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Hire Dr. Vito G.

Italy

USD 100 /hr

Senior Computational Chemist | Expert in Enzimology and Nucleic Acids via Multiscale Molecular Dynamics Simulation.

Profile Summary

Background In 2013, in the group of Prof. Dal Peraro (EPFL, Lausanne, Switzerland), I started a MD-based project focused on the two-metal-aided catalysis performed by human DNA Polymerase-η (Pol-η), an enzyme bypassing DNA lesions ensuring correct genetic inheritance. Interestingly, Pol-η was found aberrantly expressed in melanoma cells, therefore, the discovery of a Pol-η inhibitor was a challenge of great scientific interest. For this reason, in late 2013 I moved in the group of Dr. Marco De Vivo at the Italian Institute of Technology where I started my PhD in the field enzyme-mediated nucleic acids editing. Thanks to the collaboration between IIT and EPFL results of my research were published on NAR (Cover article), JACS (Cover article), Nat. Chem. (Cover article) and more with me as first author. Once having described the dynamics of Pol-η, I started investigating Pol-η reaction mechanism for subsequent structure-based drug design efforts. To do so, in 2015 I moved in the group of Prof. Paolo Carloni, at Forschungszentrum Jülich, Germany; one of the most important players in the field Car-Parrinello quantum-mechanics/molecular-mechanics (CP QM/MM) simulations; an expensive computational approach which, differently to FF-based simulations, permits the investigation of breaking/forming chemical bonds. To run CP QM/MM simulations I gained two important grants funded by the John von Neumann Institute. Results of CP QM/MM simulations were recently published in JACS. The work shad a large echo in the scientific community and have been selected by JACS editors as cover article. Moreover, the paper has also been highlighted in JACS spotlights. Thanks to these intense investigations, we gain precious insights regarding Pol- catalytic activity, all this information was exploited to start a drug discovery project (Pol- inhibitor) which, at the time of this proposal, is reached the in vitro stage at IIT. Concomitantly, at IIT, I started a project on the characterization of group-II intron in collaboration with the group of Dr. Marco Marcia at EMBL (Grenoble). We have found that a common structural motif features the active site of different biomolecule spanning from RNAzymes, DNAzymes to Spliceosome. These results have been published in Structure and Nat. Comm. Considering my professional experience, I feel motivated to face Drug Discovery challenge with new transversal thinking; by imitating nature strategies. Indeed, I am now focused on the rational design and optimization (via both computational and experimental approaches) of biotherapeutic short natural and non-natural nucleic acids sequences for gene silencing therapies. This has been the topic of a project that EMBO has funded me with a Long-Term Fellowship I have carried on in the group of Prof. Modesto Orozco, a worldwide leading scientist in the field of integrative modeling, system biology and theoretical investigations of nucleic acids, located at IRB-Barcelona, Spain. Current Research Work My research focuses on three topics: 1) Dissecting the physicochemical properties of hybrid duplexes/triplexes to gain insights on their sequence-dependent flexibility and thermal stability for therapeutic gene silencing approaches. 2) Designing of a Mg2+-triggered RNA-endonuclease XNAzyme (constituted by 2’-Fluoroarabino NA) to selectively hydrolyze MALAT-1 non-coding RNA whose overexpression has been strictly linked to lung-cancer onset in humans. 3) Unveiling the driving-force leading RatG13 virus to evolve toward SARS-CoV-2 by analyzing all possible mutations to decipher its evolution-mechanism and host-selection process and avoid possibile future alpha- and beta-coronavirus pandemics (funded by Spanish Minister of Health). Academi Activity In 2013 I have been nominated “Best Student of the Year” by University of Cagliari having completed the master in Biochemistry in 13 months and with the highest marks In 2014 I got a fellowship from the University of Bologna for my PhD ad the Italian Institute of Technology. In 2014, thanks to the success of my Pol-mediated DNA-synthesis project, I have been awarded with the “Marco Polo Fellowship” to move in Germany to extend my background/project. There, I have been also awarded with two grants by John von Neumann Institute. In 2015 I was one of the co-organizers of the FZJ campus retreat of Institute of Advanced Simulation at FZJ Germany. In 2018 I got the EMBO Excellence in Life Science Long-Term Fellowship to start designing the RNA-endonuclease XNAzyme to hydrolyze the highly oncogenic MALAT-1 non-coding RNA and Dr. Philipp Holliger (EMBO referee) having appreciated the scientific vision, joined our project with an ongoing collaboration. Meanwhile, I have been nominated referee for several high-impact Wiley, NPG and ACS journals. Recently, I have start investigated SARS-CoV-2 evolution mechanism and this project has been funded with a research grant from the Spanish Minister of health. Very recently I have also been awarded by the Spanish Minister of Health with the Juan De La Cierva grant. Results of my investigations have been presented to numerous international conferences organized by CECAM, EMBO and Gordon Research to name few. Also, from 2017 I am co-supervising two PhD students at the Italian Institute of Technology.

