Publications & Inventions
ARTICLES - REVIEWS - BOOKS
* Indicates when MarcoDV is the only or joint corresponding author
102. I. Geronimo, P. Vidossich, M. De Vivo*
On the Role of Molecular Conformation of the 8-Oxoguanine Lesion in Damaged DNA Processing by Polymerases
J. Chem. Inf. Model., 2023, In Press
101. S. Franco-Ulloa, L. Riccardi, F. Rimembrana, E. Grottin, M. Pini, M. De Vivo*
"NanoModeler CG: A tool for modeling and engineering functional nanoparticles at a coarse-grained resolution"
J. Chem. Theory Comput., 2023, In Press
100. N. Brindani, F. Munafò, A. Menichetti, E. Donati, M. Nigro, G. Ottonello, A. Armirotti, M. De Vivo*
"Design, synthesis, docking, and biochemical characterization of non nucleoside SARS-CoV-2 RdRp inhibitors"
Bioorganic & Medicinal Chemistry, 2023, In press
99. M. De Vivo*
"JCTC: In Pursuit of Excellence"
J. Chem. Theory Comput., 2023, Avail. online
98. A. Savardi, A. Patricelli Malizia, M. De Vivo, L. Cancedda, M. Borgogno
"Preclinical development of the Na-K-2Cl cotransporter-1 (NKCC1) inhibitor ARN23746 for the treatment of neurodevelopmental disorders"
ACS Pharmacol.Transl. Sci, 2023, In press.
97. T. Kouba, A. Dubankova, P. Drncova, E. Donati, P. Vidossich, V. Speranzini, A. Pflug, J. Huchting, C. Meier, M. De Vivo, S. Cusack
"Direct observation of backtracking by influenza A and B polymerases upon consecutive incorporation of nucleoside analogue T1106"
Cell Rep., 2023, 42, 111901
96. F. Munafò,# M. Nigro,# N. Brindani, J. Manigrasso, I. Geronimo, G. Ottonello, A. Armirotti, M. De Vivo*
#Equally contributed
"Computer-aided identification, synthesis, and biological evaluation of DNA polymerase η inhibitors for the treatment of cancer"
Eur. J. Med. Chem., 2022, In press
95. I. Geronimo, M. De Vivo*
"Alchemical Free Energy Calculations of Watson–Crick and Hoogsteen Base Pairing Interconversion in DNA"
J. Chem. Theory Comput., 2022, 18, 11, 6966–6973 (Link)
94. Y. Zhao, J. Shen, Q. Wang, M. J. Ruiz Munevar, P. Vidossich, M. De Vivo, M. Zhou, E. Cao
"Structure of the Human Cation-chloride Cotransport KCC1 in an Outward-open State"
Proc. Natl. Acad. Sci. U.S.A., 2022, 119 (27) e2109083119 (Link)
93. F. Munafò, E. Donati, N. Brindani, G. Ottonello, A. Armirotti, M. De Vivo*
“Quercetin and Luteolin are single-digit micromolar inhibitors of the SARS-CoV-2 RNA-dependent RNA polymerase”
Sci. Rep., 2022, 12, Article number: 10571 (Link)
92. A. Colini Baldeschi, M. Zattoni, S. Vanni, L. Nikolic, C. Ferracin, G. La Sala, M. Summa, R. Bertorelli, S. M. Bertozzi, P. Carloni, M. L. Bolognesi, M. De Vivo, G. Legname
"Innovative non-PrP-targeted drug strategy designed to enhance prion clearance"
J. Med. Chem., 2022, 65, 13, 8998–9010 (Link)
91. M. A. La Serra, P. Vidossich, I. Acquistapace, A.K. Ganesan, M De Vivo*
"Alchemical free energy calculations to investigate protein-protein interactions: the case of the CDC42/PAK1 complex"
J. Chem. Inf. Model., 2022, 62, 12, 3023–3033 (Link)
90. O. Zhao, K. Roy, P. Vidossich, L. Cancedda, M. De Vivo, B. Forbush, E. Cao
"Structural basis for inhibition of the Cation-chloride cotransporter NKCC1 by the diuretic drug bumetanide"
Nat. Comm., 2022, 13. Article number: 2747 (Link)
89. S. Jahid, J. A. Ortega, L. M. Vuong, S. J. Hachey, J. L. Flesher, M. A. La Serra, N. Brindani, G. La Sala, J. Manigrasso, J. M. Arencibia, S. M. Bertozzi, M. Summa, R. Bertorelli, A. Armirotti, C. Chen, C. C. W. Hughes, R. Edwards, M. De Vivo*, A. K. Ganesan
"Structure-based Design of CDC42 Effector Interaction Inhibitors For the Treatment of Cancer"
Cell Rep., 2022, Apr 5;39(1):110641 (Link)
