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Chen K, Xu R, Hu X, Li D, Hou T, Kang Y. Recent advances in the development of DprE1 inhibitors using AI/CADD approaches. Drug Discov Today 2024; 29:103987. [PMID: 38670256 DOI: 10.1016/j.drudis.2024.103987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/22/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024]
Abstract
Tuberculosis (TB) is a global lethal disease caused by Mycobacterium tuberculosis (Mtb). The flavoenzyme decaprenylphosphoryl-β-d-ribose 2'-oxidase (DprE1) plays a crucial part in the biosynthesis of lipoarabinomannan and arabinogalactan for the cell wall of Mtb and represents a promising target for anti-TB drug development. Therefore, there is an urgent need to discover DprE1 inhibitors with novel scaffolds, improved bioactivity and high drug-likeness. Recent studies have shown that artificial intelligence/computer-aided drug design (AI/CADD) techniques are powerful tools in the discovery of novel DprE1 inhibitors. This review provides an overview of the discovery of DprE1 inhibitors and their underlying mechanism of action and highlights recent advances in the discovery and optimization of DprE1 inhibitors using AI/CADD approaches.
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Affiliation(s)
- Kepeng Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ruolan Xu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xueping Hu
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao, Shandong 266237, China
| | - Dan Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Yu Kang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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2
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Hart EM, Lyerly E, Bernhardt TG. The conserved σD envelope stress response monitors multiple aspects of envelope integrity in corynebacteria. PLoS Genet 2024; 20:e1011127. [PMID: 38829907 PMCID: PMC11175481 DOI: 10.1371/journal.pgen.1011127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 06/13/2024] [Accepted: 05/15/2024] [Indexed: 06/05/2024] Open
Abstract
The cell envelope fortifies bacterial cells against antibiotics and other insults. Species in the Mycobacteriales order have a complex envelope that includes an outer layer of mycolic acids called the mycomembrane (MM) and a cell wall composed of peptidoglycan and arabinogalactan. This envelope architecture is unique among bacteria and contributes significantly to the virulence of pathogenic Mycobacteriales like Mycobacterium tuberculosis. Characterization of pathways that govern envelope biogenesis in these organisms is therefore critical in understanding their biology and for identifying new antibiotic targets. To better understand MM biogenesis, we developed a cell sorting-based screen for mutants defective in the surface exposure of a porin normally embedded in the MM of the model organism Corynebacterium glutamicum. The results revealed a requirement for the conserved σD envelope stress response in porin export and identified MarP as the site-1 protease, respectively, that activate the response by cleaving the membrane-embedded anti-sigma factor. A reporter system revealed that the σD pathway responds to defects in mycolic acid and arabinogalactan biosynthesis, suggesting that the stress response has the unusual property of being induced by activating signals that arise from defects in the assembly of two distinct envelope layers. Our results thus provide new insights into how C. glutamicum and related bacteria monitor envelope integrity and suggest a potential role for members of the σD regulon in protein export to the MM.
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Affiliation(s)
- Elizabeth M. Hart
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Evan Lyerly
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Thomas G. Bernhardt
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
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3
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Kelly SD, Duong NH, Nothof JT, Lowary TL, Whitfield C. Three-component systems represent a common pathway for extracytoplasmic addition of pentofuranose sugars into bacterial glycans. Proc Natl Acad Sci U S A 2024; 121:e2402554121. [PMID: 38748580 PMCID: PMC11127046 DOI: 10.1073/pnas.2402554121] [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: 02/05/2024] [Accepted: 04/18/2024] [Indexed: 05/27/2024] Open
Abstract
Cell surface glycans are major drivers of antigenic diversity in bacteria. The biochemistry and molecular biology underpinning their synthesis are important in understanding host-pathogen interactions and for vaccine development with emerging chemoenzymatic and glycoengineering approaches. Structural diversity in glycostructures arises from the action of glycosyltransferases (GTs) that use an immense catalog of activated sugar donors to build the repeating unit and modifying enzymes that add further heterogeneity. Classical Leloir GTs incorporate α- or β-linked sugars by inverting or retaining mechanisms, depending on the nucleotide sugar donor. In contrast, the mechanism of known ribofuranosyltransferases is confined to β-linkages, so the existence of α-linked ribofuranose in some glycans dictates an alternative strategy. Here, we use Citrobacter youngae O1 and O2 lipopolysaccharide O antigens as prototypes to describe a widespread, versatile pathway for incorporating side-chain α-linked pentofuranoses by extracytoplasmic postpolymerization glycosylation. The pathway requires a polyprenyl phosphoribose synthase to generate a lipid-linked donor, a MATE-family flippase to transport the donor to the periplasm, and a GT-C type GT (founding the GT136 family) that performs the final glycosylation reaction. The characterized system shares similarities, but also fundamental differences, with both cell wall arabinan biosynthesis in mycobacteria, and periplasmic glucosylation of O antigens first discovered in Salmonella and Shigella. The participation of auxiliary epimerases allows the diversification of incorporated pentofuranoses. The results offer insight into a broad concept in microbial glycobiology and provide prototype systems and bioinformatic guides that facilitate discovery of further examples from diverse species, some in currently unknown glycans.
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Affiliation(s)
- Steven D. Kelly
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ONN1G 2W1, Canada
| | - Nam Ha Duong
- Institute of Biological Chemistry, Academia Sinica, Nangang, Taipei11529, Taiwan
- Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Nangang, Taipei11529, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu300044, Taiwan
| | - Jeremy T. Nothof
- Department of Chemistry, University of Alberta, Edmonton, ABT6G 2G2, Canada
| | - Todd L. Lowary
- Institute of Biological Chemistry, Academia Sinica, Nangang, Taipei11529, Taiwan
- Department of Chemistry, University of Alberta, Edmonton, ABT6G 2G2, Canada
- Institute of Biochemical Sciences, National Taiwan University, Taipei10617, Taiwan
| | - Chris Whitfield
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ONN1G 2W1, Canada
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4
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Rana N, Grover P, Singh H. Recent Developments and Future Perspectives of Purine Derivatives as a Promising Scaffold in Drug Discovery. Curr Top Med Chem 2024; 24:541-579. [PMID: 38288806 DOI: 10.2174/0115680266290152240110074034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/17/2023] [Accepted: 12/27/2023] [Indexed: 05/31/2024]
Abstract
Numerous purine-containing compounds have undergone extensive investigation for their medical efficacy across various diseases. The swift progress in purine-based medicinal chemistry has brought to light the therapeutic capabilities of purine-derived compounds in addressing challenging medical conditions. Defined by a heterocyclic ring comprising a pyrimidine ring linked with an imidazole ring, purine exhibits a diverse array of therapeutic attributes. This review systematically addresses the multifaceted potential of purine derivatives in combating various diseases, including their roles as anticancer agents, antiviral compounds (anti-herpes, anti-HIV, and anti-influenzae), autoimmune and anti-inflammatory agents, antihyperuricemic and anti-gout solutions, antimicrobial agents, antitubercular compounds, anti-leishmanial agents, and anticonvulsants. Emphasis is placed on the remarkable progress made in developing purine-based compounds, elucidating their significant target sites. The article provides a comprehensive exploration of developments in both natural and synthetic purines, offering insights into their role in managing a diverse range of illnesses. Additionally, the discussion delves into the structure-activity relationships and biological activities of the most promising purine molecules. The intriguing capabilities revealed by these purine-based scaffolds unequivocally position them at the forefront of drug candidate development. As such, this review holds potential significance for researchers actively involved in synthesizing purine-based drug candidates, providing a roadmap for the continued advancement of this promising field.
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Affiliation(s)
- Neha Rana
- School of Pharmacy (SOP), Noida International University, Yamuna Expressway, Gautam Budh Nagar, 203201, India
| | - Parul Grover
- KIET School of Pharmacy, KIET Group of Institutions, Delhi-NCR, Ghaziabad, 201206, India
| | - Hridayanand Singh
- Dr. K. N. Modi Institute of Pharmaceutical Education and Research, Modinagar, 201204, Uttar Pradesh, India
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5
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Finger V, Kucera T, Kafkova R, Muckova L, Dolezal R, Kubes J, Novak M, Prchal L, Lakatos L, Andrs M, Hympanova M, Marek J, Kufa M, Spiwok V, Soukup O, Mezeiova E, Janousek J, Nevosadova L, Benkova M, Kitson RRA, Kratky M, Bősze S, Mikusova K, Hartkoorn R, Roh J, Korabecny J. 2,6-Disubstituted 7-(naphthalen-2-ylmethyl)-7H-purines as a new class of potent antitubercular agents inhibiting DprE1. Eur J Med Chem 2023; 258:115611. [PMID: 37421887 DOI: 10.1016/j.ejmech.2023.115611] [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: 05/04/2023] [Revised: 06/27/2023] [Accepted: 06/27/2023] [Indexed: 07/10/2023]
Abstract
Phenotypic screening of an in-house library of small molecule purine derivatives against Mycobacterium tuberculosis (Mtb) led to the identification of 2-morpholino-7-(naphthalen-2-ylmethyl)-1,7-dihydro-6H-purin-6-one 10 as a potent antimycobacterial agent with MIC99 of 4 μM. Thorough structure-activity relationship studies revealed the importance of 7-(naphthalen-2-ylmethyl) substitution for antimycobacterial activity, yet opened the possibility of structural modifications at positions 2 and 6 of the purine core. As the result, optimized analogues with 6-amino or ethylamino substitution 56 and 64, respectively, were developed. These compounds showed strong in vitro antimycobacterial activity with MIC of 1 μM against Mtb H37Rv and against several clinically isolated drug-resistant strains, had limited toxicity to mammalian cell lines, medium clearance with respect to phase I metabolic deactivation (27 and 16.8 μL/min/mg), sufficient aqueous solubility (>90 μM) and high plasma stability. Interestingly, investigated purines, including compounds 56 and 64, lacked activity against a panel of Gram-negative and Gram-positive bacterial strains, indicating a specific mycobacterial molecular target. To investigate the mechanism of action, Mtb mutants resistant to hit compound 10 were isolated and their genomes were sequenced. Mutations were found in dprE1 (Rv3790), which encodes decaprenylphosphoryl-β-d-ribose oxidase DprE1, enzyme essential for the biosynthesis of arabinose, a vital component of the mycobacterial cell wall. Inhibition of DprE1 by 2,6-disubstituted 7-(naphthalen-2-ylmethyl)-7H-purines was proved using radiolabelling experiments in Mtb H37Rv in vitro. Finally, structure-binding relationships between selected purines and DprE1 using molecular modeling studies in tandem with molecular dynamic simulations revealed the key structural features for effective drug-target interaction.
