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Yang Y, Xu Y, Yue Y, Wang H, Cui Y, Pan M, Zhang X, Zhang L, Li H, Xu M, Tang Y, Chen S. Investigate Natural Product Indolmycin and the Synthetically Improved Analogue Toward Antimycobacterial Agents. ACS Chem Biol 2022; 17:39-53. [PMID: 34908399 DOI: 10.1021/acschembio.1c00394] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Indolmycin (IND) is a microbial natural product that selectively inhibits bacterial tryptophanyl-tRNA synthetase (TrpRS). The tryptophan biosynthesis pathway was recently shown to be an important target for developing new antibacterial agents against Mycobacterium tuberculosis (Mtb). We investigated the antibacterial activity of IND against several mycobacterial model strains. A TrpRS biochemical assay was developed to analyze a library of synthetic IND analogues. The 4″-methylated IND compound, Y-13, showed improved anti-Mtb activity with a minimum inhibitory concentration (MIC) of 1.88 μM (∼0.5 μg/mL). The MIC increased significantly when overexpression of TrpRS was induced in the genetically engineered surrogate M. bovis BCG. The cocrystal structure of Mtb TrpRS complexed with IND and ATP has revealed that the amino acid pocket is in a state between the open form of apo protein and the closed complex with the reaction intermediate. In whole-cell-based experiments, we studied the combination effect of Y-13 paired with different antibacterial agents. We evaluated the killing kinetics, the frequency of resistance to INDs, and the mode of resistance of IND-resistant mycobacteria by genome sequencing. The synergistic interaction of Y-13 with the TrpE allosteric inhibitor, indole propionic acid, suggests that prospective IND analogues could shut down tryptophan biosynthesis and protein biosynthesis in pathogens, leading to a new class of antibiotics. Finally, we discuss a strategy to expand the genome mining of antibiotic-producing microbes specifically for antimycobacterial development.
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Affiliation(s)
- Yuhong Yang
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Yuanyuan Xu
- Global Health Drug Discovery Institute, Haidian, Beijing 100192, China
| | - Yuan Yue
- Ministry of Education Key Laboratory of Protein Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Heng Wang
- Global Health Drug Discovery Institute, Haidian, Beijing 100192, China
| | - Yumeng Cui
- Global Health Drug Discovery Institute, Haidian, Beijing 100192, China
| | - Miaomiao Pan
- Global Health Drug Discovery Institute, Haidian, Beijing 100192, China
| | - Xi Zhang
- Global Health Drug Discovery Institute, Haidian, Beijing 100192, China
| | - Lin Zhang
- Global Health Drug Discovery Institute, Haidian, Beijing 100192, China
| | - Haitao Li
- Ministry of Education Key Laboratory of Protein Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Min Xu
- Global Health Drug Discovery Institute, Haidian, Beijing 100192, China
| | - Yefeng Tang
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Shawn Chen
- Global Health Drug Discovery Institute, Haidian, Beijing 100192, China
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