1
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Moreau F, Atamanyuk D, Blaukopf M, Barath M, Herczeg M, Xavier NM, Monbrun J, Airiau E, Henryon V, Leroy F, Floquet S, Bonnard D, Szabla R, Brown C, Junop MS, Kosma P, Gerusz V. Potentiating Activity of GmhA Inhibitors on Gram-Negative Bacteria. J Med Chem 2024; 67:6610-6623. [PMID: 38598312 PMCID: PMC11056994 DOI: 10.1021/acs.jmedchem.4c00037] [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: 01/05/2024] [Revised: 02/28/2024] [Accepted: 03/29/2024] [Indexed: 04/12/2024]
Abstract
Inhibition of the biosynthesis of bacterial heptoses opens novel perspectives for antimicrobial therapies. The enzyme GmhA responsible for the first committed biosynthetic step catalyzes the conversion of sedoheptulose 7-phosphate into d-glycero-d-manno-heptose 7-phosphate and harbors a Zn2+ ion in the active site. A series of phosphoryl- and phosphonyl-substituted derivatives featuring a hydroxamate moiety were designed and prepared from suitably protected ribose or hexose derivatives. High-resolution crystal structures of GmhA complexed to two N-formyl hydroxamate inhibitors confirmed the binding interactions to a central Zn2+ ion coordination site. Some of these compounds were found to be nanomolar inhibitors of GmhA. While devoid of HepG2 cytotoxicity and antibacterial activity of their own, they demonstrated in vitro lipopolysaccharide heptosylation inhibition in Enterobacteriaceae as well as the potentiation of erythromycin and rifampicin in a wild-type Escherichia coli strain. These inhibitors pave the way for a novel treatment of Gram-negative infections.
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Affiliation(s)
- François Moreau
- Mutabilis, 102 Avenue Gaston Roussel, Romainville 93230, France
| | | | - Markus Blaukopf
- Department
of Chemistry, University of Natural Resources
and Life Sciences, Muthgasse
18, Vienna A-1190, Austria
| | - Marek Barath
- Department
of Chemistry, University of Natural Resources
and Life Sciences, Muthgasse
18, Vienna A-1190, Austria
- Institute
of Chemistry, Center for Glycomics, Slovak
Academy of Sciences, Dúbravská cesta 9, Bratislava SK-845 38, Slovakia
| | - Mihály Herczeg
- Department
of Chemistry, University of Natural Resources
and Life Sciences, Muthgasse
18, Vienna A-1190, Austria
- Department
of Pharmaceutical Chemistry, University
of Debrecen, Debrecen 4032, Hungary
| | - Nuno M. Xavier
- Department
of Chemistry, University of Natural Resources
and Life Sciences, Muthgasse
18, Vienna A-1190, Austria
- Centro
de Química Estrutural, Institute of Molecular Sciences, Faculdade de Ciências, Universidade de Lisboa, Ed. C8, 5° Piso, Campo Grande, Lisboa 1749-016, Portugal
| | | | | | | | - Frédéric Leroy
- Carbosynth
Limited, 8&9 Old
Station Business Park, Compton, Berkshire RG20 6NE, U.K.
| | | | - Damien Bonnard
- Mutabilis, 102 Avenue Gaston Roussel, Romainville 93230, France
| | - Robert Szabla
- Department
of Biochemistry, University of Western Ontario, London, ON N6A 3K7, Canada
| | - Chris Brown
- Department
of Biochemistry, University of Western Ontario, London, ON N6A 3K7, Canada
| | - Murray S. Junop
- Department
of Biochemistry, University of Western Ontario, London, ON N6A 3K7, Canada
| | - Paul Kosma
- Department
of Chemistry, University of Natural Resources
and Life Sciences, Muthgasse
18, Vienna A-1190, Austria
| | - Vincent Gerusz
- Mutabilis, 102 Avenue Gaston Roussel, Romainville 93230, France
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2
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Seregina TA, Petrushanko IY, Zaripov PI, Shakulov RS, A. Sklyarova S, Mitkevich VA, Makarov AA, Mironov AS. Activation of Purine Biosynthesis Suppresses the Sensitivity of E. coli gmhA Mutant to Antibiotics. Int J Mol Sci 2023; 24:16070. [PMID: 38003258 PMCID: PMC10671730 DOI: 10.3390/ijms242216070] [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: 09/29/2023] [Revised: 11/01/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
Inactivation of enzymes responsible for biosynthesis of the cell wall component of ADP-glycero-manno-heptose causes the development of oxidative stress and sensitivity of bacteria to antibiotics of a hydrophobic nature. The metabolic precursor of ADP-heptose is sedoheptulose-7-phosphate (S7P), an intermediate of the non-oxidative branch of the pentose phosphate pathway (PPP), in which ribose-5-phosphate and NADPH are generated. Inactivation of the first stage of ADP-heptose synthesis (ΔgmhA) prevents the outflow of S7P from the PPP, and this mutant is characterized by a reduced biosynthesis of NADPH and of the Glu-Cys-Gly tripeptide, glutathione, molecules known to be involved in the resistance to oxidative stress. We found that the derepression of purine biosynthesis (∆purR) normalizes the metabolic equilibrium in PPP in ΔgmhA mutants, suppressing the negative effects of gmhA mutation likely via the over-expression of the glycine-serine pathway that is under the negative control of PurR and might be responsible for the enhanced synthesis of NADPH and glutathione. Consistently, the activity of the soxRS system, as well as the level of glutathionylation and oxidation of proteins, indicative of oxidative stress, were reduced in the double ΔgmhAΔpurR mutant compared to the ΔgmhA mutant.
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3
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Sidor K, Skirecki T. A Bittersweet Kiss of Gram-Negative Bacteria: The Role of ADP-Heptose in the Pathogenesis of Infection. Microorganisms 2023; 11:1316. [PMID: 37317291 DOI: 10.3390/microorganisms11051316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023] Open
Abstract
Due to the global crisis caused by the dramatic rise of drug resistance among Gram-negative bacteria, there is an urgent need for a thorough understanding of the pathogenesis of infections of such an etiology. In light of the limited availability of new antibiotics, therapies aimed at host-pathogen interactions emerge as potential treatment modalities. Thus, understanding the mechanism of pathogen recognition by the host and immune evasion appear to be the key scientific issues. Until recently, lipopolysaccharide (LPS) was recognized as a major pathogen-associated molecular pattern (PAMP) of Gram-negative bacteria. However, recently, ADP-L-glycero-β-D-manno-heptose (ADP-heptose), an intermediate carbohydrate metabolite of the LPS biosynthesis pathway, was discovered to activate the hosts' innate immunity. Therefore, ADP-heptose is regarded as a novel PAMP of Gram-negative bacteria that is recognized by the cytosolic alpha kinase-1 (ALPK1) protein. The conservative nature of this molecule makes it an intriguing player in host-pathogen interactions, especially in the context of changes in LPS structure or even in its loss by certain resistant pathogens. Here, we present the ADP-heptose metabolism, outline the mechanisms of its recognition and the activation of its immunity, and summarize the role of ADP-heptose in the pathogenesis of infection. Finally, we hypothesize about the routes of the entry of this sugar into cytosol and point to emerging questions that require further research.
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Affiliation(s)
- Karolina Sidor
- Department of Translational Immunology and Experimental Intensive Care, Centre of Postgraduate Medical Education, Marymoncka 99/103, 01-813 Warsaw, Poland
| | - Tomasz Skirecki
- Department of Translational Immunology and Experimental Intensive Care, Centre of Postgraduate Medical Education, Marymoncka 99/103, 01-813 Warsaw, Poland
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4
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The Inactivation of LPS Biosynthesis Genes in E. coli Cells Leads to Oxidative Stress. Cells 2022; 11:cells11172667. [PMID: 36078074 PMCID: PMC9454879 DOI: 10.3390/cells11172667] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/22/2022] [Accepted: 08/25/2022] [Indexed: 11/17/2022] Open
Abstract
Impaired lipopolysaccharide biosynthesis in Gram-negative bacteria results in the “deep rough” phenotype, which is characterized by increased sensitivity of cells to various hydrophobic compounds, including antibiotics novobiocin, actinomycin D, erythromycin, etc. The present study showed that E. coli mutants carrying deletions of the ADP-heptose biosynthesis genes became hypersensitive to a wide range of antibacterial drugs: DNA gyrase inhibitors, protein biosynthesis inhibitors (aminoglycosides, tetracycline), RNA polymerase inhibitors (rifampicin), and β-lactams (carbenicillin). In addition, it was found that inactivation of the gmhA, hldE, rfaD, and waaC genes led to dramatic changes in the redox status of cells: a decrease in the pool of reducing NADPH and ATP equivalents, the concentration of intracellular cysteine, a change in thiol homeostasis, and a deficiency in the formation of hydrogen sulfide. In “deep rough” mutants, intensive formation of reactive oxygen species was observed, which, along with a lack of reducing agents, such as reactive sulfur species or NADPH, leads to oxidative stress and an increase in the number of dead cells in the population. Within the framework of modern ideas about the role of oxidative stress as a universal mechanism of the bactericidal action of antibiotics, inhibition of the enzymes of ADP-heptose biosynthesis is a promising direction for increasing the effectiveness of existing antibiotics and solving the problem of multidrug resistance.
