1
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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: 0] [Impact Index Per Article: 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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2
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Cui Z, Ayva CE, Liew YJ, Guo Z, Mutschler R, Dreier B, Fiorito MM, Walden P, Howard CB, Ely F, Plückthun A, Pretorius C, Ungerer JPJ, Buckle AM, Alexandrov K. mRNA Display Pipeline for Protein Biosensor Construction. ACS Sens 2024; 9:2846-2857. [PMID: 38807313 PMCID: PMC11218749 DOI: 10.1021/acssensors.3c02471] [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: 11/20/2023] [Revised: 05/01/2024] [Accepted: 05/21/2024] [Indexed: 05/30/2024]
Abstract
Despite the significant potential of protein biosensors, their construction remains a trial-and-error process. The most obvious approach for addressing this is to utilize modular biosensor architectures where specificity-conferring modalities can be readily generated to recognize new targets. Toward this goal, we established a workflow that uses mRNA display-based selection of hyper-stable monobody domains for the target of choice or ribosome display to select equally stable DARPins. These binders were integrated into a two-component allosteric biosensor architecture based on a calmodulin-reporter chimera. This workflow was tested by developing biosensors for liver toxicity markers such as cytosolic aspartate aminotransferase, mitochondrial aspartate aminotransferase, and alanine aminotransferase 1. We demonstrate that our pipeline consistently produced >103 unique binders for each target within a week. Our analysis revealed that the affinity of the binders for their targets was not a direct predictor of the binder's performance in a biosensor context. The interactions between the binding domains and the reporter module affect the biosensor activity and the dynamic range. We conclude that following binding domain selection, the multiplexed biosensor assembly and prototyping appear to be the most promising approach for identifying biosensors with the desired properties.
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Affiliation(s)
- Zhenling Cui
- ARC
Centre of Excellence in Synthetic Biology, Brisbane, Queensland 4001, Australia
- Centre
for Agriculture and the Bioeconomy, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
- School
of Biology and Environmental Science, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
| | - Cagla Ergun Ayva
- Centre
for Agriculture and the Bioeconomy, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
- School
of Biology and Environmental Science, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
| | - Yi Jin Liew
- CSIRO
Health & Biosecurity, Westmead, New South Wales 2145,Australia
| | - Zhong Guo
- ARC
Centre of Excellence in Synthetic Biology, Brisbane, Queensland 4001, Australia
- Centre
for Agriculture and the Bioeconomy, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
- School
of Biology and Environmental Science, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
| | - Roxane Mutschler
- Centre
for Agriculture and the Bioeconomy, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
- School
of Biology and Environmental Science, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
| | - Birgit Dreier
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Maria M Fiorito
- Centre
for Agriculture and the Bioeconomy, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
- School
of Biology and Environmental Science, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
| | - Patricia Walden
- Centre
for Agriculture and the Bioeconomy, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
- School
of Biology and Environmental Science, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
| | - Christopher B Howard
- Australian
Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
| | | | - Andreas Plückthun
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Carel Pretorius
- Department
of Chemical Pathology, Pathology Queensland, Brisbane, Queensland 4006, Australia
- Faculty
of Health and Behavioural Sciences, The
University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jacobus PJ Ungerer
- Department
of Chemical Pathology, Pathology Queensland, Brisbane, Queensland 4006, Australia
- Faculty
of Health and Behavioural Sciences, The
University of Queensland, Brisbane, Queensland 4072, Australia
| | | | - Kirill Alexandrov
- ARC
Centre of Excellence in Synthetic Biology, Brisbane, Queensland 4001, Australia
- Centre
for Agriculture and the Bioeconomy, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
- School
of Biology and Environmental Science, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
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3
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Fujino T, Sonoda R, Higashinagata T, Mishiro-Sato E, Kano K, Murakami H. Ser/Leu-swapped cell-free translation system constructed with natural/in vitro transcribed-hybrid tRNA set. Nat Commun 2024; 15:4143. [PMID: 38755134 PMCID: PMC11099018 DOI: 10.1038/s41467-024-48056-z] [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: 08/22/2023] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
The Ser/Leu-swapped genetic code can act as a genetic firewall, mitigating biohazard risks arising from horizontal gene transfer in genetically modified organisms. Our prior work demonstrated the orthogonality of this swapped code to the standard genetic code using a cell-free translation system comprised of 21 in vitro transcribed tRNAs. In this study, to advance this system for protein engineering, we introduce a natural/in vitro transcribed-hybrid tRNA set. This set combines natural tRNAs from Escherichia coli (excluding Ser, Leu, and Tyr) and in vitro transcribed tRNAs, encompassing anticodon-swapped tRNASerGAG and tRNALeuGGA. This approach reduces the number of in vitro transcribed tRNAs required from 21 to only 4. In this optimized system, the production of a model protein, superfolder green fluorescent protein, increases to 3.5-fold. With this hybrid tRNA set, the Ser/Leu-swapped cell-free translation system will stand as a potent tool for protein production with reduced biohazard concerns in future biological endeavors.
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MESH Headings
- Cell-Free System
- Protein Biosynthesis
- Escherichia coli/genetics
- Escherichia coli/metabolism
- RNA, Transfer, Leu/genetics
- RNA, Transfer, Leu/metabolism
- RNA, Transfer, Ser/metabolism
- RNA, Transfer, Ser/genetics
- Genetic Code
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Green Fluorescent Proteins/metabolism
- Green Fluorescent Proteins/genetics
- Protein Engineering/methods
- Transcription, Genetic
- Anticodon/genetics
- Anticodon/metabolism
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Affiliation(s)
- Tomoshige Fujino
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Ryogo Sonoda
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Taito Higashinagata
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Emi Mishiro-Sato
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
| | - Keiko Kano
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
| | - Hiroshi Murakami
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan.
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, Japan.
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4
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Kobayashi T, Yamazaki K, Shinada J, Mizunuma M, Furukawa K, Chuman Y. Identification of Inhibitors of the Disease-Associated Protein Phosphatase Scp1 Using Antibody Mimetic Molecules. Int J Mol Sci 2024; 25:3737. [PMID: 38612548 PMCID: PMC11011526 DOI: 10.3390/ijms25073737] [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: 02/28/2024] [Revised: 03/18/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024] Open
Abstract
Protein phosphorylation is a prevalent translational modification, and its dysregulation has been implicated in various diseases, including cancer. Despite its significance, there is a lack of specific inhibitors of the FCP/SCP-type Ser/Thr protein phosphatase Scp1, characterized by high specificity and affinity. In this study, we focused on adnectin, an antibody-mimetic protein, aiming to identify Scp1-specific binding molecules with a broad binding surface that target the substrate-recognition site of Scp1. Biopanning of Scp1 was performed using an adnectin-presenting phage library with a randomized FG loop. We succeeded in identifying FG-1Adn, which showed high affinity and specificity for Scp1. Ala scanning analysis of the Scp1-binding sequence in relation to the FG-1 peptide revealed that hydrophobic residues, including aromatic amino acids, play important roles in Scp1 recognition. Furthermore, FG-1Adn was found to co-localize with Scp1 in cells, especially on the plasma membrane. In addition, Western blotting analysis showed that FG-1Adn increased the phosphorylation level of the target protein of Scp1 in cells, indicating that FG-1Adn can inhibit the function of Scp1. These results suggest that FG-1Adn can be used as a specific inhibitor of Scp1.
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Affiliation(s)
| | | | | | | | | | - Yoshiro Chuman
- Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181, Japan; (T.K.); (K.Y.); (J.S.); (M.M.); (K.F.)
