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Kapoor Y, Khurana H, Dutta D, Chakraborty A, Priya A, Singh A, Kamat SS, Dhar N, Pucadyil TJ, Nandicoori VK. Wag31, a membrane tether, is crucial for lipid homeostasis in mycobacteria. eLife 2025; 14:RP104268. [PMID: 40402572 PMCID: PMC12097788 DOI: 10.7554/elife.104268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2025] Open
Abstract
The mycobacterial cytoskeletal protein Wag31 is necessary for maintaining cell shape and directing cellular growth and elongation. Wag31 has a characteristic N-terminal DivIVA-domain and a C-terminal coiled-coil domain. While the role of Wag31 in polar elongation is known, there is limited mechanistic insight on how it orchestrates growth and elongation. In this report, we delineate roles of the N- and C-terminal domains of Wag31 using genetics, state-of-the-art multi-omics, biochemical, and imaging approaches. We show that Wag31 predominantly interacts with several membrane-associated proteins involved in lipid metabolism, cell wall synthesis, and division. Native levels of Wag31 are critical for the maintenance and distribution of membrane lipids. Both depletion and overexpression of Wag31 perturb lipid homeostasis, leading to the formation of intracellular lipid inclusions (ILIs). Protein-lipid crosslinking and imaging studies reveal that purified Wag31 can bind and effectively tether cardiolipin (CL)-containing liposomes. We further show that the tethering activity lies in the DivIVA-domain containing N-terminal of Wag31 while the C-terminal mediates protein-protein interactions of Wag31. Despite retaining its ability to interact with partner proteins, the DivIVA-domain-deleted Wag31 mutant shows defects in liposome tethering in vitro and non-polar localization of CL in vivo, which eventually causes lethality. Our study suggests that membrane tethering 'licenses' Wag31 to form scaffolds that help orchestrate protein-lipid and protein-protein interactions necessary for mycobacterial growth and survival.
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Affiliation(s)
- Yogita Kapoor
- CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB)HyderabadIndia
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadIndia
| | - Himani Khurana
- Indian Institute of Science Education and Research PunePuneIndia
| | - Debatri Dutta
- CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB)HyderabadIndia
| | | | - Anshu Priya
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadIndia
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB)New DelhiIndia
| | - Archana Singh
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadIndia
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB)New DelhiIndia
| | - Siddhesh S Kamat
- Indian Institute of Science Education and Research PunePuneIndia
| | - Neeraj Dhar
- Vaccine and Infectious Disease Organisation, University of SaskatchewanSaskatoonCanada
- Department of Biochemistry, Microbiology and Immunology, University of SaskatchewanSaskatoonCanada
| | | | - Vinay Kumar Nandicoori
- CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB)HyderabadIndia
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadIndia
- National Institute of ImmunologyDelhiIndia
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2
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Palathoti N, Jupudi S, Azam MA. Exploring the Catalytic Nature of Reported Aminoquinazoline-based Hemophilus influenza N-acetylglucosamine-1-phosphate Uridyltransferase Enzyme Inhibitors by Using In-Silico Strategies. Chem Biodivers 2025:e202403428. [PMID: 40192480 DOI: 10.1002/cbdv.202403428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2024] [Revised: 03/29/2025] [Accepted: 03/31/2025] [Indexed: 04/14/2025]
Abstract
Inhibiting cell wall biogenesis has proven to be a fruitful strategy for emerging effective antibacterial agents. The bifunctional enzyme N-acetylglucosamine-1-phosphate uridyltransferase (GlmU) is essential for both Gram-positive and Gram-negative bacteria to produce peptidoglycan. The aminoquinazoline inhibitors, 1-10 that were active against Hemophilus influenza GlmU (HiGlmU), extra-precision docking, molecular mechanics-generalized born surface area (MM-GBSA), molecular dynamic (MD) simulation and thermal MMGBSA in-silico strategies were performed in our current research to explore the catalytic behaviour at the binding site. Reported compounds 1-10 occupied the N-terminal domain of the active pocket and showed hydrophobic and hydrogen bonding interactions. We observe that Coulomb and van der Waals binding free energy components are beneficial for the binding of inhibitors. A 150 ns MD simulation of complex 1/HiGlmU was performed in triplicate with different seed numbers which validated our docking protocols. These investigations interested us in designing new molecules. Based on the above findings, we further designed four novel molecules D1-D4, which exhibited high binding affinity to HiGlmU. A 100 ns MD simulation was executed for the D1/HiGlmU complex to explore the catalytic behaviour. Absorption, distribution, metabolism, excretion, and toxicity screening are also performed to predict the drug-likeness. The findings of the currently mentioned investigation may be used in the design and development of potent inhibitors of HiGlmU.
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Affiliation(s)
- Nagarjuna Palathoti
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty, India
| | - Srikanth Jupudi
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty, India
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3
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Keller MR, Soni V, Brown M, Rosch KM, Saleh A, Rhee K, Doerr T. Sugar phosphate-mediated inhibition of peptidoglycan precursor synthesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.13.623475. [PMID: 39605520 PMCID: PMC11601392 DOI: 10.1101/2024.11.13.623475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
Abstract
Antibiotic tolerance, the widespread ability of diverse pathogenic bacteria to sustain viability in the presence of typically bactericidal antibiotics for extended time periods, is an understudied steppingstone towards antibiotic resistance. The Gram-negative pathogen Vibrio cholerae, the causative agent of cholera, is highly tolerant to β-lactam antibiotics. We previously found that the disruption of glycolysis, via deletion of pgi (vc0374, glucose-6-phosphate isomerase), resulted in significant cell wall damage and increased sensitivity towards β-lactam antibiotics. Here, we uncover the mechanism of this resulting damage. We find that glucose causes growth inhibition, partial lysis, and a damaged cell envelope in Δpgi. Supplementation with N-acetylglucosamine, but not other carbon sources (either from upper glycolysis, TCA cycle intermediates, or cell wall precursors) restored growth, re-established antibiotic resistance towards β-lactams, and recovered cellular morphology of a pgi mutant exposed to glucose. Targeted metabolomics revealed the cell wall precursor synthetase enzyme GlmU (vc2762, coding for the bifunctional enzyme that converts glucosamine-1P to UDP-GlcNAc) as a critical bottleneck and mediator of glucose toxicity in Δpgi. In vitro assays of GlmU revealed that sugar phosphates (primarily glucose-1-phosphate) inhibit the acetyltransferase activity of GlmU (likely competitively), resulting in compromised PG and LPS biosynthesis. These findings identify GlmU as a critical branchpoint enzyme between central metabolism and cell envelope integrity and reveal the molecular mechanism of Δpgi glucose toxicity in Vibrio cholerae.
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Affiliation(s)
- Megan R. Keller
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca NY 14853, USA
| | - Vijay Soni
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY 10021
| | - Megan Brown
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY 10021
| | - Kelly M. Rosch
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca NY 14853, USA
| | - Anas Saleh
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY 10021
| | - Kyu Rhee
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca NY 14853, USA
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY 10021
| | - Tobias Doerr
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Department of Microbiology, Cornell University, Ithaca NY 14853, USA
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca NY 14853, USA
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4
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Agarwal M, Bhaskar A, Singha B, Mukhopadhyay S, Pahuja I, Singh A, Chaturvedi S, Agarwal N, Dwivedi VP, Nandicoori VK. Depletion of essential mycobacterial gene glmM reduces pathogen survival and induces host-protective immune responses against tuberculosis. Commun Biol 2024; 7:949. [PMID: 39107377 PMCID: PMC11303689 DOI: 10.1038/s42003-024-06620-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 07/23/2024] [Indexed: 08/10/2024] Open
Abstract
The limitations of TB treatment are the long duration and immune-dampening effects of anti-tuberculosis therapy. The Cell wall plays a crucial role in survival and virulence; hence, enzymes involved in its biosynthesis are good therapeutic targets. Here, we identify Mycobacterium tuberculosis (Mtb) GlmM, (GlmMMtb) engaged in the UDP-GlcNAc synthesis pathway as an essential enzyme. We generated a conditional knockdown strain, Rv-glmMkD using the CRISPR interference-mediated gene silencing approach. Depletion of GlmMMtb affects the morphology and thickness of the cell wall. The Rv-glmMkD strain attenuated Mtb survival in vitro, in the host macrophages (ex vivo), and in a murine mice infection model (in vivo). Results suggest that the depletion of GlmMMtb induces M1 macrophage polarization, prompting a pro-inflammatory cytokine response, apparent from the upregulation of activation markers, including IFNɣ and IL-17 that resists the growth of Mtb. These observations provide a rationale for exploring GlmMMtb as a potential therapeutic target.
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Affiliation(s)
- Meetu Agarwal
- Signal Transduction Laboratory, National Institute of Immunology, New Delhi, India.
