1
|
Liu X, Wang Y, Sun L, Xiao G, Hou N, Chen J, Wang W, Xu X, Gu Y. Screening and optimization of shark nanobodies against SARS-CoV-2 spike RBD. Antiviral Res 2024; 226:105898. [PMID: 38692413 DOI: 10.1016/j.antiviral.2024.105898] [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: 01/01/2024] [Revised: 03/28/2024] [Accepted: 04/28/2024] [Indexed: 05/03/2024]
Abstract
SARS-CoV-2 continues to threaten human health, antibody therapy is one way to control the infection. Because new SARS-CoV-2 mutations are constantly emerging, there is an urgent need to develop broadly neutralizing antibodies to block the viral entry into host cells. VNAR from sharks is the smallest natural antigen binding domain, with the advantages of small size, flexible paratopes, good stability, and low manufacturing cost. Here, we used recombinant SARS-CoV-2 Spike-RBD to immunize sharks and constructed a VNAR phage display library. VNAR R1C2, selected from the library, efficiently binds to the RBD domain and blocks the infection of ACE2-positive cells by pseudovirus. Next, homologous bivalent VNARs were constructed through the tandem fusion of two R1C2 units, which enhanced both the affinity and neutralizing activity of R1C2. R1C2 was predicted to bind to a relatively conserved region within the RBD. By introducing mutations at four key binding sites within the CDR3 and HV2 regions of R1C2, the affinity and neutralizing activity of R1C2 were significantly improved. Furthermore, R1C2 also exhibits an effective capacity of binding to the Omicron variants (BA.2 and XBB.1). Together, these results suggest that R1C2 could serve as a valuable candidate for preventing and treating SARS-CoV-2 infections.
Collapse
Affiliation(s)
- Xiaochun Liu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Marine Biomedical Research Institute of Qingdao, Qingdao, 266071, China
| | - Yanqing Wang
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Lishan Sun
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Guokai Xiao
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Ning Hou
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Jin Chen
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Wei Wang
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Ximing Xu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Marine Biomedical Research Institute of Qingdao, Qingdao, 266071, China.
| | - Yuchao Gu
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
| |
Collapse
|
2
|
Han Q, Wang S, Wang Z, Zhang C, Wang X, Feng N, Wang T, Zhao Y, Chi H, Yan F, Xia X. Nanobodies with cross-neutralizing activity provide prominent therapeutic efficacy in mild and severe COVID-19 rodent models. Virol Sin 2023; 38:787-800. [PMID: 37423308 PMCID: PMC10590698 DOI: 10.1016/j.virs.2023.07.003] [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: 03/16/2023] [Accepted: 07/04/2023] [Indexed: 07/11/2023] Open
Abstract
The weakened protective efficacy of COVID-19 vaccines and antibodies caused by SARS-CoV-2 variants presents a global health emergency, which underscores the urgent need for universal therapeutic antibody intervention for clinical patients. Here, we screened three alpacas-derived nanobodies (Nbs) with neutralizing activity from twenty RBD-specific Nbs. The three Nbs were fused with the Fc domain of human IgG, namely aVHH-11-Fc, aVHH-13-Fc and aVHH-14-Fc, which could specifically bind RBD protein and competitively inhibit the binding of ACE2 receptor to RBD. They effectively neutralized SARS-CoV-2 pseudoviruses D614G, Alpha, Beta, Gamma, Delta, and Omicron sub-lineages BA.1, BA.2, BA.4, and BA.5 and authentic SARS-CoV-2 prototype, Delta, and Omicron BA.1, BA.2 strains. In mice-adapted COVID-19 severe model, intranasal administration of aVHH-11-Fc, aVHH-13-Fc and aVHH-14-Fc effectively protected mice from lethal challenges and reduced viral loads in both the upper and lower respiratory tracts. In the COVID-19 mild model, aVHH-13-Fc, which represents the optimal neutralizing activity among the above three Nbs, effectively protected hamsters from the challenge of SARS-CoV-2 prototype, Delta, Omicron BA.1 and BA.2 by significantly reducing viral replication and pathological alterations in the lungs. In structural modeling of aVHH-13 and RBD, aVHH-13 binds to the receptor-binding motif region of RBD and interacts with some highly conserved epitopes. Taken together, our study illustrated that alpaca-derived Nbs offered a therapeutic countermeasure against SARS-CoV-2, including those Delta and Omicron variants which have evolved into global pandemic strains.
Collapse
Affiliation(s)
- Qiuxue Han
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100021, China; Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 132122, China
| | - Shen Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 132122, China
| | - Zhenshan Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 132122, China
| | - Cheng Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 132122, China
| | - Xinyue Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 132122, China
| | - Na Feng
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 132122, China
| | - Tiecheng Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 132122, China
| | - Yongkun Zhao
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 132122, China; Jiangsu Co-innovation Centre for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
| | - Hang Chi
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 132122, China.
