Friday, 25 October 2013

New Drug Approvals 2013 - Pt. XVII - Macitentan (Opsumit ®)












ATC Code: C02KX (imcomplete)


Wikipedia: Macitentan


ChEMBL: CHEMBL2103873




On October 13th the FDA approved Macitentan (trade name Opsumit ®) for the treatment of pulmonary arterial hypertension (PAH). Macitentan is an endothelin receptor antagonist (with affinities to both Endothelin ET-A (ETA) and Endothelin ET-B (ETB) receptor subtypes, similar in mechanism of action to the previously licensed drug Bosentan, CHEMBLID957).




Target(s)

The Endothelin receptor ET-A (ETA, CHEMBLID252 ; Uniprot P25101) and Endothelin receptor ET-B (ETB, CHEMBLID1785 ; Uniprot P24530) receptors mediate a number of physiological effects via the natural peptide agonist Endothelin-1 (ET1 , CHEMBL437472 ; Uniprot P05305). In addition to normal roles in supporting homeostasis, these effects can include pathologies such as inflammation, vasoconstriction, fibrosis and hypertrophy.



Macitentan acts as an antagonist for both receptors with both a high affinity and long residence time in human pulmonary arterial smooth muscle cells. Hence it counteracts vasoconstriction and relieves hypertension. One of the metabolites of Macitentan is also pharmacologically active at the ET receptors and is estimated to be about 20% as potent as the parent drug in vitro








Macitentan (CHEMBL2103873 ; Pubchem : 16004692 ) is a small molecule drug with a molecular weight of 588.3 Da, an AlogP of 3.67, 11 rotatable bonds, and 1 rule of 5 violation.






Canonical SMILES : CCCNS(=O)(=O)Nc1ncnc(OCCOc2ncc(Br)cn2)c1c3ccc(Br)cc3

InChi: InChI=1S/C19H20Br2N6O4S/c1-2-7-26-32(28,29)27-17-16(13-3-5-14(20)6-4-13)18(25-12-24-17)30-8-9-31-19-22-10-15(21)11-23-19/h3-6,10-12,26H,2,7-9H2,1H3,(H,24,25,27)





Dosage

10 mg once daily. Doses higher than 10 mg once daily have not been studied in patients with PAH and are not recommended.



Metabolism and Elimination 

Following oral administration, the apparent elimination half-lives of macitentan and its active metabolite are approximately 16 hours and 48 hours, respectively. Macitentan is metabolized primarily by oxidative depropylation of the sulfamide to form the pharmacologically active metabolite. This reaction is dependent on the cytochrome P450 (CYP) system, mainly CYP3A4 with a minor contribution of CYP2C19. It is interesting to note the presence of bromine atoms in two of the aryl rings, typically a lighter halogen, typically fluorine is used to block oxidative P450-mediated metabolism at these exposed aromatic positions.



At steady state in PAH patients, the systemic exposure to the active metabolite is 3-times the exposure to macitentan and is expected to contribute approximately 40% of the total pharmacologic activity. In a study in healthy subjects with radiolabeled macitentan, approximately 50% of radioactive drug material was eliminated in urine but none was in the form of unchanged drug or the active metabolite. About 24% of the radioactive drug material was recovered from feces.



Pregnancy

Macitentan may cause fetal harm when administered to a pregnant woman. Macitentan is contraindicated in females who are pregnant.



Hepatotoxicity

Other ERAs have caused elevations of aminotransferases, hepatotoxicity, and liver failure. Obtain liver enzyme tests prior to initiation of Macitentan and repeat during treatment as clinically indicated.



Hemoglobin Decrease 

Decreases in hemoglobin concentration and hematocrit have occurred following administration

of other ERAs and were observed in clinical studies with Macitentan. These decreases occurred

early and stabilized thereafter Initiation of Macitentan is not recommended in patients with severe anemia. Measure hemoglobin prior to initiation of treatment and repeat during treatment as clinically indicated.



Strong CYP3A4 Inducers / Inhibitors


Strong inducers of CYP3A4 such as rifampin significantly reduce macitentan exposure whereas concomitant use of strong CYP3A4 inhibitors like ketoconazole approximately double macitentan exposure. Many HIV drugs like ritonavir (CHEMBL163) are strong inhibitors of CYP3A4.