88. I. Geronimo, P. Vidossich, M. De Vivo*
"Local Structural Dynamics at the Metal-Centered Catalytic Site of Polymerases is Critical for Fidelity"
ACS Catal., 2021, 11, 22, 14110–14121 (Link)
87. E. Donati, P. Vidossich, M. De Vivo*
"Molecular mechanism of phosphate steering for DNA binding, cleavage localization, and substrate release in nucleases"
ACS Catal., 2021, 11, 21, 13244–13254 (Link)
86. A. Savardi, M. Borgogno, M. De Vivo,* L. Cancedda
"Pharmacological tools to target NKCC1 in brain disorders"
Trends in Pharmacol. Sci. (Cell Press), 2021, Vol. 42, No. 12 (Link)
85. J. Manigrasso, M. Marcia, M. De Vivo*
"Computer-aided design of RNA-targeted small molecules: a growing need in drug discovery"
Chem (Cell Press), 2021, Volume 7, Issue 11, Pages 2965-2988 (Link)
84. J. Manigrasso, M. De Vivo*, G. Palermo
"Controlled Trafficking of Multiple and Diverse Cations Prompts Nucleic Acid Hydrolysis"
ACS Catal., 2021, 11, 14, 8786-8797 (Link)
Cover Article
83. M. Marcia, J. Manigrasso, M. De Vivo,*
"Finding the ion in the RNA-stack: Can computational models accurately predict key functional elements in large macromolecular complexes?"
J. Chem. Inf. Model., 2021, 61, 6, 2511–2515 (Link)
82. A. Pecina, D. Rosa-Gastaldo, L. Riccardi, S. Franco-Ulloa, E. Milan, P. Scrimin, F. Mancin, M. De Vivo*
"On the Metal-Aided Catalytic Mechanism for Phosphodiester Bond Cleavage Performed by Nanozymes"
ACS Catal., 2021, 11, 14, 8736–8748 (Link)
Cover Article
81. M. Borgogno, A. Savardi, J. Manigrasso, A. Turci, C. Portioli, G. Ottonello, S. M. Bertozzi, A. Armirotti, A. Contestabile, L. Cancedda, M. De Vivo*
"Design, synthesis, in vitro and in vivo characterization of selective NKCC1 inhibitors for the treatment of core symptoms in Down syndrome and other brain disorders"
J. Med. Chem., 2021, 64, 14, 10203–10229 (Link)
Cover Article
80. L. Riccardi, S. Decherchi, W. Rocchia, G. Zanoni, A. Cavalli, F. Mancin, M. De Vivo*
"Molecular recognition by gold nanoparticle-based receptors as defined through surface morphology and pockets fingerprint"
J. Phys. Chem. Lett., 2021, 12, 23, 5616–5622 (Link)
Cover Article
79. C. Portioli, M. J. Ruiz Munevar, M. De Vivo*, L. Cancedda
"Cation-coupled chloride cotransporters: chemical insights and disease implications"
Trends Chem. (Cell Press), 2021, 3, 10, 832–849 (Link)
Cover Article
78. S. Franco-Ulloa, D. Guarnieri, L. Riccardi, P. Pompa and M. De Vivo*
"Association mechanism of peptide-coated metal nanoparticles with model membranes: A coarse-grained study"
J. Chem. Theory Comput., 2021, 17, 7, 4512-4523 (Link)
Cover Article
77. P. Vidossich and M. De Vivo*
"The role of first principles simulations in studying (Bio)catalytic processes"
Chem Catalysis (Cell Press), 2021, 1, 1, 69-87 (Link)
76. L. Morillas-Becerril, S. Franco-Ulloa, I. Fortunati, R. Marotta, X. Sun, G. Zanoni, M. De Vivo*, F. Mancin
"Specific and nondisruptive interaction of guanidium-functionalized gold nanoparticles with neutral phospholipid bilayers"
Communications Chemistry (Nature), 2021, 4, 93 (Link)
75. I, Geronimo, P. Vidossich, E. Donati, M. De Vivo*
"Computational investigations of polymerase enzymes: Structure, function, inhibition, and biotechnology"
WIREs Computational Molecular Science, 2021, 11, 6 (Link)
Cover Article
74. M. Prejanò, P. Vidossich, N. Russo, M. De Vivo*, T. Marino
"Insights into the catalytic mechanism of domains CD1 and CD2 in Histone Deacetylase 6 from quantum calculations"
ACS Catal., 2021, 11, 5, 3084–3093 (Link)
73. P. Vidossich, M. Castañeda, E. Luis, C. Mota, D. de Sanctis, G. P. Miscione, M. De Vivo*
