review) (Link)
16. D. Branduardi, M. De Vivo, N. Rega, V. Barone, A. Cavalli
"Methylphosphate 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) (Link)
15. M. De Vivo*
"Bridging Quantum Mechanics and Structure-Based Drug Design"
Front Biosci., 2011, Jan 1; 16: 1619-1633. (Review) (Link)
14. 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. (Link)
13. 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. (Link)
12. 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. (Link)
• Highlighted in JACS select 2008, 130 (50),16824–16827.
11. 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. (Link)
1o. 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. (Link)
9. 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. (Link)
8. 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. (Link)
7. 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. (Link)
6. 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) (Link)
5. 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. (Link)
F1000 Prime Recommended (by Prof. A. Warshel) (Link)
4. 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. (Link)
3. 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. (Link)
2. 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. (Link)
1. 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. (Link)
_________________________________________________________
BOOK CHAPTERS
5. M. De Vivo*, M. Masetti, G. Rossetti
“Molecular modelling and simulations applied to challenging drug discovery targets”
in “Computational Tools for Chemical Biology”, Royal Society of Chemistry, 2017 (Link)
Edited: Sonsoles Martín-Santamaría - Invited contribution
4. J. Dreyer, G. Brancato, E. Ippoliti, V. Genna, M. De Vivo, P. Carloni, U. Rothlisberger
“First Principle Methods in Biology: From Continuum Models to Hybrid Ab Initio Quantum Mechanics/Molecular Mechanics”
in "Simulating Enzyme Reactivity" - Published by The Royal Society of Chemistry, 2017 (Link)
Edited by Iñaki Tuñón and Vicente Moliner - Invited contribution
3. G. Palermo, M. De Vivo*
“Computational Chemistry for Drug Discovery"
Encyclopedia of Nanotechnology, Springer – 2015, pp 1-15 (Link) - Invited contribution
2. M. Cascella, M. Dal Peraro, M. De Vivo*
“Computational chemistry strategies tackling function and inhibition of pharmaceutically relevant targets”
Pp. 290-343 (54) in Volume 1 of the eBooks series entitled
“Frontiers in Computational Chemistry” by Bentham Science Publishers – 2015 (Link) - Invited contribution
1. 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 (Link) - Invited contribution
_________________________________________________________
BOOK REVIEW
"Enzyme Technologies: Pluripotent Players in Discovering Therapeutic Agents."
Edited by Hsiu-Chiung Yang, Wu-Kuang Yeh, James R. McCarthy (Wiley)
Dr. Marco De Vivo
ChemMedChem
Volume 10, Issue 8, page 1443, August 2015 (Link) - Invited contribution
PATENTS AND INVENTIONS .
Inventions at IIT:
12. IT 102019000004929
Patent filed on new compounds targeting Intracellular chloride concentration
"Modulators Of Intracellular Chloride Concentration"
Cancedda L., De Vivo M., Contestabile A., Borgogno M., Savardi A., Ortega Martinez J. A.
11. EP18170092.3
Patent filed on new compounds targeting the prion protein
“Serpin inhibitors for the treatment of prion and prion-like diseases”
Legname G., Vanni S., Carloni P., De Vivo M.
10. IT 102017000047189
Patent filed on new compounds targeting the protein RhoJ
“Compounds and composition for the treatment of cancer, retinal disorders, and cardiomyopathies.”
De Vivo M., Ganesan A., Ortega Martinez J. A., Jahid S.
9. IT 102017000028709
Patent filed on new anticancer compounds targeting topoisomerases
“5-carboxamide-2-thiobarbituric acids and use thereof as medicaments.”
De Vivo M., Ortega Martinez J. A., Arencibia Jimenez J. M., Sissi C.
8. IT 102017000012144
Patent filed on new anticancer compounds targeting the acid ceramidase enzyme
“Acid Ceramidase inhibitors, and their use as medicaments”
De Vivo M., Ortega Martinez J.O., Arencibia Jimenez J. M.
7. IT 102016000130706 (UA2016A009452)
Patent filed on new anticancer compounds targeting topoisomerases
“4-amino-2-pyrido-bicyclic pyrimidines as type II topoisomerase inhibitors and use thereof as medicaments.”
