Mechanism-Based Inactivation of Mycobacterium tuberculosis Isocitrate Lyase 1 by (2R,3S)-2-Hydroxy-3-(nitromethyl)succinic acid.

Abstract

The isocitrate lyase paralogs of Mycobacterium tuberculosis (ICL1 and 2) are essential for mycobacterial persistence and constitute targets for the development of antituberculosis agents. We report that (2R,3S)-2-hydroxy-3-(nitromethyl)succinic acid (5-NIC) undergoes apparent retro-aldol cleavage as catalyzed by ICL1 to produce glyoxylate and 3-nitropropionic acid (3-NP), the latter of which is a covalent-inactivating agent of ICL1. Kinetic analysis of this reaction identified that 5-NIC serves as a robust and efficient mechanism-based inactivator of ICL1 (kinact/KI = (1.3 ± 0.1) × 103 M-1 s-1) with a partition ratio <1. Using enzyme kinetics, mass spectrometry, and X-ray crystallography, we identified that the reaction of the 5-NIC-derived 3-NP with the Cys191 thiolate of ICL1 results in formation of an ICL1-thiohydroxamate adduct as predicted. One aspect of the design of 5-NIC was to lower its overall charge compared to isocitrate to assist with cell permeability. Accordingly, the absence of the third carboxylate group will simplify the synthesis of pro-drug forms of 5-NIC for characterization in cell-infection models of M. tuberculosis.

• Authors: Drake M Mellott, Dan Torres, Inna V Krieger, Scott A Cameron, Zahra Moghadamchargari, Arthur Laganowsky, James C Sacchettini, Thomas D Meek, Lawrence D Harris
• Journal: Journal of the American Chemical Society (J Am Chem Soc) Vol. 143 Issue 42 Pg. 17666-17676 (10 27 2021) ISSN: 1520-5126 [Electronic] United States
• PMID: 34664502 (Publication Type: Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't)

Chemical References

• Enzyme Inhibitors
• Glyoxylates
• Nitro Compounds
• Propionates
• Succinates
• Isocitrate Lyase
• glyoxylic acid
• 3-nitropropionic acid

Topics

• Enzyme Inhibitors (chemical synthesis, chemistry, metabolism)
• Glyoxylates (chemistry, metabolism)
• Isocitrate Lyase (antagonists & inhibitors, chemistry, metabolism)
• Kinetics
• Models, Chemical
• Mycobacterium tuberculosis (enzymology)
• Nitro Compounds (chemistry, metabolism)
• Propionates (chemistry, metabolism)
• Protein Binding
• Succinates (chemical synthesis, chemistry, metabolism)