The license holder is Actelion Pharmaceuticals US the full prescribing information can be found here.

Wednesday, 23 October 2013

Some Gamification of ChEMBL



Here's a small toy app built from the ChEMBL API - really just a technology exemplar - but also pointing towards some interesting potential crowdsourced things that could be done - for example community classification of the drug-likeness of compounds, or the identification of complex toxicophores - the sort of thing where capturing 'expert' tacit knowledge is needed - and the best way to learn is through analysis of examples.



So, have a play, and see how well you do.



There's a small interesting story behind this app - I originally thought we should do a dirty hack (a mapped gif - the shame of it) - but no, the development pixies, did a proper job, and in a very short time....



The first load of the app is slow. So settle down, clear your mind, and get ready to test your skills. The obvious next feature for this is one of those buttons to tweet a score, saying something like - "I got to level 7 on the ChEMBL-brain-O-thon"



Oh, the url for this won't be stable, and may well disappear completely, so be quick and waste some valuable work time now!



jpo

Tuesday, 22 October 2013

ChEMBL Web Service Update 3: Image Rendering Changes









If you are a follower of this blog you will have seen some earlier posts (here and here) providing details on changes we are making to our Web Services. I recommend reviewing the previous posts, but in summary we have setup a temporary base URL to allow existing ChEMBL Web Service users to test the new ChEMBL API powered Web Services. The new temporary base URL is:




https://www.ebi.ac.uk/chemblws2



As well as providing users with all existing functionality we have also added a couple of extra features, one of which is improved molecule rendering options. The current live Web Services provides the following REST call to allow you to get a molecule image: 








  








You are able to provide a dimension argument (pixels) to change the size of the image:














The image quality has deteriorated, this is because the image returned is simply re-sized version of the first image. The new ChEMBL API powered Web Services addresses this issue by dynamically generating the images, using either the RDKit or the Indgio chemistry toolkits (defaults to RDKit). So, to get an image using the new services, you just need to add '2' to the base URL:














When using the dimensions argument with the new Web Services you now get the following improved smaller image:











The coordinates used to generate the image are based on those found in the ChEMBL192 molfile. All current ChEMBL images are produced using Pipeline Pilot, which is currently setup to ignore the molfile coordinates and layout molecule how it sees best. This explains why the layout of the first two images are different to the second two. We can get the new Web Services to ignore coordinates and get the chemical toolkit to layout molecule coordinates how it sees best using the ignoreCoords=1 argument:


















If you would prefer to use Indigo to generate your ChEMBL molecule images you can use the engine argument:














Finally, it is also possible to use any combination of the 3 arguments mentioned above:












In summary, the new Web Service base URL extends the the current image generating functionality, by improving the dimensions argument and introducing the ignoreCoords and engine arguments. More details in table below:









Argument Name Argument Description Argument Options Default
dimensions Size of image in pixels 1-500 500
ignoreCoords Choose to use or ignore coordinates in ChEMBL molfiles 1 or 0 0 (Use ChEMBL molfile coordinates)
engine Chemical toolkit used to generate image RDKit or indigo RDKit




We hope you find these image  rendering changes useful and if you have any questions please let us know via mail to "chembl-help at ebi.ac.uk" if you have any questions.





The ChEMBL Team











Friday, 18 October 2013

ChEMBL KNIME training?

                                    



We recently did some KNIME training for ChEMBL at a workshop, and it was very popular. It made us think a little about just how much was available within Knime for ChEMBL, and we thought we'd ask if there was interest in us running a specific, detailed course on ChEMBL/KNIME next year.



So here's a poll. We'll keep this open for a month (i.e. closes 18th November 2013) and then decide what to do (if anything).



The stoopid free poll server I sued doesn't like the browser safari - so I'll transfer across to another system over the weekend, and try and transfer votes. Thank you to those that have voted so far.









Would you be interested in Knime ChEMBL training?





Yes - I'd like a two day course at the EBI next year


Yes - I'd like webinars


Yes - I'd like you to visit our lab (charge involved)


Yes - but not from you guys.


