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Nur A, Lai JY, Ch'ng ACW, Choong YS, Wan Isa WYH, Lim TS. A review of in vitro stochastic and non-stochastic affinity maturation strategies for phage display derived monoclonal antibodies. Int J Biol Macromol 2024; 277:134217. [PMID: 39069045 DOI: 10.1016/j.ijbiomac.2024.134217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/24/2024] [Accepted: 07/25/2024] [Indexed: 07/30/2024]
Abstract
Monoclonal antibodies identified using display technologies like phage display occasionally suffers from a lack of affinity making it unsuitable for application. This drawback is circumvented with the application of affinity maturation. Affinity maturation is an essential step in the natural evolution of antibodies in the immune system. The evolution of molecular based methods has seen the development of various mutagenesis approaches. This allows for the natural evolutionary process during somatic hypermutation to be replicated in the laboratories for affinity maturation to fine-tune the affinity and selectivity of antibodies. In this review, we will discuss affinity maturation strategies for mAbs generated through phage display systems. The review will highlight various in vitro stochastic and non-stochastic affinity maturation approaches that includes but are not limited to random mutagenesis, site-directed mutagenesis, and gene synthesis.
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Affiliation(s)
- Alia Nur
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Jing Yi Lai
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Angela Chiew Wen Ch'ng
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Wan Yus Haniff Wan Isa
- School of Medical Sciences, Department of Medicine, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia; Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 Penang, Malaysia.
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2
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Sandei I, Gaule T, Batchelor M, Paci E, Kim YY, Kulak AN, Tomlinson DC, Meldrum FC. Phage display identifies Affimer proteins that direct calcium carbonate polymorph formation. Biomater Sci 2024. [PMID: 39206560 PMCID: PMC11358866 DOI: 10.1039/d4bm00165f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 07/24/2024] [Indexed: 09/04/2024]
Abstract
A key factor in biomineralization is the use of organic molecules to direct the formation of inorganic materials. However, identification of molecules that can selectively produce the calcium carbonate polymorphs calcite or aragonite has proven extremely challenging. Here, we use a phage display approach to identify proteins - rather than the short peptides typically identified using this method - that can direct calcium carbonate formation. A 1.3 × 1010 library of Affimer proteins was displayed on modified M13 phage, where an Affimer is a ≈13 kDa protein scaffold that displays two variable regions of 9-13 residues. The phage displaying the Affimer library were then screened in binding assays against calcite and aragonite at pH 7.4, and four different strongly-binding proteins were identified. The two aragonite-binding proteins generated aragonite when calcium and magnesium ions were present at a 1 : 1 ratio, while the calcite-binding proteins produce magnesium-calcite under the same conditions. Calcite alone formed in the presence of all four proteins in the absence of magnesium ions. In combination with molecular dynamics simulations to evaluate the conformations of the proteins in solution, this work demonstrates the importance of conformation in polymorph control, and highlights the importance of magnesium ions, which are abundant in seawater, to reduce the energetic barriers associated with aragonite formation.
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Affiliation(s)
- Ilaria Sandei
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK.
| | - Thembaninkosi Gaule
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK.
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Matthew Batchelor
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Emanuele Paci
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Yi-Yeoun Kim
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK.
| | | | - Darren C Tomlinson
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Fiona C Meldrum
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK.
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Pierzynowska K, Morcinek-Orłowska J, Gaffke L, Jaroszewicz W, Skowron PM, Węgrzyn G. Applications of the phage display technology in molecular biology, biotechnology and medicine. Crit Rev Microbiol 2024; 50:450-490. [PMID: 37270791 DOI: 10.1080/1040841x.2023.2219741] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 10/17/2022] [Accepted: 05/25/2023] [Indexed: 06/06/2023]
Abstract
The phage display technology is based on the presentation of peptide sequences on the surface of virions of bacteriophages. Its development led to creation of sophisticated systems based on the possibility of the presentation of a huge variability of peptides, attached to one of proteins of bacteriophage capsids. The use of such systems allowed for achieving enormous advantages in the processes of selection of bioactive molecules. In fact, the phage display technology has been employed in numerous fields of biotechnology, as diverse as immunological and biomedical applications (in both diagnostics and therapy), the formation of novel materials, and many others. In this paper, contrary to many other review articles which were focussed on either specific display systems or the use of phage display in selected fields, we present a comprehensive overview of various possibilities of applications of this technology. We discuss an usefulness of the phage display technology in various fields of science, medicine and the broad sense of biotechnology. This overview indicates the spread and importance of applications of microbial systems (exemplified by the phage display technology), pointing to the possibility of developing such sophisticated tools when advanced molecular methods are used in microbiological studies, accompanied with understanding of details of structures and functions of microbial entities (bacteriophages in this case).
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Affiliation(s)
- Karolina Pierzynowska
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | | | - Lidia Gaffke
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Weronika Jaroszewicz
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Piotr M Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdańsk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
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4
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Jahandar-Lashaki S, Farajnia S, Faraji-Barhagh A, Hosseini Z, Bakhtiyari N, Rahbarnia L. Phage Display as a Medium for Target Therapy Based Drug Discovery, Review and Update. Mol Biotechnol 2024:10.1007/s12033-024-01195-6. [PMID: 38822912 DOI: 10.1007/s12033-024-01195-6] [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: 11/01/2023] [Accepted: 05/07/2024] [Indexed: 06/03/2024]
Abstract
Phage libraries are now amongst the most prominent approaches for the identification of high-affinity antibodies/peptides from billions of displayed phages in a specific library through the biopanning process. Due to its ability to discover potential therapeutic candidates that bind specifically to targets, phage display has gained considerable attention in targeted therapy. Using this approach, peptides with high-affinity and specificity can be identified for potential therapeutic or diagnostic use. Furthermore, phage libraries can be used to rapidly screen and identify novel antibodies to develop immunotherapeutics. The Food and Drug Administration (FDA) has approved several phage display-derived peptides and antibodies for the treatment of different diseases. In the current review, we provided a comprehensive insight into the role of phage display-derived peptides and antibodies in the treatment of different diseases including cancers, infectious diseases and neurological disorders. We also explored the applications of phage display in targeted drug delivery, gene therapy, and CAR T-cell.
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Affiliation(s)
- Samaneh Jahandar-Lashaki
- Medical Biotechnology Department, Faculty of Advanced Medical Science, Tabriz University of Medical Sciences, Tabriz, Iran
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Safar Farajnia
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Aref Faraji-Barhagh
- Medical Biotechnology Department, Faculty of Advanced Medical Science, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zahra Hosseini
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Nasim Bakhtiyari
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Leila Rahbarnia
- Infectious and Tropical Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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5
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Rosas-Murrieta NH, Rodríguez-Enríquez A, Herrera-Camacho I, Millán-Pérez-Peña L, Santos-López G, Rivera-Benítez JF. Comparative Review of the State of the Art in Research on the Porcine Epidemic Diarrhea Virus and SARS-CoV-2, Scope of Knowledge between Coronaviruses. Viruses 2024; 16:238. [PMID: 38400014 PMCID: PMC10892376 DOI: 10.3390/v16020238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/17/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024] Open
Abstract
This review presents comparative information corresponding to the progress in knowledge of some aspects of infection by the porcine epidemic diarrhea virus (PEDV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) coronaviruses. PEDV is an alphacoronavirus of great economic importance due to the million-dollar losses it generates in the pig industry. PEDV has many similarities to the SARS-CoV-2 betacoronavirus that causes COVID-19 disease. This review presents possible scenarios for SARS-CoV-2 based on the collected literature on PEDV and the tools or strategies currently developed for SARS-CoV-2 that would be useful in PEDV research. The speed of the study of SARS-CoV-2 and the generation of strategies to control the pandemic was possible due to the knowledge derived from infections caused by other human coronaviruses such as severe acute respiratory syndrome (SARS) and middle east respiratory syndrome (MERS). Therefore, from the information obtained from several coronaviruses, the current and future behavior of SARS-CoV-2 could be inferred and, with the large amount of information on the virus that causes COVID-19, the study of PEDV could be improved and probably that of new emerging and re-emerging coronaviruses.
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Affiliation(s)
- Nora H. Rosas-Murrieta
- Centro de Química, Laboratorio de Bioquímica y Biología Molecular, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico; (A.R.-E.); (I.H.-C.); (L.M.-P.-P.)
| | - Alan Rodríguez-Enríquez
- Centro de Química, Laboratorio de Bioquímica y Biología Molecular, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico; (A.R.-E.); (I.H.-C.); (L.M.-P.-P.)
- Posgrado en Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico
| | - Irma Herrera-Camacho
- Centro de Química, Laboratorio de Bioquímica y Biología Molecular, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico; (A.R.-E.); (I.H.-C.); (L.M.-P.-P.)
| | - Lourdes Millán-Pérez-Peña
- Centro de Química, Laboratorio de Bioquímica y Biología Molecular, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico; (A.R.-E.); (I.H.-C.); (L.M.-P.-P.)
| | - Gerardo Santos-López
- Centro de Investigación Biomédica de Oriente, Laboratorio de Biología Molecular y Virología, Instituto Mexicano del Seguro Social (IMSS), Metepec 74360, Mexico;
| | - José F. Rivera-Benítez
- Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Ciudad de México 38110, Mexico;
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Samson R, Dharne M, Khairnar K. Bacteriophages: Status quo and emerging trends toward one health approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168461. [PMID: 37967634 DOI: 10.1016/j.scitotenv.2023.168461] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/30/2023] [Accepted: 11/07/2023] [Indexed: 11/17/2023]
Abstract
The alarming rise in antimicrobial resistance (AMR) among the drug-resistant pathogens has been attributed to the ESKAPEE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, Enterobacter sp., and Escherichia coli). Recently, these AMR microbes have become difficult to treat, as they have rendered the existing therapeutics ineffective. Thus, there is an urgent need for effective alternatives to lessen or eliminate the current infections and limit the spread of emerging diseases under the "One Health" framework. Bacteriophages (phages) are naturally occurring biological resources with extraordinary potential for biomedical, agriculture/food safety, environmental protection, and energy production. Specific unique properties of phages, such as their bactericidal activity, host specificity, potency, and biocompatibility, make them desirable candidates in therapeutics. The recent biotechnological advancement has broadened the repertoire of phage applications in nanoscience, material science, physical chemistry, and soft-matter research. Herein, we present a comprehensive review, coupling the substantial aspects of phages with their applicability status and emerging opportunities in several interdependent areas under one health concept. Consolidating the recent state-of-the-art studies that integrate human, animal, plant, and environment health, the following points have been highlighted: (i) The biomedical and pharmacological advantages of phages and their antimicrobial derivatives with particular emphasis on in-vivo and clinical studies. (ii) The remarkable potential of phages to be altered, improved, and applied for drug delivery, biosensors, biomedical imaging, tissue engineering, energy, and catalysis. (iii) Resurgence of phages in biocontrol of plant, food, and animal-borne pathogens. (iv) Commercialization of phage-based products, current challenges, and perspectives.
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Affiliation(s)
- Rachel Samson
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Mahesh Dharne
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India.
| | - Krishna Khairnar
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Environmental Virology Cell (EVC), CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur 440020, India.
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7
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Nguyen HM, Watanabe S, Sharmin S, Kawaguchi T, Tan XE, Wannigama DL, Cui L. RNA and Single-Stranded DNA Phages: Unveiling the Promise from the Underexplored World of Viruses. Int J Mol Sci 2023; 24:17029. [PMID: 38069353 PMCID: PMC10707117 DOI: 10.3390/ijms242317029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/26/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
RNA and single-stranded DNA (ssDNA) phages make up an understudied subset of bacteriophages that have been rapidly expanding in the last decade thanks to advancements in metaviromics. Since their discovery, applications of genetic engineering to ssDNA and RNA phages have revealed their immense potential for diverse applications in healthcare and biotechnology. In this review, we explore the past and present applications of this underexplored group of phages, particularly their current usage as therapeutic agents against multidrug-resistant bacteria. We also discuss engineering techniques such as recombinant expression, CRISPR/Cas-based genome editing, and synthetic rebooting of phage-like particles for their role in tailoring phages for disease treatment, imaging, biomaterial development, and delivery systems. Recent breakthroughs in RNA phage engineering techniques are especially highlighted. We conclude with a perspective on challenges and future prospects, emphasizing the untapped diversity of ssDNA and RNA phages and their potential to revolutionize biotechnology and medicine.
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Affiliation(s)
- Huong Minh Nguyen
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Shinya Watanabe
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Sultana Sharmin
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Tomofumi Kawaguchi
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Xin-Ee Tan
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Dhammika Leshan Wannigama
- Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata 990-2292, Yamagata, Japan;
| | - Longzhu Cui
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
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Kumar A, Yadav A. Synthetic phage and its application in phage therapy. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 200:61-89. [PMID: 37739560 DOI: 10.1016/bs.pmbts.2023.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Synthetic phage analysis has been implemented in progressive various areas of biology, such as genetics, molecular biology, and synthetic biology. Many phage-derived technologies have been altered for developing gene circuits to program biological systems. Due to their extremely potent potency, phages also provide greater medical availability against bacterial agents and bacterial diagnostic agents. Its host specificity and our growing ability to manipulate, them further expand its possibility. New Phages also genetically redesign programmable biomaterials with highly tunable properties. Moreover, new phages are central to powerful directed evolution platforms. It is used to enhance existing biological, functions to create new phages. In other sites, the mining of antibiotics, and the emergence and dissemination of more than one type of drug-resistant microbe, a human health concerns. The major point in controlling and treating microbial infections. At present, genetic modifications and biochemical treatments are used to modify phages. Among these, genetic engineering involves the identification of defective proteins, modification of host bodies, recognized receptors, and disruption of bacterial phage resistance signaling gateways.