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5
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Yamano K, Sawada M, Kikuchi R, Nagataki K, Kojima W, Endo R, Kinefuchi H, Sugihara A, Fujino T, Watanabe A, Tanaka K, Hayashi G, Murakami H, Matsuda N. Optineurin provides a mitophagy contact site for TBK1 activation. EMBO J 2024; 43:754-779. [PMID: 38287189 PMCID: PMC10907724 DOI: 10.1038/s44318-024-00036-1] [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: 11/09/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 01/31/2024] Open
Abstract
Tank-binding kinase 1 (TBK1) is a Ser/Thr kinase that is involved in many intracellular processes, such as innate immunity, cell cycle, and apoptosis. TBK1 is also important for phosphorylating the autophagy adaptors that mediate the selective autophagic removal of damaged mitochondria. However, the mechanism by which PINK1-Parkin-mediated mitophagy activates TBK1 remains largely unknown. Here, we show that the autophagy adaptor optineurin (OPTN) provides a unique platform for TBK1 activation. Both the OPTN-ubiquitin and the OPTN-pre-autophagosomal structure (PAS) interaction axes facilitate assembly of the OPTN-TBK1 complex at a contact sites between damaged mitochondria and the autophagosome formation sites. At this assembly point, a positive feedback loop for TBK1 activation is initiated that accelerates hetero-autophosphorylation of the protein. Expression of monobodies engineered here to bind OPTN impaired OPTN accumulation at contact sites, as well as the subsequent activation of TBK1, thereby inhibiting mitochondrial degradation. Taken together, these data show that a positive and reciprocal relationship between OPTN and TBK1 initiates autophagosome biogenesis on damaged mitochondria.
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Affiliation(s)
- Koji Yamano
- Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan.
| | - Momoha Sawada
- Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Reika Kikuchi
- Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Kafu Nagataki
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Waka Kojima
- Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Ryu Endo
- Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Hiroki Kinefuchi
- Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Atsushi Sugihara
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Tomoshige Fujino
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Aiko Watanabe
- Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Keiji Tanaka
- Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Gosuke Hayashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Hiroshi Murakami
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Noriyuki Matsuda
- Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
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6
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Zeng Y, Woolley M, Chockalingam K, Thomas B, Arora S, Hook M, Chen Z. Click display: a rapid and efficient in vitro protein display method for directed evolution. Nucleic Acids Res 2023; 51:e89. [PMID: 37548398 PMCID: PMC10484664 DOI: 10.1093/nar/gkad643] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/20/2023] [Accepted: 07/22/2023] [Indexed: 08/08/2023] Open
Abstract
We describe a novel method for in vitro protein display-click display-that does not depend on maintaining RNA integrity during biopanning and yields covalently linked protein-cDNA complexes from double-stranded input DNA within 2 h. The display is achieved in a one-pot format encompassing transcription, translation and reverse transcription reactions in series. Stable linkage between proteins and the encoding cDNA is mediated by a modified DNA linker-ML-generated via a click chemistry reaction between a puromycin-containing oligo and a cDNA synthesis primer. Biopanning of a click-displayed mock library coupled with next-generation sequencing analysis revealed >600-fold enrichment of target binders within a single round of panning. A synthetic library of Designed Ankyrin Repeat Proteins (DARPins) with ∼1012 individual members was generated using click display in a 25-μl reaction and six rounds of library panning against a model protein yielded a panel of nanomolar binders. This study establishes click display as a powerful tool for protein binder discovery/engineering and provides a convenient platform for in vitro biopanning selection even in RNase-rich environments such as on whole cells.
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Affiliation(s)
- Yu Zeng
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Michael Woolley
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Karuppiah Chockalingam
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Benjamin Thomas
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, Houston, TX 77030, USA
| | - Srishtee Arora
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX 77030, USA
| | - Magnus Hook
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX 77030, USA
| | - Zhilei Chen
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, Houston, TX 77030, USA
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7
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Umemoto S, Kondo T, Fujino T, Hayashi G, Murakami H. Large-scale analysis of mRNA sequences localized near the start and amber codons and their impact on the diversity of mRNA display libraries. Nucleic Acids Res 2023; 51:7465-7479. [PMID: 37395404 PMCID: PMC10415131 DOI: 10.1093/nar/gkad555] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 06/14/2023] [Accepted: 06/18/2023] [Indexed: 07/04/2023] Open
Abstract
Extremely diverse libraries are essential for effectively selecting functional peptides or proteins, and mRNA display technology is a powerful tool for generating such libraries with over 1012-1013 diversity. Particularly, the protein-puromycin linker (PuL)/mRNA complex formation yield is determining for preparing the libraries. However, how mRNA sequences affect the complex formation yield remains unclear. To study the effects of N-terminal and C-terminal coding sequences on the complex formation yield, puromycin-attached mRNAs containing three random codons after the start codon (32768 sequences) or seven random bases next to the amber codon (6480 sequences) were translated. Enrichment scores were calculated by dividing the appearance rate of every sequence in protein-PuL/mRNA complexes by that in total mRNAs. The wide range of enrichment scores (0.09-2.10 for N-terminal and 0.30-4.23 for C-terminal coding sequences) indicated that the N-terminal and C-terminal coding sequences strongly affected the complex formation yield. Using C-terminal GGC-CGA-UAG-U sequences, which resulted in the highest enrichment scores, we constructed highly diverse libraries of monobodies and macrocyclic peptides. The present study provides insights into how mRNA sequences affect the protein/mRNA complex formation yield and will accelerate the identification of functional peptides and proteins involved in various biological processes and having therapeutic applications.
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Affiliation(s)
- Shun Umemoto
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Taishi Kondo
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Tomoshige Fujino
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Gosuke Hayashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
- Japan Science and Technology Agency (JST), PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Hiroshi Murakami
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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8
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Chonira V, Kwon YD, Gorman J, Case JB, Ku Z, Simeon R, Casner RG, Harris DR, Olia AS, Stephens T, Shapiro L, Bender MF, Boyd H, Teng IT, Tsybovsky Y, Krammer F, Zhang N, Diamond MS, Kwong PD, An Z, Chen Z. A potent and broad neutralization of SARS-CoV-2 variants of concern by DARPins. Nat Chem Biol 2023; 19:284-291. [PMID: 36411391 PMCID: PMC10294592 DOI: 10.1038/s41589-022-01193-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 09/30/2022] [Indexed: 11/22/2022]
Abstract
We report the engineering and selection of two synthetic proteins-FSR16m and FSR22-for the possible treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. FSR16m and FSR22 are trimeric proteins composed of DARPin SR16m or SR22 fused with a T4 foldon. Despite selection by a spike protein from a now historical SARS-CoV-2 strain, FSR16m and FSR22 exhibit broad-spectrum neutralization of SARS-CoV-2 strains, inhibiting authentic B.1.351, B.1.617.2 and BA.1.1 viruses, with respective IC50 values of 3.4, 2.2 and 7.4 ng ml-1 for FSR16m. Cryo-EM structures revealed that these DARPins recognize a region of the receptor-binding domain (residues 456, 475, 486, 487 and 489) overlapping a critical portion of the angiotensin-converting enzyme 2 (ACE2)-binding surface. K18-hACE2 transgenic mice inoculated with B.1.617.2 and receiving intranasally administered FSR16m showed less weight loss and 10-100-fold lower viral burden in upper and lower respiratory tracts. The strong and broad neutralization potency makes FSR16m and FSR22 promising candidates for the prevention and treatment of infection by SARS-CoV-2.
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Affiliation(s)
- Vikas Chonira
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX, USA
| | - Young D Kwon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - James Brett Case
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA
| | - Zhiqiang Ku
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Rudo Simeon
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX, USA
| | - Ryan G Casner
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Darcy R Harris
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Adam S Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tyler Stephens
- Vaccine Research Center Electron Microscopy Unit, Cancer Research Technology Program, Leidos Biomedical Research Inc, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Michael F Bender
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Hannah Boyd
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yaroslav Tsybovsky
- Vaccine Research Center Electron Microscopy Unit, Cancer Research Technology Program, Leidos Biomedical Research Inc, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai (ISMMS), New York City, NY, USA
- Department of Pathology, Molecular and Cell based Medicine, ISMMS, New York City, NY, USA
| | - Ningyan Zhang
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA.
- Department of Pathology and Immunology, Department of Molecular Microbiology, and The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO, USA.
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA.
| | - Zhilei Chen
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX, USA.