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Affiliation(s)
- Vladimir Finger
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika, Heyrovskeho 1203, 50005, Hradec Králové, Czech Republic; Biomedical Research Center, University Hospital Hradec Králové, Sokolska 581, 500 05, Hradec Králové, Czech Republic
| | - Tomas Kucera
- Faculty of Military Health Sciences, University of Defence, Trebesska, 1575, 500 01, Hradec Králové, Czech Republic
| | - Radka Kafkova
- Faculty of Natural Sciences, Department of Biochemistry, Comenius University in Bratislava, Mlynská Dolina, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | - Lubica Muckova
- Biomedical Research Center, University Hospital Hradec Králové, Sokolska 581, 500 05, Hradec Králové, Czech Republic; Faculty of Military Health Sciences, University of Defence, Trebesska, 1575, 500 01, Hradec Králové, Czech Republic
| | - Rafael Dolezal
- Biomedical Research Center, University Hospital Hradec Králové, Sokolska 581, 500 05, Hradec Králové, Czech Republic
| | - Jan Kubes
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika, Heyrovskeho 1203, 50005, Hradec Králové, Czech Republic
| | - Martin Novak
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika, Heyrovskeho 1203, 50005, Hradec Králové, Czech Republic; Biomedical Research Center, University Hospital Hradec Králové, Sokolska 581, 500 05, Hradec Králové, Czech Republic
| | - Lukas Prchal
- Biomedical Research Center, University Hospital Hradec Králové, Sokolska 581, 500 05, Hradec Králové, Czech Republic
| | - Levente Lakatos
- ELKH-ELTE Research Group of Peptide Chemistry, Eötvös Loránd University, Pázmány Péter Sétány 1/A, H-1117, Budapest, Hungary; National Public Health Center, Albert Flórián út 2-6, Budapest, 1097, Hungary
| | - Martin Andrs
- Biomedical Research Center, University Hospital Hradec Králové, Sokolska 581, 500 05, Hradec Králové, Czech Republic
| | - Michaela Hympanova
- Biomedical Research Center, University Hospital Hradec Králové, Sokolska 581, 500 05, Hradec Králové, Czech Republic; Faculty of Military Health Sciences, University of Defence, Trebesska, 1575, 500 01, Hradec Králové, Czech Republic
| | - Jan Marek
- Biomedical Research Center, University Hospital Hradec Králové, Sokolska 581, 500 05, Hradec Králové, Czech Republic; Faculty of Military Health Sciences, University of Defence, Trebesska, 1575, 500 01, Hradec Králové, Czech Republic
| | - Martin Kufa
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika, Heyrovskeho 1203, 50005, Hradec Králové, Czech Republic; Biomedical Research Center, University Hospital Hradec Králové, Sokolska 581, 500 05, Hradec Králové, Czech Republic
| | - Vojtech Spiwok
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Technicka 5, 166 28, Prague, Czech Republic
| | - Ondrej Soukup
- Biomedical Research Center, University Hospital Hradec Králové, Sokolska 581, 500 05, Hradec Králové, Czech Republic
| | - Eva Mezeiova
- Biomedical Research Center, University Hospital Hradec Králové, Sokolska 581, 500 05, Hradec Králové, Czech Republic
| | - Jiri Janousek
- Biomedical Research Center, University Hospital Hradec Králové, Sokolska 581, 500 05, Hradec Králové, Czech Republic
| | - Lenka Nevosadova
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika, Heyrovskeho 1203, 50005, Hradec Králové, Czech Republic
| | - Marketa Benkova
- Biomedical Research Center, University Hospital Hradec Králové, Sokolska 581, 500 05, Hradec Králové, Czech Republic
| | - Russell R A Kitson
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika, Heyrovskeho 1203, 50005, Hradec Králové, Czech Republic
| | - Martin Kratky
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika, Heyrovskeho 1203, 50005, Hradec Králové, Czech Republic
| | - Szilvia Bősze
- ELKH-ELTE Research Group of Peptide Chemistry, Eötvös Loránd University, Pázmány Péter Sétány 1/A, H-1117, Budapest, Hungary; National Public Health Center, Albert Flórián út 2-6, Budapest, 1097, Hungary
| | - Katarina Mikusova
- Faculty of Natural Sciences, Department of Biochemistry, Comenius University in Bratislava, Mlynská Dolina, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | - Ruben Hartkoorn
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Jaroslav Roh
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika, Heyrovskeho 1203, 50005, Hradec Králové, Czech Republic.
| | - Jan Korabecny
- Biomedical Research Center, University Hospital Hradec Králové, Sokolska 581, 500 05, Hradec Králové, Czech Republic.
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6
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Rossini NDO, Dias MVB. Mutations and insights into the molecular mechanisms of resistance of Mycobacterium tuberculosis to first-line. Genet Mol Biol 2023; 46:e20220261. [PMID: 36718771 PMCID: PMC9887390 DOI: 10.1590/1678-4685-gmb-2022-0261] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 12/18/2022] [Indexed: 01/28/2023] Open
Abstract
Genetically antimicrobial resistance in Mycobacterium tuberculosis is currently one of the most important aspects of tuberculosis, considering that there are emerging resistant strains for almost every known drug used for its treatment. There are multiple antimicrobials used for tuberculosis treatment, and the most effective ones are the first-line drugs, which include isoniazid, pyrazinamide, rifampicin, and ethambutol. In this context, understanding the mechanisms of action and resistance of these molecules is essential for proposing new therapies and strategies of treatment. Additionally, understanding how and where mutations arise conferring a resistance profile to the bacteria and their effect on bacterial metabolism is an important requisite to be taken in producing safer and less susceptible drugs to the emergence of resistance. In this review, we summarize the most recent literature regarding novel mutations reported between 2017 and 2022 and the advances in the molecular mechanisms of action and resistance against first-line drugs used in tuberculosis treatment, highlighting recent findings in pyrazinamide resistance involving PanD and, additionally, resistance-conferring mutations for novel drugs such as bedaquiline, pretomanid, delamanid and linezolid.
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Affiliation(s)
- Nicolas de Oliveira Rossini
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil. Universidade de São PauloInstituto de Ciências BiomédicasDepartamento de MicrobiologiaSão PauloSPBrazil
| | - Marcio Vinicius Bertacine Dias
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil. Universidade de São PauloInstituto de Ciências BiomédicasDepartamento de MicrobiologiaSão PauloSPBrazil,University of Warwick, Department of Chemistry, Coventry, United Kingdom. University of WarwickDepartment of ChemistryCoventryUnited Kingdom
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7
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Abstract
The genus Mycobacterium contains several slow-growing human pathogens, including Mycobacterium tuberculosis, Mycobacterium leprae, and Mycobacterium avium. Mycobacterium smegmatis is a nonpathogenic and fast growing species within this genus. In 1990, a mutant of M. smegmatis, designated mc2155, that could be transformed with episomal plasmids was isolated, elevating M. smegmatis to model status as the ideal surrogate for mycobacterial research. Classical bacterial models, such as Escherichia coli, were inadequate for mycobacteria research because they have low genetic conservation, different physiology, and lack the novel envelope structure that distinguishes the Mycobacterium genus. By contrast, M. smegmatis encodes thousands of conserved mycobacterial gene orthologs and has the same cell architecture and physiology. Dissection and characterization of conserved genes, structures, and processes in genetically tractable M. smegmatis mc2155 have since provided previously unattainable insights on these same features in its slow-growing relatives. Notably, tuberculosis (TB) drugs, including the first-line drugs isoniazid and ethambutol, are active against M. smegmatis, but not against E. coli, allowing the identification of their physiological targets. Furthermore, Bedaquiline, the first new TB drug in 40 years, was discovered through an M. smegmatis screen. M. smegmatis has become a model bacterium, not only for M. tuberculosis, but for all other Mycobacterium species and related genera. With a repertoire of bioinformatic and physical resources, including the recently established Mycobacterial Systems Resource, M. smegmatis will continue to accelerate mycobacterial research and advance the field of microbiology.
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8
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Structural Identification of Lipid-α: A Glycosyl Lipid Involved in Oligo- And Polysaccharides Metabolism in Streptococcus agalactiae (Group B Streptococcus). Curr Microbiol 2022; 80:16. [PMID: 36459236 DOI: 10.1007/s00284-022-03117-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 11/09/2022] [Indexed: 12/04/2022]
Abstract
Streptococcus agalactiae (group B Streptococcus, GBS) is a gram-positive bacterium that is an asymptomatic colonizer commonly found in the gastrointestinal and genitourinary tract of healthy adults. GBS is also the most common cause of life-threatening bacterial infections in newborns and is emerging as a pathogen in immunocompromised and diabetic adults. The GBS cell wall and covalently linked capsular polysaccharides (CPS) are vital to the protection of the bacterial cell and act as virulence factors. GBS-CPS have been successfully used to produce conjugate vaccines for all currently identified GBS serotypes. However, the mechanisms of biosynthesis and assembly of CPS and the other cell wall components remain poorly defined due to their complex surface structures. In this biosynthetic study of the GBS cell wall-CPS complex, glycolipids with varying lengths of glycosyl-chains were discovered. Among those, one of the smallest glycolipids (named GBS Lipid-α) was structurally characterized. Lipid-α is involved in GBS saccharide metabolism and presumably acts as a glycosyl acceptor to elongate the glycosyl chain. GBS Lipid-α was determined to be a 3-monosaccharide 1,2 acyl glycerol with a molecular mass in the range of m/z = 724-808. GBS Lipid-α is highly heterogenic with various acyl groups and glycosyl moieties. This knowledge will pave the way for future studies to elucidate the entire metabolic pathway and genes involved. The Lipid-α pathway may also exist in other bacterial species and has the potential to be a biomarker for future drug development.