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Affiliation(s)
- Ajay Kumar
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University, Kanpur, Uttar Pradesh, India.
| | - Anuj Yadav
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University, Kanpur, Uttar Pradesh, India
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Bisht D, Sajjanar BK, Saxena S, Kakodia B, Dighe V, Thakuria D, Kharayat NS, Chanu KV, Kumar S. Identification and characterization of phage display-selected peptides having affinity to Peste des petits ruminants virus. J Immunol Methods 2023; 515:113455. [PMID: 36893896 DOI: 10.1016/j.jim.2023.113455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/23/2023] [Accepted: 03/03/2023] [Indexed: 03/09/2023]
Abstract
Phage display is a well-established technique used for selecting novel ligands having affinity to a plethora of targets including proteins, viruses, whole bacterial and mammalian cells as well as lipid targets. In the present study, phage display technology was used to identify peptides having affinity to PPRV. The binding capacity of these peptides was characterized through various formats of ELISA using phage clones, linear and multiple antigenic peptides. The whole PPRV was used as an immobilized target in a surface biopanning process using a 12-mer phage display random peptide library. After five rounds of biopanning, forty colonies were picked and amplified followed by DNA isolation and amplification for sequencing. Sequencing suggested 12 different clones expressing different peptide sequence Phage-ELISA was performed using all 12 phage clones. Results indicated that four phage clones i.e., P4, P8, P9 and P12 had a specific binding activity to PPR virus. Linear peptides displayed by all 12 clones were synthesized using solid phase peptide synthesis and subjected to virus capture ELISA. No significant binding of the linear peptides with PPRV was evident which may be due to loss of conformation of linear peptide after coating. When the four selected phage clones displayed peptide sequences were synthesized in Multiple antigenic peptide (MAP) format and used in virus capture ELISA, the results indicated significant binding of PPRV to the MAPs. It may be due to increased avidity and/or better projection of binding residues in 4-armed MAPs as compared to linear peptides. MAP-peptides were also conjugated on gold nanoparticles (AuNPs). Visual colour change from wine red to purple was observed on addition of PPRV in MAP-conjugated AuNPs solution. This colour change may be attributable to the networking of PPRV with MAP -conjugated AuNPs resulting in aggregation of AuNPs. All these results supported the hypothesis that the phage display selected peptides were capable of binding to the PPRV. The potential of these peptides to develop novel diagnostic or therapeutic agents remains to be investigated.
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Affiliation(s)
- Deepika Bisht
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122, India; Division of Virology, ICAR-Indian Veterinary Research Institute, Mukteswar, Nainital, Uttarakhand 263138, India.
| | - B K Sajjanar
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122, India.
| | - Shikha Saxena
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122, India.
| | - Bhuvna Kakodia
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122, India
| | - Vikas Dighe
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122, India.
| | - Dimpal Thakuria
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122, India; ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, Nainital, Uttarakhand 263136, India.
| | - Nitish S Kharayat
- Temperate Animal Husbandry Division, ICAR-Indian Veterinary Research Institute, Mukteswar Campus, Nainital, Uttarakhand 263138, India.
| | | | - Satish Kumar
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122, India.
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10
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Huang J, Fu X, Xue Q, Ma P, Yin Y, Jiang M, Lu Y, Ying Q, Jiang J, He H, Wu D. Peptide ARHGEF9 Inhibits Glioma Progression via PI3K/AKT/mTOR Pathway. DISEASE MARKERS 2023; 2023:7146589. [PMID: 36852158 PMCID: PMC9966571 DOI: 10.1155/2023/7146589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/03/2022] [Accepted: 01/18/2023] [Indexed: 02/20/2023]
Abstract
Background The most prevalent malignant tumor in a human brain nervous system is called glioma. Peptide is a compound formed by the peptide bond of α-amino acids, and the development of polypeptide drugs has been widely used in many fields. We plan to investigate the underlying peptides with clinical value in glioma. Method Based on public databases, we targeted the common genes between glioma differentially expressed genes (DEGs) and peptide genes related to glioma prognosis. Then, these common genes were analyzed by LASSO-Cox analysis, prognostic risk model, and nomogram to identify key prognostic peptide genes and the target gene in this study. Next, the mechanism of target gene in glioma was explored by bioinformatics analysis and functional experiments. Results We obtained a total of 26 overlapping genes for the following study. After that, 6 independent prognostic factors (REPIN1, PSD3, RDX, CDK4, FANCI, and ARHGEF9) were obtained and applied to construct the prognostic nomogram, and ARHGEF9 was the target gene in the study. Next, peptide ARHGEF9 was found to inhibit glioma cell development. Through Spearman's correlation analysis, ARHGEF9 had a close relation with PI3K/AKT/mTOR pathway. In functional experiments, peptide ARHGEF9 could suppress the protein expressions of p-PIK3K, p-AKT and p-mTOR, while IGF-1 could reverse this effect. Conclusion This study identifies 6 new prognostic biomarkers for glioma patients. Among them, peptide ARHGEF9 gene is an inhibitory gene functioning by targeting PI3K/AKT/mTOR pathway.
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Affiliation(s)
- Jie Huang
- Department of Neurosurgery, Third Affiliated Hospital, Navy Medical University, Shanghai, China 200432
| | - Xiaoling Fu
- Department of Medical Psychology, The Fourth Medical Center of PLA General Hospital, 51 Fu Cheng Road, Beijing, China 100048
| | - Qiang Xue
- Department of Neurosurgery, Third Affiliated Hospital, Navy Medical University, Shanghai, China 200432
| | - Peng Ma
- Department of Neurosurgery, Third Affiliated Hospital, Navy Medical University, Shanghai, China 200432
| | - Yating Yin
- Department of Neurosurgery, Third Affiliated Hospital, Navy Medical University, Shanghai, China 200432
| | - Minjie Jiang
- Department of Neurosurgery, Yixing People's Hospital, Yixing, Jiangsu Province, China 214200
| | - Yunpeng Lu
- Department of Neurosurgery, Yixing People's Hospital, Yixing, Jiangsu Province, China 214200
| | - Qi Ying
- Department of Neurosurgery, Third Affiliated Hospital, Navy Medical University, Shanghai, China 200432
| | - Jun Jiang
- Endoscopy Center, Minhang Hospital, Fudan University, Shanghai, China
| | - Hua He
- Department of Neurosurgery, Third Affiliated Hospital, Navy Medical University, Shanghai, China 200432
| | - Da Wu
- Department of Neurosurgery, Yixing People's Hospital, Yixing, Jiangsu Province, China 214200
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11
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Recombinant antibodies by phage display for bioanalytical applications. Biosens Bioelectron 2023; 222:114909. [PMID: 36462427 DOI: 10.1016/j.bios.2022.114909] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 10/08/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022]
Abstract
Antibody phage display, aimed at preparing antibodies to defined antigens, is a useful replacement for hybridoma technology. The phage system replaces all work stages that follow animal immunization with simple procedures for manipulating DNA and bacteria. It enables the time needed to generate stable antibody-producing clones to be shortened considerably, making the process noticeably cheaper. Antibodies prepared by phage display undergo several affinity selection steps and can be used as selective receptors in biosensors. This article briefly describes the techniques used in the making of phage antibodies to various antigens. The possibilities and prospects are discussed of using phage antibodies as selective agents in analytical systems, including biosensors.
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Selection of Listeria monocytogenes InlA-Binding Peptides Using Phage Display—Novel Compounds for Diagnostic Applications? Appl Microbiol 2022. [DOI: 10.3390/applmicrobiol2040070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Listeria monocytogenes is a pathogenic, gram-positive bacterium causing foodborne infections and listeriosis, an infection responsible for serious medical conditions, especially for pregnant women, newborns, or people with a weak immune system. Even after antibiotic treatment, 30% of clinical infections result in death. L. monocytogenes is able to enter and multiply in mammalian cells. Invasion into epithelial cells in the human intestine is mediated by the interaction of the bacterial surface protein internalin A (InlA) with the host cell receptor E-cadherin (E-cad). We have used phage display to select InlA-specific peptides consisting of 12 amino acids using a randomized, recombinant peptide library. We could demonstrate that the selected peptides bound to recombinant InlA protein as well as to L. monocytogenes cells. In vitro, some of the peptides inhibited the interaction between recombinant InlA and human E-cad. As far as we know, this is the first publication on the development of InlA-specific peptide ligands. In the future, our peptides might be used for the development of innovative diagnostic tools or even therapeutic approaches.
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13
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Wang T, Xu J, Wang B, Wang Y, Zhao W, Xiang B, Xue Y, Yuan Q, Wang Y. Receptor-binding domain-anchored peptides block binding of severe acute respiratory syndrome coronavirus 2 spike proteins with cell surface angiotensin-converting enzyme 2. Front Microbiol 2022; 13:910343. [PMID: 36177466 PMCID: PMC9513850 DOI: 10.3389/fmicb.2022.910343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 08/18/2022] [Indexed: 12/14/2022] Open
Abstract
Background The COVID-19 pandemic has killed over 6 million people worldwide. Despite the accumulation of knowledge about the causative pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the pathogenesis of this disease, cures remain to be discovered. We searched for certain peptides that might interfere with spike protein (S protein)-angiotensin-converting enzyme 2 (ACE2) interactions. Methods Phage display (PhD)-12 peptide library was screened against recombinant spike trimer (S-trimer) or receptor-binding domain (S-RBD) proteins. The resulting enriched peptide sequences were obtained, and their potential binding sites on S-trimer and S-RBD 3D structure models were searched. Synthetic peptides corresponding to these and other reference sequences were tested for their efficacy in blocking the binding of S-trimer protein onto recombinant ACE2 proteins or ACE2-overexpressing cells. Results After three rounds of phage selections, two peptide sequences (C2, DHAQRYGAGHSG; C6, HWKAVNWLKPWT) were enriched by S-RBD, but only C2 was present in S-trimer selected phages. When the 3D structures of static monomeric S-RBD (6M17) and S-trimer (6ZGE, 6ZGG, 7CAI, and 7CAK, each with different status of S-RBDs in the three monomer S proteins) were scanned for potential binding sites of C2 and C6 peptides, C6 opt to bind the saddle of S-RBD in both 6M17 and erected S-RBD in S-trimers, but C2 failed to cluster there in the S-trimers. In the competitive S-trimer-ACE2-binding experiments, synthetic C2 and C6 peptides inhibited S-trimer binding onto 293T-ACE2hR cells at high concentrations (50 μM) but not at lower concentrations (10 μM and below), neither for the settings of S-trimer binding onto recombinant ACE2 proteins. Conclusion Using PhD methodology, two peptides were generated bearing potentials to interfere with S protein-ACE2 interaction, which might be further exploited to produce peptidomimetics that block the attachment of SARS-CoV-2 virus onto host cells, hence diminishing the pathogenesis of COVID-19.
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Affiliation(s)
- Ting Wang
- Oncology Department of Integrated Traditional Chinese and Western Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Jie Xu
- Central Laboratory, Xiang’an Hospital of Xiamen University, Xiang’an University Medical Center, Xiamen University, Xiamen, Fujian, China
- Eye Institute of Xiamen University, Medical College, Xiamen University, Xiamen, Fujian, China
| | - Beibei Wang
- Center for Advanced Materials Research, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, Guangdong, China
| | - Yulian Wang
- Eye Institute of Xiamen University, Medical College, Xiamen University, Xiamen, Fujian, China
| | - Wei Zhao
- Eye Institute of Xiamen University, Medical College, Xiamen University, Xiamen, Fujian, China
| | - Bin Xiang
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Yuhua Xue
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Quan Yuan
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, Fujian, China
| | - Yiqiang Wang
- Central Laboratory, Xiang’an Hospital of Xiamen University, Xiang’an University Medical Center, Xiamen University, Xiamen, Fujian, China
- Wisdom Lake Academy of Pharmacy, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
- *Correspondence: Yiqiang Wang,
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Nanoparticle Emulsions Enhance the Inhibition of NLRP3. Int J Mol Sci 2022; 23:ijms231710168. [PMID: 36077562 PMCID: PMC9456257 DOI: 10.3390/ijms231710168] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Antibacterial delivery emulsions are potential materials for treating bacterial infections. Few studies have focused on the role and mechanism of emulsions in inflammation relief. Therefore, based on our previous analysis, in which the novel and natural Pickering emulsions stabilized by antimicrobial peptide nanoparticles were prepared, the regulation effect of emulsion on inflammasome was explored in silico, in vitro and in vivo. Firstly, the interactions between inflammasome components and parasin I or Pickering emulsion were predicted by molecular docking. Then, the inflammasome stimulation by different doses of the emulsion was tested in RAW 264.7 and THP-1 cells. Finally, in Kunming mice with peritonitis, NLRP3 and IL-1β expression in the peritoneum were evaluated. The results showed that the Pickering emulsion could combine with ALK, casp-1, NEK7, or NLRP3 to affect the assembly of the NLRP3 and further relieve inflammation. LPNE showed a dose–dependent inhibition effect on the release of IL-1β and casp-1. With the concentration of parasin I increased from 1.5 mg/mL to 3 mg/mL, the LDH activity decreased in the chitosan peptide-embedded nanoparticles emulsion (CPENE) and lipid/peptide nanoparticles emulsion (LPNE) groups. However, from 1.5 to 6 mg/mL, LPNE had a dose–dependent effect on the release of casp-1. The CPENE and parasin I-conjugated chitosan nanoparticles emulsion (PCNE) may decrease the release of potassium and chloride ions. Therefore, it can be concluded that the LPNE may inhibit the activation of the inflammasome by decreasing LDH activity, potassium and chloride ions through binding with compositions of NLRP3.