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5
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Hassan BA, Liu ZA, Milicaj J, Kim MS, Tyson M, Sham YY, Taylor EA. Kinetic Characterization and Computational Modeling of Escherichia coli Heptosyltransferase II: Exploring the Role of Protein Dynamics in Catalysis for GT-B Glycosyltransferase. Biochemistry 2022; 61:1572-1584. [PMID: 35861590 DOI: 10.1021/acs.biochem.2c00329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Glycosyltransferase (GT) enzymes promote the formation of glycosidic bonds between a sugar molecule and a diversity of substrates. Heptosyltransferase II (HepII) is a GT involved in the lipopolysaccharide (LPS) biosynthetic pathway that transfers the seven-carbon sugar (l-glycero-d-manno-heptose, Hep) onto a lipid-anchored glycopolymer (heptosylated Kdo2-Lipid A, Hep-Kdo2-Lipid A, or HLA). LPS plays a key role in Gram-negative bacterial sepsis, biofilm formation, and host colonization, and as such, LPS biosynthetic enzymes are targets for novel antimicrobial therapeutics. Three heptosyltransferases are involved in the inner-core LPS biosynthesis, with Escherichia coli HepII being the last to be quantitatively characterized in vivo. HepII shares modest sequence similarity with heptosyltransferase I (HepI) while maintaining a high degree of structural homology. Here, we report the first kinetic and biophysical characterization of HepII and demonstrate the properties of HepII that are shared with HepI, including sugar donor promiscuity and sugar acceptor-induced secondary structural changes, which results in significant thermal stabilization. HepII also has an increased catalytic efficiency and a significantly tighter binding affinity for both of its substrates compared to HepI. A structural model of the HepII ternary complex, refined by molecular dynamics simulations, was developed to probe the potentially important substrate-protein contacts. Ligand binding-induced changes in Trp fluorescence in HepII enabled the determination of substrate dissociation constants. Combined, these efforts meaningfully enhance our understanding of the heptosyltransferase family of enzymes and will aid in future efforts to design novel, potent, and specific inhibitors for this family of enzymes.
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Affiliation(s)
- Bakar A Hassan
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, United States
| | - Zhiqi A Liu
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, United States
| | - Jozafina Milicaj
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, United States
| | - Mia S Kim
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, United States
| | - Meka Tyson
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, United States
| | - Yuk Y Sham
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, Minnesota 55455, United States.,Department of Integrative Biology and Physiology, Medical School, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Erika A Taylor
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, United States
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6
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Yakovlieva L, Fülleborn JA, Walvoort MTC. Opportunities and Challenges of Bacterial Glycosylation for the Development of Novel Antibacterial Strategies. Front Microbiol 2021; 12:745702. [PMID: 34630370 PMCID: PMC8498110 DOI: 10.3389/fmicb.2021.745702] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 08/27/2021] [Indexed: 12/29/2022] Open
Abstract
Glycosylation is a ubiquitous process that is universally conserved in nature. The various products of glycosylation, such as polysaccharides, glycoproteins, and glycolipids, perform a myriad of intra- and extracellular functions. The multitude of roles performed by these molecules is reflected in the significant diversity of glycan structures and linkages found in eukaryotes and prokaryotes. Importantly, glycosylation is highly relevant for the virulence of many bacterial pathogens. Various surface-associated glycoconjugates have been identified in bacteria that promote infectious behavior and survival in the host through motility, adhesion, molecular mimicry, and immune system manipulation. Interestingly, bacterial glycosylation systems that produce these virulence factors frequently feature rare monosaccharides and unusual glycosylation mechanisms. Owing to their marked difference from human glycosylation, bacterial glycosylation systems constitute promising antibacterial targets. With the rise of antibiotic resistance and depletion of the antibiotic pipeline, novel drug targets are urgently needed. Bacteria-specific glycosylation systems are especially promising for antivirulence therapies that do not eliminate a bacterial population, but rather alleviate its pathogenesis. In this review, we describe a selection of unique glycosylation systems in bacterial pathogens and their role in bacterial homeostasis and infection, with a focus on virulence factors. In addition, recent advances to inhibit the enzymes involved in these glycosylation systems and target the bacterial glycan structures directly will be highlighted. Together, this review provides an overview of the current status and promise for the future of using bacterial glycosylation to develop novel antibacterial strategies.
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Affiliation(s)
- Liubov Yakovlieva
- Faculty of Science and Engineering, Stratingh Institute for Chemistry, University of Groningen, Groningen, Netherlands
| | - Julius A Fülleborn
- Faculty of Science and Engineering, Stratingh Institute for Chemistry, University of Groningen, Groningen, Netherlands
| | - Marthe T C Walvoort
- Faculty of Science and Engineering, Stratingh Institute for Chemistry, University of Groningen, Groningen, Netherlands
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7
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Kim S, Jo S, Kim MS, Shin DH. A triple-targeting inhibitory activity of Rose Bengal on polysaccharide biosynthesis of Burkholderia pseudomallei. Arch Pharm (Weinheim) 2021; 354:e2000360. [PMID: 33555065 DOI: 10.1002/ardp.202000360] [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: 09/22/2020] [Revised: 12/31/2020] [Accepted: 01/15/2021] [Indexed: 11/08/2022]
Abstract
Sugar nucleotidyltransferases (SNTs) participate in various biosynthesis pathways constructing polysaccharides in Gram-negative bacteria. In this study, a triple-targeting inhibitory activity of Rose Bengal against SNTs such as d-glycero-α-d-manno-heptose-1-phosphate guanylyltransferase (HddC), d-glycero-β-d-manno-heptose-1-phosphate adenylyltransferase (HldC), and 3-deoxy-d-manno-oct-2-ulosonic acid cytidylyltransferase (KdsB) from Burkholderia pseudomallei is provided. Rose Bengal effectively suppresses the nucleotidyltransferase activity of the three SNTs, and its IC50 values are 10.42, 0.76, and 5.31 µM, respectively. Interestingly, Rose Bengal inhibits the three enzymes regardless of their primary, secondary, tertiary, and quaternary structural differences. The experimental results indicate that Rose Bengal possesses the plasticity to shape its conformation suitable to interact with the three SNTs. As HddC functions in the formation of capsular polysaccharides and HldC and KdsB produce building blocks to constitute the inner core of lipopolysaccharide, Rose Bengal is a potential candidate to design antibiotics in a new category. In particular, it can be developed as a specific antimelioidosis agent. As the mortality rate of the infected people caused by B. pseudomallei is quite high, there is an urgent need for specific antimelioidosis agents. Therefore, a further study is being carried out with derivatives of Rose Bengal.
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Affiliation(s)
- Suwon Kim
- Department of Pharmacy, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Seri Jo
- Department of Pharmacy, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Mi-Sun Kim
- Department of Pharmacy, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Dong H Shin
- Department of Pharmacy, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
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8
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Karan S, Pratap B, Yadav SP, Ashish F, Saxena AK. Structural and functional characterization of M. tuberculosis sedoheptulose- 7-phosphate isomerase, a critical enzyme involved in lipopolysaccharide biosynthetic pathway. Sci Rep 2020; 10:20813. [PMID: 33257730 PMCID: PMC7705670 DOI: 10.1038/s41598-020-77230-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 10/15/2020] [Indexed: 11/09/2022] Open
Abstract
M. tuberculosis GmhA enzyme catalyzes the isomerization of D-sedoheptulose 7-phosphate into D-glycero-D-α-manno-heptose-7-phosphate in GDP-D-glycero-α-D-manno-heptose biosynthetic pathway. The D-glycero-α-D-manno-heptose is a major constituent of lipopolysaccharide and contributes to virulence and antibiotic resistance to mycobacteria. In current study, we have performed the structural and biochemical analysis of M. tuberculosis GmhA, the first enzyme involved in D-sedoheptulose 7-phosphate isomerization in GDP-D-α-D-heptose biosynthetic pathway. The MtbGmhA enzyme exits as tetramer and small angle X-ray scattering analysis also yielded tetrameric envelope in solution. The MtbGmhA enzyme binds to D-sedoheptulose 7-phosphate with Km ~ 0.31 ± 0.06 mM-1 and coverts it to D-glycero-D-α-manno-heptose-7-phosphate with catalytic efficiency (kcat/Km) ~ 1.45 mM-1 s-1. The residues involved in D-sedoheptulose 7-phosphate and Zn2+ binding were identified using modeled MtbGmhA + D-sedoheptulose 7-phosphate + Zn2+ structure. To understand the role in catalysis, six site directed mutants of MtbGmhA were generated, which showed significant decrease in catalytic activity. The circular dichroism analysis showed ~ 46% α-helix, ~ 19% β-sheet and ~ 35% random coil structures of MtbGmhA enzyme and melting temperature ~ 53.5 °C. Small angle X-ray scattering analysis showed the tetrameric envelope, which fitted well with modeled MtbGmhA tetramer in closed conformation. The MtbGmhA dynamics involved in D-sedoheptulose 7-phosphate and Zn2+ binding was identified using dynamics simulation and showed enhanced stability in presence of these ligands. Our biochemical data and structural knowledge have provided insight into mechanism of action of MtbGmhA enzyme, which can be targeted for novel antibiotics development against M. tuberculosis.