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Miranda-Velez M, Sarker GS, Ramisetty P, Geden S, Bartolomeu Halicki PC, Annamalai T, Tse-Dinh YC, Rohde KH, Moon JH. Proton Motive Force-Disrupting Antimycobacterial Guanylurea Polymer. Biomacromolecules 2022; 23:4668-4677. [DOI: 10.1021/acs.biomac.2c00902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Michelle Miranda-Velez
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., Miami, Florida 33199, United States
| | - Golam Sabbir Sarker
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., Miami, Florida 33199, United States
| | - Priya Ramisetty
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., Miami, Florida 33199, United States
| | - Sandra Geden
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd., Orlando, Florida 32827, United States
| | - Priscila Cristina Bartolomeu Halicki
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd., Orlando, Florida 32827, United States
| | - Thirunavukkarasu Annamalai
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., Miami, Florida 33199, United States
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., Miami, Florida 33199, United States
- Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St., Miami, Florida 33199, United States
| | - Kyle H. Rohde
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd., Orlando, Florida 32827, United States
| | - Joong Ho Moon
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., Miami, Florida 33199, United States
- Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St., Miami, Florida 33199, United States
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10
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London JA, Taylor SL, Barsukov I, Cartmell A, Yates EA. Exploration of expanded carbohydrate chemical space to access biological activity using microwave-induced acid condensation of simple sugars. RSC Adv 2022; 12:11075-11083. [PMID: 35425031 PMCID: PMC8992359 DOI: 10.1039/d2ra01463g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 03/30/2022] [Indexed: 11/30/2022] Open
Abstract
Complex glycans are ubiquitous in nature and essential to life. Despite their diverse roles, however, only a fraction of their potential chemical space has been explored. New regions of this chemical space can, nevertheless, be accessed by generating structures that do not occur in nature or by modifying naturally-occurring polysaccharide structures – collectively, termed new polysaccharides (NPs). Two synthetic routes to NPs are described; the de novo route, directly from monosaccharide starting materials and the functionalization route, involving glycosylation of existing polysaccharides. The reaction involves a simple condensation step under microwave heating, catalysed by environmentally benign organic acids and is illustrated by the generation of structures with biological activities ranging from cell signalling and inhibition of bacterial growth, to mimicking carbohydrate antigens of pathogenic microorganisms. The method is as applicable to fine chemicals as it is to industrial waste, for example, biotechnologically-derived d-allulose (d-psicose), or the waste products of biofermentation. Accessing this chemical space unlocks new functionalities, generating complex glycans with applications in the biological, medical, biotechnological and materials science arenas. Condensation of simple sugars provides new polysaccharides with diverse biological activities, expanding access to carbohydrate chemical space.![]()
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Affiliation(s)
- James Andrew London
- Department of Biochemistry & Systems Biology, ISMIB, University of Liverpool Liverpool L69 7ZB UK
| | - Sarah Louise Taylor
- Department of Biochemistry & Systems Biology, ISMIB, University of Liverpool Liverpool L69 7ZB UK
| | - Igor Barsukov
- Department of Biochemistry & Systems Biology, ISMIB, University of Liverpool Liverpool L69 7ZB UK
| | - Alan Cartmell
- Department of Biochemistry & Systems Biology, ISMIB, University of Liverpool Liverpool L69 7ZB UK
| | - Edwin Alexander Yates
- Department of Biochemistry & Systems Biology, ISMIB, University of Liverpool Liverpool L69 7ZB UK
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11
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Tan YZ, Mancia F. Structure and Function of Mycobacterial Arabinofuranosyltransferases. Subcell Biochem 2022; 99:379-391. [PMID: 36151383 DOI: 10.1007/978-3-031-00793-4_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The mycobacteria genus is responsible for numerous infectious diseases that have afflicted the human race since antiquity-tuberculosis and leprosy in particular. An important contributor to their evolutionary success is their unique cell envelope, which constitutes a quasi-impermeable barrier, protecting the microorganism from external threats, antibiotics included. The arabinofuranosyltransferases are a family of enzymes, unique to the Actinobacteria family that mycobacteria genus belongs to, that are critical to building of this cell envelope. In this chapter, we will analyze available structures of members of the mycobacterial arabinofuranosyltransferase, clarify their function, as well as explore the common themes present amongst this family of enzymes, as revealed by recent research.
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Affiliation(s)
- Yong Zi Tan
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
- Disease Intervention Technology Laboratory (DITL), Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, NY, USA
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Gharwalová L, Palyzová A, Marešová H, Kolouchová I, Kyselová L, Řezanka T. Identification of Homologous Polyprenols from Thermophilic Bacteria. Microorganisms 2021; 9:microorganisms9061168. [PMID: 34071687 PMCID: PMC8226974 DOI: 10.3390/microorganisms9061168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 11/24/2022] Open
Abstract
Sixteen strains of five genera of thermophilic bacteria, i.e., Alicyclobacillus, Brevibacillus, Geobacillus, Meiothermus, and Thermus, were cultivated at a temperature from 42 to 70 °C. Twelve strains were obtained from the Czech Collection of Microorganisms, while four were directly isolated and identified by 16S rRNA gene sequencing from the hot springs of the world-famous Carlsbad spa (Czech Republic). Polyprenol homologs from C40 to C65 as well as free undecaprenol (C55), undecaprenyl phosphate, and undecaprenyl diphosphate were identified by shotgun analysis and RP-HPLC/MS-ESI+ (reverse phase high-performance liquid chromatography–high-resolution positive electrospray ionization mass spectrometry). The limit of detection (50 pM) was determined for individual homologs and free polyprenols and their phosphates. Thus, it has been shown that at least some thermophilic bacteria produce not just the major C55 polyprenol as previously described, but a mixture of homologs.
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Affiliation(s)
- Lucia Gharwalová
- Department of Biotechnology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, 166 28 Prague, Czech Republic; (L.G.); (I.K.)
| | - Andrea Palyzová
- Institute of Microbiology, The Czech Academy of Sciences, 142 20 Prague, Czech Republic; (A.P.); (H.M.)
| | - Helena Marešová
- Institute of Microbiology, The Czech Academy of Sciences, 142 20 Prague, Czech Republic; (A.P.); (H.M.)
| | - Irena Kolouchová
- Department of Biotechnology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, 166 28 Prague, Czech Republic; (L.G.); (I.K.)
| | - Lucie Kyselová
- Research Institute of Brewing and Malting, 120 44 Prague, Czech Republic;
| | - Tomáš Řezanka
- Institute of Microbiology, The Czech Academy of Sciences, 142 20 Prague, Czech Republic; (A.P.); (H.M.)
- Correspondence:
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An ABC transporter Wzm-Wzt catalyzes translocation of lipid-linked galactan across the plasma membrane in mycobacteria. Proc Natl Acad Sci U S A 2021; 118:2023663118. [PMID: 33879617 DOI: 10.1073/pnas.2023663118] [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] [Indexed: 12/12/2022] Open
Abstract
Mycobacterium tuberculosis, one of the deadliest pathogens in human history, is distinguished by a unique, multilayered cell wall, which offers the bacterium a high level of protection from the attacks of the host immune system. The primary structure of the cell wall core, composed of covalently linked peptidoglycan, branched heteropolysaccharide arabinogalactan, and mycolic acids, is well known, and numerous enzymes involved in the biosynthesis of its components are characterized. The cell wall biogenesis takes place at both cytoplasmic and periplasmic faces of the plasma membrane, and only recently some of the specific transport systems translocating the metabolic intermediates between these two compartments have been characterized [M. Jackson, C. M. Stevens, L. Zhang, H. I. Zgurskaya, M. Niederweis, Chem. Rev., 10.1021/acs.chemrev.0c00869 (2020)]. In this work, we use CRISPR interference methodology in Mycobacterium smegmatis to functionally characterize an ATP-binding cassette (ABC) transporter involved in the translocation of galactan precursors across the plasma membrane. We show that genetic knockdown of the transmembrane subunit of the transporter results in severe morphological changes and the accumulation of an aberrantly long galactan precursor. Based on similarities with structures and functions of specific O-antigen ABC transporters of gram-negative bacteria [C. Whitfield, D. M. Williams, S. D. Kelly, J. Biol. Chem. 295, 10593-10609 (2020)], we propose a model for coupled synthesis and export of the galactan polymer precursor in mycobacteria.
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14
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High Throughput Expression Screening of Arabinofuranosyltransferases from Mycobacteria. Processes (Basel) 2021. [DOI: 10.3390/pr9040629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Studies on membrane proteins can help to develop new drug targets and treatments for a variety of diseases. However, membrane proteins continue to be among the most challenging targets in structural biology. This uphill endeavor can be even harder for membrane proteins from Mycobacterium species, which are notoriously difficult to express in heterologous systems. Arabinofuranosyltransferases are involved in mycobacterial cell wall synthesis and thus potential targets for antituberculosis drugs. A set of 96 mycobacterial genes coding for Arabinofuranosyltransferases was selected, of which 17 were successfully expressed in E. coli and purified by metal-affinity chromatography. We herein present an efficient high-throughput strategy to screen in microplates a large number of targets from Mycobacteria and select the best conditions for large-scale protein production to pursue functional and structural studies. This methodology can be applied to other targets, is cost and time effective and can be implemented in common laboratories.
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The thick waxy coat of mycobacteria, a protective layer against antibiotics and the host's immune system. Biochem J 2020; 477:1983-2006. [PMID: 32470138 PMCID: PMC7261415 DOI: 10.1042/bcj20200194] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/30/2020] [Accepted: 05/04/2020] [Indexed: 12/22/2022]
Abstract
Tuberculosis, caused by the pathogenic bacterium Mycobacterium tuberculosis (Mtb), is the leading cause of death from an infectious disease, with a mortality rate of over a million people per year. This pathogen's remarkable resilience and infectivity is largely due to its unique waxy cell envelope, 40% of which comprises complex lipids. Therefore, an understanding of the structure and function of the cell wall lipids is of huge indirect clinical significance. This review provides a synopsis of the cell envelope and the major lipids contained within, including structure, biosynthesis and roles in pathogenesis.
