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Zhang J, Liu Y, Zhi X, Xu L, Tao J, Cui D, Liu TF. Tryptophan catabolism via the kynurenine pathway regulates infection and inflammation: from mechanisms to biomarkers and therapies. Inflamm Res 2024; 73:979-996. [PMID: 38592457 DOI: 10.1007/s00011-024-01878-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/24/2024] [Accepted: 03/27/2024] [Indexed: 04/10/2024] Open
Abstract
BACKGROUND L-Tryptophan (L-Trp), an essential amino acid, is the only amino acid whose level is regulated specifically by immune signals. Most proportions of Trp are catabolized via the kynurenine (Kyn) pathway (KP) which has evolved to align the food availability and environmental stimulation with the host pathophysiology and behavior. Especially, the KP plays an indispensable role in balancing the immune activation and tolerance in response to pathogens. SCOPE OF REVIEW In this review, we elucidate the underlying immunological regulatory network of Trp and its KP-dependent catabolites in the pathophysiological conditions by participating in multiple signaling pathways. Furthermore, the KP-based regulatory roles, biomarkers, and therapeutic strategies in pathologically immune disorders are summarized covering from acute to chronic infection and inflammation. MAJOR CONCLUSIONS The immunosuppressive effects dominate the functions of KP induced-Trp depletion and KP-produced metabolites during infection and inflammation. However, the extending minor branches from the KP are not confined to the immune tolerance, instead they go forward to various functions according to the specific condition. Nevertheless, persistent efforts should be made before the clinical use of KP-based strategies to monitor and cure infectious and inflammatory diseases.
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Affiliation(s)
- Jingpu Zhang
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Highway, Shanghai, 201508, People's Republic of China.
| | - Yanlei Liu
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Xiao Zhi
- Shanghai Institute of Virology, Shanghai Jiao Tong University School of Medicine, 227 South Chongqing Road, Shanghai, 200025, People's Republic of China
| | - Li Xu
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Highway, Shanghai, 201508, People's Republic of China
| | - Jie Tao
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Highway, Shanghai, 201508, People's Republic of China
| | - Daxiang Cui
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Tie Fu Liu
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Highway, Shanghai, 201508, People's Republic of China.
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Han X, Gao Y, Zhou B, Hameed HMA, Fang C, Ju Y, He J, Fang X, Liu Z, Yu W, Xiong X, Zhong N, Zhang T. Indole Propionic Acid Disturbs the Normal Function of Tryptophanyl-tRNA Synthetase in Mycobacterium tuberculosis. ACS Infect Dis 2024; 10:1201-1211. [PMID: 38457660 DOI: 10.1021/acsinfecdis.3c00585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2024]
Abstract
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-tRNATrp by transferring Trp to tRNATrp. 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 (TrpRSMtb), 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.
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Affiliation(s)
- Xingli Han
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou 510530, China
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Yamin Gao
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou 510530, China
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Biao Zhou
- Guangzhou Laboratory, Guangzhou Medical University, Guangzhou 511436, China
- Guangzhou International Bio Island, Guangzhou 510320, China
| | - H M Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou 510530, China
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Cuiting Fang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou 510530, China
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Yanan Ju
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou 510530, China
| | - Jing He
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou 510530, China
| | - Xiange Fang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou 510530, China
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Zhiyong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou 510530, China
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
- Guangzhou Laboratory, Guangzhou Medical University, Guangzhou 511436, China
| | - Wei Yu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou 510530, China
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
- Guangzhou Laboratory, Guangzhou Medical University, Guangzhou 511436, China
| | - Xiaoli Xiong
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou 510530, China
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Nanshan Zhong
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou 510530, China