- Department of Molecular Medicine, Jamia Hamdard University, New Delhi, India.
| | - Ashima Bhaskar
- Immunobiology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Biplab Singha
- Signal Transduction Laboratory, National Institute of Immunology, New Delhi, India
| | - Suparba Mukhopadhyay
- Immunobiology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Isha Pahuja
- Immunobiology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Archna Singh
- CSIR - Institute of Genomics and Integrative Biology, Mall Road, Delhi, India
| | - Shivam Chaturvedi
- Immunobiology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Nisheeth Agarwal
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | - Ved Prakash Dwivedi
- Immunobiology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Vinay Kumar Nandicoori
- Signal Transduction Laboratory, National Institute of Immunology, New Delhi, India.
- CSIR-Centre for Cellular and Molecular Biology, Habsiguda, Hyderabad, Telangana, India.
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5
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Angrish N, Lalwani N, Khare G. In silico virtual screening for the identification of novel inhibitors against dihydrodipicolinate reductase (DapB) of Mycobacterium tuberculosis, a key enzyme of diaminopimelate pathway. Microbiol Spectr 2023; 11:e0135923. [PMID: 37855602 PMCID: PMC10714930 DOI: 10.1128/spectrum.01359-23] [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: 03/29/2023] [Accepted: 09/02/2023] [Indexed: 10/20/2023] Open
Abstract
IMPORTANCE Non-compliance to lengthy antituberculosis (TB) treatment regimen, associated side effects, and emergence of drug-resistant strains of Mycobacterium tuberculosis (M. tb) emphasize the need to develop more effective anti-TB drugs. Here, we have evaluated the role of M. tb dihydrodipicolinate reductase (DapB), a component of the diaminopimelate pathway, which is involved in the biosynthesis of both lysine and mycobacterial cell wall. We showed that DapB is essential for the in vitro as well as intracellular growth of M. tb. We further utilized M. tb DapB, as a target for identification of inhibitors by employing in silico virtual screening, and conducted various in vitro screening assays to identify inhibitors with potential to inhibit DapB activity and in vitro and intracellular growth of M. tb with no significant cytotoxicity against various mammalian cell lines. Altogether, M. tb DapB serves as an important drug target and a hit molecule, namely, 4-(3-Phenylazoquinoxalin-2-yl) butanoic acid methyl ester has been identified as an antimycobacterial molecule in our study.
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Affiliation(s)
- Nupur Angrish
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Neha Lalwani
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Garima Khare
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
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6
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Jia J, Zheng M, Zhang C, Li B, Lu C, Bai Y, Tong Q, Hang X, Ge Y, Zeng L, Zhao M, Song F, Zhang H, Zhang L, Hong K, Bi H. Killing of Staphylococcus aureus persisters by a multitarget natural product chrysomycin A. SCIENCE ADVANCES 2023; 9:eadg5995. [PMID: 37540745 PMCID: PMC10403215 DOI: 10.1126/sciadv.adg5995] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 07/05/2023] [Indexed: 08/06/2023]
Abstract
Staphylococcus aureus poses a severe public health problem as one of the vital causative agents of healthcare- and community-acquired infections. There is a globally urgent need for new drugs with a novel mode of action (MoA) to combat S. aureus biofilms and persisters that tolerate antibiotic treatment. We demonstrate that a benzonaphthopyranone glycoside, chrysomycin A (ChryA), is a rapid bactericide that is highly active against S. aureus persisters, robustly eradicates biofilms in vitro, and shows a sustainable killing efficacy in vivo. ChryA was suggested to target multiple critical cellular processes. A wide range of genetic and biochemical approaches showed that ChryA directly binds to GlmU and DapD, involved in the biosynthetic pathways for the cell wall peptidoglycan and lysine precursors, respectively, and inhibits the acetyltransferase activities by competition with their mutual substrate acetyl-CoA. Our study provides an effective antimicrobial strategy combining multiple MoAs onto a single small molecule for treatments of S. aureus persistent infections.
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Affiliation(s)
- Jia Jia
- Department of Pathogen Biology, Jiangsu Key Laboratory of Pathogen Biology, Nanjing Medical University, Nanjing 211166, China
| | - Mingxin Zheng
- Department of Pathogen Biology, Jiangsu Key Laboratory of Pathogen Biology, Nanjing Medical University, Nanjing 211166, China
| | - Chongwen Zhang
- Department of Pathogen Biology, Jiangsu Key Laboratory of Pathogen Biology, Nanjing Medical University, Nanjing 211166, China
| | - Binglei Li
- Department of Pathogen Biology, Jiangsu Key Laboratory of Pathogen Biology, Nanjing Medical University, Nanjing 211166, China
| | - Cai Lu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yuefan Bai
- Department of Pathogen Biology, Jiangsu Key Laboratory of Pathogen Biology, Nanjing Medical University, Nanjing 211166, China
| | - Qian Tong
- Department of Pathogen Biology, Jiangsu Key Laboratory of Pathogen Biology, Nanjing Medical University, Nanjing 211166, China
| | - Xudong Hang
- Department of Pathogen Biology, Jiangsu Key Laboratory of Pathogen Biology, Nanjing Medical University, Nanjing 211166, China
| | - Yixin Ge
- Department of Pathogen Biology, Jiangsu Key Laboratory of Pathogen Biology, Nanjing Medical University, Nanjing 211166, China
| | - Liping Zeng
- Department of Pathogen Biology, Jiangsu Key Laboratory of Pathogen Biology, Nanjing Medical University, Nanjing 211166, China
| | - Ming Zhao
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Fuhang Song
- School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Huawei Zhang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China
| | - Liang Zhang
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Kui Hong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Hongkai Bi
- Department of Pathogen Biology, Jiangsu Key Laboratory of Pathogen Biology, Nanjing Medical University, Nanjing 211166, China
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7
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Soni V, Rosenn EH, Venkataraman R. Insights into the central role of N-acetyl-glucosamine-1-phosphate uridyltransferase (GlmU) in peptidoglycan metabolism and its potential as a therapeutic target. Biochem J 2023; 480:1147-1164. [PMID: 37498748 DOI: 10.1042/bcj20230173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/07/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023]
Abstract
Several decades after the discovery of the first antibiotic (penicillin) microbes have evolved novel mechanisms of resistance; endangering not only our abilities to combat future bacterial pandemics but many other clinical challenges such as acquired infections during surgeries. Antimicrobial resistance (AMR) is attributed to the mismanagement and overuse of these medications and is complicated by a slower rate of the discovery of novel drugs and targets. Bacterial peptidoglycan (PG), a three-dimensional mesh of glycan units, is the foundation of the cell wall that protects bacteria against environmental insults. A significant percentage of drugs target PG, however, these have been rendered ineffective due to growing drug resistance. Identifying novel druggable targets is, therefore, imperative. Uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) is one of the key building blocks in PG production, biosynthesized by the bifunctional enzyme N-acetyl-glucosamine-1-phosphate uridyltransferase (GlmU). UDP-GlcNAc metabolism has been studied in many organisms, but it holds some distinctive features in bacteria, especially regarding the bacterial GlmU enzyme. In this review, we provide an overview of different steps in PG biogenesis, discuss the biochemistry of GlmU, and summarize the characteristic structural elements of bacterial GlmU vital to its catalytic function. Finally, we will discuss various studies on the development of GlmU inhibitors and their significance in aiding future drug discoveries.
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Affiliation(s)
- Vijay Soni
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10065, U.S.A
| | - Eric H Rosenn
- Tel Aviv University School of Medicine, Tel Aviv 6997801, Israel
| | - Ramya Venkataraman
- Laboratory of Innate Immunity, National Institute of Immunology, New Delhi 110067, India
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8
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Ayu Eka Pitaloka D, Izzati A, Rafa Amirah S, Abdan Syakuran L, Muhammad Irham L, Darumas Putri A, Adikusuma W. Bioinformatics Analysis to Uncover the Potential Drug Targets Responsible for Mycobacterium tuberculosis Peptidoglycan and Lysine Biosynthesis. Bioinform Biol Insights 2023; 17:11779322231171774. [PMID: 37187890 PMCID: PMC10176782 DOI: 10.1177/11779322231171774] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 04/07/2023] [Indexed: 05/17/2023] Open
Abstract
Drug-resistant tuberculosis (TB), which results mainly from the selection of naturally resistant strains of Mycobacterium tuberculosis (MTB) due to mismanaged treatment, poses a severe challenge to the global control of TB. Therefore, screening novel and unique drug targets against this pathogen is urgently needed. The metabolic pathways of Homo sapiens and MTB were compared using the Kyoto Encyclopedia of Genes and Genomes tool, and further, the proteins that are involved in the metabolic pathways of MTB were subtracted and proceeded to protein-protein interaction network analysis, subcellular localization, drug ability testing, and gene ontology. The study aims to identify enzymes for the unique pathways for further screening to determine the feasibility of the therapeutic targets. The qualitative characteristics of 28 proteins identified as drug target candidates were studied. The results showed that 12 were cytoplasmic, 2 were extracellular, 12 were transmembrane, and 3 were unknown. Furthermore, druggability analysis revealed 14 druggable proteins, of which 12 were novel and responsible for MTB peptidoglycan and lysine biosynthesis. The novel targets obtained in this study are used to develop antimicrobial treatments against pathogenic bacteria. Future studies should further shed light on the clinical implementation to identify antimicrobial therapies against MTB.
