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Wongnak R, Brindha S, Oba M, Yoshizue T, Islam MD, Islam MM, Takemae H, Mizutani T, Kuroda Y. Non-Glycosylated SARS-CoV-2 Omicron BA.5 Receptor Binding Domain (RBD) with a Native-like Conformation Induces a Robust Immune Response with Potent Neutralization in a Mouse Model. Molecules 2024; 29:2676. [PMID: 38893549 PMCID: PMC11173568 DOI: 10.3390/molecules29112676] [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: 05/02/2024] [Revised: 05/24/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024] Open
Abstract
The Omicron BA.5 variant of SARS-CoV-2 is known for its high transmissibility and its capacity to evade immunity provided by vaccine protection against the (original) Wuhan strain. In our prior research, we successfully produced the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein in an E. coli expression system. Extensive biophysical characterization indicated that, even without glycosylation, the RBD maintained native-like conformational and biophysical properties. The current study explores the immunogenicity and neutralization capacity of the E. coli-expressed Omicron BA.5 RBD using a mouse model. Administration of three doses of the RBD without any adjuvant elicited high titer antisera of up to 7.3 × 105 and up to 1.6 × 106 after a booster shot. Immunization with RBD notably enhanced the population of CD44+CD62L+ T cells, indicating the generation of T cell memory. The in vitro assays demonstrated the antisera's protective efficacy through significant inhibition of the interaction between SARS-CoV-2 and its human receptor, ACE2, and through potent neutralization of a pseudovirus. These findings underscore the potential of our E. coli-expressed RBD as a viable vaccine candidate against the Omicron variant of SARS-CoV-2.
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Affiliation(s)
- Rawiwan Wongnak
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Nakamachi 2-24-16, Tokyo 184-8588, Japan; (R.W.); (S.B.); (T.Y.); (M.D.I.)
| | - Subbaian Brindha
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Nakamachi 2-24-16, Tokyo 184-8588, Japan; (R.W.); (S.B.); (T.Y.); (M.D.I.)
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Tokyo 183-8538, Japan; (M.O.); (H.T.); (T.M.)
| | - Mami Oba
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Tokyo 183-8538, Japan; (M.O.); (H.T.); (T.M.)
- Center for Infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-Cho, Fuchu-shi 183-8509, Japan
| | - Takahiro Yoshizue
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Nakamachi 2-24-16, Tokyo 184-8588, Japan; (R.W.); (S.B.); (T.Y.); (M.D.I.)
| | - Md. Din Islam
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Nakamachi 2-24-16, Tokyo 184-8588, Japan; (R.W.); (S.B.); (T.Y.); (M.D.I.)
| | - M. Monirul Islam
- Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh;
| | - Hitoshi Takemae
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Tokyo 183-8538, Japan; (M.O.); (H.T.); (T.M.)
- Center for Infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-Cho, Fuchu-shi 183-8509, Japan
| | - Tetsuya Mizutani
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Tokyo 183-8538, Japan; (M.O.); (H.T.); (T.M.)
- Center for Infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-Cho, Fuchu-shi 183-8509, Japan
| | - Yutaka Kuroda
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Nakamachi 2-24-16, Tokyo 184-8588, Japan; (R.W.); (S.B.); (T.Y.); (M.D.I.)
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Tokyo 183-8538, Japan; (M.O.); (H.T.); (T.M.)
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Tu T, Rathnayaka T, Kato T, Mizutani K, Saotome T, Noguchi K, Kidokoro SI, Kuroda Y. Design and Escherichia coli Expression of a Natively Folded Multi-Disulfide Bonded Influenza H1N1-PR8 Receptor-Binding Domain (RBD). Int J Mol Sci 2024; 25:3943. [PMID: 38612753 PMCID: PMC11012049 DOI: 10.3390/ijms25073943] [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: 01/29/2024] [Revised: 03/22/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024] Open
Abstract
Refolding multi-disulfide bonded proteins expressed in E. coli into their native structure is challenging. Nevertheless, because of its cost-effectiveness, handiness, and versatility, the E. coli expression of viral envelope proteins, such as the RBD (Receptor-Binding Domain) of the influenza Hemagglutinin protein, could significantly advance research on viral infections. Here, we show that H1N1-PR8-RBD (27 kDa, containing four cysteines forming two disulfide bonds) expressed in E. coli and was purified with nickel affinity chromatography, and reversed-phase HPLC was successfully refolded into its native structure, as assessed with several biophysical and biochemical techniques. Analytical ultracentrifugation indicated that H1N1-PR8-RBD was monomeric with a hydrodynamic radius of 2.5 nm. Thermal denaturation, monitored with DSC and CD at a wavelength of 222 nm, was cooperative with a midpoint temperature around 55 °C, strongly indicating a natively folded protein. In addition, the 15N-HSQC NMR spectrum exhibited several 1H-15N resonances indicative of a beta-sheeted protein. Our results indicate that a significant amount (40 mg/L) of pure and native H1N1-PR8-RBD can be produced using an E. coli expression system with our refolding procedure, offering potential insights into the molecular characterization of influenza virus infection.
