1
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Rotsides P, Lee PJ, Webber N, Grasty KC, Beld J, Loll PJ. Diazirine Photoprobes for the Identification of Vancomycin-Binding Proteins. ACS BIO & MED CHEM AU 2024; 4:86-94. [PMID: 38645928 PMCID: PMC11027123 DOI: 10.1021/acsbiomedchemau.3c00067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/15/2023] [Accepted: 11/15/2023] [Indexed: 04/23/2024]
Abstract
Vancomycin's interactions with cellular targets drive its antimicrobial activity and also trigger expression of resistance against the antibiotic. Interaction partners for vancomycin have previously been identified using photoaffinity probes, which have proven to be useful tools for exploring vancomycin's interactome. This work seeks to develop diazirine-based vancomycin photoprobes that display enhanced specificity and bear fewer chemical modifications as compared to previous photoprobes. Using proteins fused to vancomycin's main cell-wall target, d-alanyl-d-alanine, we used mass spectrometry to show that these photoprobes specifically label known vancomycin-binding partners within minutes. In a complementary approach, we developed a Western-blot strategy targeting the vancomycin adduct of the photoprobes, eliminating the need for affinity tags and simplifying the analysis of photolabeling reactions. Together, the probes and identification strategy provide a novel and streamlined pipeline for identifying vancomycin-binding proteins.
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Affiliation(s)
- Photis Rotsides
- Department
of Biochemistry & Molecular Biology and Department of Microbiology &
Immunology, Drexel University College of
Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Paula J. Lee
- Department
of Biochemistry & Molecular Biology and Department of Microbiology &
Immunology, Drexel University College of
Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Nakoa Webber
- Department
of Biochemistry & Molecular Biology and Department of Microbiology &
Immunology, Drexel University College of
Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Kimberly C. Grasty
- Department
of Biochemistry & Molecular Biology and Department of Microbiology &
Immunology, Drexel University College of
Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Joris Beld
- Department
of Biochemistry & Molecular Biology and Department of Microbiology &
Immunology, Drexel University College of
Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Patrick J. Loll
- Department
of Biochemistry & Molecular Biology and Department of Microbiology &
Immunology, Drexel University College of
Medicine, Philadelphia, Pennsylvania 19102, United States
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2
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Walrant A, Sachon E. Photoaffinity labeling coupled to MS to identify peptide biological partners: Secondary reactions, for better or for worse? MASS SPECTROMETRY REVIEWS 2024. [PMID: 38576378 DOI: 10.1002/mas.21880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 02/22/2024] [Accepted: 03/13/2024] [Indexed: 04/06/2024]
Abstract
Affinity photolabeling is a smart method to study noncovalent and transient interactions and provide a submolecular picture of the contacts between interacting partners. In this review, we will focus on the identification of peptide partners using photoaffinity labeling coupled to mass spectrometry in different contexts such as in vitro with a purified potential partner, in model systems such as model membranes, and with live cells using both targeted and nontargeted proteomics studies. Different biological partners will be described, among which glycoconjugates, oligonucleotides, peptides, proteins, and lipids, with the photoreactive label inserted either on the peptide of interest or on the potential partner. Particular attention will be paid to the observation and characterization of specific rearrangements following the photolabeling reaction, which can help characterize photoadducts and provide a better understanding of the interacting systems and environment.
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Affiliation(s)
- Astrid Walrant
- Laboratoire des Biomolécules, LBM, Sorbonne Université, École normale supérieure, PSL University, CNRS, Paris, France
| | - Emmanuelle Sachon
- Laboratoire des Biomolécules, LBM, Sorbonne Université, École normale supérieure, PSL University, CNRS, Paris, France
- Sorbonne Université, Mass Spectrometry Sciences Sorbonne Université, MS3U platform, Fédération de Chimie moléculaire de Paris centre, Paris, France
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3
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Gao Y, Ma M, Li W, Lei X. Chemoproteomics, A Broad Avenue to Target Deconvolution. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305608. [PMID: 38095542 PMCID: PMC10885659 DOI: 10.1002/advs.202305608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/29/2023] [Indexed: 12/22/2023]
Abstract
As a vital project of forward chemical genetic research, target deconvolution aims to identify the molecular targets of an active hit compound. Chemoproteomics, either with chemical probe-facilitated target enrichment or probe-free, provides a straightforward and effective approach to profile the target landscape and unravel the mechanisms of action. Canonical methods rely on chemical probes to enable target engagement, enrichment, and identification, whereas click chemistry and photoaffinity labeling techniques improve the efficiency, sensitivity, and spatial accuracy of target recognition. In comparison, recently developed probe-free methods detect protein-ligand interactions without the need to modify the ligand molecule. This review provides a comprehensive overview of different approaches and recent advancements for target identification and highlights the significance of chemoproteomics in investigating biological processes and advancing drug discovery processes.
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Affiliation(s)
- Yihui Gao
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
| | - Mingzhe Ma
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
- Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijing100871China
| | - Wenyang Li
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
| | - Xiaoguang Lei
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
- Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijing100871China
- Academy for Advanced Interdisciplinary StudiesPeking UniversityBeijing100871China
- Institute for Cancer ResearchShenzhen Bay LaboratoryShenzhenChina
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4
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Weerawarna PM, Schiefer IT, Soares P, Fox S, Morimoto RI, Melani RD, Kelleher NL, Luan CH, Silverman RB. Target Identification of a Class of Pyrazolone Protein Aggregation Inhibitor Therapeutics for Amyotrophic Lateral Sclerosis. ACS CENTRAL SCIENCE 2024; 10:87-103. [PMID: 38292603 PMCID: PMC10823514 DOI: 10.1021/acscentsci.3c00213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 11/01/2023] [Accepted: 11/27/2023] [Indexed: 02/01/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with no cure, and current treatment options are very limited. Previously, we performed a high-throughput screen to identify small molecules that inhibit protein aggregation caused by a mutation in the gene that encodes superoxide dismutase 1 (SOD1), which is responsible for about 25% of familial ALS. This resulted in three hit series of compounds that were optimized over several years to give three compounds that were highly active in a mutant SOD1 ALS model. Here we identify the target of two of the active compounds (6 and 7) with the use of photoaffinity labeling, chemical biology reporters, affinity purification, proteomic analysis, and fluorescent/cellular thermal shift assays. Evidence is provided to demonstrate that these two pyrazolone compounds directly interact with 14-3-3-E and 14-3-3-Q isoforms, which have chaperone activity and are known to interact with mutant SOD1G93A aggregates and become insoluble in the subcellular JUNQ compartment, leading to apoptosis. Because protein aggregation is the hallmark of all neurodegenerative diseases, knowledge of the target compounds that inhibit protein aggregation allows for the design of more effective molecules for the treatment of ALS and possibly other neurodegenerative diseases.
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Affiliation(s)
- Pathum M. Weerawarna
- Department
of Chemistry, Chemistry of Life Processes Institute, Center for Developmental
Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Isaac T. Schiefer
- Department
of Chemistry, Chemistry of Life Processes Institute, Center for Developmental
Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Pedro Soares
- Department
of Chemistry, Chemistry of Life Processes Institute, Center for Developmental
Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Susan Fox
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Richard I. Morimoto
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Rafael D. Melani
- Department
of Chemistry and Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L. Kelleher
- Department
of Chemistry, Chemistry of Life Processes Institute, Center for Developmental
Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
- Proteomics
Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Chi-Hao Luan
- High
Throughput
Analysis Laboratory, Chemistry of Life Processes Institute, and Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Richard B. Silverman
- Department
of Chemistry, Chemistry of Life Processes Institute, Center for Developmental
Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
- Department
of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, United States
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5
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Wu Y, Bertran MT, Joshi D, Maslen SL, Hurd C, Walport LJ. Identification of photocrosslinking peptide ligands by mRNA display. Commun Chem 2023; 6:103. [PMID: 37258712 PMCID: PMC10232439 DOI: 10.1038/s42004-023-00898-2] [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: 03/07/2023] [Accepted: 05/05/2023] [Indexed: 06/02/2023] Open
Abstract
Photoaffinity labelling is a promising method for studying protein-ligand interactions. However, obtaining a specific, efficient crosslinker can require significant optimisation. We report a modified mRNA display strategy, photocrosslinking-RaPID (XL-RaPID), and exploit its ability to accelerate the discovery of cyclic peptides that photocrosslink to a target of interest. As a proof of concept, we generated a benzophenone-containing library and applied XL-RaPID screening against a model target, the second bromodomain of BRD3. This crosslinking screening gave two optimal candidates that selectively labelled the target protein in cell lysate. Overall, this work introduces direct photocrosslinking screening as a versatile technique for identifying covalent peptide ligands from mRNA display libraries incorporating reactive warheads.
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Affiliation(s)
- Yuteng Wu
- Protein-Protein Interaction Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, UK
| | - M Teresa Bertran
- Protein-Protein Interaction Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Dhira Joshi
- Chemical Biology, The Francis Crick Institute, London, NW1 1AT, UK
| | - Sarah L Maslen
- Proteomics, The Francis Crick Institute, London, NW1 1AT, UK
| | - Catherine Hurd
- Protein-Protein Interaction Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- Crick-GSK Biomedical LinkLabs, GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - Louise J Walport
- Protein-Protein Interaction Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, UK.
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6
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Malarney KP, Chang PV. Chemoproteomic Approaches for Unraveling Prokaryotic Biology. Isr J Chem 2023; 63:e202200076. [PMID: 37842282 PMCID: PMC10575470 DOI: 10.1002/ijch.202200076] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Indexed: 03/07/2023]
Abstract
Bacteria are ubiquitous lifeforms with important roles in the environment, biotechnology, and human health. Many of the functions that bacteria perform are mediated by proteins and enzymes, which catalyze metabolic transformations of small molecules and modifications of proteins. To better understand these biological processes, chemical proteomic approaches, including activity-based protein profiling, have been developed to interrogate protein function and enzymatic activity in physiologically relevant contexts. Here, chemoproteomic strategies and technological advances for studying bacterial physiology, pathogenesis, and metabolism are discussed. The development of chemoproteomic approaches for characterizing protein function and enzymatic activity within bacteria remains an active area of research, and continued innovations are expected to provide breakthroughs in understanding bacterial biology.