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9
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Nakata Y, Ode H, Kubota M, Kasahara T, Matsuoka K, Sugimoto A, Imahashi M, Yokomaku Y, Iwatani Y. Cellular APOBEC3A deaminase drives mutations in the SARS-CoV-2 genome. Nucleic Acids Res 2023; 51:783-795. [PMID: 36610792 PMCID: PMC9881129 DOI: 10.1093/nar/gkac1238] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/07/2022] [Accepted: 12/13/2022] [Indexed: 01/09/2023] Open
Abstract
The number of genetic variations in the SARS-CoV-2 genome has been increasing primarily due to continuous viral mutations. Here, we report that the human APOBEC3A (A3A) cytidine deaminase plays a critical role in the induction of C-to-U substitutions in the SARS-CoV-2 genome. Bioinformatic analysis of the chronological genetic changes in a sequence database indicated that the largest UC-to-UU mutation signature, consistent with APOBEC-recognized nucleotide motifs, was predominant in single-stranded RNA regions of the viral genome. In SARS-CoV-2-infected cells, exogenous expression of A3A but not expression of other APOBEC proteins induced UC-to-UU mutations in viral RNA (vRNA). Additionally, the mutated C bases were often located at the tips in bulge or loop regions in the vRNA secondary structure. Interestingly, A3A mRNA expression was drastically increased by interferons (IFNs) and tumour necrosis factor-α (TNF-α) in epithelial cells derived from the respiratory system, a site of efficient SARS-CoV-2 replication. Moreover, the UC-to-UU mutation rate was increased in SARS-CoV-2 produced from lung epithelial cells treated with IFN-ß and TNF-α, but not from CRISPR/Cas9-based A3A knockout cells. Collectively, these findings demonstrate that A3A is a primary host factor that drives mutations in the SARS-CoV-2 RNA genome via RNA editing.
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Affiliation(s)
- Yoshihiro Nakata
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan,Department of AIDS Research, Division of Basic Medicine, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Hirotaka Ode
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Mai Kubota
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Takaaki Kasahara
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan,Department of Respiratory Medicine, Division of Internal Medicine, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Kazuhiro Matsuoka
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Atsuko Sugimoto
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Mayumi Imahashi
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Yoshiyuki Yokomaku
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Yasumasa Iwatani
- To whom correspondence should be addressed. Tel: +81 52 951 1111; Fax: +81 52 963 3970;
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10
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Abstract
INTRODUCTION The SARS-CoV-2 pandemic, and the subsequent limitations on standard diagnostics, has vastly expanded the user base of Reverse Transcription Loop-mediated isothermal Amplification (RT-LAMP) in fundamental research and development. RT-LAMP has also penetrated commercial markets, with emergency use authorizations for clinical diagnosis. AREAS COVERED This review discusses the role of RT-LAMP within the context of other technologies like RT-qPCR and rapid antigen tests, progress in sample preparation strategies to enable simplified workflow for RT-LAMP directly from clinical specimens, new challenges with primer and assay design for the evolving pandemic, prominent detection modalities including colorimetric and CRISPR-mediated methods, and translational research and commercial development of RT-LAMP for clinical applications. EXPERT OPINION RT-LAMP occupies a middle ground between RT-qPCR and rapid antigen tests. The simplicity approaches that of rapid antigen tests, making it suitable for point-of-care use, but the sensitivity nears that of RT-qPCR. RT-LAMP still lags RT-qPCR in fundamental understanding of the mechanism, and the interplay between sample preparation and assay performance. Industry is now beginning to address issues around scalability and usability, which could finally enable LAMP and RT-LAMP to find future widespread application as a diagnostic for other conditions, including other pathogens with pandemic potential.
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Affiliation(s)
- Gihoon Choi
- Biotechnology & Bioengineering Department, Sandia National Laboratories, Livermore, CA, USA
| | - Taylor J Moehling
- Biotechnology & Bioengineering Department, Sandia National Laboratories, Livermore, CA, USA
| | - Robert J Meagher
- Biotechnology & Bioengineering Department, Sandia National Laboratories, Livermore, CA, USA
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11
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Li Y, Qiao J, Han X, Zhao Z, Kou J, Zhang W, Man S, Ma L. Needs, Challenges and Countermeasures of SARS-CoV-2 Surveillance in Cold-Chain Foods and Packaging to Prevent Possible COVID-19 Resurgence: A Perspective from Advanced Detections. Viruses 2022; 15:120. [PMID: 36680157 PMCID: PMC9864631 DOI: 10.3390/v15010120] [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: 12/01/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/03/2023] Open
Abstract
The pandemic caused by SARS-CoV-2 has a huge impact on the global economy. SARS-CoV-2 could possibly and potentially be transmitted to humans through cold-chain foods and packaging (namely good-to-human), although it mainly depends on a human-to-human route. It is imperative to develop countermeasures to cope with the spread of viruses and fulfil effective surveillance of cold-chain foods and packaging. This review outlined SARS-CoV-2-related cold-chain food incidents and current methods for detecting SARS-CoV-2. Then the needs, challenges and practicable countermeasures for SARS-CoV-2 detection, specifically for cold-chain foods and packaging, were underlined. In fact, currently established detection methods for SARS-CoV-2 are mostly used for humans; thus, these may not be ideally applied to cold-chain foods directly. Therefore, it creates a need to develop novel methods and low-cost, automatic, mini-sized devices specifically for cold-chain foods and packaging. The review intended to draw people's attention to the possible spread of SARS-CoV-2 with cold-chain foods and proposed perspectives for futuristic cold-chain foods monitoring during the pandemic.
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Affiliation(s)
- Yaru Li
- State Key Laboratory of Food Nutrition and Safety, Tianjin 300457, China
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin 300457, China
- Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin 300457, China
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin 300457, China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Jiali Qiao
- State Key Laboratory of Food Nutrition and Safety, Tianjin 300457, China
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin 300457, China
- Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin 300457, China
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin 300457, China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Xiao Han
- State Key Laboratory of Food Nutrition and Safety, Tianjin 300457, China
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin 300457, China
- Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin 300457, China
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin 300457, China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Zhiying Zhao
- State Key Laboratory of Food Nutrition and Safety, Tianjin 300457, China
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin 300457, China
- Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin 300457, China
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin 300457, China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Jun Kou
- State Key Laboratory of Food Nutrition and Safety, Tianjin 300457, China
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin 300457, China
- Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin 300457, China
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin 300457, China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Wenlu Zhang
- State Key Laboratory of Food Nutrition and Safety, Tianjin 300457, China
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin 300457, China
- Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin 300457, China
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin 300457, China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Shuli Man
- State Key Laboratory of Food Nutrition and Safety, Tianjin 300457, China
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin 300457, China
- Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin 300457, China
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin 300457, China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Long Ma
- State Key Laboratory of Food Nutrition and Safety, Tianjin 300457, China
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin 300457, China
- Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin 300457, China
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin 300457, China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
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12
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Takamure K, Sakamoto Y, Iwatani Y, Amano H, Yagi T, Uchiyama T. Characteristics of collection and inactivation of virus in air flowing inside a winding conduit equipped with 280 nm deep UV-LEDs. ENVIRONMENT INTERNATIONAL 2022; 170:107580. [PMID: 36252438 DOI: 10.1016/j.envint.2022.107580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 10/06/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
A general-purpose virus inactivation unit that can inactivate viruses was developed using deep ultraviolet (DUV) LEDs that emit DUV rays with a wavelength of 280 nm. The inside of the virus inactivation unit is a rectangular conduit with a sharp turn of 180° (sharp-turned rectangular conduit). Virus inactivation is attempted by directly irradiating the air passing through the conduit with DUV rays. The flow characteristics of air and virus particles inside the virus inactivation unit were investigated using numerical simulations. The air was locally accelerated at the sharp turn parts and flowed along the partition plate in the sharp-turned rectangular conduit. The aerosol particles moving in the sharp-turned rectangular conduit were greatly bent in orbit at the sharp turn parts, and then rapidly approached the partition plate at the lower part of the conduit. Consequently, many particles collided with the partition plates behind the sharp-turn parts. SARS-CoV-2 virus was nebulized in the virus inactivation unit, and the RNA concentration and virus inactivation rate with and without the emission of DUV-LEDs were measured in the experiment. The concentration of SARS-CoV-2 RNA was reduced to 60% through DUV-LED irradiation. In addition, SARS-CoV-2 passing through the virus inactivation unit was inactivated below the detection limit by the emission of DUV-LEDs. The virus inactivation rate and the value of the detection limit corresponded to 99.38% and 35.36 TCID50/mL, respectively.