"Functional Implications of Second-shell Basic Residues for dUTPase DR2231 Enzymatic Specificity"
ACS Catal., 2020, 10, 23, 13825–13833 (Link)
72. J. A. Ortega, J. Arencibia, E. Minniti, J.O. Byl, S. Franco-Ulloa, M. Borgogno, V. Genna, M. Summa, S. M. Bertozzi, R. Bertorelli, A. Armirotti, A. Minarini, C. Sissi, N. Osheroff, M. De Vivo*
"A novel, potent, and drug-like tetrahydroquinazoline inhibitor that is highly selective for human topoisomerase II α over β"
J. Med. Chem. 2020, 21, 12873–12886 (Link)
71. S. Franco-Ulloa , G. Tatulli , S. Løland Bore , M. Moglianetti , P. P. Pompa ,M. Cascella, M. De Vivo*
"Dispersion state phase diagram of citrate-coated metallic nanoparticles in saline solutions"
Nat. Comm. 2020, 11, 5422 (Link)
70. J. Czescik, S. Zamolo, T. Darbre, C. Sissi, A. Pecina, L. Riccardi, M. De Vivo*, F. Mancin, P. Scrimin
"A gold nanoparticle nanonuclease relying on a Zn(II) mononuclear complex"
Angewandte Chemie, 2020, 59, 2–12 (Link)
69. A. Savardi, M Borgogno, R. Narducci, G. La Sala, J. Ortega, M. Summa, A. Armirotti, R. Bertorelli, A. Contestabile, M. De Vivo*, L Cancedda
"Discovery of a small molecule drug candidate for selective NKCC1 inhibition in brain disorders"
Chem (Cell Press), 2020, 6, 1–24 (Link)
68. J. Manigrasso, I. Chillón, V. Genna, P. Vidossich, S. Somarowthu, A. M. Pyle, M. De Vivo,* M. Marcia
"Visualizing group II intron dynamics between the first and second steps of splicing”
Nat. Comm., 2020, 11, 2837 (Link)
67. E. Catanzaro, N. Betari, J. M. Arencibia, S. Montanari, C. Sissi, A. De Simone, I. Vassura, A. Santini, V. Andrisano, V. Tumiatti, M. De Vivo, D. V. Krysko, M. B.L. Rocchi, C. Fimognari, A. Milelli
"Targeting topoisomerase II with trypthantrin derivatives: discovery of 7-((2-(dimethylamino)ethyl)amino)indolo[2,1-b]quinazoline-6,12-dione as an antiproliferative agent to treat cancer”
Eur. J. Med. Chem., 2020, 202 (15), 112504 (Link)
66. D. Duarte, A. Lamontanara, G. La Sala, S. Jeong, Y-K Sohn, A. Panjkovich, S. Georgeon, T. Kükenshöner, M. Marcaida, F. Pojer, M. De Vivo, D. Svergun, H-S Kim, M. Dal Peraro, O. Hantschel
"Btk SH2-kinase interface is critical for allosteric kinase activation and its targeting inhibits B-cell neoplasms"
Nat. Comm., 2020, 11, 2319 (Link)
65. J. Arencibia, N. Brindani, S. Franco-Ulloa, M. Nigro, J. A. Kuriappan, G. Ottonello, S. Mandrup Bertozzi, M. Summa, S. Girotto, R. Bertorelli, A. Armirotti, M. De Vivo*
"Design, synthesis, dynamic docking, biochemical characterization, and in vivo pharmacokinetics studies of novel topoisomerase II poisons with promising antiproliferative activity"
J. Med. Chem., 2020, 63 (7), pp 3508–3521 (Link)
64. 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, 142 (6), pp 2823-2834 (Link)
Cover Article
63. 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)
62. 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)
Cover Article
61. 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)
60. 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)
59. 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)
58. 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
57. 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)
56. 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)
55. 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)
54. L. Riccardi, V. Genna, M. De Vivo*
"Metal-ligand interactions in drug design" (Perspective)
Nature Reviews Chemistry, 2018, 2, 100–112 (Link)
Cover Article
53. 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)
52. 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
51. 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)