| | - Feihu Yan
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 132122, China; Jiangsu Co-innovation Centre for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
| | - Xianzhu Xia
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100021, China; Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 132122, China; Jiangsu Co-innovation Centre for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
| |
Collapse
|
3
|
Jiang X, Sun L, Hu C, Zheng F, Lyu Z, Shao J. Shark IgNAR: The Next Broad Application Antibody in Clinical Diagnoses and Tumor Therapies? Mar Drugs 2023; 21:496. [PMID: 37755109 PMCID: PMC10532743 DOI: 10.3390/md21090496] [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: 08/21/2023] [Revised: 09/14/2023] [Accepted: 09/14/2023] [Indexed: 09/28/2023] Open
Abstract
Antibodies represent a relatively mature detection means and serve as therapeutic drug carriers in the clinical diagnosis and treatment of cancer-among which monoclonal antibodies (mAbs) currently occupy a dominant position. However, the emergence and development of small-molecule monodomain antibodies are inevitable due to the many limitations of mAbs, such as their large size, complex structure, and sensitivity to extreme temperature, and tumor microenvironments. Thus, since first discovered in Chondroid fish in 1995, IgNAR has become an alternative therapeutic strategy through which to replace monoclonal antibodies, thus entailing that this novel type of immunoglobulin has received wide attention with respect to clinical diagnoses and tumor therapies. The variable new antigen receptor (VNAR) of IgNAR provides an advantage for the development of new antitumor drugs due to its small size, high stability, high affinity, as well as other structural and functional characteristics. In that respect, a better understanding of the unique characteristics and therapeutic potential of IgNAR/VNAR in clinical and anti-tumor treatment is needed. This article reviews the advantages of its unique biochemical conditions and molecular structure for clinical diagnoses and novel anti-tumor drugs. At the same time, the main advantages of the existing conjugated drugs, which are based on single-domain antibodies, are introduced here, thereby providing new ideas and methods for the development of clinical diagnoses and anti-tumor therapies in the future.
Collapse
Affiliation(s)
- Xiaofeng Jiang
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China; (L.S.); (C.H.); (Z.L.)
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
- Jiangsu Baiying Biotech Co., Ltd., Taizhou 225300, China;
| | - Ling Sun
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China; (L.S.); (C.H.); (Z.L.)
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Chengwu Hu
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China; (L.S.); (C.H.); (Z.L.)
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Feijian Zheng
- Jiangsu Baiying Biotech Co., Ltd., Taizhou 225300, China;
| | - Zhengbing Lyu
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China; (L.S.); (C.H.); (Z.L.)
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Jianzhong Shao
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| |
Collapse
|
4
|
Cabanillas-Bernal O, Valdovinos-Navarro BJ, Cervantes-Luevano KE, Sanchez-Campos N, Licea-Navarro AF. Unleashing the power of shark variable single domains (VNARs): broadly neutralizing tools for combating SARS-CoV-2. Front Immunol 2023; 14:1257042. [PMID: 37753081 PMCID: PMC10518403 DOI: 10.3389/fimmu.2023.1257042] [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: 07/11/2023] [Accepted: 08/18/2023] [Indexed: 09/28/2023] Open
Abstract
The pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) generated a joint global effort to develop vaccines and other treatments that could mitigate the negative effects and the rapid spread of the virus. Single-domain antibodies derived from various sources, including cartilaginous fish, camelids, and humans, have gained attention as promising therapeutic tools against coronavirus disease 2019. Shark-derived variable new antigen receptors (VNARs) have emerged as the smallest naturally occurring antigen-binding molecules. Here, we compile and review recent published studies on VNARs with the capacity to recognize and/or neutralize SARS-CoV-2. We found a close balance between the use of natural immune libraries and synthetic VNAR libraries for the screening against SARS-CoV-2, with phage display being the preferred display technology for the selection of VNARs against this virus. In addition, we discuss potential modifications and engineering strategies employed to improve the neutralization potential of VNARs, such as exploring fusion with the Fc domain of human Immunoglobulin G (IgG) to increase avidity and therapeutic potential. This research highlights the potential of VNARs as powerful molecular tools in the fight against infectious diseases.
Collapse
Affiliation(s)
| | | | | | | | - Alexei F. Licea-Navarro
- Biomedical Innovation Department, Centro de Investigación Científica y Educación Superior de Ensenada, (CICESE), Ensenada, Baja California, Mexico
| |
Collapse
|
5
|
Lim HT, Kok BH, Leow CY, Leow CH. Exploring shark VNAR antibody against infectious diseases using phage display technology. FISH & SHELLFISH IMMUNOLOGY 2023; 140:108986. [PMID: 37541634 DOI: 10.1016/j.fsi.2023.108986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/29/2023] [Accepted: 08/01/2023] [Indexed: 08/06/2023]
Abstract
Antibody with high affinity and specificity to antigen has widely used as a tool to combat various diseases. The variable domain of immunoglobulin new antigen receptor (VNAR) naturally found in shark contains autonomous function as single-domain antibody. Due to its excellent characteristics, the small, non-complex, and highly stable have made shark VNAR can acquires the antigen-binding capability that might not be reached by conventional antibody. Phage display technology enables shark VNAR to be presented on the surface of phage, allowing the exploration of shark VNAR as an alternative antibody format to target antigens from various infectious diseases. The application of phage-displayed shark VNAR in antibody library and biopanning eventually leads to the discovery and isolation of antigen-specific VNARs with diagnostic and therapeutic potential towards infectious diseases. This review provides an overview of the shark VNAR antibody, the types of phage display technology with comparison to the other types of display system, as well as the application and case studies of phage-displayed shark VNAR antibodies against infectious diseases.
Collapse
Affiliation(s)
- Hui Ting Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia
| | - Boon Hui Kok
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia
| | - Chiuan Yee Leow
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia
| | - Chiuan Herng Leow
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia.
| |
Collapse
|
6
|
Feng X, Wang H. Emerging Landscape of Nanobodies and Their Neutralizing Applications against SARS-CoV-2 Virus. ACS Pharmacol Transl Sci 2023; 6:925-942. [PMID: 37470012 PMCID: PMC10275483 DOI: 10.1021/acsptsci.3c00042] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Indexed: 07/21/2023]
Abstract
The new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes the coronavirus disease 2019 (COVID-19) has significantly altered people's way of life. Despite widespread knowledge of vaccination, mask use, and avoidance of close contact, COVID-19 is still spreading around the world. Numerous research teams are examining the SARS-CoV-2 infection process to discover strategies to identify, prevent, and treat COVID-19 to limit the spread of this chronic coronavirus illness and restore lives to normalcy. Nanobodies have advantages over polyclonal and monoclonal antibodies (Ab) and Ab fragments, including reduced size, high stability, simplicity in manufacture, compatibility with genetic engineering methods, and lack of solubility and aggregation issues. Recent studies have shown that nanobodies that target the SARS-CoV-2 receptor-binding domain and disrupt ACE2 interactions are helpful in the prevention and treatment of SARS-CoV-2-infected animal models, despite the lack of evidence in human patients. The creation and evaluation of nanobodies, as well as their diagnostic and therapeutic applications against COVID-19, are discussed in this paper.
