1
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Zheng Y, Zhu X, Jiang M, Cao F, You Q, Chen X. Development and Applications of D-Amino Acid Derivatives-based Metabolic Labeling of Bacterial Peptidoglycan. Angew Chem Int Ed Engl 2024; 63:e202319400. [PMID: 38284300 DOI: 10.1002/anie.202319400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/28/2024] [Accepted: 01/29/2024] [Indexed: 01/30/2024]
Abstract
Peptidoglycan, an essential component within the cell walls of virtually all bacteria, is composed of glycan strands linked by stem peptides that contain D-amino acids. The peptidoglycan biosynthesis machinery exhibits high tolerance to various D-amino acid derivatives. D-amino acid derivatives with different functionalities can thus be specifically incorporated into and label the peptidoglycan of bacteria, but not the host mammalian cells. This metabolic labeling strategy is highly selective, highly biocompatible, and broadly applicable, which has been utilized in various fields. This review introduces the metabolic labeling strategies of peptidoglycan by using D-amino acid derivatives, including one-step and two-step strategies. In addition, we emphasize the various applications of D-amino acid derivative-based metabolic labeling, including bacterial peptidoglycan visualization (existence, biosynthesis, and dynamics, etc.), bacterial visualization (including bacterial imaging and visualization of growth and division, metabolic activity, antibiotic susceptibility, etc.), pathogenic bacteria-targeted diagnostics and treatment (positron emission tomography (PET) imaging, photodynamic therapy, photothermal therapy, gas therapy, immunotherapy, etc.), and live bacteria-based therapy. Finally, a summary of this metabolic labeling and an outlook is provided.
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Affiliation(s)
- Yongfang Zheng
- Fujian-Taiwan Science and Technology Cooperation Base of Biomedical Materials and Tissue Engineering, Engineering Research Center of Industrial Biocatalysis, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Provincial Key Laboratory of Polymer Materials, College of Chemistry and Materials Science, Fujian Normal University, 32 Shangsan Road, Fuzhou, 350007, P.R. China
| | - Xinyu Zhu
- Fujian-Taiwan Science and Technology Cooperation Base of Biomedical Materials and Tissue Engineering, Engineering Research Center of Industrial Biocatalysis, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Provincial Key Laboratory of Polymer Materials, College of Chemistry and Materials Science, Fujian Normal University, 32 Shangsan Road, Fuzhou, 350007, P.R. China
| | - Mingyi Jiang
- Fujian-Taiwan Science and Technology Cooperation Base of Biomedical Materials and Tissue Engineering, Engineering Research Center of Industrial Biocatalysis, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Provincial Key Laboratory of Polymer Materials, College of Chemistry and Materials Science, Fujian Normal University, 32 Shangsan Road, Fuzhou, 350007, P.R. China
| | - Fangfang Cao
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, Singapore, 119074, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
| | - Qing You
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, Singapore, 119074, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
| | - Xiaoyuan Chen
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, Singapore, 119074, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
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2
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Zheng Y, Jiang M, Zhu X, Chen Y, Feng L, Zhu H. Metabolic labeling-mediated visualization, capture, and inactivation of Gram-positive bacteria via biotin-streptavidin interactions. Chem Commun (Camb) 2024. [PMID: 38477080 DOI: 10.1039/d4cc00517a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
We introduce a biotinylated D-amino acid probe capable of metabolically incorporating into bacterial PG. Leveraging the robust affinity between biotin and streptavidin, the probe has demonstrated efficacy in imaging, capture, and targeted inactivation of Gram-positive bacteria through synergistic pairings with commercially available streptavidin-modified fluorescent dyes and nanomaterials. The versatility of the probe is underscored by its compatibility with a variety of commercially available streptavidin-modified reagents. This adaptability allows the probe to be applied across diverse scenarios by integrating with these commercial reagents.
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Affiliation(s)
- Yongfang Zheng
- Fujian-Taiwan Science and Technology Cooperation Base of Biomedical Materials and Tissue Engineering, Engineering Research Center of Industrial Biocatalysis, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Provincial Key Laboratory of Polymer Materials, College of Chemistry and Materials Science, Fujian Normal University, 32 Shangsan Road, Fuzhou 350007, China.
| | - Mingyi Jiang
- Fujian-Taiwan Science and Technology Cooperation Base of Biomedical Materials and Tissue Engineering, Engineering Research Center of Industrial Biocatalysis, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Provincial Key Laboratory of Polymer Materials, College of Chemistry and Materials Science, Fujian Normal University, 32 Shangsan Road, Fuzhou 350007, China.
| | - Xinyu Zhu
- Fujian-Taiwan Science and Technology Cooperation Base of Biomedical Materials and Tissue Engineering, Engineering Research Center of Industrial Biocatalysis, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Provincial Key Laboratory of Polymer Materials, College of Chemistry and Materials Science, Fujian Normal University, 32 Shangsan Road, Fuzhou 350007, China.
| | - Yuyuan Chen
- Fujian-Taiwan Science and Technology Cooperation Base of Biomedical Materials and Tissue Engineering, Engineering Research Center of Industrial Biocatalysis, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Provincial Key Laboratory of Polymer Materials, College of Chemistry and Materials Science, Fujian Normal University, 32 Shangsan Road, Fuzhou 350007, China.
| | - Lisha Feng
- Fujian-Taiwan Science and Technology Cooperation Base of Biomedical Materials and Tissue Engineering, Engineering Research Center of Industrial Biocatalysis, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Provincial Key Laboratory of Polymer Materials, College of Chemistry and Materials Science, Fujian Normal University, 32 Shangsan Road, Fuzhou 350007, China.
| | - Hu Zhu
- Fujian-Taiwan Science and Technology Cooperation Base of Biomedical Materials and Tissue Engineering, Engineering Research Center of Industrial Biocatalysis, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Provincial Key Laboratory of Polymer Materials, College of Chemistry and Materials Science, Fujian Normal University, 32 Shangsan Road, Fuzhou 350007, China.
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3
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Quintana ILL, Paul A, Chowdhury A, Moulton KD, Kulkarni SS, Dube DH. Thioglycosides Act as Metabolic Inhibitors of Bacterial Glycan Biosynthesis. ACS Infect Dis 2023; 9:2025-2035. [PMID: 37698279 PMCID: PMC10580310 DOI: 10.1021/acsinfecdis.3c00324] [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: 07/07/2023] [Indexed: 09/13/2023]
Abstract
Glycans that coat the surface of bacteria are compelling antibiotic targets because they contain distinct monosaccharides that are linked to pathogenesis and are absent in human cells. Disrupting glycan biosynthesis presents a path to inhibiting the ability of a bacterium to infect the host. We previously demonstrated that O-glycosides act as metabolic inhibitors and disrupt bacterial glycan biosynthesis. Inspired by a recent study which showed that thioglycosides (S-glycosides) are 10 times more effective than O-glycosides at inhibiting glycan biosynthesis in mammalian cells, we crafted a panel of S-glycosides based on rare bacterial monosaccharides. The novel thioglycosides altered glycan biosynthesis and fitness in pathogenic bacteria but had no notable effect on glycosylation or growth in beneficial bacteria or mammalian cells. In contrast to findings in mammalian cells, S-glycosides and O-glycosides exhibited comparable potency in bacteria. However, S-glycosides exhibited enhanced selectivity relative to O-glycosides. These novel metabolic inhibitors will allow selective perturbation of the bacterial glycocalyx for functional studies and set the stage to expand our antibiotic arsenal.
