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Showing posts from August, 2009

Kinase SARfari - looking for testers

We are testing a number of interfaces to our data at the moment, and have just flipped Kinase SARfari to a public facing server. We are looking for some people willing to test the interface on a number of differing platforms, so if you are interested, please mail us. An install package is also available, for those wishing to try things on their own machines (however, you'll need some experience in web server config, Catalyst (the MVC, not the modelling package), an Oracle database, and a chemical data cartridge...)

Meeting: Translating Protein Structures into Drugs, September 10th, London

There is an excellent meeting on protein structures and drug design at King's College London on September 10th 2009 (i.e. very soon now). In order of importance 1) There are some very good speakers 2) it is one day long, and 3) It is free. Here is a link to the meeting website.

New Drug Approvals - Pt. XVI - Vigabatrin (Sabril)

The next approval for this year, on August 21st, was Vigabatrin (trade name Sabril). Vigabatrin (previously known by the research code MDL-71,754) is an antiepileptic drug indicated as a monotherapy for pedriatic patients 1 month to 2 years of age with infantile spasms (IS) and as an adjunctive therapy for adult patients with refractory complex partial seizures (CPS) who have inadequately responded to several alternative treatments. Vigabatrin has previously been approved in the UK, Mexican, Canadian and Danish markets. Vigabatrin is the first therapy approved for the treatment of IS and a new option as add-on therapy for the adults with CPS. Vigabatrin is an irreversible inhibitor of gamma-aminobutyric acid transaminase (GABA-T), the enzyme responsible for the metabolism of the inhibitory neurotransmitter GABA; blockade of GABA-T leads to increased levels of GABA in the central nervous system. This enzyme can also be irreversible inhibited by Gabaculine, a naturally occurring bacte…

Software: #songsincode

I always catch onto these internet phenomenom too late, and here is another example - #songsincode { 'name':'Lola', 'occupation':'showgirl', 'fashion':['music','passion'], 'location':[-22.970834, -43.191665] } And the next.... var i = {shot:{sheriff:true,deputy:false}} and.... if(man.silhouetto.size=='small'){scaramouche.do(fandango);if(thunderbolt&&lightning){me.frightened=true}} If you like them, google and thou shalt find more (many, many more). Great kudos via http://tinyurl.com/lrh2rl

Books: Molecules and Medicine

The ACS exhibition hall has got the usual selection of publishers, and I'm drawn, just like a tramp (as in vagrant) to a pile of discarded cardboard, to the book stands. Todays book is Molecules and Medicine by Corey, Czakó and Kürti. It covers a wide range of range of drugs presented as monographs organised by therapeutic area. Additionally, there is an explanation at the front of some key chemistry concepts that help non-chemists understand the array of representational forms of molecules - most people either 'get' chemistry or they don't, and this introduction may well help. As a minor criticism, I personally find the typesetting and illustrations fussy and inconsistently styled, and it just seems too colorful, but this may well add to the attraction of the book overall for a wider audience. In summary a good book, buy it as a present, either for yourself, or for elderly relatives, they are always really interested in drugs and disease (but if you do the latter, r…

Books: Drug Truths

Large pharma gets a pretty hard time in the press, and it would be fair to say that the public's impression of the industry is negative at the current time, and it is difficult to see how this will change in the short to medium term. This is a shame, and probably largely undeserved - a lot of scientists have a lot of pride in their work and the companies they work for (as of course do salespeople, facilties, manufacturing staff, etc.). However, Health, Politics and Money are a heady and potent mix, as the current discussions over 'Obama's' healthcare reforms show. Let's be clear, this book is a polemic, and all the better for it! It addresses and challenges a series of widespread media myths about drug discovery ('most drugs are discovered in academic labs with public money', 'large pharma aren't interested in diseases from the third world', 'they're evil manipulative baby snatchers', ad nauseum). The book does this well (actually…

Updated Drug Icons...

