The Molecular Modeling and Drug Discovery Lab develops and applies computational methods to understand, characterize, and design chemical systems capable of recognizing, signalling, interacting with, and transforming other entities. These systems include pharmaceutically relevant enzymes and functionalized nanoparticles for chemosensing and catalysis. The final goal is to achieve an atomic-level comprehension of those systems, and use this information to design nanoparticles with programmed properties, and potent inhibitors as a promising starting point for drug discovery programs.
Structure, dynamics and catalysis of the chemical systems of interest are studied by means of classical molecular dynamics (MD) simulations coupled with first-principles-based computational methods (e.g. QM/MM simulations) and enhanced sampling techniques for free energy estimation. This multiscale computational approach includes also docking, virtual screening, de novo small molecules computational design and in silico ADMET evaluation (for drug design). These computational efforts are integrated with medicinal chemistry and molecular biology to identify and optimize novel small molecules able to inhibit the enzymatic function of interest. The goal is to understand the general principles that control molecular recognition and catalysis and use this information to design intelligent nanosystems and potent inhibitors for drug discovery.
Our lab comprehends a core of computational chemists, with access to CPU and GPU processors for computational simulations. We also take advantage of allocated time on external supercomputers. This computational activity is fully integrated with medicinal chemistry and molecular biology experiments, within the group. Our med chemists and molecular biologists work in the brand-new laboratories of the department of drug discovery and development in IIT, which offers state-of-the-art instrumentation.
Our research is highly interdisciplinary and collaborative. We have a number of collaborators located in top institutions, all over the world:
Prof. Paolo Carloni, and with Dr. Giulia Rossetti and Dr. Alejandro Giorgetti IAS-5 / INM-9 Computational Biomedicine Forschungszentrum (Jülich, Germany).
Dr. Laura Cancedda (IIT), Prof. Fabrizio Mancin (University of Padova), Dr. Federico Rastrelli (University of Padova), Prof. Anand Ganesan (UC Irvince, USA), Prof. Matteo Dal Peraro (EPFL, Lausanne), Prof. Claudia Sissi (University of Padova), Prof. Anna Minarini (University of Bologna).