Thermodynamic principles of molecular recognition. Binding free energy, energy and entropy in the ligand-protein target interaction. Statistical mechanics approach to the evaluation of the drug-receptor equilibrium constant. Molecular mechanics (MM) computational tools in modeling biomolecular systems: atomistic force fields and computation of binding energies in molecular Docking. Computer Lab applications of binding affinities evaluation.
Knowledge acquired: the course is divided into a theoretical part and in laboratory sessions. From the theoretical standpoint, the student will be acquainted with the thermodynamic basis in molecular recognition in biological systems and with a statistical mechanics rationalization of Molecular Docking scoring functions in drug design. Exercises in computer Lab will furnish the technical skills for implementing on a Unix platform the calculation of the equilibrium constant of drug-receptor system.
Prerequisites
none
Teaching Methods
The whole course is done in the computer Lab (aula 61). Theoretical and Lab lectures are continuously intertwined in order to practically apply on the computers what is learned in theory lectures.
Further information
Lecture notes available online on the professor's homepage lx03.sm.chim.unifi/~procacci/MSB (unrestricted access)
Type of Assessment
Oral examination aimed at assessing the knowledge of both theoretical and technical/applicative aspects of the Course
Course program
FRONTAL LESSONS
Introductory Course Description. Atomic definition of the
drug-receptor system, potential functions on multidimensional spaces.
Potential bonded (non-bonded) and non-bonded INTRA molecule for ligand
and receptor NonBonded drug interaction potential in implicit solvent
protein. Generalities on Ligand-receptor association. Measure of the
binding constant (binding isotherm). Statistical Thermodynamics of
ligand-receptor binding. Microcanonical ensemble and statistical
entropy Canonical ensemble and Statistical Definition of Helmholtz
Free Energy. Translational partition function of a monoatomic ideal
gas Canonical partition function for a gas of non-interacting
molecules or of an ideal solution. Electronic, vibrational, rotational
and translational partition function Chemical equilibrium A + B = AB;
dissociation constant and molecular partition functions in implicit
solvent Drug-receptor dissociation free energy as a sum of electronic,
vibrational, rotational and translational contributions Calculation of
translational and rotational contribution to free energy-dissociation
drug-protein. Free energy "cratic". Calculation of the vibrational
contribution to the free energy of dissociation and elimination of
free "cratic" energy. Final formulation of free dissociation energy.
INFORMATIC LABORATORY LESSONS
Set up of the accounts and work environment. Unix commands from terminal: pwd, cd, ls, cp, cat; Short introduction to VMD and emacs
Linux commands from terminal: grep, less, awk, sed, and concatenation of commands with "|" ">" And "<" to generate input file for VMD.
Tutorial: PDB (protein) PUBCHEM (ligands) web databases. SMILES code and generation of ligand 3D structures with "babel".
Molecular Manipulation tools within VMD / tcl ["set menu tkcon" for generating the VMD / tcl console]
Calculation of COM via VMD / tcl and ligand rotation in binding pocket.
VMD / tcl recovery / recovery lesson; Set, moveby, ROT (subroutine), writepdb
VMD / tcl summary exercise on FKBP12 with toluene.
Download and installation of Autodock4 and Vina.
Molecular mechanical exercise with vina: VMD/tcl preparation of the Ligand-receptor pairs (pdbqt files) and ligand pose optimization with vina.
Final individual exercise includes: 1) downloading a pdb file from the
RCSB protein data bank database 2) handling it with unix commanded
commands to isolate only the receptor structure by deleting
comments. 3) downloading the ligand SMILES code from the public
database PUBCHEM and conversion to PDB format with babel
4) Docking with Vina. 5) Output analysis and calculation of the dissociation constant.