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16
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Batt SM, Burke CE, Moorey AR, Besra GS. Antibiotics and resistance: the two-sided coin of the mycobacterial cell wall. Cell Surf 2020; 6:100044. [PMID: 32995684 PMCID: PMC7502851 DOI: 10.1016/j.tcsw.2020.100044] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/26/2020] [Accepted: 08/26/2020] [Indexed: 01/07/2023] Open
Abstract
Mycobacterium tuberculosis, the bacterium responsible for tuberculosis, is the global leading cause of mortality from an infectious agent. Part of this success relies on the unique cell wall, which consists of a thick waxy coat with tightly packed layers of complexed sugars, lipids and peptides. This coat provides a protective hydrophobic barrier to antibiotics and the host's defences, while enabling the bacterium to spread efficiently through sputum to infect and survive within the macrophages of new hosts. However, part of this success comes at a cost, with many of the current first- and second-line drugs targeting the enzymes involved in cell wall biosynthesis. The flip side of this coin is that resistance to these drugs develops either in the target enzymes or the activation pathways of the drugs, paving the way for new resistant clinical strains. This review provides a synopsis of the structure and synthesis of the cell wall and the major current drugs and targets, along with any mechanisms of resistance.
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Affiliation(s)
- Sarah M. Batt
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Christopher E. Burke
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Alice R. Moorey
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Gurdyal S. Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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17
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Liu L, Kong C, Fumagalli M, Savková K, Xu Y, Huszár S, Sammartino JC, Fan D, Chiarelli LR, Mikušová K, Sun Z, Qiao C. Design, synthesis and evaluation of covalent inhibitors of DprE1 as antitubercular agents. Eur J Med Chem 2020; 208:112773. [PMID: 32898793 DOI: 10.1016/j.ejmech.2020.112773] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/05/2020] [Accepted: 08/17/2020] [Indexed: 12/14/2022]
Abstract
Decaprenylphosphoryl-β-d-ribose 2'-oxidoreductase (DprE1) is a promising drug target for the development of novel anti-tubercular agents, and inhibitors of DprE1 are being investigated extensively. Among them, the 1,3-benzothiazinone compounds such as BTZ043, and its closer congener, PBTZ169, are undergoing clinical studies. It has been shown that both BTZ compounds are prodrugs, the nitro group is reduced to nitroso first, to which an adjacent Cys387 in the DprE1 binding pocket is covalently bound and results in suicide enzyme inhibition. We figured that replacement of the nitro with an electrophilic warhead would still achieve covalent interaction with nucleophilic Cys387, while the required reductive activation could be circumvented. To test this hypothesis, a number of covalent inhibitors of DprE1 were designed and prepared. The compounds inhibitory potency against DprE1 and anti-tubercular activity were investigated, their chemical reactivity, formation of covalent adduct between the warhead and the enzyme was demonstrated by mass spectrometry.
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Affiliation(s)
- Lingfeng Liu
- College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou, 215123, PR China
| | - Chengcheng Kong
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, 97 Ma Chang Street, Beijing, 101149, PR China
| | - Marco Fumagalli
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Karin Savková
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | - Yiwen Xu
- College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou, 215123, PR China
| | - Stanislav Huszár
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | - José C Sammartino
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100, Pavia, Italy; University School for Advanced Studies - IUSS Pavia, Piazza Della Vittoria 15, 27100, Pavia, Italy
| | - Dongguang Fan
- College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou, 215123, PR China
| | - Laurent R Chiarelli
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100, Pavia, Italy.
| | - Katarína Mikušová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 842 15, Bratislava, Slovakia.
| | - Zhaogang Sun
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, 97 Ma Chang Street, Beijing, 101149, PR China.
| | - Chunhua Qiao
- College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou, 215123, PR China.
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18
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Tan YZ, Rodrigues J, Keener JE, Zheng RB, Brunton R, Kloss B, Giacometti SI, Rosário AL, Zhang L, Niederweis M, Clarke OB, Lowary TL, Marty MT, Archer M, Potter CS, Carragher B, Mancia F. Cryo-EM structure of arabinosyltransferase EmbB from Mycobacterium smegmatis. Nat Commun 2020; 11:3396. [PMID: 32636380 PMCID: PMC7341804 DOI: 10.1038/s41467-020-17202-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/18/2020] [Indexed: 01/21/2023] Open
Abstract
Arabinosyltransferase B (EmbB) belongs to a family of membrane-bound glycosyltransferases that build the lipidated polysaccharides of the mycobacterial cell envelope, and are targets of anti-tuberculosis drug ethambutol. We present the 3.3 Å resolution single-particle cryo-electron microscopy structure of Mycobacterium smegmatis EmbB, providing insights on substrate binding and reaction mechanism. Mutations that confer ethambutol resistance map mostly around the putative active site, suggesting this to be the location of drug binding.
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Affiliation(s)
- Yong Zi Tan
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, 10032, USA
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, 10027, USA
| | - José Rodrigues
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157, Oeiras, Portugal
| | - James E Keener
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
| | - Ruixiang Blake Zheng
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Richard Brunton
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Brian Kloss
- Center on Membrane Protein Production and Analysis, New York Structural Biology Center, New York, NY, 10027, USA
| | - Sabrina I Giacometti
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Ana L Rosário
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157, Oeiras, Portugal
| | - Lei Zhang
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Michael Niederweis
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Oliver B Clarke
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, 10032, USA
- Department of Anesthesiology, Columbia University, New York, NY, 10032, USA
| | - Todd L Lowary
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
- Institute of Biological Chemistry, Academia Sinica, Academia Road, Section 2, #128, Nangang, Taipei, 11529, Taiwan
| | - Michael T Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
- Bio5 Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Margarida Archer
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157, Oeiras, Portugal
| | - Clinton S Potter
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, 10027, USA
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, 10027, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Bridget Carragher
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, 10027, USA.
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, 10027, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, 10032, USA.
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19
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Shetye GS, Franzblau SG, Cho S. New tuberculosis drug targets, their inhibitors, and potential therapeutic impact. Transl Res 2020; 220:68-97. [PMID: 32275897 DOI: 10.1016/j.trsl.2020.03.007] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/28/2020] [Accepted: 03/09/2020] [Indexed: 11/18/2022]
Abstract
The current tuberculosis (TB) predicament poses numerous challenges and therefore every incremental scientific work and all positive socio-political engagements, are steps taken in the right direction to eradicate TB. Progression of the late stage TB-drug pipeline into the clinics is an immediate deliverable of this global effort. At the same time, fueling basic research and pursuing early discovery work must be sustained to maintain a healthy TB-drug pipeline. This review encompasses a broad analysis of chemotherapeutic strategies that target the DNA replication, protein synthesis, cell wall biosynthesis, energy metabolism and proteolysis of Mycobacterium tuberculosis (Mtb). It includes a status check of the current TB-drug pipeline with a focus on the associated biology, emerging targets, and their promising chemical inhibitors. Potential synergies and/or gaps within or across different chemotherapeutic strategies are systematically reviewed as well.
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Affiliation(s)
- Gauri S Shetye
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois
| | - Scott G Franzblau
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois
| | - Sanghyun Cho
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois.
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20
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Tan YZ, Zhang L, Rodrigues J, Zheng RB, Giacometti SI, Rosário AL, Kloss B, Dandey VP, Wei H, Brunton R, Raczkowski AM, Athayde D, Catalão MJ, Pimentel M, Clarke OB, Lowary TL, Archer M, Niederweis M, Potter CS, Carragher B, Mancia F. Cryo-EM Structures and Regulation of Arabinofuranosyltransferase AftD from Mycobacteria. Mol Cell 2020; 78:683-699.e11. [PMID: 32386575 PMCID: PMC7263364 DOI: 10.1016/j.molcel.2020.04.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/21/2020] [Accepted: 04/13/2020] [Indexed: 01/21/2023]
Abstract
Mycobacterium tuberculosis causes tuberculosis, a disease that kills over 1 million people each year. Its cell envelope is a common antibiotic target and has a unique structure due, in part, to two lipidated polysaccharides-arabinogalactan and lipoarabinomannan. Arabinofuranosyltransferase D (AftD) is an essential enzyme involved in assembling these glycolipids. We present the 2.9-Å resolution structure of M. abscessus AftD, determined by single-particle cryo-electron microscopy. AftD has a conserved GT-C glycosyltransferase fold and three carbohydrate-binding modules. Glycan array analysis shows that AftD binds complex arabinose glycans. Additionally, AftD is non-covalently complexed with an acyl carrier protein (ACP). 3.4- and 3.5-Å structures of a mutant with impaired ACP binding reveal a conformational change, suggesting that ACP may regulate AftD function. Mutagenesis experiments using a conditional knockout constructed in M. smegmatis confirm the essentiality of the putative active site and the ACP binding for AftD function.
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Affiliation(s)
- Yong Zi Tan
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA; National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Lei Zhang
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - José Rodrigues
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
| | | | - Sabrina I Giacometti
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Ana L Rosário
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
| | - Brian Kloss
- Center on Membrane Protein Production and Analysis, New York Structural Biology Center, New York, NY 10027, USA
| | - Venkata P Dandey
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Hui Wei
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Richard Brunton
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Ashleigh M Raczkowski
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Diogo Athayde
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
| | - Maria João Catalão
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Madalena Pimentel
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Oliver B Clarke
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA; Department of Anesthesiology, Columbia University, New York, NY 10032, USA
| | - Todd L Lowary
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; Institute of Biological Chemistry, Academia Sinica, Academia Road, Section 2, #128 Nangang, Taipei 11529, Taiwan
| | - Margarida Archer
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
| | - Michael Niederweis
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Clinton S Potter
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Bridget Carragher
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA.
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21
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Cryo-EM snapshots of mycobacterial arabinosyltransferase complex EmbB 2-AcpM 2. Protein Cell 2020; 11:505-517. [PMID: 32363534 PMCID: PMC7305291 DOI: 10.1007/s13238-020-00726-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 11/27/2019] [Indexed: 01/26/2023] Open
Abstract
Inhibition of Mycobacterium tuberculosis (Mtb) cell wall assembly is an established strategy for anti-TB chemotherapy. Arabinosyltransferase EmbB, which catalyzes the transfer of arabinose from the donor decaprenyl-phosphate-arabinose (DPA) to its arabinosyl acceptor is an essential enzyme for Mtb cell wall synthesis. Analysis of drug resistance mutations suggests that EmbB is the main target of the front-line anti-TB drug, ethambutol. Herein, we report the cryo-EM structures of Mycobacterium smegmatis EmbB in its “resting state” and DPA-bound “active state”. EmbB is a fifteen-transmembrane-spanning protein, assembled as a dimer. Each protomer has an associated acyl-carrier-protein (AcpM) on their cytoplasmic surface. Conformational changes upon DPA binding indicate an asymmetric movement within the EmbB dimer during catalysis. Functional studies have identified critical residues in substrate recognition and catalysis, and demonstrated that ethambutol inhibits transferase activity of EmbB by competing with DPA. The structures represent the first step directed towards a rational approach for anti-TB drug discovery.