50. 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
49. 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)
48. 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)
47. 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
46. 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
45. 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)
44. M. De Vivo* and A. Cavalli
“Recent advances in dynamic docking for drug discovery”
WIREs Computational Molecular Science, 2017, 7:e1320 (Link)
Cover Article
43. 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)
42. M. De Vivo*, M. Masetti, G. Rossetti
BOOK CHAPTER
“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
41. J. Dreyer, G. Brancato, E. Ippoliti, V. Genna, M. De Vivo, P. Carloni, U. Rothlisberger
BOOK CHAPTER
“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
40. 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)
39. 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)
38. 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)
37. 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)
36. 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)
35. 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)
34. 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)
33. 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)
32. 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)
31. 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
30. 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)
29. 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)
28. G. Palermo, M. De Vivo*
BOOK CHAPTER
“Computational Chemistry for Drug Discovery"
Encyclopedia of Nanotechnology, Springer – 2015, pp 1-15 (Link) - Invited contribution
27. M. Cascella, M. Dal Peraro, M. De Vivo*
BOOK CHAPTER
“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
26. M. De Vivo*
BOOK REVIEW
"Enzyme Technologies: Pluripotent Players in Discovering Therapeutic Agents."
Edited by Hsiu-Chiung Yang, Wu-Kuang Yeh, James R. McCarthy (Wiley)
ChemMedChem - Volume 10, Issue 8, page 1443, August 2015 (Link) - Invited contribution
25. 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)
24. 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
23. 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)
22. 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)
21. 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)
20. 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)
19. A. Lodola and M. De Vivo*
BOOK CHAPTER
“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
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)
102. I. Geronimo, P. Vidossich, M. De Vivo*
On the Role of Molecular Conformation of the 8-Oxoguanine Lesion in Damaged DNA Processing by Polymerases
J. Chem. Inf. Model., 2023, In Press
101. S. Franco-Ulloa, L. Riccardi, F. Rimembrana, E. Grottin, M. Pini, M. De Vivo*
"NanoModeler CG: A tool for modeling and engineering functional nanoparticles at a coarse-grained resolution"
J. Chem. Theory Comput., 2023, In Press
100. N. Brindani, F. Munafò, A. Menichetti, E. Donati, M. Nigro, G. Ottonello, A. Armirotti, M. De Vivo*
"Design, synthesis, docking, and biochemical characterization of non nucleoside SARS-CoV-2 RdRp inhibitors"
Bioorganic & Medicinal Chemistry, 2023, In press
99. M. De Vivo*
"JCTC: In Pursuit of Excellence"
J. Chem. Theory Comput., 2023, Avail. online
98. A. Savardi, A. Patricelli Malizia, M. De Vivo, L. Cancedda, M. Borgogno
"Preclinical development of the Na-K-2Cl cotransporter-1 (NKCC1) inhibitor ARN23746 for the treatment of neurodevelopmental disorders"
ACS Pharmacol.Transl. Sci, 2023, In press.