Collapse
Affiliation(s)
- Xuemei Feng
- Department
of Microbiology and Immunology, College
of Medicine and Health Science, China Three Gorges University, Yichang 443002, China
| | - Hu Wang
- Department
of Microbiology and Immunology, College
of Medicine and Health Science, China Three Gorges University, Yichang 443002, China
- Institute
of Cell Engineering, School of Medicine, Johns Hopkins University, Baltimore 21215, United States
| |
Collapse
|
7
|
Buffington J, Duan Z, Kwon HJ, Hong J, Li D, Feng M, Xie H, Ho M. Identification of nurse shark V NAR single-domain antibodies targeting the spike S2 subunit of SARS-CoV-2. FASEB J 2023; 37:e22973. [PMID: 37191949 PMCID: PMC10715488 DOI: 10.1096/fj.202202099rr] [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: 12/17/2022] [Revised: 04/17/2023] [Accepted: 05/01/2023] [Indexed: 05/17/2023]
Abstract
SARS-CoV-2 is the etiological agent of the COVID-19 pandemic. Antibody-based therapeutics targeting the spike protein, specifically the S1 subunit or the receptor binding domain (RBD) of SARS-CoV-2, have gained attention due to their clinical efficacy in treating patients diagnosed with COVID-19. An alternative to conventional antibody therapeutics is the use of shark new antigen variable receptor domain (VNAR ) antibodies. VNAR s are small (<15 kDa) and can reach deep into the pockets or grooves of the target antigen. Here, we have isolated 53 VNAR s that bind to the S2 subunit by phage panning from a naïve nurse shark VNAR phage display library constructed in our laboratory. Among those binders, S2A9 showed the best neutralization activity against the original pseudotyped SARS-CoV-2 virus. Several binders, including S2A9, showed cross-reactivity against S2 subunits from other β coronaviruses. Furthermore, S2A9 showed neutralization activity against all variants of concern (VOCs) from alpha to omicron (including BA1, BA2, BA4, and BA5) in both pseudovirus and live virus neutralization assays. Our findings suggest that S2A9 could be a promising lead molecule for the development of broadly neutralizing antibodies against SARS-CoV-2 and emerging variants. The nurse shark VNAR phage library offers a novel platform that can be used to rapidly isolate single-domain antibodies against emerging viral pathogens.
Collapse
Affiliation(s)
- Jesse Buffington
- Antibody Engineering Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Zhijian Duan
- Antibody Engineering Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Hyung Joon Kwon
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, USA
| | - Jessica Hong
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Dan Li
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Mingqian Feng
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Hang Xie
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, USA
| | - Mitchell Ho
- Antibody Engineering Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| |
Collapse
|
8
|
Kim WS, Chae HD, Jung I, Lee WK, Lee WJ, Lee J, Gong Y, Lee D, Kim BW, Kim JK, Hwang J, Kweon DH, Jung ST, Na JH. Isolation and characterization of single domain antibodies from banded houndshark (Triakis scyllium) targeting SARS-CoV-2 spike RBD protein. FISH & SHELLFISH IMMUNOLOGY 2023; 138:108807. [PMID: 37169112 PMCID: PMC10167778 DOI: 10.1016/j.fsi.2023.108807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/02/2023] [Accepted: 05/08/2023] [Indexed: 05/13/2023]
Abstract
The COVID-19 pandemic has significantly impacted human health for three years. To mitigate the spread of SARS-CoV-2, the development of neutralizing antibodies has been accelerated, including the exploration of alternative antibody formats such as single-domain antibodies. In this study, we identified new variable antigen receptors (VNARs) specific for the receptor binding domain (RBD) of SARS-CoV-2 by immunizing a banded houndshark (Triakis scyllium) with recombinant wild-type RBD. Notably, the CoV2NAR-1 clone showed high binding affinities in the nanomolar range to various RBDs and demonstrated neutralizing activity against SARS-CoV-2 pseudoviruses. These results highlight the potential of the banded houndshark as an animal model for the development of VNAR-based therapeutics or diagnostics against future pandemics.
