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RATIONAL DRUG DESIGN - Coggle Diagram
RATIONAL DRUG DESIGN
SBDD
we need:
- Large-scale production of molecular target
- Structure determination (X-ray, NMR)
- Identification and characterization of binding site(s)
- Target-ligand interactions - active conformation, target binding requirements
- (HT) search for novel ligands, prioritization by interaction energy calculation
1. PRODUCTION
- the target is a protein and it is coded in lab
- via molecular biology techniques we can perform 'cloning' and 'expression' of these targets in large amounts
- we will then express it and and start testing the properties of this protein
- small scale expression in cells and we try to isolate large amounts of protein checking the folding conformations
- upscale and protein purification
2. CRYSTALLIZATION
X-RAY CRYSTALLOGRAPY
prerequisites:
- ~10 mg of purified protein (need to be very pure)
- homogenous
- concentrate to about 20 mg/ml
- stable enough throughout the experiment
the protein is in our solution with a medium, that has to be carefully selected.
Then we in a controlled way we take the protein to supersaturation.
We then wait and regularly observe the experiment under a microscope
crystallization can be run in
➪ the batch approach → mix solubilized protein with precipitant and we directly achieve the super-saturated sample. The protein concentration decreases as the crystal grows
➪ vapour diffusion approach → is the most popular method, the soluble protein is placed in a drop above a buffer with higher precipitant agent concentration. The drop and the reservoir equilibrate by exchanging water (vapour diffusion) and by this we achieve supersaturation, nucleation and crystal growth
➪ we can work with crystallization robots
once the crystal is made :
➨ X-ray source diffractometer (we collect the diffraction pattern from the irradiation of the crystal)
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NMR
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compared to X-ray we can get dynamic parameters and we can determine the power of binding by changing the measuring conditions and the association and dissociation constant of a compound to the protein and see the strength of the binding
In rational drug design
Saturation Transfer Difference (STD) → appear-disappear of signal for binding and non binding
NOEs→ when a small molecule is alone in the solution the NOEs are short in time and weak while when it is conjugated we can see long and strong NOEs
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LBDD
situations in which the large production of molecular target is impossible (receptors).
We have to know a series of agonists and/or antagonist with similar binding site/mode: we can use them to define the pharmacophore
PHARMACOPHORE ➔ a molecular framework that carries the essential features responsible for a drug biological activity
ways to build the pharmacophore:
➪ we start from a training set of known compounds binding an unknown target
- topology-based (groups angles and distances)
- function-based (spheres with a center, with highlighted lipophilic, hydrophilic, + or - charged areas