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Lu Y, Li Q, Fan H, Liao C, Zhang J, Hu H, Yi H, Peng Y, Lu J, Chen Z. A Multivalent and Thermostable Nanobody Neutralizing SARS-CoV-2 Omicron (B.1.1.529). Int J Nanomedicine 2023; 18:353-367. [PMID: 36700149 PMCID: PMC9869787 DOI: 10.2147/ijn.s387160] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 12/20/2022] [Indexed: 01/19/2023] Open
Abstract
Background The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variants have risen to dominance, which contains far more mutations in the spike protein in comparison to previously reported variants, compromising the efficacy of most existing vaccines or therapeutic monoclonal antibodies. Nanobody screened from high-throughput naïve libraries is a potential candidate for developing preventive and therapeutic antibodies. Methods Four nanobodies specific to the SARS-CoV-2 wild-type receptor-binding domain (RBD) were screened from a naïve phage display library. Their affinity and neutralizing activity were evaluated by surface plasmon resonance assays, surrogate virus neutralization tests, and pseudovirus neutralization assays. Preliminary identification of the binding epitopes of nanobodies by peptide-based ELISA and competition assay. Then four multivalent nanobodies were engineered by attaching the monovalent nanobodies to an antibody-binding nanoplatform constructed based on the lumazine synthase protein cage nanoparticles isolated from the Aquifex aeolicus (AaLS). Finally, the differences in potency between the monovalent and multivalent nanobodies were compared using the same methods. Results Three of the four specific nanobodies could maintain substantial inhibitory activity against the Omicron (B.1.1.529), of them, B-B2 had the best neutralizing activity against the Omicron (B.1.1.529) pseudovirus (IC50 = 1.658 μg/mL). The antiviral ability of multivalent nanobody LS-B-B2 was improved in the Omicron (B.1.1.529) pseudovirus assays (IC50 = 0.653 μg/mL). The results of peptide-based ELISA indicated that LS-B-B2 might react with the linear epitopes in the SARS-CoV-2 RBD conserved regions, which would clarify the mechanisms for the maintenance of potent neutralization of Omicron (B.1.1.529) preliminary. Conclusion Our study indicated that the AaLS could be used as an antibody-binding nanoplatform to present nanobodies on its surface and improve the potency of nanobodies. The multivalent nanobody LS-B-B2 may serve as a potential agent for the neutralization of SARS-CoV-2 variants.
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Affiliation(s)
- Yuying Lu
- One Health Center of Excellence for Research and Training, School of Public Health, Sun Yat-Sen University, Guangzhou, People’s Republic of China,National Medical Products Administration Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, Guangzhou, People’s Republic of China,Key Laboratory of Tropical Diseases Control, Sun Yat-Sen University, Ministry of Education, Guangzhou, People’s Republic of China,Research Institute of Sun Yat-Sen University in Shenzhen, Shenzhen, People’s Republic of China,Hainan Key Novel Thinktank “Hainan Medical University ‘One Health’ Research Center”, Haikou, People’s Republic of China
| | - Qianlin Li
- One Health Center of Excellence for Research and Training, School of Public Health, Sun Yat-Sen University, Guangzhou, People’s Republic of China,National Medical Products Administration Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, Guangzhou, People’s Republic of China,Key Laboratory of Tropical Diseases Control, Sun Yat-Sen University, Ministry of Education, Guangzhou, People’s Republic of China,Research Institute of Sun Yat-Sen University in Shenzhen, Shenzhen, People’s Republic of China,Hainan Key Novel Thinktank “Hainan Medical University ‘One Health’ Research Center”, Haikou, People’s Republic of China
| | - Huahao Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Conghui Liao
- One Health Center of Excellence for Research and Training, School of Public Health, Sun Yat-Sen University, Guangzhou, People’s Republic of China,National Medical Products Administration Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, Guangzhou, People’s Republic of China,Key Laboratory of Tropical Diseases Control, Sun Yat-Sen University, Ministry of Education, Guangzhou, People’s Republic of China,Research Institute of Sun Yat-Sen University in Shenzhen, Shenzhen, People’s Republic of China,Hainan Key Novel Thinktank “Hainan Medical University ‘One Health’ Research Center”, Haikou, People’s Republic of China
| | - Jingsong Zhang
- One Health Center of Excellence for Research and Training, School of Public Health, Sun Yat-Sen University, Guangzhou, People’s Republic of China,National Medical Products Administration Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, Guangzhou, People’s Republic of China,Key Laboratory of Tropical Diseases Control, Sun Yat-Sen University, Ministry of Education, Guangzhou, People’s Republic of China,Research Institute of Sun Yat-Sen University in Shenzhen, Shenzhen, People’s Republic of China,Hainan Key Novel Thinktank “Hainan Medical University ‘One Health’ Research Center”, Haikou, People’s Republic of China