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15
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Radwan O, Brothers MC, Coyle V, Chapleau ME, Chapleau RR, Kim SS, Ruiz ON. Electrochemical biosensor for rapid detection of fungal contamination in fuel systems. Biosens Bioelectron 2022; 211:114374. [DOI: 10.1016/j.bios.2022.114374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 11/26/2022]
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16
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Shahin K, Zhang L, Mehraban MH, Collard JM, Hedayatkhah A, Mansoorianfar M, Soleimani-Delfan A, Wang R. Clinical and experimental bacteriophage studies: Recommendations for possible approaches for standing against SARS-CoV-2. Microb Pathog 2022; 164:105442. [PMID: 35151823 PMCID: PMC8830156 DOI: 10.1016/j.micpath.2022.105442] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 02/05/2022] [Accepted: 02/07/2022] [Indexed: 12/23/2022]
Abstract
In 2019, the world faced a serious health challenge, the rapid spreading of a life-threatening viral pneumonia, coronavirus disease 2019 (COVID-19) caused by a betacoronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As of January 2022 WHO statistics shows more than 5.6 million death and about 350 million infection by SARS-CoV-2. One of the life threatening aspects of COVID-19 is secondary infections and reduced efficacy of antibiotics against them. Since the beginning of COVID-19 many researches have been done on identification, treatment, and vaccine development. Bacterial viruses (bacteriophages) could offer novel approaches to detect, treat and control COVID-19. Phage therapy and in particular using phage cocktails can be used to control or eliminate the bacterial pathogen as an alternative or complementary therapeutic agent. At the same time, phage interaction with the host immune system can regulate the inflammatory response. In addition, phage display and engineered synthetic phages can be utilized to develop new vaccines and antibodies, stimulate the immune system, and elicit a rapid and well-appropriate defense response. The emergence of SARS-CoV-2 new variants like delta and omicron has proved the urgent need for precise, efficient and novel approaches for vaccine development and virus detection techniques in which bacteriophages may be one of the plausible solutions. Therefore, phages with similar morphology and/or genetic content to that of coronaviruses can be used for ecological and epidemiological modeling of SARS-CoV-2 behavior and future generations of coronavirus, and in general new viral pathogens. This article is a comprehensive review/perspective of potential applications of bacteriophages in the fight against the present pandemic and the post-COVID era.
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Affiliation(s)
- Khashayar Shahin
- Center for Microbes, Development, and Health (CMDH), Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200025, China; Key Laboratory of Phage Research, International Phage Research Center, Jiangsu Academy of Agricultural, China; Institute of Food Safety and Nutrition, Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
| | - Lili Zhang
- Key Laboratory of Phage Research, International Phage Research Center, Jiangsu Academy of Agricultural, China; Institute of Food Safety and Nutrition, Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Mohammad Hossein Mehraban
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Jean-Marc Collard
- Center for Microbes, Development, and Health (CMDH), Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200025, China
| | | | | | - Abbas Soleimani-Delfan
- Key Laboratory of Phage Research, International Phage Research Center, Jiangsu Academy of Agricultural, China; Institute of Food Safety and Nutrition, Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Ran Wang
- Key Laboratory of Phage Research, International Phage Research Center, Jiangsu Academy of Agricultural, China; Institute of Food Safety and Nutrition, Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
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Cheng YW, Chuang YC, Huang SW, Liu CC, Wang JR. An auto-antibody identified from phenotypic directed screening platform shows host immunity against EV-A71 infection. J Biomed Sci 2022; 29:10. [PMID: 35130884 PMCID: PMC8822709 DOI: 10.1186/s12929-022-00794-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/01/2022] [Indexed: 02/08/2023] Open
Abstract
Background Enterovirus A71 (EV-A71) is a neurotropic virus which may cause severe neural complications, especially in infants and children. The clinical manifestations include hand-foot-and-mouth disease, herpangina, brainstem encephalitis, pulmonary edema, and other severe neurological diseases. Although there are some vaccines approved, the post-marketing surveillance is still unavailable. In addition, there is no antiviral drugs against EV-A71 available. Methods In this study, we identified a novel antibody that could inhibit viral growth through a human single chain variable fragment (scFv) library expressed in mammalian cells and panned by infection with lethal dose of EV-A71. Results We identified that the host protein α-enolase (ENO1) is the target of this scFv, and anti-ENO1 antibody was found to be more in mild cases than severe EV-A71 cases. Furthermore, we examined the antiviral activity in a mouse model. We found that the treatment of the identified 07-human IgG1 antibody increased the survival rate after virus challenge, and significantly decreased the viral RNA and the level of neural pathology in brain tissue. Conclusions Collectively, through a promising intracellular scFv library expression and screening system, we found a potential scFv/antibody which targets host protein ENO1 and can interfere with the infection of EV-A71. The results indicate that the usage and application of this antibody may offer a potential treatment against EV-A71 infection.
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Affiliation(s)
- Yu-Wei Cheng
- The Institute of Basic Medical Sciences, National Cheng Kung University, Tainan, Taiwan.,Leadgene Biomedical, Inc., Tainan, Taiwan
| | - Yung-Chun Chuang
- Leadgene Biomedical, Inc., Tainan, Taiwan.,Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Sheng-Wen Huang
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Tainan, Taiwan
| | - Ching-Chuan Liu
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan
| | - Jen-Ren Wang
- The Institute of Basic Medical Sciences, National Cheng Kung University, Tainan, Taiwan. .,Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan. .,Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan. .,National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan, Taiwan.
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18
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Benz C, Ali M, Krystkowiak I, Simonetti L, Sayadi A, Mihalic F, Kliche J, Andersson E, Jemth P, Davey NE, Ivarsson Y. Proteome-scale mapping of binding sites in the unstructured regions of the human proteome. Mol Syst Biol 2022; 18:e10584. [PMID: 35044719 PMCID: PMC8769072 DOI: 10.15252/msb.202110584] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 12/18/2022] Open
Abstract
Specific protein-protein interactions are central to all processes that underlie cell physiology. Numerous studies have together identified hundreds of thousands of human protein-protein interactions. However, many interactions remain to be discovered, and low affinity, conditional, and cell type-specific interactions are likely to be disproportionately underrepresented. Here, we describe an optimized proteomic peptide-phage display library that tiles all disordered regions of the human proteome and allows the screening of ~ 1,000,000 overlapping peptides in a single binding assay. We define guidelines for processing, filtering, and ranking the results and provide PepTools, a toolkit to annotate the identified hits. We uncovered >2,000 interaction pairs for 35 known short linear motif (SLiM)-binding domains and confirmed the quality of the produced data by complementary biophysical or cell-based assays. Finally, we show how the amino acid resolution-binding site information can be used to pinpoint functionally important disease mutations and phosphorylation events in intrinsically disordered regions of the proteome. The optimized human disorderome library paired with PepTools represents a powerful pipeline for unbiased proteome-wide discovery of SLiM-based interactions.
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Affiliation(s)
- Caroline Benz
- Department of Chemistry ‐ BMCUppsala UniversityUppsalaSweden
| | - Muhammad Ali
- Department of Chemistry ‐ BMCUppsala UniversityUppsalaSweden
| | | | | | - Ahmed Sayadi
- Department of Chemistry ‐ BMCUppsala UniversityUppsalaSweden
| | - Filip Mihalic
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - Johanna Kliche
- Department of Chemistry ‐ BMCUppsala UniversityUppsalaSweden
| | - Eva Andersson
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - Per Jemth
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - Norman E Davey
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
| | - Ylva Ivarsson
- Department of Chemistry ‐ BMCUppsala UniversityUppsalaSweden
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19
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Application of Recombinant Human scFv Antibody as a Powerful Tool to Monitor Nitrogen Fixing Biofertilizer in Rice and Legume. Microbiol Spectr 2021; 9:e0209421. [PMID: 34908451 PMCID: PMC8672896 DOI: 10.1128/spectrum.02094-21] [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: 11/20/2022] Open
Abstract
Bradyrhizobium is an endophytic bacterium under investigation as an efficient biofertilizer for sustainable legume-rice rotational cropping system. Monitoring and bio-imaging of this nitrogen fixing bacterium is essential for the study of plant-microbe evolution, soil microbiome, as well as quality control in organic farming. While phage display antibody technology has been widely used to generate recombinant antibody for myriad medical purposes, so far, this technology has been minimally applied in the agricultural sector. In this study, single-chain variable fragments (scFv) against two Bradyrhizobium strains SUTN9-2 (yiN92-1e10) and DOA9 (yiDOA9-162) were isolated from a human phage display antibody library. Specific binding of scFv was demonstrated by ELISA and confocal-immunofluorescence imaging techniques. Bradyrhizobium localization in both endophytic and bacteroid forms could be observed inside rice tissue and plant nodule, respectively. Moreover, successful application of the recombinant antibody for the evaluation of nodule occupancy was also demonstrated in comparison with standard GUS-staining method. The results of this study showed for the first time the potential use of human phage display scFv antibody for imaging and monitoring of Bradyrhizobium biofertilizer and thus could be further applied for point-of-detection of bacterial inoculum in the legume-rice rotational crop system. IMPORTANCE Human scFv antibody generated from phage display technology was successfully used for the generation of specific recombinant antibodies: yiN92-1e10 and yiDOA9-162 for the detection of Bradyrhizobium strains SUTN9-2 and DOA9, respectively. These two recombinant scFv antibodies could be used for precise detection of the rhizobia both in symbiosis with legume and endophyte in rice tissue by ELISA and immunofluorescent staining, during legume-rice rotational cropping system in the field. This methodology can be further employed for the study of other plant-microbe interactions and monitoring of biofertilizer in diverse sustainable cropping systems as well as in precision agriculture.
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20
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Ch'ng ACW, Lam P, Alassiri M, Lim TS. Application of phage display for T-cell receptor discovery. Biotechnol Adv 2021; 54:107870. [PMID: 34801662 DOI: 10.1016/j.biotechadv.2021.107870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 10/23/2021] [Accepted: 11/15/2021] [Indexed: 12/13/2022]
Abstract
The immune system is tasked to keep our body unharmed and healthy. In the immune system, B- and T-lymphocytes are the two main components working together to stop and eliminate invading threats like virus particles, bacteria, fungi and parasite from attacking our healthy cells. The function of antibodies is relatively more direct in target recognition as compared to T-cell receptors (TCR) which recognizes antigenic peptides being presented on the major histocompatibility complex (MHC). Although phage display has been widely applied for antibody presentation, this is the opposite in the case of TCR. The cell surface TCR is a relatively large and complex molecule, making presentation on phage surfaces challenging. Even so, recombinant versions and modifications have been introduced to allow the growing development of TCR in phage display. In addition, the increasing application of TCR for immunotherapy has made it an important binding motif to be developed by phage display. This review will emphasize on the application of phage display for TCR discovery as well as the engineering aspect of TCR for improved characteristics.
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Affiliation(s)
- Angela Chiew Wen Ch'ng
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Paula Lam
- CellVec Private Limited, 118518, Singapore; National University of Singapore, Department of Physiology, 117597, Singapore; Duke-NUS Graduate Medical School, Cancer and Stem Cells Biology Program, 169857, Singapore
| | - Mohammed Alassiri
- Department of Basic Sciences, College of Science and Health Professions, King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia; King Abdullah International Medical Research Center (KAIMRC), Riyadh, Saudi Arabia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia; Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 Penang, Malaysia.
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21
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Zhang N, Wu H, Liang Y, Ye J, Zhang H, Miao Y, Luo Y, Fan H, Yue T. Design and Preparation of "corn-like" SPIONs@DFK-SBP-M13 Assembly for Improvement of Effective Internalization. Int J Nanomedicine 2021; 16:7091-7102. [PMID: 34703229 PMCID: PMC8541766 DOI: 10.2147/ijn.s325282] [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] [Received: 06/17/2021] [Accepted: 09/30/2021] [Indexed: 12/20/2022] Open
Abstract
Purpose Superparamagnetic iron oxide nanoparticles (SPIONs) have exhibited preeminent diagnosis and treatment performances, but their low internalization severely limits predesigned functions. The low cell internalization is now an urgent bottleneck problem for almost all nanomaterials. To achieve more internalization of SPIONS, recombinant M13 phage was designed for targeted delivery and smart release. Methods M13 phages were designed to co-express exogenous SPARC binding peptide (SBP) and cathepsin B cleavage peptide (DFK), formed recombinant DFK-SBP-M13. 3.37± 0.06 nm of SPIONs were modified by 3, 4-dihydroxyhydrocinnamic acid (DHCA) to gain 10.80 ± 0.21 nm of DHCA-coated SPIONs, i.e., DHCA@SPIONs. Upon adjusting the proportions of DHCA@SPIONs and DFK-SBP-M13, the multi-carboxyl SPIONs assembled onto recombinant M13 phages via covalent bonding. The assemblies were co-cultured with MDA-MB-231 cells to interpret their internalization and smart release. Results The “corn-like” SPIONs@DFK-SBP-M13 (261.47±3.30 nm) assemblies have not been reported previously. The assembly was stable, dispersible, superparamagnetic and biocompatible. After co-cultivation with MDA-MB-231 cells, the SPIONs@DFK-SBP-M13 assemblies quickly bond to the cell surface and are internalized. The enrichment rate of SPIONs@DFK-SBP-M13 assembly was 13.9 times higher than free SPIONs at 0.5 h, and intracellular Fe content was 3.6 times higher at 1 h. Furthermore, the DFK peptides favored cathepsin B to cleave SPIONs from the M13 templates resulting in release of SPIONs inside cells. Conclusion The novel SPIONs@DFK-SBP-M13 assembly can rapidly deliver SPIONs to the targeted sites and enabled smart release. The combination of genetic recombination and nanotechnology is beneficial for designing and optimizing some new nanomaterials with special functions to achieve wider applications.
