Research

Future drugs and therapeutic strategies will be designed to target gene regulation via genome editing. However, the main challenge in this field is to understand the molecular basis underlying gene expression, which is incompletely understood. 

I use state-of-the-art computational methods, including molecular dynamics, quantum dynamics and novel cryo electron microscopy refinement methods, to unravel the function and improve application of key macromolecules responsible for gene regulation. My goal is to provide fundamental knowledge at the molecular level for the treatment of cancer and genetic diseases. 


CRISPR-Cas9: mechanistic understanding and rational design 

TOC4-1

CRISPR-Cas9 is a revolutionary genome editing technology, but the structural and mechanistic features underlying its function are unclear. My research aims at unravelling the mechanistic basis and at improving biological applications of this unique genome-editing machinery. Toward this aim, I am applying advanced computational methods and using the next-generation supercomputer ANTON-2. This research will be fully integrated with experiments, leading to the design of novel genome editing tools with improved specificity and/or controllable activity.

Collaborators: Prof. Martin Jinek (University of Zürich), Prof. Victor S. Batista (YALE), Prof. J. A. Doudna (UC Berkeley) and Prof. J. Andrew McCammon (UCSD, post-doctoral advisor)

Read more: J. Am. Chem. Soc. 2017, 139, pp. 16028–16031.
Proc. Natl. Acad. Sci. USA, 2017, 114, pp. 7260–7265. 
ACS Cent. Sci. 20162, pp. 756–763.


Nucleosome dynamics and chromatin drug development

mini.png

The constituents of chromatin, chromosomal DNA and the associated histone proteins, are key molecular targets for anticancer drugs. By integrating MD with X-ray crystallography and biochemical assays, we have characterized the mechanism of action of promising metal-based anticancer agents at the level of the nucleosome core particle, the fundamental unit of chromatin. We have clarified the mechanism of action at the molecular level, deciphering the corresponding relationships to cytotoxicity and impact on cancer cell function.

Collaborators: Prof. Paul J. Dyson (EPFL), Prof. Curtis A. Davey (NTU-Singapore), Prof. Ursula Rothlisberger (EPFL, post-doctoral advisor)

Read more: Nat. Commun. 2017, 8, pp. 14860.
Angew. Chem. Int. Ed. 2016, 55, pp 7441–7444
ChemMedChem. 2016, 11, pp 1199–1210


Dissecting the mechanistic basis of non-coding RNA

TOC-g2
RNA is a fundamental molecule that codes for protein and controls gene expression, playing a key regulation role in many cell responses and vital processes, such as human genetic heritance and diseases. I am interested in clarifying the molecular basis of non-coding RNA, which regulates gene expression via a variety of yet unknown mechanisms. We have suggested a mechanism for the splicing reaction in the bacterial groupII intron, paving the way for the mechanistic study of the human splicesome.

Collaborators: Prof. A. Magistrato (SISSA), Prof. Ursula Rothlisberger (EPFL, post-doctoral advisor)

Read more: J. Am. Chem. Soc. 2016138, 10374–10377
J. Chem. Theory Comput., 201713, 340–352


Catalytic Metals and Enzymatic Processing of DNA & RNA

2metal
As originally revealed by Steitz & Steitz (PNAS 1993, 90), DNA/RNA endonucleases perform phosphodiester bond cleavage via a two-metal-ion aided mechanism. I am using computational methods to clarify the two-metal aided mechanism in several endonucleases, including my recent work on CRISPR-Cas9. My interest in understanding the Steitz & Steitz mechanism has started as a graduate student, when I pursued studies on typeII topoisomerase and other endonucleases.

Collaborators: Prof. Dal Peraro (EPFL), Dr. Marco De Vivo (IIT, PhD advisor)

Read more: Acc. Chem. Res. 201548, pp 220–228
J. Chem. Theory Comput. 2013, 9, pp 857–862


                     Graduate and master student projects


Anticancer Drug Discovery: Boosting Potency of Type II Topoisomerase PoisonsUntitled

Type II Topoisomerase (topoII) is a metalloenzyme targeted by clinical antibiotics and anticancer agents. I employed molecular dynamics and free energy simulations to characterise the anticancer activity of novel topoII poisons that act as potent anticancer agents. My computations have been integrated with chemical synthesis and bio-assays, validating my mechanistic hypotheses.

Collaborators: Prof. Claudia Sissi (Univ. of Padova), Dr. Marco De Vivo (IIT, PhD advisor)

Read more: Chem. Commun. 2015, 51, pp 14310-13
J. Chem. Theory Comput. 2013, 9, pp 857–862


Mechanism of lipid selection and degradation

Untitled

The Fatty Acid Amide Hydrolase is a key membrane protein involved in the control of pain, cancer and immune diseases. By using a variety of molecular dynamics techniques, including free energy methods and quantum-based dynamics, flanked by estensive analysis using Bayesian statistics, I have clarified the mechanisms of lipid selection and degradation in the enzyme, with significant insights for the discovery of targeting drugs.

Collaborators: Dr. Marco De Vivo (IIT, PhD advisor), Prof. Daniele Piomelli (UC-Irvine), Prof. Andrea Cavalli (UniBo)

Read more: Eur. J. Med. Chem. 2015, 91, pp 15-26
J. Phys. Chem. B. 2015, 119, pp 789–801
J. Chem. Theory. Comput. 2013, 15, pp 1202-1213
J. Med. Chem. 2011, 54, pp 6612–6623


Density Functional Theory (DFT) for Solar Cells technologyobject018

Solar cells are the energy revolution of the 21th century, converting solar energy in electricity. By using Density Functional Theory (DFT), I have characterised the atomistic and electronic structure nature of hybrid organic-inorganic perovskites, novel materials for solar cells technology. Our outcomes have been integrated with the experiments of the Graetzel lab. for developing more efficient solar cells technologies.

Collaborators: Prof. M. Graetzel (EPFL), Prof. Ursula Rothlisberger (EPFL, post-doctoral advisor)

Read more: J. Phys. Chem. C. 2017, 121, 23886–23895. 
J. Mater. Chem. A. 2016, 4, pp 15997-16002.
http://arxiv.org/abs/1412.3659


A duel with pain: multi-target drug discovery

UntitledMulti-target drug discovery is promising for the development of innovative drugs. By applying molecular simulations and free energy methods, I have clarified the mechanism of action of ARN2508, a novel anti-inflammatory agent that inhibits both the Fatty Acid Amide Hydrolase (FAAH) and the cyclooxygenase (COX) enzymes. With this research, we provide the basis of dual inhibition for anti-inflammatory treatments. 

Read more: ChemMedChem 2016, 11, pp 1252 –1258


Structural elucidation of organic compounds

UntitledMy initial work has been focused on the development of methods for the prediction – based on the Karplus and Altona models – of NMR coupling constants (3JC-H), which are of key importance for the structural elucidation of bioorganic and pharmaceutically relevant compounds. Based on Density Functional Theory (DFT), I have formally derived a general 3JC-H prediction equation, which is used as a support to NMR experiments for the structural elucidation of organic compounds. 

Read more: J. Org. Chem., 201075, pp 1982–1991

 

Advertisements