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Affiliation(s)
- Kien P Malarney
- Department of Microbiology, Cornell University, Ithaca, NY 14853 (USA)
| | - Pamela V Chang
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853 (USA)
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853 (USA)
- Cornell Center for Immunology, Cornell University, Ithaca, NY 14853 (USA)
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY 14853 (USA)
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7
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Kimura K, Yasunaga T, Makikawa T, Takahashi D, Toshima K. Efficient Strategy for the Preparation of Chemical Probes of Biologically Active Glycosides Using a Boron-Mediated Aglycon Delivery (BMAD) Method. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2022. [DOI: 10.1246/bcsj.20220076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kosuke Kimura
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Takeshi Yasunaga
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Takumi Makikawa
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Daisuke Takahashi
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Kazunobu Toshima
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
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8
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Antibacterial Vancomycin@ZIF-8 Loaded PVA Nanofiber Membrane for Infected Bone Repair. Int J Mol Sci 2022; 23:ijms23105629. [PMID: 35628439 PMCID: PMC9145349 DOI: 10.3390/ijms23105629] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/13/2022] [Accepted: 05/15/2022] [Indexed: 02/06/2023] Open
Abstract
Bone substitutes with strong antibacterial properties and bone regeneration effects have an inherent potential in the treatment of severe bone tissue infections, such as osteomyelitis. In this study, vancomycin (Van) was loaded into zeolitic imidazolate framework-8 (ZIF-8) to prepare composite particles, which is abbreviated as V@Z. As a pH-responsive particle, ZIF-8 can be cleaved in the weak acid environment caused by bacterial infection to realize the effective release of drugs. Then, V@Z was loaded into polyvinyl alcohol (PVA) fiber by electrospinning to prepare PVA/V@Z composite bone filler. The drug-loading rate of V@Z was about 6.735%. The membranes exhibited super hydrophilicity, water absorption and pH-controlled Van release behavior. The properties of anti E. coli and S. aureus were studied under the pH conditions of normal physiological tissues and infected tissues (pH 7.4 and pH 6.5, respectively). It was found that the material had good surface antibacterial adhesion and antibacterial property. The PVA/V@Z membrane had the more prominent bacteria-killing effect compared with the same amount of single antibacterial agent containing membrane such as ZIF-8 or Van loaded PVA, and the antibacterial rate was up to 99%. The electrospun membrane had good biocompatibility and can promote MC3T3-E1 cell spreading on it.
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9
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Cao M, Liu C, Li M, Zhang X, Peng L, Liu L, Liao J, Yang J. Recent Research on Hybrid Hydrogels for Infection Treatment and Bone Repair. Gels 2022; 8:gels8050306. [PMID: 35621604 PMCID: PMC9140391 DOI: 10.3390/gels8050306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 11/16/2022] Open
Abstract
The repair of infected bone defects (IBDs) is still a great challenge in clinic. A successful treatment for IBDs should simultaneously resolve both infection control and bone defect repair. Hydrogels are water-swollen hydrophilic materials that maintain a distinct three-dimensional structure, helping load various antibacterial drugs and biomolecules. Hybrid hydrogels may potentially possess antibacterial ability and osteogenic activity. This review summarizes the recent progress of different kinds of antibacterial agents (including inorganic, organic, and natural) encapsulated in hydrogels. Several representative hydrogels of each category and their antibacterial mechanism and effect on bone repair are presented. Moreover, the advantages and disadvantages of antibacterial agent hybrid hydrogels are discussed. The challenge and future research directions are further prospected.
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Affiliation(s)
- Mengjiao Cao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China; (M.C.); (M.L.); (L.L.)
| | - Chengcheng Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Periodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China;
| | - Mengxin Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China; (M.C.); (M.L.); (L.L.)
| | - Xu Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China;
| | - Li Peng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China;
| | - Lijia Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China; (M.C.); (M.L.); (L.L.)
| | - Jinfeng Liao
- State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China;
- Correspondence: (J.L.); (J.Y.)
| | - Jing Yang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China; (M.C.); (M.L.); (L.L.)
- Correspondence: (J.L.); (J.Y.)
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10
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Application of antibiotic-derived fluorescent probes to bacterial studies. Methods Enzymol 2022; 665:1-28. [DOI: 10.1016/bs.mie.2021.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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11
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Demonstration of the role of cell wall homeostasis in Staphylococcus aureus growth and the action of bactericidal antibiotics. Proc Natl Acad Sci U S A 2021; 118:2106022118. [PMID: 34716264 PMCID: PMC8612353 DOI: 10.1073/pnas.2106022118] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 09/02/2021] [Indexed: 12/29/2022] Open
Abstract
Bacterial cell wall peptidoglycan is essential, maintaining both cellular integrity and morphology, in the face of internal turgor pressure. Peptidoglycan synthesis is important, as it is targeted by cell wall antibiotics, including methicillin and vancomycin. Here, we have used the major human pathogen Staphylococcus aureus to elucidate both the cell wall dynamic processes essential for growth (life) and the bactericidal effects of cell wall antibiotics (death) based on the principle of coordinated peptidoglycan synthesis and hydrolysis. The death of S. aureus due to depletion of the essential, two-component and positive regulatory system for peptidoglycan hydrolase activity (WalKR) is prevented by addition of otherwise bactericidal cell wall antibiotics, resulting in stasis. In contrast, cell wall antibiotics kill via the activity of peptidoglycan hydrolases in the absence of concomitant synthesis. Both methicillin and vancomycin treatment lead to the appearance of perforating holes throughout the cell wall due to peptidoglycan hydrolases. Methicillin alone also results in plasmolysis and misshapen septa with the involvement of the major peptidoglycan hydrolase Atl, a process that is inhibited by vancomycin. The bactericidal effect of vancomycin involves the peptidoglycan hydrolase SagB. In the presence of cell wall antibiotics, the inhibition of peptidoglycan hydrolase activity using the inhibitor complestatin results in reduced killing, while, conversely, the deregulation of hydrolase activity via loss of wall teichoic acids increases the death rate. For S. aureus, the independent regulation of cell wall synthesis and hydrolysis can lead to cell growth, death, or stasis, with implications for the development of new control regimes for this important pathogen.
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12
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Li G, Peng X, Guo Y, Gong S, Cao S, Qiu F. Currently Available Strategies for Target Identification of Bioactive Natural Products. Front Chem 2021; 9:761609. [PMID: 34660543 PMCID: PMC8515416 DOI: 10.3389/fchem.2021.761609] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/20/2021] [Indexed: 01/04/2023] Open
Abstract
In recent years, biologically active natural products have gradually become important agents in the field of drug research and development because of their wide availability and variety. However, the target sites of many natural products are yet to be identified, which is a setback in the pharmaceutical industry and has seriously hindered the translation of research findings of these natural products as viable candidates for new drug exploitation. This review systematically describes the commonly used strategies for target identification via the application of probe and non-probe approaches. The merits and demerits of each method were summarized using recent examples, with the goal of comparing currently available methods and selecting the optimum techniques for identifying the targets of bioactive natural products.
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Affiliation(s)
- Gen Li
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xuling Peng
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yajing Guo
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Shaoxuan Gong
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Shijie Cao
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Feng Qiu
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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13
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Kuang X, Zhang J, Peng X, Xie Q, Li J, Zhou X, Luo Y, Xu X. A small molecule II-6s inhibits Enterococcus faecalis biofilms. J Oral Microbiol 2021; 13:1978756. [PMID: 34552703 PMCID: PMC8451641 DOI: 10.1080/20002297.2021.1978756] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Background Limitations of current intracanal irrigants such as sodium hypochlorite (NaOCl) and chlorhexidine (CHX) necessitate the development of novel antimicrobial agents to control endodontic infection. Aim This study investigated the antimicrobial activities of a small molecule II-6s against Enterococcus faecalis associated with endodontic diseases. Methods The susceptibility of E. faecalis to II-6s was evaluated by the microdilution method and time-kill assay. Microbial resistance was assessed by repeated exposure of E. faecalis to II-6s. Cytotoxicity of II-6s was evaluated by CCK-8 assay. Virulence gene expression of the II-6s-treated E. faecalis cells was measured by RT-qPCR. Bacterial reductions in the dentinal tubules were further assessed by confocal laser scanning microscopy. Results II-6s exhibited potent antimicrobial activity against E. faecalis and down-regulated virulence-associated genes in E. faecalis. II-6s induced no drug resistance in E. faecalis with lower cytotoxicity as compared to NaOCl and CHX. More importantly, 0.003125% II-6s exhibited significant bactericidal effect against E. faecalis residing in the dentinal tubules, which was comparable to 5.25% NaOCl and 2% CHX. Conclusions II-6s has excellent antimicrobial activity, moderate cytotoxicity and induces no drug resistance, and thus is a promising agent for the treatment of endodontic infection.
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Affiliation(s)
- Xinyi Kuang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jin Zhang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xian Peng
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Qian Xie
- Department of Endodontics, College of Dentistry, University of Illinois at Chicago, Chicago, ChicagoU.S.A
| | - Jiyao Li
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Youfu Luo
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Xin Xu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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14
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Yao T, Xu X, Huang R. Recent Advances about the Applications of Click Reaction in Chemical Proteomics. Molecules 2021; 26:5368. [PMID: 34500797 PMCID: PMC8434046 DOI: 10.3390/molecules26175368] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 11/17/2022] Open
Abstract
Despite significant advances in biological and analytical approaches, a comprehensive portrait of the proteome and its dynamic interactions and modifications remains a challenging goal. Chemical proteomics is a growing area of chemical biology that seeks to design small molecule probes to elucidate protein composition, distribution, and relevant physiological and pharmacological functions. Click chemistry focuses on the development of new combinatorial chemical methods for carbon heteroatom bond (C-X-C) synthesis, which have been utilized extensively in the field of chemical proteomics. Click reactions have various advantages including high yield, harmless by-products, and simple reaction conditions, upon which the molecular diversity can be easily and effectively obtained. This paper reviews the application of click chemistry in proteomics from four aspects: (1) activity-based protein profiling, (2) enzyme-inhibitors screening, (3) protein labeling and modifications, and (4) hybrid monolithic column in proteomic analysis.
