1
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Lee NJ, Jung M, Yang HY, Shim H. A single-domain antibody library based on a stability-engineered human VH3 scaffold. Sci Rep 2024; 14:17747. [PMID: 39085444 PMCID: PMC11291719 DOI: 10.1038/s41598-024-68680-5] [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: 05/14/2024] [Accepted: 07/25/2024] [Indexed: 08/02/2024] Open
Abstract
Using conventional immunoglobulin G (IgG) molecules as therapeutic agents presents several well-known disadvantages owing to their large size and structural complexity, negatively impacting development and production efficiency. Single-domain antibodies (sdAbs) are the smallest functional antibody format (~ 15 kDa) and represent a viable alternative to IgG in many applications. However, unlike natural single-domain antibodies, such as camelid VHH, the variable domains of conventional antibodies show poor physicochemical properties when expressed as sdAbs. This report identified stable sdAb variants of human VH3-23 from a framework region 2-randomized human VH library by phage display selection under thermal challenge. Synthetic complementarity determining region diversity was introduced to one of the selected variants with high thermal stability, expression level, and monomeric content to construct a human VH sdAb library. The library was validated by panning against a panel of antigens, and target-specific binders were identified and characterized for their affinity and biophysical properties. The results of this study suggest that a synthetic sdAb library based on a stability-engineered human VH scaffold could be a facile source of high-quality sdAb for many practical applications.
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Affiliation(s)
- Nam Ju Lee
- Department of Bioinspired Sciences, Ewha Womans University, Seoul, Korea
| | - Mooyoung Jung
- Department of Bioinspired Sciences, Ewha Womans University, Seoul, Korea
| | - Hye Young Yang
- Department of Life Sciences, Ewha Womans University, Seoul, Korea
| | - Hyunbo Shim
- Department of Bioinspired Sciences, Ewha Womans University, Seoul, Korea.
- Department of Life Sciences, Ewha Womans University, Seoul, Korea.
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2
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Aksu M, Kumar P, Güttler T, Taxer W, Gregor K, Mußil B, Rymarenko O, Stegmann KM, Dickmanns A, Gerber S, Reineking W, Schulz C, Henneck T, Mohamed A, Pohlmann G, Ramazanoglu M, Mese K, Groß U, Ben-Yedidia T, Ovadia O, Fischer DW, Kamensky M, Reichman A, Baumgärtner W, von Köckritz-Blickwede M, Dobbelstein M, Görlich D. Nanobodies to multiple spike variants and inhalation of nanobody-containing aerosols neutralize SARS-CoV-2 in cell culture and hamsters. Antiviral Res 2024; 221:105778. [PMID: 38065245 DOI: 10.1016/j.antiviral.2023.105778] [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: 08/25/2023] [Revised: 11/23/2023] [Accepted: 12/04/2023] [Indexed: 12/17/2023]
Abstract
The ongoing threat of COVID-19 has highlighted the need for effective prophylaxis and convenient therapies, especially for outpatient settings. We have previously developed highly potent single-domain (VHH) antibodies, also known as nanobodies, that target the Receptor Binding Domain (RBD) of the SARS-CoV-2 Spike protein and neutralize the Wuhan strain of the virus. In this study, we present a new generation of anti-RBD nanobodies with superior properties. The primary representative of this group, Re32D03, neutralizes Alpha to Delta as well as Omicron BA.2.75; other members neutralize, in addition, Omicron BA.1, BA.2, BA.4/5, and XBB.1. Crystal structures of RBD-nanobody complexes reveal how ACE2-binding is blocked and also explain the nanobodies' tolerance to immune escape mutations. Through the cryo-EM structure of the Ma16B06-BA.1 Spike complex, we demonstrated how a single nanobody molecule can neutralize a trimeric spike. We also describe a method for large-scale production of these nanobodies in Pichia pastoris, and for formulating them into aerosols. Exposing hamsters to these aerosols, before or even 24 h after infection with SARS-CoV-2, significantly reduced virus load, weight loss and pathogenicity. These results show the potential of aerosolized nanobodies for prophylaxis and therapy of coronavirus infections.
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Affiliation(s)
- Metin Aksu
- Max Planck Institute for Multidisciplinary Sciences, Dept. of Cellular Logistics, Am Fassberg 11, 37077 Göttingen, Germany
| | - Priya Kumar
- University Medical Center Göttingen, Dept. of Molecular Oncology, Justus von Liebig Weg 11, 37077 Göttingen, Germany
| | - Thomas Güttler
- Max Planck Institute for Multidisciplinary Sciences, Dept. of Cellular Logistics, Am Fassberg 11, 37077 Göttingen, Germany; Octapharma Biopharmaceuticals GmbH, Im Neuenheimer Feld 590, 69120 Heidelberg, Germany
| | - Waltraud Taxer
- Max Planck Institute for Multidisciplinary Sciences, Dept. of Cellular Logistics, Am Fassberg 11, 37077 Göttingen, Germany
| | - Kathrin Gregor
- Max Planck Institute for Multidisciplinary Sciences, Dept. of Cellular Logistics, Am Fassberg 11, 37077 Göttingen, Germany
| | - Bianka Mußil
- Max Planck Institute for Multidisciplinary Sciences, Dept. of Cellular Logistics, Am Fassberg 11, 37077 Göttingen, Germany
| | - Oleh Rymarenko
- Max Planck Institute for Multidisciplinary Sciences, Dept. of Cellular Logistics, Am Fassberg 11, 37077 Göttingen, Germany
| | - Kim M Stegmann
- University Medical Center Göttingen, Dept. of Molecular Oncology, Justus von Liebig Weg 11, 37077 Göttingen, Germany
| | - Antje Dickmanns
- University Medical Center Göttingen, Dept. of Molecular Oncology, Justus von Liebig Weg 11, 37077 Göttingen, Germany
| | - Sabrina Gerber
- University Medical Center Göttingen, Dept. of Molecular Oncology, Justus von Liebig Weg 11, 37077 Göttingen, Germany
| | - Wencke Reineking
- Department of Pathology, University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany
| | - Claudia Schulz
- Research Center for Emerging Infections and Zoonosis (RIZ), University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany
| | - Timo Henneck
- Research Center for Emerging Infections and Zoonosis (RIZ), University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany; Department of Biochemistry, University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany
| | - Ahmed Mohamed
- Research Center for Emerging Infections and Zoonosis (RIZ), University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany; Department of Biochemistry, University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany
| | - Gerhard Pohlmann
- Fraunhofer Institute for Toxicology and Experimental Medicine ITEM, Nikolai-Fuchs Str. 1, 30625 Hannover, Germany
| | - Mehmet Ramazanoglu
