1
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Birch-Price Z, Hardy FJ, Lister TM, Kohn AR, Green AP. Noncanonical Amino Acids in Biocatalysis. Chem Rev 2024; 124:8740-8786. [PMID: 38959423 DOI: 10.1021/acs.chemrev.4c00120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
In recent years, powerful genetic code reprogramming methods have emerged that allow new functional components to be embedded into proteins as noncanonical amino acid (ncAA) side chains. In this review, we will illustrate how the availability of an expanded set of amino acid building blocks has opened a wealth of new opportunities in enzymology and biocatalysis research. Genetic code reprogramming has provided new insights into enzyme mechanisms by allowing introduction of new spectroscopic probes and the targeted replacement of individual atoms or functional groups. NcAAs have also been used to develop engineered biocatalysts with improved activity, selectivity, and stability, as well as enzymes with artificial regulatory elements that are responsive to external stimuli. Perhaps most ambitiously, the combination of genetic code reprogramming and laboratory evolution has given rise to new classes of enzymes that use ncAAs as key catalytic elements. With the framework for developing ncAA-containing biocatalysts now firmly established, we are optimistic that genetic code reprogramming will become a progressively more powerful tool in the armory of enzyme designers and engineers in the coming years.
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Affiliation(s)
- Zachary Birch-Price
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Florence J Hardy
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Thomas M Lister
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Anna R Kohn
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Anthony P Green
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
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2
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Mendive‐Tapia L, Miret‐Casals L, Barth ND, Wang J, de Bray A, Beltramo M, Robert V, Ampe C, Hodson DJ, Madder A, Vendrell M. Acid-Resistant BODIPY Amino Acids for Peptide-Based Fluorescence Imaging of GPR54 Receptors in Pancreatic Islets. Angew Chem Int Ed Engl 2023; 62:e202302688. [PMID: 36917014 PMCID: PMC10947197 DOI: 10.1002/anie.202302688] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/09/2023] [Accepted: 03/14/2023] [Indexed: 03/15/2023]
Abstract
The G protein-coupled kisspeptin receptor (GPR54 or KISS1R) is an important mediator in reproduction, metabolism and cancer biology; however, there are limited fluorescent probes or antibodies for direct imaging of these receptors in cells and intact tissues, which can help to interrogate their multiple biological roles. Herein, we describe the rational design and characterization of a new acid-resistant BODIPY-based amino acid (Trp-BODIPY PLUS), and its implementation for solid-phase synthesis of fluorescent bioactive peptides. Trp-BODIPY PLUS retains the binding capabilities of both short linear and cyclic peptides and displays notable turn-on fluorescence emission upon target binding for wash-free imaging. Finally, we employed Trp-BODIPY PLUS to prepare some of the first fluorogenic kisspeptin-based probes and visualized the expression and localization of GPR54 receptors in human cells and in whole mouse pancreatic islets by fluorescence imaging.
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Affiliation(s)
| | - Laia Miret‐Casals
- Department of Organic and Macromolecular ChemistryFaculty of SciencesGhent University9000GhentBelgium
| | - Nicole D. Barth
- Centre for Inflammation ResearchThe University of EdinburghEH16 4TJEdinburghUK
| | - Jinling Wang
- Centre for Inflammation ResearchThe University of EdinburghEH16 4TJEdinburghUK
| | - Anne de Bray
- Oxford Centre for DiabetesEndocrinology and Metabolism (OCDEM)Radcliffe Department of MedicineUniversity of OxfordOX3 7LEOxfordUK
| | - Massimiliano Beltramo
- Equipe Neuroendocrinologie Moleculaire de la ReproductionPhysiologie de la Reproduction et des ComportementsCentre INRA Val de Loire37380NouzillyFrance
| | - Vincent Robert
- Equipe Neuroendocrinologie Moleculaire de la ReproductionPhysiologie de la Reproduction et des ComportementsCentre INRA Val de Loire37380NouzillyFrance
| | - Christophe Ampe
- Department of Biomolecular MedicineFaculty of Medicine and Health SciencesGhent University9052GhentBelgium
| | - David J. Hodson
- Oxford Centre for DiabetesEndocrinology and Metabolism (OCDEM)Radcliffe Department of MedicineUniversity of OxfordOX3 7LEOxfordUK
| | - Annemieke Madder
- Department of Organic and Macromolecular ChemistryFaculty of SciencesGhent University9000GhentBelgium
| | - Marc Vendrell
- Centre for Inflammation ResearchThe University of EdinburghEH16 4TJEdinburghUK
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3
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Mendive‐Tapia L, Miret‐Casals L, Barth ND, Wang J, de Bray A, Beltramo M, Robert V, Ampe C, Hodson DJ, Madder A, Vendrell M. Acid-Resistant BODIPY Amino Acids for Peptide-Based Fluorescence Imaging of GPR54 Receptors in Pancreatic Islets. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202302688. [PMID: 38516305 PMCID: PMC10952496 DOI: 10.1002/ange.202302688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Indexed: 03/17/2023]
Abstract
The G protein-coupled kisspeptin receptor (GPR54 or KISS1R) is an important mediator in reproduction, metabolism and cancer biology; however, there are limited fluorescent probes or antibodies for direct imaging of these receptors in cells and intact tissues, which can help to interrogate their multiple biological roles. Herein, we describe the rational design and characterization of a new acid-resistant BODIPY-based amino acid (Trp-BODIPY PLUS), and its implementation for solid-phase synthesis of fluorescent bioactive peptides. Trp-BODIPY PLUS retains the binding capabilities of both short linear and cyclic peptides and displays notable turn-on fluorescence emission upon target binding for wash-free imaging. Finally, we employed Trp-BODIPY PLUS to prepare some of the first fluorogenic kisspeptin-based probes and visualized the expression and localization of GPR54 receptors in human cells and in whole mouse pancreatic islets by fluorescence imaging.