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Affiliation(s)
- Tingting Yao
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, China;
- State Key Laboratory of Natural Medicines, Key Lab of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing 210009, China
| | - Xiaowei Xu
- State Key Laboratory of Natural Medicines, Key Lab of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing 210009, China
| | - Rong Huang
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, China;
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15
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Targeting Bacterial Gyrase with Cystobactamid, Fluoroquinolone, and Aminocoumarin Antibiotics Induces Distinct Molecular Signatures in Pseudomonas aeruginosa. mSystems 2021; 6:e0061021. [PMID: 34254824 PMCID: PMC8407119 DOI: 10.1128/msystems.00610-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The design of novel antibiotics relies on a profound understanding of their mechanism of action. While it has been shown that cellular effects of antibiotics cluster according to their molecular targets, we investigated whether compounds binding to different sites of the same target can be differentiated by their transcriptome or metabolome signatures. The effects of three fluoroquinolones, two aminocoumarins, and two cystobactamids, all inhibiting bacterial gyrase, on Pseudomonas aeruginosa at subinhibitory concentrations could be distinguished clearly by RNA sequencing as well as metabolomics. We observed a strong (2.8- to 212-fold) induction of autolysis-triggering pyocins in all gyrase inhibitors, which correlated with extracellular DNA (eDNA) release. Gyrase B-binding aminocoumarins induced the most pronounced changes, including a strong downregulation of phenazine and rhamnolipid virulence factors. Cystobactamids led to a downregulation of a glucose catabolism pathway. The study implies that clustering cellular mechanisms of action according to the primary target needs to take class-dependent variances into account. IMPORTANCE Novel antibiotics are urgently needed to tackle the growing worldwide problem of antimicrobial resistance. Bacterial pathogens possess few privileged targets for a successful therapy: the majority of existing antibiotics as well as current candidates in development target the complex bacterial machinery for cell wall synthesis, protein synthesis, or DNA replication. An important mechanistic question addressed by this study is whether inhibiting such a complex target at different sites with different compounds has similar or differentiated cellular consequences. Using transcriptomics and metabolomics, we demonstrate that three different classes of gyrase inhibitors can be distinguished by their molecular signatures in P. aeruginosa. We describe the cellular effects of a promising, recently identified gyrase inhibitor class, the cystobactamids, in comparison to those of the established gyrase A-binding fluoroquinolones and the gyrase B-binding aminocoumarins. The study results have implications for mode-of-action discovery approaches based on target-specific reference compounds, as they highlight the intraclass variability of cellular compound effects.
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16
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Lim Y, Kuang Y, Wu J, Yao SQ. Late‐Stage C(sp
2
)−H Functionalization: A Powerful Toolkit To Arm Natural Products for In Situ Proteome Profiling? Chemistry 2020; 27:3575-3580. [DOI: 10.1002/chem.202004373] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/04/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Ying‐Jie Lim
- Department of Chemistry National University of Singapore 3 Science Drive 3 Singapore 117543 Singapore
| | - Yulong Kuang
- Department of Chemistry National University of Singapore 3 Science Drive 3 Singapore 117543 Singapore
| | - Jie Wu
- Department of Chemistry National University of Singapore 3 Science Drive 3 Singapore 117543 Singapore
| | - Shao Q. Yao
- Department of Chemistry National University of Singapore 3 Science Drive 3 Singapore 117543 Singapore
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17
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Zhao W, Deng J, Ren Y, Xie L, Li W, Wang Q, Li S, Liu S. Antibacterial application and toxicity of metal-organic frameworks. Nanotoxicology 2020; 15:311-330. [PMID: 33259255 DOI: 10.1080/17435390.2020.1851420] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Metal-organic frameworks (MOFs), which are also referred to as coordination polymers, have been widely used in adsorption separation and catalysis, especially in the field of physical chemistry in the past few years, because of their unique physical structure and potential chemical properties. In recent years, particularly with the continuous expansion of the research field, deepening of research levels, and sustained advancements in science and technology, powerful and diverse MOFs that have demonstrated great biomedical application potential have been successively developed. Consequently, this study summarizes the origin, development, and common synthesis methods of MOFs, with major emphasis on their antibacterial application and safety evaluation in biomedicine.
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Affiliation(s)
- Wanling Zhao
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China.,Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jinqiong Deng
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China.,Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yan Ren
- Guangdong Provincial People's Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Liyuan Xie
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Weirong Li
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qi Wang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shengqing Li
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Sijun Liu
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
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18
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Ghasemiyeh P, Vazin A, Zand F, Azadi A, Karimzadeh I, Mohammadi-Samani S. A simple and validated HPLC method for vancomycin assay in plasma samples: the necessity of TDM center development in Southern Iran. Res Pharm Sci 2020; 15:529-540. [PMID: 33828596 PMCID: PMC8020853 DOI: 10.4103/1735-5362.301337] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 06/08/2020] [Accepted: 11/08/2020] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND AND PURPOSE Vancomycin is a glycopeptide antibiotic which is the drug of choice against methicillin-resistant Staphylococcus aureus. It has a narrow therapeutic index, and thus therapeutic drug monitoring (TDM), and clinical pharmacokinetic assessment are necessary in order to prevent adverse drug reactions such as nephrotoxicity. In this study, we aimed to develop a simple and validated HPLC method for vancomycin assay in order to establish a TDM center for patients admitted to the ICU of Nemazee Hospital in southern Iran. EXPERIMENTAL APPROACH In this study, a brief review of different parameters and variables which could affect the sensitivity, selectivity of the validated HPLC method for vancomycin determination were considered. According to the previous studies a simple, fast, and the relatively low-cost method was established for vancomycin determination in plasma samples. FINDINGS/RESULTS The developed HPLC assay indicated a calibration curve with R-square of > 0.999, acceptable selectivity, the accuracy of 90-105%, CV% of less than 15%, the limit of quantification of 1 μg/mL, and limit of detection of 300 ng/mL. Vancomycin trough level, the area under the curve, renal clearance, the volume of distribution, and elimination constant were measured in patients using this validated method. CONCLUSION AND IMPLICATIONS Validated method for assay of vancomycin plasma levels was used to quantify vancomycin levels of four patients who were admitted to the ICU of Nemazee Hospital. According to the results, two of these patients showed lower levels than recommended therapeutic purposes while one of them showed a toxic level. According to the results, the TDM assessment of vancomycin is strongly recommended for patients who are hospitalized in ICU.
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Affiliation(s)
- Parisa Ghasemiyeh
- Department of Clinical Pharmacy, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, I.R. Iran
- Department of Pharmaceutics, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, I.R. Iran
| | - Afsaneh Vazin
- Department of Clinical Pharmacy, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, I.R. Iran
| | - Farid Zand
- Anesthesiology and Critical Care Research Center, Nemazee Hospital, Shiraz University of Medical Sciences, Shiraz, I.R. Iran
| | - Amir Azadi
- Department of Pharmaceutics, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, I.R. Iran
| | - Iman Karimzadeh
- Department of Clinical Pharmacy, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, I.R. Iran
| | - Soliman Mohammadi-Samani
- Department of Pharmaceutics, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, I.R. Iran
- Center for Nanotechnology in Drug delivery, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, I.R. Iran
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19
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Álvarez-Martínez FJ, Barrajón-Catalán E, Micol V. Tackling Antibiotic Resistance with Compounds of Natural Origin: A Comprehensive Review. Biomedicines 2020; 8:E405. [PMID: 33050619 PMCID: PMC7601869 DOI: 10.3390/biomedicines8100405] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/08/2020] [Accepted: 10/09/2020] [Indexed: 12/13/2022] Open
Abstract
Drug-resistant bacteria pose a serious threat to human health worldwide. Current antibiotics are losing efficacy and new antimicrobial agents are urgently needed. Living organisms are an invaluable source of antimicrobial compounds. The antimicrobial activity of the most representative natural products of animal, bacterial, fungal and plant origin are reviewed in this paper. Their activity against drug-resistant bacteria, their mechanisms of action, the possible development of resistance against them, their role in current medicine and their future perspectives are discussed. Electronic databases such as PubMed, Scopus and ScienceDirect were used to search scientific contributions until September 2020, using relevant keywords. Natural compounds of heterogeneous origins have been shown to possess antimicrobial capabilities, including against antibiotic-resistant bacteria. The most commonly found mechanisms of antimicrobial action are related to protein biosynthesis and alteration of cell walls and membranes. Various natural compounds, especially phytochemicals, have shown synergistic capacity with antibiotics. There is little literature on the development of specific resistance mechanisms against natural antimicrobial compounds. New technologies such as -omics, network pharmacology and informatics have the potential to identify and characterize new natural antimicrobial compounds in the future. This knowledge may be useful for the development of future therapeutic strategies.
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Affiliation(s)
- Francisco Javier Álvarez-Martínez
- Institute of Research, Development and Innovation in Health Biotechnology of Elche (IDiBE), Universitas Miguel Hernández (UMH), 03202 Elche, Spain; (F.J.Á.-M.); (V.M.)
| | - Enrique Barrajón-Catalán
- Institute of Research, Development and Innovation in Health Biotechnology of Elche (IDiBE), Universitas Miguel Hernández (UMH), 03202 Elche, Spain; (F.J.Á.-M.); (V.M.)
| | - Vicente Micol
- Institute of Research, Development and Innovation in Health Biotechnology of Elche (IDiBE), Universitas Miguel Hernández (UMH), 03202 Elche, Spain; (F.J.Á.-M.); (V.M.)