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Affiliation(s)
- Isabella
de la Luz Quintana
- Department
of Chemistry & Biochemistry, Bowdoin
College, 6600 College Station, Brunswick, Maine 04011, United States
| | - Ankita Paul
- Department
of Chemistry, Indian Institute of Technology
Bombay, Powai, Mumbai 400-076, India
| | - Aniqa Chowdhury
- Department
of Chemistry & Biochemistry, Bowdoin
College, 6600 College Station, Brunswick, Maine 04011, United States
| | - Karen D. Moulton
- Department
of Chemistry & Biochemistry, Bowdoin
College, 6600 College Station, Brunswick, Maine 04011, United States
| | - Suvarn S. Kulkarni
- Department
of Chemistry, Indian Institute of Technology
Bombay, Powai, Mumbai 400-076, India
| | - Danielle H. Dube
- Department
of Chemistry & Biochemistry, Bowdoin
College, 6600 College Station, Brunswick, Maine 04011, United States
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4
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Dzigba P, Rylski AK, Angera IJ, Banahene N, Kavunja HW, Greenlee-Wacker MC, Swarts BM. Immune Targeting of Mycobacteria through Cell Surface Glycan Engineering. ACS Chem Biol 2023; 18:1548-1556. [PMID: 37306676 PMCID: PMC10782841 DOI: 10.1021/acschembio.3c00155] [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] [Indexed: 06/13/2023]
Abstract
Mycobacteria and other organisms in the order Mycobacteriales cause a range of significant human diseases, including tuberculosis, leprosy, diphtheria, Buruli ulcer, and non-tuberculous mycobacterial (NTM) disease. However, the intrinsic drug tolerance engendered by the mycobacterial cell envelope undermines conventional antibiotic treatment and contributes to acquired drug resistance. Motivated by the need to augment antibiotics with novel therapeutic approaches, we developed a strategy to specifically decorate mycobacterial cell surface glycans with antibody-recruiting molecules (ARMs), which flag bacteria for binding to human-endogenous antibodies that enhance macrophage effector functions. Mycobacterium-specific ARMs consisting of a trehalose targeting moiety and a dinitrophenyl hapten (Tre-DNPs) were synthesized and shown to specifically incorporate into outer-membrane glycolipids of Mycobacterium smegmatis via trehalose metabolism, enabling recruitment of anti-DNP antibodies to the mycobacterial cell surface. Phagocytosis of Tre-DNP-modified M. smegmatis by macrophages was significantly enhanced in the presence of anti-DNP antibodies, demonstrating proof-of-concept that our strategy can augment the host immune response. Because the metabolic pathways responsible for cell surface incorporation of Tre-DNPs are conserved in all Mycobacteriales organisms but absent from other bacteria and humans, the reported tools may be enlisted to interrogate host-pathogen interactions and develop immune-targeting strategies for diverse mycobacterial pathogens.
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Affiliation(s)
- Priscilla Dzigba
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, 48859, USA
- Department of Biology, Central Michigan University, Mount Pleasant, MI, 48859, USA
- Biochemistry, Cell, and Molecular Biology Graduate Programs, Central Michigan University, Mount Pleasant, MI, 48859 United States
| | - Adrian K. Rylski
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, 48859, USA
| | - Isaac J. Angera
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, 48859, USA
| | - Nicholas Banahene
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, 48859, USA
- Biochemistry, Cell, and Molecular Biology Graduate Programs, Central Michigan University, Mount Pleasant, MI, 48859 United States
| | - Herbert W. Kavunja
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, 48859, USA
| | - Mallary C. Greenlee-Wacker
- Department of Biology, Central Michigan University, Mount Pleasant, MI, 48859, USA
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA, 93407, USA
| | - Benjamin M. Swarts
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, 48859, USA
- Biochemistry, Cell, and Molecular Biology Graduate Programs, Central Michigan University, Mount Pleasant, MI, 48859 United States
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5
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Liu Z, Lepori I, Chordia MD, Dalesandro BE, Guo T, Dong J, Siegrist MS, Pires MM. A Metabolic-Tag-Based Method for Assessing the Permeation of Small Molecules Across the Mycomembrane in Live Mycobacteria. Angew Chem Int Ed Engl 2023; 62:e202217777. [PMID: 36700874 PMCID: PMC10159989 DOI: 10.1002/anie.202217777] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/05/2023] [Accepted: 01/24/2023] [Indexed: 01/27/2023]
Abstract
The general lack of permeability of small molecules observed for Mycobacterium tuberculosis (Mtb) is most ascribed to its unique cell envelope. More specifically, the outer mycomembrane is hypothesized to be the principal determinant for access of antibiotics to their molecular targets. We describe a novel assay that combines metabolic tagging of the peptidoglycan, which sits directly beneath the mycomembrane, click chemistry of test molecules, and a fluorescent labeling chase step, to measure the permeation of small molecules. We showed that the assay workflow was robust and compatible with high-throughput analysis in mycobacteria by testing a small panel of azide-tagged molecules. The general trend is similar across the two types of mycobacteria with some notable exceptions. We anticipate that this assay platform will lay the foundation for medicinal chemistry efforts to understand and improve uptake of both existing drugs and newly-discovered compounds into mycobacteria.
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Affiliation(s)
- Zichen Liu
- Department of Chemistry, University of Virginia, Charlottesville, United States
| | - Irene Lepori
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, United States
- Department of Microbiology, University of Massachusetts, Amherst, United States
| | - Mahendra D. Chordia
- Department of Chemistry, University of Virginia, Charlottesville, United States
| | | | - Taijie Guo
- Institute of Translational Medicine, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200232, China
| | - Jiajia Dong
- Institute of Translational Medicine, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200232, China
| | - M. Sloan Siegrist
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, United States
- Department of Microbiology, University of Massachusetts, Amherst, United States
| | - Marcos M. Pires
- Department of Chemistry, University of Virginia, Charlottesville, United States
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6
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Copling A, Akantibila M, Kumaresan R, Fleischer G, Cortes D, Tripathi RS, Carabetta VJ, Vega SL. Recent Advances in Antimicrobial Peptide Hydrogels. Int J Mol Sci 2023; 24:7563. [PMID: 37108725 PMCID: PMC10139150 DOI: 10.3390/ijms24087563] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
Advances in the number and type of available biomaterials have improved medical devices such as catheters, stents, pacemakers, prosthetic joints, and orthopedic devices. The introduction of a foreign material into the body comes with a risk of microbial colonization and subsequent infection. Infections of surgically implanted devices often lead to device failure, which leads to increased patient morbidity and mortality. The overuse and improper use of antimicrobials has led to an alarming rise and spread of drug-resistant infections. To overcome the problem of drug-resistant infections, novel antimicrobial biomaterials are increasingly being researched and developed. Hydrogels are a class of 3D biomaterials consisting of a hydrated polymer network with tunable functionality. As hydrogels are customizable, many different antimicrobial agents, such as inorganic molecules, metals, and antibiotics have been incorporated or tethered to them. Due to the increased prevalence of antibiotic resistance, antimicrobial peptides (AMPs) are being increasingly explored as alternative agents. AMP-tethered hydrogels are being increasingly examined for antimicrobial properties and practical applications, such as wound-healing. Here, we provide a recent update, from the last 5 years of innovations and discoveries made in the development of photopolymerizable, self-assembling, and AMP-releasing hydrogels.
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Affiliation(s)
- Aryanna Copling
- Department of Molecular & Cellular Biosciences, Rowan University, Glassboro, NJ 08028, USA;
| | - Maxwell Akantibila
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ 08103, USA; (M.A.); (G.F.); (D.C.); (R.S.T.)
| | - Raaha Kumaresan
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA;
| | - Gilbert Fleischer
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ 08103, USA; (M.A.); (G.F.); (D.C.); (R.S.T.)
| | - Dennise Cortes
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ 08103, USA; (M.A.); (G.F.); (D.C.); (R.S.T.)
| | - Rahul S. Tripathi
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ 08103, USA; (M.A.); (G.F.); (D.C.); (R.S.T.)
| | - Valerie J. Carabetta
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ 08103, USA; (M.A.); (G.F.); (D.C.); (R.S.T.)
| | - Sebastián L. Vega
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA;
- Department of Orthopedic Surgery, Cooper Medical School of Rowan University, Camden, NJ 08103, USA
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7
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Dalesandro BE, Pires MM. Immunotargeting of Gram-Positive Pathogens via a Cell Wall Binding Tick Antifreeze Protein. J Med Chem 2023; 66:503-515. [PMID: 36563000 DOI: 10.1021/acs.jmedchem.2c01464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Immunological agents that supplement or modulate the host immune response have proven to have powerful therapeutic potential, although this modality is less explored against bacterial pathogens. We describe the application of a bacterial binding protein to re-engage the immune system toward pathogenic bacteria. More specifically, a hapten was conjugated to a protein expressed by Ixodes scapularis ticks, called I. scapularis antifreeze glycoprotein (IAFGP), that has high affinity for the d-alanine residue on the bacterial peptidoglycan. We showed that a fragment of this protein retained high surface binding affinity. Moreover, conjugation of a hapten to this peptide led to the display of haptens on the cell surface of vancomycin-resistant Enterococcus faecalis. Hapten display then induced the recruitment of antibodies and promoted uptake of bacterial pathogens by immune cells. These results demonstrate the feasibility in using cell wall binding agents as the basis of a class of bacterial immunotherapies.
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Affiliation(s)
- Brianna E Dalesandro
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Marcos M Pires
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
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8
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Apostolos AJ, Chordia MD, Kolli SH, Dalesandro BE, Rutkowski MR, Pires MM. Real-time non-invasive fluorescence imaging of gut commensal bacteria to detect dynamic changes in the microbiome of live mice. Cell Chem Biol 2022; 29:S2451-9456(22)00416-0. [PMID: 36516833 PMCID: PMC10239791 DOI: 10.1016/j.chembiol.2022.11.010] [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: 05/27/2022] [Revised: 10/20/2022] [Accepted: 11/18/2022] [Indexed: 12/15/2022]
Abstract
In mammals, gut commensal microbiota interact extensively with the host, and the same interactions can be dysregulated in diseased states. Animal imaging is a powerful technique that is widely used to diagnose, measure, and track biological changes in model organisms such as laboratory mice. Several imaging techniques have been discovered and adopted by the research community that provide dynamic, non-invasive assessment of live animals, but these gains have not been universal across all fields of biology. Herein, we describe a method to non-invasively image commensal bacteria based on the specific metabolic labeling of bacterial cell walls to illuminate the gut bacteria of live mice. This tagging strategy may additionally provide unprecedented insight into cell wall turnover of gut commensals, which has implications for bacterial cellular growth and division, in a live animal.