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Affiliation(s)
| | - Laia Miret‐Casals
- Department of Organic and Macromolecular ChemistryFaculty of SciencesGhent University9000GhentBelgium
| | - Nicole D. Barth
- Centre for Inflammation ResearchThe University of EdinburghEH16 4TJEdinburghUK
| | - Jinling Wang
- Centre for Inflammation ResearchThe University of EdinburghEH16 4TJEdinburghUK
| | - Anne de Bray
- Oxford Centre for DiabetesEndocrinology and Metabolism (OCDEM)Radcliffe Department of MedicineUniversity of OxfordOX3 7LEOxfordUK
| | - Massimiliano Beltramo
- Equipe Neuroendocrinologie Moleculaire de la ReproductionPhysiologie de la Reproduction et des ComportementsCentre INRA Val de Loire37380NouzillyFrance
| | - Vincent Robert
- Equipe Neuroendocrinologie Moleculaire de la ReproductionPhysiologie de la Reproduction et des ComportementsCentre INRA Val de Loire37380NouzillyFrance
| | - Christophe Ampe
- Department of Biomolecular MedicineFaculty of Medicine and Health SciencesGhent University9052GhentBelgium
| | - David J. Hodson
- Oxford Centre for DiabetesEndocrinology and Metabolism (OCDEM)Radcliffe Department of MedicineUniversity of OxfordOX3 7LEOxfordUK
| | - Annemieke Madder
- Department of Organic and Macromolecular ChemistryFaculty of SciencesGhent University9000GhentBelgium
| | - Marc Vendrell
- Centre for Inflammation ResearchThe University of EdinburghEH16 4TJEdinburghUK
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4
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Incorporation of Non-Canonical Amino Acids into Antimicrobial Peptides: Advances, Challenges, and Perspectives. Appl Environ Microbiol 2022; 88:e0161722. [PMID: 36416555 PMCID: PMC9746297 DOI: 10.1128/aem.01617-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The emergence of antimicrobial resistance is a global health concern and calls for the development of novel antibiotic agents. Antimicrobial peptides seem to be promising candidates due to their diverse sources, mechanisms of action, and physicochemical characteristics, as well as the relatively low emergence of resistance. The incorporation of noncanonical amino acids into antimicrobial peptides could effectively improve their physicochemical and pharmacological diversity. Recently, various antimicrobial peptides variants with improved or novel properties have been produced by the incorporation of single and multiple distinct noncanonical amino acids. In this review, we summarize strategies for the incorporation of noncanonical amino acids into antimicrobial peptides, as well as their features and suitabilities. Recent applications of noncanonical amino acid incorporation into antimicrobial peptides are also presented. Finally, we discuss the related challenges and prospects.
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5
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Werner M, Pampel J, Pham TL, Thomas F. Late‐Stage Functionalisation of Peptides on the Solid Phase by an Iodination‐Substitution Approach. Chemistry 2022; 28:e202201339. [PMID: 35700354 PMCID: PMC9545490 DOI: 10.1002/chem.202201339] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Indexed: 11/20/2022]
Abstract
The functionalisation of peptides at a late synthesis stage holds great potential, for example, for the synthesis of peptide pharmaceuticals, fluorescent biosensors or peptidomimetics. Here we describe an on‐resin iodination‐substitution reaction sequence on homoserine that is also suitable for peptide modification in a combinatorial format. The reaction sequence is accessible to a wide range of sulfur nucleophiles with various functional groups including boronic acids, hydroxy groups or aromatic amines. In this way, methionine‐like thioethers or thioesters and thiosulfonates are accessible. Next to sulfur nucleophiles, selenols, pyridines and carboxylic acids were successfully used as nucleophiles, whereas phenols did not react. The late‐stage iodination‐substitution approach is not only applicable to short peptides but also to the more complex 34‐amino‐acid WW domains. We applied this strategy to introduce 7‐mercapto‐4‐methylcoumarin into a switchable ZnII responsive WW domain to design an iFRET‐based ZnII sensor.