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Affiliation(s)
- Na Zhang
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, 710069, People's Republic of China
| | - Hui Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Yingzhi Liang
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, 710069, People's Republic of China
| | - Jianming Ye
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, 710069, People's Republic of China
| | - Huan Zhang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, Shaanxi, 710069, People's Republic of China
| | - Yuqing Miao
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, Shaanxi, 710069, People's Republic of China
| | - Yane Luo
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, 710069, People's Republic of China
| | - Haiming Fan
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, Shaanxi, 710069, People's Republic of China
| | - Tianli Yue
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, 710069, People's Republic of China.,Laboratory of Quality and Safety Risk Assessment for Agro-Products (Yangling), Ministry of Agriculture, Beijing, People's Republic of China
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22
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Jaroszewicz W, Morcinek-Orłowska J, Pierzynowska K, Gaffke L, Węgrzyn G. Phage display and other peptide display technologies. FEMS Microbiol Rev 2021; 46:6407522. [PMID: 34673942 DOI: 10.1093/femsre/fuab052] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 10/19/2021] [Indexed: 12/13/2022] Open
Abstract
Phage display technology, which is based on the presentation of peptide sequences on the surface of bacteriophage virions, was developed over 30 years ago. Improvements in phage display systems have allowed us to employ this method in numerous fields of biotechnology, as diverse as immunological and biomedical applications, the formation of novel materials and many others. The importance of phage display platforms was recognized by awarding the Nobel Prize in 2018 "for the phage display of peptides and antibodies". In contrast to many review articles concerning specific applications of phage display systems published in recent years, we present an overview of this technology, including a comparison of various display systems, their advantages and disadvantages, and examples of applications in various fields of science, medicine, and the broad sense of biotechnology. Other peptide display technologies, which employ bacterial, yeast and mammalian cells, as well as eukaryotic viruses and cell-free systems, are also discussed. These powerful methods are still being developed and improved; thus, novel sophisticated tools based on phage display and other peptide display systems are constantly emerging, and new opportunities to solve various scientific, medical and technological problems can be expected to become available in the near future.
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Affiliation(s)
- Weronika Jaroszewicz
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | | | - Karolina Pierzynowska
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Lidia Gaffke
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
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Chikaev AN, Chikaev AN, Rudometov AP, Merkulyeva YA, Karpenko LI. Phage display as a tool for identifying HIV-1 broadly neutralizing antibodies. Vavilovskii Zhurnal Genet Selektsii 2021; 25:562-572. [PMID: 34595378 PMCID: PMC8453360 DOI: 10.18699/vj21.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/14/2021] [Accepted: 03/22/2021] [Indexed: 11/19/2022] Open
Abstract
Combinatorial biology methods offer a good solution for targeting interactions of specif ic molecules
by a high-throughput screening and are widely used for drug development, diagnostics, identif ication of novel
monoclonal antibodies, search for linear peptide mimetics of discontinuous epitopes for the development of
immunogens or vaccine components. Among all currently available techniques, phage display remains one of
the most popular approaches. Despite being a fairly old method, phage display is still widely used for studying
protein-protein, peptide-protein and DNA-protein interactions due to its relative simplicity and versatility. Phage
display allows highly representative libraries of peptides, proteins or their fragments to be created. Each phage
particle in a library displays peptides or proteins fused to its coat protein and simultaneously carries the DNA
sequence encoding the displayed peptide/protein in its genome. The biopanning procedure allows isolation of
specif ic clones for almost any target, and due to the physical link between the genotype and the phenotype of
recombinant phage particles it is possible to determine the structure of selected molecules. Phage display technology
continues to play an important role in HIV research. A major obstacle to the development of an effective
HIV vaccine is an extensive genetic and antigenic variability of the virus. According to recent data, in order to provide
protection against HIV infection, the so-called broadly neutralizing antibodies that are cross-reactive against
multiple viral strains of HIV must be induced, which makes the identif ication of such antibodies a key area of HIV
vaccinology. In this review, we discuss the use of phage display as a tool for identif ication of HIV-specif ic antibodies
with broad neutralizing activity. We provide an outline of phage display technology, brief ly describe the
design of antibody phage libraries and the affinity selection procedure, and discuss the biology of HIV-1-specif ic
broadly neutralizing antibodies. Finally, we summarize the studies aimed at identif ication of broadly neutralizing
antibodies using various types of phage libraries.
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Affiliation(s)
| | - A N Chikaev
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A P Rudometov
- State Research Center of Virology and Biotechnology "Vector", Rospotrebnadzor, Koltsovo, Novosibirsk region, Russia
| | - Yu A Merkulyeva
- State Research Center of Virology and Biotechnology "Vector", Rospotrebnadzor, Koltsovo, Novosibirsk region, Russia
| | - L I Karpenko
- State Research Center of Virology and Biotechnology "Vector", Rospotrebnadzor, Koltsovo, Novosibirsk region, Russia
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Soltanmohammadi B, Piri‐Gavgani S, Basardeh E, Ghanei M, Azizi M, Khaksar Z, Sharifzadeh Z, Badmasti F, Soezi M, Fateh A, Azimi P, Siadat SD, Shooraj F, Bouzari S, Omrani MD, Rahimi‐Jamnani F. Bactericidal fully human single-chain fragment variable antibodies protect mice against methicillin-resistant Staphylococcus aureus bacteraemia. Clin Transl Immunology 2021; 10:e1302. [PMID: 34221401 PMCID: PMC8240403 DOI: 10.1002/cti2.1302] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 05/01/2021] [Accepted: 05/30/2021] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES The increasing prevalence of antibiotic-resistant Staphylococcus aureus, besides the inadequate numbers of effective antibiotics, emphasises the need to find new therapeutic agents against this lethal pathogen. METHODS In this study, to obtain antibody fragments against S. aureus, a human single-chain fragment variable (scFv) library was enriched against living methicillin-resistant S. aureus (MRSA) cells, grown in three different conditions, that is human peripheral blood mononuclear cells with plasma, whole blood and biofilm. The antibacterial activity of scFvs was evaluated by the growth inhibition assay in vitro. Furthermore, the therapeutic efficacy of anti-S. aureus scFvs was appraised in a mouse model of bacteraemia. RESULTS Three scFv antibodies, that is MEH63, MEH158 and MEH183, with unique sequences, were found, which exhibited significant binding to S. aureus and reduced the viability of S. aureus in in vitro inhibition assays. Based on the results, MEH63, MEH158 and MEH183, in addition to their combination, could prolong the survival rate, reduce the bacterial burden in the blood and prevent inflammation and tissue destruction in the kidneys and spleen of mice with MRSA bacteraemia compared with the vehicle group (treated with normal saline). CONCLUSION The combination therapy with anti-S. aureus scFvs and conventional antibiotics might shed light on the treatment of patients with S. aureus infections.
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Affiliation(s)
- Behnoush Soltanmohammadi
- Department of Mycobacteriology and Pulmonary ResearchPasteur Institute of IranTehranIran
- Microbiology Research CenterPasteur Institute of IranTehranIran
| | - Somayeh Piri‐Gavgani
- Department of Mycobacteriology and Pulmonary ResearchPasteur Institute of IranTehranIran
- Microbiology Research CenterPasteur Institute of IranTehranIran
| | - Eilnaz Basardeh
- Department of Mycobacteriology and Pulmonary ResearchPasteur Institute of IranTehranIran
- Microbiology Research CenterPasteur Institute of IranTehranIran
| | - Mostafa Ghanei
- Chemical Injuries Research CenterSystems Biology and Poisoning InstituteBaqiyatallah University of Medical SciencesTehranIran
| | - Masoumeh Azizi
- Molecular Medicine Department, Biotechnology Research CenterPasteur Institute of IranTehranIran
| | - Zabihollah Khaksar
- Department of Basic SciencesSchool of Veterinary MedicineShiraz UniversityShirazIran
| | | | - Farzad Badmasti
- Department of BacteriologyPasteur Institute of IranTehranIran
| | - Mahdieh Soezi
- Department of Mycobacteriology and Pulmonary ResearchPasteur Institute of IranTehranIran
- Microbiology Research CenterPasteur Institute of IranTehranIran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary ResearchPasteur Institute of IranTehranIran
- Microbiology Research CenterPasteur Institute of IranTehranIran
| | - Parisa Azimi
- Department of Mycobacteriology and Pulmonary ResearchPasteur Institute of IranTehranIran
- Microbiology Research CenterPasteur Institute of IranTehranIran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary ResearchPasteur Institute of IranTehranIran
- Microbiology Research CenterPasteur Institute of IranTehranIran
| | - Fahimeh Shooraj
- Department of Mycobacteriology and Pulmonary ResearchPasteur Institute of IranTehranIran
- Microbiology Research CenterPasteur Institute of IranTehranIran
| | - Saeid Bouzari
- Molecular Biology DepartmentPasteur Institute of IranTehranIran
| | - Mir Davood Omrani
- Department of Medical GeneticsSchool of MedicineShahid Beheshti University of Medical SciencesTehranIran
| | - Fatemeh Rahimi‐Jamnani
- Department of Mycobacteriology and Pulmonary ResearchPasteur Institute of IranTehranIran
- Microbiology Research CenterPasteur Institute of IranTehranIran
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25
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Aikawa C, Kawashima K, Fukuzaki C, Nakakido M, Murase K, Nozawa T, Tsumoto K, Nakagawa I. Single-chain variable fragment (scFv) targeting streptolysin O controls group A Streptococcus infection. Biochem Biophys Res Commun 2021; 566:177-183. [PMID: 34129965 DOI: 10.1016/j.bbrc.2021.06.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 06/04/2021] [Indexed: 10/21/2022]
Abstract
Streptococcus pyogenes (Group A Streptococcus, GAS) causes a range of human diseases, including life-threatening and severe invasive GAS infections, such as streptococcal toxic shock syndrome (STSS). Several antibiotics, including penicillin, are effective against GAS. Still, invasive GAS diseases have a high mortality rate (>30%). Clinical isolates from STSS patients show higher expression of pore-forming streptolysin O (SLO). Thus, SLO is an important pathogenic factor for GAS and may be an effective target for treatment of GAS disease. We succeeded in obtaining a single-chain variable fragment (scFv) SLO-I4 capable of recognizing SLO, which significantly inhibited GAS-induced cell lytic activity in erythrocytes, macrophages, and epithelial cells. In epithelial cells, SLO-I4 significantly reduced SLO-mediated endosomal membrane damage, which consequently prevented bacterial escape from the endosome. The effectiveness of anti-SLO scFv in counteracting SLO function suggests that it might be beneficial against GAS infections.
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Affiliation(s)
- Chihiro Aikawa
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, 606-8501, Japan
| | - Kiyosumi Kawashima
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, 606-8501, Japan
| | - Chihiro Fukuzaki
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, 606-8501, Japan
| | - Makoto Nakakido
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, 108-8639, Japan; Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Kazunori Murase
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, 606-8501, Japan
| | - Takashi Nozawa
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, 606-8501, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, 108-8639, Japan; Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, 108-8639, Japan; Laboratory of Medical Proteomics, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Ichiro Nakagawa
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, 606-8501, Japan.
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26
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Sokullu E, Gauthier MS, Coulombe B. Discovery of Antivirals Using Phage Display. Viruses 2021; 13:v13061120. [PMID: 34200959 PMCID: PMC8230593 DOI: 10.3390/v13061120] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/05/2021] [Accepted: 06/07/2021] [Indexed: 02/06/2023] Open
Abstract
The latest coronavirus disease outbreak, COVID-19, has brought attention to viral infections which have posed serious health threats to humankind throughout history. The rapid global spread of COVID-19 is attributed to the increased human mobility of today's world, yet the threat of viral infections to global public health is expected to increase continuously in part due to increasing human-animal interface. Development of antiviral agents is crucial to combat both existing and novel viral infections. Recently, there is a growing interest in peptide/protein-based drug molecules. Antibodies are becoming especially predominant in the drug market. Indeed, in a remarkably short period, four antibody therapeutics were authorized for emergency use in COVID-19 treatment in the US, Russia, and India as of November 2020. Phage display has been one of the most widely used screening methods for peptide/antibody drug discovery. Several phage display-derived biologics are already in the market, and the expiration of intellectual property rights of phage-display antibody discovery platforms suggests an increment in antibody drugs in the near future. This review summarizes the most common phage display libraries used in antiviral discovery, highlights the approaches employed to enhance the antiviral potency of selected peptides/antibody fragments, and finally provides a discussion about the present status of the developed antivirals in clinic.