97. T. Kouba, A. Dubankova, P. Drncova, E. Donati, P. Vidossich, V. Speranzini, A. Pflug, J. Huchting, C. Meier, M. De Vivo, S. Cusack
"Direct observation of backtracking by influenza A and B polymerases upon consecutive incorporation of nucleoside analogue T1106"
Cell Rep., 2023, 42, 111901
96. F. Munafò,# M. Nigro,# N. Brindani, J. Manigrasso, I. Geronimo, G. Ottonello, A. Armirotti, M. De Vivo*
#Equally contributed
"Computer-aided identification, synthesis, and biological evaluation of DNA polymerase η inhibitors for the treatment of cancer"
Eur. J. Med. Chem., 2022, In press
95. I. Geronimo, M. De Vivo*
"Alchemical Free Energy Calculations of Watson–Crick and Hoogsteen Base Pairing Interconversion in DNA"
J. Chem. Theory Comput., 2022, 18, 11, 6966–6973 (Link)
94. Y. Zhao, J. Shen, Q. Wang, M. J. Ruiz Munevar, P. Vidossich, M. De Vivo, M. Zhou, E. Cao
"Structure of the Human Cation-chloride Cotransport KCC1 in an Outward-open State"
Proc. Natl. Acad. Sci. U.S.A., 2022, 119 (27) e2109083119 (Link)
93. F. Munafò, E. Donati, N. Brindani, G. Ottonello, A. Armirotti, M. De Vivo*
“Quercetin and Luteolin are single-digit micromolar inhibitors of the SARS-CoV-2 RNA-dependent RNA polymerase”
Sci. Rep., 2022, 12, Article number: 10571 (Link)
92. A. Colini Baldeschi, M. Zattoni, S. Vanni, L. Nikolic, C. Ferracin, G. La Sala, M. Summa, R. Bertorelli, S. M. Bertozzi, P. Carloni, M. L. Bolognesi, M. De Vivo, G. Legname
"Innovative non-PrP-targeted drug strategy designed to enhance prion clearance"
J. Med. Chem., 2022, 65, 13, 8998–9010 (Link)
91. M. A. La Serra, P. Vidossich, I. Acquistapace, A.K. Ganesan, M De Vivo*
"Alchemical free energy calculations to investigate protein-protein interactions: the case of the CDC42/PAK1 complex"
J. Chem. Inf. Model., 2022, 62, 12, 3023–3033 (Link)
90. O. Zhao, K. Roy, P. Vidossich, L. Cancedda, M. De Vivo, B. Forbush, E. Cao
"Structural basis for inhibition of the Cation-chloride cotransporter NKCC1 by the diuretic drug bumetanide"
Nat. Comm., 2022, 13. Article number: 2747 (Link)
89. S. Jahid, J. A. Ortega, L. M. Vuong, S. J. Hachey, J. L. Flesher, M. A. La Serra, N. Brindani, G. La Sala, J. Manigrasso, J. M. Arencibia, S. M. Bertozzi, M. Summa, R. Bertorelli, A. Armirotti, C. Chen, C. C. W. Hughes, R. Edwards, M. De Vivo*, A. K. Ganesan
"Structure-based Design of CDC42 Effector Interaction Inhibitors For the Treatment of Cancer"
Cell Rep., 2022, Apr 5;39(1):110641 (Link)
88. I. Geronimo, P. Vidossich, M. De Vivo*
"Local Structural Dynamics at the Metal-Centered Catalytic Site of Polymerases is Critical for Fidelity"
ACS Catal., 2021, 11, 22, 14110–14121 (Link)
87. E. Donati, P. Vidossich, M. De Vivo*
"Molecular mechanism of phosphate steering for DNA binding, cleavage localization, and substrate release in nucleases"
ACS Catal., 2021, 11, 21, 13244–13254 (Link)
86. A. Savardi, M. Borgogno, M. De Vivo,* L. Cancedda
"Pharmacological tools to target NKCC1 in brain disorders"
Trends in Pharmacol. Sci. (Cell Press), 2021, Vol. 42, No. 12 (Link)
85. J. Manigrasso, M. Marcia, M. De Vivo*
"Computer-aided design of RNA-targeted small molecules: a growing need in drug discovery"
Chem (Cell Press), 2021, Volume 7, Issue 11, Pages 2965-2988 (Link)
84. J. Manigrasso, M. De Vivo*, G. Palermo
"Controlled Trafficking of Multiple and Diverse Cations Prompts Nucleic Acid Hydrolysis"
ACS Catal., 2021, 11, 14, 8786-8797 (Link)
Cover Article
83. M. Marcia, J. Manigrasso, M. De Vivo,*
"Finding the ion in the RNA-stack: Can computational models accurately predict key functional elements in large macromolecular complexes?"
