Exploring Covalent Allosteric Inhibition of Antigen 85C from Mycobacterium tuberculosis by Ebselen Derivatives

ACS Infect Dis. 2017 May 12;3(5):378-387. doi: 10.1021/acsinfecdis.7b00003. Epub 2017 Mar 21.


Previous studies identified ebselen as a potent in vitro and in vivo inhibitor of the Mycobacterium tuberculosis (Mtb) antigen 85 (Ag85) complex, comprising three homologous enzymes required for the biosynthesis of the mycobacterial cell wall. In this study, the Mtb Ag85C enzyme was cocrystallized with azido and adamantyl ebselen derivatives, resulting in two crystallographic structures of 2.01 and 1.30 Å resolution, respectively. Both structures displayed the anticipated covalent modification of the solvent accessible, noncatalytic Cys209 residue forming a selenenylsulfide bond. Continuous difference density for both thiol modifiers allowed for the assessment of interactions that influence ebselen binding and inhibitor orientation that were unobserved in previous Ag85C ebselen structures. The kinact/KI values for ebselen, adamantyl ebselen, and azido ebselen support the importance of observed constructive chemical interactions with Arg239 for increased in vitro efficacy toward Ag85C. To better understand the in vitro kinetic properties of these ebselen derivatives, the energetics of specific protein-inhibitor interactions and relative reaction free energies were calculated for ebselen and both derivatives using density functional theory. These studies further support the different in vitro properties of ebselen and two select ebselen derivatives from our previously published ebselen library with respect to kinetics and protein-inhibitor interactions. In both structures, the α9 helix was displaced farther from the enzyme active site than the previous Ag85C ebselen structure, resulting in the restructuring of a connecting loop and imparting a conformational change to residues believed to play a role in substrate binding specific to Ag85C. These notable structural changes directly affect protein stability, reducing the overall melting temperature by up to 14.5 °C, resulting in the unfolding of protein at physiological temperatures. Additionally, this structural rearrangement due to covalent allosteric modification creates a sizable solvent network that encompasses the active site and extends to the modified Cys209 residue. In all, this study outlines factors that influence enzyme inhibition by ebselen and its derivatives while further highlighting the effects of the covalent modification of Cys209 by said inhibitors on the structure and stability of Ag85C. Furthermore, the results suggest a strategy for developing new classes of Ag85 inhibitors with increased specificity and potency.

Keywords: Mycobacterium tuberculosis; allosteric covalent inhibition; antigen 85 complex; ebselen.

MeSH terms

  • Acyltransferases / antagonists & inhibitors
  • Acyltransferases / chemistry*
  • Acyltransferases / genetics
  • Acyltransferases / metabolism
  • Adamantane / chemistry
  • Allosteric Regulation
  • Allosteric Site
  • Amino Acid Motifs
  • Antigens, Bacterial / chemistry*
  • Antigens, Bacterial / genetics
  • Antigens, Bacterial / metabolism
  • Antitubercular Agents / chemical synthesis
  • Antitubercular Agents / chemistry*
  • Azides / chemistry
  • Azoles / chemical synthesis
  • Azoles / chemistry*
  • Catalytic Domain
  • Cell Wall / chemistry*
  • Cell Wall / enzymology
  • Cloning, Molecular
  • Crystallography, X-Ray
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Gene Expression
  • Isoindoles
  • Kinetics
  • Models, Molecular
  • Mycobacterium tuberculosis / chemistry*
  • Mycobacterium tuberculosis / enzymology
  • Organoselenium Compounds / chemical synthesis
  • Organoselenium Compounds / chemistry*
  • Plasmids / chemistry
  • Plasmids / metabolism
  • Protein Binding
  • Protein Conformation, alpha-Helical
  • Protein Conformation, beta-Strand
  • Protein Interaction Domains and Motifs
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Thermodynamics


  • Antigens, Bacterial
  • Antitubercular Agents
  • Azides
  • Azoles
  • Isoindoles
  • Organoselenium Compounds
  • Recombinant Proteins
  • ebselen
  • Acyltransferases
  • antigen 85C, Mycobacterium tuberculosis
  • Adamantane