- Guangzhou Laboratory, Guangzhou Medical University, Guangzhou 511436, China
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, The National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou 510530, China
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
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3
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Kumar S, Sega S, Lynn-Barbe JK, Harris DL, Koehn JT, Crans DC, Crick DC. Proline Dehydrogenase and Pyrroline 5 Carboxylate Dehydrogenase from Mycobacterium tuberculosis: Evidence for Substrate Channeling. Pathogens 2023; 12:1171. [PMID: 37764979 PMCID: PMC10537722 DOI: 10.3390/pathogens12091171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/25/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
In Mycobacterium tuberculosis, proline dehydrogenase (PruB) and ∆1-pyrroline-5-carboxylate (P5C) dehydrogenase (PruA) are monofunctional enzymes that catalyze proline oxidation to glutamate via the intermediates P5C and L-glutamate-γ-semialdehyde. Both enzymes are essential for the replication of pathogenic M. tuberculosis. Highly active enzymes were expressed and purified using a Mycobacterium smegmatis expression system. The purified enzymes were characterized using natural substrates and chemically synthesized analogs. The structural requirements of the quinone electron acceptor were examined. PruB displayed activity with all tested lipoquinone analogs (naphthoquinone or benzoquinone). In PruB assays utilizing analogs of the native naphthoquinone [MK-9 (II-H2)] specificity constants Kcat/Km were an order of magnitude greater for the menaquinone analogs than the benzoquinone analogs. In addition, mycobacterial PruA was enzymatically characterized for the first time using exogenous chemically synthesized P5C. A Km value of 120 ± 0.015 µM was determined for P5C, while the Km value for NAD+ was shown to be 33 ± 4.3 µM. Furthermore, proline competitively inhibited PruA activity and coupled enzyme assays, suggesting that the recombinant purified monofunctional PruB and PruA enzymes of M. tuberculosis channel substrate likely increase metabolic flux and protect the bacterium from methylglyoxal toxicity.
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Affiliation(s)
- Santosh Kumar
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-1682, USA; (S.K.)
| | - Steven Sega
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-1682, USA; (S.K.)
| | - Jamie K. Lynn-Barbe
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-1682, USA; (S.K.)
| | - Dannika L. Harris
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-1682, USA; (S.K.)
| | - Jordan T. Koehn
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA;
| | - Debbie C. Crans
- Chemistry Department, Colorado State University, Fort Collins, CO 80523-1682, USA;
| | - Dean C. Crick
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-1682, USA; (S.K.)
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4
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Miles SA, Nillama JA, Hunter L. Tinker, Tailor, Soldier, Spy: The Diverse Roles That Fluorine Can Play within Amino Acid Side Chains. Molecules 2023; 28:6192. [PMID: 37687021 PMCID: PMC10489206 DOI: 10.3390/molecules28176192] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/17/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023] Open
Abstract
Side chain-fluorinated amino acids are useful tools in medicinal chemistry and protein science. In this review, we outline some general strategies for incorporating fluorine atom(s) into amino acid side chains and for elaborating such building blocks into more complex fluorinated peptides and proteins. We then describe the diverse benefits that fluorine can offer when located within amino acid side chains, including enabling 19F NMR and 18F PET imaging applications, enhancing pharmacokinetic properties, controlling molecular conformation, and optimizing target-binding.
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Affiliation(s)
| | | | - Luke Hunter
- School of Chemistry, The University of New South Wales (UNSW), Sydney 2052, Australia
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5
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Xia C, Zeng X, Peng L, Pan D, Wu Z, Guo Y, Cai Z. The function of uridine diphosphate glucose pyrophosphorylase in the lyophilization-stress response of Lactobacillus acidophilus. ANN MICROBIOL 2022. [DOI: 10.1186/s13213-022-01680-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Purpose
Uridine diphosphate glucose pyrophosphorylase (UGPase) plays an important role in glucose metabolism, catalyzing the reversible formation and decomposition of UDP-glucose (UDPG). In previous work, we found that UGPase is a key enzyme in lyophilization response for Lactobacillus acidophilus (L. acidophilus). However, its function and regulatory mechanism in the freeze-drying stress response are unknown. Herein, the effect of UGPase on freeze-drying survival rate of Staphylococcus carnosus (S. carnosus) was studied.