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Affiliation(s)
- Marius Werner
- Institute of Organic Chemistry Heidelberg University Im Neuenheimer Feld 270 69120 Heidelberg Germany
- Centre for Advanced Materials (CAM) Heidelberg University Im Neuenheimer Feld 225 69120 Heidelberg Germany
- Department of Medicinal Chemistry Institute of Pharmacy and Molecular Biotechnology (IPMB) Heidelberg University Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Julius Pampel
- Department of Chemical Biology Max Planck Institute for Medical Research Jahnstraße 29 69120 Heidelberg Germany
| | - Truc Lam Pham
- Institute of Organic Chemistry Heidelberg University Im Neuenheimer Feld 270 69120 Heidelberg Germany
- Centre for Advanced Materials (CAM) Heidelberg University Im Neuenheimer Feld 225 69120 Heidelberg Germany
| | - Franziska Thomas
- Institute of Organic Chemistry Heidelberg University Im Neuenheimer Feld 270 69120 Heidelberg Germany
- Centre for Advanced Materials (CAM) Heidelberg University Im Neuenheimer Feld 225 69120 Heidelberg Germany
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6
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Wu Y, Chau H, Yeung Y, Thor W, Kai H, Chan W, Wong K. Versatile Synthesis of Multivalent Porphyrin–Peptide Conjugates by Direct Porphyrin Construction on Resin. Angew Chem Int Ed Engl 2022; 61:e202207532. [PMID: 35730925 PMCID: PMC9543522 DOI: 10.1002/anie.202207532] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Indexed: 11/17/2022]
Abstract
Multifunctional porphyrin–peptide conjugates with different propensities for self‐assembly into various supramolecular nanoarchitectures play important roles in advanced materials and biomedical research. However, preparing prefunctionalized core porphyrins by traditional low‐yielding statistical synthesis and purifying them after peptide ligation through many rounds of HPLC purification is tedious and unsustainable. Herein, we report a novel integrated solid‐phase synthetic protocol for the construction of porphyrin moieties from simple aldehydes and dipyrromethanes on resin‐bound peptides directly to form mono‐, cis/trans‐di‐, and trivalent porphyrin–peptide conjugates in a highly efficient and controllable manner; moreover, only single final‐stage HPLC purification of the products is needed. This efficient strategy enables the rapid, greener, and substrate‐controlled diversity‐oriented synthesis of multivalent porphyrin–(long) peptide conjugate libraries for multifarious biological and materials applications.
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Affiliation(s)
- Yue Wu
- Department of Chemistry Hong Kong Baptist University 224 Waterloo Rd Kowloon Tong, Kowloon, Hong Kong SAR China
| | - Ho‐Fai Chau
- Department of Chemistry Hong Kong Baptist University 224 Waterloo Rd Kowloon Tong, Kowloon, Hong Kong SAR China
| | - Yik‐Hoi Yeung
- Department of Chemistry Hong Kong Baptist University 224 Waterloo Rd Kowloon Tong, Kowloon, Hong Kong SAR China
| | - Waygen Thor
- Department of Chemistry Hong Kong Baptist University 224 Waterloo Rd Kowloon Tong, Kowloon, Hong Kong SAR China
| | - Hei‐Yui Kai
- Department of Chemistry Hong Kong Baptist University 224 Waterloo Rd Kowloon Tong, Kowloon, Hong Kong SAR China
| | - Wai‐Lun Chan
- Department of Applied Biology and Chemical Technology The Hong Kong Polytechnic University Hung Hom, Hong Kong SAR China
| | - Ka‐Leung Wong
- Department of Chemistry Hong Kong Baptist University 224 Waterloo Rd Kowloon Tong, Kowloon, Hong Kong SAR China
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7
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Li X, Xie C, Zha S, Tam WS, Jiang M, Wong KL. Biocompatible Porphyrin-Peptide Conjugates as Theranostic Agents Targeting the Epstein-Barr Virus. Chempluschem 2022; 87:e202200184. [PMID: 36036545 DOI: 10.1002/cplu.202200184] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 08/03/2022] [Indexed: 02/18/2024]
Abstract
Epstein-Barr virus (EBV) is a common human-infected virus related to many diseases and cancers. Recently, some peptides have been found to serve targeting and therapeutic roles by inhibiting EBNA1, an oncoprotein of the EBV. We herein report the conjugation of the EBNA1-targeting peptides and porphyrins which can bring synergistic effects by both introducing more specific treatments (photodynamic therapy) and improving the biocompatibility of the photosensitizer and the peptides. One of our compounds exhibited significant photo-cytotoxicity where the Lethal Concentration 50 (LC50 )=6.1 μM in EBV-positive cells. Besides, in vitro cell imaging and co-staining can also be achieved simultaneously and suggested the binding inside nucleus.
