Development of a Single-Chain Variable Fragment of CR3022 for a Plasmonic-Based Biosensor Targeting the SARS-CoV-2 Spike Protein
Taufik Ramdani Tohari,
Isa Anshori,
Umi Baroroh,
Antonius Eko Nugroho,
Gilang Gumilar,
Shinta Kusumawardani,
Sari Syahruni,
Brian Yuliarto,
Wyanda Arnafia,
Irvan Faizal,
Yeni Wahyuni Hartati,
Toto Subroto,
Muhammad Yusuf
Affiliations
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
Umi Baroroh
Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40133, 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
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
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
Yeni Wahyuni Hartati
Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40133, Indonesia
Toto Subroto
Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40133, Indonesia
Muhammad Yusuf
Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40133, Indonesia
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.
