What’s new in DistilBio?

The last few weeks have seen a lot of new features added in DistilBio. While looking at the queries run by users and based on user feedback, we realized that the following were areas for improvement

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  • Ability to filter, refine and analyse results
  • “Ease of use of DistilBio”
  • Missing results which were known and relevant
  • Queries yielding no results

Let’s look at the issues a little closely and the measures taken by the DistilBio team to handle this. (Watch demo video)

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Where does this piece of Data come from?

DistilBio integrates data sets from various sources like Entrez Gene, Uniprot, DrugBank, PharmGKB, CTD, CHEMBL, protein interaction databases like IntAct, MINT etc. Each connection is backed by a data source.

Let us look at an example to see how data sources can be viewed in DistilBio.

I ran a query for breast cancer, the drugs used in the treatment and the proteins targeted by these drugs.

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DistilBio featured in Semantic Web

This week DistilBio was featured in semanticweb.com. The article discusses how bench biologists can leverage the wealth of information available across various datasets using DistilBio.

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“How does a user say what are the drugs used for Alzheimer’s disease and do they have certain protein targets and are those protein targets implicated in other diseases?”

Check out the Sitagliptin example featured in the post to see how DistilBio can be used. You can also check out more use cases from earlier posts about drug molecular side effects, drug repurposing and comparison of drugs.

For more on Metaome and DistilBio, read the original post - Metaome Helps Bench Biologists Get More Value From Linked Data [Semantic Web]

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Aspirin – Old drug, new roles?

In my last post, I looked at the different mechanism of actions of 3 OTC drugs – Aspirin, Acetaminophen and Ibuprofen. Aspirin a drug discovered ~100 years ago and in use for more than 50 years is one of the most common OTC drugs used. Aspirin is reported to be an analgesic, anti-pyretic, anti-inflammatory and anti-platelet agent. Recently I read a few reports that discussed the role of Aspirin in the prevention of cancer (1,2,3,4). This was really intriguing, that such a widely used drug with so many uses could also play a role in prevention of cancer.

As shown in my last post, aspirin and targets the COX1 and COX2 proteins and inhibits the formation of prostaglandins. Aspirin is also known to target other proteins.

I looked up DistilBio to find the protein targets of Aspirin. Continue reading

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Different strokes – Common painkillers and their mechanisms

We find a lot of over-the-counter (OTC) painkillers like aspirin, acetaminophen, ibuprofen. All these drugs though relieve pain and control fever, act in different ways and have different properties.  I thought it would be interesting to look at how these drugs act and the differences between the drugs.

First, I ran a query for aspirin, acetaminophen and ibuprofen in Distilbio to look at what I could find. Aspirin and Ibuprofen are categorized as NSAIDs (Non-steroidal anti-inflammatory drug) whereas acetaminophen is not an NSAID. I also ran a query to check if there are any common targets between these drugs. Continue reading

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Breast cancer gene BRCA and Heart disease

Recently I came across very interesting papers that report for the first time that women with risk of breast and ovarian cancer may have a higher risk of developing heart disease.

Mutations in the genes BRCA1 and BRCA2 have been associated with risk of breast and ovarian cancer. But now new research published in Nature Communications and the Journal of Biological Chemistry has found a new role for BRCA1 and BRCA2 as a “gatekeeper” of cardiac function and survival. Continue reading

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Understanding Drug Databases

While searching for information on Lumiracoxib in a few drug databases, I came across some confusing results. Lumiracoxib, is a non-steroidal anti-inflammatory drug that acts specifically on COX2. This drug was withdrawn in 2007 in Australia and subsequently in Canada and New Zealand due to concerns that it may cause liver damage.

I wanted to dig deeper into this and see how data for the same drug is represented by different databases, specifically the “drug to disease” relationship.  This made me look at a couple of more drugs, Cerivastatin and Ximelagatran that have been withdrawn from the market. Continue reading

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Drug Re-purposing – DistilBio Use Case

A very interesting and new approach adopted by Pharma companies is Drug re-purposing or re-positioning. Drug re-purposing is the use of already approved drug for disease indications that they were not initially developed to combat. This means that the drugs have already been through extensive toxicity tests and clinical trials, and failure due to adverse toxicology is reduced.

The most famous example of drug repurposing is of Sildenafil (Viagra), developed by Pfizer. Initially developed as a treatment for high blood pressure, which failed, but its side effect led to a new line of therapy (1).

Drugs, though intended to bind to a single target, generally bind to its primary target and several other proteins that could either lead to its efficacy or side-effects. Looking at these secondary targets will be interesting and probable targets for other disease areas.

As an example, I have selected the drug Rabeprazole, an anti-ulcer drug. Now lets see if Rabeprazole, an approved drug, can be re-purposed for any other disease area.

The first query is for Rabeprazole and the disease areas associated with it.

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Query: Rabeprazole > disease                          Run Query

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Disease to Drug and Molecular Side Effects – DistilBio Use Case

Since my last post on Drug target search for Sitagliptin, I have been thinking about other ways to verify the results I got using DistilBio. One of the things that came to my mind was to work backwards from diabetes and see if I could get comparable results.

To start with, I ran a query of Type 2 Diabetes (previously known as Non Insulin Dependant Diabetes Mellitus – NIDDM) and the proteins associated with it.

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Query: diabetes mellitus, noninsulin-dependent; niddm > protein

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Drug Target Search – DistilBio Use Case

Over the past month I have been exploring DistilBio to look at specific use cases that would be useful to someone working in the area of drug discovery.  I came up with several interesting and encouraging results. In this post, the first in this series, I will show you how DistilBio can be used to search for the target of a drug.

The drug I have chosen is Sitagliptin (Trade Name: Januvia), an anti-diabetic drug developed and marketed by Merck & Co. Lets see what DistilBio tells me about this drug.

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First, lets look at what is Sitagliptin and the associated disease indication.

Query: Sitagliptin > disease indication

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