- CIBER, Fisiopatología de la Obesidad y la Nutrición, CIBERobn, Instituto de Salud Carlos III (CB12/03/30038), 28220 Madrid, Spain
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20
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Tavares TD, Antunes JC, Padrão J, Ribeiro AI, Zille A, Amorim MTP, Ferreira F, Felgueiras HP. Activity of Specialized Biomolecules against Gram-Positive and Gram-Negative Bacteria. Antibiotics (Basel) 2020; 9:E314. [PMID: 32526972 PMCID: PMC7344598 DOI: 10.3390/antibiotics9060314] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/01/2020] [Accepted: 06/08/2020] [Indexed: 11/24/2022] Open
Abstract
The increased resistance of bacteria against conventional pharmaceutical solutions, the antibiotics, has raised serious health concerns. This has stimulated interest in the development of bio-based therapeutics with limited resistance, namely, essential oils (EOs) or antimicrobial peptides (AMPs). This study envisaged the evaluation of the antimicrobial efficacy of selected biomolecules, namely LL37, pexiganan, tea tree oil (TTO), cinnamon leaf oil (CLO) and niaouli oil (NO), against four bacteria commonly associated to nosocomial infections: Staphylococcus aureus, Staphylococcus epidermidis, Escherichia coli and Pseudomonas aeruginosa. The antibiotic vancomycin and silver nanoparticles (AgNPs) were used as control compounds for comparison purposes. The biomolecules were initially screened for their antibacterial efficacy using the agar-diffusion test, followed by the determination of minimal inhibitory concentrations (MICs), kill-time kinetics and the evaluation of the cell morphology upon 24 h exposure. All agents were effective against the selected bacteria. Interestingly, the AgNPs required a higher concentration (4000-1250 µg/mL) to induce the same effects as the AMPs (500-7.8 µg/mL) or EOs (365.2-19.7 µg/mL). Pexiganan and CLO were the most effective biomolecules, requiring lower concentrations to kill both Gram-positive and Gram-negative bacteria (62.5-7.8 µg/mL and 39.3-19.7 µg/mL, respectively), within a short period of time (averaging 2 h 15 min for all bacteria). Most biomolecules apparently disrupted the bacteria membrane stability due to the observed cell morphology deformation and by effecting on the intracellular space. AMPs were observed to induce morphological deformations and cellular content release, while EOs were seen to split and completely envelope bacteria. Data unraveled more of the potential of these new biomolecules as replacements for the conventional antibiotics and allowed us to take a step forward in the understanding of their mechanisms of action against infection-related bacteria.
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Affiliation(s)
| | | | | | | | | | | | | | - Helena P. Felgueiras
- Centre for Textile Science and Technology (2C2T), Department of Textile Engineering, University of Minho, Campus of Azurém, 4800-058 Guimarães, Portugal; (T.D.T.); (J.C.A.); (J.P.); (A.I.R.); (A.Z.); (M.T.P.A.); (F.F.)
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21
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Chen X, Wang Y, Ma N, Tian J, Shao Y, Zhu B, Wong YK, Liang Z, Zou C, Wang J. Target identification of natural medicine with chemical proteomics approach: probe synthesis, target fishing and protein identification. Signal Transduct Target Ther 2020; 5:72. [PMID: 32435053 PMCID: PMC7239890 DOI: 10.1038/s41392-020-0186-y] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/30/2020] [Accepted: 04/30/2020] [Indexed: 12/14/2022] Open
Abstract
Natural products are an important source of new drugs for the treatment of various diseases. However, developing natural product-based new medicines through random moiety modification is a lengthy and costly process, due in part to the difficulties associated with comprehensively understanding the mechanism of action and the side effects. Identifying the protein targets of natural products is an effective strategy, but most medicines interact with multiple protein targets, which complicate this process. In recent years, an increasing number of researchers have begun to screen the target proteins of natural products with chemical proteomics approaches, which can provide a more comprehensive array of the protein targets of active small molecules in an unbiased manner. Typically, chemical proteomics experiments for target identification consist of two key steps: (1) chemical probe design and synthesis and (2) target fishing and identification. In recent decades, five different types of chemical proteomic probes and their respective target fishing methods have been developed to screen targets of molecules with different structures, and a variety of protein identification approaches have been invented. Presently, we will classify these chemical proteomics approaches, the application scopes and characteristics of the different types of chemical probes, the different protein identification methods, and the advantages and disadvantages of these strategies.
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Affiliation(s)
- Xiao Chen
- School of Medicine & Holistic Integrative Medicine, and College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
- School of Biopharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Yutong Wang
- School of Medicine & Holistic Integrative Medicine, and College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Nan Ma
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jing Tian
- School of Medicine & Holistic Integrative Medicine, and College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yurou Shao
- School of Medicine & Holistic Integrative Medicine, and College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Bo Zhu
- School of Medicine & Holistic Integrative Medicine, and College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
- School of Biopharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Yin Kwan Wong
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, 518020, China
| | - Zhen Liang
- The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, 518020, China.
| | - Chang Zou
- The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, 518020, China.
| | - Jigang Wang
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
- The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, 518020, China.
- Department of Toxicology, School of Public Health, Guangxi Medical University, Nanning, 530021, China.
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22
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Steiger AK, Fansler SJ, Whidbey C, Miller CJ, Wright AT. Probe-enabled approaches for function-dependent cell sorting and characterization of microbiome subpopulations. Methods Enzymol 2020; 638:89-107. [PMID: 32416923 DOI: 10.1016/bs.mie.2020.03.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Understanding the roles that individual species or communities play within a microbiome is a significant challenge. The complexity and heterogeneity of microbiomes presents a challenge to researchers looking to unravel the function that microbiomes serve within larger environments. While identification of the species and proteins present in a microbiome can be accomplished through genomics approaches, strategies that report on enzyme activity are limited. In this chapter, we describe the application of small molecule chemical probes in the isolation and subsequent characterization of microbiome subpopulations based on enzymatic function. We will cover protocols for labeling microbes with appropriate probes, microbiome sample preparation, and using fluorescence-activated cell sorting to isolate subpopulations based on function. We hope that the strategies outlined here will serve as a resource for researchers studying the functional role that microbiomes play in the gut and soil.
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Affiliation(s)
- Andrea K Steiger
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States
| | - Sarah J Fansler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States
| | - Christopher Whidbey
- Department of Chemistry, Seattle University, Seattle, Washington, United States
| | - Carson J Miller
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States
| | - Aaron T Wright
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States; The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington, United States.
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23
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Parker CG, Pratt MR. Click Chemistry in Proteomic Investigations. Cell 2020; 180:605-632. [PMID: 32059777 PMCID: PMC7087397 DOI: 10.1016/j.cell.2020.01.025] [Citation(s) in RCA: 187] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/09/2020] [Accepted: 01/16/2020] [Indexed: 01/20/2023]
Abstract
Despite advances in genetic and proteomic techniques, a complete portrait of the proteome and its complement of dynamic interactions and modifications remains a lofty, and as of yet, unrealized, objective. Specifically, traditional biological and analytical approaches have not been able to address key questions relating to the interactions of proteins with small molecules, including drugs, drug candidates, metabolites, or protein post-translational modifications (PTMs). Fortunately, chemists have bridged this experimental gap through the creation of bioorthogonal reactions. These reactions allow for the incorporation of chemical groups with highly selective reactivity into small molecules or protein modifications without perturbing their biological function, enabling the selective installation of an analysis tag for downstream investigations. The introduction of chemical strategies to parse and enrich subsets of the "functional" proteome has empowered mass spectrometry (MS)-based methods to delve more deeply and precisely into the biochemical state of cells and its perturbations by small molecules. In this Primer, we discuss how one of the most versatile bioorthogonal reactions, "click chemistry", has been exploited to overcome limitations of biological approaches to enable the selective marking and functional investigation of critical protein-small-molecule interactions and PTMs in native biological environments.
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Affiliation(s)
- Christopher G Parker
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA.
| | - Matthew R Pratt
- Departments of Chemistry and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
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24
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Lee CC, Southgate R, Jiao C, Gersz E, Owen JR, Kates SL, Beck CA, Xie C, Daiss JL, Post V, Moriarty TF, Zeiter S, Schwarz EM, Muthukrishnan G. Deriving a dose and regimen for anti-glucosaminidase antibody passive-immunisation for patients with Staphylococcus aureus osteomyelitis. Eur Cell Mater 2020; 39:96-107. [PMID: 32003439 PMCID: PMC7236896 DOI: 10.22203/ecm.v039a06] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Staphylococcus aureus (S. aureus) osteomyelitis remains a major clinical problem. Anti-glucosaminidase (Gmd) antibodies (1C11) are efficacious in prophylactic and therapeutic murine models. Feasibility, safety and pharmacokinetics of 1C11 passive immunisation in sheep and endogenous anti-Gmd levels were quantified in osteomyelitis patients. 3 sheep received a 500 mg intravenous (i.v.) bolus of 1C11 and its levels in sera were determined by enzyme-linked immunosorbent assay (ELISA) over 52 d. A humanised anti-Gmd monoclonal antibody, made by grafting the antigen-binding fragment (Fab) portion of 1C11 onto the fragment crystallisable region (Fc) of human IgG1, was used to make a standard curve of mean fluorescent intensity versus concentration of anti-Gmd. Anti-Gmd serum levels were determined in 297 patients with culture-confirmed S. aureus osteomyelitis and 40 healthy controls. No complications or adverse events were associated with the sheep 1C11 i.v. infusion and the estimated circulating half-life of 1C11 was 23.7 d. Endogenous anti-Gmd antibody levels in sera of osteomyelitis patients ranged from < 1 ng/mL to 300 µg/mL, with a mean concentration of 21.7 µg/mL. The estimated circulating half-life of endogenous anti-Gmd antibodies in sera of 12 patients with cured osteomyelitis was 120.4 d. A clinically relevant administration of anti-Gmd (500 mg i.v. = 7 mg/kg/70 kg human) was safe in sheep. This dose was 8 times more than the endogenous anti-Gmd levels observed in osteomyelitis patients and was predicted to have a half-life of > 3 weeks. Anti-Gmd passive immunisation has potential to prevent and treat S. aureus osteomyelitis. Further clinical development is warranted.