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22
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Zhang L, Zhao Y, Gao Y, Wu L, Gao R, Zhang Q, Wang Y, Wu C, Wu F, Gurcha SS, Veerapen N, Batt SM, Zhao W, Qin L, Yang X, Wang M, Zhu Y, Zhang B, Bi L, Zhang X, Yang H, Guddat LW, Xu W, Wang Q, Li J, Besra GS, Rao Z. Structures of cell wall arabinosyltransferases with the anti-tuberculosis drug ethambutol. Science 2020; 368:1211-1219. [PMID: 32327601 DOI: 10.1126/science.aba9102] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/06/2020] [Accepted: 04/14/2020] [Indexed: 11/02/2022]
Abstract
The arabinosyltransferases EmbA, EmbB, and EmbC are involved in Mycobacterium tuberculosis cell wall synthesis and are recognized as targets for the anti-tuberculosis drug ethambutol. In this study, we determined cryo-electron microscopy and x-ray crystal structures of mycobacterial EmbA-EmbB and EmbC-EmbC complexes in the presence of their glycosyl donor and acceptor substrates and with ethambutol. These structures show how the donor and acceptor substrates bind in the active site and how ethambutol inhibits arabinosyltransferases by binding to the same site as both substrates in EmbB and EmbC. Most drug-resistant mutations are located near the ethambutol binding site. Collectively, our work provides a structural basis for understanding the biochemical function and inhibition of arabinosyltransferases and the development of new anti-tuberculosis agents.
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Affiliation(s)
- Lu Zhang
- Shanghai Institute for Advanced Immunochemical Studies, iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Response, College of Life Sciences, College of Pharmacy, Nankai University, Tianjin 300353, China
| | - Yao Zhao
- Shanghai Institute for Advanced Immunochemical Studies, iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Gao
- Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China
| | - Lijie Wu
- Shanghai Institute for Advanced Immunochemical Studies, iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ruogu Gao
- University of Chinese Academy of Sciences, Beijing 100101, China.,National Laboratory of Biomacromolecules and Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, CAS, Beijing 100101, China
| | - Qi Zhang
- Shanghai Institute for Advanced Immunochemical Studies, iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yinan Wang
- Shanghai Institute for Advanced Immunochemical Studies, iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100101, China
| | - Chengyao Wu
- Shanghai Institute for Advanced Immunochemical Studies, iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Fangyu Wu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Response, College of Life Sciences, College of Pharmacy, Nankai University, Tianjin 300353, China
| | - Sudagar S Gurcha
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Natacha Veerapen
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Sarah M Batt
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Wei Zhao
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Response, College of Life Sciences, College of Pharmacy, Nankai University, Tianjin 300353, China
| | - Ling Qin
- Shanghai Institute for Advanced Immunochemical Studies, iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiuna Yang
- Shanghai Institute for Advanced Immunochemical Studies, iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Manfu Wang
- Shanghai Institute for Advanced Immunochemical Studies, iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yan Zhu
- Shanghai Institute for Advanced Immunochemical Studies, iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Bing Zhang
- Shanghai Institute for Advanced Immunochemical Studies, iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Lijun Bi
- National Laboratory of Biomacromolecules and Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, CAS, Beijing 100101, China
| | - Xian'en Zhang
- National Laboratory of Biomacromolecules and Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, CAS, Beijing 100101, China
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies, iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Wenqing Xu
- Shanghai Institute for Advanced Immunochemical Studies, iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Quan Wang
- Shanghai Institute for Advanced Immunochemical Studies, iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China. .,National Laboratory of Biomacromolecules and Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, CAS, Beijing 100101, China
| | - Jun Li
- Shanghai Institute for Advanced Immunochemical Studies, iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
| | - Gurdyal S Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
| | - Zihe Rao
- Shanghai Institute for Advanced Immunochemical Studies, iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China. .,State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Response, College of Life Sciences, College of Pharmacy, Nankai University, Tianjin 300353, China.,Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China.,National Laboratory of Biomacromolecules and Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, CAS, Beijing 100101, China
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Mycobacterial Cell Wall: A Source of Successful Targets for Old and New Drugs. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10072278] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Eighty years after the introduction of the first antituberculosis (TB) drug, the treatment of drug-susceptible TB remains very cumbersome, requiring the use of four drugs (isoniazid, rifampicin, ethambutol and pyrazinamide) for two months followed by four months on isoniazid and rifampicin. Two of the drugs used in this “short”-course, six-month chemotherapy, isoniazid and ethambutol, target the mycobacterial cell wall. Disruption of the cell wall structure can enhance the entry of other TB drugs, resulting in a more potent chemotherapy. More importantly, inhibition of cell wall components can lead to mycobacterial cell death. The complexity of the mycobacterial cell wall offers numerous opportunities to develop drugs to eradicate Mycobacterium tuberculosis, the causative agent of TB. In the past 20 years, researchers from industrial and academic laboratories have tested new molecules to find the best candidates that will change the face of TB treatment: drugs that will shorten TB treatment and be efficacious against active and latent, as well as drug-resistant TB. Two of these new TB drugs block components of the mycobacterial cell wall and have reached phase 3 clinical trial. This article reviews TB drugs targeting the mycobacterial cell wall in use clinically and those in clinical development.
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Abstract
Macozinone, a piperazine-benzothiazinone PBTZ169, is currently undergoing Phase 1/2 clinical studies for the treatment of tuberculosis (TB). In this review we summarize the key findings that led to the development of this compound and to identification of its target, decaprenylphospohoryl ribose oxidase DprE1, which is involved in the synthesis of the essential arabinan polymers of the cell wall in a TB pathogen, Mycobacterium tuberculosis. We present the results of the pilot clinical studies, which raise optimism regarding its further development towards more efficient TB drug regimens.
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Biosynthesis of Galactan in Mycobacterium tuberculosis as a Viable TB Drug Target? Antibiotics (Basel) 2020; 9:antibiotics9010020. [PMID: 31935842 PMCID: PMC7168186 DOI: 10.3390/antibiotics9010020] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 12/27/2019] [Accepted: 01/02/2020] [Indexed: 12/21/2022] Open
Abstract
While target-based drug design has proved successful in several therapeutic areas, this approach has not yet provided compelling outcomes in the field of antibacterial agents. This statement remains especially true for the development of novel therapeutic interventions against tuberculosis, an infectious disease that is among the top ten leading causes of death globally. Mycobacterial galactan is an important component of the protective cell wall core of the tuberculosis pathogen and it could provide a promising target for the design of new drugs. In this review, we summarize the current knowledge on galactan biosynthesis in Mycobacterium tuberculosis, including landmark findings that led to the discovery and understanding of three key enzymes in this pathway: UDP-galactose mutase, and galactofuranosyl transferases GlfT1 and GlfT2. Moreover, we recapitulate the efforts aimed at their inhibition. The predicted common transition states of the three enzymes provide the lucrative possibility of multitargeting in pharmaceutical development, a favourable property in the mitigation of drug resistance. We believe that a tight interplay between target-based computational approaches and experimental methods will result in the development of original inhibitors that could serve as the basis of a new generation of drugs against tuberculosis.
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Characterization of Arabinosyl Transfer Reactions in the Biosynthesis of Mycobacterial Cell Envelope (Lipo)Polysaccharides. Methods Mol Biol 2019. [PMID: 30864132 DOI: 10.1007/978-1-4939-9154-9_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
D-Arabinofuranose is a major glycosyl constituent of mycobacteria found in two essential cell envelope heteropolysaccharides, arabinogalactan and lipoarabinomannan. Seven different arabinosyltransferases at least are required to synthesize the arabinan domain of these two major glycans. Because of their interest from the perspective of drug development, these enzymes have been the object of intense investigations. In this chapter, we describe the protocols used to perform nonradioactive arabinosyltransferase assays with synthetic acceptor and donor substrates and characterize the enzymatic products of the reactions by mass spectrometry.
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27
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Liu K, Wang L, Guo Z. An extensive review of studies on mycobacterium cell wall polysaccharide-related oligosaccharides – part III: synthetic studies and biological applications of arabinofuranosyl oligosaccharides and their analogs, derivatives and conjugates. J Carbohydr Chem 2019. [DOI: 10.1080/07328303.2019.1630841] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Kechun Liu
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Ji′nan, Shandong, China
| | - Lizhen Wang
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Ji′nan, Shandong, China
| | - Zhongwu Guo
- Department of Chemistry, University of Florida, Gainesville, FL, USA
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28
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Calabretta PJ, Hodges HL, Kraft MB, Marando VM, Kiessling LL. Bacterial Cell Wall Modification with a Glycolipid Substrate. J Am Chem Soc 2019; 141:9262-9272. [PMID: 31081628 DOI: 10.1021/jacs.9b02290] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite the ubiquity and importance of glycans in biology, methods to probe their structures in cells are limited. Mammalian glycans can be modulated using metabolic incorporation, a process in which non-natural sugars are taken up by cells, converted to nucleotide-sugar intermediates, and incorporated into glycans via biosynthetic pathways. These studies have revealed that glycan intermediates can be shunted through multiple pathways, and this complexity can be heightened in bacteria, as they can catabolize diverse glycans. We sought to develop a strategy that probes structures recalcitrant to metabolic incorporation and that complements approaches focused on nucleotide sugars. We reasoned that lipid-linked glycans, which are intermediates directly used in glycan biosynthesis, would offer an alternative. We generated synthetic arabinofuranosyl phospholipids to test this strategy in Corynebacterium glutamicum and Mycobacterium smegmatis, organisms that serve as models of Mycobacterium tuberculosis. Using a C. glutamicum mutant that lacks arabinan, we identified synthetic glycosyl donors whose addition restores cell wall arabinan, demonstrating that non-natural glycolipids can serve as biosynthetic intermediates and function in chemical complementation. The addition of an isotopically labeled glycan substrate facilitated cell wall characterization by NMR. Structural analysis revealed that all five known arabinofuranosyl transferases could process the exogenous lipid-linked sugar donor, allowing for the full recovery of the cell envelope. The lipid-based probe could also rescue wild-type cells treated with an inhibitor of cell wall biosynthesis. Our data indicate that surrogates of natural lipid-linked glycans can intervene in the cell's traditional workflow, indicating that biosynthetic incorporation is a powerful strategy for probing glycan structure and function.