- Fraunhofer Institute for Toxicology and Experimental Medicine ITEM, Nikolai-Fuchs Str. 1, 30625 Hannover, Germany
| | - Kemal Mese
- University Medical Center Göttingen, Dept. of Medical Microbiology and Virology, Kreuzbergring 57, 37075 Göttingen, Germany
| | - Uwe Groß
- University Medical Center Göttingen, Dept. of Medical Microbiology and Virology, Kreuzbergring 57, 37075 Göttingen, Germany
| | - Tamar Ben-Yedidia
- Scinai Immunotherapeutics Ltd., Jerusalem BioPark, Hadassah Ein Kerem, Jerusalem, 9112001, Israel
| | - Oded Ovadia
- Scinai Immunotherapeutics Ltd., Jerusalem BioPark, Hadassah Ein Kerem, Jerusalem, 9112001, Israel
| | - Dalit Weinstein Fischer
- Scinai Immunotherapeutics Ltd., Jerusalem BioPark, Hadassah Ein Kerem, Jerusalem, 9112001, Israel
| | - Merav Kamensky
- Scinai Immunotherapeutics Ltd., Jerusalem BioPark, Hadassah Ein Kerem, Jerusalem, 9112001, Israel
| | - Amir Reichman
- Scinai Immunotherapeutics Ltd., Jerusalem BioPark, Hadassah Ein Kerem, Jerusalem, 9112001, Israel
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany
| | - Maren von Köckritz-Blickwede
- Research Center for Emerging Infections and Zoonosis (RIZ), University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany; Department of Biochemistry, University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany
| | - Matthias Dobbelstein
- Max Planck Institute for Multidisciplinary Sciences, Dept. of Cellular Logistics, Am Fassberg 11, 37077 Göttingen, Germany; University Medical Center Göttingen, Dept. of Molecular Oncology, Justus von Liebig Weg 11, 37077 Göttingen, Germany.
| | - Dirk Görlich
- Max Planck Institute for Multidisciplinary Sciences, Dept. of Cellular Logistics, Am Fassberg 11, 37077 Göttingen, Germany.
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3
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Yang J, Lin S, Chen Z, Yang F, Guo L, Wang L, Duan Y, Zhang X, Dai Y, Yin K, Yu C, Yuan X, Sun H, He B, Cao Y, Ye H, Dong H, Liu X, Chen B, Li J, Zhao Q, Lu G. Development of a bispecific nanobody conjugate broadly neutralizes diverse SARS-CoV-2 variants and structural basis for its broad neutralization. PLoS Pathog 2023; 19:e1011804. [PMID: 38033141 PMCID: PMC10688893 DOI: 10.1371/journal.ppat.1011804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 11/07/2023] [Indexed: 12/02/2023] Open
Abstract
The continuous emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with increased transmissibility and profound immune-escape capacity makes it an urgent need to develop broad-spectrum therapeutics. Nanobodies have recently attracted extensive attentions due to their excellent biochemical and binding properties. Here, we report two high-affinity nanobodies (Nb-015 and Nb-021) that target non-overlapping epitopes in SARS-CoV-2 S-RBD. Both nanobodies could efficiently neutralize diverse viruses of SARS-CoV-2. The neutralizing mechanisms for the two nanobodies are further delineated by high-resolution nanobody/S-RBD complex structures. In addition, an Fc-based tetravalent nanobody format is constructed by combining Nb-015 and Nb-021. The resultant nanobody conjugate, designated as Nb-X2-Fc, exhibits significantly enhanced breadth and potency against all-tested SARS-CoV-2 variants, including Omicron sub-lineages. These data demonstrate that Nb-X2-Fc could serve as an effective drug candidate for the treatment of SARS-CoV-2 infection, deserving further in-vivo evaluations in the future.
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Affiliation(s)
- Jing Yang
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Sheng Lin
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zimin Chen
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Fanli Yang
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Liyan Guo
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lingling Wang
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yanping Duan
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xindan Zhang
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yushan Dai
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Keqing Yin
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Chongzhang Yu
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xin Yuan
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Honglu Sun
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Bin He
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yu Cao
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Disaster Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Haoyu Ye
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Haohao Dong
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xianbo Liu
- CHENGDU NB BIOLAB CO., LTD, Chengdu, Sichuan, China
| | - Bo Chen
- CHENGDU NB BIOLAB CO., LTD, Chengdu, Sichuan, China
| | - Jian Li
- School of Basic Medical Sciences, Chengdu University, Chengdu, Sichuan, China
| | - Qi Zhao
- College of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Guangwen Lu
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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4
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Li J, Howard CB, Dey S, Lowry K, Whiley DM, Puttick S, Rose S, Lobb RJ, Wuethrich A, Edwardraja S, Trau M. A universal reagent for detection of emerging diseases using bioengineered multifunctional yeast nanofragments. NATURE NANOTECHNOLOGY 2023; 18:1222-1229. [PMID: 37291255 DOI: 10.1038/s41565-023-01415-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 05/04/2023] [Indexed: 06/10/2023]
Abstract
Accurate and early detection of biomarkers provides the molecular evidence for disease management, allowing prompt actions and timely treatments to save lives. Multivalent biomolecular interactions between the probe and biomarker as well as controlled probe orientation on material surfaces are keys for highly sensitive detection. Here we report the bioengineering of programmable and multifunctional nanoprobes, which can provide rapid, specific and highly sensitive detection of emerging diseases in a range of widely used diagnostic systems. These nanoprobes composed of nanosized cell wall fragments, termed as synthetic bionanofragments (SynBioNFs), are generated by the fragmentation of genetically programmed yeast cells. SynBioNFs display multiple copies of biomolecules for high-affinity target binding and molecular handles for the precisely orientated attachment on surfaces used in diagnostic platforms. SynBioNFs are demonstrated for the capture and detection of SARS-CoV-2 virions using multiple diagnostic platforms, including surface-enhanced Raman scattering, fluorescence, electrochemical and colorimetric-based lateral flow systems with sensitivity comparable with the gold-standard reverse-transcription quantitative polymerase chain reaction.