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Affiliation(s)
- Dian Ayu Eka Pitaloka
- Department of Pharmacology and Clinical
Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang, Indonesia
- Center for Translational Biomarker
Research, Universitas Padjadjaran, Sumedang, Indonesia
| | - Afifah Izzati
- Department of Pharmacology and Clinical
Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang, Indonesia
| | - Siti Rafa Amirah
- Department of Pharmacology and Clinical
Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang, Indonesia
| | - Luqman Abdan Syakuran
- Genetics and Molecular Laboratory,
Faculty of Biology, Jenderal Soedirman University, Purwokerto, Indonesia
| | - Lalu Muhammad Irham
- Faculty of Pharmacy, Universitas Ahmad
Dahlan, Yogyakarta, Indonesia
- Research Center for Pharmaceutical
Ingrediensts and Traditional Medicine, National Research and Inovation Agency
(BRIN), South Tangerang, Indonesia
| | | | - Wirawan Adikusuma
- Department of Pharmacy, Faculty of
Health Science, Universitas Muhammadiyah Mataram, Mataram, Indonesia
- Research Center for Vaccine and Drugs,
National Research and Inovation Agency (BRIN), South Tangerang, Indonesia
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9
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Kaur K, Sharma S, Abhishek S, Kaur P, Saini UC, Dhillon MS, Karakousis PC, Verma I. Metabolic switching and cell wall remodelling of Mycobacterium tuberculosis during bone tuberculosis. J Infect 2023; 86:134-146. [PMID: 36549425 DOI: 10.1016/j.jinf.2022.12.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
OBJECTIVES Bone tuberculosis (TB) is the third most common types of extrapulmonary tuberculosis. It is critical to understand mycobacterial adaptive strategies within bone lesions to identify mycobacterial factors that may have role in disease pathogenesis. METHODS Whole genome microarray was used to characterize the in-vivo transcriptome of Mycobacterium tuberculosis (M.tb) within bone TB specimens. Mycobacterial virulent proteins were identified by bioinformatic software. An in vitro osteoblast cell line model was used to study the role of these proteins in bone TB pathogenesis. RESULTS 914 mycobacterial genes were significantly overexpressed and 1688 were repressed in bone TB specimens. Pathway analysis of differentially expressed genes demonstrated a non-replicative and hypometabolic state of M.tb, reinforcement of the mycobacterial cell wall and induction of DNA damage repair responses, suggesting possible survival strategies of M.tb within bone. Bioinformatics mining of microarray data led to identification of five virulence proteins. The genes encoding these proteins were also upregulated in the in vitro MC3T3 osteoblast cell line model of bone TB. Further, exposure of osteoblast cells to two of these virulence proteins (Rv1046c and Rv3663c) significantly inhibited osteoblast differentiation. CONCLUSION M.tb alters its transcriptome to establish infection in bone by upregulating certain virulence genes which play a key role in disturbing bone homeostasis.
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Affiliation(s)
- Khushpreet Kaur
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Sumedha Sharma
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Sudhanshu Abhishek
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Prabhdeep Kaur
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Uttam Chand Saini
- Department of Orthopaedics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Mandeep Singh Dhillon
- Department of Orthopaedics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Petros C Karakousis
- Centers for Tuberculosis Research and Systems Approaches for Infectious Diseases, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Indu Verma
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, India.
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10
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Singha B, Behera D, Khan MZ, Singh NK, Sowpati DT, Gopal B, Nandicoori VK. The unique N-terminal region of Mycobacterium tuberculosis sigma factor A plays a dominant role in the essential function of this protein. J Biol Chem 2023; 299:102933. [PMID: 36690275 PMCID: PMC10011835 DOI: 10.1016/j.jbc.2023.102933] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 01/11/2023] [Accepted: 01/14/2023] [Indexed: 01/22/2023] Open
Abstract
SigA (σA) is an essential protein and the primary sigma factor in Mycobacterium tuberculosis (Mtb). However, due to the absence of genetic tools, our understanding of the role and regulation of σA activity and its molecular attributes that help modulate Mtb survival is scant. Here, we generated a conditional gene replacement of σA in Mtb and showed that its depletion results in a severe survival defect in vitro, ex vivo, and in vivo in a murine infection model. Our RNA-seq analysis suggests that σA either directly or indirectly regulates ∼57% of the Mtb transcriptome, including ∼28% of essential genes. Surprisingly, we note that despite having ∼64% similarity with σA, overexpression of the primary-like σ factor SigB (σB) fails to compensate for the absence of σA, suggesting minimal functional redundancy. RNA-seq analysis of the Mtb σB deletion mutant revealed that 433 genes are regulated by σB, of which 283 overlap with the σA transcriptome. Additionally, surface plasmon resonance, in vitro transcription, and functional complementation experiments reveal that σA residues between 132-179 that are disordered and missing from all experimentally determined σA-RNAP structural models are imperative for σA function. Moreover, phosphorylation of σA in the intrinsically disordered N-terminal region plays a regulatory role in modulating its activity. Collectively, these observations and analysis provide a rationale for the centrality of σA for the survival and pathogenicity of this bacillus.
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Affiliation(s)
- Biplab Singha
- National Institute of Immunology, New Delhi, India; CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Debashree Behera
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | | | | | | | | | - Vinay Kumar Nandicoori
- National Institute of Immunology, New Delhi, India; CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.
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11
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Wyllie JA, McKay MV, Barrow AS, Soares da Costa TP. Biosynthesis of uridine diphosphate N-Acetylglucosamine: An underexploited pathway in the search for novel antibiotics? IUBMB Life 2022; 74:1232-1252. [PMID: 35880704 PMCID: PMC10087520 DOI: 10.1002/iub.2664] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/04/2022] [Indexed: 11/06/2022]
Abstract
Although the prevalence of antibiotic resistance is increasing at an alarming rate, there are a dwindling number of effective antibiotics available. Thus, the development of novel antibacterial agents should be of utmost importance. Peptidoglycan biosynthesis has been and is still an attractive source for antibiotic targets; however, there are several components that remain underexploited. In this review, we examine the enzymes involved in the biosynthesis of one such component, UDP-N-acetylglucosamine, an essential building block and precursor of bacterial peptidoglycan. Furthermore, given the presence of a similar biosynthesis pathway in eukaryotes, we discuss the current knowledge on the differences and similarities between the bacterial and eukaryotic enzymes. Finally, this review also summarises the recent advances made in the development of inhibitors targeting the bacterial enzymes.
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Affiliation(s)
- Jessica A Wyllie
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Mirrin V McKay
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Andrew S Barrow
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Tatiana P Soares da Costa
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, South Australia, Australia
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12
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Gupta S, Mishra DK, Khan MZ, Saini V, Mehta D, Kumar S, Yadav A, Mitra M, Rani P, Singh M, Nandi CK, Das P, Ahuja V, Nandicoori VK, Bajaj A. Development of a Highly Specific, Selective, and Sensitive Fluorescent Probe for Detection of Mycobacteria in Human Tissues. Adv Healthc Mater 2022; 11:e2102640. [PMID: 35038229 DOI: 10.1002/adhm.202102640] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/07/2022] [Indexed: 11/08/2022]
Abstract
Tuberculosis (TB), including extrapulmonary TB, is responsible for more than one million deaths in a year worldwide. Existing methods of mycobacteria detection have poor sensitivity, selectivity, and specificity, especially in human tissues. Herein, the synthesis of a cholic acid-derived fluorescent probe (P4) that can specifically stain the mycobacterium species is presented. It is shown that P4 probe specifically binds with mycobacterial lipids, trehalose monomycolate, and phosphatidylinositol mannoside 6. P4 probe can detect mycobacteria in polymicrobial planktonic cultures and biofilms with high specificity, selectivity, and sensitivity. Moreover, it can detect a single mycobacterium in the presence of 10 000 other bacilli. Unlike the probes that depend on active mycobacterial enzymes, the membrane-specific P4 probe can detect mycobacteria even in formalin-fixed paraffin-embedded mice and human tissue sections. Therefore, the ability of the P4 probe to detect mycobacteria in different biological milieu makes it a potential candidate for diagnostic and prognostic applications in clinical settings.
