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DrugBugDB:

DrugBugDB database which contains the prediction results for all the FDA approved drugs. These results obtained using a hybrid approach developed in our laboratory via implementing machine learning and similarity search approaches. This database constructed using metabolic proteins from 491 gut microbial genomes, 2036 EC numbers (with representative PDB ID and domains present) and 1689 FDA approved drugs. Gut microbial species capable of metabolizing a drug molecule with their specific metabolizing enzymes present at the database that can be browse by the user.

Significance:

Gut microbiota harbours approximately 1000 different bacterial species, hence possessing a vast metabolic potential other than coded by host genome. Recent reports have shown that the some of the drug molecule can be metabolized in the gut lumen by specific gut microbial species. These reports have shifted the focus towards the identification of mechanism by which gut microbe can metabolize a drug molecule. Most of the orally administered drugs first encounter the gut microbes and their metabolic enzymes prior to their absorption into blood therefore these gut bacterial species plays an important role in deciding upon the actual physiological activity of the drug molecule via altering their pharmacokinetic and pharmacodynamic properties. This gut microbial mediated metabolism can ultimately affects the overall efficacy and toxicity of these drugs. Considering the variation in gut microbial community between different individuals, thus, this gut microbiota mediated metabolism of drug molecules can ultimately lead to the individual and/or population specific differences in the drug response.

We have created a database called “DrugbugDB” which contains the information of gut bacterial species and corresponding metabolic enzymes capable of metabolising the FDA approved drug molecules. The structural properties of known substrate molecules belonging to particular enzyme class and subclass have been used to train machine learning algorithm for the prediction of enzyme class and subclass, and the same properties have been also used for the similarity search, against substrate database of particular enzyme subclass, in order to assign exact EC number to new (drug) molecules. Human gut microbes that contain drug metabolizing enzymes provided in the database along with the representative 3-dimentional structure of enzyme and the functional domains required for the metabolism. Contribution of specific gut bacterial phylum, genus and species to the metabolism of FDA approved drugs has been predicted and include in the database. DrugbugDB is repeatedly updated and well compatible with the integration of new data regarding gut bacterial species and drug molecules. We hope that this database will be useful for the researchers working in the field of gut microbial metabolism and will provide valuable information on the metabolism of all the available drugs.

The flowchart of DrugBugDB approach is shown below.

Browsing         Steps

Please browse the DrugBugDB database using following steps.
  1. Database can be browse by drug categories, where all the FDA approved drugs have been classified in to its broad pharmacological category. User can select one or multiple categories resultantly all the drugs belong to selected category will be dislayed. Individual drug can be selected to know more about metabolic details
  2. Database can be browse by bacterial phylum, resultantly all the bacterial species belong to selected phylum will be displayed. Individual species can be selected to list out the number of drugs that can be metabolized by this species. Individual drug can be selected to know more about metabolic details