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Affiliation(s)
- Junrong Li
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland, Australia
| | - Christopher B Howard
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland, Australia.
| | - Shuvashis Dey
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland, Australia
| | - Kym Lowry
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
- Queensland Paediatric Infectious Diseases (QPID) Sakzewski Laboratory, Queensland Children's Hospital, Brisbane, Queensland, Australia
| | - David M Whiley
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Simon Puttick
- Probing Biosystems Future Science Platform, Commonwealth Scientific and Industrial Research Organization, Brisbane, Queensland, Australia
| | - Stephen Rose
- Probing Biosystems Future Science Platform, Commonwealth Scientific and Industrial Research Organization, Brisbane, Queensland, Australia
| | - Richard J Lobb
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland, Australia
| | - Alain Wuethrich
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland, Australia.
| | - Selvakumar Edwardraja
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland, Australia.
| | - Matt Trau
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland, Australia.
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.
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5
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Jiang J, Boughter CT, Ahmad J, Natarajan K, Boyd LF, Meier-Schellersheim M, Margulies DH. SARS-CoV-2 antibodies recognize 23 distinct epitopic sites on the receptor binding domain. Commun Biol 2023; 6:953. [PMID: 37726484 PMCID: PMC10509263 DOI: 10.1038/s42003-023-05332-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 09/07/2023] [Indexed: 09/21/2023] Open
Abstract
The COVID-19 pandemic and SARS-CoV-2 variants have dramatically illustrated the need for a better understanding of antigen (epitope)-antibody (paratope) interactions. To gain insight into the immunogenic characteristics of epitopic sites (ES), we systematically investigated the structures of 340 Abs and 83 nanobodies (Nbs) complexed with the Receptor Binding Domain (RBD) of the SARS-CoV-2 spike protein. We identified 23 distinct ES on the RBD surface and determined the frequencies of amino acid usage in the corresponding CDR paratopes. We describe a clustering method for analysis of ES similarities that reveals binding motifs of the paratopes and that provides insights for vaccine design and therapies for SARS-CoV-2, as well as a broader understanding of the structural basis of Ab-protein antigen (Ag) interactions.
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Affiliation(s)
- Jiansheng Jiang
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA.
| | - Christopher T Boughter
- Computational Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Javeed Ahmad
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Kannan Natarajan
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Lisa F Boyd
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Martin Meier-Schellersheim
- Computational Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - David H Margulies
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA.
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6
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Nguyen H, Nguyen HL, Lan PD, Thai NQ, Sikora M, Li MS. Interaction of SARS-CoV-2 with host cells and antibodies: experiment and simulation. Chem Soc Rev 2023; 52:6497-6553. [PMID: 37650302 DOI: 10.1039/d1cs01170g] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the devastating global COVID-19 pandemic announced by WHO in March 2020. Through unprecedented scientific effort, several vaccines, drugs and antibodies have been developed, saving millions of lives, but the fight against COVID-19 continues as immune escape variants of concern such as Delta and Omicron emerge. To develop more effective treatments and to elucidate the side effects caused by vaccines and therapeutic agents, a deeper understanding of the molecular interactions of SARS-CoV-2 with them and human cells is required. With special interest in computational approaches, we will focus on the structure of SARS-CoV-2 and the interaction of its spike protein with human angiotensin-converting enzyme-2 (ACE2) as a prime entry point of the virus into host cells. In addition, other possible viral receptors will be considered. The fusion of viral and human membranes and the interaction of the spike protein with antibodies and nanobodies will be discussed, as well as the effect of SARS-CoV-2 on protein synthesis in host cells.
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Affiliation(s)
- Hung Nguyen
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
| | - Hoang Linh Nguyen
- Institute of Fundamental and Applied Sciences, Duy Tan University, Ho Chi Minh City 700000, Vietnam
- Faculty of Environmental and Natural Sciences, Duy Tan University, Da Nang 550000, Vietnam
| | - Pham Dang Lan
- Life Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, 729110 Ho Chi Minh City, Vietnam
- Faculty of Physics and Engineering Physics, VNUHCM-University of Science, 227, Nguyen Van Cu Street, District 5, 749000 Ho Chi Minh City, Vietnam
| | - Nguyen Quoc Thai
- Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap, Vietnam
| | - Mateusz Sikora
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
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7
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Shen H, Yang H. Binding of synthetic nanobodies to the SARS-CoV-2 receptor-binding domain: the importance of salt bridges. Phys Chem Chem Phys 2023; 25:24129-24142. [PMID: 37655617 DOI: 10.1039/d3cp02628k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
In this study, five different SARS-CoV-2 receptor-binding domain (RBD) models were created based on the crystal structures of RBD complexes with two synthetic nanobodies (Sb16 and Sb45). Microsecond all-atom MD simulations revealed that Sb16 and Sb45 substantially stabilized the flexible RBD loop (residues GLU471-SER494) due to the salt bridges and hydrogen bonding interactions between RBD and the synthetic nanobodies. However, the calculation of binding free energy displayed that Sb45 had a higher binding affinity to RBD than Sb16, in agreement with the experimental result. This is because Sb45 has stronger electrostatic attraction to RBD as compared to Sb16. In particular, the salt bridge GLU484-ARG33 in Sb45-RBD is stronger than the GLU484-LYS32 in Sb16-RBD. Furthermore, by comparing the binding affinity of Sb16 for two RBD mutants (E484K and K417N), we found that E484K mutation substantially reduced the binding affinity to Sb16, and K417N mutation had no significant effect, qualitatively in agreement with experimental studies. According to the binding free energy calculation, the strong electrostatic repulsion between LYS32 and LYS484 caused by E484K mutation destroys the salt bridge between LYS32 and GLU484 in the RBD wild type (WT). In contrast, the binding of the K417N mutant to Sb16 effectively maintains the salt bridge between LYS32 and GLU484. Therefore, our research suggests that the salt bridges between RBD and synthetic nanobodies are crucial for binding synthetic nanobodies to RBD, and a SARS-CoV-2 variant can escape neutralization from nanobodies by creating electrostatic repulsion between them.
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Affiliation(s)
- Hujun Shen
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Education University, Guiyang, 550018, China.
| | - Hengxiu Yang
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Education University, Guiyang, 550018, China.