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Affiliation(s)
- Phillip J Calabretta
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | | | | | - Victoria M Marando
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Laura L Kiessling
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
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29
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Abstract
Actinobacteria is a group of diverse bacteria. Most species in this class of bacteria are filamentous aerobes found in soil, including the genus Streptomyces perhaps best known for their fascinating capabilities of producing antibiotics. These bacteria typically have a Gram-positive cell envelope, comprised of a plasma membrane and a thick peptidoglycan layer. However, there is a notable exception of the Corynebacteriales order, which has evolved a unique type of outer membrane likely as a consequence of convergent evolution. In this chapter, we will focus on the unique cell envelope of this order. This cell envelope features the peptidoglycan layer that is covalently modified by an additional layer of arabinogalactan . Furthermore, the arabinogalactan layer provides the platform for the covalent attachment of mycolic acids , some of the longest natural fatty acids that can contain ~100 carbon atoms per molecule. Mycolic acids are thought to be the main component of the outer membrane, which is composed of many additional lipids including trehalose dimycolate, also known as the cord factor. Importantly, a subset of bacteria in the Corynebacteriales order are pathogens of human and domestic animals, including Mycobacterium tuberculosis. The surface coat of these pathogens are the first point of contact with the host immune system, and we now know a number of host receptors specific to molecular patterns exposed on the pathogen's surface, highlighting the importance of understanding how the cell envelope of Actinobacteria is structured and constructed. This chapter describes the main structural and biosynthetic features of major components found in the actinobacterial cell envelopes and highlights the key differences between them.
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Affiliation(s)
- Kathryn C Rahlwes
- Department of Microbiology, University of Massachusetts, 639 North Pleasant Street, Amherst, MA, 01003, USA
| | - Ian L Sparks
- Department of Microbiology, University of Massachusetts, 639 North Pleasant Street, Amherst, MA, 01003, USA
| | - Yasu S Morita
- Department of Microbiology, University of Massachusetts, 639 North Pleasant Street, Amherst, MA, 01003, USA.
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30
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31
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Recent therapeutic approaches for the management of tuberculosis: Challenges and opportunities. Biomed Pharmacother 2018; 99:735-745. [DOI: 10.1016/j.biopha.2018.01.115] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/23/2018] [Accepted: 01/24/2018] [Indexed: 11/19/2022] Open
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32
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Anti-tubercular drug discovery: in silico implications and challenges. Eur J Pharm Sci 2017; 104:1-15. [PMID: 28341614 DOI: 10.1016/j.ejps.2017.03.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/08/2017] [Accepted: 03/19/2017] [Indexed: 12/18/2022]
Abstract
Tuberculosis (TB) has been reported as a major public health concern, especially in the developing countries. WHO report on tuberculosis 2016 shows a high mortality rate caused by TB leading to 1.8 million deaths worldwide (including deaths due to TB in HIV positive individuals), which is one of the top 10 causes of mortality in 2015. However, the main therapy used for the treatment of TB is still the Direct Observed Therapy Short-course (DOTS) that consists of four main first-line drugs. Due to the prolonged and unorganized use of these drugs, Mycobacterium tuberculosis (Mtb) has developed drug-resistance against them. To overcome this drug-resistance, efforts are continuously being made to develop new therapeutics. New drug-targets of Mtb are pursued by the researchers to develop their inhibitors. For this, new methodologies that comprise of the computational drug designing techniques are vigorously applied. A major limitation that is found with these techniques is the inability of the newly identified target-based inhibitors to inhibit the whole cell bacteria. A foremost factor for this limitation is the inability of these inhibitors to penetrate the bacterial cell wall. In this regard, various strategies to overcome this limitation have been discussed in detail in this review, along with new targets and new methodologies. A bunch of in silico tools available for the prediction of physicochemical properties that need to be explored to deal with the permeability issue of the Mtb inhibitors has also been discussed.
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33
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Angala SK, McNeil MR, Shi L, Joe M, Pham H, Zuberogoitia S, Nigou J, Boot CM, Lowary TL, Gilleron M, Jackson M. Biosynthesis of the Methylthioxylose Capping Motif of Lipoarabinomannan in Mycobacterium tuberculosis. ACS Chem Biol 2017; 12:682-691. [PMID: 28075556 DOI: 10.1021/acschembio.6b01071] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Lipoarabinomannan (LAM) is a lipoglycan found in abundant quantities in the cell envelope of all mycobacteria. The nonreducing arabinan termini of LAM display species-specific structural microheterogeneity that impacts the biological activity of the entire molecule. Mycobacterium tuberculosis, for instance, produces mannoside caps made of one to three α-(1 → 2)-Manp-linked residues that may be further substituted with an α-(1 → 4)-linked methylthio-d-xylose (MTX) residue. While the biological functions and catalytic steps leading to the formation of the mannoside caps of M. tuberculosis LAM have been well established, the biosynthetic origin and biological relevance of the MTX motif remain elusive. We here report on the discovery of a five-gene cluster dedicated to the biosynthesis of the MTX capping motif of M. tuberculosis LAM, and on the functional characterization of two glycosyltransferases, MtxS and MtxT, responsible, respectively, for the production of decaprenyl-phospho-MTX (DP-MTX) and the transfer of MTX from DP-MTX to the mannoside caps of LAM. Collectively, our NMR spectroscopic and mass spectrometric analyses of mtxS and mtxT overexpressors and knockout mutants support a biosynthetic model wherein the conversion of 5'-methylthioadenosine, which is a ubiquitous byproduct of spermidine biosynthesis, into 5'-methylthioribose-1-phosphate precedes the formation of a 5'-methylthioribose nucleotide sugar, followed by the epimerization at C-3 of the ribose residue, and the transfer of MTX from the nucleotide sugar to decaprenyl-phosphate yielding the substrate for transfer onto LAM. The conservation of the MTX biosynthetic genes in a number of Actinomycetes suggests that this discrete glycosyl substituent may be more widespread in prokaryotes than originally thought.
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Affiliation(s)
- Shiva kumar Angala
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology and
Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, United States
| | - Michael R. McNeil
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology and
Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, United States
| | - Libin Shi
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology and
Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, United States
| | - Maju Joe
- Alberta
Glycomics Centre and Department of Chemistry, The University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Ha Pham
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology and
Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, United States
| | - Sophie Zuberogoitia
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 205 route de Narbonne, F-31077 Toulouse, France
| | - Jérôme Nigou
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 205 route de Narbonne, F-31077 Toulouse, France
| | - Claudia M. Boot
- Central
Instrumentation Facility, Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872, United States
| | - Todd L. Lowary
- Alberta
Glycomics Centre and Department of Chemistry, The University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Martine Gilleron
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 205 route de Narbonne, F-31077 Toulouse, France
| | - Mary Jackson
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology and
Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, United States
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Abstract
Mycobacterium tuberculosis (Mtb), the etiological agent of tuberculosis (TB), is recognized as a global health emergency as promoted by the World Health Organization. Over 1 million deaths per year, along with the emergence of multi- and extensively-drug resistant strains of Mtb, have triggered intensive research into the pathogenicity and biochemistry of this microorganism, guiding the development of anti-TB chemotherapeutic agents. The essential mycobacterial cell wall, sharing some common features with all bacteria, represents an apparent ‘Achilles heel’ that has been targeted by TB chemotherapy since the advent of TB treatment. This complex structure composed of three distinct layers, peptidoglycan, arabinogalactan and mycolic acids, is vital in supporting cell growth, virulence and providing a barrier to antibiotics. The fundamental nature of cell wall synthesis and assembly has rendered the mycobacterial cell wall as the most widely exploited target of anti-TB drugs. This review provides an overview of the biosynthesis of the prominent cell wall components, highlighting the inhibitory mechanisms of existing clinical drugs and illustrating the potential of other unexploited enzymes as future drug targets.
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Islam MM, Hameed HMA, Mugweru J, Chhotaray C, Wang C, Tan Y, Liu J, Li X, Tan S, Ojima I, Yew WW, Nuermberger E, Lamichhane G, Zhang T. Drug resistance mechanisms and novel drug targets for tuberculosis therapy. J Genet Genomics 2016; 44:21-37. [PMID: 28117224 DOI: 10.1016/j.jgg.2016.10.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/26/2016] [Accepted: 10/10/2016] [Indexed: 10/20/2022]
Abstract
Drug-resistant tuberculosis (TB) poses a significant challenge to the successful treatment and control of TB worldwide. Resistance to anti-TB drugs has existed since the beginning of the chemotherapy era. New insights into the resistant mechanisms of anti-TB drugs have been provided. Better understanding of drug resistance mechanisms helps in the development of new tools for the rapid diagnosis of drug-resistant TB. There is also a pressing need in the development of new drugs with novel targets to improve the current treatment of TB and to prevent the emergence of drug resistance in Mycobacterium tuberculosis. This review summarizes the anti-TB drug resistance mechanisms, furnishes some possible novel drug targets in the development of new agents for TB therapy and discusses the usefulness using known targets to develop new anti-TB drugs. Whole genome sequencing is currently an advanced technology to uncover drug resistance mechanisms in M. tuberculosis. However, further research is required to unravel the significance of some newly discovered gene mutations in their contribution to drug resistance.