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Affiliation(s)
- Siddhi Gupta
- Laboratory of Nanotechnology and Chemical Biology Regional Centre for Biotechnology NCR Biotech Science Cluster 3rd Milestone, Faridabad‐Gurgaon Expressway Faridabad Haryana 121001 India
| | - Deepak Kumar Mishra
- Laboratory of Nanotechnology and Chemical Biology Regional Centre for Biotechnology NCR Biotech Science Cluster 3rd Milestone, Faridabad‐Gurgaon Expressway Faridabad Haryana 121001 India
| | - Mehak Zahoor Khan
- National Institute of Immunology Aruna Asaf Ali Marg New Delhi 110067 India
| | - Varsha Saini
- Laboratory of Nanotechnology and Chemical Biology Regional Centre for Biotechnology NCR Biotech Science Cluster 3rd Milestone, Faridabad‐Gurgaon Expressway Faridabad Haryana 121001 India
| | - Devashish Mehta
- Laboratory of Nanotechnology and Chemical Biology Regional Centre for Biotechnology NCR Biotech Science Cluster 3rd Milestone, Faridabad‐Gurgaon Expressway Faridabad Haryana 121001 India
| | - Sandeep Kumar
- Laboratory of Nanotechnology and Chemical Biology Regional Centre for Biotechnology NCR Biotech Science Cluster 3rd Milestone, Faridabad‐Gurgaon Expressway Faridabad Haryana 121001 India
| | - Aditya Yadav
- School of Basic Sciences Indian Institute of Technology Mandi Mandi HP 175005 India
| | - Madhurima Mitra
- Laboratory of Nanotechnology and Chemical Biology Regional Centre for Biotechnology NCR Biotech Science Cluster 3rd Milestone, Faridabad‐Gurgaon Expressway Faridabad Haryana 121001 India
| | - Parul Rani
- Laboratory of Nanotechnology and Chemical Biology Regional Centre for Biotechnology NCR Biotech Science Cluster 3rd Milestone, Faridabad‐Gurgaon Expressway Faridabad Haryana 121001 India
| | - Mukesh Singh
- Department of Gastroenterology All India Institute of Medical Sciences New Delhi 110029 India
| | - Chayan Kanti Nandi
- School of Basic Sciences Indian Institute of Technology Mandi Mandi HP 175005 India
| | - Prasenjit Das
- Department of Pathology All India Institute of Medical Sciences New Delhi 110029 India
| | - Vineet Ahuja
- Department of Gastroenterology All India Institute of Medical Sciences New Delhi 110029 India
| | | | - Avinash Bajaj
- Laboratory of Nanotechnology and Chemical Biology Regional Centre for Biotechnology NCR Biotech Science Cluster 3rd Milestone, Faridabad‐Gurgaon Expressway Faridabad Haryana 121001 India
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13
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Identification of Mtb GlmU Uridyltransferase Domain Inhibitors by Ligand-Based and Structure-Based Drug Design Approaches. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092805. [PMID: 35566155 PMCID: PMC9105790 DOI: 10.3390/molecules27092805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/04/2022] [Accepted: 04/07/2022] [Indexed: 01/09/2023]
Abstract
Targeting enzymes that play a role in the biosynthesis of the bacterial cell wall has long been a strategy for antibacterial discovery. In particular, the cell wall of Mycobacterium tuberculosis (Mtb) is a complex of three layers, one of which is Peptidoglycan, an essential component providing rigidity and strength. UDP-GlcNAc, a precursor for the synthesis of peptidoglycan, is formed by GlmU, a bi-functional enzyme. Inhibiting GlmU Uridyltransferase activity has been proven to be an effective anti-bacterial, but its similarity with human enzymes has been a deterrent to drug development. To develop Mtb selective hits, the Mtb GlmU substrate binding pocket was compared with structurally similar human enzymes to identify selectivity determining factors. Substrate binding pockets and conformational changes upon substrate binding were analyzed and MD simulations with substrates were performed to quantify crucial interactions to develop critical pharmacophore features. Thereafter, two strategies were applied to propose potent and selective bacterial GlmU Uridyltransferase domain inhibitors: (i) optimization of existing inhibitors, and (ii) identification by virtual screening. The binding modes of hits identified from virtual screening and ligand growing approaches were evaluated further for their ability to retain stable contacts within the pocket during 20 ns MD simulations. Hits that are predicted to be more potent than existing inhibitors and selective against human homologues could be of great interest for rejuvenating drug discovery efforts towards targeting the Mtb cell wall for antibacterial discovery.
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14
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Mycobacterium tuberculosis Transcription Factor EmbR Regulates the Expression of Key Virulence Factors That Aid in Ex Vivo and In Vivo Survival. mBio 2022; 13:e0383621. [PMID: 35471080 PMCID: PMC9239209 DOI: 10.1128/mbio.03836-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis encodes ~200 transcription factors that modulate gene expression under different microenvironments in the host. Even though high-throughput chromatin immunoprecipitation sequencing and transcriptome sequencing (RNA-seq) studies have identified the regulatory network for ~80% of transcription factors, many transcription factors remain uncharacterized. EmbR is one such transcription factor whose in vivo regulon and biological function are yet to be elucidated. Previous in vitro studies suggested that phosphorylation of EmbR by PknH upregulates the embCAB operon. Using a gene replacement mutant of embR, we investigated its role in modulating cellular morphology, antibiotic resistance, and survival in the host. Contrary to the prevailing hypothesis, under normal growth conditions, EmbR is neither phosphorylated nor impacted by ethambutol resistance through the regulation of the embCAB operon. The embR deletion mutant displayed attenuated M. tuberculosis survival in vivo. RNA-seq analysis suggested that EmbR regulates operons involved in the secretion pathway, lipid metabolism, virulence, and hypoxia, including well-known hypoxia-inducible genes devS and hspX. Lipidome analysis revealed that EmbR modulates levels of all lysophospholipids, several phospholipids, and M. tuberculosis-specific lipids, which is more pronounced under hypoxic conditions. We found that the EmbR mutant is hypersusceptible to hypoxic stress, and RNA sequencing performed under hypoxic conditions indicated that EmbR majorly regulates genes involved in response to acidic pH, hypoxia, and fatty acid metabolism. We observed condition-specific phosphorylation of EmbR, which contributes to EmbR-mediated transcription of several essential genes, ensuring enhanced survival. Collectively, the study establishes EmbR as a key modulator of hypoxic response that facilitates mycobacterial survival in the host.
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15
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Mi J, Gong W, Wu X. Advances in Key Drug Target Identification and New Drug Development for Tuberculosis. BIOMED RESEARCH INTERNATIONAL 2022; 2022:5099312. [PMID: 35252448 PMCID: PMC8896939 DOI: 10.1155/2022/5099312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 02/14/2022] [Indexed: 12/15/2022]
Abstract
Tuberculosis (TB) is a severe infectious disease worldwide. The increasing emergence of drug-resistant Mycobacterium tuberculosis (Mtb) has markedly hampered TB control. Therefore, there is an urgent need to develop new anti-TB drugs to treat drug-resistant TB and shorten the standard therapy. The discovery of targets of drug action will lay a theoretical foundation for new drug development. With the development of molecular biology and the success of Mtb genome sequencing, great progress has been made in the discovery of new targets and their relevant inhibitors. In this review, we summarized 45 important drug targets and 15 new drugs that are currently being tested in clinical stages and several prospective molecules that are still at the level of preclinical studies. A comprehensive understanding of the drug targets of Mtb can provide extensive insights into the development of safer and more efficient drugs and may contribute new ideas for TB control and treatment.
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Affiliation(s)
- Jie Mi
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing 100091, China
| | - Wenping Gong
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing 100091, China
| | - Xueqiong Wu
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing 100091, China
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16
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N-Acetylglucosamine Sensing and Metabolic Engineering for Attenuating Human and Plant Pathogens. Bioengineering (Basel) 2022; 9:bioengineering9020064. [PMID: 35200417 PMCID: PMC8869657 DOI: 10.3390/bioengineering9020064] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/22/2022] [Accepted: 02/03/2022] [Indexed: 11/17/2022] Open
Abstract
During evolution, both human and plant pathogens have evolved to utilize a diverse range of carbon sources. N-acetylglucosamine (GlcNAc), an amino sugar, is one of the major carbon sources utilized by several human and phytopathogens. GlcNAc regulates the expression of many virulence genes of pathogens. In fact, GlcNAc catabolism is also involved in the regulation of virulence and pathogenesis of various human pathogens, including Candida albicans, Vibrio cholerae, Leishmania donovani, Mycobacterium, and phytopathogens such as Magnaporthe oryzae. Moreover, GlcNAc is also a well-known structural component of many bacterial and fungal pathogen cell walls, suggesting its possible role in cell signaling. Over the last few decades, many studies have been performed to study GlcNAc sensing, signaling, and metabolism to better understand the GlcNAc roles in pathogenesis in order to identify new drug targets. In this review, we provide recent insights into GlcNAc-mediated cell signaling and pathogenesis. Further, we describe how the GlcNAc metabolic pathway can be targeted to reduce the pathogens’ virulence in order to control the disease prevalence and crop productivity.
