KCC Seminar: Thermodynamics and kinetics of drug-target binding through molecular simulations

May 11 2017 01:30 PM - May 11 2017 02:30 PM

Prof. Andrea Cavalli 
University of Bologna and Italian Institute of Technology, Italy​


Andrea Cavalli is Professor of Medicinal Chemistry at the University of Bologna and Director of CompuNet at the Italian Istitute of Tecnology, Genova, Italy. Prof. Cavalli received his PhD in Pharmaceutical Sciences from the University of Bologna in 1999 and did postdoctoral work at SISSA (Trieste, Italy) and ETH (Zurich, Switzerland). Prof. Cavalli’s research has combined computational chemistry with drug discovery, focusing on neurodegenerative diseases, cancer, and neglected tropical diseases. He has developed and applied algorithms and protocols to accelerate and enhance the discovery of novel lead and drug candidates. In particular, he has been a pioneer in the use of molecular dynamics simulations and related approaches to drug discovery. In an interdisciplinary effort, these approaches led to the identification and characterization of lead candidates within the framework of multitarget drug discovery and polypharmacology. He is an author of more than 190 scientific papers and inventor in several international patents. He has delivered more than 100 invited lectures and seminars at international congresses and prestigious institutions. He is member of the Editorial Board of several international journals, and in 2014 he founded a high-tech startup company (BiKi Technologies s.r.l.) focused on molecular dynamics and enhanced sampling in drug discovery. In 2003, he was awarded the Farmindustria Prize for Pharmaceutical Research.


De Vivo, M.; Masetti, M.; Bottegoni, G.; Cavalli, A. Role of Molecular Dynamics and Related Methods in Drug Discovery. J. Med. Chem. 2016, 59, 4035-4061.
Mollica, L.; Theret, I.; Antoine, M.; Perron-Sierra, F.; Charton, Y.; Fourquez, J.M.; Wierzbicki, M.; Boutin, J.A.; Ferry, G.; Decherchi, S.; Bottegoni, G.; Ducrot, P.; Cavalli, A. Molecular Dynamics Simulations and Kinetic Measurements to Estimate and Predict Protein-Ligand Residence Times. J. Med. Chem. 2016, 59, 7167-7176.
Decherchi, S.; Berteotti, A.; Bottegoni, G.; Rocchia, W.; Cavalli, A. The ligand binding mechanism to purine nucleoside phosphorylase elucidated via molecular dynamics and machine learning. Nature Commun. 2015, 6, 6155.
Cavalli, A.; Spitaleri, A.; Saladino, G.; Gervasio, F.L. Investigating Drug-Target Association and Dissociation Mechanisms Using Metadynamics-Based Algorithms. Acc. Chem. Res. 2015, 48, 277-85.
Patel, J.S.; Berteotti, A.; Ronsisvalle, S.; Rocchia, W.; Cavalli, A. Steered Molecular Dynamics Simulations for Studying Protein-Ligand Interaction in Cyclin-Dependent Kinase 5. J. Chem. Inf. Model. 2014, 54, 470-80.
Grazioso, G.; Limongelli, V.; Branduardi, D.; Novellino, E.; De Micheli, C.; Cavalli, A.; Parrinello, M. Investigating the Mechanism of Substrate Uptake and Release in the Glutamate Transporter Homologue GltPh through Metadynamics Simulations. J. Am. Chem. Soc. 2012,134, 453-463.
Colizzi, F.; Perozzo, R.; Scapozza, L.; Recanatini, M.; Cavalli, A. Single-Molecule Pulling Simulations Can Discern Active from Inactive Enzyme Inhibitors. J. Am. Chem. Soc. 2010, 132, 7361-71.