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Affiliation(s)
- Md Mahmudul Islam
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - H M Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Julius Mugweru
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chiranjibi Chhotaray
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Changwei Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Institute of Chemical Biology and Drug Discovery, Stony Brook University-State University of New York, Stony Brook, NY 11794-3400, USA
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Xinjie Li
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Shouyong Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Iwao Ojima
- Institute of Chemical Biology and Drug Discovery, Stony Brook University-State University of New York, Stony Brook, NY 11794-3400, USA
| | - Wing Wai Yew
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Eric Nuermberger
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, MD 21231-1002, USA
| | - Gyanu Lamichhane
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, MD 21231-1002, USA
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Mikušová K, Ekins S. Learning from the past for TB drug discovery in the future. Drug Discov Today 2016; 22:534-545. [PMID: 27717850 DOI: 10.1016/j.drudis.2016.09.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 09/25/2016] [Accepted: 09/28/2016] [Indexed: 12/14/2022]
Abstract
Tuberculosis drug discovery has shifted in recent years from a primarily target-based approach to one that uses phenotypic high-throughput screens. As examples of this, through our EU-funded FP7 collaborations, New Medicines for Tuberculosis was target-based and our more-recent More Medicines for Tuberculosis project predominantly used phenotypic screening. From these projects we have examples of success (DprE1) and failure (PimA) going from drug to target and from target to drug, respectively. It is clear that we still have much to learn about the drug targets and the complex effects of the drugs on Mycobacterium tuberculosis. We propose a more integrated approach that learns from earlier drug discovery efforts that could help to move drug discovery forward.
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Affiliation(s)
- Katarína Mikušová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Sean Ekins
- Collaborative Drug Discovery, Inc., 1633 Bayshore Highway, Suite 342, Burlingame, CA 94010, USA; Collaborations in Chemistry, 5616 Hilltop Needmore Road, Fuquay Varina, NC 27526, USA.
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Abstract
The cell wall of Mycobacterium tuberculosis is unique in that it differs significantly from those of both Gram-negative and Gram-positive bacteria. The thick, carbohydrate- and lipid-rich cell wall with distinct lipoglycans enables mycobacteria to survive under hostile conditions such as shortage of nutrients and antimicrobial exposure. The key features of this highly complex cell wall are the mycolyl-arabinogalactan-peptidoglycan (mAGP)-based and phosphatidyl-myo-inositol-based macromolecular structures, with the latter possessing potent immunomodulatory properties. These structures are crucial for the growth, viability, and virulence of M. tuberculosis and therefore are often the targets of effective chemotherapeutic agents against tuberculosis. Over the past decade, sophisticated genomic and molecular tools have advanced our understanding of the primary structure and biosynthesis of these macromolecules. The availability of the full genome sequences of various mycobacterial species, including M. tuberculosis, Mycobacterium marinum, and Mycobacterium bovis BCG, have greatly facilitated the identification of large numbers of drug targets and antigens specific to tuberculosis. Techniques to manipulate mycobacteria have also improved extensively; the conditional expression-specialized transduction essentiality test (CESTET) is currently used to determine the essentiality of individual genes. Finally, various biosynthetic assays using either purified proteins or synthetic cell wall acceptors have been developed to study enzyme function. This article focuses on the recent advances in determining the structural details and biosynthesis of arabinogalactan, lipoarabinomannan, and related glycoconjugates.
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Abstract
This article summarizes what is currently known of the structures, physiological roles, involvement in pathogenicity, and biogenesis of a variety of noncovalently bound cell envelope lipids and glycoconjugates of Mycobacterium tuberculosis and other Mycobacterium species. Topics addressed in this article include phospholipids; phosphatidylinositol mannosides; triglycerides; isoprenoids and related compounds (polyprenyl phosphate, menaquinones, carotenoids, noncarotenoid cyclic isoprenoids); acyltrehaloses (lipooligosaccharides, trehalose mono- and di-mycolates, sulfolipids, di- and poly-acyltrehaloses); mannosyl-beta-1-phosphomycoketides; glycopeptidolipids; phthiocerol dimycocerosates, para-hydroxybenzoic acids, and phenolic glycolipids; mycobactins; mycolactones; and capsular polysaccharides.
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Synthesis and anti-tuberculosis activity of glycitylamines. Bioorg Med Chem 2016; 24:693-702. [PMID: 26810833 DOI: 10.1016/j.bmc.2015.12.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 12/16/2015] [Accepted: 12/22/2015] [Indexed: 11/23/2022]
Abstract
A series of glycitylamines, which were prepared in few steps from readily available carbohydrates, were tested for their ability to inhibit tuberculosis growth in an Alamar Blue BCG colourimetric assay. Several derivatives, including (2R,3R)-1-(hexadecylamine)pent-4-ene-2,3-diol, (2R,3R)-1-(hexadecylmethylamino)pent-4-ene-2,3-diol and 5-deoxy-5-hexadecylmethylamino-D-arabinitol, were prepared in good to excellent (44-90%) overall yield and exhibited micromolar (20-41μM) inhibitory activity that was similar to the first line tuberculosis (TB) drug ethambutol (39μM) in the same assay. The ease and low cost of the synthesis of the glycitylamines offers definite advantages for their use as potential TB drugs.
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40
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Abstract
In this chapter we review the molecular mechanisms of drug resistance to the major first- and second-line antibiotics used to treat tuberculosis.
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41
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Batt SM, Cacho Izquierdo M, Castro Pichel J, Stubbs CJ, Vela-Glez Del Peral L, Pérez-Herrán E, Dhar N, Mouzon B, Rees M, Hutchinson JP, Young RJ, McKinney JD, Barros Aguirre D, Ballell L, Besra GS, Argyrou A. Whole Cell Target Engagement Identifies Novel Inhibitors of Mycobacterium tuberculosis Decaprenylphosphoryl-β-d-ribose Oxidase. ACS Infect Dis 2015; 1:615-26. [PMID: 27623058 DOI: 10.1021/acsinfecdis.5b00065] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We have targeted the Mycobacterium tuberculosis decaprenylphosphoryl-β-d-ribose oxidase (Mt-DprE1) for potential chemotherapeutic intervention of tuberculosis. A multicopy suppression strategy that overexpressed Mt-DprE1 in M. bovis BCG was used to profile the publically available GlaxoSmithKline antimycobacterial compound set, and one compound (GSK710) was identified that showed an 8-fold higher minimum inhibitory concentration relative to the control strain. Analogues of GSK710 show a clear relationship between whole cell potency and in vitro activity using an enzymatic assay employing recombinant Mt-DprE1, with binding affinity measured by fluorescence quenching of the flavin cofactor of the enzyme. M. bovis BCG spontaneous resistant mutants to GSK710 and a closely related analogue were isolated and sequencing of ten such mutants revealed a single point mutation at two sites, E221Q or G248S within DprE1, providing further evidence that DprE1 is the main target of these compounds. Finally, time-lapse microscopy experiments showed that exposure of M. tuberculosis to a compound of this series arrests bacterial growth rapidly followed by a slower cytolysis phase.
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Affiliation(s)
- Sarah M. Batt
- School
of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | | | | | | | | | | | - Neeraj Dhar
- School
of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | | | | | | | | | - John D. McKinney
- School
of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | | | | | - Gurdyal S. Besra
- School
of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
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42
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Jayawardana KW, Wijesundera SA, Yan M. Aggregation-based detection of M. smegmatis using D-arabinose-functionalized fluorescent silica nanoparticles. Chem Commun (Camb) 2015; 51:15964-6. [PMID: 26379182 PMCID: PMC4618767 DOI: 10.1039/c5cc05772h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fluorescein-doped silica nanoparticles (FSNPs) functionalized with D-arabinose (Ara) showed strong interactions with Mycobacterium smegmatis (M. smegmatis) and caused the bacteria to aggregate. This aggregate formation was used as a means to detect M. smegmatis at the concentration of 10(4) CFU per mL.
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Affiliation(s)
- Kalana W Jayawardana
- Department of Chemistry, University of Massachusetts Lowell, Lowell, MA 01854, USA.
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43
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Affiliation(s)
- Monika Jankute
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom;
| | - Jonathan A.G. Cox
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom;
| | - James Harrison
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom;
| | - Gurdyal S. Besra
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom;
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44
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GtrA Protein Rv3789 Is Required for Arabinosylation of Arabinogalactan in Mycobacterium tuberculosis. J Bacteriol 2015; 197:3686-97. [PMID: 26369580 DOI: 10.1128/jb.00628-15] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 09/07/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Mycobacterium tuberculosis possesses a thick and highly hydrophobic cell wall principally composed of a mycolyl-arabinogalactan-peptidoglycan complex, which is critical for survival and virulence. DprE1 is a well-characterized component of decaprenyl-phospho-ribose epimerase, which produces decaprenyl-phospho-arabinose (DPA) for the biosynthesis of mycobacterial arabinans. Upstream of dprE1 lies rv3789, which encodes a short transmembrane protein of the GtrA family, whose members are often involved in the synthesis of cell surface polysaccharides. We demonstrate that rv3789 and dprE1 are cotranscribed from a common transcription start site situated 64 bp upstream of rv3789. Topology mapping revealed four transmembrane domains in Rv3789 and a cytoplasmic C terminus consistent with structural models built using analysis of sequence coevolution. To investigate its role, we generated an unmarked rv3789 deletion mutant in M. tuberculosis. The mutant was characterized by impaired growth and abnormal cell morphology, since the cells were shorter and more swollen than wild-type cells. This phenotype likely stems from the decreased incorporation of arabinan into arabinogalactan and was accompanied by an accumulation of DPA. A role for Rv3789 in arabinan biosynthesis was further supported by its interaction with the priming arabinosyltransferase AftA, as demonstrated by a two-hybrid approach. Taken together, the data suggest that Rv3789 does not act as a DPA flippase but, rather, recruits AftA for arabinogalactan biosynthesis. IMPORTANCE Upstream of the essential dprE1 gene, encoding a key enzyme of the decaprenyl phospho-arabinose (DPA) pathway, lies rv3789, coding for a short transmembrane protein of unknown function. In this study, we demonstrated that rv3789 and dprE1 are cotranscribed from a common transcription start site located 64 bp upstream of rv3789 in M. tuberculosis. Furthermore, the deletion of rv3789 led to a reduction in arabinan content and to an accumulation of DPA, confirming that Rv3789 plays a role in arabinan biosynthesis. Topology mapping, structural modeling, and protein interaction studies suggest that Rv3789 acts as an anchor protein recruiting AftA, the first arabinosyl transferase. This investigation provides deeper insight into the mechanism of arabinan biosynthesis in mycobacteria.
