Methodology And Tools ( Python, Java Or R) For Drug-Target-Fishing

Question

[Pradeep]

Please suggest me accepted methodology and tools for fishing the targets for a molecule to find mode of action.

I have a molecule for which mechanism of action is not known. Micro array data is available ( Experimental groups: Disease, Wild type, Disease + Drug, Wild type + Drug)

Problem: Micro array analysis gives > 500 DEGs in several pathways/processes related to disease.

Need to find: Short list and rank targets for the molecule.

Please suggest: methodology ( publications, tutorials, videos) more importantly need information about any freely available software / code / libraries -- preferably for R/Python/Java environment.

Thank you.

[Malachi Griffith]

This post describes many potentially relevant resources: Drug To Target/Gene/Protein Interaction Databases

Answer 1

[Istvan Albert]

Here is a new resource DGIdb - Mining the Druggable Genome posted by Obi Griffith

Answer 2

[David Westergaard]

I find it very difficult to believe you can elucidate the molecular mechanism of a compound just by microarray data. Microarray data can be useful in many connections, and can tell you something about the pathways perturbed, but I don't think it's very good for this purpose.

What I suggest instead:

• The link Istvan Albert posted
• Search existing bioactivity databases. E.g. ChEMBL, who also just released a VirtualMachine, complete with a RDKit installation for similarity searching (see the RDKit Chemical Cartridge page for more help

Also, other suggestions largely depend on which disease you are dealing with. Since you mention there is a "Wild type," I assume it is some form of genetic disease. Are you aware of the exact mechanism of the disease? You mention that the 500 DEGs are in pathways/processes related to the disease. Also, be aware, if the compound has not been fine tuned, it could potentially be a multi-target affector of some sort, e.g like Regorafenib, which inhibits ~18 different kinases, and is used in the treatment of colecteral cancer.