Increasing the structural coverage of tuberculosis drug targets

Abstract

High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus “homolog-rescue” strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. Of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structures would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Cα RMSD <1Å, >85% side chain identity, and ≥80% PSAPF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases.

Structures of the calcium-activated, non-selective cation channel TRPM4

“…2a). Structural homology search using DALI server 29 identified an AMP-binding phosphoribohydrolase named lonely guy (LOG) protein 30,31 that has the highest structural similarity to the NBD of TRPM4 (Extended Data Fig. 7a).…”

Functional, structural and epitopic prediction of hypothetical proteins of Mycobacterium tuberculosis H37Rv: An in silico approach for prioritizing the targets

“…We have found many of these proteins template are in TBSGC server and in published literature those may play key role in drug discovery/further analysis [119][120][121][122].…”

Crystal Structures of Apo and Liganded 4-Oxalocrotonate Decarboxylase Uncover a Structural Basis for the Metal-Assisted Decarboxylation of a Vinylogous β-Keto Acid

“…Only one member of each cluster (quite often a dimeric protein) was chosen to represent the overall fold of the group. Representative tertiary and quaternary structures of enzymes from ( A ) Mus musculus (PDB entry 1QCN (30) and Burkholderia cenocepacia (PDB entry 4QKU); ( B ) Sulfolobus solfataricus (PDB entry 2Q18 (32) ; ( C ) Mycobacterium marinum (PDB entry 3QDF (39) , Thermus thermophilus (PDB entry 2DFU and PDB entry 1WZO), M. abscessos (PDB entry 3RR6 (39) , Corynebacterium glutamicum (PDB entry 4DBF (33) , and M. smegmatis (PDB entry 4PFZ); ( D ) M. abscessos (PDB entry 3R6O (39) and Sinorhizobium meliloti (PDB entry 3LZK); ( E ) Homo sapiens (PDB entry 1SAW (31) , E. coli (PDB entry 1NR9), Yersinia pestis (PDB entry 3S52), Oleispira antarctica (PDB entry 3V77 (40) , B. cenocepacia (PDB entry 4MAQ) and Saccharomyces cerevisiae (PDB entry 1NKQ); ( F ) E. coli HpcE (PDB entry 1GTT (10) and ( G ) E. coli HpcG (PDB entry 2EB4 (11) , E. coli MhpD (PDB entry 2WQT (9) and P. putida NahK (this work). ( H ) Superposition of representative monomers showing the conserved CTD (incomplete β-barrel and β-sheet) and the position of each NTD.…”