Drug design: My latest paper explained without the jargon

Our latest paper has just appeared in the Journal of Physical Chemistry A.  If you don't have access to this journal you can find a free version of an earlier draft here. It's ultimately related to making better drugs so first some background.

Background

Designing new drugs currently involves a lot of trial-and-error, so you have to pay a lot of smart scientists a lot of money for a long time to design new drugs - a cost that is ultimately passed on to you and I as consumers.  There are many, many reasons why drug design is so difficult. One of them is that we often don't know fundamental properties of drug-candidates such as the charge of the molecule at a given pH. Obviously, it is hard to figure out whether or how a drug-candidate interact with the body if you don't even know whether it is postive, negative or neutral.

It is not too difficult to measure the charge at a given pH, but modern day drug design involves the screening of hundreds of thousands of molecules and it is simply not feasible to measure them all. Besides, you have to make the molecules to do the measurement, which may be a waster of time if it turn out to have the wrong charge. There are several computer programs that can predict the charge at a given pH very quickly but they have been known to fail quite badly from time to time.  The main problem it that these programs rely on a database of experimental data and if the molecule of interest doesn't resemble anything in the database this approach will fail.

Last year we developed a "new" method for predicting the charge of a molecule that relies less on experimental data but it fast enough to be of practical use in drug design. We showed that the basic approach works reasonably well for small prototypical molecules and we even tested one drug-like molecule where one of the commercial programs fail and show that our new method performs better (but not great). 

The New Study

We test the method on 48 drug molecules and show that it works reasonably well.  It is not quite as accurate as the methods that rely on experimental data, but this is probably because many of the molecules we test are in the databases that the programs use.  But we felt we had to test these molecules first because they are some of the first molecules other users will try to test the method. The next step is to test the method on molecules where some of the existing methods perform poorly. We also have to think about how best to make this method available to researchers who are acutually doing the drug design.



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