Collapse
Affiliation(s)
- Woo Sung Kim
- Department of Pharmaceutical Engineering, Sangji University, Wonju, 26339, Republic of Korea
| | - Hee Do Chae
- Department of Pharmaceutical Engineering, Sangji University, Wonju, 26339, Republic of Korea
| | - Inji Jung
- Department of Biomedical Sciences, Graduate School, Korea University, Seoul, 02841, Republic of Korea; BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, 02841, Republic of Korea
| | - Won-Kyu Lee
- New Drug Development Center, Osong Medical Innovation Foundation (Kbiohealth), Chungbuk, 28160, Republic of Korea
| | - Woo Jun Lee
- Department of Marine Biology, Pukyong National University, Busan, 48513, Republic of Korea
| | - Jisun Lee
- Department of Biomedical Sciences, Graduate School, Korea University, Seoul, 02841, Republic of Korea; BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, 02841, Republic of Korea
| | - Yejin Gong
- Department of Pharmaceutical Engineering, Sangji University, Wonju, 26339, Republic of Korea
| | - Dohyun Lee
- New Drug Development Center, Osong Medical Innovation Foundation (Kbiohealth), Chungbuk, 28160, Republic of Korea
| | - Byeong-Won Kim
- New Drug Development Center, Osong Medical Innovation Foundation (Kbiohealth), Chungbuk, 28160, Republic of Korea
| | - Jin-Koo Kim
- Department of Marine Biology, Pukyong National University, Busan, 48513, Republic of Korea
| | - Jaehyeon Hwang
- Department of Integrative Biotechnology, Sungkyunkwan University, Seoburo 2066, Suwon, Gyeonggi, 16419, Republic of Korea
| | - Dae-Hyuk Kweon
- Department of Integrative Biotechnology, Sungkyunkwan University, Seoburo 2066, Suwon, Gyeonggi, 16419, Republic of Korea
| | - Sang Taek Jung
- Department of Biomedical Sciences, Graduate School, Korea University, Seoul, 02841, Republic of Korea; BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, 02841, Republic of Korea.
| | - Jung-Hyun Na
- Department of Pharmaceutical Engineering, Sangji University, Wonju, 26339, Republic of Korea.
| |
Collapse
|
9
|
Manoutcharian K, Gevorkian G. Shark VNAR phage display libraries: An alternative source for therapeutic and diagnostic recombinant antibody fragments. FISH & SHELLFISH IMMUNOLOGY 2023; 138:108808. [PMID: 37169114 DOI: 10.1016/j.fsi.2023.108808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/02/2023] [Accepted: 05/08/2023] [Indexed: 05/13/2023]
Abstract
The development of recombinant antibody fragments as promising alternatives to full-length immunoglobulins offers vast opportunities for biomedicine. Antibody fragments have important advantages compared with conventional monoclonal antibodies that make them attractive for the biotech industry: superior stability and solubility, reduced immunogenicity, higher specificity and affinity, capacity to target the hidden epitope and cross the blood-brain barrier, the ability to refold after heat denaturation and inexpensive and easy large-scale production. Different antibody formats such as antigen-binding fragments (Fab), single-chain fragment variable (scFv) consisting of the antigen-binding domains of Ig heavy (VH) and light (VL) chain regions connected by a flexible peptide linker, single-domain antibody fragments (sdAbs) like camelid heavy-chain variable domains (VHHs) and shark variable new antigen receptor (VNARs), and bispecific antibodies (bsAbs) are currently being evaluated as diagnostics or therapeutics in preclinical studies and clinical trials. In the present review, we summarize and discuss studies on VNARs, the smallest recombinant antibody fragment, obtained after the screening of different types of phage display antibody libraries. Results published until March 2023 are discussed.
Collapse
Affiliation(s)
- Karen Manoutcharian
- Instituto de Investigaciones Biomedicas, Universidad Nacional Autonoma de Mexico (UNAM), Mexico, DF, Mexico
| | - Goar Gevorkian
- Instituto de Investigaciones Biomedicas, Universidad Nacional Autonoma de Mexico (UNAM), Mexico, DF, Mexico.
| |
Collapse
|
10
|
Dueñas S, Escalante T, Gasperin-Bulbarela J, Bernáldez-Sarabia J, Cervantes-Luévano K, Jiménez S, Sánchez-Campos N, Cabanillas-Bernal O, Valdovinos-Navarro BJ, Álvarez-Lee A, De León-Nava MA, Licea-Navarro AF. Chimeric Peptides from Californiconus californicus and Heterodontus francisci with Antigen-Binding Capacity: A Conotoxin Scaffold to Create Non-Natural Antibodies (NoNaBodies). Toxins (Basel) 2023; 15:toxins15040269. [PMID: 37104207 PMCID: PMC10141372 DOI: 10.3390/toxins15040269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/08/2023] Open
Abstract
Research into various proteins capable of blocking metabolic pathways has improved the detection and treatment of multiple pathologies associated with the malfunction and overexpression of different metabolites. However, antigen-binding proteins have limitations. To overcome the disadvantages of the available antigen-binding proteins, the present investigation aims to provide chimeric antigen-binding peptides by binding a complementarity-determining region 3 (CDR3) of variable domains of new antigen receptors (VNARs) with a conotoxin. Six non-natural antibodies (NoNaBodies) were obtained from the complexes of conotoxin cal14.1a with six CDR3s from the VNARs of Heterodontus francisci and two NoNaBodies from the VNARs of other shark species. The peptides cal_P98Y vs. vascular endothelial growth factor 165 (VEGF165), cal_T10 vs. transforming growth factor beta (TGF-β), and cal_CV043 vs. carcinoembryonic antigen (CEA) showed in-silico and in vitro recognition capacity. Likewise, cal_P98Y and cal_CV043 demonstrated the capacity to neutralize the antigens for which they were designed.