| | - Huan Hu
- One Health Center of Excellence for Research and Training, School of Public Health, Sun Yat-Sen University, Guangzhou, People’s Republic of China,National Medical Products Administration Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, Guangzhou, People’s Republic of China,Key Laboratory of Tropical Diseases Control, Sun Yat-Sen University, Ministry of Education, Guangzhou, People’s Republic of China,Research Institute of Sun Yat-Sen University in Shenzhen, Shenzhen, People’s Republic of China,Hainan Key Novel Thinktank “Hainan Medical University ‘One Health’ Research Center”, Haikou, People’s Republic of China
| | - Huaimin Yi
- One Health Center of Excellence for Research and Training, School of Public Health, Sun Yat-Sen University, Guangzhou, People’s Republic of China,National Medical Products Administration Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, Guangzhou, People’s Republic of China,Key Laboratory of Tropical Diseases Control, Sun Yat-Sen University, Ministry of Education, Guangzhou, People’s Republic of China,Research Institute of Sun Yat-Sen University in Shenzhen, Shenzhen, People’s Republic of China,Hainan Key Novel Thinktank “Hainan Medical University ‘One Health’ Research Center”, Haikou, People’s Republic of China
| | - Yuanli Peng
- One Health Center of Excellence for Research and Training, School of Public Health, Sun Yat-Sen University, Guangzhou, People’s Republic of China,National Medical Products Administration Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, Guangzhou, People’s Republic of China,Key Laboratory of Tropical Diseases Control, Sun Yat-Sen University, Ministry of Education, Guangzhou, People’s Republic of China,Research Institute of Sun Yat-Sen University in Shenzhen, Shenzhen, People’s Republic of China,Hainan Key Novel Thinktank “Hainan Medical University ‘One Health’ Research Center”, Haikou, People’s Republic of China
| | - Jiahai Lu
- One Health Center of Excellence for Research and Training, School of Public Health, Sun Yat-Sen University, Guangzhou, People’s Republic of China,National Medical Products Administration Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, Guangzhou, People’s Republic of China,Key Laboratory of Tropical Diseases Control, Sun Yat-Sen University, Ministry of Education, Guangzhou, People’s Republic of China,Research Institute of Sun Yat-Sen University in Shenzhen, Shenzhen, People’s Republic of China,Hainan Key Novel Thinktank “Hainan Medical University ‘One Health’ Research Center”, Haikou, People’s Republic of China,Correspondence: Jiahai Lu; Zeliang Chen, One Health Center of Excellence for Research and Training, School of Public Health, Sun Yat-Sen University, Guangzhou, People’s Republic of China, Email ;
| | - Zeliang Chen
- One Health Center of Excellence for Research and Training, School of Public Health, Sun Yat-Sen University, Guangzhou, People’s Republic of China,National Medical Products Administration Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, Guangzhou, People’s Republic of China,Key Laboratory of Tropical Diseases Control, Sun Yat-Sen University, Ministry of Education, Guangzhou, People’s Republic of China,Key Laboratory of Zoonose Prevention and Control at Universities of Inner Mongolia Autonomous Region, Medical College, Inner Mongolia Minzu University, Tongliao, People’s Republic of China
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Ikeuchi E, Kuroda D, Nakakido M, Murakami A, Tsumoto K. Delicate balance among thermal stability, binding affinity, and conformational space explored by single-domain V HH antibodies. Sci Rep 2021; 11:20624. [PMID: 34663870 PMCID: PMC8523659 DOI: 10.1038/s41598-021-98977-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 09/08/2021] [Indexed: 11/29/2022] Open
Abstract
The high binding affinities and specificities of antibodies have led to their use as drugs and biosensors. Single-domain VHH antibodies exhibit high specificity and affinity but have higher stability and solubility than conventional antibodies as they are single-domain proteins. In this work, based on physicochemical measurements and molecular dynamics (MD) simulations, we have gained insight that will facilitate rational design of single-chain VHH antibodies. We first assessed two homologous VHH antibodies by differential scanning calorimetry (DSC); one had a high (64.8 °C) and the other a low (58.6 °C) melting temperature. We then generated a series of the variants of the low stability antibody and analyzed their thermal stabilities by DSC and characterized their structures through MD simulations. We found that a single mutation that resulted in 8.2 °C improvement in melting temperature resulted in binding affinity an order of magnitude lower than the parent antibody, likely due to a shift of conformational space explored by the single-chain VHH antibody. These results suggest that the delicate balance among conformational stability, binding capability, and conformational space explored by antibodies must be considered in design of fully functional single-chain VHH antibodies.
