The TB-drugome is a structural proteome-wide drug-target network that includes 274 drugs and 1730 proteins from Mycobacterium tuberculosis (M.tb). It was constructed by associating the putative ligand binding sites of the M.tb proteins with the known binding sites of approved drugs for which structural information was available. The premise being that two entirely unrelated proteins can bind similar ligands if they share similar ligand binding sites, since the ligand binding site can be considered as a negative image of the ligand. In this way, an M.tb protein can be connected to a drug through the drug target, irrespective of whether that protein target is from human or another organism. The binding site comparison software SMAP (http://funsite.sdsc.edu), was used for this purpose in an all-drug-against-all-target manner. For each identified drug-target pair, the atomic details of the interaction were studied using protein-ligand docking. The TB-drugome reveals that approximately one-third of the drugs examined have the potential to be repositioned to treat tuberculosis and that many currently unexploited M.tb receptors may be druggable and could serve as novel anti-tubercular targets.

TB-Drugome.tar.gz (220 M)

The compressed file includes the following files and directories:

This file contains information about the 274 approved drugs that were identified in the PDB. For each drug, its name, PDB ligand code, isomeric SMILES string and known targets are listed, and the PDB codes of the protein structures with which it has been crystallized are given.

This file contains information about the M.tb proteins with solved structure(s) in the RCSB PDB that were used in TB-drugome. For each protein, the gene name (if available), gene accession number, protein name and corresponding PDB codes are given.

This file contains information about the reliable homology models of M.tb proteins from ModBase that were used in TB-drugome. For each homology model, the ModBase model code is given, as well as the gene accession number, gene name and description of the M.tb protein. N.B. Further information about each homology model can be found on the ModBase website.

This file contains a list of the cross-fold drug-target pairs with a SMAP P-value < 1.0e-5, for solved M.tb structures only. For each pair, information about the drug and target structures is given, as well as the corresponding SMAP P-value (indicating the significance of the binding site similarity) and eHiTS energy score (from docking the drug into the predicted binding site in the M.tb protein).

This file contains a list of the cross-fold drug-target pairs with a SMAP P-value < 1.0e-5, for homology models of M.tb proteins only. For each pair, information about the drug and target structures is given, as well as the corresponding SMAP P-value (indicating the significance of the binding site similarity) and eHiTS energy score (from docking the drug into the predicted binding site in the M.tb protein).

This directory contains the eHiTS predicted binding poses (in SDF format) for all cross-fold drug-target pairs (solved M.tb structures only) with SMAP P-values < 1.0e-5. N.B. A blank file indicates that docking failed for that particular drug-target pair. Each drug binding pose can be viewed within its corresponding M.tb protein structure using molecular graphics software. The biological unit PDB files of all solved M.tb structures have also been provided for this purpose. In addition, the structures of the proteins with which the drugs were originally crystallized in the PDB have also been provided. These structures have been aligned onto the relevant solved M.tb protein structures using SMAP.

This directory contains the eHiTS predicted binding poses (in SDF format) for all cross-fold drug-target pairs (homology models of M.tb proteins only) with SMAP P-values < 1.0e-5. N.B. A blank file indicates that docking failed for that particular drug-target pair. Each drug binding pose can be viewed within its corresponding M.tb homology model using molecular graphics software. The homology model PDB files have also been provided for this purpose. In addition, the structures of the proteins with which the drugs were originally crystallized in the PDB have also been provided. These structures have been aligned onto the relevant homology models using SMAP.

The TB-drugome is supported by the National Institutes of Heath (NIH) grant number GM078596 and is located within the Skaggs School of Pharmacy and Pharmaceutical Sciences and the San Diego Supercomputer Center (SDSC) at the University of California San Diego (UCSD).

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