Collapse
Affiliation(s)
- Salvador Dueñas
- Departamento de Innovación Biomédica, CICESE, Carretera Ensenada-Tijuana 3918, Ensenada C.P. 22860, Mexico
| | - Teresa Escalante
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José 11501, Costa Rica
| | | | - Johanna Bernáldez-Sarabia
- Departamento de Innovación Biomédica, CICESE, Carretera Ensenada-Tijuana 3918, Ensenada C.P. 22860, Mexico
| | - Karla Cervantes-Luévano
- Departamento de Innovación Biomédica, CICESE, Carretera Ensenada-Tijuana 3918, Ensenada C.P. 22860, Mexico
| | - Samanta Jiménez
- Departamento de Innovación Biomédica, CICESE, Carretera Ensenada-Tijuana 3918, Ensenada C.P. 22860, Mexico
| | - Noemí Sánchez-Campos
- Departamento de Innovación Biomédica, CICESE, Carretera Ensenada-Tijuana 3918, Ensenada C.P. 22860, Mexico
| | - Olivia Cabanillas-Bernal
- Departamento de Innovación Biomédica, CICESE, Carretera Ensenada-Tijuana 3918, Ensenada C.P. 22860, Mexico
| | | | - Angélica Álvarez-Lee
- Departamento de Innovación Biomédica, CICESE, Carretera Ensenada-Tijuana 3918, Ensenada C.P. 22860, Mexico
| | - Marco A. De León-Nava
- Departamento de Innovación Biomédica, CICESE, Carretera Ensenada-Tijuana 3918, Ensenada C.P. 22860, Mexico
| | - Alexei F. Licea-Navarro
- Departamento de Innovación Biomédica, CICESE, Carretera Ensenada-Tijuana 3918, Ensenada C.P. 22860, Mexico
| |
Collapse
|
11
|
Bhattacharya M, Chatterjee S, Lee SS, Chakraborty C. Therapeutic applications of nanobodies against SARS-CoV-2 and other viral infections: Current update. Int J Biol Macromol 2023; 229:70-80. [PMID: 36586649 PMCID: PMC9797221 DOI: 10.1016/j.ijbiomac.2022.12.284] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/15/2022] [Accepted: 12/25/2022] [Indexed: 12/30/2022]
Abstract
In the last two years, the world encountered the SARS-CoV-2 virus, which is still dominating the population due to the absence of a viable treatment. To eradicate the global pandemic, scientists, doctors, and researchers took an exceptionally significant initiative towards the development of effective therapeutics to save many lifes. This review discusses about the single-domain antibodies (sdAbs), also called nanobodies, their structure, and their types against the infections of dreadful SARS-CoV-2 virus. A precise description highlights the nanobodies and their therapeutic application against the other selected viruses. It aims to focus on the extraordinary features of these antibodies compared to the conventional therapeutics like mAbs, convalescent plasma therapy, and vaccines. The stable structure of these nanobodies along with the suitable mechanism of action also confers greater resistance to the evolving variants with numerous mutations. The nanobodies developed against SARS-CoV-2 and its mutant variants have shown the greater neutralization potential than the primitive ones. Engineering of these specialized antibodies by modern biotechnological approaches will surely be more beneficial in treating this COVID-19 pandemic along with certain other viral infections.
Collapse
Affiliation(s)
- Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore 756020, Odisha, India
| | - Srijan Chatterjee
- Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si 24252, Gangwon-do, Republic of Korea
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si 24252, Gangwon-do, Republic of Korea
| | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal 700126, India.
| |
Collapse
|
12
|
Xi X, Xiao G, An G, Liu L, Liu X, Hao P, Wang JY, Song D, Yu W, Gu Y. A novel shark single-domain antibody targeting OGT as a tool for detection and intracellular localization. Front Immunol 2023; 14:1062656. [PMID: 36855630 PMCID: PMC9968394 DOI: 10.3389/fimmu.2023.1062656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/09/2023] [Indexed: 02/14/2023] Open
Abstract
Introduction O-GlcNAcylation is a type of reversible post-translational modification on Ser/Thr residues of intracellular proteins in eukaryotic cells, which is generated by the sole O-GlcNAc transferase (OGT) and removed by O-GlcNAcase (OGA). Thousands of proteins, that are involved in various physiological and pathological processes, have been found to be O-GlcNAcylated. However, due to the lack of favorable tools, studies of the O-GlcNAcylation and OGT were impeded. Immunoglobulin new antigen receptor (IgNAR) derived from shark is attractive to research tools, diagnosis and therapeutics. The variable domain of IgNARs (VNARs) have several advantages, such as small size, good stability, low-cost manufacture, and peculiar paratope structure. Methods We obtained shark single domain antibodies targeting OGT by shark immunization, phage display library construction and panning. ELISA and BIACORE were used to assess the affinity of the antibodies to the antigen and three shark single-domain antibodies with high affinity were successfully screened. The three antibodies were assessed for intracellular function by flow cytometry and immunofluorescence co-localization. Results In this study, three anti-OGT VNARs (2D9, 3F7 and 4G2) were obtained by phage display panning. The affinity values were measured using surface plasmon resonance (SPR) that 2D9, 3F7 and 4G2 bound to OGT with KD values of 35.5 nM, 53.4 nM and 89.7 nM, respectively. Then, the VNARs were biotinylated and used for the detection and localization of OGT by ELISA, flow cytometry and immunofluorescence. 2D9, 3F7 and 4G2 were exhibited the EC50 values of 102.1 nM, 40.75 nM and 120.7 nM respectively. VNAR 3F7 was predicted to bind the amino acid residues of Ser375, Phe377, Cys379 and Tyr 380 on OGT. Discussion Our results show that shark single-domain antibodies targeting OGT can be used for in vitro detection and intracellular co-localization of OGT, providing a powerful tool for the study of OGT and O-GlcNAcylation.
