Discovery of antimicrobial agent targeting tryptophan synthase

Yuliana K. Bosken, Rizi Ai, Eduardo Hilario, Rittik K. Ghosh, Michael F. Dunn, Shih-Hsin Kan, Dimitri Niks, Huanbin Zhou, Wenbo Ma, Leonard J. Mueller, Li Fan, Chia-En A. Chang

Research output: Contribution to journalArticlepeer-review

2 Citations (SciVal)

Abstract

Antibiotic resistance is a continually growing challenge in the treatment of various bacterial infections worldwide. New drugs and new drug targets are necessary to curb the threat of infectious diseases caused by multidrug-resistant pathogens. The tryptophan biosynthesis pathway is essential for bacterial growth but is absent in higher animals and humans. Drugs that can inhibit the bacterial biosynthesis of tryptophan offer a new class of antibiotics. In this work, we combined a structure-based strategy using in silico docking screening and molecular dynamics (MD) simulations to identify compounds targeting the α subunit of tryptophan synthase with experimental methods involving the whole-cell minimum inhibitory concentration (MIC) test, solution state NMR, and crystallography to confirm the inhibition of L-tryptophan biosynthesis. Screening 1,800 compounds from the National Cancer Institute Diversity Set I against α subunit revealed 28 compounds for experimental validation; four of the 28 hit compounds showed promising activity in MIC testing. We performed solution state NMR experiments to demonstrate that a one successful inhibitor, 3-amino-3-imino-2-phenyldiazenylpropanamide (Compound 1) binds to the α subunit. We also report a crystal structure of Salmonella enterica serotype Typhimurium tryptophan synthase in complex with Compound 1 which revealed a binding site at the αβ interface of the dimeric enzyme. MD simulations were carried out to examine two binding sites for the compound. Our results show that this small molecule inhibitor could be a promising lead for future drug development.

Original languageEnglish
Pages (from-to)432-442
Number of pages11
JournalProtein Science
Volume31
Issue number2
Early online date12 Nov 2021
DOIs
Publication statusPublished - 7 Feb 2022

Keywords

  • antimicrobial agents
  • computer-aided drug discovery
  • crystal structure
  • enzyme inhibitor
  • essential bacterial pathway
  • molecular docking
  • structure-based drug discovery
  • virtual screening

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