Lecture 11: Molecular Drug Design Flashcards
True or false:
Molecular mechanics can be used to model the electrons of a molecule.
False.
True or false:
Molecular mechanics can be used to model chemical reactions.
False.
Molecules exist in ______ energy forms most of the time.
Low
Why is quantum mechanics seldom used for molecular modelling?
It is computationally difficult (and slow) to solve this equation. The size of the calculation increases exponentially with the number of electrons in the molecule
Molecular mechanics force fields
Self-consistent set of molecular mechanics equations and parameters that describe how atoms interact
Most of the time, molecules exist in ____ energy forms
low
Forces that drive drug-receptor binding
Charge-charge interactions
Van der Waals interactions
Steric interactions
Hydrophobic interactions
Homology modelling can produce high-quality models if there is a high degree of sequence similarity of __ % between the template and the target
> 60%
“Good” homology models can be produced when the degree of sequence similarity is ____ %
> 40%
Which regions of homologous proteins are often among the better-conserved?
The active or binding sites
What is molecular docking?
Technology that attempts to predict how drugs bind to proteins
For molecular docking, what must be known?
Protein structure
Structure Based Design: Docking
Ligand database –> Calculate ligand 3D structure and charge –> Fit ligand to protein –> Score result
Limitations of current docking programs
- Usually use a rigid protein to simplify the calculation
- Drug-receptor interactions are usually pre-calculated and less accurate in order to speed up the docking process
- The molecular-mechanics force field used has limitations
- Solvent is usually ignored