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Affiliation(s)
- Xiong Li
- Department of Chemistry, Hong Kong Baptist University Kowloon, Hong Kong S.A.R., P. R. China
| | - Chen Xie
- Department of Chemistry, Hong Kong Baptist University Kowloon, Hong Kong S.A.R., P. R. China
| | - Shuai Zha
- Department of Chemistry, Hong Kong Baptist University Kowloon, Hong Kong S.A.R., P. R. China
| | - Wing Sze Tam
- Department of Chemistry, Hong Kong Baptist University Kowloon, Hong Kong S.A.R., P. R. China
| | - Mingjun Jiang
- Department of Chemistry, Hong Kong Baptist University Kowloon, Hong Kong S.A.R., P. R. China
| | - Ka-Leung Wong
- Department of Chemistry, Hong Kong Baptist University Kowloon, Hong Kong S.A.R., P. R. China
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8
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Dey S, Rout AK, Behera BK, Ghosh K. Plastisphere community assemblage of aquatic environment: plastic-microbe interaction, role in degradation and characterization technologies. ENVIRONMENTAL MICROBIOME 2022; 17:32. [PMID: 35739580 PMCID: PMC9230103 DOI: 10.1186/s40793-022-00430-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/14/2022] [Indexed: 05/03/2023]
Abstract
It is undeniable that plastics are ubiquitous and a threat to global ecosystems. Plastic waste is transformed into microplastics (MPs) through physical and chemical disruption processes within the aquatic environment. MPs are detected in almost every environment due to their worldwide transportability through ocean currents or wind, which allows them to reach even the most remote regions of our planet. MPs colonized by biofilm-forming microbial communities are known as the ''plastisphere". The revelation that this unique substrate can aid microbial dispersal has piqued interest in the ground of microbial ecology. MPs have synergetic effects on the development, transportation, persistence, and ecology of microorganisms. This review summarizes the studies of plastisphere in recent years and the microbial community assemblage (viz. autotrophs, heterotrophs, predators, and pathogens). We also discussed plastic-microbe interactions and the potential sources of plastic degrading microorganisms. Finally, it also focuses on current technologies used to characterize those microbial inhabitants and recommendations for further research.
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Affiliation(s)
- Sujata Dey
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, 700120, India
| | - Ajaya Kumar Rout
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, 700120, India
| | - Bijay Kumar Behera
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, 700120, India.
| | - Koushik Ghosh
- Aquaculture Laboratory, Department of Zoology, The University of Burdwan, Golapbag, Burdwan, West Bengal, 713104, India.
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9
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Wu Y, Chau HF, Yeung YH, Thor W, Kai HY, Chan WL, Wong KL. Versatile Synthesis of Multivalent Porphyrin–Peptide Conjugates by Direct Porphyrin Construction on Resin. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yue Wu
- Hong Kong Baptist University Department of Chemistry 224 Waterloo Rd 000000 Kowloon Tong HONG KONG
| | - Ho-Fai Chau
- Hong Kong Baptist University Department of Chemistry 224 Waterloo Rd Kowloon Tong HONG KONG
| | - Yik-Hoi Yeung
- Hong Kong Baptist University Department of Chemistry 224 Waterloo Rd 000000 Kowloon Tong HONG KONG
| | - Waygen Thor
- Hong Kong Baptist University Department of Chemistry 224 Waterloo Rd 000000 Kowloon Tong HONG KONG
| | - Hei-Yui Kai
- Hong Kong Baptist University Department of Chemistry 224 Waterloo Rd 000000 Kowloon Tong HONG KONG
| | - Wai-Lun Chan
- The Hong Kong Polytechnic University Department of Applied Biology and Chemical Technology 11 Yuk Choi Rd 000000 Hung Hom HONG KONG
| | - Ka-Leung Wong
- Hong Kong Baptist University Department of Chemistry Kowloon Tong Nil Hong Kong HONG KONG
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10
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Roy SK, Purkait A, Shome R, Das S, Das D, Ghosh SS, Jana CK. Proline selective labeling via on-site construction of naphthoxazole (NapOx). Chem Commun (Camb) 2022; 58:5909-5912. [PMID: 35475487 DOI: 10.1039/d2cc01268e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chemoselective construction of naphthoxazoles (NapOx) via a three-component annulation reaction enables proline selective labeling of peptides in solution or in solid-phase synthesis. The fluorogenic peptides possess low cytotoxicity, efficient cell membrane permeability and excellent bioimaging potential for biomedical applications.