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Affiliation(s)
- Kotaro Takamure
- Institute of Materials and Systems for Sustainability, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.
| | - Yasuaki Sakamoto
- Graduate School of Informatics, Nagoya University, Nagoya 464-8601, Japan
| | - Yasumasa Iwatani
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya 460-0001, Japan.
| | - Hiroshi Amano
- Institute of Materials and Systems for Sustainability, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.
| | - Tetsuya Yagi
- Department of Infectious Diseases, Nagoya University Hospital, Nagoya 466-0065, Japan.
| | - Tomomi Uchiyama
- Institute of Materials and Systems for Sustainability, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.
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13
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Chen L, Zhang H, Li M, Wu B, Zhang Z, Gong R. An intranasal vaccine targeting the receptor binding domain of SARS-CoV-2 elicits a protective immune response. Front Immunol 2022; 13:1005321. [DOI: 10.3389/fimmu.2022.1005321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/21/2022] [Indexed: 11/17/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogen responsible for COVID-19, has caused an ongoing worldwide pandemic. Due to the rapid emergence of variants of concern (VOCs), novel vaccines and vaccination strategies are urgently needed. We developed an intranasal vaccine consisting of the SARS-CoV-2 receptor binding domain (RBD) fused to the antibody Fc fragment (RBD-Fc). RBD-Fc could induce strong humoral immune responses via intranasal vaccination. Notably, this immunogen could efficiently induce IgG and IgA and establish mucosal immunity in the respiratory tract. The induced antibodies could efficiently neutralize wild-type SARS-CoV-2 and currently identified SARS-CoV-2 VOCs, including the Omicron variant. In a mouse model, intranasal immunization could provide complete protection against a lethal SARS-CoV-2 challenge. Unfortunately, the limitation of our study is the small number of animals used in the immune response analysis. Our results suggest that recombinant RBD-Fc delivered via intranasal vaccination has considerable potential as a mucosal vaccine that may reduce the risk of SARS-CoV-2 infection.
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14
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Woolley M, Chen Z. A PCR-free rapid protocol for one-pot construction of highly diverse genetic libraries. PLoS One 2022; 17:e0276338. [PMID: 36315516 PMCID: PMC9621413 DOI: 10.1371/journal.pone.0276338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 10/04/2022] [Indexed: 11/05/2022] Open
Abstract
In vitro protein display methods can access extensive libraries (e.g., 1012-1014) and play an increasingly important role in protein engineering. However, the preparation of large libraries remains a laborious and time-consuming process. Here we report an efficient one-pot ligation & elongation (L&E) method for sizeable synthetic library preparation free of PCR amplification or any purification steps. As a proof of concept, we constructed an ankyrin repeat protein templated synthetic library with 1011 variants in 150 μL volume. The entire process from the oligos to DNA template ready for transcription is linearly scalable and took merely 90 minutes. We believe this L&E method can significantly simplify the preparation of synthetic libraries and accelerate in vitro protein display experiments.
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Affiliation(s)
- Michael Woolley
- Microbial Pathogenesis and Immunology Department, Texas A&M Health Science Center, Bryan, Texas, United States of America
| | - Zhilei Chen
- Microbial Pathogenesis and Immunology Department, Texas A&M Health Science Center, Bryan, Texas, United States of America
- * E-mail:
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15
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Bruncsics B, Errington WJ, Sarkar CA. MVsim is a toolset for quantifying and designing multivalent interactions. Nat Commun 2022; 13:5029. [PMID: 36068204 PMCID: PMC9448752 DOI: 10.1038/s41467-022-32496-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 08/03/2022] [Indexed: 11/17/2022] Open
Abstract
Arising through multiple binding elements, multivalency can specify the avidity, duration, cooperativity, and selectivity of biomolecular interactions, but quantitative prediction and design of these properties has remained challenging. Here we present MVsim, an application suite built around a configurational network model of multivalency to facilitate the quantification, design, and mechanistic evaluation of multivalent binding phenomena through a simple graphical user interface. To demonstrate the utility and versatility of MVsim, we first show that both monospecific and multispecific multivalent ligand-receptor interactions, with their noncanonical binding kinetics, can be accurately simulated. Further, to illustrate the conceptual insights into multivalent systems that MVsim can provide, we apply it to quantitatively predict the ultrasensitivity and performance of multivalent-encoded protein logic gates, evaluate the inherent programmability of multispecificity for selective receptor targeting, and extract rate constants of conformational switching for the SARS-CoV-2 spike protein and model its binding to ACE2 as well as multivalent inhibitors of this interaction. MVsim and instructional tutorials are freely available at https://sarkarlab.github.io/MVsim/ .
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Affiliation(s)
- Bence Bruncsics
- Department of Measurement and Information Systems, Budapest University of Technology and Economics, Budapest, H-1111, Hungary
| | - Wesley J Errington
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN, 55455-0215, USA
| | - Casim A Sarkar
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN, 55455-0215, USA.
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16
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Development of Antibody-like Proteins Targeting the Oncogenic Ser/Thr Protein Phosphatase PPM1D. Processes (Basel) 2022. [DOI: 10.3390/pr10081501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
PPM1D, a protein Ser/Thr phosphatase, is overexpressed in various cancers and functions as an oncogenic protein by inactivating the p53 pathway. Therefore, molecules that bind PPM1D are expected to be useful anti-cancer agents. In this study, we constructed a phage display library based on the antibody-like small molecule protein adnectin and screened for PPM1D-specific binding molecules. We identified two adnectins, PMDB-1 and PMD-24, that bind PPM1D specific B-loop and PPM1D430 as targets, respectively. Specificity analyses of these recombinant proteins using other Ser/Thr protein phosphatases showed that these molecules bind to only PPM1D. Expression of PMDB-1 in breast cancer-derived MCF-7 cells overexpressing endogenous PPM1D stabilized p53, indicating that PMDB-1 functions as an inhibitor of PPM1D. Furthermore, MTT assay exhibited that MCF-7 cells expressing PMDB-1 showed inhibition of cell proliferation. These data suggest that the adnectin PMDB-1 identified in this study can be used as a lead compound for anti-cancer drugs targeting intracellular PPM1D.
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17
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Ahan RE, Hanifehnezhad A, Kehribar EŞ, Oguzoglu TC, Földes K, Özçelik CE, Filazi N, Öztop S, Palaz F, Önder S, Bozkurt EU, Ergünay K, Özkul A, Şeker UÖŞ. A Highly Potent SARS-CoV-2 Blocking Lectin Protein. ACS Infect Dis 2022; 8:1253-1264. [PMID: 35426678 PMCID: PMC9017247 DOI: 10.1021/acsinfecdis.2c00006] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
The COVID-19 (coronavirus
disease-19) pandemic affected more than
180 million people around the globe, causing more than five million
deaths as of January 2022. SARS-CoV-2 (severe acute respiratory syndrome
coronavirus 2), the new coronavirus, has been identified as the primary
cause of the infection. The number of vaccinated people is increasing;
however, prophylactic drugs are highly demanded to ensure secure social
contact. A number of drug molecules have been repurposed to fight
against SARS-CoV-2, and some of them have been proven to be effective
in preventing hospitalization or ICU admissions. Here, we demonstrated
griffithsin (GRFT), a lectin protein, to block the entry of SARS-CoV-2
and its variants, Delta and Omicron, into the Vero E6 cell lines and
IFNAR–/– mouse models by attaching to the
spike protein of SARS-CoV-2. Given the current mutation frequency
of SARS-CoV-2, we believe that GRFT protein-based drugs will have
a high impact in preventing the transmission of both the Wuhan strain
as well as any other emerging variants, including Delta and Omicron
variants, causing the high-speed spread of COVID-19.