Collapse
Affiliation(s)
- Xiaozhi Xi
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Ocean University of China, Qingdao, China
| | - Guokai Xiao
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Ocean University of China, Qingdao, China
| | - Guiqi An
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Lin Liu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Xiaochun Liu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Peiyu Hao
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Ocean University of China, Qingdao, China
| | - Jennifer Yiyang Wang
- College of Letters and Science Dept. of Microbiology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Dandan Song
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Ocean University of China, Qingdao, China
| | - Wengong Yu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Ocean University of China, Qingdao, China
| | - Yuchao Gu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Ocean University of China, Qingdao, China
| |
Collapse
|
13
|
Zhang T, Liu C, Zheng H, Han X, Lin H, Cao L, Sui J. The specific biopanning of single-domain antibody against haptens based on a functionalized cryogel. J Mol Recognit 2023; 36:e2999. [PMID: 36225143 DOI: 10.1002/jmr.2999] [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: 07/19/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 12/15/2022]
Abstract
Phage display technology is commonly applied for high-throughput screening of single-domain antibodies (sdAbs), and the problem of non-specific adsorption caused by carrier proteins seriously affects the biopanning of single-domain antibodies specific to haptens. In this paper, enrofloxacin (ENR)-functionalized cryogels were prepared by the ethylenediamine (EDA) and carbodiimide methods for application in the biopanning of ENR-specific phages. To improve the efficiency of biopanning, double blocking, a wash solution flow rate of 1 mL/min, and phage pre-incubation were applied to the biopanning process through single-factor experiments. Results of flat colony counting showed that the phage output of AG-ENR cryogels was 15 times higher than that of AG cryogels for the same input amount. And seven complete sequences of ENR-specific shark sdAbs were obtained by monoclonal phage ELISA and sequence alignment. All these results indicate that functionalized cryogels could be used as a novel and efficient method for phage biopanning for single-domain antibodies to haptens.
Collapse
Affiliation(s)
- Tianjiao Zhang
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Chang Liu
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Hongwei Zheng
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Xiangning Han
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Hong Lin
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Limin Cao
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Jianxin Sui
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao, China
| |
Collapse
|
14
|
Kolmar H, Grzeschik J, Könning D, Krah S, Zielonka S. Construction of Semisynthetic Shark vNAR Yeast Surface Display Antibody Libraries. Methods Mol Biol 2023; 2702:227-243. [PMID: 37679622 DOI: 10.1007/978-1-0716-3381-6_11] [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] [Indexed: 09/09/2023]
Abstract
The adaptive immune system of sharks comprises a unique heavy chain-only antibody isotype, termed immunoglobulin new antigen receptor (IgNAR), in which antigen binding is mediated by a single variable domain, referred to as vNAR. In recent years, efforts were made to harness these domains for biomedical and biotechnological applications particularly due to their high affinity and specificity combined with a small size and high stability. Herein, we describe protocols for the construction of semisynthetic, CDR3-randomized vNAR libraries for the isolation of target-specific paratopes by yeast surface display. Additionally, we provide guidance for affinity maturation of a panel of antigen-enriched vNAR domains through CDR1 diversification of the FACS-selected, antigen-enriched population and sublibrary establishment.
Collapse
Affiliation(s)
- Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany.
| | - Julius Grzeschik
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Doreen Könning
- Antibody-Drug Conjugates and Targeted NBE Therapeutics, Merck KGaA, Darmstadt, Germany
| | - Simon Krah
- Antibody Discovery & Protein Engineering, Merck KGaA, Darmstadt, Germany
| | - Stefan Zielonka
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany.
- Antibody Discovery & Protein Engineering, Merck KGaA, Darmstadt, Germany.
| |
Collapse
|
15
|
Lim HT, Kok BH, Lim CP, Abdul Majeed AB, Leow CY, Leow CH. Single domain antibodies derived from ancient animals as broadly neutralizing agents for SARS-CoV-2 and other coronaviruses. BIOMEDICAL ENGINEERING ADVANCES 2022; 4:100054. [PMID: 36158162 PMCID: PMC9482557 DOI: 10.1016/j.bea.2022.100054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 09/06/2022] [Accepted: 09/16/2022] [Indexed: 11/28/2022] Open
Abstract
With severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as an emergent human virus since December 2019, the world population is susceptible to coronavirus disease 2019 (COVID-19). SARS-CoV-2 has higher transmissibility than the previous coronaviruses, associated by the ribonucleic acid (RNA) virus nature with high mutation rate, caused SARS-CoV-2 variants to arise while circulating worldwide. Neutralizing antibodies are identified as immediate and direct-acting therapeutic against COVID-19. Single-domain antibodies (sdAbs), as small biomolecules with non-complex structure and intrinsic stability, can acquire antigen-binding capabilities comparable to conventional antibodies, which serve as an attractive neutralizing solution. SARS-CoV-2 spike protein attaches to human angiotensin-converting enzyme 2 (ACE2) receptor on lung epithelial cells to initiate viral infection, serves as potential therapeutic target. sdAbs have shown broad neutralization towards SARS-CoV-2 with various mutations, effectively stop and prevent infection while efficiently block mutational escape. In addition, sdAbs can be developed into multivalent antibodies or inhaled biotherapeutics against COVID-19.