J. Chem. Inf. Model., 2021, 61, 6, 2511–2515 (Link)
82. A. Pecina, D. Rosa-Gastaldo, L. Riccardi, S. Franco-Ulloa, E. Milan, P. Scrimin, F. Mancin, M. De Vivo*
"On the Metal-Aided Catalytic Mechanism for Phosphodiester Bond Cleavage Performed by Nanozymes"
ACS Catal., 2021, 11, 14, 8736–8748 (Link)
Cover Article
81. M. Borgogno, A. Savardi, J. Manigrasso, A. Turci, C. Portioli, G. Ottonello, S. M. Bertozzi, A. Armirotti, A. Contestabile, L. Cancedda, M. De Vivo*
"Design, synthesis, in vitro and in vivo characterization of selective NKCC1 inhibitors for the treatment of core symptoms in Down syndrome and other brain disorders"
J. Med. Chem., 2021, 64, 14, 10203–10229 (Link)
Cover Article
80. L. Riccardi, S. Decherchi, W. Rocchia, G. Zanoni, A. Cavalli, F. Mancin, M. De Vivo*
"Molecular recognition by gold nanoparticle-based receptors as defined through surface morphology and pockets fingerprint"
J. Phys. Chem. Lett., 2021, 12, 23, 5616–5622 (Link)
Cover Article
79. C. Portioli, M. J. Ruiz Munevar, M. De Vivo*, L. Cancedda
"Cation-coupled chloride cotransporters: chemical insights and disease implications"
Trends Chem. (Cell Press), 2021, 3, 10, 832–849 (Link)
Cover Article
78. S. Franco-Ulloa, D. Guarnieri, L. Riccardi, P. Pompa and M. De Vivo*
"Association mechanism of peptide-coated metal nanoparticles with model membranes: A coarse-grained study"
J. Chem. Theory Comput., 2021, 17, 7, 4512-4523 (Link)
Cover Article
77. P. Vidossich and M. De Vivo*
"The role of first principles simulations in studying (Bio)catalytic processes"
Chem Catalysis (Cell Press), 2021, 1, 1, 69-87 (Link)
76. L. Morillas-Becerril, S. Franco-Ulloa, I. Fortunati, R. Marotta, X. Sun, G. Zanoni, M. De Vivo*, F. Mancin
"Specific and nondisruptive interaction of guanidium-functionalized gold nanoparticles with neutral phospholipid bilayers"
Communications Chemistry (Nature), 2021, 4, 93 (Link)
75. I, Geronimo, P. Vidossich, E. Donati, M. De Vivo*
"Computational investigations of polymerase enzymes: Structure, function, inhibition, and biotechnology"
WIREs Computational Molecular Science, 2021, 11, 6 (Link)
Cover Article
74. M. Prejanò, P. Vidossich, N. Russo, M. De Vivo*, T. Marino
"Insights into the catalytic mechanism of domains CD1 and CD2 in Histone Deacetylase 6 from quantum calculations"
ACS Catal., 2021, 11, 5, 3084–3093 (Link)
73. P. Vidossich, M. Castañeda, E. Luis, C. Mota, D. de Sanctis, G. P. Miscione, M. De Vivo*
"Functional Implications of Second-shell Basic Residues for dUTPase DR2231 Enzymatic Specificity"
ACS Catal., 2020, 10, 23, 13825–13833 (Link)
72. J. A. Ortega, J. Arencibia, E. Minniti, J.O. Byl, S. Franco-Ulloa, M. Borgogno, V. Genna, M. Summa, S. M. Bertozzi, R. Bertorelli, A. Armirotti, A. Minarini, C. Sissi, N. Osheroff, M. De Vivo*
"A novel, potent, and drug-like tetrahydroquinazoline inhibitor that is highly selective for human topoisomerase II α over β"
J. Med. Chem. 2020, 21, 12873–12886 (Link)
71. S. Franco-Ulloa , G. Tatulli , S. Løland Bore , M. Moglianetti , P. P. Pompa ,M. Cascella, M. De Vivo*
"Dispersion state phase diagram of citrate-coated metallic nanoparticles in saline solutions"
Nat. Comm. 2020, 11, 5422 (Link)
70. J. Czescik, S. Zamolo, T. Darbre, C. Sissi, A. Pecina, L. Riccardi, M. De Vivo*, F. Mancin, P. Scrimin
"A gold nanoparticle nanonuclease relying on a Zn(II) mononuclear complex"
Angewandte Chemie, 2020, 59, 2–12 (Link)
69. A. Savardi, M Borgogno, R. Narducci, G. La Sala, J. Ortega, M. Summa, A. Armirotti, R. Bertorelli, A. Contestabile, M. De Vivo*, L Cancedda
"Discovery of a small molecule drug candidate for selective NKCC1 inhibition in brain disorders"
Chem (Cell Press), 2020, 6, 1–24 (Link)
68. J. Manigrasso, I. Chillón, V. Genna, P. Vidossich, S. Somarowthu, A. M. Pyle, M. De Vivo,* M. Marcia
"Visualizing group II intron dynamics between the first and second steps of splicing”
Nat. Comm., 2020, 11, 2837 (Link)
67. E. Catanzaro, N. Betari, J. M. Arencibia, S. Montanari, C. Sissi, A. De Simone, I. Vassura, A. Santini, V. Andrisano, V. Tumiatti, M. De Vivo, D. V. Krysko, M. B.L. Rocchi, C. Fimognari, A. Milelli
"Targeting topoisomerase II with trypthantrin derivatives: discovery of 7-((2-(dimethylamino)ethyl)amino)indolo[2,1-b]quinazoline-6,12-dione as an antiproliferative agent to treat cancer”
Eur. J. Med. Chem., 2020, 202 (15), 112504 (Link)