Methods
In this work, the genes LBA1719 encoding UGPase of L. acidophilus ATCC4356 were inserted into plasmid pMG-36e to construct the recombinant plasmid pMG-LBA1719 and then overexpressed in S. carnosus; the control group was S. carnosus transformed by pMG-36e. The lyophilization-survival rate of overexpressed S. carnosus was determined, and the differentially expressed genes (DEGs) were analyzed by transcriptome to disclose the mechanism of LBA1719 in regulating the lyophilization-survival rate.
Results
Compared with the control group, the UGPase activities of the overexpressed S. carnosus increased by 35.49%, while the lyophilization-survival rates decreased by 11.17% (p < 0.05). Overexpression of LBA1719 decreased the expression of genes gapA, gapB, and pgiA in carbohydrate metabolism and dapA, dapB, and dapE in amino acid metabolism, significantly changing the physiological characteristics of S. carnosus and decreasing its lyophilization-survival rate.
Conclusion
In summary, overexpression of UGPase accelerated the growth rate of S. carnosus and reduced its lyophilization-survival rates. GapA, gapB, pgiA, dapA, dapB, and dapE are vital to lyophilization protection in lactic acid bacteria (LAB). These findings provide new theoretical basis for analyzing the regulatory and molecular mechanisms of lyophilization resistance in LABs.
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6
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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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7
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Consalvi S, Venditti G, Zhu J, Boshoff HI, Arora K, De Logu A, Ioerger TR, Rubin EJ, Biava M, Poce G. 6-Fluorophenylbenzohydrazides inhibit Mycobacterium tuberculosis growth through alteration of tryptophan biosynthesis. Eur J Med Chem 2021; 226:113843. [PMID: 34520959 PMCID: PMC10994514 DOI: 10.1016/j.ejmech.2021.113843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/31/2021] [Accepted: 09/07/2021] [Indexed: 11/22/2022]
Abstract
A major constraint in reducing tuberculosis epidemic is the emergence of strains resistant to one or more of clinically approved antibiotics, which emphasizes the need of novel drugs with novel targets. Genetic knockout strains of Mycobacterium tuberculosis (Mtb) have established that tryptophan (Trp) biosynthesis is essential for the bacterium to survive in vivo and cause disease in animal models. An anthranilate-like compound, 6-FABA, was previously shown to synergize with the host immune response to Mtb infection in vivo. Herein, we present a class of anthranilate-like compounds endowed with good antimycobacterial activity and low cytotoxicity. We show how replacing the carboxylic moiety with a hydrazide led to a significant improvement in both activity and cytotoxicity relative to the parent compound 6-FABA. Several new benzohydrazides (compounds 20-31, 33, 34, 36, 38 and 39) showed good activities against Mtb (0.625 ≤ MIC≤6.25 μM) and demonstrated no detectable cytotoxicity against Vero cell assay (CC50 ≥ 1360 μM). The target preliminary studies confirmed the hypothesis that this new class of compounds inhibits Trp biosynthesis. Taken together, these findings indicate that fluorophenylbenzohydrazides represent good candidates to be assessed for drug discovery.
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Affiliation(s)
- Sara Consalvi
- Department of Chemistry and Technologies of Drug, Sapienza University of Rome, Piazzale A. Moro 5, 00185, Rome, Italy
| | - Giulia Venditti
- Department of Chemistry and Technologies of Drug, Sapienza University of Rome, Piazzale A. Moro 5, 00185, Rome, Italy
| | - Junhao Zhu
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, 02115, USA
| | - Helena I Boshoff
- National Institute of Allergy and Infectious Diseases, Laboratory of Clinical Immunology and Microbiology, 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - Kriti Arora
- National Institute of Allergy and Infectious Diseases, Laboratory of Clinical Immunology and Microbiology, 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - Alessandro De Logu
- Department of Life and Environmental Sciences, University of Cagliari, via Ospedale 72, 09124, Cagliari, Italy
| | - Thomas R Ioerger
- Department of Computer Science, Texas A&M University, 3112 TAMU, College Station, TX, 77843, USA
| | - Eric J Rubin
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, 02115, USA
| | - Mariangela Biava
- Department of Chemistry and Technologies of Drug, Sapienza University of Rome, Piazzale A. Moro 5, 00185, Rome, Italy.
| | - Giovanna Poce
- Department of Chemistry and Technologies of Drug, Sapienza University of Rome, Piazzale A. Moro 5, 00185, Rome, Italy.