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8
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Modhiran N, Lauer SM, Amarilla AA, Hewins P, Lopes van den Broek SI, Low YS, Thakur N, Liang B, Nieto GV, Jung J, Paramitha D, Isaacs A, Sng JD, Song D, Jørgensen JT, Cheuquemilla Y, Bürger J, Andersen IV, Himelreichs J, Jara R, MacLoughlin R, Miranda-Chacon Z, Chana-Cuevas P, Kramer V, Spahn C, Mielke T, Khromykh AA, Munro T, Jones ML, Young PR, Chappell K, Bailey D, Kjaer A, Herth MM, Jurado KA, Schwefel D, Rojas-Fernandez A, Watterson D. A nanobody recognizes a unique conserved epitope and potently neutralizes SARS-CoV-2 omicron variants. iScience 2023; 26:107085. [PMID: 37361875 PMCID: PMC10251734 DOI: 10.1016/j.isci.2023.107085] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/12/2023] [Accepted: 06/06/2023] [Indexed: 06/28/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) Omicron variant sub-lineages spread rapidly worldwide, mostly due to their immune-evasive properties. This has put a significant part of the population at risk for severe disease and underscores the need for effective anti-SARS-CoV-2 agents against emergent strains in vulnerable patients. Camelid nanobodies are attractive therapeutic candidates due to their high stability, ease of large-scale production, and potential for delivery via inhalation. Here, we characterize the receptor binding domain (RBD)-specific nanobody W25 and show superior neutralization activity toward Omicron sub-lineages in comparison to all other SARS-CoV2 variants. Structure analysis of W25 in complex with the SARS-CoV2 spike glycoprotein shows that W25 engages an RBD epitope not covered by any of the antibodies previously approved for emergency use. In vivo evaluation of W25 prophylactic and therapeutic treatments across multiple SARS-CoV-2 variant infection models, together with W25 biodistribution analysis in mice, demonstrates favorable pre-clinical properties. Together, these data endorse W25 for further clinical development.
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Affiliation(s)
- Naphak Modhiran
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
- Australian Institute for Bioengineering and Nanotechnology, Brisbane, QLD, Australia
| | - Simon Malte Lauer
- Institute of Medical Physics and Biophysics, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Alberto A. Amarilla
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
| | - Peter Hewins
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Sara Irene Lopes van den Broek
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100 Copenhagen, Denmark
| | - Yu Shang Low
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
| | - Nazia Thakur
- The Pirbright Institute, Ash Road, Guildford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Benjamin Liang
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
| | - Guillermo Valenzuela Nieto
- Institute of Medicine, Faculty of Medicine & Center for Interdisciplinary Studies on the Nervous System, CISNE, Universidad Austral de Chile, Valdivia, Chile
| | - James Jung
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
| | - Devina Paramitha
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
| | - Ariel Isaacs
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
| | - Julian D.J. Sng
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
| | - David Song
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Jesper Tranekjær Jørgensen
- Department of Clinical Physiology, Nuclear Medicine & PET, Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
- Cluster for Molecular Imaging, Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Yorka Cheuquemilla
- Institute of Medicine, Faculty of Medicine & Center for Interdisciplinary Studies on the Nervous System, CISNE, Universidad Austral de Chile, Valdivia, Chile
| | - Jörg Bürger
- Institute of Medical Physics and Biophysics, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
- Microscopy and Cryo-Electron Microscopy Service Group, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Ida Vang Andersen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100 Copenhagen, Denmark
- Department of Clinical Physiology, Nuclear Medicine & PET, Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Johanna Himelreichs
- Institute of Medicine, Faculty of Medicine & Center for Interdisciplinary Studies on the Nervous System, CISNE, Universidad Austral de Chile, Valdivia, Chile
| | - Ronald Jara
- Institute of Medicine, Faculty of Medicine & Center for Interdisciplinary Studies on the Nervous System, CISNE, Universidad Austral de Chile, Valdivia, Chile
| | - Ronan MacLoughlin
- Research and Development, Science and Emerging Technologies, Aerogen Limited, Galway Business Park, H91 HE94 Galway, Ireland
| | | | - Pedro Chana-Cuevas
- CETRAM & Faculty of Medical Science Universidad de Santiago de Chile, Chile
| | - Vasko Kramer
- PositronPharma SA, Rancagua 878, 7500921 Providencia, Santiago, Chile
| | - Christian Spahn
- Institute of Medical Physics and Biophysics, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Thorsten Mielke
- Microscopy and Cryo-Electron Microscopy Service Group, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Alexander A. Khromykh
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD, Australia
| | - Trent Munro
- Australian Institute for Bioengineering and Nanotechnology, Brisbane, QLD, Australia
| | - Martina L. Jones
- Australian Institute for Bioengineering and Nanotechnology, Brisbane, QLD, Australia
| | - Paul R. Young
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
- Australian Institute for Bioengineering and Nanotechnology, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD, Australia
| | - Keith Chappell
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
- Australian Institute for Bioengineering and Nanotechnology, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD, Australia
| | - Dalan Bailey
- The Pirbright Institute, Ash Road, Guildford, UK
| | - Andreas Kjaer
- Department of Clinical Physiology, Nuclear Medicine & PET, Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
- Cluster for Molecular Imaging, Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Matthias Manfred Herth
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100 Copenhagen, Denmark
- Department of Clinical Physiology, Nuclear Medicine & PET, Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Kellie Ann Jurado
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - David Schwefel
- Institute of Medical Physics and Biophysics, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Alejandro Rojas-Fernandez
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Berking Biotechnology, Valdivia, Chile
| | - Daniel Watterson
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
- Australian Institute for Bioengineering and Nanotechnology, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD, Australia
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9
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Rahman MS, Han MJ, Kim SW, Kang SM, Kim BR, Kim H, Lee CJ, Noh JE, Kim H, Lee JO, Jang SK. Structure-Guided Development of Bivalent Aptamers Blocking SARS-CoV-2 Infection. Molecules 2023; 28:4645. [PMID: 37375202 DOI: 10.3390/molecules28124645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused devastation to human society through its high virulence, infectivity, and genomic mutations, which reduced the efficacy of vaccines. Here, we report the development of aptamers that effectively interfere with SARS-CoV-2 infection by targeting its spike protein, which plays a pivotal role in host cell entry of the virus through interaction with the viral receptor angiotensin-converting enzyme 2 (ACE2). To develop highly effective aptamers and to understand their mechanism in inhibiting viral infection, we determined the three-dimensional (3D) structures of aptamer/receptor-binding domain (RBD) complexes using cryogenic electron microscopy (cryo-EM). Moreover, we developed bivalent aptamers targeting two distinct regions of the RBD in the spike protein that directly interact with ACE2. One aptamer interferes with the binding of ACE2 by blocking the ACE2-binding site in RBD, and the other aptamer allosterically inhibits ACE2 by binding to a distinct face of RBD. Using the 3D structures of aptamer-RBD complexes, we minimized and optimized these aptamers. By combining the optimized aptamers, we developed a bivalent aptamer that showed a stronger inhibitory effect on virus infection than the component aptamers. This study confirms that the structure-based aptamer-design approach has a high potential in developing antiviral drugs against SARS-CoV-2 and other viruses.