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Affiliation(s)
- Charles C. Lee
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, USA
| | - Richard Southgate
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, USA
| | - Cindy Jiao
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, USA
| | - Elaine Gersz
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, USA
| | - John R. Owen
- Department of Orthopaedic Surgery, Virginia Commonwealth University, Richmond, VA, USA
| | - Stephen L. Kates
- Department of Orthopaedic Surgery, Virginia Commonwealth University, Richmond, VA, USA
| | - Christopher A. Beck
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, USA
| | - Chao Xie
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, USA
| | - John L. Daiss
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, USA
| | | | | | | | - Edward M. Schwarz
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, USA,Corresponding Author: Edward M. Schwarz, Ph.D., Burton Professor of Orthopaedics, Director of Center for Musculoskeletal Research, University of Rochester Medical Center, 601 Elmwood Avenue, Box 665, Rochester, NY 14642, Phone: (585) 275-3063, FAX: (585) 276-2177,
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25
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Wang H, Chen T, Chen Y, Luo T, Tan B, Chen H, Xin H. Evaluation of the inhibitory effects of vaginal microorganisms on sperm motility in vitro. Exp Ther Med 2019; 19:535-544. [PMID: 31853321 PMCID: PMC6909777 DOI: 10.3892/etm.2019.8237] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 10/31/2019] [Indexed: 12/16/2022] Open
Abstract
Female infertility usually occurs as a result of ageing, physical impairment, hormone disturbances and lifestyle or environmental factors. However, the potential role of Lactobacillus in female infertility has remained largely unexplored. In the present study, high-throughput sequencing, real-time PCR, bacterial adherence assays and sperm motility assays were used to evaluate the microbial diversity, adherence properties and effect on sperm motility of sperm bacteria, vaginal bacteria and vaginal bacteria that had been co-cultured with sperm. The results indicated that in the co-culture group, Lactobacillus adhered to sperm cells in numbers that were 332-fold higher than those of control species Enterococcus and analysis of sequencing data using the Kyoto Encyclopedia of Genes and Genomes indicated that adhered microbes reduced sperm cell motility. Vaginal isolates, as well as bacterial strains used as controls, were co-cultured with sperm and it was indicated that all strains were able to adhere to sperm cells in large numbers. The probiotic Lactobacillus (L.) strains L. crispatus, L. acidophilus, L. helveticus and L. gasseri significantly reduced sperm motility (based on measurements of general, straightforward and non-straightforward progressive motility, total motility and average path velocity; P<0.05). Furthermore, L. crispatus, L. acidophilus, L. salivarius, L. helveticus and L. gasseri markedly reduced sperm penetration in a viscous medium. Based on these results, it may be hypothesized that the weakening effect of Lactobacillus on sperm motility may be beneficial for healthy couples to prevent the combination of abnormal sperms and eggs, but may be detrimental for males with severe asthenospermia, oligospermia or aspermia.
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Affiliation(s)
- Huan Wang
- School of Life Sciences, Institute of Translational Medicine, Nanchang University, Nanchang, Jiangxi 330031, P.R. China
| | - Tingtao Chen
- School of Life Sciences, Institute of Translational Medicine, Nanchang University, Nanchang, Jiangxi 330031, P.R. China
| | - Yidan Chen
- School of Life Sciences, Institute of Translational Medicine, Nanchang University, Nanchang, Jiangxi 330031, P.R. China
| | - Tao Luo
- National Engineering Research Center for Bioengineering Drugs and Technologies, Institute of Translational Medicine, Nanchang University, Nanchang, Jiangxi 330031, P.R. China
| | - Buzhen Tan
- Department of Obstetrics and Gynaecology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Houyang Chen
- Reproductive Medical Centre, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi 330031, P.R. China
| | - Hongbo Xin
- School of Life Sciences, Institute of Translational Medicine, Nanchang University, Nanchang, Jiangxi 330031, P.R. China
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26
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Stone MRL, Masi M, Phetsang W, Pagès JM, Cooper MA, Blaskovich MAT. Fluoroquinolone-derived fluorescent probes for studies of bacterial penetration and efflux. MEDCHEMCOMM 2019; 10:901-906. [PMID: 31303987 PMCID: PMC6596217 DOI: 10.1039/c9md00124g] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 04/16/2019] [Indexed: 12/21/2022]
Abstract
Fluorescent probes derived from the fluoroquinolone antibiotic ciprofloxacin were synthesised using a Cu(i)-catalysed azide–alkyne cycloaddition (CuAAC) to link a ciprofloxacin azide derivative with alkyne-substituted green and blue fluorophores.
Fluorescent probes derived from the fluoroquinolone antibiotic ciprofloxacin were synthesised using a Cu(i)-catalysed azide–alkyne cycloaddition (CuAAC) to link a ciprofloxacin azide derivative with alkyne-substituted green and blue fluorophores. The azide (2) and fluorophore (3 and 4) derivatives retained antimicrobial activity against Gram-positive and Gram-negative bacteria. The use of confocal fluorescent microscopy showed intracellular penetration, which was substantially enhanced in the presence of carbonyl cyanide 3-chlorophenylhydrazone as an efflux pump inhibitor in Escherichia coli.
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Affiliation(s)
- M Rhia L Stone
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia .
| | - Muriel Masi
- Membranes et Cibles Thérapeutiques , UMR_MD1 , Inserm U1261 , Aix-Marseille Univ & IRBA , Facultés de Médecine et de Pharmacie , 27 Bd Jean Moulin , 13005 Marseille , France
| | - Wanida Phetsang
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia .
| | - Jean-Marie Pagès
- Membranes et Cibles Thérapeutiques , UMR_MD1 , Inserm U1261 , Aix-Marseille Univ & IRBA , Facultés de Médecine et de Pharmacie , 27 Bd Jean Moulin , 13005 Marseille , France
| | - Matthew A Cooper
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia .
| | - Mark A T Blaskovich
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia .
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27
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Highly-branched poly(N-isopropyl acrylamide) functionalised with pendant Nile red and chain end vancomycin for the detection of Gram-positive bacteria. Acta Biomater 2019; 87:197-206. [PMID: 30711663 PMCID: PMC6401204 DOI: 10.1016/j.actbio.2019.01.066] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 01/27/2019] [Accepted: 01/30/2019] [Indexed: 12/02/2022]
Abstract
This study shows how highly branched poly(N-isopropyl acrylamide) (HB-PNIPAM) with a chain pendant solvatochromic dye (Nile red) could provide a fluorescence signal, as end groups bind to bacteria and chain segments become desolvated, indicating the presence of bacteria. Vancomycin was attached to chain ends of HB-PNIPAM or as pendant groups on linear polymers each containing Nile red. Location of the dye was varied between placement in the core of the branched polymer coil or the outer domains. Both calorimetric and fluorescence data showed that branched polymers responded to binding of both the peptide target (D-Ala-D-Aa) and bacteria in a different manner than analogous linear polymers; binding and response was more extensive in the branched variant. The fluorescence data showed that only segments located in the outer domains of branched polymers responded to binding of Gram-positive bacteria with little response when linear analogous polymer or branched polymer with the dye in the inner core was exposed to Staphylococcus aureus.
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28
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Chauhan D, Hati S, Priyadarshini R, Sen S. Transcriptome analysis predicts mode of action of benzimidazole molecules against
Staphylococcus aureus
UAMS‐1. Drug Dev Res 2019; 80:490-503. [DOI: 10.1002/ddr.21523] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 01/23/2019] [Accepted: 01/26/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Deepika Chauhan
- Department of Life Science, School of Natural SciencesShiv Nadar University Dadri Uttar Pradesh India
| | - Santanu Hati
- Department of Chemistry, School of Natural SciencesShiv Nadar University Dadri Uttar Pradesh India
- Department of Medicinal Chemistry, College of PharmacyUniversity of Florida Gainesville Florida
| | - Richa Priyadarshini
- Department of Life Science, School of Natural SciencesShiv Nadar University Dadri Uttar Pradesh India
| | - Subhabrata Sen
- Department of Chemistry, School of Natural SciencesShiv Nadar University Dadri Uttar Pradesh India
- Department of ChemistrySRM University Amaravati Andhra Pradesh India
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29
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Yokogawa N, Ishikawa M, Nishitani K, Beck CA, Tsuchiya H, Mesfin A, Kates SL, Daiss JL, Xie C, Schwarz EM. Immunotherapy synergizes with debridement and antibiotic therapy in a murine 1-stage exchange model of MRSA implant-associated osteomyelitis. J Orthop Res 2018; 36:1590-1598. [PMID: 29405452 PMCID: PMC6541030 DOI: 10.1002/jor.23801] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 10/31/2017] [Indexed: 02/04/2023]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) reinfection following revision surgery remains a major orthopaedic problem. Toward the development of immunotherapy with anti-glucosaminidase monoclonal antibodies (anti-Gmd), we aimed to: (i) develop a murine 1-stage exchange model of bioluminescent MRSA (USA300LAC::lux) contaminated femoral implants; and (ii) utilize this model to demonstrate the synergistic effects of combination vancomycin and anti-Gmd therapy on reinfection and bone healing. Following an infection surgery, the original plate and two screws were removed on day 7, and exchanged with sterile implants. Mice were randomized to five groups: (i) no infection control; (ii) infected placebo; (iii) anti-Gmd; (iv) vancomycin; and (v) combination therapy. Bioluminescent imaging (BLI) was performed on days 0, 1, 3, 5, 7, 8, 10, 12, and 14. Mice were euthanized on day 14 (day 7 post-revision), and efficacy was assessed via colony forming units (CFU) on explanted hardware, micro-CT, and histology. As monotherapies, anti-Gmd inhibited Staphylococcus abscess communities, and vancomycin reduced CFU on the implants. However, only combination therapy prevented increased BLI post-revision surgery, with a significant 6.5-fold reduction on day 10 (p < 0.05 vs. placebo), and achieved sterile implant levels by day 12. Synergistic effects were also apparent from reduced osteolysis and increased new bone formation around the screws only observed following combination therapy. Taken together, we find that: (i) this murine femoral plate 1-stage revision model can efficiently evaluate therapies to prevent reinfection; and (ii) immunotherapy plays a distinct role from antibiotics to reduce reinfection following revision surgery, such that synergy to achieve osseointegration is possible. © 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:1590-1598, 2018.