Collapse
Affiliation(s)
- H T Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Penang 11800, Malaysia
| | - B H Kok
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Penang 11800, Malaysia
| | - C P Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Penang 11800, Malaysia
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor, Penang 11800, Malaysia
| | - A B Abdul Majeed
- Faculty of Pharmacy, Universiti Teknologi MARA, Kampus Puncak Alam, Bandar Puncak Alam, Selangor 42300, Malaysia
| | - C Y Leow
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor, Penang 11800, Malaysia
| | - C H Leow
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Penang 11800, Malaysia
| |
Collapse
|
16
|
Valdovino-Navarro BJ, Dueñas S, Flores-Acosta GI, Gasperin-Bulbarela J, Bernaldez-Sarabia J, Cabanillas-Bernal O, Cervantes-Luevano KE, Licea-Navarro AF. Neutralizing Ability of a Single Domain VNAR Antibody: In Vitro Neutralization of SARS-CoV-2 Variants of Concern. Int J Mol Sci 2022; 23:ijms232012267. [PMID: 36293124 PMCID: PMC9603574 DOI: 10.3390/ijms232012267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 is the causal pathogen of coronavirus disease 2019 (COVID-19). The emergence of new variants with different mutational patterns has limited the therapeutic options available and complicated the development of effective neutralizing antibodies targeting the spike (S) protein. Variable New Antigen Receptors (VNARs) constitute a neutralizing antibody technology that has been introduced into the list of possible therapeutic options against SARS-CoV-2. The unique qualities of VNARs, such as high affinities for target molecules, capacity for paratope reformatting, and relatively high stability, make them attractive molecules to counteract the emerging SARS-CoV-2 variants. In this study, we characterized a VNAR antibody (SP240) that was isolated from a synthetic phage library of VNAR domains. In the phage display, a plasma with high antibody titers against SARS-CoV-2 was used to selectively displace the VNAR antibodies bound to the antigen SARS-CoV-2 receptor binding domain (RBD). In silico data suggested that the SP240 binding epitopes are located within the ACE2 binding interface. The neutralizing ability of SP240 was tested against live Delta and Omicron SARS-CoV-2 variants and was found to clear the infection of both variants in the lung cell line A549-ACE2-TMPRSS2. This study highlights the potential of VNARs to act as neutralizing antibodies against emerging SARS-CoV-2 variants.
Collapse
|
17
|
Chen YL, Lin JJ, Ma H, Zhong N, Xie XX, Yang Y, Zheng P, Zhang LJ, Jin T, Cao MJ. Screening and Characterization of Shark-Derived VNARs against SARS-CoV-2 Spike RBD Protein. Int J Mol Sci 2022; 23:ijms231810904. [PMID: 36142819 PMCID: PMC9502636 DOI: 10.3390/ijms231810904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/11/2022] [Accepted: 09/15/2022] [Indexed: 12/03/2022] Open
Abstract
The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein is the major target for antibody therapeutics. Shark-derived variable domains of new antigen receptors (VNARs) are the smallest antibody fragments with flexible paratopes that can recognize protein motifs inaccessible to classical antibodies. This study reported four VNARs binders (JM-2, JM-5, JM-17, and JM-18) isolated from Chiloscyllium plagiosum immunized with SARS-CoV-2 RBD. Biolayer interferometry showed that the VNARs bound to the RBD with an affinity KD ranging from 38.5 to 2720 nM, and their Fc fusions had over ten times improved affinity. Gel filtration chromatography revealed that JM-2-Fc, JM-5-Fc, and JM-18-Fc could form stable complexes with RBD in solution. In addition, five bi-paratopic VNARs, named JM-2-5, JM-2-17, JM-2-18, JM-5-18, and JM-17-18, were constructed by fusing two VNARs targeting distinct RBD epitopes based on epitope grouping results. All these bi-paratopic VNARs except for JM-5-18 showed higher RBD binding affinities than its component VNARs, and their Fc fusions exhibited further enhanced binding affinities, with JM-2-5-Fc, JM-2-17-Fc, JM-2-18-Fc, and JM-5-18-Fc having KD values lower than 1 pM. Among these Fc fusions of bi-paratopic VNARs, JM-2-5-Fc, JM-2-17-Fc, and JM-2-18-Fc could block the angiotensin-converting enzyme 2 (ACE2) binding to the RBD of SARS-CoV-2 wildtype, Delta, Omicron, and SARS-CoV, with inhibition rates of 48.9~84.3%. Therefore, these high-affinity VNAR binders showed promise as detectors and therapeutics of COVID-19.
Collapse
Affiliation(s)
- Yu-Lei Chen
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Jin-Jin Lin
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Huan Ma
- CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei 230007, China
| | - Ning Zhong
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Xin-Xin Xie
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Yunru Yang
- CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei 230007, China
| | - Peiyi Zheng
- CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei 230007, China
| | - Ling-Jing Zhang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Tengchuan Jin
- CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei 230007, China
- Correspondence: (T.J.); (M.-J.C.); Tel.: +86-551-6360-0720 (T.J.); +86-592-618-3955 (M.-J.C.)
| | - Min-Jie Cao
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
- Correspondence: (T.J.); (M.-J.C.); Tel.: +86-551-6360-0720 (T.J.); +86-592-618-3955 (M.-J.C.)
| |
Collapse
|
18
|
Feng B, Chen Z, Sun J, Xu T, Wang Q, Yi H, Niu X, Zhu J, Fan M, Hou R, Shao Y, Huang S, Li C, Hu P, Zheng P, He P, Luo J, Yan Q, Xiong X, Liu J, Zhao J, Chen L. A Class of Shark-Derived Single-Domain Antibodies can Broadly Neutralize SARS-Related Coronaviruses and the Structural Basis of Neutralization and Omicron Escape. SMALL METHODS 2022; 6:e2200387. [PMID: 35583124 PMCID: PMC9347709 DOI: 10.1002/smtd.202200387] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/09/2022] [Indexed: 05/26/2023]
Abstract
The identification of a novel class of shark-derived single domain antibodies, named vnarbodies that show picomolar affinities binding to the receptor binding domain (RBD) of Wuhan and Alpha, Beta, Kappa, Delta, Delta-plus, and Lambda variants, is reported. Vnarbody 20G6 and 17F6 have broad neutralizing activities against all these SARS-CoV-2 viruses as well as other sarbecoviruses, including Pangolin coronavirus and Bat coronavirus. Intranasal administration of 20G6 effectively protects mice from the challenges of SARS-CoV-2 Wuhan and Beta variants. 20G6 and 17F6 contain a unique "WXGY" motif in the complementary determining region 3 that binds to a hidden epitope on RBD, which is highly conserved in sarbecoviruses through a novel β-sheet interaction. It is found that the S375F mutation on Omicron RBD disrupts the structure of β-strand, thus impair the binding with 20G6. The study demonstrates that shark-derived vnarbodies offer a prophylactic and therapeutic option against most SARS-CoV-2 variants and provide insights into antibody evasion by the Omicron variant.