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8
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An antitubercular prodrug leaves Mycobacterium tuberculosis facing a difficult choice, poisoning or starvation? Cell Chem Biol 2021; 28:1101-1103. [PMID: 34416139 DOI: 10.1016/j.chembiol.2021.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this issue of Cell Chemical Biology, Libardo et al. (2021) identify prodrugs that kill Mtb through poisoning of its L-tryptophan biosynthetic pathway. Determination of the mechanisms of resistance evolved by the bacterium highlights the importance of metabolic flux modulation in TB drug resistance.
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9
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The tryptophan biosynthetic pathway is essential for Mycobacterium tuberculosis to cause disease. Biochem Soc Trans 2021; 48:2029-2037. [PMID: 32915193 PMCID: PMC7609029 DOI: 10.1042/bst20200194] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/21/2020] [Accepted: 08/26/2020] [Indexed: 12/19/2022]
Abstract
Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), is the most significant cause of death from a single infectious agent worldwide. Antibiotic-resistant strains of M. tuberculosis represent a threat to effective treatment, and the long duration, toxicity and complexity of current chemotherapy for antibiotic-resistant disease presents a need for new therapeutic approaches with novel modes of action. M. tuberculosis is an intracellular pathogen that must survive phagocytosis by macrophages, dendritic cells or neutrophils to establish an infection. The tryptophan biosynthetic pathway is required for bacterial survival in the phagosome, presenting a target for new classes of antitubercular compound. The enzymes responsible for the six catalytic steps that produce tryptophan from chorismate have all been characterised in M. tuberculosis, and inhibitors have been described for some of the steps. The innate immune system depletes cellular tryptophan in response to infection in order to inhibit microbial growth, and this effect is likely to be important for the efficacy of tryptophan biosynthesis inhibitors as new antibiotics. Allosteric inhibitors of both the first and final enzymes in the pathway have proven effective, including by a metabolite produced by the gut biota, raising the intriguing possibility that the modulation of tryptophan biosynthesis may be a natural inter-bacterial competition strategy.
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10
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Libardo MDJ, Duncombe CJ, Green SR, Wyatt PG, Thompson S, Ray PC, Ioerger TR, Oh S, Goodwin MB, Boshoff HIM, Barry CE. Resistance of Mycobacterium tuberculosis to indole 4-carboxamides occurs through alterations in drug metabolism and tryptophan biosynthesis. Cell Chem Biol 2021; 28:1180-1191.e20. [PMID: 33765439 PMCID: PMC8379015 DOI: 10.1016/j.chembiol.2021.02.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/22/2021] [Accepted: 02/25/2021] [Indexed: 01/22/2023]
Abstract
Tryptophan biosynthesis represents an important potential drug target for new anti-TB drugs. We identified a series of indole-4-carboxamides with potent antitubercular activity. In vitro, Mycobacterium tuberculosis (Mtb) acquired resistance to these compounds through three discrete mechanisms: (1) a decrease in drug metabolism via loss-of-function mutations in the amidase that hydrolyses these carboxamides, (2) an increased biosynthetic rate of tryptophan precursors via loss of allosteric feedback inhibition of anthranilate synthase (TrpE), and (3) mutation of tryptophan synthase (TrpAB) that decreased incorporation of 4-aminoindole into 4-aminotryptophan. Thus, these indole-4-carboxamides act as prodrugs of a tryptophan antimetabolite, 4-aminoindole.
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Affiliation(s)
- M Daben J Libardo
- Tuberculosis Research Section, Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Caroline J Duncombe
- Tuberculosis Research Section, Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Simon R Green
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Paul G Wyatt
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Stephen Thompson
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Peter C Ray
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Thomas R Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Sangmi Oh
- Tuberculosis Research Section, Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael B Goodwin
- Tuberculosis Research Section, Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Helena I M Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Clifton E Barry
- Tuberculosis Research Section, Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Institute for Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7935, South Africa.
