Computational screening for new inhibitors of M. tuberculosis mycolyltransferases antigen 85 group of proteins as potential drug targets.
The group of antigen 85 proteins of Mycobacterium tuberculosis is responsible for converting trehalose monomycolate to trehalose dimycolate, which contributes to cell wall stability. Here, we have used a serial enrichment approach to identify new potential inhibitors by searching the libraries of compounds using both 2D atom pair descriptors and binary fingerprints followed by molecular docking. Three different docking softwares AutoDock, GOLD, and LigandFit were used for docking calculations. In addition, we applied the criteria of selecting compounds with binding efficiency close to the starting known inhibitor and showing potential to form hydrogen bonds with the active site amino acid residues. The starting inhibitor was ethyl-3-phenoxybenzyl-butylphosphonate, which had IC(50) value of 2.0 μM in mycolyltransferase inhibition assay. Our search from more than 34 million compounds from public libraries yielded 49 compounds. Subsequently, selection was restricted to compounds conforming to the Lipinski rule of five and exhibiting hydrogen bonding to any of the amino acid residues in the active site pocket of all three proteins of antigen 85A, 85B, and 85C. Finally, we selected those ligands which were ranked top in the table with other known decoys in all the docking results. The compound NIH415032 from tuberculosis antimicrobial acquisition and coordinating facility was further examined using molecular dynamics simulations for 10 ns. These results showed that the binding is stable, although some of the hydrogen bond atom pairs varied through the course of simulation. The NIH415032 has antitubercular properties with IC(90) at 20 μg/ml (53.023 μM). These results will be helpful to the medicinal chemists for developing new antitubercular molecules for testing.
G.N. Ramachandran Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110 007, India.
Shachi
S
Gahoi
Rahul Shubhra
RS
Mandal
Nikita
N
Ivanisenko
Priyanka
P
Shrivastava
Sriyans
S
Jain
Ashish Kumar
AK
Singh
Muthukurrusi Varieth
MV
Raghunandanan
Swarna
S
Kanchan
Bhupesh
B
Taneja
Chhabinath
C
Mandal
Vladimir A
VA
Ivanisenko
Anil
A
Kumar
Rita
R
Kumar
Srinivasan
S
Ramachandran
D000217:Acyltransferases / Q000737:chemistry* / Q000378:metabolism; D000942:Antigens, Bacterial / Q000737:chemistry* / Q000378:metabolism; D000995:Antitubercular Agents / Q000737:chemistry* / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D015195:Drug Design; D006860:Hydrogen Bonding; D008024:Ligands; D062105:Molecular Docking Simulation; D009169:Mycobacterium tuberculosis / Q000201:enzymology*
D000942:Antigens, Bacterial; D000995:Antitubercular Agents; D001426:Bacterial Proteins; D008024:Ligands; D000217:Acyltransferases; C121433:antigen 85B, Mycobacterium tuberculosis