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Affiliation(s)
- Sumita Karan
- Rm-403/440, Structural Biology Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Bhanu Pratap
- Rm-403/440, Structural Biology Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Shiv Pratap Yadav
- Protein Science and Engineering Division, Institute of Microbial Technology, Sector 39-A, Chandigarh, 160036, India
| | - Fnu Ashish
- Protein Science and Engineering Division, Institute of Microbial Technology, Sector 39-A, Chandigarh, 160036, India
| | - Ajay K Saxena
- Rm-403/440, Structural Biology Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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Cascioferro S, Parrino B, Carbone D, Schillaci D, Giovannetti E, Cirrincione G, Diana P. Thiazoles, Their Benzofused Systems, and Thiazolidinone Derivatives: Versatile and Promising Tools to Combat Antibiotic Resistance. J Med Chem 2020; 63:7923-7956. [PMID: 32208685 PMCID: PMC7997583 DOI: 10.1021/acs.jmedchem.9b01245] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
Thiazoles,
their benzofused systems, and thiazolidinone derivatives
are widely recognized as nuclei of great value for obtaining molecules
with various biological activities, including analgesic, anti-inflammatory,
anti-HIV, antidiabetic, antitumor, and antimicrobial. In particular,
in the past decade, many compounds bearing these heterocycles have
been studied for their promising antibacterial properties due to their
action on different microbial targets. Here we assess the recent development
of this class of compounds to address mechanisms underlying antibiotic
resistance at both bacterial-cell and community levels (biofilms).
We also explore the SAR and the prospective clinical application of
thiazole and its benzofused derivatives, which act as inhibitors of
mechanisms underlying antibiotic resistance in the treatment of severe
drug-resistant infections. In addition, we examined all bacterial
targets involved in their antimicrobial activity reporting, when described,
their spontaneous frequencies of resistance.
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Affiliation(s)
- Stella Cascioferro
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Barbara Parrino
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Daniela Carbone
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Domenico Schillaci
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Elisa Giovannetti
- Department of Medical Oncology, VU University Medical Center, Cancer Center Amsterdam, DeBoelelaan 1117, 1081HV, Amsterdam, The Netherlands.,Cancer Pharmacology Lab, Fondazione Pisana per la Scienza, via Giovannini 13, 56017 San Giuliano Terme, Pisa, Italy
| | - Girolamo Cirrincione
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Patrizia Diana
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
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10
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Klobucar K, French S, Côté JP, Howes JR, Brown ED. Genetic and Chemical-Genetic Interactions Map Biogenesis and Permeability Determinants of the Outer Membrane of Escherichia coli. mBio 2020; 11:e00161-20. [PMID: 32156814 PMCID: PMC7064757 DOI: 10.1128/mbio.00161-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 01/29/2020] [Indexed: 02/08/2023] Open
Abstract
Gram-negative bacteria are intrinsically resistant to many antibiotics due to their outer membrane barrier. Although the outer membrane has been studied for decades, there is much to uncover about the biology and permeability of this complex structure. Investigating synthetic genetic interactions can reveal a great deal of information about genetic function and pathway interconnectivity. Here, we performed synthetic genetic arrays (SGAs) in Escherichia coli by crossing a subset of gene deletion strains implicated in outer membrane permeability with nonessential gene and small RNA (sRNA) deletion collections. Some 155,400 double-deletion strains were grown on rich microbiological medium with and without subinhibitory concentrations of two antibiotics excluded by the outer membrane, vancomycin and rifampin, to probe both genetic interactions and permeability. The genetic interactions of interest were synthetic sick or lethal (SSL) gene deletions that were detrimental to the cell in combination but had a negligible impact on viability individually. On average, there were ∼30, ∼36, and ∼40 SSL interactions per gene under no-drug, rifampin, and vancomycin conditions, respectively; however, many of these involved frequent interactors. Our data sets have been compiled into an interactive database called the Outer Membrane Interaction (OMI) Explorer, where genetic interactions can be searched, visualized across the genome, compared between conditions, and enriched for gene ontology (GO) terms. A set of SSL interactions revealed connectivity and permeability links between enterobacterial common antigen (ECA) and lipopolysaccharide (LPS) of the outer membrane. This data set provides a novel platform to generate hypotheses about outer membrane biology and permeability.IMPORTANCE Gram-negative bacteria are a major concern for public health, particularly due to the rise of antibiotic resistance. It is important to understand the biology and permeability of the outer membrane of these bacteria in order to increase the efficacy of antibiotics that have difficulty penetrating this structure. Here, we studied the genetic interactions of a subset of outer membrane-related gene deletions in the model Gram-negative bacterium E. coli We systematically combined these mutants with 3,985 nonessential gene and small RNA deletion mutations in the genome. We examined the viability of these double-deletion strains and probed their permeability characteristics using two antibiotics that have difficulty crossing the outer membrane barrier. An understanding of the genetic basis for outer membrane integrity can assist in the development of new antibiotics with favorable permeability properties and the discovery of compounds capable of increasing outer membrane permeability to enhance the activity of existing antibiotics.
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Affiliation(s)
- Kristina Klobucar
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Shawn French
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Jean-Philippe Côté
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - James R Howes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
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11
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Hu X, Yang C, Wang PG, Zhang GL. ADP-heptose: A new innate immune modulator. Carbohydr Res 2019; 473:123-128. [DOI: 10.1016/j.carres.2018.12.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 12/18/2018] [Accepted: 12/18/2018] [Indexed: 11/16/2022]
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12
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Beare PA, Jeffrey BM, Long CM, Martens CM, Heinzen RA. Genetic mechanisms of Coxiella burnetii lipopolysaccharide phase variation. PLoS Pathog 2018; 14:e1006922. [PMID: 29481553 PMCID: PMC5843353 DOI: 10.1371/journal.ppat.1006922] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 03/08/2018] [Accepted: 02/05/2018] [Indexed: 12/30/2022] Open
Abstract
Coxiella burnetii is an intracellular pathogen that causes human Q fever, a disease that normally presents as a severe flu-like illness. Due to high infectivity and disease severity, the pathogen is considered a risk group 3 organism. Full-length lipopolysaccharide (LPS) is required for full virulence and disease by C. burnetii and is the only virulence factor currently defined by infection of an immunocompetent animal. Transition of virulent phase I bacteria with smooth LPS, to avirulent phase II bacteria with rough LPS, occurs during in vitro passage. Semi-rough intermediate forms are also observed. Here, the genetic basis of LPS phase conversion was investigated to obtain a more complete understanding of C. burnetii pathogenesis. Whole genome sequencing of strains producing intermediate and/or phase II LPS identified several common mutations in predicted LPS biosynthesis genes. After passage in broth culture for 30 weeks, phase I strains from different genomic groups exhibited similar phase transition kinetics and elevation of mutations in LPS biosynthesis genes. Targeted mutagenesis and genetic complementation using a new C. burnetii nutritional selection system based on lysine auxotrophy confirmed that six of the mutated genes were necessary for production of phase I LPS. Disruption of two of these genes in a C. burnetii phase I strain resulted in production of phase II LPS, suggesting inhibition of the encoded enzymes could represent a new therapeutic strategy for treatment of Q fever. Additionally, targeted mutagenesis of genes encoding LPS biosynthesis enzymes can now be used to construct new phase II strains from different genomic groups for use in pathogen-host studies at a risk group 2 level.
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Affiliation(s)
- Paul A. Beare
- Coxiella Pathogenesis Section, Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Brendan M. Jeffrey
- Bioinformatics and Computational Biosciences Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Carrie M. Long
- Coxiella Pathogenesis Section, Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Craig M. Martens
- Research Technologies Section, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Robert A. Heinzen
- Coxiella Pathogenesis Section, Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
- * E-mail:
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13
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Vivoli M, Pang J, Harmer NJ. A half-site multimeric enzyme achieves its cooperativity without conformational changes. Sci Rep 2017; 7:16529. [PMID: 29184087 PMCID: PMC5705639 DOI: 10.1038/s41598-017-16421-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 11/02/2017] [Indexed: 11/09/2022] Open
Abstract
Cooperativity is a feature many multimeric proteins use to control activity. Here we show that the bacterial heptose isomerase GmhA displays homotropic positive and negative cooperativity among its four protomers. Most similar proteins achieve this through conformational changes: GmhA instead employs a delicate network of hydrogen bonds, and couples pairs of active sites controlled by a unique water channel. This network apparently raises the Lewis acidity of the catalytic zinc, thus increasing the activity at one active site at the cost of preventing substrate from adopting a reactive conformation at the paired negatively cooperative site – a “half-site” behavior. Our study establishes the principle that multimeric enzymes can exploit this cooperativity without conformational changes to maximize their catalytic power and control. More broadly, this subtlety by which enzymes regulate functions could be used to explore new inhibitor design strategies.