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Affiliation(s)
- Recep E. Ahan
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - Alireza Hanifehnezhad
- Faculty of Veterinary Medicine, Department of Virology, Ankara University, Ankara 06110, Turkey
| | - Ebru Ş. Kehribar
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - Tuba C. Oguzoglu
- Faculty of Veterinary Medicine, Department of Virology, Ankara University, Ankara 06110, Turkey
| | - Katalin Földes
- Faculty of Veterinary Medicine, Department of Virology, Ankara University, Ankara 06110, Turkey
| | - Cemile E. Özçelik
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - Nazlican Filazi
- Faculty of Veterinary Medicine, Department of Virology, Ankara University, Ankara 06110, Turkey
| | - Sıdıka Öztop
- Adana Dr. Turgut Noyan Medical and Research Center, Department of Immunology, Baskent University, Adana 01250, Turkey
| | - Fahreddin Palaz
- Faculty of Medicine, Hacettepe University, Ankara 06230, Turkey
| | - Sevgen Önder
- Faculty of Medicine, Department of Medical Pathology, Hacettepe University, Ankara 06230, Turkey
| | - Eray U. Bozkurt
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - Koray Ergünay
- Faculty of Medicine, Department of Medical Microbiology, Virology Unit, Hacettepe University, Ankara 06230, Turkey
| | - Aykut Özkul
- Faculty of Veterinary Medicine, Department of Virology, Ankara University, Ankara 06110, Turkey
- Biotechnology Institute, Ankara University, Ankara 06135, Turkey
| | - Urartu Özgür Şafak Şeker
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
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18
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Kondo T, Matsuoka K, Umemoto S, Fujino T, Hayashi G, Iwatani Y, Murakami H. Monobodies with potent neutralizing activity against SARS-CoV-2 Delta and other variants of concern. Life Sci Alliance 2022; 5:5/6/e202101322. [PMID: 35256514 PMCID: PMC8906176 DOI: 10.26508/lsa.202101322] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 11/24/2022] Open
Abstract
Neutralizing antibodies against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are useful for patients' treatment of the coronavirus disease 2019 (COVID-19). We report here affinity maturation of monobodies against the SARS-CoV-2 spike protein and their neutralizing activity against SARS-CoV-2 B.1.1 (Pango v.3.1.14) as well as four variants of concern. We selected matured monobodies from libraries with multi-site saturation mutagenesis on the recognition loops through in vitro selection. One clone, the C4-AM2 monobody, showed extremely high affinity (K D < 0.01 nM) against the receptor-binding domain of the SARS-CoV-2 B.1.1, even in monomer form. Furthermore, the C4-AM2 monobody efficiently neutralized the SARS-CoV-2 B.1.1 (IC 50 = 46 pM, 0.62 ng/ml), and the Alpha (IC 50 = 77 pM, 1.0 ng/ml), Beta (IC 50 = 0.54 nM, 7.2 ng/ml), Gamma (IC 50 = 0.55 nM, 7.4 ng/ml), and Delta (IC 50 = 0.59 nM, 8.0 ng/ml) variants. The obtained monobodies would be useful as neutralizing proteins against current and potentially hazardous future SARS-CoV-2 variants.
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Affiliation(s)
- Taishi Kondo
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Kazuhiro Matsuoka
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Shun Umemoto
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Tomoshige Fujino
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Gosuke Hayashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan.,Japan Science and Technology Agency (JST), PRESTO, Kawaguchi, Japan
| | - Yasumasa Iwatani
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan .,Division of Basic Medicine, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Hiroshi Murakami
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan.,Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, Japan
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19
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Liang Z, Peng T, Jiao X, Zhao Y, Xie J, Jiang Y, Meng B, Fang X, Yu X, Dai X. Latex Microsphere-Based Bicolor Immunochromatography for Qualitative Detection of Neutralizing Antibody against SARS-CoV-2. BIOSENSORS 2022; 12:bios12020103. [PMID: 35200362 PMCID: PMC8869495 DOI: 10.3390/bios12020103] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/26/2022] [Accepted: 02/02/2022] [Indexed: 05/12/2023]
Abstract
Neutralizing antibody (NAb) is a family of antibodies with special functions, which afford a degree of protection against infection and/or reduce the risk of clinically severe infection. Receptor binding domain (RBD) in the spike protein of SARS-CoV-2, a portion of the S1 subunit, can stimulate the immune system to produce NAb after infection and vaccination. The detection of NAb against SARS-CoV-2 is a simple and direct approach for evaluating a vaccine's effectiveness. In this study, a direct, rapid, and point-of-care bicolor lateral flow immunoassay (LFIA) was developed for NAb against SARS-CoV-2 detection without sample pretreatment, and which was based on the principle of NAb-mediated blockage of the interaction between RBD and angiotensin-converting enzyme 2. In the bicolor LFIA, red and blue latex microspheres (LMs) were used to locate the test and control lines, leading to avoidance of erroneous interpretations of one-colored line results. Under the optimal conditions, NAb against SARS-CoV-2 detection carried out using the bicolor LFIA could be completed within 9 min, and the visible limit of detection was about 48 ng/mL. Thirteen serum samples were analyzed, and the results showed that the NAb levels in three positive serum samples were equal to, or higher than, 736 ng/mL. The LM-based bicolor LFIA allows one-step, rapid, convenient, inexpensive, and user-friendly determination of NAb against SARS-CoV-2 in serum.
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Affiliation(s)
- Zhanwei Liang
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (Z.L.); (X.J.)
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China; (T.P.); (Y.Z.); (J.X.); (Y.J.); (B.M.); (X.F.)
| | - Tao Peng
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China; (T.P.); (Y.Z.); (J.X.); (Y.J.); (B.M.); (X.F.)
| | - Xueshima Jiao
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (Z.L.); (X.J.)
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China; (T.P.); (Y.Z.); (J.X.); (Y.J.); (B.M.); (X.F.)
| | - Yang Zhao
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China; (T.P.); (Y.Z.); (J.X.); (Y.J.); (B.M.); (X.F.)
| | - Jie Xie
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China; (T.P.); (Y.Z.); (J.X.); (Y.J.); (B.M.); (X.F.)
| | - You Jiang
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China; (T.P.); (Y.Z.); (J.X.); (Y.J.); (B.M.); (X.F.)
| | - Bo Meng
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China; (T.P.); (Y.Z.); (J.X.); (Y.J.); (B.M.); (X.F.)
| | - Xiang Fang
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China; (T.P.); (Y.Z.); (J.X.); (Y.J.); (B.M.); (X.F.)
| | - Xiaoping Yu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (Z.L.); (X.J.)
- Correspondence: (X.Y.); (X.D.); Tel./Fax: +86-010-645-24962 (X.D.)
| | - Xinhua Dai
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China; (T.P.); (Y.Z.); (J.X.); (Y.J.); (B.M.); (X.F.)
- Correspondence: (X.Y.); (X.D.); Tel./Fax: +86-010-645-24962 (X.D.)
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20
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Guleken Z, Jakubczyk P, Wiesław P, Krzysztof P, Bulut H, Öten E, Depciuch J, Tarhan N. Characterization of Covid-19 infected pregnant women sera using laboratory indexes, vibrational spectroscopy, and machine learning classifications. Talanta 2022; 237:122916. [PMID: 34736654 PMCID: PMC8491955 DOI: 10.1016/j.talanta.2021.122916] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 09/19/2021] [Accepted: 09/29/2021] [Indexed: 01/08/2023]
Abstract
Herein, we show differences in blood serum of asymptomatic and symptomatic pregnant women infected with COVID-19 and correlate them with laboratory indexes, ATR FTIR and multivariate machine learning methods. We collected the sera of COVID-19 diagnosed pregnant women, in the second trimester (n = 12), third-trimester (n = 7), and second-trimester with severe symptoms (n = 7) compared to the healthy pregnant (n = 11) women, which makes a total of 37 participants. To assign the accuracy of FTIR spectra regions where peak shifts occurred, the Random Forest algorithm, traditional C5.0 single decision tree algorithm and deep neural network approach were used. We verified the correspondence between the FTIR results and the laboratory indexes such as: the count of peripheral blood cells, biochemical parameters, and coagulation indicators of pregnant women. CH2 scissoring, amide II, amide I vibrations could be used to differentiate the groups. The accuracy calculated by machine learning methods was higher than 90%. We also developed a method based on the dynamics of the absorbance spectra allowing to determine the differences between the spectra of healthy and COVID-19 patients. Laboratory indexes of biochemical parameters associated with COVID-19 validate changes in the total amount of proteins, albumin and lipase.