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11
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Yelamanchi SD, Surolia A. Targeting amino acid metabolism of Mycobacterium tuberculosis for developing inhibitors to curtail its survival. IUBMB Life 2021; 73:643-658. [PMID: 33624925 DOI: 10.1002/iub.2455] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 12/31/2020] [Accepted: 12/31/2020] [Indexed: 12/29/2022]
Abstract
Tuberculosis caused by the bacterium, Mycobacterium tuberculosis (Mtb), continues to remain one of the most devastating infectious diseases afflicting humans. Although there are several drugs for treating tuberculosis available currently, the emergence of the drug resistant forms of this pathogen has made its treatment and eradication a challenging task. While the replication machinery, protein synthesis and cell wall biogenesis of Mtb have been targeted often for anti-tubercular drug development a number of essential metabolic pathways crucial to its survival have received relatively less attention. In this context a number of amino acid biosynthesis pathways have recently been shown to be essential for the survival and pathogenesis of Mtb. Many of these pathways and or their key enzymes homologs are absent in humans hence they could be harnessed for anti-tubercular drug development. In this review, we describe comprehensively the amino acid metabolic pathways essential in Mtb and the key enzymes involved therein that are being investigated for developing inhibitors that compromise the survival and pathogenesis caused by this pathogen.
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Affiliation(s)
| | - Avadhesha Surolia
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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12
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Xie L, Chen Z, Liu W, Gu D, Yu Y, Chen X, Wu Y, Xu N, Xie J, Zhao G, Ruan BH. A sensitive EZMTT method provides microscale, quantitative and high-throughput evaluation of drug efficacy in the treatment of Mycobacterium tuberculosis infectious diseases. J Microbiol Methods 2021; 181:106136. [PMID: 33422524 DOI: 10.1016/j.mimet.2021.106136] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 01/05/2021] [Accepted: 01/05/2021] [Indexed: 12/22/2022]
Abstract
Drug resistance has become a serious public health problem in mycobacterial infectious diseases. Here, we investigated a water soluble tetrazolium salt (EZMTT)-based detection method to provide an easy, safe and quantitative antimycobacterial susceptibility test (AMST) method, especially for targeting early detection of loss of drug susceptibility in mycobacteria. After a single addition of the EZMTT detection reagent at the inoculation of mycobacteria culture, the AMST was continuously analyzed in a sealed 96-well plate (100 μl), or a sealed tube to ensure biosafety. Using Mycobacterium tuberculosis H37Ra as the model strain, the EZMTT assay was developed with high reproducibility (Z factor of 0.64) for facile measurements of growth and drug susceptibility. In the comparative AMST study, the 7-day EZMTT method identified not only the same set of drug resistance as the other two methods (the 30-day traditional Löwenstein Jensen solid medium assay and the 10-14 day 8 ml Mycobacteria Growth Indicator Tube liquid method), but also additional strains with loss of drug susceptibility. In conclusion, we demonstrated that the EZMTT-based AMST assay in a sealed microtiter plate has great potential for routine use in medical diagnosis and drug screening to battle the unmet medical need in the treatment of multi- and extensive-drug resistant mycobacteria.
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Affiliation(s)
- Li Xie
- Center for M. tuberculosis Research, Hangzhou, 310021, China
| | - Zhao Chen
- College of Pharmaceutical Science, Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, IDD & CB, Zhejiang University of Technology, Hangzhou 310014, China
| | - Wei Liu
- Center for M. tuberculosis Research, Hangzhou, 310021, China
| | - Dongshi Gu
- College of Pharmaceutical Science, Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, IDD & CB, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yan Yu
- College of Pharmaceutical Science, Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, IDD & CB, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xinrou Chen
- College of Pharmaceutical Science, Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, IDD & CB, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yefei Wu
- Center for M. tuberculosis Research, Hangzhou, 310021, China
| | - Ning Xu
- College of Pharmaceutical Science, Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, IDD & CB, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jie Xie
- Center for M. tuberculosis Research, Hangzhou, 310021, China
| | - Gang Zhao
- Center for M. tuberculosis Research, Hangzhou, 310021, China.
| | - Benfang Helen Ruan
- College of Pharmaceutical Science, Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, IDD & CB, Zhejiang University of Technology, Hangzhou 310014, China.