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17
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Han X, Chen C, Wang H, Kang J, Yan Q, Ma Y, Wang W, Wu S, Wang C, Ma X. GlmU inhibitor from the roots of Euphorbia ebracteolata as an anti-tuberculosis agent. RSC Adv 2022; 12:18266-18273. [PMID: 35800323 PMCID: PMC9214920 DOI: 10.1039/d2ra02044k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/16/2022] [Indexed: 11/21/2022] Open
Abstract
Ebractenoid F was identified to be a GlmU inhibitor from Euphorbia ebracteolata, which could inhibit the cell wall biosynthesis of M. tb H37Ra, along with the biofilm formation.
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Affiliation(s)
- Xiuyan Han
- Second Affiliated Hospital, Institute of Integrative Medicine, Dalian Medical University, Dalian 116023, P.R. of China
- College of Pharmacy, Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, P.R. of China
| | - Changming Chen
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang 550001, P.R. of China
| | - Honglei Wang
- College of Pharmacy, Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, P.R. of China
| | - Jian Kang
- College of Pharmacy, Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, P.R. of China
| | - Qiulong Yan
- College of Pharmacy, Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, P.R. of China
| | - Yufang Ma
- College of Pharmacy, Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, P.R. of China
| | - Wenxin Wang
- College of Pharmacy, Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, P.R. of China
| | - Shan Wu
- College of Pharmacy, Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, P.R. of China
| | - Chao Wang
- Second Affiliated Hospital, Institute of Integrative Medicine, Dalian Medical University, Dalian 116023, P.R. of China
- College of Pharmacy, Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, P.R. of China
| | - Xiaochi Ma
- Second Affiliated Hospital, Institute of Integrative Medicine, Dalian Medical University, Dalian 116023, P.R. of China
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18
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Zheng M, Zheng M, Epstein S, Harnagel AP, Kim H, Lupoli TJ. Chemical Biology Tools for Modulating and Visualizing Gram-Negative Bacterial Surface Polysaccharides. ACS Chem Biol 2021; 16:1841-1865. [PMID: 34569792 DOI: 10.1021/acschembio.1c00341] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Bacterial cells present a wide diversity of saccharides that decorate the cell surface and help mediate interactions with the environment. Many Gram-negative cells express O-antigens, which are long sugar polymers that makeup the distal portion of lipopolysaccharide (LPS) that constitutes the surface of the outer membrane. This review highlights chemical biology tools that have been developed in recent years to facilitate the modulation of O-antigen synthesis and composition, as well as related bacterial polysaccharide pathways, and the detection of unique glycan sequences. Advances in the biochemistry and structural biology of O-antigen biosynthetic machinery are also described, which provide guidance for the design of novel chemical and biomolecular probes. Many of the tools noted here have not yet been utilized in biological systems and offer researchers the opportunity to investigate the complex sugar architecture of Gram-negative cells.
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Affiliation(s)
- Meng Zheng
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Maggie Zheng
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Samuel Epstein
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Alexa P. Harnagel
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Hanee Kim
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Tania J. Lupoli
- Department of Chemistry, New York University, New York, 10003 New York, United States
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19
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Pal S, Soni V, Kumar S, Jha SK, Medatwal N, Rana K, Yadav P, Mehta D, Jain D, Sharma P, Kar R, Srivastava A, Patil VS, Dasgupta U, Nandicoori VK, Bajaj A. A hydrogel-based implantable multidrug antitubercular formulation outperforms oral delivery. NANOSCALE 2021; 13:13225-13230. [PMID: 34477730 DOI: 10.1039/d0nr08806d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We present a non-immunogenic, injectable, low molecular weight, amphiphilic hydrogel-based drug delivery system (TB-Gel) that can entrap a cocktail of four front-line antitubercular drugs, isoniazid, rifampicin, pyrazinamide, and ethambutol. We showed that TB-Gel is more effective than oral delivery of the combination of four drugs in reducing the mycobacterial infection in mice. Results show that half the dose of chemotherapeutic drugs is sufficient to achieve a comparable therapeutic effect to that of oral delivery.
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Affiliation(s)
- Sanjay Pal
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad-121001, Haryana, India.
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20
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Unique C-terminal extension and interactome of Mycobacterium tuberculosis GlmU impacts it's in vivo function and the survival of pathogen. Biochem J 2021; 478:2081-2099. [PMID: 33955473 DOI: 10.1042/bcj20210170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/01/2021] [Accepted: 05/06/2021] [Indexed: 11/17/2022]
Abstract
N-acetyl glucosamine-1-phosphate uridyltransferase (GlmU) is a bifunctional enzyme involved in the biosynthesis of Uridine diphosphate N-acetylglucosamine (UDP-GlcNAc). UDP-GlcNAc is a critical precursor for the synthesis of peptidoglycan and other cell wall components. The absence of a homolog in eukaryotes makes GlmU an attractive target for therapeutic intervention. Mycobacterium tuberculosis GlmU (GlmUMt) has features, such as a C-terminal extension, that are not present in GlmUorthologs from other bacteria. Here, we set out to determine the uniqueness of GlmUMt by performing in vivo complementation experiments using RvΔglmU mutant. We find that any deletion of the carboxy-terminal extension region of GlmUMt abolishes its ability to complement the function of GlmUMt. Results show orthologs of GlmU, including its closest ortholog, from Mycobacterium smegmatis, cannot complement the function of GlmUMt. Furthermore, the co-expression of GlmUMt domain deletion mutants with either acetyl or uridyltransferase activities failed to rescue the function. However, co-expression of GlmUMt point mutants with either acetyl or uridyltransferase activities successfully restored the biological function of GlmUMt, likely due to the formation of heterotrimers. Based on the interactome experiments, we speculate that GlmUMt participates in unique interactions essential for its in vivo function.
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21
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Dubey N, Khan MZ, Kumar S, Sharma A, Das L, Bhaduri A, Singh Y, Nandicoori VK. Mycobacterium tuberculosis PPiA interacts with host integrin receptor to exacerbate disease progression. J Infect Dis 2021; 224:1383-1393. [PMID: 33580239 DOI: 10.1093/infdis/jiab081] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 02/05/2021] [Indexed: 11/14/2022] Open
Abstract
Attenuated intracellular survival of Mycobacterium tuberculosis (Mtb) secretory gene mutants exemplifies their role as virulence factors. Mtb peptidyl prolyl isomerase A (PPiA) assists in protein folding through cis/trans isomerization of prolyl bonds. Here, we show that PPiA abets Mtb survival and aids in the disease progression by exploiting host-associated factors. While the deletion of PPiA has no discernable effect on the bacillary survival in a murine infection model, it compromises the formation of granuloma-like lesions and promotes host cell death through ferroptosis. Overexpression of PPiA enhances the bacillary load and exacerbates pathology in mice lungs. Importantly, PPiA interacts with the integrin α5β1 receptor through a conserved surface-exposed RGD motif. The secretion of PPiA as well as interaction with integrin contributes to the disease progression by upregulating multiple host matrix metalloproteinases. Collectively, we identified a novel non-chaperone role of PPiA that is critical in facilitating host-pathogen interaction ensuing disease progression.
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Affiliation(s)
- Neha Dubey
- Department of Zoology, University of Delhi, Mall Road, Delhi, India.,Current Department of Molecular Microbiology, WUSTL, St. Louis, USA
| | - Mehak Zahoor Khan
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
| | - Suresh Kumar
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
| | - Aditya Sharma
- Department of Zoology, University of Delhi, Mall Road, Delhi, India.,Current Department of Pharmacological and Pharmaceutical Sciences, University of Houston, College of Pharmacy, Texas, USA
| | - Lahari Das
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, India.,Current Department of Pharmacological and Pharmaceutical Sciences, University of Houston, College of Pharmacy, Texas, USA
| | - Asani Bhaduri
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, India.,Current Cluster Innovation Center, University of Delhi, Mall Road, Delhi, India
| | - Yogendra Singh
- Department of Zoology, University of Delhi, Mall Road, Delhi, India
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22
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Comprehensive analysis of protein acetyltransferases of human pathogen Mycobacterium tuberculosis. Biosci Rep 2020; 39:221456. [PMID: 31820790 PMCID: PMC6923341 DOI: 10.1042/bsr20191661] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 11/20/2019] [Accepted: 11/26/2019] [Indexed: 12/12/2022] Open
Abstract
Tuberculosis (TB), a leading infectious disease caused by Mycobacterium tuberculosis strain, takes four human lives every minute globally. Paucity of knowledge on M. tuberculosis virulence and antibiotic resistance is the major challenge for tuberculosis control. We have identified 47 acetyltransferases in the M. tuberculosis, which use diverse substrates including antibiotic, amino acids, and other chemical molecules. Through comparative analysis of the protein file of the virulent M. tuberculosis H37Rv strain and the avirulent M. tuberculosis H37Ra strain, we identified one acetyltransferase that shows significant variations with N-terminal deletion, possibly influencing its physicochemical properties. We also found that one acetyltransferase has three types of post-translation modifications (lysine acetylation, succinylation, and glutarylation). The genome context analysis showed that many acetyltransferases with their neighboring genes belong to one operon. By data mining from published transcriptional profiles of M. tuberculosis exposed to diverse treatments, we revealed that several acetyltransferases may be functional during M. tuberculosis infection. Insights obtained from the present study can potentially provide clues for developing novel TB therapeutic interventions.