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45
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Islam M, Gayatri G, Hotha S. Influence of Steric Crowding on Diastereoselective Arabinofuranosylations. J Org Chem 2015. [PMID: 26195010 DOI: 10.1021/acs.joc.5b00964] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The occurrence of arabinofuranosides on the cell surface of Mycobacterium tuberculosis (Mtb) and their significance in controlling disease spurred interest in developing strategies for their diastereoselective synthesis. Mtb uses enzymes to achieve diastereoselectivity through noncovalent interactions. Of the two possible glycosidic linkages, chemically, 1,2-trans linkage is relatively easy to synthesize by taking advantage of neighboring group participation, whereas synthesis of the 1,2-cis linkage is notoriously difficult. In this article, stereochemical effects on the diastereoselectivity of arabinofuranosidation are investigated with thiopyridyl, imidate, and thiotolyl donors as well as differently crowded glycosyl acceptors; subtle differences in the stereochemical environment of the acceptors were observed to alter the diastereoselectivity of the furanoside formation. Results from this endeavor suggest that 1,2-cis arabinofuranosides can be synthesized conveniently by conducting the reaction at lower temperature on sterically demanding and less reactive substrates.
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Affiliation(s)
- Maidul Islam
- †Department of Chemistry, Indian Institute of Science Education and Research, Pune 411 008, India
| | - Gaddamanugu Gayatri
- ‡Centre for Molecular Modelling, Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - Srinivas Hotha
- †Department of Chemistry, Indian Institute of Science Education and Research, Pune 411 008, India
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46
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The sweet tooth of bacteria: common themes in bacterial glycoconjugates. Microbiol Mol Biol Rev 2015; 78:372-417. [PMID: 25184559 DOI: 10.1128/mmbr.00007-14] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Humans have been increasingly recognized as being superorganisms, living in close contact with a microbiota on all their mucosal surfaces. However, most studies on the human microbiota have focused on gaining comprehensive insights into the composition of the microbiota under different health conditions (e.g., enterotypes), while there is also a need for detailed knowledge of the different molecules that mediate interactions with the host. Glycoconjugates are an interesting class of molecules for detailed studies, as they form a strain-specific barcode on the surface of bacteria, mediating specific interactions with the host. Strikingly, most glycoconjugates are synthesized by similar biosynthesis mechanisms. Bacteria can produce their major glycoconjugates by using a sequential or an en bloc mechanism, with both mechanistic options coexisting in many species for different macromolecules. In this review, these common themes are conceptualized and illustrated for all major classes of known bacterial glycoconjugates, with a special focus on the rather recently emergent field of glycosylated proteins. We describe the biosynthesis and importance of glycoconjugates in both pathogenic and beneficial bacteria and in both Gram-positive and -negative organisms. The focus lies on microorganisms important for human physiology. In addition, the potential for a better knowledge of bacterial glycoconjugates in the emerging field of glycoengineering and other perspectives is discussed.
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47
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Jiang T, Cai L, Zhao X, He L, Ma Y, Zang S, Zhang C, Li X, Xin Y. Functional identification of MSMEG_6402 protein from Mycobacterium smegmatis in decaprenylphosphoryl-D-arabinose biosynthesis. Microb Pathog 2014; 76:44-50. [PMID: 25223716 DOI: 10.1016/j.micpath.2014.09.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Revised: 08/18/2014] [Accepted: 09/11/2014] [Indexed: 11/24/2022]
Abstract
The arabinogalactan (AG) of the mycobacterial cell wall consists of an arabinan region, a galactan region and a disaccharide linker. Decaprenylphosphoryl-D-arabinose (DPA) is the donor for arabinofuran residues, which are formed from phosphoribose diphosphate (PRPP) and decaprenyl phosphate (DP). DP is sequentially catalyzed by a three-step process that involves a transferase, a phosphatase and an epimerase. Rv3807c is a putative phospholipid phosphatase that might generate the intermediate product of decaprenyl-phosphoryl-ribose (DPR) in DPA biosynthesis. Mycobacterium smegmatis MSMEG_6402 is a homolog gene of Mycobacterium tuberculosis Rv3807c and was substituted for the functional identification of Rv3807c. Previously, we generated a conditional MSMEG_6402 gene knockout strain (M. sm-ΔM_6402) that exhibited significantly affected cell wall structure. To understand the function of MSMEG_6402 in DPA biosynthesis, this gene was amplified and expressed, and the resulting protein was identified and purified using a His-tagged approach. A MSMEG_6402 enzymatic reaction system with PRPP and DP as substrates was utilized, and the reaction products were separated using thin layer chromatography (TLC). The results revealed a specific lipid-linked sugar band that appeared in the reaction with the addition of MSMEG_6402. Furthermore, ESI-MS detection was utilized in this study, and the results revealed that the enzymatic reaction products involving MSMEG_6402 included DPPR and a sodium ion adduct of DPR. Additionally, the phosphatase activity of MSMEG_6402 was also determined through phosphate group detection using the colorimetric method. Based on our results together with the results of previous studies, including the functional identification and bioinformatics analysis of M. tuberculosis Rv3807c, we propose that MSMEG_6402, as a phosphatase, has an intimate relationship with DPA biosynthesis.
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Affiliation(s)
- Tao Jiang
- Department of Biotechnology, Dalian Medical University, Dalian 116044, China
| | - Lina Cai
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China
| | - Xiaojiao Zhao
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China
| | - Lianqi He
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China
| | - Yufang Ma
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China
| | - Shizhu Zang
- Department of Biotechnology, Dalian Medical University, Dalian 116044, China
| | - Cuili Zhang
- Department of Biotechnology, Dalian Medical University, Dalian 116044, China
| | - Xinli Li
- Department of Biotechnology, Dalian Medical University, Dalian 116044, China
| | - Yi Xin
- Department of Biotechnology, Dalian Medical University, Dalian 116044, China.
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48
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Angala SK, Belardinelli JM, Huc-Claustre E, Wheat WH, Jackson M. The cell envelope glycoconjugates of Mycobacterium tuberculosis. Crit Rev Biochem Mol Biol 2014; 49:361-99. [PMID: 24915502 PMCID: PMC4436706 DOI: 10.3109/10409238.2014.925420] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Tuberculosis (TB) remains the second most common cause of death due to a single infectious agent. The cell envelope of Mycobacterium tuberculosis (Mtb), the causative agent of the disease in humans, is a source of unique glycoconjugates and the most distinctive feature of the biology of this organism. It is the basis of much of Mtb pathogenesis and one of the major causes of its intrinsic resistance to chemotherapeutic agents. At the same time, the unique structures of Mtb cell envelope glycoconjugates, their antigenicity and essentiality for mycobacterial growth provide opportunities for drug, vaccine, diagnostic and biomarker development, as clearly illustrated by recent advances in all of these translational aspects. This review focuses on our current understanding of the structure and biogenesis of Mtb glycoconjugates with particular emphasis on one of the most intriguing and least understood aspect of the physiology of mycobacteria: the translocation of these complex macromolecules across the different layers of the cell envelope. It further reviews the rather impressive progress made in the last 10 years in the discovery and development of novel inhibitors targeting their biogenesis.
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Affiliation(s)
- Shiva Kumar Angala
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University , Fort Collins, CO , USA
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49
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Alvin A, Miller KI, Neilan BA. Exploring the potential of endophytes from medicinal plants as sources of antimycobacterial compounds. Microbiol Res 2014; 169:483-95. [PMID: 24582778 PMCID: PMC7126926 DOI: 10.1016/j.micres.2013.12.009] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2013] [Revised: 12/19/2013] [Accepted: 12/27/2013] [Indexed: 12/03/2022]
Abstract
Natural product drug discovery has regained interest due to low production costs, structural diversity, and multiple uses of active compounds to treat various diseases. Attention has been directed towards medicinal plants as these plants have been traditionally used for generations to treat symptoms of numerous diseases. It is established that plants harbour microorganisms, collectively known as endophytes. Exploring the as-yet untapped natural products from the endophytes increases the chances of finding novel compounds. The concept of natural products targeting microbial pathogens has been applied to isolate novel antimycobacterial compounds, and the rapid development of drug-resistant Mycobacterium tuberculosis has significantly increased the need for new treatments against this pathogen. It remains important to continuously screen for novel compounds from natural sources, particularly from rarely encountered microorganisms, such as the endophytes. This review focuses on bioprospecting for polyketides and small peptides exhibiting antituberculosis activity, although current treatments against tuberculosis are described. It is established that natural products from these structure classes are often biosynthesised by microorganisms. Therefore it is hypothesised that some bioactive polyketides and peptides originally isolated from plants are in fact produced by their endophytes. This is of interest for further endophyte natural product investigations.
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Affiliation(s)
- Alfonsus Alvin
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Kristin I Miller
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Brett A Neilan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
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50
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Huang SH, Wu WS, Huang LY, Huang WF, Fu WC, Chen PT, Fang JM, Cheng WC, Cheng TJR, Wong CH. New continuous fluorometric assay for bacterial transglycosylase using Förster resonance energy transfer. J Am Chem Soc 2013; 135:17078-89. [PMID: 24131464 DOI: 10.1021/ja407985m] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The emergence of antibiotic resistance has prompted scientists to search for new antibiotics. Transglycosylase (TGase) is an attractive target for new antibiotic discovery due to its location on the outer membrane of bacteria and its essential role in peptidoglycan synthesis. Though there have been a few molecules identified as TGase inhibitors in the past thirty years, none of them have been developed into antibiotics for humans. The slow pace of development is perhaps due to the lack of continuous, quantitative, and high-throughput assay available for the enzyme. Herein, we report a new continuous fluorescent assay based on Förster resonance energy transfer, using lipid II analogues with a dimethylamino-azobenzenesulfonyl quencher in the lipid chain and a coumarin fluorophore in the peptide chain. During the process of transglycosylation, the quencher-appended polyprenol is released and the fluorescence of coumarin can be detected. Using this system, the substrate specificity and affinity of lipid II analogues bearing various numbers and configurations of isoprene units were investigated. Moreover, the inhibition constants of moenomycin and two previously identified small molecules were also determined. In addition, a high-throughput screening using the new assay was conducted to identify potent TGase inhibitors from a 120,000 compound library. This new continuous fluorescent assay not only provides an efficient and convenient way to study TGase activities, but also enables the high-throughput screening of potential TGase inhibitors for antibiotic discovery.
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Affiliation(s)
- Shih-Hsien Huang
- Genomics Research Center, Academia Sinica , 128 Academia Road, Section 2, Nankang, Taipei, 115, Taiwan
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