My research is focused on the development and application of advanced computational methods – including all-atom molecular dynamics, quantum dynamics and novel cryo electron microscopy refinement methods – and of their integration with experiments to unravel the function and improve applications of key macromolecular assemblies involved in DNA cleavage and replication, RNA transcription and translation, with important therapeutic applications for the treatment of cancer and genetic diseases.
CRISPR-Cas9: mechanistic understanding and rational design
CRISPR-Cas9 is a transformative 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.
Nucleosome dynamics and chromatin drug development
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.
Dissecting the mechanistic basis of non-coding RNA
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.
Catalytic Metals and Enzymatic Processing of DNA & RNA
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.
Graduate and master student projects
Anticancer Drug Discovery: Boosting Potency of Type II Topoisomerase Poisons
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.
Mechanism of lipid selection and degradation
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.
Density Functional Theory (DFT) for Solar Cells technology
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.
A duel with pain: multi-target drug discovery
Multi-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
As a master student, I have been working at 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., 2010, 75, pp 1982–1991