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23
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Maitra A, Munshi T, Healy J, Martin LT, Vollmer W, Keep NH, Bhakta S. Cell wall peptidoglycan in Mycobacterium tuberculosis: An Achilles' heel for the TB-causing pathogen. FEMS Microbiol Rev 2020; 43:548-575. [PMID: 31183501 PMCID: PMC6736417 DOI: 10.1093/femsre/fuz016] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 06/07/2019] [Indexed: 02/06/2023] Open
Abstract
Tuberculosis (TB), caused by the intracellular pathogen Mycobacterium tuberculosis, remains one of the leading causes of mortality across the world. There is an urgent requirement to build a robust arsenal of effective antimicrobials, targeting novel molecular mechanisms to overcome the challenges posed by the increase of antibiotic resistance in TB. Mycobacterium tuberculosis has a unique cell envelope structure and composition, containing a peptidoglycan layer that is essential for maintaining cellular integrity and for virulence. The enzymes involved in the biosynthesis, degradation, remodelling and recycling of peptidoglycan have resurfaced as attractive targets for anti-infective drug discovery. Here, we review the importance of peptidoglycan, including the structure, function and regulation of key enzymes involved in its metabolism. We also discuss known inhibitors of ATP-dependent Mur ligases, and discuss the potential for the development of pan-enzyme inhibitors targeting multiple Mur ligases.
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Affiliation(s)
- Arundhati Maitra
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Tulika Munshi
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Jess Healy
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Liam T Martin
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Waldemar Vollmer
- The Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Nicholas H Keep
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Sanjib Bhakta
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
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24
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Chen C, Han X, Yan Q, Wang C, Jia L, Taj A, Zhao L, Ma Y. The Inhibitory Effect of GlmU Acetyltransferase Inhibitor TPSA on Mycobacterium tuberculosis May Be Affected Due to Its Methylation by Methyltransferase Rv0560c. Front Cell Infect Microbiol 2019; 9:251. [PMID: 31380295 PMCID: PMC6652808 DOI: 10.3389/fcimb.2019.00251] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 06/27/2019] [Indexed: 01/01/2023] Open
Abstract
Mycobacterium tuberculosis bifunctional enzyme GlmU is a novel target for anti-TB drugs and is involved in glycosyl donor UDP-N-acetylglucosamine biosynthesis. Here, we found that TPSA (2-[5-(2-{[4-(2-thienyl)-2-pyrimidinyl]sulfanyl}acetyl)-2-thienyl]acetic acid) was a novel inhibitor for GlmU acetyltransferase activity (IC50: 5.3 μM). The interaction sites of GlmU and TPSA by molecular docking were confirmed by site-directed mutagenesis. TPSA showed an inhibitory effect on Mtb H37Ra growth and intracellular H37Ra in macrophage cells (MIC: 66.5 μM). To investigate why TPSA at a higher concentration (66.5 μM) was able to inhibit H37Ra growth, proteome and transcriptome of H37Ra treated with TPSA were analyzed. The expression of two methyltransferases MRA_0565 (Rv0558) and MRA_0567 (Rv0560c) were markedly increased. TPSA was pre-incubated with purified Rv0558 and Rv0560c in the presence of S-adenosylmethionine (methyl donor) respectively, resulting in its decreased inhibitory effect of GlmU on acetyltransferase activity. The inhibition of TPSA on growth of H37Ra with overexpressed Rv0558 and Rv0560c was reduced. These implied that methyltransferases could modify TPSA. The methylation of TPSA catalyzed by Rv0560c was subsequently confirmed by LC-MS. Therefore, TPSA as a GlmU acetyltransferase activity inhibitor may offer a structural basis for new anti-tuberculosis drugs. TPSA needs to be modified further by some groups to prevent its methylation by methyltransferases.
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Affiliation(s)
- Changming Chen
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Xiuyan Han
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Qiulong Yan
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Chao Wang
- College of Pharmacy, Dalian Medical University, Dalian, China
| | - Liqiu Jia
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Ayaz Taj
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Lizhe Zhao
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Yufang Ma
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China.,Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
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25
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Di Somma A, Caterino M, Soni V, Agarwal M, di Pasquale P, Zanetti S, Molicotti P, Cannas S, Nandicoori VK, Duilio A. The bifunctional protein GlmU is a key factor in biofilm formation induced by alkylating stress in Mycobacterium smegmatis. Res Microbiol 2019; 170:171-181. [DOI: 10.1016/j.resmic.2019.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/21/2019] [Accepted: 03/21/2019] [Indexed: 10/27/2022]
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26
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Yadav K, Yavvari PS, Pal S, Kumar S, Mishra D, Gupta S, Mitra M, Soni V, Khare N, Sharma P, Srikanth CV, Kapil A, Singh A, Nandicoori VK, Bajaj A. Oral Delivery of Cholic Acid-Derived Amphiphile Helps in Combating Salmonella-Mediated Gut Infection and Inflammation. Bioconjug Chem 2019; 30:721-732. [DOI: 10.1021/acs.bioconjchem.8b00880] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Kavita Yadav
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Third Milestone, Faridabad-Gurgaon
Expressway, Faridabad-121001, Haryana, India
- Manipal Academy of Higher Education, Manipal-576104, Karnataka, India
| | - Prabhu Srinivas Yavvari
- Department of Chemistry, Indian Institute of Science Education and Research, Bhopal-462026, Madhya Pradesh, India
| | - Sanjay Pal
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Third Milestone, Faridabad-Gurgaon
Expressway, Faridabad-121001, Haryana, India
- Kalinga Institute of Industrial Technology, Bhubaneswar-751024, Odisha India,
| | - Sandeep Kumar
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Third Milestone, Faridabad-Gurgaon
Expressway, Faridabad-121001, Haryana, India
- Manipal Academy of Higher Education, Manipal-576104, Karnataka, India
| | - Deepakkumar Mishra
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Third Milestone, Faridabad-Gurgaon
Expressway, Faridabad-121001, Haryana, India
| | - Siddhi Gupta
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Third Milestone, Faridabad-Gurgaon
Expressway, Faridabad-121001, Haryana, India
| | - Madhurima Mitra
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Third Milestone, Faridabad-Gurgaon
Expressway, Faridabad-121001, Haryana, India
| | - Vijay Soni
- National Institute of Immunology, Aruna Asaf Ali
Marg, New Delhi-110067, India
| | - Neha Khare
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Third Milestone, Faridabad-Gurgaon
Expressway, Faridabad-121001, Haryana, India
| | - Priyanka Sharma
- Department of Microbiology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi-110029, India
| | - Chittur V. Srikanth
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Third Milestone, Faridabad-Gurgaon
Expressway, Faridabad-121001, Haryana, India
| | - Arti Kapil
- Department of Microbiology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi-110029, India
| | - Archana Singh
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi-110025, India
| | | | - Avinash Bajaj
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Third Milestone, Faridabad-Gurgaon
Expressway, Faridabad-121001, Haryana, India
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Jain P, Malakar B, Khan MZ, Lochab S, Singh A, Nandicoori VK. Delineating FtsQ-mediated regulation of cell division in Mycobacterium tuberculosis. J Biol Chem 2018; 293:12331-12349. [PMID: 29903917 DOI: 10.1074/jbc.ra118.003628] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 05/31/2018] [Indexed: 11/06/2022] Open
Abstract
Identifying and characterizing the individual contributors to bacterial cellular elongation and division will improve our understanding of their impact on cell growth and division. Here, we delineated the role of ftsQ, a terminal gene of the highly conserved division cell wall (dcw) operon, in growth, survival, and cell length maintenance in the human pathogen Mycobacterium tuberculosis (Mtb). We found that FtsQ overexpression significantly increases the cell length and number of multiseptate cells. FtsQ depletion in Mtb resulted in cells that were shorter than WT cells during the initial growth stages (4 days after FtsQ depletion) but were longer than WT cells at later stages (10 days after FtsQ depletion) and compromised the survival in vitro and in differentiated THP1 macrophages. Overexpression of N- and C-terminal FtsQ regions altered the cell length, and the C-terminal domain alone complemented the FtsQ depletion phenotype. MS analyses suggested robust FtsQ phosphorylation on Thr-24, and although phosphoablative and -mimetic mutants rescued the FtsQ depletion-associated cell viability defects, they failed to complement the cell length defects. MS and coimmunoprecipitation experiments identified 63 FtsQ-interacting partners, and we show that the interaction of FtsQ with the recently identified cell division protein SepIVA is independent of FtsQ phosphorylation and suggests a role of FtsQ in modulating cell division. FtsQ exhibited predominantly septal localization in both the presence and absence of SepIVA. Our results suggest a role for FtsQ in modulating the length, division, and survival of Mtb cells both in vitro and in the host.