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Affiliation(s)
- Mirella Vivoli
- Department of Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Jiayun Pang
- Department of Pharmaceutical, Chemical and Environmental Sciences, Faculty of Engineering and Science,University of Greenwich, Medway Campus, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK
| | - Nicholas J Harmer
- Department of Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK. .,Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
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14
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Cote JM, Ramirez-Mondragon CA, Siegel ZS, Czyzyk DJ, Gao J, Sham YY, Mukerji I, Taylor EA. The Stories Tryptophans Tell: Exploring Protein Dynamics of Heptosyltransferase I from Escherichia coli. Biochemistry 2017; 56:886-895. [PMID: 28098447 DOI: 10.1021/acs.biochem.6b00850] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Heptosyltransferase I (HepI) catalyzes the addition of l-glycero-β-d-manno-heptose to Kdo2-Lipid A, as part of the biosynthesis of the core region of lipopolysaccharide (LPS). Gram-negative bacteria with gene knockouts of HepI have reduced virulence and enhanced susceptibility to hydrophobic antibiotics, making the design of inhibitors of HepI of interest. Because HepI protein dynamics are partially rate-limiting, disruption of protein dynamics might provide a new strategy for inhibiting HepI. Discerning the global mechanism of HepI is anticipated to aid development of inhibitors of LPS biosynthesis. Herein, dynamic protein rearrangements involved in the HepI catalytic cycle were probed by combining mutagenesis with intrinsic tryptophan fluorescence and circular dichroism analyses. Using wild-type and mutant forms of HepI, multiple dynamic regions were identified via changes in Trp fluorescence. Interestingly, Trp residues (Trp199 and Trp217) in the C-terminal domain (which binds ADP-heptose) are in a more hydrophobic environment upon binding of ODLA to the N-terminal domain. These residues are adjacent to the ADP-heptose binding site (with Trp217 in van der Waals contact with the adenine ring of ADP-heptose), suggesting that the two binding sites interact to report on the occupancy state of the enzyme. ODLA binding was also accompanied by a significant stabilization of HepI (heating to 95 °C fails to denature the protein when it is in the presence of ODLA). These results suggest that conformational rearrangements, from an induced fit model of substrate binding to HepI, are important for catalysis, and the disruption of these conformational dynamics may serve as a novel mechanism for inhibiting this and other glycosyltransferase enzymes.
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Affiliation(s)
- Joy M Cote
- Department of Chemistry, Wesleyan University , Middletown, Connecticut 06459, United States
| | | | - Zarek S Siegel
- Department of Chemistry, Wesleyan University , Middletown, Connecticut 06459, United States
| | - Daniel J Czyzyk
- Department of Chemistry, Wesleyan University , Middletown, Connecticut 06459, United States
| | | | | | - Ishita Mukerji
- Molecular Biophysics Program, Department of Molecular Biology and Biochemistry, Wesleyan University , Middletown, Connecticut 06459, United States
| | - Erika A Taylor
- Department of Chemistry, Wesleyan University , Middletown, Connecticut 06459, United States
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15
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Functional characterization of Helicobacter pylori 26695 sedoheptulose 7-phosphate isomerase encoded by hp0857 and its association with lipopolysaccharide biosynthesis and adhesion. Biochem Biophys Res Commun 2016; 477:794-800. [DOI: 10.1016/j.bbrc.2016.06.137] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 06/27/2016] [Indexed: 11/17/2022]
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16
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Vivoli M, Isupov MN, Nicholas R, Hill A, Scott AE, Kosma P, Prior JL, Harmer NJ. Unraveling the B. pseudomallei Heptokinase WcbL: From Structure to Drug Discovery. ACTA ACUST UNITED AC 2016; 22:1622-32. [PMID: 26687481 PMCID: PMC4691232 DOI: 10.1016/j.chembiol.2015.10.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 10/20/2015] [Accepted: 10/31/2015] [Indexed: 11/25/2022]
Abstract
Gram-negative bacteria utilize heptoses as part of their repertoire of extracellular polysaccharide virulence determinants. Disruption of heptose biosynthesis offers an attractive target for novel antimicrobials. A critical step in the synthesis of heptoses is their 1-O phosphorylation, mediated by kinases such as HldE or WcbL. Here, we present the structure of WcbL from Burkholderia pseudomallei. We report that WcbL operates through a sequential ordered Bi-Bi mechanism, loading the heptose first and then ATP. We show that dimeric WcbL binds ATP anti-cooperatively in the absence of heptose, and cooperatively in its presence. Modeling of WcbL suggests that heptose binding causes an elegant switch in the hydrogen-bonding network, facilitating the binding of a second ATP molecule. Finally, we screened a library of drug-like fragments, identifying hits that potently inhibit WcbL. Our results provide a novel mechanism for control of substrate binding and emphasize WcbL as an attractive anti-microbial target for Gram-negative bacteria.
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Affiliation(s)
- Mirella Vivoli
- Department of Biosciences, University of Exeter, Henry Wellcome Building, Stocker Road, Exeter EX4 4QD, UK
| | - Michail N Isupov
- Department of Biosciences, University of Exeter, Henry Wellcome Building, Stocker Road, Exeter EX4 4QD, UK
| | - Rebecca Nicholas
- Department of Biosciences, University of Exeter, Henry Wellcome Building, Stocker Road, Exeter EX4 4QD, UK
| | - Andrew Hill
- Department of Biosciences, University of Exeter, Henry Wellcome Building, Stocker Road, Exeter EX4 4QD, UK
| | - Andrew E Scott
- Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire SP4 0JQ, UK
| | - Paul Kosma
- University of Natural Resources and Life Sciences-Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Joann L Prior
- Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire SP4 0JQ, UK
| | - Nicholas J Harmer
- Department of Biosciences, University of Exeter, Henry Wellcome Building, Stocker Road, Exeter EX4 4QD, UK.
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17
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Muheim C, Bakali A, Engström O, Wieslander Å, Daley DO, Widmalm G. Identification of a Fragment-Based Scaffold that Inhibits the Glycosyltransferase WaaG from Escherichia coli. Antibiotics (Basel) 2016; 5:E10. [PMID: 27025525 PMCID: PMC4810412 DOI: 10.3390/antibiotics5010010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 01/19/2016] [Accepted: 01/21/2016] [Indexed: 01/04/2023] Open
Abstract
WaaG is a glycosyltransferase that is involved in the biosynthesis of lipopolysaccharide in Gram-negative bacteria. Inhibitors of WaaG are highly sought after as they could be used to inhibit the biosynthesis of the core region of lipopolysaccharide, which would improve the uptake of antibiotics. Herein, we establish an activity assay for WaaG using (14)C-labeled UDP-glucose and LPS purified from a ∆waaG strain of Escherichia coli. We noted that addition of the lipids phosphatidylglycerol (PG) and cardiolipin (CL), as well as the detergent 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS) increased activity. We then use the assay to determine if three molecular scaffolds, which bind to WaaG, could inhibit its activity in vitro. We show that 4-(2-amino-1,3-thiazol-4-yl)phenol inhibits WaaG (IC50 1.0 mM), but that the other scaffolds do not. This study represents an important step towards an inhibitor of WaaG by fragment-based lead discovery.
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Affiliation(s)
- Claudio Muheim
- Arrhenius Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm S-106 91, Sweden; (C.M.); (A.B.)
| | - Amin Bakali
- Arrhenius Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm S-106 91, Sweden; (C.M.); (A.B.)
| | - Olof Engström
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, Stockholm S-106 91, Sweden;
| | - Åke Wieslander
- Arrhenius Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm S-106 91, Sweden; (C.M.); (A.B.)
| | - Daniel O. Daley
- Arrhenius Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm S-106 91, Sweden; (C.M.); (A.B.)
| | - Göran Widmalm
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, Stockholm S-106 91, Sweden;
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19
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Loutet SA, El-Halfawy OM, Jassem AN, López JMS, Medarde AF, Speert DP, Davies JE, Valvano MA. Identification of synergists that potentiate the action of polymyxin B against Burkholderia cenocepacia. Int J Antimicrob Agents 2015; 46:376-80. [PMID: 26187366 DOI: 10.1016/j.ijantimicag.2015.05.010] [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: 03/06/2015] [Revised: 04/19/2015] [Accepted: 05/11/2015] [Indexed: 10/23/2022]
Abstract
Burkholderia cenocepacia and other members of the Burkholderia cepacia complex (BCC) are highly multidrug-resistant bacteria that cause severe pulmonary infections in patients with cystic fibrosis. A screen of 2686 compounds derived from marine organisms identified molecules that could synergise with polymyxin B (PMB) to inhibit the growth of B. cenocepacia. At 1 μg/mL, five compounds synergised with PMB and inhibited the growth of B. cenocepacia by ≥70% compared with growth in PMB alone. Follow-up testing revealed that one compound from the screen, the aminocoumarin antibiotic novobiocin, synergised with PMB and colistin against tobramycin-resistant clinical isolates of B. cenocepacia and Burkholderia multivorans. In parallel, we show that novobiocin sensitivity is common among BCC species and that these bacteria are even more susceptible to an alternative aminocoumarin, clorobiocin, which also had an additive effect with PMB against B. cenocepacia. These studies support using aminocoumarin antibiotics to treat BCC infections and show that synergisers can be found to increase the efficacy of antimicrobial peptides and polymyxins against BCC bacteria.