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Affiliation(s)
- Subhra Kanti Roy
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, India.
| | - Anisha Purkait
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, India.
| | - Rajib Shome
- Department of Biosciences and Engineering, Indian Institute of Technology Guwahati, 781039, India
| | - Saurav Das
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, India.
| | - Debapratim Das
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, India.
| | - Siddhartha Sankar Ghosh
- Department of Biosciences and Engineering, Indian Institute of Technology Guwahati, 781039, India
| | - Chandan K Jana
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, India.
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11
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Mendive‐Tapia L, Mendive‐Tapia D, Zhao C, Gordon D, Benson S, Bromley MJ, Wang W, Wu J, Kopp A, Ackermann L, Vendrell M. Rationales Design von Phe-BODIPY-Aminosäuren als fluorogene Bausteine für den peptidbasierten Nachweis von Candida-Infektionen im Harntrakt. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202117218. [PMID: 38505242 PMCID: PMC10946803 DOI: 10.1002/ange.202117218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Indexed: 11/08/2022]
Abstract
AbstractPilzinfektionen, die durch Candida‐Arten verursacht werden, gehören zu den häufigsten Infektionen bei Krankenhauspatienten. Die derzeitigen Methoden zum Nachweis von Candida‐Pilzzellen in klinischen Proben beruhen jedoch auf zeitaufwändigen Analysen, die eine schnelle und zuverlässige Diagnose erschweren. In diesem Beitrag beschreiben wir die rationale Entwicklung neuer Phe‐BODIPY‐Aminosäuren als kleine fluorogene Bausteine und ihre Anwendung zur Erzeugung fluoreszierender antimikrobieller Peptide für die schnelle Markierung von Candida‐Zellen im Urin. Mit Hilfe von computergestützten Berechnungen haben wir das fluorogene Verhalten von BODIPY‐substituierten aromatischen Aminosäuren analysiert und Bioaktivitäts‐ und konfokale Mikroskopieexperimente bei verschiedenen Stämmen durchgeführt, um den Nutzen und die Vielseitigkeit von Peptiden mit Phe‐BODIPYs zu bestätigen. Schließlich haben wir einen einfachen und sensitiven fluoreszensbasierten Test zum Nachweis von Candida albicans in menschlichen Urinproben entwickelt.
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Affiliation(s)
- Lorena Mendive‐Tapia
- Zentrum für EntzündungsforschungDie Universität von EdinburghEH16 4TJEdinburghGroßbritannien
| | - David Mendive‐Tapia
- Abteilung Theoretische ChemiePhysikalisch-Chemisches InstitutUniversität Heidelberg69120HeidelbergDeutschland
| | - Can Zhao
- Manchester Fungal Infection GroupAbteilung für EvolutionInfektion und GenomikM139NTManchesterGroßbritannien
| | - Doireann Gordon
- Zentrum für EntzündungsforschungDie Universität von EdinburghEH16 4TJEdinburghGroßbritannien
| | - Sam Benson
- Zentrum für EntzündungsforschungDie Universität von EdinburghEH16 4TJEdinburghGroßbritannien
| | - Michael J. Bromley
- Manchester Fungal Infection GroupAbteilung für EvolutionInfektion und GenomikM139NTManchesterGroßbritannien
| | - Wei Wang
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität37077GöttingenDeutschland
| | - Jun Wu
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität37077GöttingenDeutschland
| | - Adelina Kopp
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität37077GöttingenDeutschland
| | - Lutz Ackermann
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität37077GöttingenDeutschland
| | - Marc Vendrell
- Zentrum für EntzündungsforschungDie Universität von EdinburghEH16 4TJEdinburghGroßbritannien
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12
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Mendive‐Tapia L, Mendive‐Tapia D, Zhao C, Gordon D, Benson S, Bromley MJ, Wang W, Wu J, Kopp A, Ackermann L, Vendrell M. Rational Design of Phe‐BODIPY Amino Acids as Fluorogenic Building Blocks for Peptide‐Based Detection of Urinary Tract
Candida
Infections. Angew Chem Int Ed Engl 2022; 61:e202117218. [PMID: 35075763 PMCID: PMC9305947 DOI: 10.1002/anie.202117218] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Indexed: 12/11/2022]
Abstract
Fungal infections caused by Candida species are among the most prevalent in hospitalized patients. However, current methods for the detection of Candida fungal cells in clinical samples rely on time‐consuming assays that hamper rapid and reliable diagnosis. Herein, we describe the rational development of new Phe‐BODIPY amino acids as small fluorogenic building blocks and their application to generate fluorescent antimicrobial peptides for rapid labelling of Candida cells in urine. We have used computational methods to analyse the fluorogenic behaviour of BODIPY‐substituted aromatic amino acids and performed bioactivity and confocal microscopy experiments in different strains to confirm the utility and versatility of peptides incorporating Phe‐BODIPYs. Finally, we have designed a simple and sensitive fluorescence‐based assay for the detection of Candida albicans in human urine samples.
