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Bio <-> Chem

Technical notes from the interface between bioinformatics and cheminformatics by Chris Southan
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PubChemBiologieEnglisch
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Autor Christopher Southan

Context to this concatenated blog series is given below at the beginning of the set. This most recent one completes the top-13 sources. I'm now inclined to look at some of the smaller but more bioactivity-rich sources as detailed single posts in the future.

BACE1BiologieEnglisch
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Autor Christopher Southan

Updates : 09 June. The F1000 recommendation is now live but note it is pay-walled so you only see the first line A new detailed review has appeared "The amyloid cascade hypothesis: are we poised for success or failure?" (PMID 27255958) that is relevant to the topic of BACE1 targeting for AD The lead compound described below is now ligand 9197

Chemistry LinkingPatentsBiologieEnglisch
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Autor Christopher Southan

Congratulations are due to the authors (three of whom I have met) of "Big Data from Pharmaceutical Patents: A Computational Analysis of Medicinal Chemists' Bread and Butter" (PMID 27028220).  You can find extra context in the NextMove blog (including an"In the Pipeline" review. This post looks at intersects between their work and the important general question " can I find a synthetic description for structure X ?

BIA-10-2474BiologieEnglisch
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Autor Christopher Southan

Context in  two earlier blog posts, "The unfortunate case of BIA 10-2474" and  "Molecular details related to BIA 10-2474" Update; 13 Aug  FDA press release "The Agency has found, based on the available information, that BIA 10-2474 exhibits a unique toxicity that does not extend to other drugs in the class, called fatty acid amide hydrolase (FAAH) inhibitors".

AntinfectivesBiologieEnglisch
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Autor Christopher Southan

The general good news is the release of not only the physical MMV pathogen box   but also the accompanying structures and activity data sheet. The less good personal news was that none of my antimalarial recommendations made it into the selected 400 :(.  Notwithstanding, the domain split of the new box is shown below.

PoluproteinsZikaBiologieEnglisch
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Autor Christopher Southan

Update 07 Aug  Via Twitter I was alerted to a blogpost on essentially the same theme "What is the SARS-CoV-2 molecular parts list?" Update 06  April 2020 .  Three years on this post becomes topical again since very similar principles and database consequences now apply to  COVID19.

AntimalarialsOSMPubChemBiologieEnglisch
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Autor Christopher Southan

This post is related to an  OSM Github  Open Science proposal  for SCINDR - the SCIcience INntroDduction Robot.  In a nutshell, the idea is to develop a way to connect, in real time, globally disparate researchers who are doing similar open drug discovery science  so that they can make contact to work better and faster towards the development of new medicines.

ZikaBiologieEnglisch
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Autor Christopher Southan

Update: 18 Oct,  Our paper "Illustrating and homology modeling the proteins of the Zika virus" has finally made all the way through to PMID 27746901, so thanks to the Open refereeing (links at F1000research).  Not also, as an update to the supplementary data in the paper and a blog post about Flavivirus polyproteins,  the graphic below displays the high-scoring PDB hits (mostly Dengue but now joined by

BIA-10-2474BiologieEnglisch
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Autor Christopher Southan

Update: Sept 2018.  The long-overdue primary med chem report from BIAL on the early characterisation of the 10-2747 series SAR is finally out but turns out to be a bit of a letdown (see GtoPdb blogpost). Update: 11 Nov 2017.

BIA-10-2474BlindingPatentsBiologieEnglisch
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Autor Christopher Southan

Update  20 April: The full official report (13K words) was  published yesterday. Update 15 April: The plot thickens, viz Le Figaro has just released an article on the trial. SE has commented on this and pasted a Google translate into his blogpost. There is some new detail in the piece (rather damming in fact) but it's still short on scientific technicalities.

Drug ApprovalsBiologieEnglisch
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Autor Christopher Southan

Update : 2nd Feb, a statistical review from C&ENews (n.b. Blogger is loosing some of the link highlighting later in the post, but, via mouse-over, you can get out to them). This is an annual follow-on from previous years (e.g.2014,  2013 and 2012). Adding the 45 NMEs and the  biologicals comes to 51. Good news for a good year then but I shall link to the pundit commentaries as they surface.