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Affiliation(s)
- Zozan Guleken
- Department of Physiology, Uskudar University Faculty of Medicine, Istanbul, Turkey.
| | | | - Paja Wiesław
- College of Natural Sciences, University of Rzeszów, Poland
| | | | - Huri Bulut
- Department of Medical Biochemistry, Faculty of Medicine Istinye University, Istanbul, Turkey
| | - Esra Öten
- Health Science University Istanbul Kanuni Sultan Suleyman Training and Research Hospital, Department of Obstetrics and Gynecology, Turkey
| | - Joanna Depciuch
- Institute of Nuclear Physics Polish Academy of Science, 31-342, Krakow, Poland.
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21
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Luong AD, Buzid A, Vashist SK, Luong JHT. Perspectives on electrochemical biosensing of COVID-19. CURRENT OPINION IN ELECTROCHEMISTRY 2021; 30:100794. [PMID: 34250313 PMCID: PMC8254385 DOI: 10.1016/j.coelec.2021.100794] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Rapid detection of human coronavirus disease 2019, termed as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or COVID-19 infection, is urgently needed for containment strategy owing to its unprecedented spreading. Novel biosensors can be deployed in remote clinical settings without central facilities for infection screening. Electrochemical biosensors serve as analytical tools for rapid detection of viral structure proteins, mainly spike (S) and nucleocapsid (N) proteins, human immune responses, reactive oxygen species, viral ribonucleic acid, polymerase chain reaction by-products, and other potential biomarkers. The development of point-of-care testing devices is challenging due to the requirement of extensive validation, a time-consuming and expensive step. Together with specific biorecognition molecules, nanomaterial-based biosensors have emerged for the fast detection of early viral infections.
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Affiliation(s)
- Albert D Luong
- Department of Surgery, Jacobs School of Medicine, University of Buffalo, Buffalo, NY, 14215, USA
| | - Alyah Buzid
- Department of Chemistry, College of Science, King Faisal University, P.O. Box 380, Al-Ahsa, 31982, Saudi Arabia
| | - Sandeep K Vashist
- Pictor Pvt. Ltd., 24 Balfour Road Parnell, Auckland, 1052, New Zealand
| | - John H T Luong
- Innovative Chromatography Group, Irish Separation Science Cluster (ISSC), School of Chemistry and Analytical & Biological Chemistry Research Facility (ABCRF), University College Cork, College Road, Cork, T12 YN60, Ireland
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22
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Akkapeddi P, Teng KW, Koide S. Monobodies as tool biologics for accelerating target validation and druggable site discovery. RSC Med Chem 2021; 12:1839-1853. [PMID: 34820623 PMCID: PMC8597423 DOI: 10.1039/d1md00188d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/26/2021] [Indexed: 12/21/2022] Open
Abstract
Despite increased investment and technological advancement, new drug approvals have not proportionally increased. Low drug approval rates, particularly for new targets, are linked to insufficient target validation at early stages. Thus, there remains a strong need for effective target validation techniques. Here, we review the use of synthetic binding proteins as tools for drug target validation, with focus on the monobody platform among several advanced synthetic binding protein platforms. Monobodies with high affinity and high selectivity can be rapidly developed against challenging targets, such as KRAS mutants, using protein engineering technologies. They have strong tendency to bind to functional sites and thus serve as drug-like molecules, and they can serve as targeting ligands for constructing bio-PROTACs. Genetically encoded monobodies are effective "tool biologics" for validating intracellular targets. They promote crystallization and help reveal the atomic structures of the monobody-target interface, which can inform drug design. Using case studies, we illustrate the potential of the monobody technology in accelerating target validation and small-molecule drug discovery.
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Affiliation(s)
- Padma Akkapeddi
- Perlmutter Cancer Center, New York University Langone Medical Center New York NY USA
| | - Kai Wen Teng
- Perlmutter Cancer Center, New York University Langone Medical Center New York NY USA
| | - Shohei Koide
- Perlmutter Cancer Center, New York University Langone Medical Center New York NY USA
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine New York NY USA
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23
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Havranek B, Chan KK, Wu A, Procko E, Islam SM. Computationally Designed ACE2 Decoy Receptor Binds SARS-CoV-2 Spike (S) Protein with Tight Nanomolar Affinity. J Chem Inf Model 2021; 61:4656-4669. [PMID: 34427448 PMCID: PMC8409145 DOI: 10.1021/acs.jcim.1c00783] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Indexed: 12/25/2022]
Abstract
Even with the availability of vaccines, therapeutic options for COVID-19 still remain highly desirable, especially in hospitalized patients with moderate or severe disease. Soluble ACE2 (sACE2) is a promising therapeutic candidate that neutralizes SARS CoV-2 infection by acting as a decoy. Using computational mutagenesis, we designed a number of sACE2 derivatives carrying three to four mutations. The top-predicted sACE2 decoy based on the in silico mutagenesis scan was subjected to molecular dynamics and free-energy calculations for further validation. After illuminating the mechanism of increased binding for our designed sACE2 derivative, the design was verified experimentally by flow cytometry and BLI-binding experiments. The computationally designed sACE2 decoy (ACE2-FFWF) bound the receptor-binding domain of SARS-CoV-2 tightly with low nanomolar affinity and ninefold affinity enhancement over the wild type. Furthermore, cell surface expression was slightly greater than wild-type ACE2, suggesting that the design is well-folded and stable. Having an arsenal of high-affinity sACE2 derivatives will help to buffer against the emergence of SARS CoV-2 variants. Here, we show that computational methods have become sufficiently accurate for the design of therapeutics for current and future viral pandemics.
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Affiliation(s)
- Brandon Havranek
- Department of Chemistry, University of
Illinois at Chicago, Chicago, Illinois 60607, United
States
| | - Kui K. Chan
- Orthogonal Biologics Inc.,
Urbana, Illinois 61801, United States
| | - Austin Wu
- Department of Computer Science,
Northwestern University, Evanston, Illinois 60208,
United States
| | - Erik Procko
- Department of Biochemistry and Cancer Center at
Illinois, University of Illinois, Urbana, Illinois 61801,
United States
| | - Shahidul M. Islam
- Department of Chemistry, University of
Illinois at Chicago, Chicago, Illinois 60607, United
States
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24
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Huo J, Mikolajek H, Le Bas A, Clark JJ, Sharma P, Kipar A, Dormon J, Norman C, Weckener M, Clare DK, Harrison PJ, Tree JA, Buttigieg KR, Salguero FJ, Watson R, Knott D, Carnell O, Ngabo D, Elmore MJ, Fotheringham S, Harding A, Moynié L, Ward PN, Dumoux M, Prince T, Hall Y, Hiscox JA, Owen A, James W, Carroll MW, Stewart JP, Naismith JH, Owens RJ. A potent SARS-CoV-2 neutralising nanobody shows therapeutic efficacy in the Syrian golden hamster model of COVID-19. Nat Commun 2021; 12:5469. [PMID: 34552091 PMCID: PMC8458290 DOI: 10.1038/s41467-021-25480-z] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/12/2021] [Indexed: 12/18/2022] Open
Abstract
SARS-CoV-2 remains a global threat to human health particularly as escape mutants emerge. There is an unmet need for effective treatments against COVID-19 for which neutralizing single domain antibodies (nanobodies) have significant potential. Their small size and stability mean that nanobodies are compatible with respiratory administration. We report four nanobodies (C5, H3, C1, F2) engineered as homotrimers with pmolar affinity for the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. Crystal structures show C5 and H3 overlap the ACE2 epitope, whilst C1 and F2 bind to a different epitope. Cryo Electron Microscopy shows C5 binding results in an all down arrangement of the Spike protein. C1, H3 and C5 all neutralize the Victoria strain, and the highly transmissible Alpha (B.1.1.7 first identified in Kent, UK) strain and C1 also neutralizes the Beta (B.1.35, first identified in South Africa). Administration of C5-trimer via the respiratory route showed potent therapeutic efficacy in the Syrian hamster model of COVID-19 and separately, effective prophylaxis. The molecule was similarly potent by intraperitoneal injection.