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Affiliation(s)
- Slade A Loutet
- Centre for Human Immunology, Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada; Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Omar M El-Halfawy
- Centre for Human Immunology, Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada; Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Agatha N Jassem
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | | | | | - David P Speert
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada; Department of Pathology, University of British Columbia, Vancouver, BC, Canada
| | - Julian E Davies
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Miguel A Valvano
- Centre for Human Immunology, Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada; Centre for Infection and Immunity, Queen's University Belfast, Belfast, UK.
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20
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Vincent SP, Tikad A. β-Selective One-Pot Fluorophosphorylation ofd,d-Heptosylglycals Mediated by Selectfluor. Isr J Chem 2015. [DOI: 10.1002/ijch.201400148] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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21
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Comparative genomics study for identification of drug and vaccine targets in Vibrio cholerae: MurA ligase as a case study. Genomics 2013; 103:83-93. [PMID: 24368230 DOI: 10.1016/j.ygeno.2013.12.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Revised: 12/11/2013] [Accepted: 12/12/2013] [Indexed: 12/15/2022]
Abstract
A systematic workflow consisting of comparative genomics, metabolic pathways analysis and additional drug prioritization parameters identified 264 proteins of Vibrio cholerae which were predicted to be absent in Homo sapiens. Among these, 40 proteins were identified as essential proteins that could serve as potential drug and vaccine targets. Additional prioritization parameters characterized 11 proteins as vaccine candidates while druggability of each of the identified proteins as evaluated by the Drug Bank database which prioritized 16 proteins suitable for drug targets. As a case study, we built a homology model of one of the potential drug targets, MurA ligase, using MODELLER (9v12) software. The model has been further explored for in silico docking with inhibitors having druggability potential from the Drug Bank database. Results from this study could facilitate selecting V. cholerae proteins for drug design and vaccine production pipelines in future.
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22
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Li T, Wen L, Williams A, Wu B, Li L, Qu J, Meisner J, Xiao Z, Fang J, Wang PG. Chemoenzymatic synthesis of ADP-d-glycero-β-d-manno-heptose and study of the substrate specificity of HldE. Bioorg Med Chem 2013; 22:1139-47. [PMID: 24412338 DOI: 10.1016/j.bmc.2013.12.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 12/03/2013] [Accepted: 12/12/2013] [Indexed: 11/16/2022]
Abstract
An efficient one-pot three enzymes strategy for chemoenzymatic synthesis of ADP-d-glycero-β-d-manno-heptose (ADP-d, d-heptose) was reported using chemically synthesized d, d-heptose-7-phosphate and the ADP-d, d-heptose biosynthetic enzymes HldE and GmhB. Moreover, the result of investigating substrate specificity of the kinase action of HldE revealed that HldE had highly restricted substrate specificity towards structurally modified heptose-7-phosphate analogs.
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Affiliation(s)
- Tiehai Li
- Department of Chemistry, Center for Therapeutics and Diagnostics, Georgia State University, Atlanta, GA 30303, USA
| | - Liuqing Wen
- Department of Chemistry, Center for Therapeutics and Diagnostics, Georgia State University, Atlanta, GA 30303, USA
| | - Adriel Williams
- Department of Chemistry, Center for Therapeutics and Diagnostics, Georgia State University, Atlanta, GA 30303, USA
| | - Baolin Wu
- Department of Chemistry, Center for Therapeutics and Diagnostics, Georgia State University, Atlanta, GA 30303, USA
| | - Lei Li
- Department of Chemistry, Center for Therapeutics and Diagnostics, Georgia State University, Atlanta, GA 30303, USA
| | - Jingyao Qu
- Department of Chemistry, Center for Therapeutics and Diagnostics, Georgia State University, Atlanta, GA 30303, USA
| | - Jeffrey Meisner
- Department of Chemistry, Center for Therapeutics and Diagnostics, Georgia State University, Atlanta, GA 30303, USA
| | - Zhongying Xiao
- Department of Chemistry, Center for Therapeutics and Diagnostics, Georgia State University, Atlanta, GA 30303, USA
| | - Junqiang Fang
- National Glycoengineering Research Center, Shandong University, Jinan, Shandong 250100, People's Republic of China
| | - Peng George Wang
- Department of Chemistry, Center for Therapeutics and Diagnostics, Georgia State University, Atlanta, GA 30303, USA; National Glycoengineering Research Center, Shandong University, Jinan, Shandong 250100, People's Republic of China.
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23
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Laxminarayan R, Duse A, Wattal C, Zaidi AKM, Wertheim HFL, Sumpradit N, Vlieghe E, Hara GL, Gould IM, Goossens H, Greko C, So AD, Bigdeli M, Tomson G, Woodhouse W, Ombaka E, Peralta AQ, Qamar FN, Mir F, Kariuki S, Bhutta ZA, Coates A, Bergstrom R, Wright GD, Brown ED, Cars O. Antibiotic resistance-the need for global solutions. THE LANCET. INFECTIOUS DISEASES 2013; 13:1057-98. [PMID: 24252483 DOI: 10.1016/s1473-3099(13)70318-9] [Citation(s) in RCA: 2558] [Impact Index Per Article: 232.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The causes of antibiotic resistance are complex and include human behaviour at many levels of society; the consequences affect everybody in the world. Similarities with climate change are evident. Many efforts have been made to describe the many different facets of antibiotic resistance and the interventions needed to meet the challenge. However, coordinated action is largely absent, especially at the political level, both nationally and internationally. Antibiotics paved the way for unprecedented medical and societal developments, and are today indispensible in all health systems. Achievements in modern medicine, such as major surgery, organ transplantation, treatment of preterm babies, and cancer chemotherapy, which we today take for granted, would not be possible without access to effective treatment for bacterial infections. Within just a few years, we might be faced with dire setbacks, medically, socially, and economically, unless real and unprecedented global coordinated actions are immediately taken. Here, we describe the global situation of antibiotic resistance, its major causes and consequences, and identify key areas in which action is urgently needed.
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Affiliation(s)
- Ramanan Laxminarayan
- Center for Disease Dynamics, Economics and Policy, Washington, DC, USA; Princeton University, Princeton NJ, USA; Public Health Foundation of India, New Delhi, India
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24
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Desroy N, Denis A, Oliveira C, Atamanyuk D, Briet S, Faivre F, LeFralliec G, Bonvin Y, Oxoby M, Escaich S, Floquet S, Drocourt E, Vongsouthi V, Durant L, Moreau F, Verhey TB, Lee TW, Junop MS, Gerusz V. Novel HldE-K Inhibitors Leading to Attenuated Gram Negative Bacterial Virulence. J Med Chem 2013; 56:1418-30. [DOI: 10.1021/jm301499r] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Theodore B. Verhey
- Department of Biochemistry and
Biomedical Sciences and Michael G. DeGroote Institute for Infectious
Disease Research, McMaster University,
1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
| | - Ting-Wai Lee
- Department of Biochemistry and
Biomedical Sciences and Michael G. DeGroote Institute for Infectious
Disease Research, McMaster University,
1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
| | - Murray S. Junop
- Department of Biochemistry and
Biomedical Sciences and Michael G. DeGroote Institute for Infectious
Disease Research, McMaster University,
1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
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25
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Lee TW, Verhey TB, Antiperovitch PA, Atamanyuk D, Desroy N, Oliveira C, Denis A, Gerusz V, Drocourt E, Loutet SA, Hamad MA, Stanetty C, Andres SN, Sugiman-Marangos S, Kosma P, Valvano MA, Moreau F, Junop MS. Structural-functional studies of Burkholderia cenocepacia D-glycero-β-D-manno-heptose 7-phosphate kinase (HldA) and characterization of inhibitors with antibiotic adjuvant and antivirulence properties. J Med Chem 2013; 56:1405-17. [PMID: 23256532 PMCID: PMC3585733 DOI: 10.1021/jm301483h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
As an essential constituent of the outer membrane of Gram-negative bacteria, lipopolysaccharide contributes significantly to virulence and antibiotic resistance. The lipopolysaccharide biosynthetic pathway therefore serves as a promising therapeutic target for antivirulence drugs and antibiotic adjuvants. Here we report the structural-functional studies of D-glycero-β-D-manno-heptose 7-phosphate kinase (HldA), an absolutely conserved enzyme in this pathway, from Burkholderia cenocepacia. HldA is structurally similar to members of the PfkB carbohydrate kinase family and appears to catalyze heptose phosphorylation via an in-line mechanism mediated mainly by a conserved aspartate, Asp270. Moreover, we report the structures of HldA in complex with two potent inhibitors in which both inhibitors adopt a folded conformation and occupy the nucleotide-binding sites. Together, these results provide important insight into the mechanism of HldA-catalyzed heptose phosphorylation and necessary information for further development of HldA inhibitors.