No - Knime, what's that



free poll


Thursday, 17 October 2013

New Bot on the Blog









Following the success of our ChEMBL Bot, there is now a new faithful bot out there which answers to the name @MalariaSARLit and is looking for new followers. Its job is to tenaciously monitor PubMed for new malaria-related publications, score them according to our ChEMBL-likeness score and tweet a ChEMBL-like one daily at noon GMT. Followers of the bot will get a free and reliable antimalarial SAR paper alert every day in their twitter feed.  





George (NKOTB fan)


Sunday, 13 October 2013

New Drug Approvals 2013 - Pt. XVI - Riociguat (AdempasTM)








ATC code: not yet assigned


Wikipedia: Riociguat





On October 8, 2013, the FDA approved riociguat for the treatment of
patients suffering from two forms of pulmonary hypertension - chronic thromboembolic pulmonary hypertension (CTEPH), and pulmonary arterial hypertension (PAH).



Pulmonary hypertension (PH) is a disease characterized by abnormally high blood pressure in the lungs, which increases the workload for the right ventricle of the heart. Some of the symptoms of PH are dizziness, shortness of breath and water deposits in the legs and joints. PH progresses slowly and can lead to severe and often fatal circulatory and respiratory complications. CTEPH is a form of PH caused by blood clots obstructing the passage of blood through the vessels in the lung, often after a pulmonary embolism has occurred. PAH on the other hand is caused by a chronic tightening or constriction of blood vessels.



Riociguat (CHEMBL2107834) is a stimulator of soluble guanylate cyclase (sGC), an ezyme that is activated by increased levels of nitric oxide (NO). Downstream signalling of increased levels of cGMP (CHEBI:28181) causes the dilation of the endothelium in blood vessels. SGc is a heterodimer consisting of an alpha- and beta-subunit. There are two known isoforms for each subunit (Uniprot-ids, alpha: P33402, Q02108 ; beta: Q02153, O75343). Stimulation of the kinase by riociguat and other sGC stimulators depends on the presence of a reduced heme group in the sGC beta-subunit. The activation of sGC by this class of compounds is synergistic with NO signalling. Some other compounds in this class are YC-1 (CHEMBL333985) and BAY 41-8543 (CHEMBL1916024). In contrast, the sGC can also be targeted through activators that work independently of NO signalling. 







Canonical SMILES: COC(=O)N(C)c1c(N)nc(nc1N)c2nn(Cc3ccccc3F)c4ncccc24

Std-InChI:  InChI=1S/C20H19FN8O2/c1-28(20(30)31-2)15-16(22)25-18(26-17(15)23)14-12-7-5-9-24-19(12)29(27-14)10-11-6-3-4-8-13(11)21/h3-9H,10H2,1-2H3,(H4,22,23,25,26)

Std-InChI key: WXXSNCNJFUAIDG-UHFFFAOYSA-N



Riociguat has a molecular weight of 422.42 Da. The calculated LogP for riociguat is 2.34 and the compound has no stereo-centers.



The compound is administered orally and was approved through the FDA priorities review program. It has a black box warning because it can harm fetuses and is therefore not prescribed to pregnant women. Other adverse effects of riociguat include headache, dizziness, indigestion, peripheral edema, nausea, diarrhea and vomiting.



Riociguat is a first-in-class compound and was developed by Bayer HealthCare Pharmaceuticals.



Riociguat will be marketed as a prescription medicine under the name Adempas.








Wednesday, 9 October 2013

EMBL-EBI RDF Platform













Yesterday saw the release of the EMBL-EBI RDF Platform, the official announcement can be found here. The purpose of this new platform is to act as a central resource for all RDF and Semantic Technology focused work being carried out at the EMBL-EBI. The benefit to users of the RDF version of the ChEMBL database is that you now have access to documentation, a SPARQL endpoint, example SPARQL queries and a Linked Data browser.



Other EMBL-EBI resources involved in this project include BioModels, BioSamples, Expression Atlas, Reactome and UniProt - we expect the number of resources offering RDF versions of their data to grow over the coming year.



One of the very cool things the new platform offers users is the ability to run federated SPARQL queries across the separate resources listed above. Essentially this is removing the data integration burden, which would have previously been required in order to answer the questions asked by the federated queries. Example federated SPARQL queries include:



 We hope you find the new resource useful and please use this page to provide feedback