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MESH Headings
- Administration, Intranasal
- Animals
- Antibodies, Neutralizing/administration & dosage
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/pharmacology
- Cryoelectron Microscopy
- Crystallography, X-Ray
- Disease Models, Animal
- Dose-Response Relationship, Immunologic
- Epitopes/chemistry
- Epitopes/metabolism
- Female
- Male
- Mesocricetus
- Neutralization Tests
- SARS-CoV-2/drug effects
- Single-Domain Antibodies/administration & dosage
- Single-Domain Antibodies/immunology
- Single-Domain Antibodies/metabolism
- Single-Domain Antibodies/pharmacology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/metabolism
- COVID-19 Drug Treatment
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Affiliation(s)
- Jiandong Huo
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Science Campus, Didcot, UK
| | | | - Audrey Le Bas
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Science Campus, Didcot, UK
| | - Jordan J Clark
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Parul Sharma
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Anja Kipar
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Joshua Dormon
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK
- Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Science Campus, Didcot, UK
| | - Chelsea Norman
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK
- Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Science Campus, Didcot, UK
| | - Miriam Weckener
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK
| | - Daniel K Clare
- Diamond Light Source Ltd, Harwell Science Campus, Didcot, UK
| | - Peter J Harrison
- Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Science Campus, Didcot, UK
- Diamond Light Source Ltd, Harwell Science Campus, Didcot, UK
| | - Julia A Tree
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Karen R Buttigieg
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | | | - Robert Watson
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Daniel Knott
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Oliver Carnell
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Didier Ngabo
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Michael J Elmore
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Susan Fotheringham
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Adam Harding
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Lucile Moynié
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK
| | - Philip N Ward
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Science Campus, Didcot, UK
| | - Maud Dumoux
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK
| | - Tessa Prince
- Diamond Light Source Ltd, Harwell Science Campus, Didcot, UK
| | - Yper Hall
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Julian A Hiscox
- Diamond Light Source Ltd, Harwell Science Campus, Didcot, UK
- Department of Preventive Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
- Infectious Diseases Horizontal Technology Centre (ID HTC), A*STAR, Singapore, Singapore
| | - Andrew Owen
- Department of Pharmacology and Therapeutics, Centre of Excellence in Long-acting Therapeutics (CELT), University of Liverpool, Liverpool, UK
| | - William James
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Miles W Carroll
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - James P Stewart
- Diamond Light Source Ltd, Harwell Science Campus, Didcot, UK
- Department of Preventive Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
- Department of Infectious Disease, University of Georgia, Georgia, USA
| | - James H Naismith
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK.
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Science Campus, Didcot, UK.
| | - Raymond J Owens
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK.
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Science Campus, Didcot, UK.
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25
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Kamalinia G, Grindel BJ, Takahashi TT, Millward SW, Roberts RW. Directing evolution of novel ligands by mRNA display. Chem Soc Rev 2021; 50:9055-9103. [PMID: 34165126 PMCID: PMC8725378 DOI: 10.1039/d1cs00160d] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
mRNA display is a powerful biological display platform for the directed evolution of proteins and peptides. mRNA display libraries covalently link the displayed peptide or protein (phenotype) with the encoding genetic information (genotype) through the biochemical activity of the small molecule puromycin. Selection for peptide/protein function is followed by amplification of the linked genetic material and generation of a library enriched in functional sequences. Iterative selection cycles are then performed until the desired level of function is achieved, at which time the identity of candidate peptides can be obtained by sequencing the genetic material. The purpose of this review is to discuss the development of mRNA display technology since its inception in 1997 and to comprehensively review its use in the selection of novel peptides and proteins. We begin with an overview of the biochemical mechanism of mRNA display and its variants with a particular focus on its advantages and disadvantages relative to other biological display technologies. We then discuss the importance of scaffold choice in mRNA display selections and review the results of selection experiments with biological (e.g., fibronectin) and linear peptide library architectures. We then explore recent progress in the development of "drug-like" peptides by mRNA display through the post-translational covalent macrocyclization and incorporation of non-proteogenic functionalities. We conclude with an examination of enabling technologies that increase the speed of selection experiments, enhance the information obtained in post-selection sequence analysis, and facilitate high-throughput characterization of lead compounds. We hope to provide the reader with a comprehensive view of current state and future trajectory of mRNA display and its broad utility as a peptide and protein design tool.
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Affiliation(s)
- Golnaz Kamalinia
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA.
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26
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Kondo T, Eguchi M, Tsuzuki N, Murata N, Fujino T, Hayashi G, Murakami H. Construction of a Highly Diverse mRNA Library for in vitro Selection of Monobodies. Bio Protoc 2021; 11:e4125. [PMID: 34541043 DOI: 10.21769/bioprotoc.4125] [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: 01/03/2021] [Revised: 05/07/2021] [Accepted: 05/16/2021] [Indexed: 11/02/2022] Open
Abstract
Recently, we developed transcription/translation coupled with the association of puromycin linker (TRAP) display as a quick in vitro selection method to obtain antibody-like proteins. For the in vitro selection, it is important to prepare mRNA libraries among which the diversity is high. Here, we describe a method for the preparation of monobody mRNA libraries with greater than 1013 theoretical diversity. First, we synthesized two long single-stranded DNAs that corresponded to fragments of monobody DNA, with random codons in the BC and FG loops. These oligonucleotides were ligated by T4 DNA ligase with the support of guide oligonucleotides containing 3' ends that were protected by a modification. After amplifying the product DNAs by PCR, one end of each DNA fragment was digested with the type II restriction enzyme BsaI, and the resulting DNA fragments were ligated using T4 DNA ligase. After amplification of the DNA product, mRNAs were synthesized by T7 RNA polymerase. This method is simple and could be used for the preparation of mRNA libraries for various antibody-like proteins. Graphic abstract: Construction of a highly diverse mRNA library.
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Affiliation(s)
- Taishi Kondo
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Minori Eguchi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Nariaki Tsuzuki
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Naoya Murata
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Tomoshige Fujino
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Gosuke Hayashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan.,Japan Science and Technology Agency (JST), PRESTO, Japan
| | - Hiroshi Murakami
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan.,Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, Japan
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27
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Bruncsics B, Errington WJ, Sarkar CA. MVsim : a toolset for quantifying and designing multivalent interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.08.01.454686. [PMID: 34373856 PMCID: PMC8351779 DOI: 10.1101/2021.08.01.454686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Arising through multiple binding elements, multivalency can specify the avidity, duration, cooperativity, and selectivity of biomolecular interactions, but quantitative prediction and design of these properties has remained challenging. Here we present MVsim , an application suite built around a configurational network model of multivalency to facilitate the quantification, design, and mechanistic evaluation of multivalent binding phenomena through a simple graphical user interface. To demonstrate the utility and versatility of MVsim , we first show that both monospecific and multispecific multivalent ligand-receptor interactions, with their noncanonical binding kinetics, can be accurately simulated. We then quantitatively predict the ultrasensitivity and performance of multivalent-encoded protein logic gates, evaluate the inherent programmability of multispecificity for selective receptor targeting, and extract rate constants of conformational switching for the SARS-CoV-2 spike protein and model its binding to ACE2 as well as multivalent inhibitors of this interaction. MVsim is freely available at https://sarkarlab.github.io/MVsim/ .
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Affiliation(s)
- Bence Bruncsics
- Department of Measurement and Information Systems, Budapest University of Technology and Economics, Budapest H-1111, Hungary
| | - Wesley J. Errington
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455-0215, USA
| | - Casim A. Sarkar
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455-0215, USA
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28
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Norman A, Franck C, Christie M, Hawkins PME, Patel K, Ashhurst AS, Aggarwal A, Low JKK, Siddiquee R, Ashley CL, Steain M, Triccas JA, Turville S, Mackay JP, Passioura T, Payne RJ. Discovery of Cyclic Peptide Ligands to the SARS-CoV-2 Spike Protein Using mRNA Display. ACS CENTRAL SCIENCE 2021; 7:1001-1008. [PMID: 34230894 PMCID: PMC8189037 DOI: 10.1021/acscentsci.0c01708] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Indexed: 05/03/2023]
Abstract
The COVID-19 pandemic, caused by SARS-CoV-2, has led to substantial morbidity, mortality, and disruption globally. Cellular entry of SARS-CoV-2 is mediated by the viral spike protein, and affinity ligands to this surface protein have the potential for applications as antivirals and diagnostic reagents. Here, we describe the affinity selection of cyclic peptide ligands to the SARS-CoV-2 spike protein receptor binding domain (RBD) from three distinct libraries (in excess of a trillion molecules each) by mRNA display. We identified six high affinity molecules with dissociation constants (K D) in the nanomolar range (15-550 nM) to the RBD. The highest affinity ligand could be used as an affinity reagent to detect the spike protein in solution by ELISA, and the cocrystal structure of this molecule bound to the RBD demonstrated that it binds to a cryptic binding site, displacing a β-strand near the C-terminus. Our findings provide key mechanistic insight into the binding of peptide ligands to the SARS-CoV-2 spike RBD, and the ligands discovered in this work may find future use as reagents for diagnostic applications.