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Affiliation(s)
- Md Shafiqur Rahman
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea
| | - Min Jung Han
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea
| | - Sang Won Kim
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea
| | - Seong Mu Kang
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea
| | - Bo Ri Kim
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea
| | - Heesun Kim
- Division of Integrative Bioscience & Biotechnology, POSTECH Biotech Center, Pohang University of Science and Technology, Nam-gu, Pohang-si 37673, Republic of Korea
| | - Chang Jun Lee
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea
| | - Jung Eun Noh
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea
| | - Hanseong Kim
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea
| | - Jie-Oh Lee
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea
| | - Sung Key Jang
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea
- Division of Integrative Bioscience & Biotechnology, POSTECH Biotech Center, Pohang University of Science and Technology, Nam-gu, Pohang-si 37673, Republic of Korea
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10
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Dormeshkin D, Katsin M, Stegantseva M, Golenchenko S, Shapira M, Dubovik S, Lutskovich D, Kavaleuski A, Meleshko A. Design and Immunogenicity of SARS-CoV-2 DNA Vaccine Encoding RBD-PVXCP Fusion Protein. Vaccines (Basel) 2023; 11:1014. [PMID: 37376403 DOI: 10.3390/vaccines11061014] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/16/2023] [Accepted: 03/21/2023] [Indexed: 06/29/2023] Open
Abstract
The potential of immune-evasive mutation accumulation in the SARS-CoV-2 virus has led to its rapid spread, causing over 600 million confirmed cases and more than 6.5 million confirmed deaths. The huge demand for the rapid development and deployment of low-cost and effective vaccines against emerging variants has renewed interest in DNA vaccine technology. Here, we report the rapid generation and immunological evaluation of novel DNA vaccine candidates against the Wuhan-Hu-1 and Omicron variants based on the RBD protein fused with the Potato virus X coat protein (PVXCP). The delivery of DNA vaccines using electroporation in a two-dose regimen induced high-antibody titers and profound cellular responses in mice. The antibody titers induced against the Omicron variant of the vaccine were sufficient for effective protection against both Omicron and Wuhan-Hu-1 virus infections. The PVXCP protein in the vaccine construct shifted the immune response to the favorable Th1-like type and provided the oligomerization of RBD-PVXCP protein. Naked DNA delivery by needle-free injection allowed us to achieve antibody titers comparable with mRNA-LNP delivery in rabbits. These data identify the RBD-PVXCP DNA vaccine platform as a promising solution for robust and effective SARS-CoV-2 protection, supporting further translational study.
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Affiliation(s)
- Dmitri Dormeshkin
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, 220084 Minsk, Belarus
| | - Mikalai Katsin
- Immunofusion, LLC, 210004 Vitebsk, Belarus
- Imunovakcina, UAB, LT-08102 Vilnius, Lithuania
| | | | | | - Michail Shapira
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, 220084 Minsk, Belarus
| | - Simon Dubovik
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, 220084 Minsk, Belarus
| | | | - Anton Kavaleuski
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Alexander Meleshko
- Immunofusion, LLC, 210004 Vitebsk, Belarus
- Imunovakcina, UAB, LT-08102 Vilnius, Lithuania
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11
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Jiang J, Boughter CT, Ahmad J, Natarajan K, Boyd LF, Meier-Schellersheim M, Margulies DH. SARS-CoV-2 antibodies recognize 23 distinct epitopic sites on the receptor binding domain. RESEARCH SQUARE 2023:rs.3.rs-2800118. [PMID: 37333174 PMCID: PMC10275037 DOI: 10.21203/rs.3.rs-2800118/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The COVID-19 pandemic and SARS-CoV-2 variants have dramatically illustrated the need for a better understanding of antigen (epitope)-antibody (paratope) interactions. To gain insight into the immunogenic characteristics of epitopic sites (ES), we systematically investigated the structures of 340 Abs and 83 nanobodies (Nbs) complexed with the Receptor Binding Domain (RBD) of the SARS-CoV-2 spike protein. We identified 23 distinct ES on the RBD surface and determined the frequencies of amino acid usage in the corresponding CDR paratopes. We describe a clustering method for analysis of ES similarities that reveals binding motifs of the paratopes and that provides insights for vaccine design and therapies for SARS-CoV-2, as well as a broader understanding of the structural basis of Ab-protein antigen (Ag) interactions.
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Affiliation(s)
- Jiansheng Jiang
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 10892, USA
| | - Christopher T. Boughter
- Computational Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 10892, USA
| | - Javeed Ahmad
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 10892, USA
| | - Kannan Natarajan
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 10892, USA
| | - Lisa F. Boyd
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 10892, USA
| | - Martin Meier-Schellersheim
- Computational Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 10892, USA
| | - David H. Margulies
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 10892, USA
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12
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Kumar R. Cryo-EM technique and its application: Structure of steroid hormone receptors. VITAMINS AND HORMONES 2023; 123:385-397. [PMID: 37717991 DOI: 10.1016/bs.vh.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
In recent years, cryo-electron microscopy (cryo-EM) has become one of the most powerful tools to solve the 3-D structure of macromolecules. Unlike X-ray crystallography, the cryo-EM method has advantage of providing an in-depth insight into the dynamic behavior of macromolecules, which is particularly useful to determine 3-D structural analyses of large protein complexes. Due to recent technical advancements, cryo-EM has become the method of choice for the determination of protein structures. Among other proteins, solving 3-D structure of steroid hormone receptors (SHRs) complexed with DNA and coactivators has been a challenge for decades. The limitations with X-ray crystallography and NMR to solve SHR protein structures prompted investigators to move towards cryo-EM technique. The cryo-EM structural analyses have been successful in revealing structural dynamics of several SHRs in recent years. Though, limited by low-resolution, the structural analyses of these SHRs may be useful in understanding many receptor functions as well as provide a platform to refine high-resolution structural analyses in future. This review article discusses the cryo-EM technique in general as well as structural information gained for SHRs using cryo-EM.
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Affiliation(s)
- Raj Kumar
- Department of Pharmaceutical and Biomedical Sciences, Touro College of Pharmacy, New York, NY, United States.