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Affiliation(s)
- Emina Ikeuchi
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, 108-8639, Japan.,Panasonic Corporation Technology Division, Kyoto, 619-0237, Japan
| | - Daisuke Kuroda
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, 108-8639, Japan.,Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, 108-8639, Japan.,Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Makoto Nakakido
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, 108-8639, Japan.,Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Akikazu Murakami
- Department of Parasitology and Immunopathoetiology, Graduate School of Medicine, University of the Ryukyus, Okinawa, 903-0215, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, 108-8639, Japan. .,Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, 108-8639, Japan. .,Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan. .,Laboratory of Medical Proteomics, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan.
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Tam C, Kumar A, Zhang KYJ. NbX: Machine Learning-Guided Re-Ranking of Nanobody-Antigen Binding Poses. Pharmaceuticals (Basel) 2021; 14:ph14100968. [PMID: 34681192 PMCID: PMC8537642 DOI: 10.3390/ph14100968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/17/2021] [Accepted: 09/21/2021] [Indexed: 12/02/2022] Open
Abstract
Modeling the binding pose of an antibody is a prerequisite to structure-based affinity maturation and design. Without knowing a reliable binding pose, the subsequent structural simulation is largely futile. In this study, we have developed a method of machine learning-guided re-ranking of antigen binding poses of nanobodies, the single-domain antibody which has drawn much interest recently in antibody drug development. We performed a large-scale self-docking experiment of nanobody–antigen complexes. By training a decision tree classifier through mapping a feature set consisting of energy, contact and interface property descriptors to a measure of their docking quality of the refined poses, significant improvement in the median ranking of native-like nanobody poses by was achieved eightfold compared with ClusPro and an established deep 3D CNN classifier of native protein–protein interaction. We further interpreted our model by identifying features that showed relatively important contributions to the prediction performance. This study demonstrated a useful method in improving our current ability in pose prediction of nanobodies.
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Affiliation(s)
- Chunlai Tam
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan; (C.T.); (A.K.)
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan
| | - Ashutosh Kumar
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan; (C.T.); (A.K.)
| | - Kam Y. J. Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan; (C.T.); (A.K.)
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan
- Correspondence:
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Zabetakis D, Shriver-Lake LC, Olson MA, Goldman ER, Anderson GP. Experimental evaluation of single-domain antibodies predicted by molecular dynamics simulations to have elevated thermal stability. Protein Sci 2019; 28:1909-1912. [PMID: 31342597 DOI: 10.1002/pro.3692] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/12/2019] [Accepted: 07/16/2019] [Indexed: 01/07/2023]
Abstract
Recently Bekker et al. [Bekker G-J et al. Protein Sci. 2019;28:429-438.] described a computational strategy of applying molecular-dynamics simulations to estimate the relative stabilities of single-domain antibodies, and utilized their method to design changes with the aim of increasing the stability of a single-domain antibody with a known crystal structure. The structure from which they generated potentially stabilizing mutations is an anti-cholera toxin single domain antibody selected from a naïve library which has relatively low thermal stability, reflected by a melting point of 48°C. Their work was purely theoretical, so to examine their predictions, we prepared the parental and predicted stabilizing mutant single domain antibodies and examined their thermal stability, ability to refold and affinity. We found that the mutation that improved stability the most (~7°C) was one which changed an amino acid in CDR1 from an asparagine to an aspartic acid. This change unfortunately was also accompanied by a reduction in affinity. Thus, while their modeling did appear to successfully predict stabilizing mutations, introducing mutations in the binding regions is problematic. Of further interest, the mutations selected via their high temperature simulations, did improve refolding, suggesting that they were successful in stabilizing the structure at high temperatures and thereby decrease aggregation. Our result should permit them to reassess and refine their model and may one day lead to a usefulin silico approach to protein stabilization.
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Affiliation(s)
- Dan Zabetakis
- Center for Biomolecular Science and Engineering, Naval Research Laboratory, Washington, District of Columbia
| | - Lisa C Shriver-Lake
- Center for Biomolecular Science and Engineering, Naval Research Laboratory, Washington, District of Columbia
| | - Mark A Olson
- Systems and Structural Biology Division, USAMRIID, Frederick, Maryland
| | - Ellen R Goldman
- Center for Biomolecular Science and Engineering, Naval Research Laboratory, Washington, District of Columbia
| | - George P Anderson
- Center for Biomolecular Science and Engineering, Naval Research Laboratory, Washington, District of Columbia
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