Biological Sciences Division
Published November 17, 2022 | Version v1
Journal article Open

Label-free affinity screening, design and synthesis of inhibitors targeting the Mycobacterium tuberculosis L-alanine dehydrogenase

Creators

  • 1. Los Alamos National Laboratory
  • 2. Georgetown University Medical Center
  • 3. University of Chicago
  • 4. Array BioPharma Inc.
  • 5. Kyung-Hee University
  • 6. Seoul National University
  • 7. Chungnam National University
  • 8. University of California, Irvine
  • 9. Masan National Tuberculosis Hospital
  • 10. Korea University
  • 11. New Mexico Consortium

Description

The ability of Mycobacterium tuberculosis (Mtb) to persist in its host may enable an evolutionary advantage for drug resistant variants to emerge. A potential strategy to prevent persistence and gain drug efficacy is to directly target the activity of enzymes that are crucial for persistence. We present a method for expedited discovery and structure-based design of lead compounds by targeting the hypoxia-associated enzyme L-alanine dehydrogenase (AlaDH). Biochemical and structural analyses of AlaDH confirmed binding of nucleoside derivatives and showed a site adjacent to the nucleoside binding pocket that can confer specificity to putative inhibitors. Using a combination of dye-ligand affinity chromatography, enzyme kinetics and protein crystallographic studies, we show the development and validation of drug prototypes. Crystal structures of AlaDH-inhibitor complexes with variations at the N6 position of the adenyl-moiety of the inhibitor provide insight into the molecular basis for the specificity of these compounds. We describe a drug-designing pipeline that aims to block Mtb to proliferate upon re-oxygenation by specifically blocking NAD accessibility to AlaDH. The collective approach to drug discovery was further evaluated through in silico analyses providing additional insight into an efficient drug development strategy that can be further assessed with the incorporation of in vivo studies.

Data availability

All relevant data are within the paper and its Supporting Information files.

Files

journal.pone.0277670.pdf

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Additional details

Identifiers

DOI
10.1371/journal.pone.0277670
Other
oai:uchicago.tind.io:6332

Funding

National Institutes of Health
NIGMS PSI-Biology program
National Research Foundation
BrainPool program
Republic of Korea
2019H1D3A2A02102296
Rural Development Administration
Cooperative Research Program for Agriculture Science and Technology Development
National Research Foundation
2017R1A5A2015385

UChicago Information

Division(s)
Biological Sciences Division
Department(s)
Biophysical Sciences