- From enzymatic function to drug discovery -
We are a research group focused on the use of multiscale molecular modeling to understand function and inhibition of pharmaceutically relevant enzymes and functionalized nanoparticles. Within the group, computational insights are fully integrated with medicinal chemistry and molecular biology to design, synthesize and test promising compounds potentially endowed with the desired pharmacological effect to treat primarily cancer, neurological disorders and inflammatory-related diseases.
Enjoy your visit - and thanks for your interest !
Marco De Vivo & the group
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Dr. Marco De Vivo
Research Lab Director
Molecular Modeling & Drug Discovery Lab
Istituto Italiano di Tecnologia
Via Morego, 30 - Genoa (16163), Italy
Phone: +39 010 2897 404
Email: marco.devivo @ iit.it
-> One postdoctoral position in biochemistry and structural biology for drug discovery
We are looking for candidates with extensive experience in biochemistry and/or structural biology (protein expression, purification, crystallization and enzymatic assays). The selected candidate will play a key role in generating new inhibitors with therapeutic implications and potential for high-impact publications. (Link)
Our latest stories:
-> Insights on the specificity of the anticancer drug Etoposide between human topoisomerases II.
Our most recent article employs smoothed potential MD simulations to calculate etoposide's dissociation constants, thus shedding light on the preference of this drug for poisoning human topoisomerase IIα over the IIβ counterpart. J. Chem. Inf. Model. (Link)
-> On the computational and experimental efforts for studying lipid plasticity.
Our latest account article digs into the importance of molecular dynamics simulations when investigating membrane trafficking and selective hydrolysis of lipids, and the ancillary cooperativity with wet-lab measurements. Acc. Chem. Res. (Link)
-> Shedding light on the hydrolysis of nucleic acids
In our most recent story, classical and quantum-based molecular simulations are employed to unravel the importance of cation-pi interactions in the hydrolysis of nucleic acids by metal-dependent DNA and RNA nucleases. J. Am. Chem. Soc. (Link)
-> Rationalizing the chirality transfer in gold nanoclusters
With a combination of NMR techniques and molecular dynamics simulations, this new story sheds light on the chirality transfer of a passivated 38-atom gold nanocluster. Such study addresses the dynamics of the chirality transfer between chiral surfaces and achiral ligands. ACS Nano. (Link)
-> Rationally designing gold-supported nanoreceptors
Based on molecular dynamics simulations, this article presents the smart design of gold nanoparticles applied to analyte detection. In this study, the functional molecules grafted onto the nanoreceptors are modeled to optimize their affinity. Angewandte Chemie. (Link)
-> Towards the smart engineering of functionalized gold nanoparticles
A reliable 3D model of functionalized gold nanoparticles is determinant for the knowledge-based design of nanomaterials with novel applications. This article introduces NanoModeler, a webserver for the assembly and parametrization of monolayer-protected gold nanoparticles. J. Chem. Theory Comput. (Link) - On the journal cover!
-> Understanding the mechanism of DNA and RNA polymerases
Computational approaches, integrated with experimental data, have shed light in recent years on the mechanism of action of DNA and RNA polymerases. This perspective discusses the importance, opportunities and challenges on this growing field. ACS Catal. (Link)
-> Unraveling the allosteric communication in Protein Tyrosine Phosphatases
This study illustrates the allosteric network and reveals new sites for targeting allosteric inhibitors of Protein Tyrosine Phosphatases (PTPs), explaining the functional influence of a diverse set of disease-associated mutations. Biochemistry, (Link)
-> Inhibiting ATP-dependent phosphorylation
This study uses a broad set of biophysical analyses to evaluate the use of abietane-type diterpenoids, a biologically active class of phytometabolites with largely nonpolar structures, for the development of pharmaceutically relevant PTP inhibitors. Biochemistry, (Link)
-> Metal-ligand interactions in drug design
Atomistic understanding of the metal–ligand interactions will help us identify potent metalloenzyme inhibitors and metallodrugs. Our Perspective in Nature Reviews Chemistry, (Link)
On the cover of the Journal! Check it out!!!
-> Watson&Crick model for DNA: to be or not to be...
Our new study on how Polymerases shape the growing DNA has been published in the Journal of the American Chemical Society.
A new step forward in understanding how enzymes process DNA and RNA! - (Link)
-> Targeting bacterial Topoisomerases !
Our new study, in collaboration with Dr. Miscione at Uni Andes (CO), has been just published as part of the Special Issue "DNA Topoisomerases" in the International Journal of Molecular Sciences - (Link)
-> New inhibitors for cancer - targeting topoisomerase II
Our new study in collaboration with Dr. C. Sissi at UniPd and Dr. A. Minarini at UniBo has been published in J. Med. Chem. - Link
We disclose novel Topoisomerase II poisons with promising antiproliferative activity:
-> Two-metal-ion architecture, expanded!
Our new study in collaboration with Dr. M. Marcia, at EMBL - Check it out!
We report on newly-identified structural elements for DNA and RNA processing in different enzymes.
This study has been published on Structure (Cell Press).
-> Pocket crosstalk analysis for extended MD trajectories!
Check out our newly developed method to analyze long MD trajectories and know about pocket formation, dynamics & allostery!
This method is published in ACS Central Science.
This study will be on the cover of the journal and has been highlighted in First Reactions ACS Central Science, "Toward Understanding “the Ways” of Allosteric Drugs", by R. Amaro 2017
-> Nanoparticles like proteins!
Check out our combined computational-experimental work in collaboration with Dr. Mancin and Rastrelli and Univ of Padova, on gold NPs for chemosensing. This study has just been published on Chem (Cell Press) ! - Link
It is the Cover Article!
-> Fighting melanoma!
Check out our new paper on J. Med. Chem. reporting the design and discovery of potent inhibitors of the enzyme Acid Ceramidase - Link
-> Opinions&Comments on "dynamic docking" for drug discovery in WIREs Computational Molecular Science, read "Recent advances in dynamic docking for drug discovery" - Link