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Affiliation(s)
- Ting-Wai Lee
- Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
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26
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Page MGP. The role of the outer membrane of Gram-negative bacteria in antibiotic resistance: Ajax' shield or Achilles' heel? Handb Exp Pharmacol 2012:67-86. [PMID: 23090596 DOI: 10.1007/978-3-642-28951-4_5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
There has been an enormous increase in our knowledge of the fundamental steps in the biosynthesis and assembly of the outer membrane of Gram-negative bacteria. Lipopolysaccharide is a major component of the outer membrane of Gram-negative bacteria as is peptidoglycan. Porins, efflux pumps and other transport proteins of the outer membrane are also present. It is clear that there are numerous essential proteins that have the potential to be targets for novel antimicrobial agents. Progress, however, has been slow. Much of the emphasis has been on cytoplasmic processes that were better understood earlier on, but have the drawback that two penetration barriers, with different permeability properties, have to be crossed. With the increased understanding of the late-stage events occurring in the periplasm, it may be possible to shift focus to these more accessible targets. Nevertheless, getting drugs across the outer membrane will remain a challenge to the ingenuity of the medicinal chemist.
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27
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Apetrei CL, Tuchilus C, Aprotosoaie AC, Oprea A, Malterud KE, Miron A. Chemical, antioxidant and antimicrobial investigations of Pinus cembra L. bark and needles. Molecules 2011; 16:7773-88. [PMID: 22143542 PMCID: PMC6264604 DOI: 10.3390/molecules16097773] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Revised: 09/04/2011] [Accepted: 09/08/2011] [Indexed: 11/24/2022] Open
Abstract
The chemical constituents and biological activity of Pinus cembra L. (Pinaceae), native to the Central European Alps and the Carpathian Mountains, are not well known. The aim of the present work was to examine the phenolic content, antioxidant and antimicrobial effects of hydromethanolic extracts of Pinus cembra L. bark and needles. Bark extract had higher concentrations of total phenolics (299.3 vs. 78.22 mg gallic acid equivalents/g extract), flavonoids (125.3 vs. 19.84 mg catechin equivalents/g extract) and proanthocyanidins (74.3 vs. 12.7 mg cyanidin equivalents/g extract) than needle extract and was more active as a free radical scavenger, reducing agent and antimicrobial agent. The EC50 values in the 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2'-azino-bis(3-ethylbenzo-thiazoline-6-sulfonic acid) diammonium salt (ABTS) and reducing power assays were 71.1, 6.3 and 26 μg/mL for bark extract and 186.1, 24 and 104 μg/mL for needle extract, respectively. In addition, needle extract showed ferrous ions chelating effects (EC50 = 1,755 μg/mL). The antimicrobial effects against Staphylococcus aureus, Sarcina lutea, Bacillus cereus, Escherichia coli, Pseudomonas aeruginosa and Candida albicans were assessed by the agar diffusion method. Both extracts (4 mg/well) were active against all the microorganisms tested; bark extract showed higher inhibition on all strains. These results indicate that Pinus cembra L. bark and needles are good sources of phytochemicals with antioxidant and antimicrobial activities.
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Affiliation(s)
- Cristina Lungu Apetrei
- Department of Plant and Animal Biology, School of Pharmacy, Gr. T. Popa University of Medicine and Pharmacy, Universitatii Street Number 16, 700115 Iasi, Romania; E-Mail: (C.L.A.)
| | - Cristina Tuchilus
- Department of Microbiology, School of Medicine, Gr. T. Popa University of Medicine and Pharmacy, Universitatii Street Number 16, 700115 Iasi, Romania; E-Mail: (C.T.)
| | - Ana Clara Aprotosoaie
- Department of Pharmacognosy, School of Pharmacy, Gr. T. Popa University of Medicine and Pharmacy, Universitatii Street Number 16, 700115 Iasi, Romania; E-Mail: (A.C.A.)
| | - Adrian Oprea
- Institute of Biological Research, Lascar Catargi Street Number 47, 700107 Iasi, Romania; E-Mail: (A.O.)
| | - Karl Egil Malterud
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Oslo, P.O. 1068, Blindern, 0316 Oslo, Norway; E-Mail: (K.E.M.)
| | - Anca Miron
- Department of Pharmacognosy, School of Pharmacy, Gr. T. Popa University of Medicine and Pharmacy, Universitatii Street Number 16, 700115 Iasi, Romania; E-Mail: (A.C.A.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +40-232-301600; Fax: +40-232-211820
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Durka M, Tikad A, Périon R, Bosco M, Andaloussi M, Floquet S, Malacain E, Moreau F, Oxoby M, Gerusz V, Vincent SP. Systematic Synthesis of Inhibitors of the Two First Enzymes of the Bacterial Heptose Biosynthetic Pathway: Towards Antivirulence Molecules Targeting Lipopolysaccharide Biosynthesis. Chemistry 2011; 17:11305-13. [DOI: 10.1002/chem.201100396] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Revised: 05/26/2011] [Indexed: 11/07/2022]
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29
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Loutet SA, Valvano MA. Extreme antimicrobial peptide and polymyxin B resistance in the genus Burkholderia. Front Cell Infect Microbiol 2011; 1:6. [PMID: 22919572 PMCID: PMC3417367 DOI: 10.3389/fcimb.2011.00006] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Accepted: 07/12/2011] [Indexed: 12/12/2022] Open
Abstract
Cationic antimicrobial peptides and polymyxins are a group of naturally occurring antibiotics that can also possess immunomodulatory activities. They are considered a new source of antibiotics for treating infections by bacteria that are resistant to conventional antibiotics. Members of the genus Burkholderia, which includes various human pathogens, are inherently resistant to antimicrobial peptides. The resistance is several orders of magnitude higher than that of other Gram-negative bacteria such as Escherichia coli, Salmonella enterica, or Pseudomonas aeruginosa. This review summarizes our current understanding of antimicrobial peptide and polymyxin B resistance in the genus Burkholderia. These bacteria possess major and minor resistance mechanisms that will be described in detail. Recent studies have revealed that many other emerging Gram-negative opportunistic pathogens may also be inherently resistant to antimicrobial peptides and polymyxins and we propose that Burkholderia sp. are a model system to investigate the molecular basis of the resistance in extremely resistant bacteria. Understanding resistance in these types of bacteria will be important if antimicrobial peptides come to be used regularly for the treatment of infections by susceptible bacteria because this may lead to increased resistance in the species that are currently susceptible and may also open up new niches for opportunistic pathogens with high inherent resistance.
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Affiliation(s)
- Slade A Loutet
- Centre for Human Immunology, University of Western Ontario London, Ontario, Canada
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30
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Loutet SA, Valvano MA. Extreme antimicrobial Peptide and polymyxin B resistance in the genus burkholderia. Front Microbiol 2011; 2:159. [PMID: 21811491 PMCID: PMC3143681 DOI: 10.3389/fmicb.2011.00159] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Accepted: 07/12/2011] [Indexed: 01/04/2023] Open
Abstract
Cationic antimicrobial peptides and polymyxins are a group of naturally occurring antibiotics that can also possess immunomodulatory activities. They are considered a new source of antibiotics for treating infections by bacteria that are resistant to conventional antibiotics. Members of the genus Burkholderia, which includes various human pathogens, are inherently resistant to antimicrobial peptides. The resistance is several orders of magnitude higher than that of other Gram-negative bacteria such as Escherichia coli, Salmonella enterica, or Pseudomonas aeruginosa. This review summarizes our current understanding of antimicrobial peptide and polymyxin B resistance in the genus Burkholderia. These bacteria possess major and minor resistance mechanisms that will be described in detail. Recent studies have revealed that many other emerging Gram-negative opportunistic pathogens may also be inherently resistant to antimicrobial peptides and polymyxins and we propose that Burkholderia sp. are a model system to investigate the molecular basis of the resistance in extremely resistant bacteria. Understanding resistance in these types of bacteria will be important if antimicrobial peptides come to be used regularly for the treatment of infections by susceptible bacteria because this may lead to increased resistance in the species that are currently susceptible and may also open up new niches for opportunistic pathogens with high inherent resistance.
