Structural insights into the specific interaction between Geobacillus stearothermophilus tryptophanyl-tRNA synthetase and antimicrobial Chuangxinmycin

Fan, Shuai; Lv, Guixia; Feng, Xiao; Wu, Guoxing; Jin, Yuanyuan; Yan, Maocai; Yang, Zhaoyong

doi:10.1016/j.jbc.2022.101580

Cited by 4 publications

(5 citation statements)

References 31 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…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). We also performed isothermal titration calorimetry (ITC) binding experiments with the TrpRS Mtb and IPA (Trp as a control) and observed binding, with dissociation constant (K d ) values of 38 μM for IPA and 1.33 μM for Trp (Figure 2C).…”

Section: Ipa Targets the Trp Binding Pocket Of Trprssupporting

confidence: 54%

“…In the IND + ATP complexed structure, IND interacts with H50, D141, and Q156 of TrpRS Mtb . Another TrpRS inhibitor, CM, interacts with the TrpRS of Geobacillus stearothermophilus (GsTrpRS) involving D132, V143, and Q147 . Interestingly, these sites coincide with the interaction sites of IPA and TrpRS Mtb (D141, V152, Q156) by protein alignment (Figure B).…”

Section: Resultsmentioning

confidence: 80%

See 1 more Smart Citation

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

Han,

Gao,

Zhou

et al. 2024

ACS Infect. Dis.

View full text Add to dashboard Cite

Tuberculosis (TB) is the leading infectious disease caused by Mycobacterium tuberculosis and the second-most contagious killer after COVID-19. The emergence of drug-resistant TB has caused a great need to identify and develop new anti-TB drugs with novel targets. Indole propionic acid (IPA), a structural analog of tryptophan (Trp), is active against M. tuberculosis in vitro and in vivo. It has been verified that IPA exerts its antimicrobial effect by mimicking Trp as an allosteric inhibitor of TrpE, which is the first enzyme in the Trp synthesis pathway of M. tuberculosis. However, other Trp structural analogs, such as indolmycin, also target tryptophanyl-tRNA synthetase (TrpRS), which has two functions in bacteria: synthesis of tryptophanyl-AMP by catalyzing ATP + Trp and producing Trp-tRNA Trp by transferring Trp to tRNA Trp . So, we speculate that IPA may also target TrpRS. In this study, we found that IPA can dock into the Trp binding pocket of M. tuberculosis TrpRS (TrpRS Mtb ), which was further confirmed by isothermal titration calorimetry (ITC) assay. The biochemical analysis proved that TrpRS can catalyze the reaction between IPA and ATP to generate pyrophosphate (PPi) without Trp as a substrate. Overexpression of wild-type trpS in M. tuberculosis increased the MIC of IPA to 32-fold, and knock-down trpS in Mycolicibacterium smegmatis made it more sensitive to IPA. The supplementation of Trp in the medium abrogated the inhibition of M. tuberculosis by IPA. We demonstrated that IPA can interfere with the function of TrpRS by mimicking Trp, thereby impeding protein synthesis and exerting its anti-TB effect.

show abstract

Section: Ipa Targets the Trp Binding Pocket Of Trprssupporting

confidence: 54%

Section: Resultsmentioning

confidence: 80%

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

Han,

Gao,

Zhou

et al. 2024

ACS Infect. Dis.

View full text Add to dashboard Cite

show abstract

“…Importantly, the specific recognition of the side chain of L-Trp by Ec TrpRS involves a key hydrogen bonding interaction between Asp135 and the nitrogen of the indole moiety (Figure 7C ), and this interaction is conserved in the binding of L-Trp to all bacterial TrpRSs ( 17 ). Notably, the natural products indolmycin (PDB code: 5DK4) and chuangxinmycin (PDB code: 7CKI) both use an indole-like structure to occupy the L-Trp binding site of bacterial TrpRS, and both form key hydrogen bonding interactions with this conserved aspartate residue, similar to what substrate L-Trp does ( 20 , 21 ). However, this interaction does not exist between niraparib and Ec TrpRS.…”

Section: Resultsmentioning

confidence: 99%

“…Therefore, TrpRS is considered an attractive drug target for developing bacterial-selective inhibitors for fighting microbial infections ( 19 ). For example, two natural products, indolmycin and chuangxinmycin, have been shown to inhibit bacterial TrpRS at the nanomolar level with almost no undesired binding to human cytoplasmic TrpRS ( Hc TrpRS) ( 20 , 21 ). However, unfortunately, both inhibitors failed to enter the clinical use due to insufficient permeability or narrow antibacterial spectrum, and inhibitors against bacterial TrpRS with new scaffolds and novel mechanisms are highly desired.…”

Section: Introductionmentioning

confidence: 99%

An asymmetric structure of bacterial TrpRS supports the half-of-the-sites catalytic mechanism and facilitates antimicrobial screening

Xiang

Xia

Chen

et al. 2023

Nucleic Acids Research

View full text Add to dashboard Cite

Tryptophanyl-tRNA synthetase (TrpRS) links tryptophan to tRNATrp, thereby playing an indispensable role in protein translation. Unlike most class I aminoacyl-tRNA synthetases (AARSs), TrpRS functions as a homodimer. Herein, we captured an ‘open-closed’ asymmetric structure of Escherichia coli TrpRS (EcTrpRS) with one active site occupied by a copurified intermediate product and the other remaining empty, providing structural evidence for the long-discussed half-of-the-sites reactivity of bacterial TrpRS. In contrast to its human counterpart, bacterial TrpRS may rely on this asymmetric conformation to functionally bind with substrate tRNA. As this asymmetric conformation is probably a dominant form of TrpRS purified from bacterial cells, we performed fragment screening against asymmetric EcTrpRS to support antibacterial discovery. Nineteen fragment hits were identified, and 8 of them were successfully cocrystallized with EcTrpRS. While a fragment named niraparib bound to the L-Trp binding site of the ‘open’ subunit, the other 7 fragments all bound to an unprecedented pocket at the interface between two TrpRS subunits. Binding of these fragments relies on residues specific to bacterial TrpRS, avoiding undesired interactions with human TrpRS. These findings improve our understanding of the catalytic mechanism of this important enzyme and will also facilitate the discovery of bacterial TrpRS inhibitors with therapeutic potential.

show abstract

“…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 .…”

Section: Resultsmentioning

confidence: 99%

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

Shi

Jiang

et al. 2023

J. Nat. Prod.

View full text Add to dashboard Cite

A new congener of chuangxinmycin (CM) was identified from Actinoplanes tsinanensis CPCC 200056. Its structure was determined as 3-methylchuangxinmycin (MCM) by 1D and 2D NMR. MCM could be generated in vivo from CM by heterologous expression of the vitamin B12-dependent radical SAM enzyme CxnA/A1 responsible for methylation of 3-demethylchuangxinmycin (DCM) in CM biosynthesis, indicating that CxnA/A1 could perform iterative methylation for MCM production. In vitro assays revealed significant activities of CM, DCM, and MCM against Mycobacterium tuberculosis H37Rv and clinically isolated isoniazid/rifampin-resistant M. tuberculosis, suggesting that CM and its derivatives may have potential for antituberculosis drug development.

show abstract

Structural insights into the specific interaction between Geobacillus stearothermophilus tryptophanyl-tRNA synthetase and antimicrobial Chuangxinmycin

Cited by 4 publications

References 31 publications

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

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

An asymmetric structure of bacterial TrpRS supports the half-of-the-sites catalytic mechanism and facilitates antimicrobial screening

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

Contact Info

Product

Resources

About