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Affiliation(s)
- Esen Sokullu
- Department of Translational Proteomics, Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada;
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Correspondence: (E.S.); (B.C.)
| | - Marie-Soleil Gauthier
- Department of Translational Proteomics, Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada;
| | - Benoit Coulombe
- Department of Translational Proteomics, Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada;
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Correspondence: (E.S.); (B.C.)
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27
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Kim YJ, Lee MH, Lee SR, Chung HY, Kim K, Lee TG, Kim DY. Neutralizing Human Antibodies against Severe Acute Respiratory Syndrome Coronavirus 2 Isolated from a Human Synthetic Fab Phage Display Library. Int J Mol Sci 2021; 22:1913. [PMID: 33671877 PMCID: PMC7918989 DOI: 10.3390/ijms22041913] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/10/2021] [Accepted: 02/12/2021] [Indexed: 12/20/2022] Open
Abstract
Since it was first reported in Wuhan, China, in 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a pandemic outbreak resulting in a tremendous global threat due to its unprecedented rapid spread and an absence of a prophylactic vaccine or therapeutic drugs treating the virus. The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein is a key player in the viral entry into cells through its interaction with the angiotensin-converting enzyme 2 (ACE2) receptor protein, and the RBD has therefore been crucial as a drug target. In this study, we used phage display to develop human monoclonal antibodies (mAbs) that neutralize SARS-CoV-2. A human synthetic Fab phage display library was panned against the RBD of the SARS-CoV-2 spike protein (SARS-2 RBD), yielding ten unique Fabs with moderate apparent affinities (EC50 = 19-663 nM) for the SARS-2 RBD. All of the Fabs showed no cross-reactivity to the MERS-CoV spike protein, while three Fabs cross-reacted with the SARS-CoV spike protein. Five Fabs showed neutralizing activities in in vitro assays based on the Fabs' activities antagonizing the interaction between the SARS-2 RBD and ACE2. Reformatting the five Fabs into immunoglobulin Gs (IgGs) greatly increased their apparent affinities (KD = 0.08-1.0 nM), presumably due to the effects of avidity, without compromising their non-aggregating properties and thermal stability. Furthermore, two of the mAbs (D12 and C2) significantly showed neutralizing activities on pseudo-typed and authentic SARS-CoV-2. Given their desirable properties and neutralizing activities, we anticipate that these human anti-SARS-CoV-2 mAbs would be suitable reagents to be further developed as antibody therapeutics to treat COVID-19, as well as for diagnostics and research tools.
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Sun X, Li L, Pan L, Wang Z, Chen H, Shao C, Yu J, Ren Y, Wang X, Huang X, Zhang R, Li G. Infectious bronchitis virus: Identification of Gallus gallus APN high-affinity ligands with antiviral effects. Antiviral Res 2020; 186:104998. [PMID: 33340637 DOI: 10.1016/j.antiviral.2020.104998] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 12/12/2020] [Accepted: 12/14/2020] [Indexed: 12/12/2022]
Abstract
Infectious bronchitis virus (IBV) is a coronavirus, causes infectious bronchitis (IB) with high morbidity and mortality, and gives rise to huge economic losses for the poultry industry. Aminopeptidase N (APN) may be one of the IBV functional receptors. In this study, Gallus gallus APN (gAPN) protein was screened by phage-displayed 12-mer peptide library. Two high-affinity peptides H (HDYLYYTFTGNP) and T (TKFSPPSFWYLH) to gAPN protein were selected for in depth characterization of their anti-IBV effects. In vitro, indirect ELISA showed that these two high-affinity ligands could bind IBV S1 antibodies. Quantitative real-time PCR (qRT-PCR) assay, virus yield reduction assay and indirect immunofluorescence assay results revealed 3.125-50 μg/ml of peptide H and 6.25-50 μg/ml of peptide T reduced IBV proliferation in chicken embryo kidney cells (CEKs). In vivo, high-affinity phage-vaccinated chickens were able to induce specific IBV S1 antibodies and IBV neutralizing antibodies. QRT-PCR results confirmed that high-affinity phages reduced virus proliferation in chicken tracheas, lungs and kidneys, and alleviated IBV-induced lesions. By multiple sequence alignment, motif 'YxYY' and 'FxPPxxWxLH' of high-affinity peptides were identified in IBV S1-NTD, while another motif 'YxFxGN' located in S2. These results indicated that high affinity peptides of gAPN could present an alternative approach to IB prevention or treatment.
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Affiliation(s)
- Xiaoqi Sun
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Lanlan Li
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Long Pan
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Zheng Wang
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Huijie Chen
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Changhao Shao
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Jia Yu
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Yudong Ren
- College of Electrical and Information Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Xiurong Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Science, Harbin, 150069, China
| | - Xiaodan Huang
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Ruili Zhang
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Guangxing Li
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China.
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Kelly M, Cambray S, McCarthy KA, Wang W, Geisinger E, Ortiz-Marquez J, van Opijnen T, Gao J. Peptide Probes of Colistin Resistance Discovered via Chemically Enhanced Phage Display. ACS Infect Dis 2020; 6:2410-2418. [PMID: 32786283 DOI: 10.1021/acsinfecdis.0c00206] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Colistin is an antibiotic of last resort used to treat infections caused by multidrug-resistant Gram-negative bacterial pathogens. The recent surge in reported cases of colistin-resistant infections urgently calls for fast and reliable diagnostic methods, which can be used for the facile detection and proper treatment of these challenging infections. A major mechanism of colistin resistance involves phosphoethanolamine (PE) modification of lipopolysaccharide (LPS), the molecular target of colistin. This LPS modification mechanism has been recently reported to be transferrable via a plasmid-carried mcr-1 gene, which is particularly concerning as it may readily confer colistin resistance to a wide array of bacterial pathogens. To develop molecular tools to allow facile detection of colistin resistance, we have herein enlisted a novel phage library that incorporates dynamic covalent warheads to recognize PE modifications on bacterial cells. Screening of this chemically modified phage library against colistin-resistant pathogens revealed a number of peptide probes that readily differentiate colistin-resistant bacterial strains from their colistin-susceptible counterparts. With a fluorophore label, these peptide probes selectively stain colistin-resistant bacteria at sub-to-low micromolar concentrations. The bacterial staining is minimally inhibited by the presence of serum proteins or even blood serum. Mechanistic studies indicate that our peptide probes bind colistin-resistant bacteria primarily by targeting PE-modified lipids. However, some species-specific features of the cell surface can also contribute to the peptides' association to bacterial cells. Further elucidation of such cell surface features may give molecular probes with improved species and strain specificity, which will enable bacterial infection diagnosis with high precision.
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Affiliation(s)
- Michael Kelly
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Samantha Cambray
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Kelly A. McCarthy
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Wenjian Wang
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Edward Geisinger
- Department of Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Juan Ortiz-Marquez
- Department of Biology, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Tim van Opijnen
- Department of Biology, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Jianmin Gao
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
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30
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Selection and Characterization of YKL-40-Targeting Monoclonal Antibodies from Human Synthetic Fab Phage Display Libraries. Int J Mol Sci 2020; 21:ijms21176354. [PMID: 32883029 PMCID: PMC7504393 DOI: 10.3390/ijms21176354] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/26/2020] [Accepted: 08/28/2020] [Indexed: 12/14/2022] Open
Abstract
YKL-40, also known as chitinase-3-like 1 (CHI3L1), is a glycoprotein that is expressed and secreted by various cell types, including cancers and macrophages. Due to its implications for and upregulation in a variety of diseases, including inflammatory conditions, fibrotic disorders, and tumor growth, YKL-40 has been considered as a significant therapeutic biomarker. Here, we used a phage display to develop novel monoclonal antibodies (mAbs) targeting human YKL-40 (hYKL-40). Human synthetic antibody phage display libraries were panned against a recombinant hYKL-40 protein, yielding seven unique Fabs (Antigen-binding fragment), of which two Fabs (H1 and H2) were non-aggregating and thermally stable (75.5 °C and 76.5 °C, respectively) and had high apparent affinities (KD = 2.3 nM and 4.0 nM, respectively). Reformatting the Fabs into IgGs (Immunoglobulin Gs) increased their apparent affinities (notably, for H1 and H2, KD = 0.5 nM and 0.3 nM, respectively), presumably due to the effects of avidity, with little change to their non-aggregation property. The six anti-hYKL-40 IgGs were analyzed using a trans-well migration assay in vitro, revealing that three clones (H1, H2, and H4) were notably effective in reducing cell migration from both A549 and H460 lung cancer cell lines. The three clones were further analyzed in an in vivo animal test that assessed their anti-cancer activities, demonstrating that the tumor area and the number of tumor nodules were significantly reduced in the lung tissues treated with H1 (IgG). Given its high affinity and desirable properties, we expect that the H1 anti-hYKL-40 mAb will be a suitable candidate for developing anti-cancer therapeutics.
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31
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Alfaleh MA, Alsaab HO, Mahmoud AB, Alkayyal AA, Jones ML, Mahler SM, Hashem AM. Phage Display Derived Monoclonal Antibodies: From Bench to Bedside. Front Immunol 2020; 11:1986. [PMID: 32983137 PMCID: PMC7485114 DOI: 10.3389/fimmu.2020.01986] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/23/2020] [Indexed: 12/12/2022] Open
Abstract
Monoclonal antibodies (mAbs) have become one of the most important classes of biopharmaceutical products, and they continue to dominate the universe of biopharmaceutical markets in terms of approval and sales. They are the most profitable single product class, where they represent six of the top ten selling drugs. At the beginning of the 1990s, an in vitro antibody selection technology known as antibody phage display was developed by John McCafferty and Sir. Gregory Winter that enabled the discovery of human antibodies for diverse applications, particularly antibody-based drugs. They created combinatorial antibody libraries on filamentous phage to be utilized for generating antigen specific antibodies in a matter of weeks. Since then, more than 70 phage–derived antibodies entered clinical studies and 14 of them have been approved. These antibodies are indicated for cancer, and non-cancer medical conditions, such as inflammatory, optical, infectious, or immunological diseases. This review will illustrate the utility of phage display as a powerful platform for therapeutic antibodies discovery and describe in detail all the approved mAbs derived from phage display.
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Affiliation(s)
- Mohamed A Alfaleh
- Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia.,Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hashem O Alsaab
- Department of Pharmaceutics and Pharmaceutical Technology, College of Pharmacy, Taif University, Taif, Saudi Arabia
| | - Ahmad Bakur Mahmoud
- College of Applied Medical Sciences, Taibah University, Medina, Saudi Arabia
| | - Almohanad A Alkayyal
- Department of Medical Laboratory Technology, University of Tabuk, Tabuk, Saudi Arabia
| | - Martina L Jones
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia.,Australian Research Council Training Centre for Biopharmaceutical Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Stephen M Mahler
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia.,Australian Research Council Training Centre for Biopharmaceutical Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Anwar M Hashem
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
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Cai L, Cao M, Regenstein J. Slow-Release and Nontoxic Pickering Emulsion Platform for Antimicrobial Peptide. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:7453-7466. [PMID: 32559384 DOI: 10.1021/acs.jafc.0c00874] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The resistance in microorganisms against many conventional antibiotics has become a serious global health problem. However, antibacterial drug delivery materials are still limited in toxicity, short efficacy and reducing inflammation. The novel and natural Pickering emulsions stabilized by antimicrobial peptide nanoparticles were tested as promising platforms to control bacterial resistance development. The parasin I interacted or conjugated with lecithin or chitosan and formed nanoparticles encapsulated by Pickering emulsion. The protonation and deprotonation of amino groups in chitosan and parasin I resulted in nanoparticles in different aggregate states and changed emulsion stability. Moreover, the Pickering emulsion could induce severe bacterial agglomeration on both Gram-positive and Gram-negative bacteria than parasin I through the membrane disintegration mechanism. Furthermore, the Pickering emulsion could alleviate the cytotoxicity of human liver cells and hemolytic activity in rat blood cells. In combination with the lack of acute cytotoxicity in Kunming mice and milder, more effective anti-inflammatory effect in peritonitis demonstrated for these Pickering emulsions, especially chitosan peptide-embedded nanoparticles Pickering emulsion, a potential role in combating multidrug resistant bacteria in biomedical applications.
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Affiliation(s)
- Luyun Cai
- College of Biosystems Engineering and Food Science, National & Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang University, Hangzhou 310058, China
- Ningbo Research Institute, Zhejiang University, Ningbo 315400, China
| | - Minjie Cao
- College of Food Science and Engineering, Bohai University, Jinzhou 121013, China
| | - Joe Regenstein
- Department of Food Science, Cornell University, Ithaca, New York 14853-7201, United States
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33
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Kisil OV, Efimenko TA, Gabrielyan NI, Efremenkova OV. Development of Antimicrobial Therapy Methods to Overcome the Antibiotic Resistance of Acinetobacter baumannii. Acta Naturae 2020; 12:34-45. [PMID: 33173595 PMCID: PMC7604900 DOI: 10.32607/actanaturae.10955] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/19/2020] [Indexed: 12/29/2022] Open
Abstract
The spread of antibiotic resistance among pathogens represents a threat to human health around the world. In 2017, the World Health Organization published a list of 12 top-priority antibiotic-resistant pathogenic bacteria for which new effective antibiotics or new ways of treating the infections caused by them are needed. This review focuses on Acinetobacter baumannii, one of these top-priority pathogens. The pathogenic bacterium A. baumannii is one of the most frequently encountered infectious agents in the world; its clinically significant features include resistance to UV light, drying, disinfectants, and antibiotics. This review looks at the various attempts that have been made to tackle the problem of drug resistance relating to A. baumannii variants without the use of antibiotics. The potential of bacteriophages and antimicrobial peptides in the treatment of infections caused by A. baumannii in both planktonic and biofilm form is assessed. Such topics as research into the development of vaccines based on the outer membrane proteins of A. baumannii and the use of silver nanoparticles, as well as photodynamic and chelate therapy, are also covered.