We have made a few changes to the icon set we use for the ChEMBL-og New Drug Monographs, we will also use these (or variants thereof) in some of our other web interfaces. The changes were prompted by some of the things we wished we had included from the start. An example icon is below. Which is a synthetic small molecule drug, is rule of five compliant, is topically dosed, is dosed as a single enantiomer, and has a boxed warning. The various components mean Drug classthis can either be Synthetic small molecule Natural product-derived small molecule Peptide/protein Protein: Monoclonal antibody Protein: Enzyme Oligonucleotide Oligosaccharide. Rule of FiveAn image of the number five. This is either pass or fail - we fail a molecule if it fails to pass all the individual tests (usually people use fail one parameter). We use XlogP (the same as used by PubChem) for the calculations and use 5.0 as a cutoff New targetAn image of a 'bullseye' target. This is either true or false. …

SME Workshop on European Bioinformatics Resources - Vienna, 3rd and 4th September 2009

There is a workshop in Vienna targeted at SMEs (Small and Medium Enterprises) on the 3rd and 4th September. If you are interested in going, you'd better hurry up since the closing date for registrations is the 21st August.

New Drug Approvals - Pt. XV - Asenapine (Saphris)

On the 14th August 2009 Asenapine (tradename Saphris) was approved for the acute treatment of schizophrenia in adults and acute treatment of manic or mixed episodes associated with bipolar I disorder with or without psychotic features in adults. This class of psychiatric diseases are complex and carry a significant economic healthcare burden; approximately 24 million people worldwide are believed to suffer from schizophrenia, while ca. 67 million people are thought to suffer from bipolar I disorder. Asenapine (previously known by the research code Org-5222) is the one of a large class of drugs aimed at treating such diseases, and shows the typical broad spectrum of against a variety of receptor targets and a complicated mechanism of action, although such drugs are thought to primarily act through antagonism of D2 and 5HT2A receptors. To give some idea of the promiscuity (or polypharmacology) of Asenapine at various aminergic GPCRs, reported pKis are 5HT1A 8.6, 5HT1B 8.4, 5HT2A 10.2, …

New Drug Approvals - Pt. XIV - Pitavastatin (Livalo)

The latest FDA approval is Pitavastatin (trade name Livalo), approved on August 3rd. Pitavastatin is an HMG-CoA reductase inhibitor, indicated for the primary treatment of hypercholesterolemia (elevated levels of cholesterol in the blood) on patients unable to sufficiently lower their cholesterol levels by diet and exercise. Hypercholesterolemia is a very widespread and leads to serious cardiovascular disease in affluent and increasingly in developing societies.
Pitavastatin (also known by the research code NKS-104) has been available in Japan since 2003 and is now the sixth statin to reach the U.S. market, after Lovastatin (trade name Mecavor), Pravastatin (trade name Pravachol), Fluvastatin (trade name Lescol), Atorvastatin (trade name Lipitor) and Rosuvastatin (trade name Crestor). All of these drugs are derived from the natural product Mevastatin from the fungus Penicillium citrinum. Like the other statins, Pitavastatin lowers the cholesterol levels by competitively inhibiting H…

New Drug Approvals - Pt. XIII - Saxagliptin (Onglyza)

On the 31st July 2009 Saxagliptin (tradename Onglyza) was approved for the treatment of Type II diabetes - Type 2 Diabetes is also known as adult-onset diabetes, and also non-insulin-dependent diabetes melittus (NIDDM). It is the type of diabetes that is often associated with obesity, and so is an increasingly common disease/condition in our well-fed western and also developing world cultures. Saxagliptin (previously known by the research code BMS-477118) is the third orally-dosed Dipeptidyl peptidase-IV (or DPP-IV) inhibitor to market, and is in the same mechanistic class as other 'gliptins' - Sitagliptin (tradename Januvia) and Vildagliptin (tradename Galvus/Eucreas) which are both launched and also others such as Alogliptin (aka SYR322) and Linagliptin (aka BI-1356, and expected tradename Ondero), which are in late stage clinical trials. The DPP-IV drug class has had quite a complex development and commercial history, as web searches will readily show. Saxagliptin is a…