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Showing posts from August, 2013

New Drug Approvals 2013 - Pt. XII - Technetium Tc 99m Tilmanocept (LymphoSeekTM)

ATC code: V09IA09

On March 13th 2013, the FDA approved Technetium Tc 99m Tilmanocept (LymphoSeekTM), a radioactive diagnostic agent indicated for lymphatic mapping with a hand-held gamma counter to assist in the localisation of lymph nodes draining a primary tumour site in patients with breast cancer or melanoma
Melanoma is a malignant skin tumour, which, although rather uncommon, causes 75% of skin cancer related deaths.  Breast cancer accounts for almost 23% of all cancers in women and in 2008 caused 13.7% of cancer related deaths in women. Lymph nodes drain lymphatic fluid coming from tissues, if the tissues contain a tumour, the node will retain cancer cells coming from it. By removing and analysing the lymph node, precious informations can be obtained regarding the spread of the tumour.

Technetium Tc 99m Tilmanocept (ChEMBL: CHEMBL2108726) acts by accumulating in lymphatic tissue and selectively binding to mannose binding receptor (CD206, ChEMBL: CHEMBL2176854, Uniprot:P22897) …

Removal of Metal-Containing Compounds

Further to my post a few months ago (To Remove or Not to Remove) about removing certain problem metal-containing compounds, we have now come up with a plan of what to do. Instead of labeling this curation as ‘removal of inorganics’, or ‘removal of organometallics’, we simply want this to be known as ‘removal of some metal-containing compounds’.
The criterion that we used was to exclude a large proportion of compounds that contained a metal, apart from cases where a metal was commonly found as part of a pharmaceutical preparation (e.g. Ranitidine Bismuth Citrate CHEMBL2111286, Silver Sulfadiazine CHEMBL1382627, Bacitracin Zinc CHEMBL2096639). The reasoning behind the removal of such compounds was that most of these metals are bonded to the rest of the compound components via coordinate bonds. However, due to InChI limitations, there is no way of creating a Standard InChI that retains coordinate bond information. As we use Standard InChI as the main compound identifier of un…

2nd RDKit UGM - A reminder

For those who forgot to register, this is a gentle reminder for the 2nd RDKit User Group Meeting. The meeting will take place October 2nd-4th here the Genome Campus in Hinxton, UK. We're using a different format for the meeting this year:

Days 1 and 2: Talks, lightning talks, roundtable(s), discussion, and something new: talktorials! Talktorials are somewhere between a talk and a tutorial, they cover something interesting done with the RDKit and include the code used to do the work. During the presentation you'll give an overview of what you did and also show the pieces of the code that are central to the work. The idea is to mix the science up with the tutorial aspects.

Day 3 will be the first ever RDKit sprint: those who choose to stay will spend an intense day working in small groups to produce useful artifacts: new bits of code, KNIME nodes, KNIME workflows, tutorials, documentation, IPython notebooks, etc. We'll see who's there and what folks are interested in contr…

What is the R&D Cost of a New Medicine?

Here's a recent (2012), and excellent, analysis and estimate of the development costs of a new medicine (specifically an NME, a chemically distinct, novel molecule). There is a good overview of the historical trends in costs and attrition, and a collection of all significant previous estimates of the R&D costs of a new drug. There's some nice exploration of the sensitivity of the costs to various factors, and differential success and costs across various therapeutic areas.

In case you wanted to jump to the punchline, the costs in this study is $1,506,000,000 (i.e. $1.5bn) at 2011 USD prices.

The report is free, with only registration at the OHE website required to download the report. Great value!

%T The R&D Cost of a New Medicine %A J. Mestre-Ferrandiz %A J. Sussex %A A. Towse %I Office of Health Economics %D 2012 %O ISBN 978-1-899040-19-3
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USAN Watch: August 2013

The USANs for August 2013 have recently been published.


USAN Research Code InChIKey (Parent)Drug ClassTherapeutic classTargetapatorsen OGX-427 n/atherapeuticoligonucleotideHSP-27brincidofovirCMX-001
therapeuticsynthetic small molecule prodrugCMV DNA polymerasecensavudineBMS-986001
therapeuticnatural product derived small molecule prodrugHIV RTdaratumumab
HuMax-CD38, 3003-005

n/atherapeuticmonoclonal antibodyCD38diclofenacDCOPUUMXTXDBNB-UHFFFAOYSA-Ntherapeuticsynthetic small moleculeCOXduvelisibIPI-145; INK-1197 
therapeuticsynthetic small moleculePI3K-delta, PI3K-gammaelbasvir
therapeuticsynthetic small moleculeHCV-NS5AgrapiprantRQ-7, RQ-00000007, MR10A7, AAT-007, CJ-023, 423

therapeuticsynthetic small moleculeEP4samatasvirIDX-18719, IDX-719
therapeuticsynthetic small moleculeHCV-NS5AsotagliflozinLP-802034, LX-4211 
therapeuticsynthetic small moleculeSGLT1, SGLT2taladegibLY-2940680  SZBGQDXLNMELTB-UHFFFAOYSA-Ntherapeuticsynthetic small moleculeSMO-1veledimexINXN-1001
therapeuticsynthetic small mol…

Open PHACTS KNIME and Pipeline Pilot Components

Open PHACTS has released a collection of Pipeline Pilot and KNIME workflow components which integrate with the Open PHACTS API. Integration with these well-established graphical workflow tools allows the pharmacological and physicochemical data within the Open PHACTS Discovery Platform to be easily accessed and consumed.
Open PHACTS (Open PHArmacological Concepts Triple Store) is a project of the Innovative Medicines Initiative (IMI) and has seen SMEs, academia and the pharmaceutical industry work together to create a freely-available online platform to multiple, integrated sources of publicly available pharmacological data. The project ends in 2014 and the project’s not-for-profit successor organisation, the Open PHACTS Foundation, will continue to support and develop the infrastructure created.
The Open PHACTS Discovery Platform has been designed to answer various critical pharmacology questions, many of which can be addressed using the newly released Pipeline Pilot and KNIME nodes. T…

Compound Sets and Availability

Chemical databases come in many different types and flavours, and given that we now have UniChem up and running, and it is being actively used by at least some of you, our minds have turned a little to describing these ‘flavours’ and ‘resolutions’. One of the key things a user is interested in is how easy is it to get hold of a compound, since this is usually a key filter applied to actually doing anything with the results of a database search. The cost implications of needing to commission synthesis, or potentially try and develop new synthetic methodology to a compound are substantial, and there is a substantial literature on the computational assessment of synthetic accessibility (q.v.).

So, here is a simple five state classification that reflects the typical availability of a compounds in a chemical collection.
A compound has been previously been synthesized and is readily available from chemical vendors.A compound has been previously synthesized but would require resynthesis.A comp…