Collapse
Affiliation(s)
- Bo Feng
- State Key Laboratory of Respiratory DiseaseInstitute of Infectious DiseaseGuangzhou 8th People's Hospital & The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Guangzhou LaboratoryGuangzhouChina
| | - Zhilong Chen
- School of Medicine & School of Biomedical SciencesHuaqiao UniversityQuanzhouChina
- Xiamen United Institutes of Respiratory HealthXiamenChina
| | - Jing Sun
- State Key Laboratory of Respiratory DiseaseInstitute of Infectious DiseaseGuangzhou 8th People's Hospital & The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Tingting Xu
- State Key Laboratory of Respiratory DiseaseGuangdong Provincial Key Laboratory of Computational BiomedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina
| | - Qian Wang
- State Key Laboratory of Respiratory DiseaseInstitute of Infectious DiseaseGuangzhou 8th People's Hospital & The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Haisu Yi
- State Key Laboratory of Respiratory DiseaseInstitute of Infectious DiseaseGuangzhou 8th People's Hospital & The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Xuefeng Niu
- State Key Laboratory of Respiratory DiseaseInstitute of Infectious DiseaseGuangzhou 8th People's Hospital & The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Jiabin Zhu
- State Key Laboratory of Respiratory DiseaseInstitute of Infectious DiseaseGuangzhou 8th People's Hospital & The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Mengzhu Fan
- School of Medicine & School of Biomedical SciencesHuaqiao UniversityQuanzhouChina
| | - Ruitian Hou
- State Key Laboratory of Respiratory DiseaseGuangdong Provincial Key Laboratory of Computational BiomedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina
| | - Ying Shao
- School of Medicine & School of Biomedical SciencesHuaqiao UniversityQuanzhouChina
| | - Sihui Huang
- School of Medicine & School of Biomedical SciencesHuaqiao UniversityQuanzhouChina
| | - Cuiyun Li
- State Key Laboratory of Respiratory DiseaseGuangdong Provincial Key Laboratory of Computational BiomedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina
| | - Peiyu Hu
- Guangzhou LaboratoryGuangzhouChina
| | | | - Ping He
- State Key Laboratory of Respiratory DiseaseGuangdong Provincial Key Laboratory of Computational BiomedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina
| | - Jia Luo
- Xiamen United Institutes of Respiratory HealthXiamenChina
| | - Qihong Yan
- State Key Laboratory of Respiratory DiseaseGuangdong Provincial Key Laboratory of Computational BiomedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina
| | - Xiaoli Xiong
- State Key Laboratory of Respiratory DiseaseGuangdong Provincial Key Laboratory of Computational BiomedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina
| | - Jinsong Liu
- State Key Laboratory of Respiratory DiseaseGuangdong Provincial Key Laboratory of Computational BiomedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina
| | - Jincun Zhao
- State Key Laboratory of Respiratory DiseaseInstitute of Infectious DiseaseGuangzhou 8th People's Hospital & The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Guangzhou LaboratoryGuangzhouChina
| | - Ling Chen
- State Key Laboratory of Respiratory DiseaseInstitute of Infectious DiseaseGuangzhou 8th People's Hospital & The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Guangzhou LaboratoryGuangzhouChina
- School of Medicine & School of Biomedical SciencesHuaqiao UniversityQuanzhouChina
- State Key Laboratory of Respiratory DiseaseGuangdong Provincial Key Laboratory of Computational BiomedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina
| |
Collapse
|
19
|
Outlook of therapeutic and diagnostic competency of nanobodies against SARS-CoV-2: A systematic review. Anal Biochem 2022; 640:114546. [PMID: 34995616 PMCID: PMC8730734 DOI: 10.1016/j.ab.2022.114546] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 12/29/2021] [Accepted: 01/02/2022] [Indexed: 12/15/2022]
Abstract
PURPOSE The newly emerged coronavirus (SARS-CoV-2) continues to infect humans, and no completely efficient treatment has yet been found. Antibody therapy is one way to control infection caused by COVID-19, but the use of classical antibodies has many disadvantages. Heavy chain antibodies (HCAbs) are single-domain antibodies derived from the Camelidae family. The variable part of these antibodies (Nanobodies or VHH) has interesting properties such as small size, identify criptic epitopes, stability in harsh conditions, good tissue permeability and cost-effective production causing nanobodies have become a good candidate in the treatment and diagnosis of viral infections. METHODS Totally 157 records (up to November 10, 2021), were recognized to be reviewed in this study. 62 studies were removed after first step screening due to their deviation from inclusion criteria. The remaining 95 studies were reviewed in details. After removing articles that were not in the study area, 45 remaining studies met the inclusion criteria and were qualified to be included in the systematic review. RESULTS In this systematic review, the application of nanobodies in the treatment and detection of COVID-19 infection was reviewed. The results of this study showed that extensive and sufficient studies have been performed in the field of production of nanobodies against SARS-CoV-2 virus and the obtained nanobodies have a great potential for use in patients infected with SARS-CoV-2 virus. CONCLUSION According to the obtained results, it was found that nanobodies can be used effectively in the treatment and diagnosis of SARS-CoV-2 virus.
Collapse
|