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Affiliation(s)
- Preeti Jain
- From the National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067 and
| | - Basanti Malakar
- From the National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067 and
| | - Mehak Zahoor Khan
- From the National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067 and
| | - Savita Lochab
- From the National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067 and
| | - Archana Singh
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, New Delhi 110025, India
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28
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Craggs PD, Mouilleron S, Rejzek M, de Chiara C, Young RJ, Field RA, Argyrou A, de Carvalho LPS. The Mechanism of Acetyl Transfer Catalyzed by Mycobacterium tuberculosis GlmU. Biochemistry 2018; 57:3387-3401. [PMID: 29684272 PMCID: PMC6011181 DOI: 10.1021/acs.biochem.8b00121] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The biosynthetic pathway of peptidoglycan is essential for Mycobacterium tuberculosis. We report here the acetyltransferase substrate specificity and catalytic mechanism of the bifunctional N-acetyltransferase/uridylyltransferase from M. tuberculosis (GlmU). This enzyme is responsible for the final two steps of the synthesis of UDP- N-acetylglucosamine, which is an essential precursor of peptidoglycan, from glucosamine 1-phosphate, acetyl-coenzyme A, and uridine 5'-triphosphate. GlmU utilizes ternary complex formation to transfer an acetyl from acetyl-coenzyme A to glucosamine 1-phosphate to form N-acetylglucosamine 1-phosphate. Steady-state kinetic studies and equilibrium binding experiments indicate that GlmU follows a steady-state ordered kinetic mechanism, with acetyl-coenzyme A binding first, which triggers a conformational change in GlmU, followed by glucosamine 1-phosphate binding. Coenzyme A is the last product to dissociate. Chemistry is partially rate-limiting as indicated by pH-rate studies and solvent kinetic isotope effects. A novel crystal structure of a mimic of the Michaelis complex, with glucose 1-phosphate and acetyl-coenzyme A, helps us to propose the residues involved in deprotonation of glucosamine 1-phosphate and the loop movement that likely generates the active site required for glucosamine 1-phosphate to bind. Together, these results pave the way for the rational discovery of improved inhibitors against M. tuberculosis GlmU, some of which might become candidates for antibiotic discovery programs.
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Affiliation(s)
- Peter D Craggs
- Platform Technology and Science , GlaxoSmithKline , Stevenage , U.K
| | | | | | | | - Robert J Young
- Platform Technology and Science , GlaxoSmithKline , Stevenage , U.K
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29
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Arora D, Chawla Y, Malakar B, Singh A, Nandicoori VK. The transpeptidase PbpA and noncanonical transglycosylase RodA of Mycobacterium tuberculosis play important roles in regulating bacterial cell lengths. J Biol Chem 2018. [PMID: 29530985 DOI: 10.1074/jbc.m117.811190] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The cell wall of Mycobacterium tuberculosis (Mtb) is a complex structure that protects the pathogen in hostile environments. Peptidoglycan (PG), which helps determine the morphology of the cell envelope, undergoes substantial remodeling under stress. This meshwork of linear chains of sugars, cross-linked through attached peptides, is generated through the sequential action of enzymes termed transglycosylases and transpeptidases. The Mtb genome encodes two classical transglycosylases and four transpeptidases, the functions of which are not fully elucidated. Here, we present work on the yet uncharacterized transpeptidase PbpA and a nonclassical transglycosylase RodA. We elucidate their roles in regulating in vitro growth and in vivo survival of pathogenic mycobacteria. We find that RodA and PbpA are required for regulating cell length, but do not affect mycobacterial growth. Biochemical analyses show PbpA to be a classical transpeptidase, whereas RodA is identified to be a member of an emerging class of noncanonical transglycosylases. Phosphorylation of RodA at Thr-463 modulates its biological function. In a guinea pig infection model, RodA and PbpA are found to be required for both bacterial survival and formation of granuloma structures, thus underscoring the importance of these proteins in mediating mycobacterial virulence in the host. Our results emphasize the fact that whereas redundant enzymes probably compensate for the absence of RodA or PbpA during in vitro growth, the two proteins play critical roles for the survival of the pathogen inside its host.
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Affiliation(s)
- Divya Arora
- From the National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067 India and
| | - Yogesh Chawla
- From the National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067 India and
| | - Basanti Malakar
- From the National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067 India and
| | - Archana Singh
- CSIR-Institute of Genomics and Integrative Biology, 110025 New Delhi, India
| | - Vinay Kumar Nandicoori
- From the National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067 India and
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30
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Khan MZ, Bhaskar A, Upadhyay S, Kumari P, Rajmani RS, Jain P, Singh A, Kumar D, Bhavesh NS, Nandicoori VK. Protein kinase G confers survival advantage to Mycobacterium tuberculosis during latency-like conditions. J Biol Chem 2017; 292:16093-16108. [PMID: 28821621 DOI: 10.1074/jbc.m117.797563] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 08/16/2017] [Indexed: 11/06/2022] Open
Abstract
Protein kinase G (PknG), a thioredoxin-fold-containing eukaryotic-like serine/threonine protein kinase, is a virulence factor in Mycobacterium tuberculosis, required for inhibition of phagolysosomal fusion. Here, we unraveled novel functional facets of PknG during latency-like conditions. We found that PknG mediates persistence under stressful conditions like hypoxia and abets drug tolerance. PknG mutant displayed minimal growth in nutrient-limited conditions, suggesting its role in modulating cellular metabolism. Intracellular metabolic profiling revealed that PknG is necessary for efficient metabolic adaptation during hypoxia. Notably, the PknG mutant exhibited a reductive shift in mycothiol redox potential and compromised stress response. Exposure to antibiotics and hypoxic environment resulted in higher oxidative shift in mycothiol redox potential of PknG mutant compared with the wild type. Persistence during latency-like conditions required kinase activity and thioredoxin motifs of PknG and is mediated through phosphorylation of a central metabolic regulator GarA. Finally, using a guinea pig model of infection, we assessed the in vivo role of PknG in manifestation of disease pathology and established a role for PknG in the formation of stable granuloma, hallmark structures of latent tuberculosis. Taken together, PknG-mediated GarA phosphorylation is important for maintenance of both mycobacterial physiology and redox poise, an axis that is dispensable for survival under normoxic conditions but is critical for non-replicating persistence of mycobacteria. In conclusion, we propose that PknG probably acts as a modulator of latency-associated signals.
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Affiliation(s)
| | | | | | - Pooja Kumari
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067 and
| | - Raju S Rajmani
- the Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Preeti Jain
- From the National Institute of Immunology and
| | - Amit Singh
- the Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Dhiraj Kumar
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067 and
| | - Neel Sarovar Bhavesh
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067 and
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31
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Sengupta S, Naz S, Das I, Ahad A, Padhi A, Naik SK, Ganguli G, Pattanaik KP, Raghav SK, Nandicoori VK, Sonawane A. Mycobacterium tuberculosis EsxL inhibits MHC-II expression by promoting hypermethylation in class-II transactivator loci in macrophages. J Biol Chem 2017; 292:6855-6868. [PMID: 28209712 DOI: 10.1074/jbc.m117.775205] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 02/13/2017] [Indexed: 12/13/2022] Open
Abstract
Mycobacterium tuberculosis is known to modulate the host immune responses to facilitate its persistence inside the host cells. One of the key mechanisms includes repression of class-II transactivator (CIITA) and MHC-II expression in infected macrophages. However, the precise mechanism of CIITA and MHC-II down-regulation is not well studied. M. tuberculosis 6-kDa early secretory antigenic target (ESAT-6) is a known potent virulence and antigenic determinant. The M. tuberculosis genome encodes 23 such ESAT-6 family proteins. We herein report that M. tuberculosis and M. bovis bacillus Calmette-Guérin infection down-regulated the expression of CIITA/MHC-II by inducing hypermethylation in histone H3 lysine 9 (H3K9me2/3). Further, we showed that M. tuberculosis ESAT-6 family protein EsxL, encoded by Rv1198, is responsible for the down-regulation of CIITA/MHC-II by inducing H3K9me2/3. We further report that M. tuberculosis esxL induced the expression of nitric-oxide synthase, NO production, and p38 MAPK pathway, which in turn was responsible for the increased H3K9me2/3 in CIITA via up-regulation of euchromatic histone-lysine N-methyltransferase 2 (G9a). In contrast, inhibition of nitric-oxide synthase, p38 MAPK, and G9a abrogated H3K9me2/3, resulting in increased CIITA expression. A chromatin immunoprecipitation assay confirmed that hypermethylation at the promoter IV region of CIITA is mainly responsible for CIITA down-regulation and subsequent antigen presentation. We found that co-culture of macrophages infected with esxL-expressing M. smegmatis and mouse splenocytes led to down-regulation of IL-2, a key cytokine involved in T-cell proliferation. In summary, we demonstrate that M. tuberculosis EsxL inhibits antigen presentation by enhancing H3K9me2/3 at the CIITA promoter, thereby repressing its expression through NO and p38 MAPK activation.
