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Modern Method for Determining Binding Affinity

Metcalf

Bluelighter
Joined
Oct 23, 2005
Messages
47
Can anyone out there give me a broad overview of what techniques are used to determine the binding affinity of a particular molecule to a receptor subtype?

In addition how should I interpret the data produced and what are the limitations of such data?
 
Typically receptor-ligand binding assays are done in vitro, ie the receptors are expressed on cell membrane fragments within a test tube/plate well, however they can also be done with frog eggs are tissues expressing the receptor to get a more realistic determination of the receptor-ligand interaction in vivo. The ligand is a radioisotope, so once it is added and the reaction mixture is washed of free ligand, the amount of ligand-receptor binding can be determined with a scintillation counter.

As for any specific experiment, read the methods.
 
Also, the drawbacks can include the fact that molecule might actually behave differently under physiological conditions in vivo. In drug discovery, you can demonstrate in vitro that a particular molecule binds to a particular receptor, but what else does it do in the body? It may have lots of other effects.

There are a lot of kits out there developed by companies for specific receptor assays -- for example, the receptor tyrosine kinases are intensively studied and have many of their own assays. Some kits use protein conjugates that are fluorescent or radioactive to perform the assays, and having another molecule attached to your molecule of interest can change the kinetics of the reaction. You just have to look at each experiment individually.
 
It's a fact. Unless you have something similar so you can try substitution on lab rats you never know what you have. Notice how many drugs were discovered by accident. Librium begat the benzodiazipines (accidental rearrangement during production). Unless you are prepared to swallow the thing, you will never know it's true effects. I, for one, would be keen to taste the substituted aminorex series. I would predict activity on par with the substituted amphetamines (e.g. DOB, MDA and so on). FSDoA pointed out that it would be a natural area to investigate.
 
skybyte said:
Over my head
here ya go, hope this helps. before reading: the Ligand (in this case, the drug) binds to the Receptor (which is on the cell membrane, ie the cell wall), which causes changes in the cell
timely16 said:
Typically receptor-ligand binding assays are done in vitro, ie the receptors are expressed on cell membrane fragments within a test tube/plate well [cell membrane is the wall of a cell. the way drugs exert their action is by binding to the receptor (attaching to it) which is on the cell wall, which then causes changes inside the cell, which ultimately causes changes in the way your brain handles information. so, in vitro (in the lab), they have the receptors on a piece of cell wall in a dish and add the drug and basicly watch what happens] , however they can also be done with frog eggs are tissues expressing the receptor to get a more realistic determination of the receptor-ligand interaction in vivo [in vivo means outside the lab. using actual biological cells (frog eggs eg) they can see what the drug is doing when there are other factors present] . The ligand is a radioisotope, so once it is added and the reaction mixture is washed of free ligand, the amount of ligand-receptor binding can be determined with a scintillation counter.[the ligand (drug) is a radioisotope, which just means its modified so that it emits radiation. if my interpretation of what he said is correct (not entirely sure..), after they add the ligands and the ligands bind to the receptors (the molecule to be binded to the receptors, ie, the drug) they then wash the rest of the ligands out. what's remaining will be the ligands that binded to the receptors. using a scintillation counter, which is an instrument that measures the radiation, you can determine how much of the ligand (drug) remains (ie how much bound to the receptors) then its just a matter of math to calculate the binding affinity (how much the drug 'wants' to bind to the receptors]

As for any specific experiment, read the methods.
 
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