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Affiliation(s)
- Alexis J Apostolos
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Mahendra D Chordia
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Sree H Kolli
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA 22904, USA
| | | | - Melanie R Rutkowski
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Marcos M Pires
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA.
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9
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Weidenbacher PAB, Rodriguez-Rivera FP, Sanyal M, Visser JA, Do J, Bertozzi CR, Kim PS. Chemically Modified Bacterial Sacculi as a Vaccine Microparticle Scaffold. ACS Chem Biol 2022; 17:1184-1196. [PMID: 35412807 PMCID: PMC9127789 DOI: 10.1021/acschembio.2c00140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
Vaccine scaffolds
and carrier proteins increase the immunogenicity
of subunit vaccines. Here, we developed, characterized, and demonstrated
the efficacy of a novel microparticle vaccine scaffold comprised of
bacterial peptidoglycan (PGN), isolated as an entire sacculi. The
PGN microparticles contain bio-orthogonal chemical handles allowing
for site-specific attachment of immunogens. We first evaluated the
purification, integrity, and immunogenicity of PGN microparticles
derived from a variety of bacterial species. We then optimized PGN
microparticle modification conditions; Staphylococcus
aureus PGN microparticles containing azido-d-alanine yielded robust conjugation to immunogens. We then demonstrated
that this vaccine scaffold elicits comparable immunostimulation to
the conventional carrier protein, keyhole limpet hemocyanin (KLH).
We further modified the S. aureus PGN
microparticle to contain the SARS-CoV-2 receptor-binding domain (RBD)—this
conjugate vaccine elicited neutralizing antibody titers comparable
to those elicited by the KLH-conjugated RBD. Collectively, these findings
suggest that chemically modified bacterial PGN microparticles are
a conjugatable and biodegradable microparticle scaffold capable of
eliciting a robust immune response toward an antigen of interest.
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Affiliation(s)
- Payton A.-B. Weidenbacher
- Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Frances P. Rodriguez-Rivera
- Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Mrinmoy Sanyal
- Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
- Department of Biochemistry, School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Joshua A. Visser
- Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Jonathan Do
- Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
- Department of Biochemistry, School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Carolyn R. Bertozzi
- Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Peter S. Kim
- Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
- Department of Biochemistry, School of Medicine, Stanford University, Stanford, California 94305, United States
- Chan Zuckerberg Biohub, San Francisco, California 94158, United States
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10
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Ferraro NJ, Pires MM. Genetic Determinants of Surface Accessibility in Staphylococcus aureus. Bioconjug Chem 2022; 33:767-772. [PMID: 35499914 DOI: 10.1021/acs.bioconjchem.2c00173] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacterial cell walls represent one of the most prominent targets of antibacterial agents. These agents include natural products (e.g., vancomycin) and proteins stemming from the innate immune system (e.g., peptidoglycan-recognition proteins and lysostaphin). Among bacterial pathogens that infect humans, Staphylococcus aureus (S. aureus) continues to impose a tremendous healthcare burden across the globe. S. aureus has evolved countermeasures that can directly restrict the accessibility of innate immune proteins, effectively protecting itself from threats that target key cell well components. We recently described a novel assay that directly reports on the accessibility of molecules to the peptidoglycan layer within the bacterial cell wall of S. aureus. The assay relies on site-specific chemical remodeling of the peptidoglycan with a biorthogonal handle. Here, we disclose the application of our assay to a screen of a nonredundant transposon mutant library for susceptibility of the peptidoglycan layer with the goal of identifying genes that contribute to the control of cell surface accessibility. We discovered several genes that resulted in higher accessibility levels to the peptidoglycan layer and showed that these genes modulate sensitivity to lysostaphin. These results indicate that this assay platform can be leveraged to gain further insight into the biology of bacterial cell surfaces.
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Affiliation(s)
- Noel J Ferraro
- Department of Chemistry University of Virginia Charlottesville, Virginia 22904, United States
| | - Marcos M Pires
- Department of Chemistry University of Virginia Charlottesville, Virginia 22904, United States
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11
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Impact of crossbridge structure on peptidoglycan crosslinking: A synthetic stem peptide approach. Methods Enzymol 2022; 665:259-279. [PMID: 35379437 DOI: 10.1016/bs.mie.2021.11.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The bacterial cell wall, whose main component is peptidoglycan (PG), provides cellular rigidity and prevents lysis from osmotic pressure. Moreover, the cell wall is the main interface between the external environment and internal cellular components. Given its essentiality, many antibiotics target enzymes related to the biosynthesis of cell wall. Of these enzymes, transpeptidases (TPs) are central to proper cell wall assembly and their inactivation is the mechanism of action of many antibiotics including β-lactams. TPs are responsible for stitching together strands of PG to make the crosslinked meshwork of the cell wall. This chapter focuses on the use of solid-phase peptide synthesis to build PG analogs that become site-selectively incorporated into the cell wall of live bacterial cells. This method allows for the design of fluorescent handles on PG probes that will enable the interrogation of substrate preferences of TPs (e.g., amidation at the glutamic acid residue, crossbridge presence) by analyzing the level of probe incorporation within the native cell wall of live bacterial cells.
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12
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Banahene N, Kavunja HW, Swarts BM. Chemical Reporters for Bacterial Glycans: Development and Applications. Chem Rev 2022; 122:3336-3413. [PMID: 34905344 PMCID: PMC8958928 DOI: 10.1021/acs.chemrev.1c00729] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bacteria possess an extraordinary repertoire of cell envelope glycans that have critical physiological functions. Pathogenic bacteria have glycans that are essential for growth and virulence but are absent from humans, making them high-priority targets for antibiotic, vaccine, and diagnostic development. The advent of metabolic labeling with bioorthogonal chemical reporters and small-molecule fluorescent reporters has enabled the investigation and targeting of specific bacterial glycans in their native environments. These tools have opened the door to imaging glycan dynamics, assaying and inhibiting glycan biosynthesis, profiling glycoproteins and glycan-binding proteins, and targeting pathogens with diagnostic and therapeutic payload. These capabilities have been wielded in diverse commensal and pathogenic Gram-positive, Gram-negative, and mycobacterial species─including within live host organisms. Here, we review the development and applications of chemical reporters for bacterial glycans, including peptidoglycan, lipopolysaccharide, glycoproteins, teichoic acids, and capsular polysaccharides, as well as mycobacterial glycans, including trehalose glycolipids and arabinan-containing glycoconjugates. We cover in detail how bacteria-targeting chemical reporters are designed, synthesized, and evaluated, how they operate from a mechanistic standpoint, and how this information informs their judicious and innovative application. We also provide a perspective on the current state and future directions of the field, underscoring the need for interdisciplinary teams to create novel tools and extend existing tools to support fundamental and translational research on bacterial glycans.
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Affiliation(s)
- Nicholas Banahene
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, United States
- Biochemistry, Cell, and Molecular Biology Program, Central Michigan University, Mount Pleasant, MI, United States
| | - Herbert W. Kavunja
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, United States
- Biochemistry, Cell, and Molecular Biology Program, Central Michigan University, Mount Pleasant, MI, United States
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13
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Ferraro NJ, Kim S, Im W, Pires MM. Systematic Assessment of Accessibility to the Surface of Staphylococcus aureus. ACS Chem Biol 2021; 16:2527-2536. [PMID: 34609132 DOI: 10.1021/acschembio.1c00604] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Proteins from bacterial foes, antimicrobial peptides, and host immune proteins must navigate past a dense layer of bacterial surface biomacromolecules to reach the peptidoglycan (PG) layer of Gram-positive bacteria. A subclass of molecules (e.g., antibiotics with intracellular targets) also must permeate through the PG (in a molecular sieving manner) to reach the cytoplasmic membrane. Despite the biological and therapeutic importance of surface accessibility, systematic analyses in live bacterial cells have been lacking. We describe a live cell fluorescence assay that is robust, shows a high level of reproducibility, and reports on the permeability of molecules to and within the PG scaffold. Moreover, our study shows that teichoic acids impede the permeability of molecules of a wide range of sizes and chemical composition.
