Question: How do you test products using compucational chemistry

Diana Drennan answered on 18 Mar 2011:

OK. If you imagine a lock needing a key to open it, then, the reason the key works is that it fits into certain parts of the lock, right? You could possibly find another key that works, if it fit similarly. So a protein has a part of it that is like the lock, and the compounds are like keys. But these work not just by shape, but by charge too. The shape had to fit properly, and the charges have to attract each other (i.e. positive to negative). The compounds all have different shapes and charges, but some are similar enough that they fit, too. I make a model of the shapes and charges that are important for fitting a compound to the protein we’re interested in. I have a database with over 12 million compounds in it that we can purchase. We also invent our own compounds that have never been made before (that we can find). Then, I use that model to see if any of the available or invented compounds will fit.

Then, we have to buy or make them, test them in lots of ways to see if they work, do they fit other proteins that we don’t want them to (and give us nasty side-effects) are they stable in formulation, are they stable in the skin, are they safe, are they easy to make, are they cheap to make, etc etc etc.

Here’s a brief description and nice picture. http://www.cbuc.cl/CADD.html and another nice picture http://www.biomedcentral.com/1471-2148/8/103/figure/F3