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Tohari TR, Anshori I, Baroroh U, Nugroho AE, Gumilar G, Kusumawardani S, Syahruni S, Yuliarto B, Arnafia W, Faizal I, Hartati YW, Subroto T, Yusuf M. Development of a Single-Chain Variable Fragment of CR3022 for a Plasmonic-Based Biosensor Targeting the SARS-CoV-2 Spike Protein. Biosensors (Basel) 2022; 12:1133. [PMID: 36551102 PMCID: PMC9776105 DOI: 10.3390/bios12121133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/02/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
Two years after SARS-CoV-2 caused the first case of COVID-19, we are now in the "new normal" period, where people's activity has bounced back, followed by the easing of travel policy restrictions. The lesson learned is that the wide availability of accurate and rapid testing procedures is crucial to overcome possible outbreaks in the future. Therefore, many laboratories worldwide have been racing to develop a new point-of-care diagnostic test. To aid continuous innovation, we developed a plasmonic-based biosensor designed explicitly for portable Surface Plasmon Resonance (SPR). In this study, we designed a single chain variable fragment (scFv) from the CR3022 antibody with a particular linker that inserted a cysteine residue at the second position. It caused the linker to have a strong affinity to the gold surface through thiol-coupling and possibly become a ready-to-use bioreceptor toward a portable SPR gold chip without purification steps. The theoretical affinity of this scFv on spike protein was -64.7 kcal/mol, computed using the Molecular Mechanics Generalized Born Surface Area (MM/GBSA) method from the 100 ns molecular dynamics trajectory. Furthermore, the scFv was produced in Escherichia coli BL21 (DE3) as a soluble protein. The binding activity toward Spike Receptor Binding Domain (RBD) SARS-CoV-2 was confirmed with a spot-test, and the experimental binding free energy of -10.82 kcal/mol was determined using portable SPR spectroscopy. We hope this study will be useful in designing specific and low-cost bioreceptors, particularly early in an outbreak when the information on antibody capture is still limited.
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Affiliation(s)
- Taufik Ramdani Tohari
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40133, Indonesia
| | - Isa Anshori
- Lab-on-Chip Group, Biomedical Engineering Department, Institute of Technology, Bandung 40132, Indonesia
- Research Center for Nanoscience and Nanotechnology (RCNN), Institut Teknologi Bandung, Bandung 40132, Indonesia
| | - Umi Baroroh
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40133, Indonesia
- Department of Biotechnology, Indonesian School of Pharmacy, Bandung 40266, Indonesia
| | - Antonius Eko Nugroho
- Lab-on-Chip Group, Biomedical Engineering Department, Institute of Technology, Bandung 40132, Indonesia
| | - Gilang Gumilar
- Research Center for Nanoscience and Nanotechnology (RCNN), Institut Teknologi Bandung, Bandung 40132, Indonesia
- Advanced Functional Material Research Group, Faculty of Industrial Technology, Institut Teknologi Bandung, Bandung 40132, Indonesia
- Research and Development Division, PT. Biostark Analitika Inovasi, Bandung 40375, Indonesia
| | - Shinta Kusumawardani
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40133, Indonesia
| | - Sari Syahruni
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40133, Indonesia
| | - Brian Yuliarto
- Research Center for Nanoscience and Nanotechnology (RCNN), Institut Teknologi Bandung, Bandung 40132, Indonesia
- Advanced Functional Material Research Group, Faculty of Industrial Technology, Institut Teknologi Bandung, Bandung 40132, Indonesia
| | - Wyanda Arnafia
- Research and Development Division, PT. Tekad Mandiri Citra, Bandung 40292, Indonesia
| | - Irvan Faizal
- Centre for Vaccine and Drug Research, National Research and Innovation Agency Republic of Indonesia, Kawasan Puspiptek Serpong, Tangerang Selatan 15314, Indonesia
- Department of Biotechnology, Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, BSD Campus, Tangerang 15345, Indonesia
| | - Yeni Wahyuni Hartati
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40133, Indonesia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, Indonesia
| | - Toto Subroto
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40133, Indonesia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, Indonesia
| | - Muhammad Yusuf
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40133, Indonesia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, Indonesia
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