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Affiliation(s)
- O. V. Kisil
- Gause Institute of New Antibiotics, Moscow, 119021 Russia
| | - T. A. Efimenko
- Gause Institute of New Antibiotics, Moscow, 119021 Russia
| | - N. I. Gabrielyan
- V.I. Shumakov Federal Research Center of Transplantology and Artificial Organs, Ministry of Healthcare of the Russian Federation, Moscow, 1123182 Russia
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Pardoux É, Boturyn D, Roupioz Y. Antimicrobial Peptides as Probes in Biosensors Detecting Whole Bacteria: A Review. Molecules 2020; 25:E1998. [PMID: 32344585 PMCID: PMC7221689 DOI: 10.3390/molecules25081998] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/23/2020] [Accepted: 04/23/2020] [Indexed: 12/17/2022] Open
Abstract
Bacterial resistance is becoming a global issue due to its rapid growth. Potential new drugs as antimicrobial peptides (AMPs) are considered for several decades as promising candidates to circumvent this threat. Nonetheless, AMPs have also been used more recently in other settings such as molecular probes grafted on biosensors able to detect whole bacteria. Rapid, reliable and cost-efficient diagnostic tools for bacterial infection could prevent the spread of the pathogen from the earliest stages. Biosensors based on AMPs would enable easy monitoring of potentially infected samples, thanks to their powerful versatility and integrability in pre-existent settings. AMPs, which show a broad spectrum of interactions with bacterial membranes, can be tailored in order to design ubiquitous biosensors easily adaptable to clinical settings. This review aims to focus on the state of the art of AMPs used as the recognition elements of whole bacteria in label-free biosensors with a particular focus on the characteristics obtained in terms of threshold, volume of sample analysable and medium, in order to assess their workability in real-world applications.
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Affiliation(s)
- Éric Pardoux
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, SyMMES, 38000 Grenoble, France;
- Univ. Grenoble Alpes, CNRS, DCM, 38000 Grenoble, France;
| | - Didier Boturyn
- Univ. Grenoble Alpes, CNRS, DCM, 38000 Grenoble, France;
| | - Yoann Roupioz
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, SyMMES, 38000 Grenoble, France;
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Alfaleh MA, Alsaab HO, Mahmoud AB, Alkayyal AA, Jones ML, Mahler SM, Hashem AM. Phage Display Derived Monoclonal Antibodies: From Bench to Bedside. Front Immunol 2020. [PMID: 32983137 DOI: 10.3389/fimmu.2020.01986/bibtex] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
Abstract
Monoclonal antibodies (mAbs) have become one of the most important classes of biopharmaceutical products, and they continue to dominate the universe of biopharmaceutical markets in terms of approval and sales. They are the most profitable single product class, where they represent six of the top ten selling drugs. At the beginning of the 1990s, an in vitro antibody selection technology known as antibody phage display was developed by John McCafferty and Sir. Gregory Winter that enabled the discovery of human antibodies for diverse applications, particularly antibody-based drugs. They created combinatorial antibody libraries on filamentous phage to be utilized for generating antigen specific antibodies in a matter of weeks. Since then, more than 70 phage-derived antibodies entered clinical studies and 14 of them have been approved. These antibodies are indicated for cancer, and non-cancer medical conditions, such as inflammatory, optical, infectious, or immunological diseases. This review will illustrate the utility of phage display as a powerful platform for therapeutic antibodies discovery and describe in detail all the approved mAbs derived from phage display.
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Affiliation(s)
- Mohamed A Alfaleh
- Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hashem O Alsaab
- Department of Pharmaceutics and Pharmaceutical Technology, College of Pharmacy, Taif University, Taif, Saudi Arabia
| | - Ahmad Bakur Mahmoud
- College of Applied Medical Sciences, Taibah University, Medina, Saudi Arabia
| | - Almohanad A Alkayyal
- Department of Medical Laboratory Technology, University of Tabuk, Tabuk, Saudi Arabia
| | - Martina L Jones
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
- Australian Research Council Training Centre for Biopharmaceutical Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Stephen M Mahler
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
- Australian Research Council Training Centre for Biopharmaceutical Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Anwar M Hashem
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
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Khalaj‐Hedayati A, Chua CLL, Smooker P, Lee KW. Nanoparticles in influenza subunit vaccine development: Immunogenicity enhancement. Influenza Other Respir Viruses 2020; 14:92-101. [PMID: 31774251 PMCID: PMC6928032 DOI: 10.1111/irv.12697] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 09/14/2019] [Accepted: 10/01/2019] [Indexed: 12/25/2022] Open
Abstract
The threat of novel influenza infections has sparked research efforts to develop subunit vaccines that can induce a more broadly protective immunity by targeting selected regions of the virus. In general, subunit vaccines are safer but may be less immunogenic than whole cell inactivated or live attenuated vaccines. Hence, novel adjuvants that boost immunogenicity are increasingly needed as we move toward the era of modern vaccines. In addition, targeting, delivery, and display of the selected antigens on the surface of professional antigen-presenting cells are also important in vaccine design and development. The use of nanosized particles can be one of the strategies to enhance immunogenicity as they can be efficiently recognized by antigen-presenting cells. They can act as both immunopotentiators and delivery system for the selected antigens. This review will discuss on the applications, advantages, limitations, and types of nanoparticles (NPs) used in the preparation of influenza subunit vaccine candidates to enhance humoral and cellular immune responses.
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Affiliation(s)
- Atin Khalaj‐Hedayati
- School of BiosciencesFaculty of Health and Medical SciencesTaylor's UniversitySubang JayaMalaysia
| | - Caroline Lin Lin Chua
- School of BiosciencesFaculty of Health and Medical SciencesTaylor's UniversitySubang JayaMalaysia
| | - Peter Smooker
- Department of Biosciences and Food TechnologySchool of ScienceRMIT UniversityBundooraVictoriaAustralia
| | - Khai Wooi Lee
- School of BiosciencesFaculty of Health and Medical SciencesTaylor's UniversitySubang JayaMalaysia
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Tan P, Lai Z, Zhu Y, Shao C, Akhtar MU, Li W, Zheng X, Shan A. Multiple Strategy Optimization of Specifically Targeted Antimicrobial Peptide Based on Structure-Activity Relationships to Enhance Bactericidal Efficiency. ACS Biomater Sci Eng 2019; 6:398-414. [PMID: 33463238 DOI: 10.1021/acsbiomaterials.9b00937] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Unlike traditional broad-spectrum antibacterial agents, specifically targeted antimicrobial peptides (STAMPs) are difficult for bacteria to develop resistance to due to their unique membrane lytic mechanism. Additionally, STAMPs can maintain a normal ecological balance and provide long-term protection to the body. However, therapeutic applications of STAMPS are hindered by their weak activity and imperfect specificity, as well as lack of knowledge in understanding their structure-activity relationships. To investigate the effects of different parameters on the biological activities of STAMPs, a peptide sequence, WKKIWKDPGIKKWIK, was truncated, extended, and provided with an increased charge and altered amphipathicity. In addition, a novel template modification method for attaching a phage-displayed peptide, which recognized and bound to Escherichia coli (E. coli) cells, to the end of the sequence was introduced. Compared with the traditional template modification method, peptide 13, which contained a phage-displayed peptide at the C-terminus, exhibited superior narrow-spectrum antibacterial activity against E. coli compared to that of parental peptide 2, and the activity and specificity of peptide 13 were increased by 5.0 and 2.4 times, respectively. Additionally, peptide 13 showed low cytotoxicity and relatively desirable salt, serum, acid, alkaline and heat stability. In this study, peptide 13 specifically killed E. coli by causing cytoplasmic membrane rupture and cytosol leakage. In summary, these findings are useful for improving the activity and specificity of STAMPs and show that peptide 13 is able to combat the growing threat of E. coli infections.
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Affiliation(s)
- Peng Tan
- Laboratory of Molecular Nutrition and Immunity, The Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Zhenheng Lai
- Laboratory of Molecular Nutrition and Immunity, The Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Yongjie Zhu
- Laboratory of Molecular Nutrition and Immunity, The Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Changxuan Shao
- Laboratory of Molecular Nutrition and Immunity, The Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Muhammad Usman Akhtar
- Laboratory of Molecular Nutrition and Immunity, The Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Weifen Li
- Institute of Animal Nutrition and Feed Science, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Xin Zheng
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Anshan Shan
- Laboratory of Molecular Nutrition and Immunity, The Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
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38
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Canassa-DeLeo T, Campo VL, Rodrigues LC, Marchiori MF, Fuzo C, Brigido MM, Sandomenico A, Ruvo M, Maranhão AQ, Dias-Baruffi M. Multifaceted antibodies development against synthetic α-dystroglycan mucin glycopeptide as promising tools for dystroglycanopathies diagnostic. Glycoconj J 2019; 37:77-93. [PMID: 31823246 DOI: 10.1007/s10719-019-09893-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 10/23/2019] [Accepted: 10/31/2019] [Indexed: 01/19/2023]
Abstract
Dystroglycanopathies are diseases characterized by progressive muscular degeneration and impairment of patient's quality of life. They are associated with altered glycosylation of the dystrophin-glycoprotein (DGC) complex components, such as α-dystroglycan (α-DG), fundamental in the structural and functional stability of the muscle fiber. The diagnosis of dystroglycanopathies is currently based on the observation of clinical manifestations, muscle biopsies and enzymatic measures, and the available monoclonal antibodies are not specific for the dystrophic hypoglycosylated muscle condition. Thus, modified α-DG mucins have been considered potential targets for the development of new diagnostic strategies toward these diseases. In this context, this work describes the synthesis of the hypoglycosylated α-DG mimetic glycopeptide NHAc-Gly-Pro-Thr-Val-Thr[αMan]-Ile-Arg-Gly-BSA (1) as a potential tool for the development of novel antibodies applicable to dystroglycanopathies diagnosis. Glycopeptide 1 was used for the development of polyclonal antibodies and recombinant monoclonal antibodies by Phage Display technology. Accordingly, polyclonal antibodies were reactive to glycopeptide 1, which enables the application of anti-glycopeptide 1 antibodies in immune reactive assays targeting hypoglycosylated α-DG. Regarding monoclonal antibodies, for the first time variable heavy (VH) and variable light (VL) immunoglobulin domains were selected by Phage Display, identified by NGS and described by in silico analysis. The best-characterized VH and VL domains were cloned, expressed in E. coli Shuffle T7 cells, and used to construct a single chain fragment variable that recognized the Glycopeptide 1 (GpαDG1 scFv). Molecular modelling of glycopeptide 1 and GpαDG1 scFv suggested that their interaction occurs through hydrogen bonds and hydrophobic contacts involving amino acids from scFv (I51, Y33, S229, Y235, and P233) and R8 and α-mannose from Glycopeptide 1.
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Affiliation(s)
- Thais Canassa-DeLeo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café S/N, CEP, Ribeirão Preto, SP, 14040-903, Brazil
| | - Vanessa Leiria Campo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café S/N, CEP, Ribeirão Preto, SP, 14040-903, Brazil.,Centro Universitário Barão de Mauá, Rua Ramos de Azevedo 423, Jardim Paulista, CEP, Ribeirão Preto, 14090-180, SP, Brazil
| | - Lílian Cataldi Rodrigues
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café S/N, CEP, Ribeirão Preto, SP, 14040-903, Brazil
| | - Marcelo Fiori Marchiori
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café S/N, CEP, Ribeirão Preto, SP, 14040-903, Brazil
| | - Carlos Fuzo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café S/N, CEP, Ribeirão Preto, SP, 14040-903, Brazil
| | - Marcelo Macedo Brigido
- Instituto de Ciências Biológicas, Universidade de Brasília, Asa Norte, Brasília, DF, CEP 70910-900, Brazil
| | - Annamaria Sandomenico
- Istituto di Biostrutture e Bioimmagini, CNR, via Mezzocannone, 16, 80134, Naples, Italy
| | - Menotti Ruvo
- Istituto di Biostrutture e Bioimmagini, CNR, via Mezzocannone, 16, 80134, Naples, Italy
| | - Andrea Queiroz Maranhão
- Instituto de Ciências Biológicas, Universidade de Brasília, Asa Norte, Brasília, DF, CEP 70910-900, Brazil
| | - Marcelo Dias-Baruffi
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café S/N, CEP, Ribeirão Preto, SP, 14040-903, Brazil.