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Affiliation(s)
- Noel J. Ferraro
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Seonghoon Kim
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
| | - Wonpil Im
- Departments of Biological Sciences, Chemistry, and Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Marcos M. Pires
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
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14
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Apostolos AJ, Ferraro NJ, Dalesandro BE, Pires MM. SaccuFlow: A High-Throughput Analysis Platform to Investigate Bacterial Cell Wall Interactions. ACS Infect Dis 2021; 7:2483-2491. [PMID: 34291914 DOI: 10.1021/acsinfecdis.1c00255] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Bacterial cell walls are formidable barriers that protect bacterial cells against external insults and oppose internal turgor pressure. While cell wall composition is variable across species, peptidoglycan is the principal component of all cell walls. Peptidoglycan is a mesh-like scaffold composed of cross-linked strands that can be heavily decorated with anchored proteins. The biosynthesis and remodeling of peptidoglycan must be tightly regulated by cells because disruption to this biomacromolecule is lethal. This essentiality is exploited by the human innate immune system in resisting colonization and by a number of clinically relevant antibiotics that target peptidoglycan biosynthesis. Evaluation of molecules or proteins that interact with peptidoglycan can be a complicated and, typically, qualitative effort. We have developed a novel assay platform (SaccuFlow) that preserves the native structure of bacterial peptidoglycan and is compatible with high-throughput flow cytometry analysis. We show that the assay is facile and versatile as demonstrated by its compatibility with sacculi from Gram-positive bacteria, Gram-negative bacteria, and mycobacteria. Finally, we highlight the utility of this assay to assess the activity of sortase A from Staphylococcus aureus against potential antivirulence agents.
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Affiliation(s)
- Alexis J. Apostolos
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Noel J. Ferraro
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Brianna E. Dalesandro
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Marcos M. Pires
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
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15
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Luong P, Dube DH. Dismantling the bacterial glycocalyx: Chemical tools to probe, perturb, and image bacterial glycans. Bioorg Med Chem 2021; 42:116268. [PMID: 34130219 DOI: 10.1016/j.bmc.2021.116268] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 12/20/2022]
Abstract
The bacterial glycocalyx is a quintessential drug target comprised of structurally distinct glycans. Bacterial glycans bear unusual monosaccharide building blocks whose proper construction is critical for bacterial fitness, survival, and colonization in the human host. Despite their appeal as therapeutic targets, bacterial glycans are difficult to study due to the presence of rare bacterial monosaccharides that are linked and modified in atypical manners. Their structural complexity ultimately hampers their analytical characterization. This review highlights recent advances in bacterial chemical glycobiology and focuses on the development of chemical tools to probe, perturb, and image bacterial glycans and their biosynthesis. Current technologies have enabled the study of bacterial glycosylation machinery even in the absence of detailed structural information.
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Affiliation(s)
- Phuong Luong
- Department of Chemistry & Biochemistry, Bowdoin College, 6600 College Station, Brunswick, ME 04011, USA
| | - Danielle H Dube
- Department of Chemistry & Biochemistry, Bowdoin College, 6600 College Station, Brunswick, ME 04011, USA.
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16
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Dalesandro BE, Pires MM. Induction of Endogenous Antibody Recruitment to the Surface of the Pathogen Enterococcus faecium. ACS Infect Dis 2021; 7:1116-1125. [PMID: 33179504 DOI: 10.1021/acsinfecdis.0c00547] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
For the foreseeable future, conventional small molecule antibiotics will continue to be the predominant treatment option due to wide patient coverage and low costs. Today, however, there is already a significant portion of patients that fail to respond to small molecule antibiotics and, according to the Centers for Disease Control and Prevention, this number is poised to increase in the coming years. Therefore, this rise in drug resistant bacteria must be countered with the development of nontraditional therapies. We propose a measure based on the re-engagement of the immune system toward pathogenic bacteria by grafting bacterial cell surfaces with immunogenic agents. Herein, we describe a class of cell wall analogues that selectively graft bacterial cell surfaces with epitopes that promote their opsonization. More specifically, synthetic analogues of peptidoglycan conjugated to haptens were designed to be incorporated by the cell wall biosynthetic machinery into live Enterococcus faecium. E. faecium is a formidable human pathogen that poses a considerable burden to healthcare and often results in fatalities. We showed that treatment of E. faecium and vancomycin-resistant strains with the cell wall analogues led to the display of haptens on the cell surface, which induced the recruitment of antibodies existing in the serum of humans. These results demonstrate the feasibility in using cell wall analogues as the basis of a class of bacterial immunotherapies against dangerous pathogens.
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Affiliation(s)
- Brianna E. Dalesandro
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Marcos M. Pires
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
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17
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Abstract
Biofilms are widely involved in human lives, such as in medical infection, environmental remediation, and industrial processes. However, the control of the biofilm has still been a challenge because of its strong drug resistance. Here, we designed and synthesized an amphipathic antimicrobial peptide (Ac-DKDHDHDQDKDLDVDFDFDADK-NH2 (KKd-11)) that was composed of d-amino acids (DAAs). KKd-11 was found to self-assemble into a hydrogel with an improved long-term antimicrobial ability and a better antiprotease activity as compared to the hydrogel formed by Ac-LKLHLHLQLKLLLVLFLFLALK-NH2 (KK-11). Our results indicated that KKd-11 was not only able to inhibit the formation of biofilms but also could effectively damage preformed mature biofilms and kill the bacteria within the biofilms. Besides, cell viability assays indicated that the KKd-11 peptide had very good biocompatibility. We think d-peptide hydrogels may have great potential in the treatment of biofilm-induced infections.
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Affiliation(s)
- Zhen Guo
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.,Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yujiao Wang
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.,Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tingyuan Tan
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.,Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuwen Ji
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.,Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Hu
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.,Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Yi Zhang
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.,Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
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18
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Margison KD, Bilodeau DA, Mahmoudi F, Pezacki JP. Cycloadditions of
Trans
‐Cyclooctenes and Nitrones as Tools for Bioorthogonal Labelling. Chembiochem 2020; 21:948-951. [DOI: 10.1002/cbic.201900627] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Kaitlyn D. Margison
- Department of Chemistry and Biomolecular SciencesUniversity of Ottawa 150 Louis-Pasteur Ottawa ON K1N 6N5 Canada
| | - Didier A. Bilodeau
- Department of Chemistry and Biomolecular SciencesUniversity of Ottawa 150 Louis-Pasteur Ottawa ON K1N 6N5 Canada
| | - Farnaz Mahmoudi
- Department of Chemistry and Biomolecular SciencesUniversity of Ottawa 150 Louis-Pasteur Ottawa ON K1N 6N5 Canada
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular SciencesUniversity of Ottawa 150 Louis-Pasteur Ottawa ON K1N 6N5 Canada
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19
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Wehr J, Sikorski EL, Bloch E, Feigman MS, Ferraro NJ, Baybutt TR, Snook AE, Pires MM, Thévenin D. pH-Dependent Grafting of Cancer Cells with Antigenic Epitopes Promotes Selective Antibody-Mediated Cytotoxicity. J Med Chem 2020; 63:3713-3722. [PMID: 32196345 DOI: 10.1021/acs.jmedchem.0c00016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A growing class of immunotherapeutics work by redirecting components of the immune system to recognize markers on the surface of cancer cells. However, such modalities will remain confined to a relatively small subgroup of patients because of the lack of universal targetable tumor biomarkers among all patients. Here, we designed a unique class of agents that exploit the inherent acidity of solid tumors to selectively graft cancer cells with immuno-engager epitopes. Our targeting approach is based on pHLIP, a unique peptide that selectively targets tumors in vivo by anchoring to cancer cell surfaces in a pH-dependent manner. We established that pHLIP-antigen conjugates trigger the recruitment of antibodies to the surface of cancer cells and induce cytotoxicity by peripheral blood mononuclear and engineered NK cells. These results indicate that these agents have the potential to be applicable to treating a wide range of solid tumors and to circumvent problems associated with narrow windows of selectivity.
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Affiliation(s)
- Janessa Wehr
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Eden L Sikorski
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Elizabeth Bloch
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Mary S Feigman
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Noel J Ferraro
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Trevor R Baybutt
- Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, United States
| | - Adam E Snook
- Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, United States
| | - Marcos M Pires
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Damien Thévenin
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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20
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Idso MN, Akhade AS, Arrieta-Ortiz ML, Lai BT, Srinivas V, Hopkins JP, Gomes AO, Subramanian N, Baliga N, Heath JR. Antibody-recruiting protein-catalyzed capture agents to combat antibiotic-resistant bacteria. Chem Sci 2020; 11:3054-3067. [PMID: 34122810 PMCID: PMC8157486 DOI: 10.1039/c9sc04842a] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Antibiotic resistant infections are projected to cause over 10 million deaths by 2050, yet the development of new antibiotics has slowed. This points to an urgent need for methodologies for the rapid development of antibiotics against emerging drug resistant pathogens. We report on a generalizable combined computational and synthetic approach, called antibody-recruiting protein-catalyzed capture agents (AR-PCCs), to address this challenge. We applied the combinatorial protein catalyzed capture agent (PCC) technology to identify macrocyclic peptide ligands against highly conserved surface protein epitopes of carbapenem-resistant Klebsiella pneumoniae, an opportunistic Gram-negative pathogen with drug resistant strains. Multi-omic data combined with bioinformatic analyses identified epitopes of the highly expressed MrkA surface protein of K. pneumoniae for targeting in PCC screens. The top-performing ligand exhibited high-affinity (EC50 ∼50 nM) to full-length MrkA, and selectively bound to MrkA-expressing K. pneumoniae, but not to other pathogenic bacterial species. AR-PCCs that bear a hapten moiety promoted antibody recruitment to K. pneumoniae, leading to enhanced phagocytosis and phagocytic killing by macrophages. The rapid development of this highly targeted antibiotic implies that the integrated computational and synthetic toolkit described here can be used for the accelerated production of antibiotics against drug resistant bacteria.