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Affiliation(s)
- Noriaki Yokogawa
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY,Department of Orthopaedic Surgery, Kanazawa University, Kanazawa, Japan
| | - Masahiro Ishikawa
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY,Department of Orthopaedics Surgery, Kyoto University, Kyoto, Japan
| | - Kohei Nishitani
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY,Department of Orthopaedics Surgery, Kyoto University, Kyoto, Japan
| | - Christopher A. Beck
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY,Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY,Department of Orthopedics, University of Rochester Medical Center, Rochester, NY
| | - Hiroyuki Tsuchiya
- Department of Orthopaedic Surgery, Kanazawa University, Kanazawa, Japan
| | - Addisu Mesfin
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY,Department of Orthopedics, University of Rochester Medical Center, Rochester, NY
| | - Stephen L. Kates
- Department of Orthopedic Surgery, Virginia Commonwealth University, Richmond, VA
| | - John L. Daiss
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY,Department of Orthopedics, University of Rochester Medical Center, Rochester, NY
| | - Chao Xie
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY,Department of Orthopedics, University of Rochester Medical Center, Rochester, NY
| | - Edward M. Schwarz
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY,Department of Orthopedics, University of Rochester Medical Center, Rochester, NY
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30
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Sharifzadeh S, Shirley JD, Carlson EE. Activity-Based Protein Profiling Methods to Study Bacteria: The Power of Small-Molecule Electrophiles. Curr Top Microbiol Immunol 2018; 420:23-48. [PMID: 30232601 DOI: 10.1007/82_2018_135] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
ABPP methods have been utilized for the last two decades as a means to investigate complex proteomes in all three domains of life. Extensive use in eukaryotes has provided a more fundamental understanding of the biological processes involved in numerous diseases and has driven drug discovery and treatment campaigns. However, the use of ABPP in prokaryotes has been less common, although it has gained more attention over the last decade. The urgent need for understanding bacteriophysiology and bacterial pathogenicity at a foundational level has never been more apparent, as the rise in antibiotic resistance has resulted in the inadequate and ineffective treatment of infections. This is not only a result of resistance to clinically used antibiotics, but also a lack of new drugs and equally as important, new drug targets. ABPP provides a means for which new, clinically relevant drug targets may be identified through gaining insight into biological processes. In this chapter, we place particular focus on the discussion of ABPP strategies that have been applied to study different classes of bacterial enzymes.
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Affiliation(s)
- Shabnam Sharifzadeh
- Department of Chemistry, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA
| | - Joshua D Shirley
- Department of Medicinal Chemistry, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA
| | - Erin E Carlson
- Department of Chemistry, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA. .,Department of Medicinal Chemistry, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA. .,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA.
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31
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Shin C, Lee HN, Ryu JS, Chung HJ. Rapid naked-eye detection of Gram-positive bacteria by vancomycin-based nano-aggregation. RSC Adv 2018; 8:25094-25103. [PMID: 35542172 PMCID: PMC9082569 DOI: 10.1039/c8ra03540g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 06/26/2018] [Indexed: 12/16/2022] Open
Abstract
Development of a rapid, point-of-care assay for diagnosing bacterial infections is crucial for subsequent treatment of the patient and preventing the overuse of antibiotics. Herein, we describe a rapid, one-step colorimetric assay based on the formation of nano-aggregates using nanobeads targeting Gram-positive bacteria. Vancomycin was immobilized onto blue-colored polymeric nanobeads to induce specific and multivalent binding with the Gram-positive bacterial cell wall and subsequent agglomeration. Without any pre-processing steps, the addition of various types of Gram-positive pathogens to the nanobeads resulted in the formation of blue precipitates, which could be observed with the naked eye in ∼30 min. We also utilized a porous filter system for the assay, which allowed discrimination of Gram-positive targets with higher selectivity, and demonstrated feasibility as a simple diagnostic assay with minimal technical components. We anticipate that the nanobead aggregation assay can be potentially applied as a rapid and simple sensing platform, which can be easily miniaturized and enable point-of-care diagnosis of Gram-positive infections. A rapid, colorimetric assay based on aggregation of nanobeads functionalized with vancomycin is developed for naked-eye detection of Gram-positive bacteria.![]()
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Affiliation(s)
- Cheong Shin
- Graduate School of Nanoscience and Technology
- Korea Advanced Institute of Science and Technology
- Daejeon
- Korea
| | - Ha Neul Lee
- Graduate School of Nanoscience and Technology
- Korea Advanced Institute of Science and Technology
- Daejeon
- Korea
| | - Jea Sung Ryu
- Graduate School of Nanoscience and Technology
- Korea Advanced Institute of Science and Technology
- Daejeon
- Korea
| | - Hyun Jung Chung
- Graduate School of Nanoscience and Technology
- Korea Advanced Institute of Science and Technology
- Daejeon
- Korea
- Department of Biological Sciences
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32
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Wright MH, Sieber SA. Chemical proteomics approaches for identifying the cellular targets of natural products. Nat Prod Rep 2017; 33:681-708. [PMID: 27098809 PMCID: PMC5063044 DOI: 10.1039/c6np00001k] [Citation(s) in RCA: 258] [Impact Index Per Article: 36.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This review focuses on chemical probes to identify the protein binding partners of natural products in living systems.
Covering: 2010 up to 2016 Deconvoluting the mode of action of natural products and drugs remains one of the biggest challenges in chemistry and biology today. Chemical proteomics is a growing area of chemical biology that seeks to design small molecule probes to understand protein function. In the context of natural products, chemical proteomics can be used to identify the protein binding partners or targets of small molecules in live cells. Here, we highlight recent examples of chemical probes based on natural products and their application for target identification. The review focuses on probes that can be covalently linked to their target proteins (either via intrinsic chemical reactivity or via the introduction of photocrosslinkers), and can be applied “in situ” – in living systems rather than cell lysates. We also focus here on strategies that employ a click reaction, the copper-catalysed azide–alkyne cycloaddition reaction (CuAAC), to allow minimal functionalisation of natural product scaffolds with an alkyne or azide tag. We also discuss ‘competitive mode’ approaches that screen for natural products that compete with a well-characterised chemical probe for binding to a particular set of protein targets. Fuelled by advances in mass spectrometry instrumentation and bioinformatics, many modern strategies are now embracing quantitative proteomics to help define the true interacting partners of probes, and we highlight the opportunities this rapidly evolving technology provides in chemical proteomics. Finally, some of the limitations and challenges of chemical proteomics approaches are discussed.
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Affiliation(s)
- M H Wright
- Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85748, Garching, Germany.
| | - S A Sieber
- Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85748, Garching, Germany.
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33
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Pan S, Zhang H, Wang C, Yao SCL, Yao SQ. Target identification of natural products and bioactive compounds using affinity-based probes. Nat Prod Rep 2017; 33:612-20. [PMID: 26580476 DOI: 10.1039/c5np00101c] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Covering: 2010 to 2014.Advances in isolation, synthesis and screening strategies have made many bioactive substances available. However, in most cases their putative biological targets remain unknown. Herein, we highlight recent advances in target identification of natural products and bioactive compounds by using affinity-based probes. Aided by photoaffinity labelling, this strategy can capture potential cellular targets (on and off) of a natural product or bioactive compound in live cells directly, even when the compound-target interaction is reversible with moderate affinity. The knowledge of these targets may help uncover molecular pathways and new therapeutics for currently untreatable diseases. In this highlight, we will introduce the development of various photoactivatable groups, their synthesis and applications in target identification of natural products and bioactive compounds, with a focus on work done in recent years and from our laboratory. We will further discuss the strengths and weaknesses of each group and the outlooks for this novel proteome-wide profiling strategy.
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Affiliation(s)
- Sijun Pan
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
| | - Hailong Zhang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
| | - Chenyu Wang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
| | - Samantha C L Yao
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
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34
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Chowdhuri AR, Das B, Kumar A, Tripathy S, Roy S, Sahu SK. One-pot synthesis of multifunctional nanoscale metal-organic frameworks as an effective antibacterial agent against multidrug-resistant Staphylococcus aureus. NANOTECHNOLOGY 2017; 28:095102. [PMID: 28139466 DOI: 10.1088/1361-6528/aa57af] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Drug-resistant bacteria are an increasingly serious threat to global public health. In particular, infections from multidrug-resistant (MDR) Gram-positive bacteria (i.e. Staphylococcus aureus) are growing global health concerns. In this work, we report the first use of nanoscale metal-organic frameworks (NMOFs) coencapsulating an antibiotic (vancomycin) and targeting ligand (folic acid) in one pot to enhance therapeutic efficacy against MDR S. aureus. Zeolitic imidazolate framework (ZIF-8) NMOFs, which have globular morphologies coencapsulating vancomycin and folic acid, are characterized by transmission electron microscopy, field-emission scanning electron microscopy, powder x-ray diffraction, ulltraviolet-visible spectroscopy, and dynamic light-scattering techniques. We determined that the presence of folic acid on the surface of the NMOFs is significant in the sense of effective uptake by MDR S. aureus through endocytosis. The functionalized NMOFs transport vancomycin across the cell wall of MDR S. aureus and enhance antibacterial activity, which has been confirmed from studies of the minimum inhibitory concentration, minimum bactericidal concentration, cytotoxicity of bacterial cells, and generation of reactive oxygen species. This work shows that functionalized NMOFs hold great promise for effective treatment of MDR S. aureus.