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Affiliation(s)
- Lorena Mendive‐Tapia
- Centre for Inflammation Research The University of Edinburgh EH16 4TJ Edinburgh UK
| | - David Mendive‐Tapia
- Department Theoretische Chemie Physikalisch-Chemisches Institut Universität Heidelberg 69120 Heidelberg Germany
| | - Can Zhao
- Manchester Fungal Infection Group Division of Evolution Infection and Genomics University of Manchester M139NT Manchester UK
| | - Doireann Gordon
- Centre for Inflammation Research The University of Edinburgh EH16 4TJ Edinburgh UK
| | - Sam Benson
- Centre for Inflammation Research The University of Edinburgh EH16 4TJ Edinburgh UK
| | - Michael J. Bromley
- Manchester Fungal Infection Group Division of Evolution Infection and Genomics University of Manchester M139NT Manchester UK
| | - Wei Wang
- Institut für Organische und Biomolekulare Chemie Georg-August-Universität 37077 Göttingen Germany
| | - Jun Wu
- Institut für Organische und Biomolekulare Chemie Georg-August-Universität 37077 Göttingen Germany
| | - Adelina Kopp
- Institut für Organische und Biomolekulare Chemie Georg-August-Universität 37077 Göttingen Germany
| | - Lutz Ackermann
- Institut für Organische und Biomolekulare Chemie Georg-August-Universität 37077 Göttingen Germany
| | - Marc Vendrell
- Centre for Inflammation Research The University of Edinburgh EH16 4TJ Edinburgh UK
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13
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Du Y, Liu X, Dong X, Yin Z. A review on marine plastisphere: biodiversity, formation, and role in degradation. Comput Struct Biotechnol J 2022; 20:975-988. [PMID: 35242288 PMCID: PMC8861569 DOI: 10.1016/j.csbj.2022.02.008] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/11/2022] [Accepted: 02/11/2022] [Indexed: 12/20/2022] Open
Abstract
The pollution of plastic waste has become an increasingly serious environmental crisis. Recently, plastic has been detected in various kinds of environments, even in human tissues, which is an increasing threat to the ecosystems and humans. In the ocean, the plastic waste is eventually fragmentized into microplastics (MPs) under the disruption of physical and chemical processes. MPs are colonized by microbial communities such as fungi, diatoms, and bacteria, which form biofilms on the surface of the plastic called “plastisphere”. In this review, we summarize the studies related to microorganisms in the plastisphere in recent years and describe the microbial species in the plastisphere, mainly including bacteria, fungi, and autotrophs. Secondly, we explore the interactions between MPs and the plastisphere. The depth of MPs in the ocean and the nutrients in the surrounding seawater can have a great impact on the community structure of microorganisms in the plastisphere. Finally, we discuss the types of MP-degrading bacteria in the ocean, and use the “seed bank” theory to speculate on the potential sources of MP-degrading microorganisms. Challenges and future research prospects are also discussed.
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Affiliation(s)
- Yuhui Du
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, PR China
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, PR China
| | - Xinbei Liu
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Tai’an, PR China
| | - Xusheng Dong
- Ruminant Nutrition and Physiology Laboratory, College of Animal Science and Technology, Shandong Agricultural University, Tai’an, PR China
| | - Zhiqiu Yin
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Tai’an, PR China
- Corresponding author.
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14
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Lam PL, Wu Y, Wong KL. Incorporation of Fmoc-Dab(Mtt)-OH during solid-phase peptide synthesis: a word of caution. Org Biomol Chem 2022; 20:2601-2604. [DOI: 10.1039/d2ob00070a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
As a commercially available and orthogonally protected amino acid building block, Fmoc-Dab(Mtt)-OH showed abnormally poor coupling efficiency during solid-phase peptide synthesis (SPPS).
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Affiliation(s)
- Pak-Lun Lam
- Department of Chemistry, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Yue Wu
- Department of Chemistry, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Ka-Leung Wong
- Department of Chemistry, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
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15
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Chavda J, Bhavsar K, Gupta S, Gupta I. BODIPY-peptide conjugate: Synthesis, photo-physical and cell viability studies. J PORPHYR PHTHALOCYA 2021. [DOI: 10.1142/s1088424621501261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The synthesis and biological studies of BODIPY-GPR peptide conjugate (BD-2) are reported. As compared to the parent BODIPY (BD-1), the peptide linked BD-2showed blue shifted absorption and emission with excellent Stokes shift of 201 nm. Molecular docking studies on EGFR protein kinase indicated very efficient binding affinity of BD-2 as compared to the standard drug (Erlotinib). The cell viability experiments of BD-2on normal (HEK293T) and lung cancer (A549) cell lines indicated 85–95% viability. Bioimaging studies showed that, BD-2was able to penetrate the lung cancer cell line.