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Affiliation(s)
- Slade A Loutet
- Centre for Human Immunology, University of Western Ontario London, ON, Canada
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31
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Yi L, Velasquez MS, Holler TP, Woodard RW. A simple assay for 3-deoxy-d-manno-octulosonate cytidylyltransferase and its use as a pathway screen. Anal Biochem 2011; 416:152-8. [PMID: 21669179 DOI: 10.1016/j.ab.2011.05.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Revised: 04/22/2011] [Accepted: 05/18/2011] [Indexed: 11/28/2022]
Abstract
This article describes the adaptation of a simple colorimetric assay for inorganic pyrophosphate to the enzyme 3-deoxy-d-manno-octulosonate cytidylyltransferase (CMP-KDO synthetase, KdsB, EC 2.7.7.38), a key enzyme in the biosynthesis of lipopolysaccharide (LPS) in Gram-negative organisms. This assay is particularly useful because it can be combined with the malachite green (MG) assay for inorganic phosphate to form an assay system capable of determining inorganic phosphate and inorganic pyrophosphate in the same solution (the MG/EK (eikonogen reagent) assay). This assay system has the potential for simultaneous screening of the 3-deoxy-d-manno-octulosonate (KDO) biosynthesis pathway. We tested this potential using two enzymes, KdsB and KdsC, involved in the biosynthesis and use of the key bacterial 8-carbon sugar, KDO.
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Affiliation(s)
- Li Yi
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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32
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Fighting bacterial infections—Future treatment options. Drug Resist Updat 2011; 14:125-39. [DOI: 10.1016/j.drup.2011.02.001] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Revised: 01/31/2011] [Accepted: 01/31/2011] [Indexed: 12/13/2022]
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Abstract
The unremitting emergence of multidrug-resistant bacterial pathogens highlights a matching need for new therapeutic options. For example, new carbapenemases such as KPC (class A Klebsiella pneumoniae) and NDM-1 (New Delhi metallo-β-lactamase 1) are surfacing, resulting in almost total resistance to β-lactam antibiotics. Furthermore, resistance is quickly disseminated, not only in the healthcare sector, but also within the community at large, because many resistance determinants are carried on mobile genetic elements readily shared among pathogens. The absence of new antibiotics has led to a growing reliance on older, more toxic drugs such as colistin, but resistance to these is already arising. One approach to combat this growing problem is the use of combination drug antibiotic adjuvant therapy, which potentiates the activity of antibiotics. Here, we review the current situation and discuss potential drug combinations that may increase the potency of antibiotics in the future. Adjuvant therapies include antibiotic combinations, synergy between antibiotics and nonantibiotics, inhibition of resistance and molecules that alter the physiology of antibiotic-insensitive cells, such as those in biofilms. We provide a rationale for these multicomponent strategies, highlighting current research and important considerations for their clinical use and pharmacological properties.
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34
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Development of a multicomponent kinetic assay of the early enzymes in the Campylobacter jejuni N-linked glycosylation pathway. Bioorg Med Chem 2010; 18:8167-71. [PMID: 21036619 DOI: 10.1016/j.bmc.2010.10.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Revised: 10/01/2010] [Accepted: 10/06/2010] [Indexed: 11/23/2022]
Abstract
The human pathogen Campylobacter jejuni possesses a general N-linked glycosylation system that is known to play a role in pathogenicity; however, a detailed understanding of this role remains elusive. A considerable hindrance to studying bacterial N-glycosylation in vivo is the absence of small molecule inhibitors to reversibly control the process. This report describes a pathway-screening assay that targets the early enzymes of C. jejuni N-glycan biosynthesis that would enable identification of inhibitors to the first four steps in the pathway. The assay includes PglF, PglE, PglD, PglC, and PglA; the enzymes involved in the biosynthesis of an undecaprenyl diphosphate-linked disaccharide and monitors the transfer of [³H]GalNAc from the hydrophilic UDP-linked carrier to the lipophilic UndPP-diNAcBac (2,4-diacetamido-2,4,6-trideoxyglucose). The optimized assay has a Z'-factor calculated to be 0.77, indicating a robust assay suitable for screening. The diacylglycerol kinase from Streptococcus mutans, which provides a convenient method for phosphorylating undecaprenol, has been included in a modified version of the assay thereby allowing the screen to be conducted with entirely commercially available substrates.
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Abstract
The Burkholderia cepacia complex (Bcc) is a group of genetically related environmental bacteria that can cause chronic opportunistic infections in patients with cystic fibrosis (CF) and other underlying diseases. These infections are difficult to treat due to the inherent resistance of the bacteria to antibiotics. Bacteria can spread between CF patients through social contact and sometimes cause cepacia syndrome, a fatal pneumonia accompanied by septicemia. Burkholderia cenocepacia has been the focus of attention because initially it was the most common Bcc species isolated from patients with CF in North America and Europe. Today, B. cenocepacia, along with Burkholderia multivorans, is the most prevalent Bcc species in patients with CF. Given the progress that has been made in our understanding of B. cenocepacia over the past decade, we thought that it was an appropriate time to review our knowledge of the pathogenesis of B. cenocepacia, paying particular attention to the characterization of virulence determinants and the new tools that have been developed to study them. A common theme emerging from these studies is that B. cenocepacia establishes chronic infections in immunocompromised patients, which depend more on determinants mediating host niche adaptation than those involved directly in host cells and tissue damage.
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Affiliation(s)
- Slade A. Loutet
- Centre for Human Immunology, Department of Microbiology and Immunology, Department of Medicine, University of Western Ontario, London, Ontario, Canada
| | - Miguel A. Valvano
- Centre for Human Immunology, Department of Microbiology and Immunology, Department of Medicine, University of Western Ontario, London, Ontario, Canada
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36
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Harmer NJ. The structure of sedoheptulose-7-phosphate isomerase from Burkholderia pseudomallei reveals a zinc binding site at the heart of the active site. J Mol Biol 2010; 400:379-92. [PMID: 20447408 DOI: 10.1016/j.jmb.2010.04.058] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Revised: 04/27/2010] [Accepted: 04/28/2010] [Indexed: 11/25/2022]
Abstract
Heptoses are found in the surface polysaccharides of most bacteria, contributing to structures that are essential for virulence and antibiotic resistance. Consequently, the biosynthetic enzymes for these sugars are attractive targets for novel antibiotics. The best characterized biosynthetic enzyme is GmhA, which catalyzes the conversion of sedoheptulose-7-phosphate into D-glycero-D-manno-heptopyranose-7-phosphate, the first step in the biosynthesis of heptose. Here, the structure of GmhA from Burkholderia pseudomallei is reported. This enzyme contains a zinc ion at the heart of its active site: this ion stabilizes the active, closed form of the enzyme and presents coordinating side chains as a potential acid and base to drive catalysis. A complex with the product demonstrates that the enzyme retains activity in the crystal and thus suggests that the closed conformation is catalytically relevant and is an excellent target for the development of therapeutics. A revised mechanism for the action of GmhA is postulated on the basis of this structure and the activity of B. pseudomallei GmhA mutants.
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Affiliation(s)
- Nicholas J Harmer
- School of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK.
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38
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Taylor PL, Sugiman-Marangos S, Zhang K, Valvano MA, Wright GD, Junop MS. Structural and kinetic characterization of the LPS biosynthetic enzyme D-alpha,beta-D-heptose-1,7-bisphosphate phosphatase (GmhB) from Escherichia coli. Biochemistry 2010; 49:1033-41. [PMID: 20050699 DOI: 10.1021/bi901780j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Lipopolysaccharide is a major component of the outer membrane of gram-negative bacteria and provides a permeability barrier to many commonly used antibiotics. ADP-heptose residues are an integral part of the LPS inner core, and mutants deficient in heptose biosynthesis demonstrate increased membrane permeability. The heptose biosynthesis pathway involves phosphorylation and dephosphorylation steps not found in other pathways for the synthesis of nucleotide sugar precursors. Consequently, the heptose biosynthetic pathway has been marked as a novel target for antibiotic adjuvants, which are compounds that facilitate and potentiate antibiotic activity. D-alpha,beta-D-heptose-1,7-bisphosphate phosphatase (GmhB) catalyzes the third essential step of LPS heptose biosynthesis. This study describes the first crystal structure of GmhB and enzymatic analysis of the protein. Structure-guided mutations followed by steady state kinetic analysis, together with established precedent for HAD phosphatases, suggest that GmhB functions through a phosphoaspartate intermediate. This study provides insight into the structure-function relationship of GmhB, a new target for combatting gram-negative bacterial infection.