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Affiliation(s)
- Matthew N Idso
- Institute for Systems Biology 401 Terry Ave North Seattle 98109 USA
| | | | | | - Bert T Lai
- Indi Molecular, Inc. 6162 Bristol Parkway Culver City CA 90230 USA
| | - Vivek Srinivas
- Institute for Systems Biology 401 Terry Ave North Seattle 98109 USA
| | - James P Hopkins
- Institute for Systems Biology 401 Terry Ave North Seattle 98109 USA
| | | | | | - Nitin Baliga
- Institute for Systems Biology 401 Terry Ave North Seattle 98109 USA
| | - James R Heath
- Institute for Systems Biology 401 Terry Ave North Seattle 98109 USA
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21
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Liang Y, Liu Q, Zhou Y, Chen S, Yang L, Zhu M, Wang Q. Counting and Recognizing Single Bacterial Cells by a Lanthanide-Encoding Inductively Coupled Plasma Mass Spectrometric Approach. Anal Chem 2019; 91:8341-8349. [DOI: 10.1021/acs.analchem.9b01130] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Yong Liang
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Qian Liu
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Yang Zhou
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Shi Chen
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Limin Yang
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Min Zhu
- PerkinElmer Instruments (Shanghai) Co. Ltd., Shanghai 201203, China
| | - Qiuquan Wang
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
- State Key Lab of Marine Environmental Science, Xiamen University, Xiamen, Fujian 361005, China
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22
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Feigman MS, Kim S, Pidgeon SE, Yu Y, Ongwae GM, Patel DS, Regen S, Im W, Pires MM. Synthetic Immunotherapeutics against Gram-negative Pathogens. Cell Chem Biol 2018; 25:1185-1194.e5. [PMID: 29983273 PMCID: PMC6195440 DOI: 10.1016/j.chembiol.2018.05.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/06/2018] [Accepted: 05/29/2018] [Indexed: 12/11/2022]
Abstract
While traditional drug discovery continues to be an important platform for the search of new antibiotics, alternative approaches should also be pursued to complement these efforts. We herein designed a class of molecules that decorate bacterial cell surfaces with the goal of re-engaging components of the immune system toward Escherichia coli and Pseudomonas aeruginosa. More specifically, conjugates were assembled using polymyxin B (an antibiotic that inherently attaches to the surface of Gram-negative pathogens) and antigenic epitopes that recruit antibodies found in human serum. We established that the spacer length played a significant role in hapten display within the bacterial cell surface, a result that was confirmed both experimentally and via molecular dynamics simulations. Most importantly, we demonstrated the specific killing of bacteria by our agent in the presence of human serum. By enlisting the immune system, these agents have the potential to pave the way for a potent antimicrobial modality.
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Affiliation(s)
| | - Seonghoon Kim
- Departments of Biological Sciences and Bioengineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Sean E Pidgeon
- Department of Chemistry, Lehigh University, Bethlehem, PA 18015, USA
| | - Yuming Yu
- Department of Chemistry, Lehigh University, Bethlehem, PA 18015, USA
| | | | - Dhilon S Patel
- Departments of Biological Sciences and Bioengineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Steven Regen
- Department of Chemistry, Lehigh University, Bethlehem, PA 18015, USA
| | - Wonpil Im
- Departments of Biological Sciences and Bioengineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Marcos M Pires
- Department of Chemistry, Lehigh University, Bethlehem, PA 18015, USA.
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23
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He P, Lv F, Liu L, Wang S. Synthesis of amphiphilic poly(fluorene) derivatives for selective imaging of Staphylococcus aureus. Sci Bull (Beijing) 2018; 63:900-906. [PMID: 36658971 DOI: 10.1016/j.scib.2018.05.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Revised: 03/31/2018] [Accepted: 05/09/2018] [Indexed: 01/21/2023]
Abstract
Three amphiphilic poly(fluorene-co-phenylene) derivatives with different side chains (PFP-1, PFP-2, PFP-3) were designed and synthesized for exploring their detection and imaging of pathogens. Upon incubation with six kinds of different pathogens, it was found the three polymers could selectively interact with Staphylococcus aureus (S. aureus). Their selective imaging towards S. aureus were thus realized. The selective imaging towards S. aureus was also confirmed even under the blend of microbes. PFP-3 shows stronger fluorescence imaging signal than PFP-1 and PFP-2. Zeta potential and isothermal titration microcalorimetry (ITC) tests demonstrated that both electrostatic interactions and hydrophobic interactions played important roles in the binding between PFPs and pathogens. Thus, amphiphilic PFP-3 exhibits great potential for specific imaging of S. aureus in a simple and rapid manner.
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Affiliation(s)
- Ping He
- Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; College of Chemistry, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fengting Lv
- Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; College of Chemistry, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Libing Liu
- Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; College of Chemistry, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Shu Wang
- Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; College of Chemistry, University of Chinese Academy of Sciences, Beijing 100049, China.
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24
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2013-2014. MASS SPECTROMETRY REVIEWS 2018; 37:353-491. [PMID: 29687922 DOI: 10.1002/mas.21530] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/29/2016] [Indexed: 06/08/2023]
Abstract
This review is the eighth update of the original article published in 1999 on the application of Matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2014. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly- saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2018 Wiley Periodicals, Inc. Mass Spec Rev 37:353-491, 2018.
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Affiliation(s)
- David J Harvey
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
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25
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Feigman MJS, Pires MM. Synthetic Immunobiotics: A Future Success Story in Small Molecule-Based Immunotherapy? ACS Infect Dis 2018; 4:664-672. [PMID: 29431421 DOI: 10.1021/acsinfecdis.7b00261] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Drug resistance to our current stock of antibiotics is projected to increase to levels that threaten our ability to reduce and eliminate bacterial infections, which is now considered one of the primary health care crises of the 21st century. Traditional antibiotic agents (e.g., penicillin) paved the way for massive advances in human health, but we need novel strategies to maintain the upper hand in the battle against pathogenic bacteria. Nontraditional strategies, such as targeted immunotherapies, could prove fruitful in complementing our antibiotic arsenal.
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Affiliation(s)
- Mary J. Sabulski Feigman
- Department of Chemistry, Lehigh University, 6 E. Packer Ave., Bethlehem, Pennsylvania 18015, United States
| | - Marcos M. Pires
- Department of Chemistry, Lehigh University, 6 E. Packer Ave., Bethlehem, Pennsylvania 18015, United States
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26
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Sabulski MJ, Pidgeon SE, Pires MM. Immuno-targeting of Staphylococcus aureus via surface remodeling complexes. Chem Sci 2017; 8:6804-6809. [PMID: 29147504 PMCID: PMC5643955 DOI: 10.1039/c7sc02721d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 08/20/2017] [Indexed: 12/28/2022] Open
Abstract
Agents with novel mechanisms of action are needed to complement traditional antibiotics. Towards these goals, we have exploited the surface-homing properties of vancomycin to tag the surface of Gram-positive pathogens with immune cell attractants in two unique modes. First, vancomycin was conjugated to the small molecule hapten 2,4-dinitrophenol (DNP) to promote bacterial opsonization. Second, we built on these results by improving the tagging specificity and mechanism of incorporation by coupling it to a sortase A substrate peptide. We demonstrated, for the first time, that the surface of Staphylococcus aureus (S. aureus) can be metabolically labeled in live Caenorhabditis elegans hosts. These constructs represent a class of promising narrow-spectrum agents that target S. aureus for opsonization and establish a new surface labeling modality in live host organisms, which should be a powerful tool in dissecting features of host-pathogen interactions.
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Affiliation(s)
- Mary J Sabulski
- Department of Chemistry , Lehigh University , 6 E Packer Ave. , Bethlehem , PA 18015 , USA .
| | - Sean E Pidgeon
- Department of Chemistry , Lehigh University , 6 E Packer Ave. , Bethlehem , PA 18015 , USA .
| | - Marcos M Pires
- Department of Chemistry , Lehigh University , 6 E Packer Ave. , Bethlehem , PA 18015 , USA .
