New small molecules target TB's EccA 1 enzyme

Tuberculosis bacteria use a protein machine called the ESX-1 secretion system to send out factors that make infection worse. One essential piece of that machine is the EccA 1 enzyme, which the researchers describe as involved in the secretion of virulence factors and essential for virulence and bacterial survival within the phagosome. ajay Kumar saxena and co-authors set out to find small molecules that could shut down EccA 1 and thus disarm the bacterium rather than kill it outright. To do this, they first modeled the full-length EccA 1 structure (573 residues, Mw ∼62.4 kDa), which they report contains an N-terminal TPR domain and a C-terminal CbxX/CfqX type ATPase domain. With a full-length model in hand, the team used computational approaches to screen chemical libraries and predict how small molecules might bind the ATPase pocket, with the overall goal of developing new antivirulence drugs that abolish EccA 1 function and reduce the bacterium's ability to survive inside host cells.

The study used virtual screening, docking and dynamics simulation techniques to search the ZINC database for candidates that fit the C-terminal ATPase pocket of EccA 1. From that screen the authors identified five ZINC compounds, labeled Z1 (ZINC000004513760, -43.45 kcal/mol), Z2 (ZINC000000001793, -49.56 kcal/mol), Z3 (ZINC000005390388, -55.83 kcal/mol), Z4 (ZINC000257294577, -52.33 kcal/mol), and Z5 (ZINC000004824264, -44.44 kcal/mol). These were compared against the ADP substrate (Adenosine diphosphate, -35.00 kcal/mol) and two known p97 ATPase inhibitors, NMS873 (3-[3-cyclopentylsulfanyl-5-[[3-methyl-4-(4 methylsulfonylphenyl)phenoxy]methyl]-1,2,4-triazol-4-yl]pyridine, -48.68 kcal/mol) and CB5083 (1-[4-(benzylamino)-5H,7H,8H-pyrano[4,3-d]pyrimidin-2-yl]-2-methyl-1H-indole-4-carboxamide, -50.88 kcal/mol). The authors report that Z1-Z5 compounds exhibited good Absorption, Distribution, Metabolism, and/or Excretion properties (ADMTE), favorable pharmacokinetic properties, and met Lipinsky’s rule of five for drug-like properties. Finally, 100 ns dynamics simulation analysis on EccA 1 complexed with (i) Z1-Z5 compounds (ii) ADP substrate and (iii) NMS873 and CB5083 inhibitors showed high stability and biologically relevant conformation during dynamics simulation.

Taken together, these computational results suggest Z1-Z5 may act as potential inhibitors against EccA 1 and point toward a new antivirulence strategy against M. tuberculosis. Because EccA 1 is central to secretion of virulence factors and bacterial survival within the phagosome, molecules that bind its C-terminal ATPase pocket could prevent the bacterium from effectively harming host cells. The work stays within computational and modeling approaches: binding energies, ADMTE assessments, and 100 ns dynamics simulations all support the idea that these compounds interact stably with EccA 1. The authors are careful to note that these findings provide avenues for new antivirulence drug development after in vitro and in vivo clinical trials. In other words, Z1-Z5 are promising starting points, but laboratory experiments and clinical testing will be needed to confirm whether they can safely and effectively disarm M. tuberculosis in patients.