Investigate Natural Product Indolmycin and the Synthetically Improved Analogue Toward Antimycobacterial Agents

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.

Iterative Methylation Leads to 3-Methylchuangxinmycin Production in Actinoplanes tsinanensis CPCC 200056

“…Methylation is a ubiquitous reaction in natural product biosynthesis. Sometimes, the resulting methyl group(s) may exert significant effects on the biological activities of these natural products. − As a new congener of CM, MCM was assayed for its activity against Gram-positive and -negative bacteria. While CM displayed evident activity against some Gram-positive bacteria, both MCM and CM showed no activity against Gram-negative bacteria, including E. coli (Table S1).…”

“…The crystal structures of tryptophanyl-tRNA synthetase from Geobacillus stearothermophilus (GsTrpRS), − E. coli (EcTrpRS), Saccharomyces cerevisiae (ScTrpRS), Mycobacterium tuberculosis (MtbTrpRS), and Homo sapiens (hTrpRS) have been determined. The crystal structure of MtbTrpRS (PDB code: 7ENS) complexed with indolmycin, the bacterial tryptophanyl-tRNA synthetase inhibitor from Streptomyces , was resolved and chosen for in silico analysis of the binding and inhibition mechanism of CM, DCM, and MCM against M. tuberculosis . Molecular docking (CDOCKER module of Discovery Studio) indicates that CM, DCM, and MCM are all well accommodated into the Trp pocket of MtbTrpRS (Figure A).…”

Indole Propionic Acid Disturbs the Normal Function of Tryptophanyl-tRNA Synthetase in Mycobacterium tuberculosis

“…IPA possibly forms H bonds with the G13, Q138, and D141 sites of TrpRS Mtb and forms a salt bridge with H50 of TrpRS Mtb (Figure 2A). Yang 18 Another TrpRS inhibitor, CM, interacts with the TrpRS of Geobacillus stearothermophilus (GsTrpRS) involving D132, V143, and Q147. 26 Interestingly, these sites coincide with the interaction sites of IPA and TrpRS Mtb (D141, V152, Q156) by protein alignment (Figure 2B).…”

“…16 Bosch et al used a CRISPR interference system to titrate gene vulnerability in M. tuberculosis and found that ARSs as a class are universally vulnerable, meaning that ARSs can be new targets for drug discovery. 17 Indolmycin (IND) 18 and chuangxinmycin (CM) 19 as Trp analogs exert their antibacterial effects by inhibiting M. tuberculosis tryptophanyl-tRNA synthetase (TrpRS; chemical structures of Trp, IPA, CM, and IND are shown in Figure 1). As a prodrug, GSK3036656 20 needs covalent cyclization with ATP, AMP, and other adenosine groups; then the compound can inhibit M. tuberculosis LeuRS.…”

Total Synthesis of Carolacton and Demethylcarolactons with Potent Antiviral Activity

“…Taken together, it is imperative to develop a more concise, efficient, and modular synthetic route to access carolacton and its analogues. In line with our continuous interest in the total synthesis of natural products and related biomedical studies, we have embarked on a project to undertake this task.…”