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13
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Fontes FL, Peters BJ, Crans DC, Crick DC. The Acid-Base Equilibrium of Pyrazinoic Acid Drives the pH Dependence of Pyrazinamide-Induced Mycobacterium tuberculosis Growth Inhibition. ACS Infect Dis 2020; 6:3004-3014. [PMID: 33078607 DOI: 10.1021/acsinfecdis.0c00507] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Pyrazinamide, a first-line antibiotic used against Mycobacterium tuberculosis, has been shown to act in a pH-dependent manner in vitro. Why pyrazinamide, an antitubercle prodrug discovered more than 65 years ago, exhibits this pH-dependent activity was unclear. Upon entering mycobacterial cells, pyrazinamide is deamidated to pyrazinoate by an enzymatic process and exists in an acid-base equilibrium with pyrazinoic acid. Thus, the effects of total pyrazinoic acid (pyrazinoic acid + pyrazinoate) on M. tuberculosis growth, pH homeostasis, and proton motive force over a range of pH values found in host tissues were investigated. Although M. tuberculosis was able to maintain pH homeostasis over an external pH range of 7.0 to 5.5, total pyrazinoic acid induced growth inhibition increased as culture medium pH was decreased from 7.3 to 6.4. Consistent with growth inhibition, total pyrazinoic acid increased both acidification of the bacterial cytoplasm and dissipation of membrane potential as the environmental pH decreased when added to the bacterial suspensions. The results suggest pyrazinoic acid is the active form of the drug, which acts as an uncoupler of proton motive force, likely a protonophore, providing a mechanistic explanation for the pH dependence of the drug activity.
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Affiliation(s)
- Fabio L. Fontes
- Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, United States
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Benjamin J. Peters
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Debbie C. Crans
- Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, United States
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Dean C. Crick
- Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, United States
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
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14
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Sester A, Stüer-Patowsky K, Hiller W, Kloss F, Lütz S, Nett M. Biosynthetic Plasticity Enables Production of Fluorinated Aurachins. Chembiochem 2020; 21:2268-2273. [PMID: 32216075 PMCID: PMC7496329 DOI: 10.1002/cbic.202000166] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 03/25/2020] [Indexed: 12/15/2022]
Abstract
Enzyme promiscuity has important implications in the field of biocatalysis. In some cases, structural analogues of simple metabolic building blocks can be processed through entire pathways to give natural product derivatives that are not readily accessible by chemical means. In this study, we explored the plasticity of the aurachin biosynthesis pathway with regard to using fluoro‐ and chloroanthranilic acids, which are not abundant in the bacterial producers of these quinolone antibiotics. The incorporation rates of the tested precursor molecules disclosed a regiopreference for halogen substitution as well as steric limitations of enzymatic substrate tolerance. Three previously undescribed fluorinated aurachin derivatives were produced in preparative amounts by fermentation and structurally characterized. Furthermore, their antibacterial activities were evaluated in comparison to their natural congener aurachin D.