Subject Matter Expertise

• ★ Molecular Docking
• ★ Biotechnology & Bioengineering
• ★ Computer Simulation/Computational Modeling
• ☆ Organometallic Chemistry
• ☆ Quantum Chemistry
• ☆ Recombinant DNA
• ☆ RNA Sequencing
• ☆ Biophysics
• ☆ Protein/Enzyme Engineering
• ☆ Drug Design
• ☆ Severe Acute Respiratory Syndrome (SARS)

Services

• Writing
• Research
• Consulting
• Data & AI
• Product Development

Writing Medical Writing, Technical Writing

Research Fact Checking, Gray Literature Search, Systematic Literature Review, Secondary Data Collection

Consulting Scientific and Technical Consulting

Data & AI Statistical Analysis, Data Visualization

Product Development Formulation

Work Experience

Postdoctoral Researcher

Institut de Recerca Biomèdica

January 2018 - Present

Postdoctoral Researcher

Istituto Italiano di Tecnologia

April 2017 - December 2017

PhD-Fellow

Istituto Italiano di Tecnologia

January 2014 - April 2017

Visiting PhD-student

Forschungszentrum Jülich

September 2014 - September 2015

Internship

Istituto Italiano di Tecnologia

September 2013 - December 2013

Internship

École Polytechnique Fédérale de Lausanne

March 2013 - August 2013

Interniship

Centro Nacional de Investigaciones Oncológicas

April 2009 - July 2009

Education

Doctorate (Pharmacy and Biochemistry)

University of Bologna

January 2014 - April 2017

Master in Cellular and Molecular Biology (Biochemistry)

University of Cagliari

October 2011 - February 2013

Bachelor in Experimental Biology (Biochemitry)

University of Cagliari

August 2008 - July 2011

Certifications

• Certification details not provided.

Publications

JOURNAL ARTICLE

Vito Genna, Elisa Donati, Marco De Vivo(2020). Recruiting Mechanism and Functional Role of a Third Metal Ion in the Enzymatic Activity of 5$\prime$ Structure-Specific Nucleases . Journal of the American Chemical Society. American Chemical Society ({ACS})

Vito Genna, Marco Marcia, Marco De Vivo(2019). A Transient and Flexible Cation-$\uppi$ Interaction Promotes Hydrolysis of Nucleic Acids in {DNA} and {RNA} Nucleases . Journal of the American Chemical Society. 141. (27). p. 10770--10776. American Chemical Society ({ACS})

Vito Genna, Sebastian Arangundy-Franklin, Alexander I. Taylor, Benjamin T. Porebski, Sew Peak-Chew, Alexandra Vaisman, Roger Woodgate, Modesto Orozco, Philipp Holliger(2019). A synthetic genetic polymer with an uncharged backbone chemistry based on alkyl phosphonate nucleic acids . Nature Chemistry. 11. (6). p. 533--542. Springer Science and Business Media {LLC}

Vito Genna, Rita Petracca, Katherine A. Bowen, Lauren McSweeney, Siobhan O’Flaherty, Brendan Twamley, Marc Devocelle, Eoin M. Scanlan(2019). Chemoselective Synthesis of N-Terminal Cysteinyl Thioesters via $\upbeta$,$\upgamma$-C,S Thiol-Michael Addition . Organic Letters. American Chemical Society ({ACS})

(2019). The Origins and the Biological Consequences of the Pur/Pyr DNA·RNA Asymmetry .

Vito Genna, Elisa Donati, Marco De Vivo(2018). The Catalytic Mechanism of {DNA} and {RNA} Polymerases . {ACS} Catalysis. p. 11103--11118. American Chemical Society ({ACS})

Vito Genna, Elisa Donati, Marco De Vivo(2018). The catalytic mechanism of {DNA} and {RNA} polymerases . {ACS} Catalysis. American Chemical Society ({ACS})

Vito Genna, Laura Riccardi, Marco De Vivo(2018). Metal{\textendash}ligand interactions in drug design . Nature Reviews Chemistry. 2. (7). p. 100--112. Springer Nature

Genna V, Carloni P, De Vivo M(2018). A Strategically Located Arg/Lys Residue Promotes Correct Base Paring During Nucleic Acid Biosynthesis in Polymerases . Journal of the American Chemical Society.

Genna, V., Colombo, M., De Vivo, M., Marcia, M.(2018). Second-Shell Basic Residues Expand the Two-Metal-Ion Architecture of DNA and RNA Processing Enzymes . Structure. 26. (1). p. 40-50.e2.

Genna, V., Vidossich, P., Ippoliti, E., Carloni, P., Vivo, M.D.(2016). A Self-Activated Mechanism for Nucleic Acid Polymerization Catalyzed by DNA/RNA Polymerases . Journal of the American Chemical Society. 138. (44). p. 14592-14598.

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

Kumar, A., Melis, P., Genna, V., Cocco, E., Marrosu, M.G., Pieroni, E.(2014). Antigenic peptide molecular recognition by the DRB1-DQB1 haplotype modulates multiple sclerosis susceptibility . Molecular BioSystems. 10. (8). p. 2043-2054.

BOOK

Dreyer, J., Brancato, G., Ippoliti, E., Genna, V., De Vivo, M., Carloni, P., Rothlisberger, U.(2017). Chapter 9: First Principles Methods in Biology: From Continuum Models to Hybrid Ab initio Quantum Mechanics/Molecular Mechanics . RSC Theoretical and Computational Chemistry Series. 2017-January. (9). p. 294-339.

Pieroni, E., Kumar, A., Pisu, M., Genna, V., Concas, A., Cao, G.(2013). Combination of classical and molecular modeling approaches to investigate the effect of antipsychotic drugs on cell proliferation kinetics . Chemical Engineering Transactions. 32. p. 787-792.