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Affiliation(s)
- Patricia L Taylor
- Department of Biochemistry and Biomedical Sciences and M. G. DeGroote Institute for Infectious Disease Research, McMaster University, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada
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39
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Morar M, Bhullar K, Hughes DW, Junop M, Wright GD. Structure and Mechanism of the Lincosamide Antibiotic Adenylyltransferase LinB. Structure 2009; 17:1649-1659. [DOI: 10.1016/j.str.2009.10.013] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Revised: 10/13/2009] [Accepted: 10/14/2009] [Indexed: 11/28/2022]
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40
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Contributions of two UDP-glucose dehydrogenases to viability and polymyxin B resistance of Burkholderia cenocepacia. Microbiology (Reading) 2009; 155:2029-2039. [DOI: 10.1099/mic.0.027607-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Burkholderia cenocepacia is highly resistant to antimicrobial peptides and we hypothesized that the conversion of UDP-glucose to UDP-glucuronic acid, a reaction catalysed by the enzyme UDP-glucose dehydrogenase (Ugd) would be important for this resistance. The genome of B. cenocepacia contains three predicted ugd genes: ugdBCAL2946
, ugdBCAM0855
and ugdBCAM2034
, all of which were individually inactivated. Only inactivation of ugdBCAL2946
resulted in increased sensitivity to polymyxin B and this sensitivity could be overcome when either ugdBCAL2946
or ugdBCAM0855
but not ugdBCAM2034
was expressed from plasmids. The growth of a conditional ugdBCAL2946
mutant, created in the ΔugdBCAM0855
background, was significantly impaired under non-permissive conditions. Growth could be rescued by either ugdBCAL2946
or ugdBCAM0855
expressed in trans, but not by ugdBCAM2034
. Biochemical analysis of the purified, recombinant forms of UgdBCAL2946 and UgdBCAM0855 revealed that they are soluble homodimers with similar in vitro Ugd activity and comparable kinetic constants for their substrates UDP-glucose and NAD+. Purified UgdBCAM2034 showed no in vitro Ugd activity. Real-time PCR analysis showed that the expression of ugdBCAL2946
was 5.4- and 135-fold greater than that of ugdBCAM0855
and ugdBCAM2034
, respectively. Together, these data indicate that the combined activity of UgdBCAL2946 and UgdBCAM0855 is essential for the survival of B. cenocepacia but only the most highly expressed ugd gene, ugdBCAL2946
, is required for polymyxin B resistance.
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41
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High-throughput screening identifies novel inhibitors of the acetyltransferase activity of Escherichia coli GlmU. Antimicrob Agents Chemother 2009; 53:2306-11. [PMID: 19349513 DOI: 10.1128/aac.01572-08] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bifunctional GlmU protein catalyzes the formation of UDP-N-acetylglucosamine in a two-step reaction using the substrates glucosamine-1-phosphate, acetyl coenzyme A, and UTP. This metabolite is a common precursor to the synthesis of bacterial cell surface carbohydrate polymers, such as peptidoglycan, lipopolysaccharide, and wall teichoic acid that are involved in the maintenance of cell shape, permeability, and virulence. The C-terminal acetyltransferase domain of GlmU exhibits structural and mechanistic features unique to bacterial UDP-N-acetylglucosamine synthases, making it an excellent target for antibacterial design. In the work described here, we have developed an absorbance-based assay to screen diverse chemical libraries in high throughput for inhibitors to the acetyltransferase reaction of Escherichia coli GlmU. The primary screen of 50,000 drug-like small molecules identified 63 hits, 37 of which were specific to acetyltransferase activity of GlmU. Secondary screening and mode-of-inhibition studies identified potent inhibitors where compound binding within the acetyltransferase active site was requisite on the presence of glucosamine-1-phosphate and were competitive with the substrate acetyl coenzyme A. These molecules may represent novel chemical scaffolds for future antimicrobial drug discovery. In addition, this work outlines the utility of catalytic variants in targeting specific activities of bifunctional enzymes in high-throughput screens.
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Desroy N, Moreau F, Briet S, Le Fralliec G, Floquet S, Durant L, Vongsouthi V, Gerusz V, Denis A, Escaich S. Towards Gram-negative antivirulence drugs: new inhibitors of HldE kinase. Bioorg Med Chem 2008; 17:1276-89. [PMID: 19124251 DOI: 10.1016/j.bmc.2008.12.021] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Revised: 12/01/2008] [Accepted: 12/09/2008] [Indexed: 10/21/2022]
Abstract
Gram-negative bacteria lacking heptoses in their lipopolysaccharide (LPS) display attenuated virulence and increased sensitivity to human serum and to some antibiotics. Thus inhibition of bacterial heptose synthesis represents an attractive target for the development of new antibacterial agents. HldE is a bifunctional enzyme involved in the synthesis of bacterial heptoses. Development of a biochemical assay suitable for high-throughput screening allowed the discovery of inhibitors 1 and 2 of HldE kinase. Study of the structure-activity relationship of this series of inhibitors led to highly potent compounds.
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Affiliation(s)
- Nicolas Desroy
- MUTABILIS SA, 102 Avenue Gaston Roussel, 93230 Romainville, France.
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43
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Abstract
AbstractAntimicrobial resistance is a rapidly increasing problem impacting the successful treatment of bacterial infectious disease. To combat resistance, the development of new treatment options is required. Recent advances in technology have aided in the discovery of novel antibacterial agents, specifically through genome mining for novel natural product biosynthetic gene clusters and improved small molecule high-throughput screening methods. Novel targets such as lipopolysaccharide and fatty acid biosyntheses have been identified by essential gene studies, representing a shift from traditional antibiotic targets. Finally, inhibiting non-essential genes with small molecules is being explored as a method for rescuing the activity of ‘old’ antibiotics, providing a novel synergistic approach to antimicrobial discovery.
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44
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Abstract
Acinetobacter baumannii has emerged as a highly troublesome pathogen for many institutions globally. As a consequence of its immense ability to acquire or upregulate antibiotic drug resistance determinants, it has justifiably been propelled to the forefront of scientific attention. Apart from its predilection for the seriously ill within intensive care units, A. baumannii has more recently caused a range of infectious syndromes in military personnel injured in the Iraq and Afghanistan conflicts. This review details the significant advances that have been made in our understanding of this remarkable organism over the last 10 years, including current taxonomy and species identification, issues with susceptibility testing, mechanisms of antibiotic resistance, global epidemiology, clinical impact of infection, host-pathogen interactions, and infection control and therapeutic considerations.
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45
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Antivirulence as a new antibacterial approach for chemotherapy. Curr Opin Chem Biol 2008; 12:400-8. [DOI: 10.1016/j.cbpa.2008.06.022] [Citation(s) in RCA: 139] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2008] [Revised: 06/19/2008] [Accepted: 06/20/2008] [Indexed: 12/11/2022]
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46
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Taylor PL, Blakely KM, de Leon GP, Walker JR, McArthur F, Evdokimova E, Zhang K, Valvano MA, Wright GD, Junop MS. Structure and function of sedoheptulose-7-phosphate isomerase, a critical enzyme for lipopolysaccharide biosynthesis and a target for antibiotic adjuvants. J Biol Chem 2007; 283:2835-45. [PMID: 18056714 DOI: 10.1074/jbc.m706163200] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The barrier imposed by lipopolysaccharide (LPS) in the outer membrane of Gram-negative bacteria presents a significant challenge in treatment of these organisms with otherwise effective hydrophobic antibiotics. The absence of L-glycero-D-manno-heptose in the LPS molecule is associated with a dramatically increased bacterial susceptibility to hydrophobic antibiotics and thus enzymes in the ADP-heptose biosynthesis pathway are of significant interest. GmhA catalyzes the isomerization of D-sedoheptulose 7-phosphate into D-glycero-D-manno-heptose 7-phosphate, the first committed step in the formation of ADP-heptose. Here we report structures of GmhA from Escherichia coli and Pseudomonas aeruginosa in apo, substrate, and product-bound forms, which together suggest that GmhA adopts two distinct conformations during isomerization through reorganization of quaternary structure. Biochemical characterization of GmhA mutants, combined with in vivo analysis of LPS biosynthesis and novobiocin susceptibility, identifies key catalytic residues. We postulate GmhA acts through an enediol-intermediate isomerase mechanism.
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Affiliation(s)
- Patricia L Taylor
- Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1200 Main Street West, Hamilton, Ontario, Canada
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47
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Wright GD, Sutherland AD. New strategies for combating multidrug-resistant bacteria. Trends Mol Med 2007; 13:260-7. [PMID: 17493872 DOI: 10.1016/j.molmed.2007.04.004] [Citation(s) in RCA: 168] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2007] [Revised: 04/03/2007] [Accepted: 04/30/2007] [Indexed: 11/24/2022]
Abstract
Antibiotic resistance is a problem that continues to challenge the healthcare sector. In particular, multidrug resistance is now common in familiar pathogens such as Staphylococcus aureus and Mycobacterium tuberculosis, as well as emerging pathogens such as Acinetobacter baumannii. New antibiotics and new therapeutic strategies are needed to address this challenge. Advances in identifying new sources of antibiotic natural products and expanding antibiotic chemical diversity are providing chemical leads for new drugs. Inhibitors of resistance mechanisms and microbial virulence are orthogonal strategies that are also generating new chemicals that can extend the life of existing antibiotics. This new chemistry, coupled with a growing understanding of the mechanisms, origins and distribution of antibiotic resistance, position us to tackle the challenges of antibiotic resistance in the 21st century.
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Affiliation(s)
- Gerard D Wright
- Antimicrobial Research Centre, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1200 Main St W, Hamilton, Ontario, L8N 3Z5, Canada.
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