Hello!, and thank you for visiting In & Out Science. The term data mining is not really new in the life science world, but it is now when due to the masive overload of information and the proliferation of open source software, it has become possible to analyse huge amount of information using free applications.
Of course, the different commercial systems developed for life scince data mining are, in general, really good and without doubt they can help searching for the right information. However, if you or your company cannot afford the costs of such a wonderful systems, there are other options that in esence they do the same job.
A little bit of facts about the amount of information available nowadays, as example, if we just look into the two main chemical databases we find that CASREACT® contains more than 79.7 million reactions and Reaxys® more than 105 million compounds.
Freeware and Open Access Databases: Towards a Wiki Drug Discovery?
Presentation about the use of freeware and open access databases in drug design. Application of the "free information" workflows in the research of designing small molecules therapeutics against ZIKA virus.
All knime workflows can be found here.
Medicinal Chemistry Mining Overview
In a nutshell, all the activities shown in the ppt presentation below can in principle be done using only free available software. Nevertheless, in the examples presented in the slides, Reaxys® has been the source of data for the analysis.
After being in silence for few month (I've been very busy), I would like to bring up a topic that I believe it might be interesting (at least for me it is). Recently it has been published that AZD3293 is going to enter clinical phase III. AstraZeneca together with Eli Lilly have been very proud announcing this new milestone.
Until here it's all fine, and I am particularly happy that AZD3293 is doing so well. However, reading all different announcements about this particular compound, it's not mentioned anywhere that there were very talented scientists in the AZ Södertälje site the ones drawing for the first time that compound. It's not mention anywhere that it was Södertälje talented scientists who had to deal with a very challenging synthesis. But wait a second... now all those talented scientists are working somewhere else, uhmmm...
You can read here the last press release.
Just recently I have seen in various internet forums the famous list of the FDA Approvals in 2015. Since, each of us has a different perspective and interest, I just collected the information, added the chemical structures (when possible), calculated some simple properties and you can draw your own conclusions from the downloadable file.
My few comments to this list are based on data:
I could continue with more facts about the list and comment on the complexity of the molecules, if they follow the Lipinski rule, etc, but I leave up to you to draw your own conclusions and analysis.
- - A total of 45 approvals with 14 big molecules and 31 small molecules.
- - Considering the owners best sales estimations, the biologicals (big molecules) will have a peak sales of 20.2 billion dollars (estimates for 13 out of 14 approvals) and the small molecules 29.8 (estimates for 25 out of the 31 approvals).
- - 3 Small molecules approvals are a combination of two API's.
- - 11 of the small molecules approvals are non-chiral.
Since my first contact with Computer Aided Synthesis Design software back in 2009 I became very attracted to this kind of systems... keep reading