Active Site Flexibility of Mycobacterium Tuberculosis Isocitrate Lyase in Dimer Form

J Chem Inf Model. 2017 Sep 25;57(9):2351-2357. doi: 10.1021/acs.jcim.7b00265. Epub 2017 Sep 1.

Abstract

Tuberculosis (TB) still remains a global threat due to the emergence of a drug-resistant strain. Instead of focusing on the drug target of active stage TB, we are highlighting the isocitrate lyase (ICL) at the dormant stage TB. ICL is one of the persistent factors for Mycobacterium tuberculosis (MTB) to survive during the dormant phase. In addition, the absence of ICL in human has made ICL a potential drug target for TB therapy. However, the dynamic details of ICL which could give insights to the ICL-ligand interaction have yet to be solved. Therefore, a series of ICL dimer dynamics studies through molecular dynamics simulation were performed in this work. The ICL active site entrance gate closure is contributed to by hydrogen bonding and electrostatic interactions with the C-terminal. Analysis suggested that the open-closed behavior of the ICL active site entrance depends on the type of ligand present in the active site. We also observed four residues (Ser91, Asp108, Asp153, and Cys191) which could possibly be the nucleophiles for nucleophilic attack on the cleavage of isocitrate at the C2-C3 bond. We hope that the elucidation of ICL dynamics can benefit future works such as lead identification or antibody design against ICL for TB therapeutics.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Catalytic Domain*
  • Isocitrate Lyase / chemistry*
  • Isocitrate Lyase / metabolism
  • Molecular Dynamics Simulation*
  • Mycobacterium tuberculosis / enzymology*
  • Protein Multimerization*
  • Protein Structure, Quaternary

Substances

  • Isocitrate Lyase