Molecular Dynamics-based techniques for investigating protein flexibility and protein-ligand interaction in drug discovery.

by Prof. Francesca Spyrakis

Thursday Sep 5, 2024, 2:30 PM → 4:30 PM Europe/Rome

Dipartimento

Classical Molecular Dynamics (MD) is a physical-based method for studying the motion of atoms and molecules according to Newton’s physics. A force field is used to estimate the forces between interacting atoms and calculate the overall potential energy of the system. Then, during MD simulations, the integration of Newton’s laws of motions generates successive conformations of the system, providing trajectories that specify positions and velocities of the particles over time. From these MD trajectories, a variety of properties can be calculated, including free energy, kinetics measures, and other macroscopic quantities.

In the last years MD and related methods have become routinely applied in biophysics and drug design. Their main advantage is in explicitly treating structural flexibility and entropic effects, thus allowing a more accurate estimate of the thermodynamics and kinetics associated with drug−target recognition and binding. The availability of more performing hardware and of more accurate force fields further enhanced the applicability of MD-based methodologies.

In this seminar we will review the theoretical background of MD and enhanced sampling methods, widely used to study drug−target binding, underling advantages and main limitations. Case studies and recent applications will also be presented.

 

ZOOM LINK: https://zoom.us/j/8442946092?pwd=cGozOXJPd2hYSWZ5TXRteHd2cnZ5QT09&omn=98795996367