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Affiliation(s)
- Srabasti Sengupta
- From the School of Biotechnology, KIIT University, Bhubaneswar, Orissa 751024, India
| | - Saba Naz
- the National Institute of Immunology, New Delhi, Delhi 110067, India, and
| | - Ishani Das
- From the School of Biotechnology, KIIT University, Bhubaneswar, Orissa 751024, India
| | - Abdul Ahad
- the Institute of Life Science, Nalco Square, Bhubaneswar, Orissa 751023, India
| | - Avinash Padhi
- From the School of Biotechnology, KIIT University, Bhubaneswar, Orissa 751024, India
| | - Sumanta Kumar Naik
- From the School of Biotechnology, KIIT University, Bhubaneswar, Orissa 751024, India
| | - Geetanjali Ganguli
- From the School of Biotechnology, KIIT University, Bhubaneswar, Orissa 751024, India
| | - Kali Prasad Pattanaik
- From the School of Biotechnology, KIIT University, Bhubaneswar, Orissa 751024, India
| | - Sunil Kumar Raghav
- the Institute of Life Science, Nalco Square, Bhubaneswar, Orissa 751023, India
| | | | - Avinash Sonawane
- From the School of Biotechnology, KIIT University, Bhubaneswar, Orissa 751024, India,
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32
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Korte J, Alber M, Trujillo CM, Syson K, Koliwer-Brandl H, Deenen R, Köhrer K, DeJesus MA, Hartman T, Jacobs WR, Bornemann S, Ioerger TR, Ehrt S, Kalscheuer R. Trehalose-6-Phosphate-Mediated Toxicity Determines Essentiality of OtsB2 in Mycobacterium tuberculosis In Vitro and in Mice. PLoS Pathog 2016; 12:e1006043. [PMID: 27936238 PMCID: PMC5148154 DOI: 10.1371/journal.ppat.1006043] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 11/04/2016] [Indexed: 01/13/2023] Open
Abstract
Trehalose biosynthesis is considered an attractive target for the development of antimicrobials against fungal, helminthic and bacterial pathogens including Mycobacterium tuberculosis. The most common biosynthetic route involves trehalose-6-phosphate (T6P) synthase OtsA and T6P phosphatase OtsB that generate trehalose from ADP/UDP-glucose and glucose-6-phosphate. In order to assess the drug target potential of T6P phosphatase, we generated a conditional mutant of M. tuberculosis allowing the regulated gene silencing of the T6P phosphatase gene otsB2. We found that otsB2 is essential for growth of M. tuberculosis in vitro as well as for the acute infection phase in mice following aerosol infection. By contrast, otsB2 is not essential for the chronic infection phase in mice, highlighting the substantial remodelling of trehalose metabolism during infection by M. tuberculosis. Blocking OtsB2 resulted in the accumulation of its substrate T6P, which appears to be toxic, leading to the self-poisoning of cells. Accordingly, blocking T6P production in a ΔotsA mutant abrogated otsB2 essentiality. T6P accumulation elicited a global upregulation of more than 800 genes, which might result from an increase in RNA stability implied by the enhanced neutralization of toxins exhibiting ribonuclease activity. Surprisingly, overlap with the stress response caused by the accumulation of another toxic sugar phosphate molecule, maltose-1-phosphate, was minimal. A genome-wide screen for synthetic lethal interactions with otsA identified numerous genes, revealing additional potential drug targets synergistic with OtsB2 suitable for combination therapies that would minimize the emergence of resistance to OtsB2 inhibitors. Trehalose biosynthesis is considered an attractive target for the development of new drugs against various microbial pathogens including Mycobacterium tuberculosis. In this human pathogen, two partially redundant pathways mediate trehalose biosynthesis. The OtsA-OtsB2 pathway, which dominates in culture, involves trehalose-6-phosphate (T6P) synthase OtsA and T6P phosphatase OtsB2. While OtsA is dispensable, OtsB2 is strictly essential for growth of M. tuberculosis. Using conditional gene silencing, we here show that essentiality of OtsB2 is linked to accumulation of its substrate T6P, which exhibits direct or indirect toxic effects. Regulated gene expression in vivo revealed that OtsB2 is required to establish an acute infection of M. tuberculosis in a mouse infection model, but is surprisingly fully dispensable during the chronic infection phase. This highlights that trehalose metabolism of M. tuberculosis is substantially remodelled during infection.
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Affiliation(s)
- Jan Korte
- Institute for Pharmaceutical Biology and Biotechnology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- Institute for Medical Microbiology and Hospital Hygiene, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Marina Alber
- Institute for Medical Microbiology and Hospital Hygiene, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Carolina M. Trujillo
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Karl Syson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, Norfolk, United Kingdom
| | - Hendrik Koliwer-Brandl
- Institute for Medical Microbiology and Hospital Hygiene, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - René Deenen
- Biological and Medical Research Center (BMFZ), Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Karl Köhrer
- Biological and Medical Research Center (BMFZ), Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Michael A. DeJesus
- Department of Computer Science, Texas A&M University, College Station, Texas, United States of America
| | - Travis Hartman
- Department of Microbiology and Immunology, Howard Hughes Medical Institute, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - William R. Jacobs
- Department of Microbiology and Immunology, Howard Hughes Medical Institute, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Stephen Bornemann
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, Norfolk, United Kingdom
| | - Thomas R. Ioerger
- Department of Computer Science, Texas A&M University, College Station, Texas, United States of America
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Rainer Kalscheuer
- Institute for Pharmaceutical Biology and Biotechnology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- Institute for Medical Microbiology and Hospital Hygiene, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- * E-mail:
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33
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Sharma AK, Arora D, Singh LK, Gangwal A, Sajid A, Molle V, Singh Y, Nandicoori VK. Serine/Threonine Protein Phosphatase PstP of Mycobacterium tuberculosis Is Necessary for Accurate Cell Division and Survival of Pathogen. J Biol Chem 2016; 291:24215-24230. [PMID: 27758870 DOI: 10.1074/jbc.m116.754531] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Indexed: 02/06/2023] Open
Abstract
Protein phosphatases play vital roles in phosphorylation-mediated cellular signaling. Although there are 11 serine/threonine protein kinases in Mycobacterium tuberculosis, only one serine/threonine phosphatase, PstP, has been identified. Although PstP has been biochemically characterized and multiple in vitro substrates have been identified, its physiological role has not yet been elucidated. In this study, we have investigated the impact of PstP on cell growth and survival of the pathogen in the host. Overexpression of PstP led to elongated cells and partially compromised survival. We find that depletion of PstP is detrimental to cell survival, eventually leading to cell death. PstP depletion results in elongated multiseptate cells, suggesting a role for PstP in regulating cell division events. Complementation experiments performed with PstP deletion mutants revealed marginally compromised survival, suggesting that all of the domains, including the extracellular domain, are necessary for complete rescue. On the other hand, the catalytic activity of PstP is absolutely essential for the in vitro growth. Mice infection experiments establish a definitive role for PstP in pathogen survival within the host. Depletion of PstP from established infections causes pathogen clearance, indicating that the continued presence of PstP is necessary for pathogen survival. Taken together, our data suggest an important role for PstP in establishing and maintaining infection, possibly via the modulation of cell division events.
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Affiliation(s)
- Aditya K Sharma
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India.,the Academy of Scientific and Innovative Research (AcSIR), CSIR-IGIB, Delhi-110025, India
| | - Divya Arora
- From the National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Lalit K Singh
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India
| | - Aakriti Gangwal
- the Department of Zoology, University of Delhi Delhi-110007, India
| | - Andaleeb Sajid
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India
| | - Virginie Molle
- the Laboratoire de Dynamique des Interactions Membranaires Normales et Pathologiques, Université Montpellier 2, CNRS, UMR 5235, Montpellier, France, and
| | - Yogendra Singh
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India, .,the Department of Zoology, University of Delhi Delhi-110007, India
| | - Vinay Kumar Nandicoori
- From the National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India,
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Xue J, Song W, Yao H, Hou S, Liu S, Wang Y, Pei D, Zhu X, Qin D, Ren L. Effects of cholic acid modified glucosamine on chondrogenic differentiation. RSC Adv 2016. [DOI: 10.1039/c6ra09547j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Glucosamine hydrochloride is a widely used drug for the treatment of osteoarthritis and can be easily modified by other molecules because of its alterable functional groups.
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