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Mehdipour T, Tohidkia MR, Ata Saei A, Kazemi A, Khajeh S, Rahim Rahimi AA, Nikfarjam S, Farhadi M, Halimi M, Soleimani R, Zubarev RA, Nouri M. Tailoring subtractive cell biopanning to identify diffuse gastric adenocarcinoma-associated antigens via human scFv antibodies. Immunology 2019; 159:96-108. [PMID: 31596953 DOI: 10.1111/imm.13129] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 09/27/2019] [Accepted: 10/03/2019] [Indexed: 12/24/2022] Open
Abstract
Among various solid tumours, gastric cancer (GC) is one of the leading causes of cancer-related deaths worldwide. Expansion into the peritoneal cavity, which results from dissemination of diffuse cancer cells, is the main cause of mortality in gastric adenocarcinoma patients. Therefore, investigation of putative biomarkers involved in metastasis is prerequisite for GC management. In an effort to discover potential tumour markers associated with peritoneal metastasis of GC, a semi-synthetic human scFv library (Tomlinson I) was used to isolate novel antibody fragments recognizing MKN-45, a poorly differentiated diffuse gastric adenocarcinoma cell line. Four rounds of subtractive selection each consisting of extensive pre-absorption of phage library with NIH-3T3 murine embryonic fibroblasts and AGS (a well-differentiated intestinal gastric adenocarcinoma) cell line were carried out prior to positive selection on MKN-45 target cells. ELISA-based screening of 192 phage-displayed scFv clones indicated 21 high-affinity binders with specific staining of MKN-45 compared with AGS cells. Diversity analysis of the selected phage-scFvs resulted in five distinct sequences with multiple frequency. Further analysis by ELISA and flow cytometry verified three clones that specifically recognized MKN-45 cells. Liquid chromatography-mass spectrometry analysis of the scFv-immunoprecipitated proteins has led to identification of c-Met, HSP90 α and HSP90 β as candidate biomarkers associated with diffuse GC. Immunohistochemistry revealed the capability of purified scFvs to differentiate diffuse and intestinal gastric adenocarcinoma. Taken together, the isolated MKN-45-specific scFv fragments and their cognate antigens would be beneficial in screening and management as well as targeting and therapy of the diffuse gastric adenocarcinoma.
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Affiliation(s)
- Tayebeh Mehdipour
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Medical Biotechnology, School of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad R Tohidkia
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Amir Ata Saei
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Amir Kazemi
- Department of Microbiology, Islamic Azad University, Shahr-e-Qods Branch, Tehran, Iran
| | - Shirin Khajeh
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali A Rahim Rahimi
- Department of Microbiology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sepideh Nikfarjam
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehrdad Farhadi
- Department of Pathology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Monireh Halimi
- Department of Pathology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ramin Soleimani
- Department of Molecular Biology, Research and Diagnostic Laboratory of Dook, Sari, Iran
| | - Roman A Zubarev
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden.,Department of Pharmacological & Technological Chemistry, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Mohammad Nouri
- Department of Medical Biotechnology, School of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
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Kim Y, Lee H, Park K, Park S, Lim JH, So MK, Woo HM, Ko H, Lee JM, Lim SH, Ko BJ, Park YS, Choi SY, Song DH, Lee JY, Kim SS, Kim DY. Selection and Characterization of Monoclonal Antibodies Targeting Middle East Respiratory Syndrome Coronavirus through a Human Synthetic Fab Phage Display Library Panning. Antibodies (Basel) 2019; 8:E42. [PMID: 31544848 PMCID: PMC6783954 DOI: 10.3390/antib8030042] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/01/2019] [Accepted: 07/07/2019] [Indexed: 12/28/2022] Open
Abstract
Since its first report in the Middle East in 2012, the Middle East respiratory syndrome-coronavirus (MERS-CoV) has become a global concern due to the high morbidity and mortality of individuals infected with the virus. Although the majority of MERS-CoV cases have been reported in Saudi Arabia, the overall risk in areas outside the Middle East remains significant as inside Saudi Arabia. Additional pandemics of MERS-CoV are expected, and thus novel tools and reagents for therapy and diagnosis are urgently needed. Here, we used phage display to develop novel monoclonal antibodies (mAbs) that target MERS-CoV. A human Fab phage display library was panned against the S2 subunit of the MERS-CoV spike protein (MERS-S2P), yielding three unique Fabs (S2A3, S2A6, and S2D5). The Fabs had moderate apparent affinities (Half maximal effective concentration (EC50 = 123-421 nM) for MERS-S2P, showed no cross-reactivity to spike proteins from other CoVs, and were non-aggregating and thermostable (Tm = 61.5-80.4 °C). Reformatting the Fabs into IgGs (Immunoglobulin Gs) greatly increased their apparent affinities (KD = 0.17-1.2 nM), presumably due to the effects of avidity. These apparent affinities were notably higher than that of a previously reported anti-MERS-CoV S2 reference mAb (KD = 8.7 nM). Furthermore, two of the three mAbs (S2A3 and S2D5) bound only MERS-CoV (Erasmus Medical Center (EMC)) and not other CoVs, reflecting their high binding specificity. However, the mAbs lacked MERS-CoV neutralizing activity. Given their high affinity, specificity, and desirable stabilities, we anticipate that these anti-MERS-CoV mAbs would be suitable reagents for developing antibody-based diagnostics in laboratory or hospital settings for point-of-care testing.
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Affiliation(s)
- Yoonji Kim
- New Drug Development Center, Osong Medical Innovation Foundation, Cheongju-si, Chungcheongbuk-do 28160, Korea
| | - Hansaem Lee
- Korea Center for Disease Control, Osong Health Technology Administration Complex, Cheongju-si, Chungcheongbuk-do 28159, Korea
| | - Keunwan Park
- New Drug Development Center, Osong Medical Innovation Foundation, Cheongju-si, Chungcheongbuk-do 28160, Korea
| | - Sora Park
- New Drug Development Center, Osong Medical Innovation Foundation, Cheongju-si, Chungcheongbuk-do 28160, Korea
| | - Ju-Hyeon Lim
- New Drug Development Center, Osong Medical Innovation Foundation, Cheongju-si, Chungcheongbuk-do 28160, Korea
| | - Min Kyung So
- New Drug Development Center, Osong Medical Innovation Foundation, Cheongju-si, Chungcheongbuk-do 28160, Korea
| | - Hye-Min Woo
- Korea Center for Disease Control, Osong Health Technology Administration Complex, Cheongju-si, Chungcheongbuk-do 28159, Korea
| | - Hyemin Ko
- Korea Center for Disease Control, Osong Health Technology Administration Complex, Cheongju-si, Chungcheongbuk-do 28159, Korea
| | - Jeong-Min Lee
- Plexense, Inc., Yongin-si, Gyeonggi-do 441-813, Korea
| | - Sun Hee Lim
- Plexense, Inc., Yongin-si, Gyeonggi-do 441-813, Korea
| | - Byoung Joon Ko
- New Drug Development Center, Osong Medical Innovation Foundation, Cheongju-si, Chungcheongbuk-do 28160, Korea
| | - Yeon-Su Park
- Plexense, Inc., Yongin-si, Gyeonggi-do 441-813, Korea
| | - So-Young Choi
- New Drug Development Center, Osong Medical Innovation Foundation, Cheongju-si, Chungcheongbuk-do 28160, Korea
| | - Du Hyun Song
- New Drug Development Center, Osong Medical Innovation Foundation, Cheongju-si, Chungcheongbuk-do 28160, Korea
| | - Joo-Yeon Lee
- Korea Center for Disease Control, Osong Health Technology Administration Complex, Cheongju-si, Chungcheongbuk-do 28159, Korea
| | - Sung Soon Kim
- Korea Center for Disease Control, Osong Health Technology Administration Complex, Cheongju-si, Chungcheongbuk-do 28159, Korea
| | - Dae Young Kim
- New Drug Development Center, Osong Medical Innovation Foundation, Cheongju-si, Chungcheongbuk-do 28160, Korea.
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Sokullu E, Soleymani Abyaneh H, Gauthier MA. Plant/Bacterial Virus-Based Drug Discovery, Drug Delivery, and Therapeutics. Pharmaceutics 2019; 11:E211. [PMID: 31058814 PMCID: PMC6572107 DOI: 10.3390/pharmaceutics11050211] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/23/2019] [Accepted: 04/25/2019] [Indexed: 02/06/2023] Open
Abstract
Viruses have recently emerged as promising nanomaterials for biotechnological applications. One of the most important applications of viruses is phage display, which has already been employed to identify a broad range of potential therapeutic peptides and antibodies, as well as other biotechnologically relevant polypeptides (including protease inhibitors, minimizing proteins, and cell/organ targeting peptides). Additionally, their high stability, easily modifiable surface, and enormous diversity in shape and size, distinguish viruses from synthetic nanocarriers used for drug delivery. Indeed, several plant and bacterial viruses (e.g., phages) have been investigated and applied as drug carriers. The ability to remove the genetic material within the capsids of some plant viruses and phages produces empty viral-like particles that are replication-deficient and can be loaded with therapeutic agents. This review summarizes the current applications of plant viruses and phages in drug discovery and as drug delivery systems and includes a discussion of the present status of virus-based materials in clinical research, alongside the observed challenges and opportunities.
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Affiliation(s)
- Esen Sokullu
- Institut National de la Recherche Scientifique (INRS), EMT Research Center, Varennes, QC J3X 1S2, Canada.
| | - Hoda Soleymani Abyaneh
- Institut National de la Recherche Scientifique (INRS), EMT Research Center, Varennes, QC J3X 1S2, Canada.
| | - Marc A Gauthier
- Institut National de la Recherche Scientifique (INRS), EMT Research Center, Varennes, QC J3X 1S2, Canada.
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Munisso MC, Yamaoka T. Evolution of Phage Display Approaches to Select Highly Specific Hemocompatible Peptides. Tissue Eng Part C Methods 2019; 25:288-295. [DOI: 10.1089/ten.tec.2018.0367] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Maria Chiara Munisso
- Department of Biomedical Engineering, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka, Japan
| | - Tetsuji Yamaoka
- Department of Biomedical Engineering, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka, Japan
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43
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Jalilzadeh-Razin S, Mantegi M, Tohidkia MR, Pazhang Y, Pourseif MM, Barar J, Omidi Y. Phage antibody library screening for the selection of novel high-affinity human single-chain variable fragment against gastrin receptor: an in silico and in vitro study. ACTA ACUST UNITED AC 2019; 27:21-34. [PMID: 30607886 DOI: 10.1007/s40199-018-0233-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 12/03/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND As a membrane G protein coupled receptors (GPCRs) family, gastrin/cholecystokinin-2 receptor (CCK2R) plays a key role in the initiation and development of gastric cancer. OBJECTIVES Targeting CCK2R by immunotherapeutics such as single-chain variable fragments (scFvs) may provide an effective treatment modality against gastric cancer. Thus, the main objective of this study was to isolate scFvs specific to CCK2R. METHODS To isolate scFvs specific to the CCK2R, we capitalized on a semi-synthetic diverse phage antibody library (PAL) and a solution-phase biopanning process. The library was panned against a biotinylated peptide of the second extracellular loop (ECL2) of CCK2R. After four rounds of biopanning, the selected soluble scFv clones were screened by enzyme-linked immunosorbent assay (ELISA) and examined for specific binding to the peptide. The selected scFvs were purified using immobilized metal affinity chromatography (IMAC). The binding affinity and specificity of the scFvs were examined by the surface plasmon resonance (SPR), immunoblotting and flow cytometry assays and molecular docking using ZDOCK v3.0.2. RESULTS Ten different scFvs were isolated, which displayed binding affinity ranging from 0.68 to 8.0 (nM). Immunoblotting and molecular docking analysis revealed that eight scFvs were able to detect the denatured form of CCK2R protein. Of the isolated scFvs, two scFvs showed high-binding affinity to the human gastric adenocarcinoma AGS cells. CONCLUSIONS Based on our findings, a couple of the selected scFvs showed markedly high-binding affinity to immobilized CCK2R peptide and CCK2R-overexpressing AGS cells. Therefore, these scFvs are proposed to serve as targeting and/or treatment agents in the diagnosis and immunotherapy of CCK2R-positive tumors. Graphical abstract ᅟ.
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Affiliation(s)
- Sepideh Jalilzadeh-Razin
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Malihe Mantegi
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran.,Islamic Azad University of Urmia, Urmia, Iran
| | - Mohammad R Tohidkia
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Yaghub Pazhang
- Department of Biochemistry, Faculty of Veterinary Medicine, Urmia University, Urmia, Iran
| | - Mohammad M Pourseif
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jaleh Barar
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Pharmaceutics, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yadollah Omidi
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran. .,Department of Pharmaceutics, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.
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Ministro J, Manuel AM, Goncalves J. Therapeutic Antibody Engineering and Selection Strategies. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 171:55-86. [PMID: 31776591 DOI: 10.1007/10_2019_116] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Antibody drugs became an increasingly important element of the therapeutic landscape. Their accomplishment has been driven by many unique properties, in particular by their very high specificity and selectivity, in contrast to the off-target liabilities of small molecules (SMs). Antibodies can bring additional functionality to the table with their ability to interact with the immune system, and this can be further manipulated with advances in antibody engineering.The expansion of strategies related to discovery technologies of monoclonal antibodies (mAbs) (phage display, yeast display, ribosome display, bacterial display, mammalian cell surface display, mRNA display, DNA display, transgenic animal, and human B cell derived) opened perspectives for the screening and the selection of therapeutic antibodies for, theoretically, any target from any kind of organism. Moreover, antibody engineering technologies were developed and explored to obtain chosen characteristics of selected leading candidates such as high affinity, low immunogenicity, improved functionality, improved protein production, improved stability, and others. This chapter contains an overview of discovery technologies, mainly display methods and antibody humanization methods for the selection of therapeutic humanized and human mAbs that appeared along the development of these technologies and thereafter. The increasing applications of these technologies will be highlighted in the antibody engineering area (affinity maturation, guided selection to obtain human antibodies) giving promising perspectives for the development of future therapeutics.
