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Showing posts from October, 2014

Paper: PPDMs – A resource for mapping small molecule bioactivities from ChEMBL to Pfam-A protein domains

We've just published a Open Access paper in Bioinformatics on an approach to annotate the region of ligand binding within a target protein. This has a lot of applications in the use of ChEMBL, in particular providing greater accuracy in mapping functional effects, improving ligand-based target prediction approaches, and reducing false positives in sequence/target searching of ChEMBL. Where next for this work - well annotating to a site-specific level would be a good thing to implement (think about HIV-1 RT with the distinct nucleoside and non-nucleoside sites).

Here's the abstract...
Summary: PPDMs is a resource that maps small molecule bioactivities to protein domains from the Pfam-A collection of protein families. Small molecule bioactivities mapped to protein domains add important precision to approaches that use protein sequence searches alignments to assist applications in computational drug discovery and systems and chemical biology. We have previously proposed a mappin…

Django model describing ChEMBL database.

TL;DR: We have just open sourced our Django ORM Model, which describes the ChEMBL relational database schema. This means you no longer need to write another line of SQL code to interact with ChEMBL database. We think it is pretty cool and we are using it in the ChEMBL group to make our lives easier. Read on to find out more....


It is never a good idea to use SQL code directly in python. Let's see some basic examples explaining why:


Can you see what is wrong with the code above? SQL keyword `JOIN` was misspelled as 'JION'. But it's hard to find it quickly because most of code highlighters will apply Python syntax rules and ignore contents of strings. In our case the string is very important as it contains SQL statement.

The problem above can be easily solved using some simple Python SQL wrapper, such as edendb. This wrapper will provide set of functions to perform database operations for example 'select', 'insert', 'delete':


Now it's harder t…

myChEMBL 19 Released

We are very pleased to announce that the latest myChEMBL release, based on the ChEMBL 19 database,  is now available to download. In addition to the extra data, you will also find a number a great new features. So what's new then? More core chemoinformatics tools We have included OSRA (Optical Structure Recognition), which is useful for extracting compound structures from images. OSRA can be accessed from the command line or by very convenient web interface, provided by Beaker (described below). We've also added OpenBabel - another great open source cheminformatics toolkit. This means you can now experiment with both RDKit and OpenBabel and use whichever you prefer.
ChEMBL Beaker myChEMBL now ships with a local instance the ChEMBL Beaker service. For those not familiar with Beaker, the service provides users with an array of chemoinformatics utilities via a RESTful API. Under the hood, Beaker is using RDKit and OSRA to carry out its methods. With the addition of Beaker in myC…

New Drug Approvals 2014 - Pt. XII - Naloxegol (Movantik™)

ATC Code: A06AH03 Wikipedia: Naloxegol ChEMBL: CHEMBL2219418
On September 16th FDA approved Movantik (naloxegol, AZ-13337019), as an oral treatment for patients with opioid-induced constipation and chronic non-cancer pain.

Naloxegol
Naloxegol is an opioid receptor antagonist. Due to its similarity to noroxymorphone, a main metabolite of oxycodone, naloxegol is classed as a controlled substance. However, the FDA analysed its abuse potential and concluded that there was no risk of dependency.





Mode of Action Opioids are a class of drugs which are used to manage pain, but have a common side effect of reducing the motility of the gastrointestinal tract, making bowel movements difficult. Opioids work by binding to the mu-receptors (CHEMBL233, UniProt:P35372) in the central nervous system, thereby reducing pain. However, they are also able to bind to the mu-receptors in the gastrointestinal tract, hence causing opioid-induced constipation. 
Movantik is a peripherally-acting opioid receptor antagonis…

New Drug Approvals 2014 - Pt. XI - Idelalisib (Zydelig™)

ATC Code: L01XX47 Wikipedia: Idelalisib ChEMBL: CHEMBL2216870
On July 23rd the FDA approved Zydelig (idelalisib, GS-1101), as an orally-delivered drug to treat patients with three types of blood cancers.
•Relapsed chronic lymphocytic leukemia (CLL)
•Relapsed follicular B-cell, non-Hodgkin lymphoma  (FL)
•Relapsed small lymphocytic lymphoma (SLL)

Blood cancer The three main categories of blood cancer are leukemia, lymphoma and myeloma. Lymphoma is also split into two types: Hodgkin lymphoma and non-Hodgkin lymphoma. Both leukemia and myeloma occur in the bone marrow, whilst lymphoma is a cancer that is isolated to the lymphatic system. Acute leukemia is where there is an abundance of underdeveloped white blood cells that can’t function properly and chronic leukemia is where there are just far too many white blood cells, which is just as bad as having too few. Myeloma is where the plasma cells form tumours in the bone marrow.

Idelalisib This drug is a phosphoinositide 3-kinase inhibitor, which wo…