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Affiliation(s)
- Angshuman Ray Chowdhuri
- Department of Applied Chemistry, Indian Institute of Technology (ISM), Dhanbad-826004, Jharkhand, India
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35
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Abstract
Understanding the molecular mechanisms of bacterial pathogenesis and virulence is of great importance from both an academic and clinical perspective, especially in view of an alarming increase in bacterial resistance to existing antibiotics and antibacterial agents. Use of small molecules to dissect the basis of these dynamic processes is a very attractive approach due to their ability for rapid spatiotemporal control of specific biochemical functions. Activity-based protein profiling (ABPP), employing small molecule probes to interrogate enzyme activities in complex proteomes, has emerged as a powerful tool to study bacterial pathogenesis. In this chapter, we present a set of ABPP methods to identify and analyze enzymes essential for growth, metabolism and virulence of different pathogens including S. aureus and L. monocytogenes using natural product-inspired activity-based probes.
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36
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Dormán G, Nakamura H, Pulsipher A, Prestwich GD. The Life of Pi Star: Exploring the Exciting and Forbidden Worlds of the Benzophenone Photophore. Chem Rev 2016; 116:15284-15398. [PMID: 27983805 DOI: 10.1021/acs.chemrev.6b00342] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The widespread applications of benzophenone (BP) photochemistry in biological chemistry, bioorganic chemistry, and material science have been prominent in both academic and industrial research. BP photophores have unique photochemical properties: upon n-π* excitation at 365 nm, a biradicaloid triplet state is formed reversibly, which can abstract a hydrogen atom from accessible C-H bonds; the radicals subsequently recombine, creating a stable covalent C-C bond. This light-directed covalent attachment process is exploited in many different ways: (i) binding/contact site mapping of ligand (or protein)-protein interactions; (ii) identification of molecular targets and interactome mapping; (iii) proteome profiling; (iv) bioconjugation and site-directed modification of biopolymers; (v) surface grafting and immobilization. BP photochemistry also has many practical advantages, including low reactivity toward water, stability in ambient light, and the convenient excitation at 365 nm. In addition, several BP-containing building blocks and reagents are commercially available. In this review, we explore the "forbidden" (transitions) and excitation-activated world of photoinduced covalent attachment of BP photophores by touring a colorful palette of recent examples. In this exploration, we will see the pros and cons of using BP photophores, and we hope that both novice and expert photolabelers will enjoy and be inspired by the breadth and depth of possibilities.
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Affiliation(s)
- György Dormán
- Targetex llc , Dunakeszi H-2120, Hungary.,Faculty of Pharmacy, University of Szeged , Szeged H-6720, Hungary
| | - Hiroyuki Nakamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology , Yokohama 226-8503, Japan
| | - Abigail Pulsipher
- GlycoMira Therapeutics, Inc. , Salt Lake City, Utah 84108, United States.,Division of Head and Neck Surgery, Rhinology - Sinus and Skull Base Surgery, Department of Surgery, University of Utah School of Medicine , Salt Lake City, Utah 84108, United States
| | - Glenn D Prestwich
- Division of Head and Neck Surgery, Rhinology - Sinus and Skull Base Surgery, Department of Surgery, University of Utah School of Medicine , Salt Lake City, Utah 84108, United States
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37
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Cushnie TPT, O'Driscoll NH, Lamb AJ. Morphological and ultrastructural changes in bacterial cells as an indicator of antibacterial mechanism of action. Cell Mol Life Sci 2016; 73:4471-4492. [PMID: 27392605 PMCID: PMC11108400 DOI: 10.1007/s00018-016-2302-2] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Revised: 06/21/2016] [Accepted: 06/28/2016] [Indexed: 01/20/2023]
Abstract
Efforts to reduce the global burden of bacterial disease and contend with escalating bacterial resistance are spurring innovation in antibacterial drug and biocide development and related technologies such as photodynamic therapy and photochemical disinfection. Elucidation of the mechanism of action of these new agents and processes can greatly facilitate their development, but it is a complex endeavour. One strategy that has been popular for many years, and which is garnering increasing interest due to recent technological advances in microscopy and a deeper understanding of the molecular events involved, is the examination of treated bacteria for changes to their morphology and ultrastructure. In this review, we take a critical look at this approach. Variables affecting antibacterial-induced alterations are discussed first. These include characteristics of the test organism (e.g. cell wall structure) and incubation conditions (e.g. growth medium osmolarity). The main body of the review then describes the different alterations that can occur. Micrographs depicting these alterations are presented, together with information on agents that induce the change, and the sequence of molecular events that lead to the change. We close by highlighting those morphological and ultrastructural changes which are consistently induced by agents sharing the same mechanism (e.g. spheroplast formation by peptidoglycan synthesis inhibitors) and explaining how changes that are induced by multiple antibacterial classes (e.g. filamentation by DNA synthesis inhibitors, FtsZ disruptors, and other types of agent) can still yield useful mechanistic information. Lastly, recommendations are made regarding future study design and execution.
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Affiliation(s)
- T P Tim Cushnie
- Faculty of Medicine, Mahasarakham University, Khamriang, Kantarawichai, Maha Sarakham, 44150, Thailand.
| | - Noëlle H O'Driscoll
- School of Pharmacy and Life Sciences, Robert Gordon University, Sir Ian Wood Building, Garthdee Road, Aberdeen, AB10 7GJ, UK
| | - Andrew J Lamb
- School of Pharmacy and Life Sciences, Robert Gordon University, Sir Ian Wood Building, Garthdee Road, Aberdeen, AB10 7GJ, UK
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38
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Crump CJ, Murrey HE, Ballard TE, am Ende CW, Wu X, Gertsik N, Johnson DS, Li YM. Development of Sulfonamide Photoaffinity Inhibitors for Probing Cellular γ-Secretase. ACS Chem Neurosci 2016; 7:1166-73. [PMID: 27253220 DOI: 10.1021/acschemneuro.6b00127] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
γ-Secretase is a multiprotein complex that catalyzes intramembrane proteolysis associated with Alzheimer's disease and cancer. Here, we have developed potent sulfonamide clickable photoaffinity probes that target γ-secretase in vitro and in cells by incorporating various photoreactive groups and walking the clickable alkyne handle to different positions around the molecule. We found that benzophenone is preferred over diazirine as a photoreactive group within the sulfonamide scaffold for labeling γ-secretase. Intriguingly, the placement of the alkyne at different positions has little effect on probe potency but has a significant impact on the efficiency of labeling of γ-secretase. Moreover, the optimized clickable photoprobe, 163-BP3, was utilized as a cellular probe to effectively assess the target engagement of inhibitors with γ-secretase in primary neuronal cells. In addition, biotinylated 163-BP3 probes were developed and used to capture the native γ-secretase complex in the 3-[(3-cholamidopropyl)dimethylammonio]-2-hydroxy-1-propanesulfonate (CHAPSO) solubilized state. Taken together, these next generation clickable and biotinylated sulfonamide probes offer new tools to study γ-secretase in biochemical and cellular systems. Finally, the data provide insights into structural features of the sulfonamide inhibitor binding site in relation to the active site and into the design of clickable photoaffinity probes.
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Affiliation(s)
- Christina J. Crump
- Chemical
Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York
Avenue, New York, New York 10065, United States
| | - Heather E. Murrey
- Pfizer Worldwide Research and Development, Worldwide Medicinal Chemistry, Cambridge, Massachusetts 02139, United States
| | - T. Eric Ballard
- Pfizer Worldwide Research and Development, Worldwide
Medicinal Chemistry Groton, Connecticut 06340, United States
| | - Christopher W. am Ende
- Pfizer Worldwide Research and Development, Worldwide
Medicinal Chemistry Groton, Connecticut 06340, United States
| | - Xianzhong Wu
- Chemical
Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York
Avenue, New York, New York 10065, United States
| | - Natalya Gertsik
- Chemical
Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York
Avenue, New York, New York 10065, United States
| | - Douglas S. Johnson
- Pfizer Worldwide Research and Development, Worldwide Medicinal Chemistry, Cambridge, Massachusetts 02139, United States
| | - Yue-Ming Li
- Chemical
Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York
Avenue, New York, New York 10065, United States
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39
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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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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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41
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Moriarty TF, Kuehl R, Coenye T, Metsemakers WJ, Morgenstern M, Schwarz EM, Riool M, Zaat SA, Khana N, Kates SL, Richards RG. Orthopaedic device-related infection: current and future interventions for improved prevention and treatment. EFORT Open Rev 2016; 1:89-99. [PMID: 28461934 PMCID: PMC5367564 DOI: 10.1302/2058-5241.1.000037] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Orthopaedic and trauma device-related infection (ODRI) remains one of the major complications in modern trauma and orthopaedic surgery.Despite best practice in medical and surgical management, neither prophylaxis nor treatment of ODRI is effective in all cases, leading to infections that negatively impact clinical outcome and significantly increase healthcare expenditure.The following review summarises the microbiological profile of modern ODRI, the impact antibiotic resistance has on treatment outcomes, and some of the principles and weaknesses of the current systemic and local antibiotic delivery strategies.The emerging novel strategies aimed at preventing or treating ODRI will be reviewed. Particular attention will be paid to the potential for clinical impact in the coming decades, when such interventions are likely to be critically important.The review focuses on this problem from an interdisciplinary perspective, including basic science innovations and best practice in infectious disease. Cite this article: Moriarty TF, Kuehl R, Coenye T, et al. Orthopaedic device related infection: current and future interventions for improved prevention and treatment. EFORT Open Rev 2016;1:89-99. DOI: 10.1302/2058-5241.1.000037.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Nina Khana
- University Hospital of Basel, Switzerland
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42
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Anderson LN, Koech PK, Plymale AE, Landorf EV, Konopka A, Collart FR, Lipton MS, Romine MF, Wright AT. Live Cell Discovery of Microbial Vitamin Transport and Enzyme-Cofactor Interactions. ACS Chem Biol 2016; 11:345-54. [PMID: 26669591 DOI: 10.1021/acschembio.5b00918] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The rapid completion of microbial genomes is inducing a conundrum in functional gene discovery. Novel methods are needed to shorten the gap between characterizing a microbial genome and experimentally validating bioinformatically predicted functions. Of particular importance are transport mechanisms, which shuttle nutrients such as B vitamins and metabolites across cell membranes and are required for the survival of microbes ranging from members of environmental microbial communities to pathogens. Methods to accurately assign function and specificity for a wide range of experimentally unidentified and/or predicted membrane-embedded transport proteins, along with characterization of intracellular enzyme-cofactor associations, are needed to enable a significantly improved understanding of microbial biochemistry and physiology, microbial interactions, and microbial responses to perturbations. Chemical probes derived from B vitamins B1, B2, and B7 have allowed us to experimentally address the aforementioned needs by identifying B vitamin transporters and intracellular enzyme-cofactor associations through live cell labeling of the filamentous anoxygenic photoheterotroph, Chloroflexus aurantiacus J-10-fl, known to employ mechanisms for both B vitamin biosynthesis and environmental salvage. Our probes provide a unique opportunity to directly link cellular activity and protein function back to ecosystem and/or host dynamics by identifying B vitamin transport and cofactor-dependent interactions required for survival.