66. D. Duarte, A. Lamontanara, G. La Sala, S. Jeong, Y-K Sohn, A. Panjkovich, S. Georgeon, T. Kükenshöner, M. Marcaida, F. Pojer, M. De Vivo, D. Svergun, H-S Kim, M. Dal Peraro, O. Hantschel
"Btk SH2-kinase interface is critical for allosteric kinase activation and its targeting inhibits B-cell neoplasms"
Nat. Comm., 2020, 11, 2319 (Link)
65. J. Arencibia, N. Brindani, S. Franco-Ulloa, M. Nigro, J. A. Kuriappan, G. Ottonello, S. Mandrup Bertozzi, M. Summa, S. Girotto, R. Bertorelli, A. Armirotti, M. De Vivo*
"Design, synthesis, dynamic docking, biochemical characterization, and in vivo pharmacokinetics studies of novel topoisomerase II poisons with promising antiproliferative activity"
J. Med. Chem., 2020, 63 (7), pp 3508–3521 (Link)
64. 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, 142 (6), pp 2823-2834 (Link)
Cover Article
63. 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)
62. 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)
Cover Article
61. 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)
60. 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)
59. 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)
58. 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
57. 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)
56. 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)
55. 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)
54. L. Riccardi, V. Genna, M. De Vivo*
"Metal-ligand interactions in drug design" (Perspective)
Nature Reviews Chemistry, 2018, 2, 100–112 (Link)
Cover Article
53. 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)
52. 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
51. 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)
50. 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
49. 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)
48. 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)
47. 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
46. 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
45. 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)
44. M. De Vivo* and A. Cavalli
“Recent advances in dynamic docking for drug discovery”
WIREs Computational Molecular Science, 2017, 7:e1320 (Link)
Cover Article
43. 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)
42. M. De Vivo*, M. Masetti, G. Rossetti
BOOK CHAPTER
“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
41. J. Dreyer, G. Brancato, E. Ippoliti, V. Genna, M. De Vivo, P. Carloni, U. Rothlisberger
BOOK CHAPTER
“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
40. 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)
39. 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)
38. 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)
37. 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)
36. 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)
35. 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)
34. 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)
33. 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)
32. 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)
31. 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
30. 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)
29. 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)
28. G. Palermo, M. De Vivo*
BOOK CHAPTER
“Computational Chemistry for Drug Discovery"
Encyclopedia of Nanotechnology, Springer – 2015, pp 1-15 (Link) - Invited contribution
27. M. Cascella, M. Dal Peraro, M. De Vivo*
BOOK CHAPTER
“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
26. M. De Vivo*
BOOK REVIEW
"Enzyme Technologies: Pluripotent Players in Discovering Therapeutic Agents."
Edited by Hsiu-Chiung Yang, Wu-Kuang Yeh, James R. McCarthy (Wiley)
ChemMedChem - Volume 10, Issue 8, page 1443, August 2015 (Link) - Invited contribution
25. 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)
24. 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
23. 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)
22. 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)
21. 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)
20. 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)
19. A. Lodola and M. De Vivo*
BOOK CHAPTER
“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
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)
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.