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13
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Shark nanobodies with potent SARS-CoV-2 neutralizing activity and broad sarbecovirus reactivity. Nat Commun 2023; 14:580. [PMID: 36737435 PMCID: PMC9896449 DOI: 10.1038/s41467-023-36106-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/13/2023] [Indexed: 02/05/2023] Open
Abstract
Despite rapid and ongoing vaccine and therapeutic development, SARS-CoV-2 continues to evolve and evade, presenting a need for next-generation diverse therapeutic modalities. Here we show that nurse sharks immunized with SARS-CoV-2 recombinant receptor binding domain (RBD), RBD-ferritin (RFN), or spike protein ferritin nanoparticle (SpFN) immunogens elicit a set of new antigen receptor antibody (IgNAR) molecules that target two non-overlapping conserved epitopes on the spike RBD. Representative shark antibody variable NAR-Fc chimeras (ShAbs) targeting either of the two epitopes mediate cell-effector functions, with high affinity to all SARS-CoV-2 viral variants of concern, including the divergent Omicron strains. The ShAbs potently cross-neutralize SARS-CoV-2 WA-1, Alpha, Beta, Delta, Omicron BA.1 and BA.5, and SARS-CoV-1 pseudoviruses, and confer protection against SARS-CoV-2 challenge in the K18-hACE2 transgenic mouse model. Structural definition of the RBD-ShAb01-ShAb02 complex enabled design and production of multi-specific nanobodies with enhanced neutralization capacity, and picomolar affinity to divergent sarbecovirus clade 1a, 1b and 2 RBD molecules. These shark nanobodies represent potent immunotherapeutics both for current use, and future sarbecovirus pandemic preparation.
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14
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Hetero-bivalent nanobodies provide broad-spectrum protection against SARS-CoV-2 variants of concern including Omicron. Cell Res 2022; 32:831-842. [PMID: 35906408 PMCID: PMC9334538 DOI: 10.1038/s41422-022-00700-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 07/06/2022] [Indexed: 12/23/2022] Open
Abstract
SARS-CoV-2 variants with adaptive mutations have continued to emerge, causing fresh waves of infection even amongst vaccinated population. The development of broad-spectrum antivirals is thus urgently needed. We previously developed two hetero-bivalent nanobodies (Nbs), aRBD-2-5 and aRBD-2-7, with potent neutralization activity against the wild-type (WT) Wuhan isolated SARS-CoV-2, by fusing aRBD-2 with aRBD-5 and aRBD-7, respectively. Here, we resolved the crystal structures of these Nbs in complex with the receptor-binding domain (RBD) of the spike protein, and found that aRBD-2 contacts with highly-conserved RBD residues and retains binding to the RBD of the Alpha, Beta, Gamma, Delta, Delta plus, Kappa, Lambda, Omicron BA.1, and BA.2 variants. In contrast, aRBD-5 and aRBD-7 bind to less-conserved RBD epitopes non-overlapping with the epitope of aRBD-2, and do not show apparent binding to the RBD of some variants. However, when fused with aRBD-2, they effectively enhance the overall binding affinity. Consistently, aRBD-2-5-Fc and aRBD-2-7-Fc potently neutralized all of the tested authentic or pseudotyped viruses, including WT, Alpha, Beta, Gamma, Delta, and Omicron BA.1, BA.1.1 and BA.2. Furthermore, aRBD-2-5-Fc provided prophylactic protection against the WT and mouse-adapted SARS-CoV-2 in mice, and conferred protection against the Omicron BA.1 variant in hamsters prophylactically and therapeutically, indicating that aRBD-2-5-Fc could potentially benefit the prevention and treatment of COVID-19 caused by the emerging variants of concern. Our strategy provides new solutions in the development of broad-spectrum therapeutic antibodies for COVID-19.
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15
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Zemaitis L, Alzbutas G, Gecys D, Pautienius A, Ugenskiene R, Sukys M, Lesauskaite V. Determining the International Spread of B.1.1.523 SARS-CoV-2 Lineage with a Set of Mutations Highly Associated with Reduced Immune Neutralization. Microorganisms 2022; 10:1356. [PMID: 35889075 PMCID: PMC9320768 DOI: 10.3390/microorganisms10071356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/01/2022] [Accepted: 07/02/2022] [Indexed: 02/05/2023] Open
Abstract
Here, we report the emergence of the variant lineage B.1.1.523 that contains a set of mutations including 156_158del, E484K and S494P in the spike protein. E484K and S494P are known to significantly reduce SARS-CoV-2 neutralization by convalescent and vaccinated sera and are considered as mutations of concern. Lineage B.1.1.523 presumably originated in the Russian Federation and spread across European countries with the peak of transmission in April-May 2021. The B.1.1.523 lineage has now been reported from 31 countries. In this article, we analyze the possible origin of this mutation subset and its immune response using in silico methods.
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Affiliation(s)
- Lukas Zemaitis
- Laboratory of Molecular Cardiology, Institute of Cardiology, Lithuanian University of Health Sciences, LT-50162 Kaunas, Lithuania; (D.G.); (V.L.)
| | - Gediminas Alzbutas
- Laboratory of Translational Bioinformatics, Institute for Digestive Research, Lithuanian University of Health Sciences, LT-50162 Kaunas, Lithuania;
| | - Dovydas Gecys
- Laboratory of Molecular Cardiology, Institute of Cardiology, Lithuanian University of Health Sciences, LT-50162 Kaunas, Lithuania; (D.G.); (V.L.)
| | - Arnoldas Pautienius
- Institute of Microbiology and Virology, Lithuanian University of Health Sciences, LT-47181 Kaunas, Lithuania;
| | - Rasa Ugenskiene
- Department of Genetics and Molecular Medicine, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania; (R.U.); (M.S.)
| | - Marius Sukys
- Department of Genetics and Molecular Medicine, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania; (R.U.); (M.S.)
| | - Vaiva Lesauskaite
- Laboratory of Molecular Cardiology, Institute of Cardiology, Lithuanian University of Health Sciences, LT-50162 Kaunas, Lithuania; (D.G.); (V.L.)
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16
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Li T, Zhou B, Luo Z, Lai Y, Huang S, Zhou Y, Li Y, Gautam A, Bourgeau S, Wang S, Bao J, Tan J, Lavillette D, Li D. Structural Characterization of a Neutralizing Nanobody With Broad Activity Against SARS-CoV-2 Variants. Front Microbiol 2022; 13:875840. [PMID: 35722331 PMCID: PMC9201380 DOI: 10.3389/fmicb.2022.875840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
SARS-CoV-2 and its variants, such as the Omicron continue to threaten public health. The virus recognizes the host cell by attaching its Spike (S) receptor-binding domain (RBD) to the host receptor, ACE2. Therefore, RBD is a primary target for neutralizing antibodies and vaccines. Here, we report the isolation and biological and structural characterization of a single-chain antibody (nanobody) from RBD-immunized alpaca. The nanobody, named DL28, binds to RBD tightly with a KD of 1.56 nM and neutralizes the original SARS-CoV-2 strain with an IC50 of 0.41 μg mL−1. Neutralization assays with a panel of variants of concern (VOCs) reveal its wide-spectrum activity with IC50 values ranging from 0.35 to 1.66 μg mL−1 for the Alpha/Beta/Gamma/Delta and an IC50 of 0.66 μg mL−1 for the currently prevalent Omicron. Competition binding assays show that DL28 blocks ACE2-binding. However, structural characterizations and mutagenesis suggest that unlike most antibodies, the blockage by DL28 does not involve direct competition or steric hindrance. Rather, DL28 may use a “conformation competition” mechanism where it excludes ACE2 by keeping an RBD loop in a conformation incompatible with ACE2-binding.