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Affiliation(s)
- Angela Sester
- Department of Biochemical and Chemical Engineering Laboratory of Technical Biology, TU Dortmund, Emil-Figge-Strasse 66, 44227, Dortmund, Germany
| | - Katrin Stüer-Patowsky
- Department of Biochemical and Chemical Engineering Laboratory of Technical Biology, TU Dortmund, Emil-Figge-Strasse 66, 44227, Dortmund, Germany
| | - Wolf Hiller
- Department of Chemistry and Chemical Biology NMR Laboratory, TU Dortmund, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Florian Kloss
- Transfer Group Antiinfectives, Leibniz Institute for Natural Product Research and Infection Biology, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Stephan Lütz
- Department of Biochemical and Chemical Engineering Chair for Bioprocess Engineering, TU Dortmund, Emil-Figge-Strase 66, 44227, Dortmund, Germany
| | - Markus Nett
- Department of Biochemical and Chemical Engineering Laboratory of Technical Biology, TU Dortmund, Emil-Figge-Strasse 66, 44227, Dortmund, Germany
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15
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Consalvi S, Scarpecci C, Biava M, Poce G. Mycobacterial tryptophan biosynthesis: A promising target for tuberculosis drug development? Bioorg Med Chem Lett 2019; 29:126731. [PMID: 31627992 DOI: 10.1016/j.bmcl.2019.126731] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/17/2019] [Accepted: 10/01/2019] [Indexed: 12/25/2022]
Abstract
The biosynthetic pathways of amino acids are attractive targets for drug development against pathogens with an intracellular behavior like M. tuberculosis (Mtb). Indeed, while in the macrophages Mtb has restricted access to amino acids such as tryptophan (Trp). Auxotrophic Mtb strains, with mutations in the Trp biosynthetic pathway, showed reduced intracellular survival in cultured human and murine macrophages and failed to cause the disease in immunocompetent and immunocompromised mice. Herein we present recent efforts in the discovery of Trp biosynthesis inhibitors.
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Affiliation(s)
- Sara Consalvi
- Department of Chemistry and Technologies of Drug, Sapienza University of Rome, piazzale A. Moro 5, 00185 Rome, Italy
| | - Cristina Scarpecci
- Department of Chemistry and Technologies of Drug, Sapienza University of Rome, piazzale A. Moro 5, 00185 Rome, Italy
| | - Mariangela Biava
- Department of Chemistry and Technologies of Drug, Sapienza University of Rome, piazzale A. Moro 5, 00185 Rome, Italy
| | - Giovanna Poce
- Department of Chemistry and Technologies of Drug, Sapienza University of Rome, piazzale A. Moro 5, 00185 Rome, Italy.
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Gut Microbiota Metabolite Indole Propionic Acid Targets Tryptophan Biosynthesis in Mycobacterium tuberculosis. mBio 2019; 10:mBio.02781-18. [PMID: 30914514 PMCID: PMC6437058 DOI: 10.1128/mbio.02781-18] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
New drugs against tuberculosis are urgently needed. The tryptophan (Trp) analog indole propionic acid (IPA) is the first antitubercular metabolite produced by human gut bacteria. Here, we show that this antibiotic blocks Trp synthesis, an in vivo essential biosynthetic pathway in M. tuberculosis. Intriguingly, IPA acts by decoupling a bacterial feedback regulatory mechanism: it mimics Trp as allosteric inhibitor of anthranilate synthase, thereby switching off Trp synthesis regardless of intracellular Trp levels. The identification of IPA’s target paves the way for the discovery of more potent TrpE ligands employing rational, target-based lead optimization. Indole propionic acid (IPA), produced by the gut microbiota, is active against Mycobacterium tuberculosisin vitro and in vivo. However, its mechanism of action is unknown. IPA is the deamination product of tryptophan (Trp) and thus a close structural analog of this essential aromatic amino acid. De novo Trp biosynthesis in M. tuberculosis is regulated through feedback inhibition: Trp acts as an allosteric inhibitor of anthranilate synthase TrpE, which catalyzes the first committed step in the Trp biosynthesis pathway. Hence, we hypothesized that IPA may mimic Trp as an allosteric inhibitor of TrpE and exert its antimicrobial effect by blocking synthesis of Trp at the TrpE catalytic step. To test our hypothesis, we carried out metabolic, chemical rescue, genetic, and biochemical analyses. Treatment of mycobacteria with IPA inhibited growth and reduced the intracellular level of Trp, an effect abrogated upon supplementation of Trp in the medium. Missense mutations at the allosteric Trp binding site of TrpE eliminated Trp inhibition and caused IPA resistance. In conclusion, we have shown that IPA blocks Trp biosynthesis in M. tuberculosis via inhibition of TrpE by mimicking the physiological allosteric inhibitor of this enzyme.
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