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27
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Pidgeon SE, Pires MM. Cell Wall Remodeling of Staphylococcus aureus in Live Caenorhabditis elegans. Bioconjug Chem 2017; 28:2310-2315. [DOI: 10.1021/acs.bioconjchem.7b00363] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Sean E. Pidgeon
- Department
of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Marcos M. Pires
- Department
of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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28
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Poly(amino acid-hydroxyethyl methacrylate)s with chiral lysine and/or leucine side moieties and their antibacterial abilities for biomedical applications. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2017; 76:1112-1120. [DOI: 10.1016/j.msec.2017.03.177] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 02/07/2017] [Accepted: 03/21/2017] [Indexed: 12/27/2022]
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29
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Bandyopadhyay A, Cambray S, Gao J. Fast Diazaborine Formation of Semicarbazide Enables Facile Labeling of Bacterial Pathogens. J Am Chem Soc 2017; 139:871-878. [PMID: 27992180 PMCID: PMC6191850 DOI: 10.1021/jacs.6b11115] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Bioorthogonal conjugation chemistry has enabled the development of tools for the interrogation of complex biological systems. Although a number of bioorthogonal reactions have been documented in literature, they are less ideal for one or several reasons including slow kinetics, low stability of the conjugated product, requirement of toxic catalysts, and side reactions with unintended biomolecules. Herein we report a fast (>103 M-1 s-1) and bioorthogonal conjugation reaction that joins semicarbazide to an aryl ketone or aldehyde with an ortho-boronic acid substituent. The boronic acid moiety greatly accelerates the initial formation of a semicarbazone conjugate, which rearranges into a stable diazaborine. The diazaborine formation can be performed in blood serum or cell lysates with minimal interference from biomolecules. We further demonstrate that application of this conjugation chemistry enables facile labeling of bacteria. A synthetic amino acid D-AB3, which presents a 2-acetylphenylboronic acid moiety as its side chain, was found to incorporate into several bacterial species through cell wall remodeling, with particularly high efficiency for Escherichia coli. Subsequent D-AB3 conjugation to a fluorophore-labeled semicarbazide allows robust detection of this bacterial pathogen in blood serum.
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Affiliation(s)
- Anupam Bandyopadhyay
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02461
| | - Samantha Cambray
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02461
| | - Jianmin Gao
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02461
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30
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Lin B, Wu X, Zhao H, Tian Y, Han J, Liu J, Han S. Redirecting immunity via covalently incorporated immunogenic sialic acid on the tumor cell surface. Chem Sci 2016; 7:3737-3741. [PMID: 29997860 PMCID: PMC6008587 DOI: 10.1039/c5sc04133c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 02/23/2016] [Indexed: 12/17/2022] Open
Abstract
Techniques eliciting anti-tumor immunity are of interest for immunotherapy. We herein report the covalent incorporation of a non-self immunogen into the tumor glycocalyx by metabolic oligosaccharide engineering with 2,4-dinitrophenylated sialic acid (DNPSia). This enables marked suppression of pulmonary metastasis and subcutaneous tumor growth of B16F10 melanoma cells in mice preimmunized to produce anti-DNP antibodies. Located on the exterior glycocalyx, DNPSia is well-positioned to recruit antibodies. Given the high levels of natural anti-DNP antibodies in humans and ubiquitous sialylation across many cancers, DNPSia offers a simplified route to redirect immunity against diverse tumors without recourse to preimmunization.
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Affiliation(s)
- Bijuan Lin
- State Key Laboratory for Physical Chemistry of Solid Surfaces , Department of Chemical Biology , College of Chemistry and Chemical Engineering , The Key Laboratory for Chemical Biology of Fujian Province , The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, and Innovation Center for Cell Signaling Network , Xiamen University , Xiamen , 361005 , China . ; Tel: +86-0592-2181728
| | - Xuanjun Wu
- State Key Laboratory for Physical Chemistry of Solid Surfaces , Department of Chemical Biology , College of Chemistry and Chemical Engineering , The Key Laboratory for Chemical Biology of Fujian Province , The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, and Innovation Center for Cell Signaling Network , Xiamen University , Xiamen , 361005 , China . ; Tel: +86-0592-2181728
| | - Hu Zhao
- State Key Laboratory for Physical Chemistry of Solid Surfaces , Department of Chemical Biology , College of Chemistry and Chemical Engineering , The Key Laboratory for Chemical Biology of Fujian Province , The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, and Innovation Center for Cell Signaling Network , Xiamen University , Xiamen , 361005 , China . ; Tel: +86-0592-2181728
| | - Yunpeng Tian
- State Key Laboratory for Physical Chemistry of Solid Surfaces , Department of Chemical Biology , College of Chemistry and Chemical Engineering , The Key Laboratory for Chemical Biology of Fujian Province , The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, and Innovation Center for Cell Signaling Network , Xiamen University , Xiamen , 361005 , China . ; Tel: +86-0592-2181728
| | - Jiahuai Han
- State Key Laboratory of Cellular Stress Biology , Innovation Center for Cell Signaling Network , School of Life Sciences , Xiamen University , Xiamen , 361005 , China
| | - Jian Liu
- State Key Laboratory for Physical Chemistry of Solid Surfaces , Department of Chemical Biology , College of Chemistry and Chemical Engineering , The Key Laboratory for Chemical Biology of Fujian Province , The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, and Innovation Center for Cell Signaling Network , Xiamen University , Xiamen , 361005 , China . ; Tel: +86-0592-2181728
| | - Shoufa Han
- State Key Laboratory for Physical Chemistry of Solid Surfaces , Department of Chemical Biology , College of Chemistry and Chemical Engineering , The Key Laboratory for Chemical Biology of Fujian Province , The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, and Innovation Center for Cell Signaling Network , Xiamen University , Xiamen , 361005 , China . ; Tel: +86-0592-2181728
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31
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Sarkar S, Libby EA, Pidgeon SE, Dworkin J, Pires MM. In Vivo Probe of Lipid II-Interacting Proteins. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603441] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Sourav Sarkar
- Department of Chemistry; Lehigh University; Bethlehem PA 18015 USA
| | - Elizabeth A. Libby
- Department of Microbiology & Immunology; Columbia University; New York NY 10032 USA
| | - Sean E. Pidgeon
- Department of Chemistry; Lehigh University; Bethlehem PA 18015 USA
| | - Jonathan Dworkin
- Department of Microbiology & Immunology; Columbia University; New York NY 10032 USA
| | - Marcos M. Pires
- Department of Chemistry; Lehigh University; Bethlehem PA 18015 USA
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32
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Sarkar S, Libby EA, Pidgeon SE, Dworkin J, Pires MM. In Vivo Probe of Lipid II-Interacting Proteins. Angew Chem Int Ed Engl 2016; 55:8401-4. [PMID: 27225706 DOI: 10.1002/anie.201603441] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 04/25/2016] [Indexed: 11/11/2022]
Abstract
β-Lactams represent one of the most important classes of antibiotics discovered to date. These agents block Lipid II processing and cell wall biosynthesis through inactivation of penicillin-binding proteins (PBPs). PBPs enzymatically load cell wall building blocks from Lipid II carrier molecules onto the growing cell wall scaffold during growth and division. Lipid II, a bottleneck in cell wall biosynthesis, is the target of some of the most potent antibiotics in clinical use. Despite the immense therapeutic value of this biosynthetic pathway, the PBP-Lipid II association has not been established in live cells. To determine this key interaction, we designed an unnatural d-amino acid dipeptide that is metabolically incorporated into Lipid II molecules. By hijacking the peptidoglycan biosynthetic machinery, photoaffinity probes were installed in combination with click partners within Lipid II, thereby allowing, for the first time, demonstration of PBP interactions in vivo with Lipid II.
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Affiliation(s)
- Sourav Sarkar
- Department of Chemistry, Lehigh University, Bethlehem, PA, 18015, USA
| | - Elizabeth A Libby
- Department of Microbiology & Immunology, Columbia University, New York, NY, 10032, USA
| | - Sean E Pidgeon
- Department of Chemistry, Lehigh University, Bethlehem, PA, 18015, USA
| | - Jonathan Dworkin
- Department of Microbiology & Immunology, Columbia University, New York, NY, 10032, USA
| | - Marcos M Pires
- Department of Chemistry, Lehigh University, Bethlehem, PA, 18015, USA.
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33
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Fura JM, Pidgeon SE, Birabaharan M, Pires MM. Dipeptide-Based Metabolic Labeling of Bacterial Cells for Endogenous Antibody Recruitment. ACS Infect Dis 2016; 2:302-309. [PMID: 27294199 PMCID: PMC4898660 DOI: 10.1021/acsinfecdis.6b00007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Indexed: 02/06/2023]
Abstract
![]()
The number of antibiotic-resistant
bacterial infections has increased
dramatically over the past decade. To combat these pathogens, novel
antimicrobial strategies must be explored and developed. We previously
reported a strategy based on hapten-modified cell wall analogues to
induce recruitment of endogenous antibodies to bacterial cell surfaces.