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Affiliation(s)
- Tingting Li
- State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Bingjie Zhou
- University of CAS, Beijing, China.,CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai CAS, Shanghai, China
| | - Zhipu Luo
- Institute of Molecular Enzymology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Yanling Lai
- State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.,University of CAS, Beijing, China
| | - Suqiong Huang
- University of CAS, Beijing, China.,CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai CAS, Shanghai, China.,College of Pharmacy, Chongqing Medical University, Chongqing, China
| | - Yuanze Zhou
- Nanjing Crycision Biotech Co., Ltd., Nanjing, China
| | - Yaning Li
- State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.,University of CAS, Beijing, China
| | - Anupriya Gautam
- University of CAS, Beijing, China.,CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai CAS, Shanghai, China
| | - Salome Bourgeau
- University of CAS, Beijing, China.,CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai CAS, Shanghai, China.,Institut National de la Santé et de la Recherche Médicale, École des Hautes Etudes en Santé Publique, Institut de Recherche en Santé, Environnement et Travail, Université de Rennes, Rennes, France
| | - Shurui Wang
- Nanjing Crycision Biotech Co., Ltd., Nanjing, China
| | - Juan Bao
- State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Jingquan Tan
- Nanjing Crycision Biotech Co., Ltd., Nanjing, China
| | - Dimitri Lavillette
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai CAS, Shanghai, China.,Pasteurien College, Soochow University, Suzhou, China
| | - Dianfan Li
- State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
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17
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Strohl WR, Ku Z, An Z, Carroll SF, Keyt BA, Strohl LM. Passive Immunotherapy Against SARS-CoV-2: From Plasma-Based Therapy to Single Potent Antibodies in the Race to Stay Ahead of the Variants. BioDrugs 2022; 36:231-323. [PMID: 35476216 PMCID: PMC9043892 DOI: 10.1007/s40259-022-00529-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2022] [Indexed: 12/15/2022]
Abstract
The COVID-19 pandemic is now approaching 2 years old, with more than 440 million people infected and nearly six million dead worldwide, making it the most significant pandemic since the 1918 influenza pandemic. The severity and significance of SARS-CoV-2 was recognized immediately upon discovery, leading to innumerable companies and institutes designing and generating vaccines and therapeutic antibodies literally as soon as recombinant SARS-CoV-2 spike protein sequence was available. Within months of the pandemic start, several antibodies had been generated, tested, and moved into clinical trials, including Eli Lilly's bamlanivimab and etesevimab, Regeneron's mixture of imdevimab and casirivimab, Vir's sotrovimab, Celltrion's regdanvimab, and Lilly's bebtelovimab. These antibodies all have now received at least Emergency Use Authorizations (EUAs) and some have received full approval in select countries. To date, more than three dozen antibodies or antibody combinations have been forwarded into clinical trials. These antibodies to SARS-CoV-2 all target the receptor-binding domain (RBD), with some blocking the ability of the RBD to bind human ACE2, while others bind core regions of the RBD to modulate spike stability or ability to fuse to host cell membranes. While these antibodies were being discovered and developed, new variants of SARS-CoV-2 have cropped up in real time, altering the antibody landscape on a moving basis. Over the past year, the search has widened to find antibodies capable of neutralizing the wide array of variants that have arisen, including Alpha, Beta, Gamma, Delta, and Omicron. The recent rise and dominance of the Omicron family of variants, including the rather disparate BA.1 and BA.2 variants, demonstrate the need to continue to find new approaches to neutralize the rapidly evolving SARS-CoV-2 virus. This review highlights both convalescent plasma- and polyclonal antibody-based approaches as well as the top approximately 50 antibodies to SARS-CoV-2, their epitopes, their ability to bind to SARS-CoV-2 variants, and how they are delivered. New approaches to antibody constructs, including single domain antibodies, bispecific antibodies, IgA- and IgM-based antibodies, and modified ACE2-Fc fusion proteins, are also described. Finally, antibodies being developed for palliative care of COVID-19 disease, including the ramifications of cytokine release syndrome (CRS) and acute respiratory distress syndrome (ARDS), are described.
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Affiliation(s)
| | - Zhiqiang Ku
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Sciences Center, Houston, TX USA
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Sciences Center, Houston, TX USA
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18
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Walter JD, Scherer M, Hutter CAJ, Garaeva AA, Zimmermann I, Wyss M, Rheinberger J, Ruedin Y, Earp JC, Egloff P, Sorgenfrei M, Hürlimann LM, Gonda I, Meier G, Remm S, Thavarasah S, van Geest G, Bruggmann R, Zimmer G, Slotboom DJ, Paulino C, Plattet P, Seeger MA. Biparatopic sybodies neutralize SARS-CoV-2 variants of concern and mitigate drug resistance. EMBO Rep 2022; 23:e54199. [PMID: 35253970 PMCID: PMC8982573 DOI: 10.15252/embr.202154199] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 12/15/2022] Open
Abstract
The ongoing COVID‐19 pandemic represents an unprecedented global health crisis. Here, we report the identification of a synthetic nanobody (sybody) pair, Sb#15 and Sb#68, that can bind simultaneously to the SARS‐CoV‐2 spike RBD and efficiently neutralize pseudotyped and live viruses by interfering with ACE2 interaction. Cryo‐EM confirms that Sb#15 and Sb#68 engage two spatially discrete epitopes, influencing rational design of bispecific and tri‐bispecific fusion constructs that exhibit up to 100‐ and 1,000‐fold increase in neutralization potency, respectively. Cryo‐EM of the sybody‐spike complex additionally reveals a novel up‐out RBD conformation. While resistant viruses emerge rapidly in the presence of single binders, no escape variants are observed in the presence of the bispecific sybody. The multivalent bispecific constructs further increase the neutralization potency against globally circulating SARS‐CoV‐2 variants of concern. Our study illustrates the power of multivalency and biparatopic nanobody fusions for the potential development of therapeutic strategies that mitigate the emergence of new SARS‐CoV‐2 escape mutants.