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Affiliation(s)
- Jaydeepsinh Chavda
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj Campus, Gandhinagar, Gujarat-382355, India
| | - Krishna Bhavsar
- Department of Biological Engineering, IIT Gandhinagar, Palaj Campus, Gandhinagar, Gujarat-382355, India
| | - Sharad Gupta
- Department of Biological Engineering, IIT Gandhinagar, Palaj Campus, Gandhinagar, Gujarat-382355, India
| | - Iti Gupta
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj Campus, Gandhinagar, Gujarat-382355, India
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16
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Lechner VM, Nappi M, Deneny PJ, Folliet S, Chu JCK, Gaunt MJ. Visible-Light-Mediated Modification and Manipulation of Biomacromolecules. Chem Rev 2021; 122:1752-1829. [PMID: 34546740 DOI: 10.1021/acs.chemrev.1c00357] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chemically modified biomacromolecules-i.e., proteins, nucleic acids, glycans, and lipids-have become crucial tools in chemical biology. They are extensively used not only to elucidate cellular processes but also in industrial applications, particularly in the context of biopharmaceuticals. In order to enable maximum scope for optimization, it is pivotal to have a diverse array of biomacromolecule modification methods at one's disposal. Chemistry has driven many significant advances in this area, and especially recently, numerous novel visible-light-induced photochemical approaches have emerged. In these reactions, light serves as an external source of energy, enabling access to highly reactive intermediates under exceedingly mild conditions and with exquisite spatiotemporal control. While UV-induced transformations on biomacromolecules date back decades, visible light has the unmistakable advantage of being considerably more biocompatible, and a spectrum of visible-light-driven methods is now available, chiefly for proteins and nucleic acids. This review will discuss modifications of native functional groups (FGs), including functionalization, labeling, and cross-linking techniques as well as the utility of oxidative degradation mediated by photochemically generated reactive oxygen species. Furthermore, transformations at non-native, bioorthogonal FGs on biomacromolecules will be addressed, including photoclick chemistry and DNA-encoded library synthesis as well as methods that allow manipulation of the activity of a biomacromolecule.
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Affiliation(s)
- Vivian M Lechner
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Manuel Nappi
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Patrick J Deneny
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Sarah Folliet
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - John C K Chu
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Matthew J Gaunt
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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17
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Wu Y, Chau H, Thor W, Chan KHY, Ma X, Chan W, Long NJ, Wong K. Solid-Phase Peptide Macrocyclization and Multifunctionalization via Dipyrrin Construction. Angew Chem Int Ed Engl 2021; 60:20301-20307. [PMID: 34272794 PMCID: PMC8457249 DOI: 10.1002/anie.202108885] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Indexed: 11/11/2022]
Abstract
We introduce a new and highly efficient synthetic protocol towards multifunctional fluorescent cyclopeptides by solid-phase peptide macrocyclization via dipyrrin construction, with full scope of proteinogenic amino acids and different ring sizes. Various bicyclic peptides can be created by dipyrrin-based crosslinking and double dipyrrin-ring formation. The embedded dipyrrin can be either transformed to fluorescent BODIPY and then utilized as cancer-selective targeted protein imaging probe in vitro, or directly employed as a selective metal sensor in aqueous media. This work provides a valuable addition to the peptide macrocyclization toolbox, and a blueprint for the development of multifunctional dipyrrin linkers in cyclopeptides for a wide range of potential bioapplications.
