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 (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
Basic Thermodynamic Statistical Principles. 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 in RRHO (Rigid Rotor Harmonic Oscillator) approximation.
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. Drug-Protein random structures created for combination of PDB and PUBCHEM files displayed with graphical S/W VMD.
Download and compilation of an open-source Molecular Mechanics program to be applied to systems of biological interest.
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
Molecular Mechanics Tutorial with ORAC: input file analysis and file test execution; generating a topological file for the ligand using ORAC ancillary tools.
Molecular mechanical exercise with orac: modification of input files and minimization of ligand and pubchem / pdb proteins
Molecular mechanical exercise with orac: VMD/tcl preparation of the complex-pose and structure optimization
Comprehensive exercise for calculating the affinity constant.
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, hetero atoms and alternative structures 3) downloading the ligand File in SDF format from public database PUBCHEM and conversion to PDB format with babel/ primadorac 4) ligand and receptor minimization with ORAC 5) Generating the "pose" using the s/w VMD 6) minimizing the structure of the complex with ORAC 7) Calculation of the standard free dissociation energy (see lecture notes).