De Vivo M., Ortega Martinez J. A., Arencibia Jimenez J. M., Minarini A., Sissi C.
6. PCT/EP2015/060291
"Benzoxazolone derivatives as Acid Ceramidase inhibitors, and their use as medicaments"
Piomelli D., Pagliuca C., Pizzirani D., Bach A., Realini N., De Vivo M.
5. PCT/EP2012/065336 (Granted in EP, US, JP, IT, FR, DE, GB)
“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.
4. 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 (now, Melinta Therapeutics):
“Antimicrobial compounds and methods of making and using the same”
These three International applications have entered national stages in tens of nations/regions worldwide and have already 9 Patents granted:
3. PCT/US10/52928
Duffy E., Bhattacharjee A., O’Dowd H., De Vivo M., Du Y., Sinishtaj S., Tang Y., Wimberly B.
2. PCT/US10/052924
Duffy E., Bhattacharjee A., O’Dowd H., Chen S., De Vivo M., Lou R., Wimberly B.
1. PCT/US10/52922
Duffy E., Bhattacharjee A., O’Dowd H., De Vivo M., Kanyo Z., Martinow J., Paik I., Scheideman M., Sinishtaj S., Wimberly B., Wu Y.
Inventions at IIT:
12. IT 102019000004929
Patent filed on new compounds targeting Intracellular chloride concentration
"Modulators Of Intracellular Chloride Concentration"
Cancedda L., De Vivo M., Contestabile A., Borgogno M., Savardi A., Ortega Martinez J. A.
11. EP18170092.3
Patent filed on new compounds targeting the prion protein
“Serpin inhibitors for the treatment of prion and prion-like diseases”
Legname G., Vanni S., Carloni P., De Vivo M.
10. IT 102017000047189
Patent filed on new compounds targeting the protein RhoJ
“Compounds and composition for the treatment of cancer, retinal disorders, and cardiomyopathies.”
De Vivo M., Ganesan A., Ortega Martinez J. A., Jahid S.
9. IT 102017000028709
Patent filed on new anticancer compounds targeting topoisomerases
“5-carboxamide-2-thiobarbituric acids and use thereof as medicaments.”
De Vivo M., Ortega Martinez J. A., Arencibia Jimenez J. M., Sissi C.
8. IT 102017000012144
Patent filed on new anticancer compounds targeting the acid ceramidase enzyme
“Acid Ceramidase inhibitors, and their use as medicaments”
De Vivo M., Ortega Martinez J.O., Arencibia Jimenez J. M.
7. IT 102016000130706 (UA2016A009452)
Patent filed on new anticancer compounds targeting topoisomerases
“4-amino-2-pyrido-bicyclic pyrimidines as type II topoisomerase inhibitors and use thereof as medicaments.”
De Vivo M., Ortega Martinez J. A., Arencibia Jimenez J. M., Minarini A., Sissi C.
6. PCT/EP2015/060291
"Benzoxazolone derivatives as Acid Ceramidase inhibitors, and their use as medicaments"
Piomelli D., Pagliuca C., Pizzirani D., Bach A., Realini N., De Vivo M.
5. PCT/EP2012/065336 (Granted in EP, US, JP, IT, FR, DE, GB)
“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.
4. 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 (now, Melinta Therapeutics):
“Antimicrobial compounds and methods of making and using the same”
These three International applications have entered national stages in tens of nations/regions worldwide and have already 9 Patents granted:
3. PCT/US10/52928
Duffy E., Bhattacharjee A., O’Dowd H., De Vivo M., Du Y., Sinishtaj S., Tang Y., Wimberly B.
2. PCT/US10/052924
Duffy E., Bhattacharjee A., O’Dowd H., Chen S., De Vivo M., Lou R., Wimberly B.
1. PCT/US10/52922
Duffy E., Bhattacharjee A., O’Dowd H., De Vivo M., Kanyo Z., Martinow J., Paik I., Scheideman M., Sinishtaj S., Wimberly B., Wu Y.