Cell surface remodeling using unnatural single d-amino acid
cell wall analogues led to modification at the C-terminus of the peptidoglycan
stem peptide. During peptidoglycan processing, installed hapten-displaying
amino acids can be subsequently removed by cell wall enzymes. Herein,
we disclose a two-step dipeptide peptidoglycan remodeling strategy
aimed at introducing haptens at an alternative site within the stem
peptide to improve retention and diminish removal by cell wall enzymes.
Through this redesigned strategy, we determined size constraints of
peptidoglycan remodeling and applied these constraints to attain hapten–linker
conjugates that produced high levels of antibody recruitment to bacterial
cell surfaces.
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Affiliation(s)
- Jonathan M. Fura
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Sean E. Pidgeon
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Morgan Birabaharan
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Marcos M. Pires
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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34
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Pidgeon SE, Pires MM. Metabolic remodeling of bacterial surfaces via tetrazine ligations. Chem Commun (Camb) 2016; 51:10330-3. [PMID: 26027845 DOI: 10.1039/c5cc01693b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Bioorthogonal click ligations are extensively used for the introduction of functional groups in biological systems. Tetrazine ligations are attractive in that they are catalyst-free and display favorable kinetics. We describe the efficient remodeling of bacterial cell surfaces using unnatural d-amino acids derivatized with tetrazine ligation handles. The metabolic incorporation of these unnatural d-amino acids onto bacterial cell surfaces resulted in a site-selective installation of fluorophores.
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Affiliation(s)
- S E Pidgeon
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, USA.
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35
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Gautam S, Kim T, Lester E, Deep D, Spiegel DA. Wall teichoic acids prevent antibody binding to epitopes within the cell wall of Staphylococcus aureus. ACS Chem Biol 2016; 11:25-30. [PMID: 26502318 DOI: 10.1021/acschembio.5b00439] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Staphylococcus aureus is a Gram-positive bacterial pathogen that produces a range of infections including cellulitis, pneumonia, and septicemia. The principle mechanism in antistaphylococcal host defense is opsonization with antibodies and complement proteins, followed by phagocytic clearance. Here we use a previously developed technique for installing chemical epitopes in the peptidoglycan cell wall to show that surface glycopolymers known as wall teichoic acids conceal cell wall epitopes, preventing their recognition and opsonization by antibodies. Thus, our results reveal a previously unrecognized immunoevasive role for wall teichoic acids in S. aureus: repulsion of peptidoglycan-targeted antibodies.
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Affiliation(s)
- Samir Gautam
- Department
of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06511, United States
| | - Taehan Kim
- Department
of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06511, United States
| | - Evan Lester
- Department
of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06511, United States
| | - Deeksha Deep
- Department
of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06511, United States
| | - David A. Spiegel
- Department
of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06511, United States
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36
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Kim YT, Kim KH, Kang ES, Jo G, Ahn SY, Park SH, Kim SI, Mun S, Baek K, Kim B, Lee K, Yun WS, Kim YH. Synergistic Effect of Detection and Separation for Pathogen Using Magnetic Clusters. Bioconjug Chem 2015; 27:59-65. [PMID: 26710682 DOI: 10.1021/acs.bioconjchem.5b00681] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Early diagnosis of infectious diseases is important for treatment; therefore, selective and rapid detection of pathogenic bacteria is essential for human health. We report a strategy for highly selective detection and rapid separation of pathogenic microorganisms using magnetic nanoparticle clusters. Our approach to develop probes for pathogenic bacteria, including Salmonella, is based on a theoretically optimized model for the size of clustered magnetic nanoparticles. The clusters were modified to provide enhanced aqueous solubility and versatile conjugation sites for antibody immobilization. The clusters with the desired magnetic property were then prepared at critical micelle concentration (CMC) by evaporation-induced self-assembly (EISA). Two different types of target-specific antibodies for H- and O-antigens were incorporated on the cluster surface for selective binding to biological compartments of the flagella and cell body, respectively. For the two different specific binding properties, Salmonella were effectively captured with the O-antibody-coated polysorbate 80-coated magnetic nanoclusters (PCMNCs). The synergistic effect of combining selective targeting and the clustered magnetic probe leads to both selective and rapid detection of infectious pathogens.
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Affiliation(s)
| | | | | | | | | | | | - Sung Il Kim
- Life Science Division, Amogreentech Co. Ltd. , Seoul 137-902, Korea
| | - Saem Mun
- Life Science Division, Amogreentech Co. Ltd. , Seoul 137-902, Korea
| | - Kyuwon Baek
- Life Science Division, Amogreentech Co. Ltd. , Seoul 137-902, Korea
| | - Byeongyoon Kim
- Department of Chemistry and Research Institute for Natural Sciences, Korea University , Seoul 136-701, Korea
| | - Kwangyeol Lee
- Department of Chemistry and Research Institute for Natural Sciences, Korea University , Seoul 136-701, Korea
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37
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An Y, Bloom JWG, Wheeler SE. Quantifying the π-Stacking Interactions in Nitroarene Binding Sites of Proteins. J Phys Chem B 2015; 119:14441-50. [DOI: 10.1021/acs.jpcb.5b08126] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Yi An
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Jacob W. G. Bloom
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Steven E. Wheeler
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
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38
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Fura JM, Kearns D, Pires MM. D-Amino Acid Probes for Penicillin Binding Protein-based Bacterial Surface Labeling. J Biol Chem 2015; 290:30540-50. [PMID: 26499795 DOI: 10.1074/jbc.m115.683342] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Indexed: 02/02/2023] Open
Abstract
Peptidoglycan is an essential and highly conserved mesh structure that surrounds bacterial cells. It plays a critical role in retaining a defined cell shape, and, in the case of pathogenic Gram-positive bacteria, it lies at the interface between bacterial cells and the host organism. Intriguingly, bacteria can metabolically incorporate unnatural D-amino acids into the peptidoglycan stem peptide directly from the surrounding medium, a process mediated by penicillin binding proteins (PBPs). Metabolic peptidoglycan remodeling via unnatural D-amino acids has provided unique insights into peptidoglycan biosynthesis of live bacteria and has also served as the basis of a synthetic immunology strategy with potential therapeutic implications. A striking feature of this process is the vast promiscuity displayed by PBPs in tolerating entirely unnatural side chains. However, the chemical space and physical features of this side chain promiscuity have not been determined systematically. In this report, we designed and synthesized a library of variants displaying diverse side chains to comprehensively establish the tolerability of unnatural D-amino acids by PBPs in both Gram-positive and Gram-negative organisms. In addition, nine Bacillus subtilis PBP-null mutants were evaluated with the goal of identifying a potential primary PBP responsible for unnatural D-amino acid incorporation and gaining insights into the temporal control of PBP activity. We empirically established the scope of physical parameters that govern the metabolic incorporation of unnatural D-amino acids into bacterial peptidoglycan.
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Affiliation(s)
- Jonathan M Fura
- From the Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania and
| | - Daniel Kearns
- the Department of Biology, Indiana University, Bloomington, Indiana
| | - Marcos M Pires
- From the Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania and
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39
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Ren W, Ji A, Wang MX, Ai HW. Expanding the Genetic Code for a Dinitrophenyl Hapten. Chembiochem 2015; 16:2007-10. [PMID: 26185102 DOI: 10.1002/cbic.201500204] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Indexed: 01/20/2023]
Abstract
Haptens, such as dinitrophenyl (DNP) are small molecules that induce strong immune responses when attached to proteins or peptides and, as such, have been exploited for diverse applications. We engineered a Methanosarcina barkeri pyrrolysyl-tRNA synthetase (mbPylRS) to genetically encode a DNP-containing unnatural amino acid, N(6) -(2-(2,4-dinitrophenyl)acetyl)lysine (DnpK). Although this moiety was unstable in Escherichia coli, we found that its stability was enhanced in mammalian HEK 293T cells and was able to induce selective interactions with anti-DNP antibodies. The capability of genetically introducing DNP into proteins is expected to find broad applications in biosensing, immunology, and therapeutics.
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Affiliation(s)
- Wei Ren
- Department of Chemistry, University of California Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA
| | - Ao Ji
- Department of Chemistry, University of California Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA
| | - Michael X Wang
- Department of Chemistry, University of California Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA.,John W. North High School, 1550 3rd Street, Riverside, CA, 92507, USA
| | - Hui-wang Ai
- Department of Chemistry, University of California Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA.