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Affiliation(s)
| | - Ana Margarida Manuel
- iMed - Research Institute for Medicines, Faculty of Pharmacy at University of Lisbon, Lisbon, Portugal
| | - Joao Goncalves
- iMed - Research Institute for Medicines, Faculty of Pharmacy at University of Lisbon, Lisbon, Portugal.
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45
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Thong QX, Wong CL, Ooi MK, Kueh CL, Ho KL, Alitheen NB, Tan WS. Peptide inhibitors of Macrobrachium rosenbergii nodavirus. J Gen Virol 2018; 99:1227-1238. [PMID: 30041713 DOI: 10.1099/jgv.0.001116] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Macrobrachium rosenbergii nodavirus (MrNv) causes white tail disease (WTD) in giant freshwater prawns, which leads to devastating economic losses in the aquaculture industry. Despite extensive research on MrNv, there is still no antiviral agent to treat WTD. Thus, the main aim of this study was to identify potential anti-MrNv molecules. A 12-mer phage-displayed peptide library was biopanned against the MrNv virus-like particle (VLP). After four rounds of biopanning, two dominant phages harbouring the amino acid sequences HTKQIPRHIYSA and VSRHQSWHPHDL were selected. An equilibrium binding assay in solution was performed to determine the relative dissociation constant (KDrel) of the interaction between the MrNv VLP and the selected fusion phages. Phage-HTKQIPRHIYSA has a KDrel value of 92.4±22.8 nM, and phage-VSRHQSWHPHDL has a KDrel value of 12.7±3.8 nM. An in-cell elisa was used to determine the inhibitory effect of the synthetic peptides towards the entry of MrNv VLP into Spodoptera frugiperda (Sf9) cells. Peptides HTKQIPRHIYSA and VSRHQSWHPHDL inhibited the entry of the MrNv VLP into Sf9 cells with IC50 values of 30.4±3.6 and 26.5±8.8 µM, respectively. Combination of both peptides showed a significantly higher inhibitory effect with an IC50 of 4.9±0.4 µM. An MTT assay revealed that the viability of MrNv-infected cells increased to about 97 % in the presence of both peptides. A real-time RT-PCR assay showed that simultaneous application of both peptides significantly reduced the number of MrNv per infected cell, from 97±9 to 11±4. These peptides are lead compounds which can be further developed into potent anti-MrNv agents.
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Affiliation(s)
- Qiu Xian Thong
- 1Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Chuan Loo Wong
- 1Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Man Kwan Ooi
- 1Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.,†Present address: Virus-Host Interaction Research Group, Infectious Disease Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500 Subang Jaya, Selangor, Malaysia
| | - Chare Li Kueh
- 1Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Kok Lian Ho
- 2Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Noorjahan Banu Alitheen
- 3Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.,4Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Wen Siang Tan
- 1Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.,4Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
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Harada LK, Silva EC, Campos WF, Del Fiol FS, Vila M, Dąbrowska K, Krylov VN, Balcão VM. Biotechnological applications of bacteriophages: State of the art. Microbiol Res 2018; 212-213:38-58. [DOI: 10.1016/j.micres.2018.04.007] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/16/2018] [Accepted: 04/25/2018] [Indexed: 02/06/2023]
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47
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Gorman K, McGinnis J, Kay B. Generating FN3-Based Affinity Reagents Through Phage Display. ACTA ACUST UNITED AC 2018; 10:e39. [PMID: 29927113 DOI: 10.1002/cpch.39] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Antibodies are useful tools for detecting individual proteins in complex samples and for learning about their location, amount, binding partners, and function in cells. Unfortunately, generating antibodies is time consuming and laborious, and their affinity and/or specificity is often limited. This protocol offers a fast and inexpensive alternative to generate antibody surrogates through phage display of a library of fibronectin type III (FN3) monobody variants and affinity selection for binders. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Kevin Gorman
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois
| | - Jennifer McGinnis
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois
| | - Brian Kay
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois
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48
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Irani N, Basardeh E, Samiee F, Fateh A, Shooraj F, Rahimi A, Shahcheraghi F, Vaziri F, Masoumi M, Pazhouhandeh M, Siadat SD, Kazemi-Lomedasht F, Jamnani FR. The inhibitory effect of the combination of two new peptides on biofilm formation by Acinetobacter baumannii. Microb Pathog 2018; 121:310-317. [PMID: 29859290 DOI: 10.1016/j.micpath.2018.05.051] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 04/27/2018] [Accepted: 05/29/2018] [Indexed: 12/13/2022]
Abstract
The emergence of extensively drug-resistant (XDR) Acinetobacter baumannii strains and the limited number of efficacious antibiotics demonstrate an urgent need to develop novel agents to treat infections caused by this dangerous pathogen. To find antimicrobial peptides against A. baumannii growing either in planktonic or in biofilm mode, biopanning was carried out with a peptide library on five XDR A. baumannii strains grown in the medium containing human blood (blood biopanning) and biofilms formed by these strains (biofilm biopanning). Two groups of peptides were identified, among which two peptides N10 (from blood biopanning) and NB2 (from biofilm biopanning) were selected and synthesized for more assessments. The selected peptides showed significant binding to A. baumannii rather than to the human cell line Caco-2. Both peptides were effective against A. baumannii and showed antibacterial activities (minimum inhibitory concentration (MIC) 500 μg/ml). In the biofilm inhibition assay, NB2 reduced biofilm more efficiently (75%) than N10 (50%). The combination of the two peptides could function better than each peptide alone to prevent biofilm formation by A. baumannii. Supplementation of conventional therapy with a mixture of peptides targeting A. baumannii or using peptides to deliver antibiotics specifically to the site of infection may be promising to control A. baumannii-related diseases.
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Affiliation(s)
- Nazanin Irani
- Department of Microbiology, Islamic Azad University, Tehran North Branch, Tehran, Iran; Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran
| | - Eilnaz Basardeh
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Samiee
- Department of Microbial Biotechnology, Islamic Azad University, Pharmaceutical Sciences Branch, Tehran, Iran
| | - Abolfazl Fateh
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran; Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Fahimeh Shooraj
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran; Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Ayoub Rahimi
- Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Fereshteh Shahcheraghi
- Department of Bacteriology, Microbiology Research Center, Pasteur Institute of Iran, Iran
| | - Farzam Vaziri
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran; Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Morteza Masoumi
- Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | | | - Seyed Davar Siadat
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran; Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Kazemi-Lomedasht
- Venom & Biotherapeutics Molecules Lab, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Rahimi Jamnani
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran; Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran.
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49
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Vij R, Lin Z, Chiang N, Vernes JM, Storek KM, Park S, Chan J, Meng YG, Comps-Agrar L, Luan P, Lee S, Schneider K, Bevers J, Zilberleyb I, Tam C, Koth CM, Xu M, Gill A, Auerbach MR, Smith PA, Rutherford ST, Nakamura G, Seshasayee D, Payandeh J, Koerber JT. A targeted boost-and-sort immunization strategy using Escherichia coli BamA identifies rare growth inhibitory antibodies. Sci Rep 2018; 8:7136. [PMID: 29740124 PMCID: PMC5940829 DOI: 10.1038/s41598-018-25609-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 04/25/2018] [Indexed: 12/19/2022] Open
Abstract
Outer membrane proteins (OMPs) in Gram-negative bacteria are essential for a number of cellular functions including nutrient transport and drug efflux. Escherichia coli BamA is an essential component of the OMP β-barrel assembly machinery and a potential novel antibacterial target that has been proposed to undergo large (~15 Å) conformational changes. Here, we explored methods to isolate anti-BamA monoclonal antibodies (mAbs) that might alter the function of this OMP and ultimately lead to bacterial growth inhibition. We first optimized traditional immunization approaches but failed to identify mAbs that altered cell growth after screening >3000 hybridomas. We then developed a “targeted boost-and-sort” strategy that combines bacterial cell immunizations, purified BamA protein boosts, and single hybridoma cell sorting using amphipol-reconstituted BamA antigen. This unique workflow improves the discovery efficiency of FACS + mAbs by >600-fold and enabled the identification of rare anti-BamA mAbs with bacterial growth inhibitory activity in the presence of a truncated lipopolysaccharide layer. These mAbs represent novel tools for dissecting the BamA-mediated mechanism of β-barrel folding and our workflow establishes a new template for the efficient discovery of novel mAbs against other highly dynamic membrane proteins.
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Affiliation(s)
- Rajesh Vij
- Department of Antibody Engineering, Genentech, 1 DNA Way, South San Francisco, California, 94080, USA
| | - Zhonghua Lin
- Department of Antibody Engineering, Genentech, 1 DNA Way, South San Francisco, California, 94080, USA
| | - Nancy Chiang
- Department of Antibody Engineering, Genentech, 1 DNA Way, South San Francisco, California, 94080, USA
| | - Jean-Michel Vernes
- Department of Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California, 94080, USA
| | - Kelly M Storek
- Department of Infectious Diseases, Genentech, 1 DNA Way, South San Francisco, California, 94080, USA
| | - Summer Park
- Department of Translational Immunology, Genentech, 1 DNA Way, South San Francisco, California, 94080, USA
| | - Joyce Chan
- Department of Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California, 94080, USA
| | - Y Gloria Meng
- Department of Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California, 94080, USA
| | - Laetitia Comps-Agrar
- Department of Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California, 94080, USA
| | - Peng Luan
- Department of Antibody Engineering, Genentech, 1 DNA Way, South San Francisco, California, 94080, USA
| | - Sophia Lee
- Department of Antibody Engineering, Genentech, 1 DNA Way, South San Francisco, California, 94080, USA
| | - Kellen Schneider
- Department of Antibody Engineering, Genentech, 1 DNA Way, South San Francisco, California, 94080, USA
| | - Jack Bevers
- Department of Antibody Engineering, Genentech, 1 DNA Way, South San Francisco, California, 94080, USA
| | - Inna Zilberleyb
- Department of BioMolecular Resources, Genentech, 1 DNA Way, South San Francisco, California, 94080, USA
| | - Christine Tam
- Department of BioMolecular Resources, Genentech, 1 DNA Way, South San Francisco, California, 94080, USA
| | - Christopher M Koth
- Department of Structural Biology, Genentech, 1 DNA Way, South San Francisco, California, 94080, USA
| | - Min Xu
- Department of Translational Immunology, Genentech, 1 DNA Way, South San Francisco, California, 94080, USA
| | - Avinash Gill
- Department of Antibody Engineering, Genentech, 1 DNA Way, South San Francisco, California, 94080, USA
| | - Marcy R Auerbach
- Department of Infectious Diseases, Genentech, 1 DNA Way, South San Francisco, California, 94080, USA
| | - Peter A Smith
- Department of Infectious Diseases, Genentech, 1 DNA Way, South San Francisco, California, 94080, USA
| | - Steven T Rutherford
- Department of Infectious Diseases, Genentech, 1 DNA Way, South San Francisco, California, 94080, USA
| | - Gerald Nakamura
- Department of Antibody Engineering, Genentech, 1 DNA Way, South San Francisco, California, 94080, USA
| | - Dhaya Seshasayee
- Department of Antibody Engineering, Genentech, 1 DNA Way, South San Francisco, California, 94080, USA
| | - Jian Payandeh
- Department of Structural Biology, Genentech, 1 DNA Way, South San Francisco, California, 94080, USA.
| | - James T Koerber
- Department of Antibody Engineering, Genentech, 1 DNA Way, South San Francisco, California, 94080, USA.
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50
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McCarthy KA, Kelly MA, Li K, Cambray S, Hosseini AS, van Opijnen T, Gao J. Phage Display of Dynamic Covalent Binding Motifs Enables Facile Development of Targeted Antibiotics. J Am Chem Soc 2018; 140:6137-6145. [PMID: 29701966 DOI: 10.1021/jacs.8b02461] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Antibiotic resistance of bacterial pathogens poses an increasing threat to the wellbeing of our society and urgently calls for new strategies for infection diagnosis and antibiotic discovery. The antibiotic resistance problem at least partially arises from extensive use of broad-spectrum antibiotics. Ideally, for the treatment of infection, one would like to use a narrow-spectrum antibiotic that specifically targets and kills the disease-causing strain. This is particularly important considering the commensal bacterial species that are beneficial and sometimes even critical to the health of a human being. In this contribution, we describe a phage display platform that enables rapid identification of peptide probes for specific bacterial strains. The phage library described herein incorporates 2-acetylphenylboronic acid moieties to elicit dynamic covalent binding to the bacterial cell surface. Screening of the library against live bacterial cells yields submicromolar and highly specific binders for clinical strains of Staphylococcus aureus and Acinetobacter baumannii that display antibiotic resistance. We further show that the identified peptide probes can be readily converted to bactericidal agents that deliver generic toxins to kill the targeted bacterial strain with high specificity. The phage display platform described here is applicable to a wide array of bacterial strains, paving the way to facile diagnosis and development of strain-specific antibiotics.
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Affiliation(s)
- Kelly A McCarthy
- Department of Chemistry, Merkert Chemistry Center , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Michael A Kelly
- Department of Chemistry, Merkert Chemistry Center , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Kaicheng Li
- Department of Chemistry, Merkert Chemistry Center , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Samantha Cambray
- Department of Chemistry, Merkert Chemistry Center , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Azade S Hosseini
- Department of Chemistry, Merkert Chemistry Center , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Tim van Opijnen
- Department of Biology , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Jianmin Gao
- Department of Chemistry, Merkert Chemistry Center , Boston College , Chestnut Hill , Massachusetts 02467 , United States
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