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Affiliation(s)
- Alexander Norman
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Charlotte Franck
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
- School
of Life and Environmental Sciences, The
University of Sydney, Sydney, New South Wales 2006, Australia
| | - Mary Christie
- School
of Life and Environmental Sciences, The
University of Sydney, Sydney, New South Wales 2006, Australia
| | - Paige M. E. Hawkins
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Karishma Patel
- School
of Life and Environmental Sciences, The
University of Sydney, Sydney, New South Wales 2006, Australia
| | - Anneliese S. Ashhurst
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
- School
of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales 2006, Australia
| | | | - Jason K. K. Low
- School
of Life and Environmental Sciences, The
University of Sydney, Sydney, New South Wales 2006, Australia
| | - Rezwan Siddiquee
- School
of Life and Environmental Sciences, The
University of Sydney, Sydney, New South Wales 2006, Australia
- Sydney Analytical, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Caroline L. Ashley
- School
of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Megan Steain
- School
of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - James A. Triccas
- School
of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales 2006, Australia
| | | | - Joel P. Mackay
- School
of Life and Environmental Sciences, The
University of Sydney, Sydney, New South Wales 2006, Australia
| | - Toby Passioura
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- School
of Life and Environmental Sciences, The
University of Sydney, Sydney, New South Wales 2006, Australia
- Sydney Analytical, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Richard J. Payne
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
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29
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Bojadzic D, Alcazar O, Chen J, Chuang ST, Capcha JMC, Shehadeh LA, Buchwald P. Small-Molecule Inhibitors of the Coronavirus Spike: ACE2 Protein-Protein Interaction as Blockers of Viral Attachment and Entry for SARS-CoV-2. ACS Infect Dis 2021; 7:1519-1534. [PMID: 33979123 PMCID: PMC8130611 DOI: 10.1021/acsinfecdis.1c00070] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Indexed: 02/06/2023]
Abstract
Inhibitors of the protein-protein interaction (PPI) between the SARS-CoV-2 spike protein and human ACE2 (hACE2), which acts as a ligand-receptor pair that initiates the viral attachment and cellular entry of this coronavirus causing the ongoing COVID-19 pandemic, are of considerable interest as potential antiviral agents. While blockade of such PPIs with small molecules is more challenging than that with antibodies, small-molecule inhibitors (SMIs) might offer alternatives that are less strain- and mutation-sensitive, suitable for oral or inhaled administration, and more controllable/less immunogenic. Here, we report the identification of SMIs of this PPI by screening our compound library focused around the chemical space of organic dyes. Among promising candidates identified, several dyes (Congo red, direct violet 1, Evans blue) and novel druglike compounds (DRI-C23041, DRI-C91005) inhibited the interaction of hACE2 with the spike proteins of SARS-CoV-2 as well as SARS-CoV with low micromolar activity in our cell-free ELISA-type assays (IC50's of 0.2-3.0 μM), whereas control compounds, such as sunset yellow FCF, chloroquine, and suramin, showed no activity. Protein thermal shift assays indicated that the SMIs of interest identified here bind SARS-CoV-2-S and not hACE2. While dyes seemed to be promiscuous inhibitors, DRI-C23041 showed some selectivity and inhibited the entry of two different SARS-CoV-2-S expressing pseudoviruses into hACE2-expressing cells in a concentration-dependent manner with low micromolar IC50's (6-7 μM). This provides proof-of-principle evidence for the feasibility of small-molecule inhibition of PPIs critical for SARS-CoV-2 attachment/entry and serves as a first guide in the search for SMI-based alternative antiviral therapies for the prevention and treatment of diseases caused by coronaviruses in general and COVID-19 in particular.
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Affiliation(s)
- Damir Bojadzic
- Diabetes Research Institute, University of Miami, Miami, Florida, USA
| | - Oscar Alcazar
- Diabetes Research Institute, University of Miami, Miami, Florida, USA
| | - Jinshui Chen
- Diabetes Research Institute, University of Miami, Miami, Florida, USA
| | - Sung-Ting Chuang
- Diabetes Research Institute, University of Miami, Miami, Florida, USA
| | - Jose M. Condor Capcha
- Division of Cardiology, University of Miami, Miami, Florida, USA
- Interdisciplinary Stem Cell Institute, University of Miami, Miami, Florida, USA
| | - Lina A. Shehadeh
- Division of Cardiology, University of Miami, Miami, Florida, USA
- Interdisciplinary Stem Cell Institute, University of Miami, Miami, Florida, USA
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miami, Florida, USA
| | - Peter Buchwald
- Diabetes Research Institute, University of Miami, Miami, Florida, USA
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, Florida, USA
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30
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Kondo T, Eguchi M, Kito S, Fujino T, Hayashi G, Murakami H. cDNA TRAP display for rapid and stable in vitro selection of antibody-like proteins. Chem Commun (Camb) 2021; 57:2416-2419. [PMID: 33554979 DOI: 10.1039/d0cc07541h] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We developed a cDNA TRAP display for the rapid selection of antibody-like proteins in various conditions. By modifying the original puromycin linker in the TRAP display, a monobody was covalently attached to the cDNA. As a proof-of-concept, we demonstrated a rapid model selection of an anti-EGFR1 monobody in a solution containing ribonuclease.
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Affiliation(s)
- Taishi Kondo
- Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan.
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31
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Limsakul P, Charupanit K, Moonla C, Jeerapan I. Advances in emergent biological recognition elements and bioelectronics for diagnosing COVID-19. EMERGENT MATERIALS 2021; 4:231-247. [PMID: 33718775 PMCID: PMC7937783 DOI: 10.1007/s42247-021-00175-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 01/26/2021] [Indexed: 05/04/2023]
Abstract
Coronaviruses pose a serious threat to public health. Tremendous efforts are dedicated to advance reliable and effective detection of coronaviruses. Currently, the coronavirus disease 2019 (COVID-19) diagnosis mainly relies on the detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic materials by using reverse transcription-polymerase chain reaction (RT-PCR) assay. However, simpler and more rapid and reliable alternatives are needed to meet high demand during the pandemic. Biosensor-based diagnosis approaches become alternatives for selectively and rapidly detecting virus particles because of their biorecognition elements consisting of biomaterials that are specific to virus biomarkers. Here, we summarize biorecognition materials, including antibodies and antibody-like molecules, that are designed to recognize SARS-CoV-2 biomarkers and the advances of recently developed biosensors for COVID-19 diagnosis. The design of biorecognition materials or layers is crucial to maximize biosensing performances, such as high selectivity and sensitivity of virus detection. Additionally, the recent representative achievements in developing bioelectronics for sensing coronavirus are included. This review includes scholarly articles, mainly published in 2020 and early 2021. In addition to capturing the fast development in the fields of applied materials and biodiagnosis, the outlook of this rapidly evolving technology is summarized. Early diagnosis of COVID-19 could help prevent the spread of this contagious disease and provide significant information to medical teams to treat patients.
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Affiliation(s)
- Praopim Limsakul
- Division of Physical Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90112 Thailand
- Center of Excellence for Trace Analysis and Biosensor, Prince of Songkla University, Hat Yai, Songkhla, 90112 Thailand
| | - Krit Charupanit
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110 Thailand
| | - Chochanon Moonla
- School of Chemistry, Institute of Science, Suranaree University of Technology, 111, University Avenue, Nakhon Ratchasima, 30000 Thailand
| | - Itthipon Jeerapan
- Division of Physical Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90112 Thailand
- Center of Excellence for Trace Analysis and Biosensor, Prince of Songkla University, Hat Yai, Songkhla, 90112 Thailand
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