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Affiliation(s)
- Yue Wu
- Department of ChemistryHong Kong Baptist UniversityKowloon TongKowloonHong Kong SARChina
| | - Ho‐Fai Chau
- Department of ChemistryHong Kong Baptist UniversityKowloon TongKowloonHong Kong SARChina
| | - Waygen Thor
- Department of ChemistryHong Kong Baptist UniversityKowloon TongKowloonHong Kong SARChina
| | - Kaitlin Hao Yi Chan
- Department of ChemistryHong Kong Baptist UniversityKowloon TongKowloonHong Kong SARChina
- Department of Applied Biology and Chemical TechnologyHong Kong Polytechnic UniversityHung HomHong Kong SARChina
| | - Xia Ma
- Department of ChemistryHong Kong Baptist UniversityKowloon TongKowloonHong Kong SARChina
| | - Wai‐Lun Chan
- Department of Applied Biology and Chemical TechnologyHong Kong Polytechnic UniversityHung HomHong Kong SARChina
| | - Nicholas J. Long
- Department of ChemistryImperial College London, Molecular Sciences Research HubLondonUK
| | - Ka‐Leung Wong
- Department of ChemistryHong Kong Baptist UniversityKowloon TongKowloonHong Kong SARChina
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18
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Wu Y, Chau H, Thor W, Chan KHY, Ma X, Chan W, Long NJ, Wong K. Solid‐Phase Peptide Macrocyclization and Multifunctionalization via Dipyrrin Construction. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202108885] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Yue Wu
- Department of Chemistry Hong Kong Baptist University Kowloon Tong Kowloon Hong Kong SAR China
| | - Ho‐Fai Chau
- Department of Chemistry Hong Kong Baptist University Kowloon Tong Kowloon Hong Kong SAR China
| | - Waygen Thor
- Department of Chemistry Hong Kong Baptist University Kowloon Tong Kowloon Hong Kong SAR China
| | - Kaitlin Hao Yi Chan
- Department of Chemistry Hong Kong Baptist University Kowloon Tong Kowloon Hong Kong SAR China
- Department of Applied Biology and Chemical Technology Hong Kong Polytechnic University Hung Hom Hong Kong SAR China
| | - Xia Ma
- Department of Chemistry Hong Kong Baptist University Kowloon Tong Kowloon Hong Kong SAR China
| | - Wai‐Lun Chan
- Department of Applied Biology and Chemical Technology Hong Kong Polytechnic University Hung Hom Hong Kong SAR China
| | - Nicholas J. Long
- Department of Chemistry Imperial College London, Molecular Sciences Research Hub London UK
| | - Ka‐Leung Wong
- Department of Chemistry Hong Kong Baptist University Kowloon Tong Kowloon Hong Kong SAR China
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19
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Liu D, Wen L, Chen X, Yan J, Zheng K, Liu X, Hu Y, Zhang N. Substituent effects on opticalproperties of pyrrolizine-fused BOPYIN. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 254:119681. [PMID: 33744704 DOI: 10.1016/j.saa.2021.119681] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/22/2021] [Accepted: 03/02/2021] [Indexed: 06/12/2023]
Abstract
Three new pyrrolizine-fused BOPYINs (DAB-H, DAB-OMe, DAB-ester) have been reported in 26-35% yield. The relationship between structures and optical spectra was investigated, which all the compounds show large Stokes Shift (3146-3884 cm-1) and high quantum yield (up to 99%) in solvents. Among these dyes, the decoration of electron donating/withdrawing groups on indole, pyrrole and pyrrolizine units has a significant impact on optical properties, especially emission spectra. The results suggested that electron withdrawing group on pyrrole and pyrrolizine units has hypsochromic shift on emission spectra (DAB-H, DAB-OMe, DAB-ester versus DAB-1,4,5). The optimized structure, electron distribution on frontier molecular orbital, energy gap and simulated stick spectra of DABs are discussed by Density Functional Theory (DFT) calculation. We claim the agreement between the experimental and theoretical absorption spectra.
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Affiliation(s)
- Debao Liu
- College of Materials and Chemical Engineering, Medical College, Key Laboratory of Inorganic Nonmetallic Crystalline and Energy Conversion Materials, China; Three Gorges University, Yichang, Hubei 443002, China
| | - Liu Wen
- College of Materials and Chemical Engineering, Medical College, Key Laboratory of Inorganic Nonmetallic Crystalline and Energy Conversion Materials, China; Three Gorges University, Yichang, Hubei 443002, China
| | - Xi Chen
- College of Materials and Chemical Engineering, Medical College, Key Laboratory of Inorganic Nonmetallic Crystalline and Energy Conversion Materials, China; Three Gorges University, Yichang, Hubei 443002, China
| | - Jiaying Yan
- College of Materials and Chemical Engineering, Medical College, Key Laboratory of Inorganic Nonmetallic Crystalline and Energy Conversion Materials, China; Three Gorges University, Yichang, Hubei 443002, China
| | - Kaibo Zheng
- College of Materials and Chemical Engineering, Medical College, Key Laboratory of Inorganic Nonmetallic Crystalline and Energy Conversion Materials, China; Three Gorges University, Yichang, Hubei 443002, China
| | - Xiang Liu
- College of Materials and Chemical Engineering, Medical College, Key Laboratory of Inorganic Nonmetallic Crystalline and Energy Conversion Materials, China; Three Gorges University, Yichang, Hubei 443002, China
| | - Yuanyuan Hu
- College of Materials and Chemical Engineering, Medical College, Key Laboratory of Inorganic Nonmetallic Crystalline and Energy Conversion Materials, China; Three Gorges University, Yichang, Hubei 443002, China.
| | - Nuonuo Zhang
- College of Materials and Chemical Engineering, Medical College, Key Laboratory of Inorganic Nonmetallic Crystalline and Energy Conversion Materials, China; Three Gorges University, Yichang, Hubei 443002, China.
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