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Affiliation(s)
- Lindsey N. Anderson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 United States
| | - Phillip K. Koech
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 United States
| | - Andrew E. Plymale
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 United States
| | - Elizabeth V. Landorf
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439 United States
| | - Allan Konopka
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 United States
| | - Frank R. Collart
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439 United States
| | - Mary S. Lipton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 United States
| | - Margaret F. Romine
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 United States
| | - Aaron T. Wright
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 United States
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43
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Lehmann J, Wright MH, Sieber SA. Making a Long Journey Short: Alkyne Functionalization of Natural Product Scaffolds. Chemistry 2016; 22:4666-78. [PMID: 26752308 DOI: 10.1002/chem.201504419] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Indexed: 01/09/2023]
Abstract
Biological selection makes natural products promising scaffolds for drug development and the ever growing number of newly identified, structurally diverse molecules helps to fill the gaps in chemical space. Elucidating the function of a small molecule, such as identifying its protein binding partners, its on- and off-targets, is becoming increasingly important. Activity- and affinity-based protein profiling are modern strategies to acquire such molecular-level information. Introduction of a molecular handle (azide, alkyne, biotin) can shed light on the mode of action of small molecules. This Concept article covers central points on synthetic methodology for integrating a terminal alkyne into a molecule of interest.
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Affiliation(s)
- Johannes Lehmann
- Center for Integrated Protein Science, Munich (CIPSM), Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85747, Garching, Germany
| | - Megan H Wright
- Center for Integrated Protein Science, Munich (CIPSM), Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85747, Garching, Germany
| | - Stephan A Sieber
- Center for Integrated Protein Science, Munich (CIPSM), Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85747, Garching, Germany.
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44
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Farha MA, Brown ED. Strategies for target identification of antimicrobial natural products. Nat Prod Rep 2016; 33:668-80. [DOI: 10.1039/c5np00127g] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Despite a pervasive decline in natural product research at many pharmaceutical companies over the last two decades, natural products have undeniably been a prolific and unsurpassed source for new lead antibacterial compounds.
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Affiliation(s)
- Maya A. Farha
- M.G. DeGroote Institute for Infectious Disease Research and Department of Biochemistry and Biomedical Sciences
- McMaster University
- Hamilton
- Canada
| | - Eric D. Brown
- M.G. DeGroote Institute for Infectious Disease Research and Department of Biochemistry and Biomedical Sciences
- McMaster University
- Hamilton
- Canada
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45
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Recent developments and applications of clickable photoprobes in medicinal chemistry and chemical biology. Future Med Chem 2015; 7:2143-71. [DOI: 10.4155/fmc.15.136] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Photoaffinity labeling is a well-known biochemical technique that has grown significantly since the turn of the century, principally due to its combination with bioorthogonal/click chemistry reactions. This review highlights new developments and applications of clickable photoprobes in medicinal chemistry and chemical biology. In particular, recent examples of clickable photoprobes for target identification, activity- or affinity-based protein profiling (ABPP or AfBPP), characterization of sterol– or lipid–protein interactions and characterization of ligand-binding sites are presented.
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46
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Zheng W, Li G, Li X. Affinity purification in target identification: the specificity challenge. Arch Pharm Res 2015; 38:1661-85. [DOI: 10.1007/s12272-015-0635-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 07/07/2015] [Indexed: 12/16/2022]
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Arntzen MØ, Karlskås IL, Skaugen M, Eijsink VGH, Mathiesen G. Proteomic Investigation of the Response of Enterococcus faecalis V583 when Cultivated in Urine. PLoS One 2015; 10:e0126694. [PMID: 25915650 PMCID: PMC4411035 DOI: 10.1371/journal.pone.0126694] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 04/07/2015] [Indexed: 11/19/2022] Open
Abstract
Enterococcus faecalis is a robust bacterium, which is able to survive in and adapt to hostile environments such as the urinary tract and bladder. In this label-free quantitative proteomic study based on MaxQuant LFQ algorithms, we identified 127 proteins present in the secretome of the clinical vancomycin-resistant isolate E. faecalis V583 and we compared proteins secreted in the initial phase of cultivation in urine with the secretome during cultivation in standard laboratory medium, 2xYT. Of the 54 identified proteins predicted to be secreted, six were exclusively found after cultivation in urine including the virulence factor EfaA ("endocarditis specific antigen") and its homologue EF0577 ("adhesion lipoprotein"). These two proteins are both involved in manganese transport, known to be an important determinant of colonization and infection, and may additionally function as adhesins. Other detected urine-specific proteins are involved in peptide transport (EF0063 and EF3106) and protease inhibition (EF3054). In addition, we found an uncharacterized protein (EF0764), which had not previously been linked to the adaptation of V583 to a urine environment, and which is unique to E. faecalis. Proteins found in both environments included a histone-like protein, EF1550, that was up-regulated during cultivation in urine and that has a homologue in streptococci (HlpA) known to be involved in bacterial adhesion to host cells. Up-regulated secreted proteins included autolysins. These results from secretome analyses are largely compatible with previously published data from transcriptomics studies. All in all, the present data indicate that transport, in particular metal transport, adhesion, cell wall remodelling and the unknown function carried out by the unique EF0764 are important for enterococcal adaptation to the urine environment. These results provide a basis for a more targeted exploration of novel proteins involved in the adaptability and pathogenicity of E. faecalis.
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Affiliation(s)
- Magnus Øverlie Arntzen
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, N-1432 Ås, Norway
- * E-mail:
| | - Ingrid Lea Karlskås
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, N-1432 Ås, Norway
| | - Morten Skaugen
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, N-1432 Ås, Norway
| | - Vincent G. H. Eijsink
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, N-1432 Ås, Norway
| | - Geir Mathiesen
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, N-1432 Ås, Norway
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48
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Novel developments in the prevention, diagnosis, and treatment of periprosthetic joint infections. J Am Acad Orthop Surg 2015; 23 Suppl:S32-43. [PMID: 25808968 DOI: 10.5435/jaaos-d-14-00455] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Periprosthetic joint infection (PJI) is one of the most challenging complications compromising the outcome of an otherwise successful operation. Considerable efforts have been invested in the recent years to address paradigm shifts in our understanding of the complex microbiological phenomena that contribute to the pathophysiology of PJI, such as microbial adherence, biofilm formation, and resistance to antibiotics. This article is an introduction to some of the recent advancements in the prevention, diagnosis, and treatment of PJI. It describes how industry, academic researchers, and government are increasing collaboration to address PJI through development of novel technologies, therapeutic strategies, and regulatory science that specifically target the unique biofilm-associated aspects of its pathogenesis.
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49
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Yang P, Liu K. Activity-based protein profiling: recent advances in probe development and applications. Chembiochem 2015; 16:712-24. [PMID: 25652106 DOI: 10.1002/cbic.201402582] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Indexed: 11/08/2022]
Abstract
The completion of the human genome sequencing project has provided a wealth of new information regarding the genomic blueprint of the cell. Although, to date, there are roughly 20,000 genes in the human genome, the functions of only a handful of proteins are clear. The major challenge lies in translating genomic information into an understanding of their cellular functions. The recently developed activity-based protein profiling (ABPP) is an unconventional approach that is complementary for gene expression analysis and an ideal utensil in decoding this overflow of genomic information. This approach makes use of synthetic small molecules that covalently modify a set of related proteins and subsequently facilitates identification of the target protein, enabling rapid biochemical analysis and inhibitor discovery. This tutorial review introduces recent advances in the field of ABPP and its applications.
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Affiliation(s)
- Pengyu Yang
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037 (USA)
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50
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Activity-based protein profiling of microbes. Curr Opin Chem Biol 2014; 24:139-44. [PMID: 25531039 DOI: 10.1016/j.cbpa.2014.10.022] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 10/24/2014] [Accepted: 10/27/2014] [Indexed: 12/22/2022]
Abstract
Activity-based protein profiling (ABPP) in conjunction with multimodal characterization techniques has yielded impactful findings in microbiology, particularly in pathogen, bioenergy, drug discovery, and environmental research. Using small molecule chemical probes that react irreversibly with specific proteins or protein families in complex systems has provided insights in enzyme functions in central metabolic pathways, drug-protein interactions, and regulatory protein redox, for systems ranging from photoautotrophic cyanobacteria to mycobacteria, and combining live cell or cell extract ABPP with proteomics, molecular biology, modeling, and other techniques has greatly expanded our understanding of these systems. New opportunities for application of ABPP to microbial systems can enhance protein annotation, characterize protein activities in myriad environments, and reveal signal transduction and regulatory mechanisms in microbial systems.
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