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40
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Fura JM, Pires MM. d-amino carboxamide-based recruitment of dinitrophenol antibodies to bacterial surfaces via peptidoglycan remodeling. Biopolymers 2015; 104:351-9. [DOI: 10.1002/bip.22618] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Revised: 01/12/2015] [Accepted: 01/14/2015] [Indexed: 12/13/2022]
Affiliation(s)
| | - Marcos M. Pires
- Department of Chemistry; Lehigh University; Bethlehem PA 18015
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41
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Siegrist MS, Aditham AK, Espaillat A, Cameron TA, Whiteside SA, Cava F, Portnoy DA, Bertozzi CR. Host actin polymerization tunes the cell division cycle of an intracellular pathogen. Cell Rep 2015; 11:499-507. [PMID: 25892235 DOI: 10.1016/j.celrep.2015.03.046] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 02/23/2015] [Accepted: 03/22/2015] [Indexed: 02/02/2023] Open
Abstract
Growth and division are two of the most fundamental capabilities of a bacterial cell. While they are well described for model organisms growing in broth culture, very little is known about the cell division cycle of bacteria replicating in more complex environments. Using a D-alanine reporter strategy, we found that intracellular Listeria monocytogenes (Lm) spend a smaller proportion of their cell cycle dividing compared to Lm growing in broth culture. This alteration to the cell division cycle is independent of bacterial doubling time. Instead, polymerization of host-derived actin at the bacterial cell surface extends the non-dividing elongation period and compresses the division period. By decreasing the relative proportion of dividing Lm, actin polymerization biases the population toward cells with the highest propensity to form actin tails. Thus, there is a positive-feedback loop between the Lm cell division cycle and a physical interaction with the host cytoskeleton.
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Affiliation(s)
- M Sloan Siegrist
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Arjun K Aditham
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Akbar Espaillat
- Department of Molecular Biology, Umeå University, Umeå 901 87, Sweden; Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå 901 87, Sweden
| | - Todd A Cameron
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Sarah A Whiteside
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Felipe Cava
- Department of Molecular Biology, Umeå University, Umeå 901 87, Sweden; Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå 901 87, Sweden
| | - Daniel A Portnoy
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Carolyn R Bertozzi
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
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42
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Pidgeon SE, Fura JM, Leon W, Birabaharan M, Vezenov D, Pires MM. Metabolic Profiling of Bacteria by Unnatural C-terminated D-Amino Acids. Angew Chem Int Ed Engl 2015; 54:6158-62. [PMID: 25832713 DOI: 10.1002/anie.201409927] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Indexed: 01/03/2023]
Abstract
Bacterial peptidoglycan is a mesh-like network comprised of sugars and oligopeptides. Transpeptidases cross-link peptidoglycan oligopeptides to provide vital cell wall rigidity and structural support. It was recently discovered that the same transpeptidases catalyze the metabolic incorporation of exogenous D-amino acids onto bacterial cell surfaces with vast promiscuity for the side-chain identity. It is now shown that this enzymatic promiscuity is not exclusive to side chains, but that C-terminus variations can also be accommodated across a diverse range of bacteria. Atomic force microscopy analysis revealed that the incorporation of C-terminus amidated D-amino acids onto bacterial surfaces substantially reduced the cell wall stiffness. We exploited the promiscuity of bacterial transpeptidases to develop a novel assay for profiling different bacterial species.
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Affiliation(s)
- Sean E Pidgeon
- Department of Chemistry, Lehigh University, 6 E. Packer Ave., Bethlehem, PA 18015 (USA)
| | - Jonathan M Fura
- Department of Chemistry, Lehigh University, 6 E. Packer Ave., Bethlehem, PA 18015 (USA)
| | - William Leon
- Department of Chemistry, Lehigh University, 6 E. Packer Ave., Bethlehem, PA 18015 (USA)
| | - Morgan Birabaharan
- Department of Chemistry, Lehigh University, 6 E. Packer Ave., Bethlehem, PA 18015 (USA)
| | - Dmitri Vezenov
- Department of Chemistry, Lehigh University, 6 E. Packer Ave., Bethlehem, PA 18015 (USA)
| | - Marcos M Pires
- Department of Chemistry, Lehigh University, 6 E. Packer Ave., Bethlehem, PA 18015 (USA).
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43
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Pidgeon SE, Fura JM, Leon W, Birabaharan M, Vezenov D, Pires MM. Metabolic Profiling of Bacteria by Unnatural C-terminatedD-Amino Acids. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201409927] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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44
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Siegrist MS, Swarts BM, Fox DM, Lim SA, Bertozzi CR. Illumination of growth, division and secretion by metabolic labeling of the bacterial cell surface. FEMS Microbiol Rev 2015; 39:184-202. [PMID: 25725012 DOI: 10.1093/femsre/fuu012] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The cell surface is the essential interface between a bacterium and its surroundings. Composed primarily of molecules that are not directly genetically encoded, this highly dynamic structure accommodates the basic cellular processes of growth and division as well as the transport of molecules between the cytoplasm and the extracellular milieu. In this review, we describe aspects of bacterial growth, division and secretion that have recently been uncovered by metabolic labeling of the cell envelope. Metabolite derivatives can be used to label a variety of macromolecules, from proteins to non-genetically-encoded glycans and lipids. The embedded metabolite enables precise tracking in time and space, and the versatility of newer chemoselective detection methods offers the ability to execute multiple experiments concurrently. In addition to reviewing the discoveries enabled by metabolic labeling of the bacterial cell envelope, we also discuss the potential of these techniques for translational applications. Finally, we offer some guidelines for implementing this emerging technology.
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Affiliation(s)
- M Sloan Siegrist
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Benjamin M Swarts
- Department of Chemistry, Central Michigan University, Mount Pleasant, MI 48859, USA
| | - Douglas M Fox
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Shion An Lim
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Carolyn R Bertozzi
- Department of Chemistry, University of California, Berkeley, CA 94720, USA Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
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45
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Kuru E, Tekkam S, Hall E, Brun YV, VanNieuwenhze MS. Synthesis of fluorescent D-amino acids and their use for probing peptidoglycan synthesis and bacterial growth in situ. Nat Protoc 2015; 10:33-52. [PMID: 25474031 PMCID: PMC4300143 DOI: 10.1038/nprot.2014.197] [Citation(s) in RCA: 201] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Fluorescent D-amino acids (FDAAs) are efficiently incorporated into the peptidoglycans (PGs) of diverse bacterial species at the sites of PG biosynthesis, allowing specific and covalent probing of bacterial growth with minimal perturbation. Here we provide a protocol for the synthesis of four FDAAs emitting light in blue (HCC-amino-D-alanine, HADA), green (NBD-amino-D-alanine, NADA, and fluorescein-D-lysine, FDL) or red (TAMRA-D-lysine, TDL) and for their use in PG labeling of live bacteria. Our modular synthesis protocol gives easy access to a library of different FDAAs made with commercially available fluorophores and diamino acid starting materials. Molecules can be synthesized in a typical chemistry laboratory in 2-3 d using standard chemical transformations. The simple labeling procedure involves the addition of the FDAAs to a bacterial sample for the desired labeling duration and stopping further label incorporation by fixing the cells with cold 70% (vol/vol) ethanol or by washing away excess dye. We discuss several scenarios for the use of these labels in fluorescence microscopy applications, including short or long labeling durations, and the combination of different labels in pure culture (e.g., for 'virtual time-lapse' microscopy) or in situ labeling of complex environmental samples. Depending on the experiment, FDAA labeling can take as little as 30 s for a rapidly growing species such as Escherichia coli.
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Affiliation(s)
- Erkin Kuru
- Indiana University, Bloomington, IN 47405
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Qiao Y, Lebar MD, Schirner K, Schaefer K, Tsukamoto H, Kahne D, Walker S. Detection of lipid-linked peptidoglycan precursors by exploiting an unexpected transpeptidase reaction. J Am Chem Soc 2014; 136:14678-81. [PMID: 25291014 PMCID: PMC4210121 DOI: 10.1021/ja508147s] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
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Penicillin-binding
proteins (PBPs) are involved in the synthesis
and remodeling of bacterial peptidoglycan (PG). Staphylococcus
aureus expresses four PBPs. Genetic studies in S.
aureus have implicated PBP4 in the formation of highly cross-linked
PG, but biochemical studies have not reached a consensus on its primary
enzymatic activity. Using synthetic Lipid II, we show here that PBP4
preferentially acts as a transpeptidase (TP) in vitro. Moreover, it is the PBP primarily responsible for incorporating
exogenous d-amino acids into cellular PG, implying that it
also has TP activity in vivo. Notably, PBP4 efficiently
exchanges d-amino acids not only into PG polymers but also
into the PG monomers Lipid I and Lipid II. This is the first demonstration
that any TP domain of a PBP can activate the PG monomer building blocks.
Exploiting the promiscuous TP activity of PBP4, we developed a simple,
highly sensitive assay to detect cellular pools of lipid-linked PG
precursors, which are of notoriously low abundance. This method, which
addresses a longstanding problem, is useful for assessing how genetic
and pharmacological perturbations affect precursor levels, and may
facilitate studies to elucidate antibiotic mechanism of action.
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Affiliation(s)
- Yuan Qiao
- Chemical Biology Program, Harvard University , Cambridge, Massachusetts 02138, United States
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