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Affiliation(s)
- Thao Tu
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei-shi 184-8588, Tokyo, Japan; (T.T.); (T.R.)
| | - Tharangani Rathnayaka
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei-shi 184-8588, Tokyo, Japan; (T.T.); (T.R.)
| | - Toshiyo Kato
- NMR Group, Smart-Core-Facility Promotion Organization, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei-shi 184-8588, Tokyo, Japan; (T.K.); (K.N.)
| | - Kenji Mizutani
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama 230-0045, Kanagawa, Japan;
| | - Tomonori Saotome
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka-cho, Nagaoka-shi 940-2188, Niigata, Japan; (T.S.); (S.-i.K.)
| | - Keiichi Noguchi
- NMR Group, Smart-Core-Facility Promotion Organization, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei-shi 184-8588, Tokyo, Japan; (T.K.); (K.N.)
| | - Shun-ichi Kidokoro
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka-cho, Nagaoka-shi 940-2188, Niigata, Japan; (T.S.); (S.-i.K.)
| | - Yutaka Kuroda
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei-shi 184-8588, Tokyo, Japan; (T.T.); (T.R.)
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Sam S, Ofoghi H, Farahmand B. Developing of SARS-CoV-2 fusion protein expressed in E. coli Shuffle T7 for enhanced ELISA detection sensitivity - an integrated experimental and bioinformatic approach. J Biomol Struct Dyn 2024:1-16. [PMID: 38234051 DOI: 10.1080/07391102.2024.2302941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024]
Abstract
In the recent COVID-19 pandemic, developing effective diagnostic assays is crucial for controlling the spread of the SARS-CoV-2 virus. Multi-domain fusion proteins are a promising approach to detecting SARS-CoV-2 antibodies. In this study, we designed an antigen named CoV2-Pro, containing two RBD domains from SARS-CoV-2 Omicron and Delta variants and one CTD domain of the nucleoprotein in the order of RBD-RBD-N, linked by a super flexible glycine linker. We evaluated the suitability of E. coli Shuffle T7 and BL21 (DE3) strain for expressing CoV2-Pro. Moreover, Bioinformatic studies were conducted first to analyze the tertiary structure of CoV2-Pro. The CoV2-Pro sequences were cloned into a pET-32b (+) vector for expression in E. coli Shuffle T7 and BL21 (DE3). SDS-PAGE and western blot confirmed the protein expression and folding structure. The CoV2-Pro-TRX was purified by Ni-NTA affinity chromatography. Dot blot analysis was performed to evaluate the antigenic characterization of the CoV2-Pro. A molecular docking simulation was conducted to assess the binding affinity of CoV2-Pro with LY-COV555 (Bamlanivimab) monoclonal antibody. A molecular dynamic was performed to analyze the stability of the structure. Bioinformatic and experimental studies revealed a stable conformational 3D structure of the CoV2-Pro. The CoV2-Pro interacted with SARS-CoV-2 antibodies, confirming the correct antigenic structure. We assert with confidence that CoV2-Pro is ideal for developing an ELISA assay for precise diagnosis and rigorous vaccine evaluation during the COVID-19 prevalence.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sohrab Sam
- Department of Biotechnology, Iranian Research Organization for Science and Technology (IROST), Tehran, Iran
| | - Hamideh Ofoghi
- Department of Biotechnology, Iranian Research Organization for Science and Technology (IROST), Tehran, Iran
| | - Behrokh Farahmand
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
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