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Affiliation(s)
- Justin D Walter
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Melanie Scherer
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Cedric A J Hutter
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Alisa A Garaeva
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,Department of Membrane Enzymology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Iwan Zimmermann
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,Linkster Therapeutics AG, Zurich, Switzerland
| | - Marianne Wyss
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jan Rheinberger
- Department of Structural Biology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Yelena Ruedin
- Institute of Virology and Immunology, Bern & Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jennifer C Earp
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Pascal Egloff
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,Linkster Therapeutics AG, Zurich, Switzerland
| | - Michèle Sorgenfrei
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Lea M Hürlimann
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Imre Gonda
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Gianmarco Meier
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Sille Remm
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Sujani Thavarasah
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Geert van Geest
- Interfaculty Bioinformatics Unit and Swiss, Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss, Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Gert Zimmer
- Institute of Virology and Immunology, Bern & Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Dirk J Slotboom
- Department of Membrane Enzymology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Cristina Paulino
- Department of Membrane Enzymology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.,Department of Structural Biology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Philippe Plattet
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
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19
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Verkhivker G. Structural and Computational Studies of the SARS-CoV-2 Spike Protein Binding Mechanisms with Nanobodies: From Structure and Dynamics to Avidity-Driven Nanobody Engineering. Int J Mol Sci 2022; 23:ijms23062928. [PMID: 35328351 PMCID: PMC8951411 DOI: 10.3390/ijms23062928] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 03/06/2022] [Accepted: 03/07/2022] [Indexed: 11/28/2022] Open
Abstract
Nanobodies provide important advantages over traditional antibodies, including their smaller size and robust biochemical properties such as high thermal stability, high solubility, and the ability to be bioengineered into novel multivalent, multi-specific, and high-affinity molecules, making them a class of emerging powerful therapies against SARS-CoV-2. Recent research efforts on the design, protein engineering, and structure-functional characterization of nanobodies and their binding with SARS-CoV-2 S proteins reflected a growing realization that nanobody combinations can exploit distinct binding epitopes and leverage the intrinsic plasticity of the conformational landscape for the SARS-CoV-2 S protein to produce efficient neutralizing and mutation resistant characteristics. Structural and computational studies have also been instrumental in quantifying the structure, dynamics, and energetics of the SARS-CoV-2 spike protein binding with nanobodies. In this review, a comprehensive analysis of the current structural, biophysical, and computational biology investigations of SARS-CoV-2 S proteins and their complexes with distinct classes of nanobodies targeting different binding sites is presented. The analysis of computational studies is supplemented by an in-depth examination of mutational scanning simulations and identification of binding energy hotspots for distinct nanobody classes. The review is focused on the analysis of mechanisms underlying synergistic binding of multivalent nanobodies that can be superior to single nanobodies and conventional nanobody cocktails in combating escape mutations by effectively leveraging binding avidity and allosteric cooperativity. We discuss how structural insights and protein engineering approaches together with computational biology tools can aid in the rational design of synergistic combinations that exhibit superior binding and neutralization characteristics owing to avidity-mediated mechanisms.
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Affiliation(s)
- Gennady Verkhivker
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; ; Tel.: +1-714-516-4586
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
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20
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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.
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21
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Wang J, Kang G, Yuan H, Cao X, Huang H, de Marco A. Research Progress and Applications of Multivalent, Multispecific and Modified Nanobodies for Disease Treatment. Front Immunol 2022; 12:838082. [PMID: 35116045 PMCID: PMC8804282 DOI: 10.3389/fimmu.2021.838082] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 12/30/2021] [Indexed: 12/22/2022] Open
Abstract
Recombinant antibodies such as nanobodies are progressively demonstrating to be a valid alternative to conventional monoclonal antibodies also for clinical applications. Furthermore, they do not solely represent a substitute for monoclonal antibodies but their unique features allow expanding the applications of biotherapeutics and changes the pattern of disease treatment. Nanobodies possess the double advantage of being small and simple to engineer. This combination has promoted extremely diversified approaches to design nanobody-based constructs suitable for particular applications. Both the format geometry possibilities and the functionalization strategies have been widely explored to provide macromolecules with better efficacy with respect to single nanobodies or their combination. Nanobody multimers and nanobody-derived reagents were developed to image and contrast several cancer diseases and have shown their effectiveness in animal models. Their capacity to block more independent signaling pathways simultaneously is considered a critical advantage to avoid tumor resistance, whereas the mass of these multimeric compounds still remains significantly smaller than that of an IgG, enabling deeper penetration in solid tumors. When applied to CAR-T cell therapy, nanobodies can effectively improve the specificity by targeting multiple epitopes and consequently reduce the side effects. This represents a great potential in treating malignant lymphomas, acute myeloid leukemia, acute lymphoblastic leukemia, multiple myeloma and solid tumors. Apart from cancer treatment, multispecific drugs and imaging reagents built with nanobody blocks have demonstrated their value also for detecting and tackling neurodegenerative, autoimmune, metabolic, and infectious diseases and as antidotes for toxins. In particular, multi-paratopic nanobody-based constructs have been developed recently as drugs for passive immunization against SARS-CoV-2 with the goal of impairing variant survival due to resistance to antibodies targeting single epitopes. Given the enormous research activity in the field, it can be expected that more and more multimeric nanobody molecules will undergo late clinical trials in the next future. Systematic Review Registration.
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Affiliation(s)
- Jiewen Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- Institute of Shaoxing, Tianjin University, Zhejiang, China
| | - Guangbo Kang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- Institute of Shaoxing, Tianjin University, Zhejiang, China
| | - Haibin Yuan
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- Institute of Shaoxing, Tianjin University, Zhejiang, China
| | - Xiaocang Cao
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - He Huang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- Institute of Shaoxing, Tianjin University, Zhejiang, China
| | - Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Nova Gorica, Slovenia
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22
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Abstract
The spike protein (S-protein) of SARS-CoV-2, the protein that enables the virus to infect human cells, is the basis for many vaccines and a hotspot of concerning virus evolution. Here, we discuss the outstanding progress in structural characterization of the S-protein and how these structures facilitate analysis of virus function and evolution. We emphasize the differences in reported structures and that analysis of structure-function relationships is sensitive to the structure used. We show that the average residue solvent exposure in nearly complete structures is a good descriptor of open vs closed conformation states. Because of structural heterogeneity of functionally important surface-exposed residues, we recommend using averages of a group of high-quality protein structures rather than a single structure before reaching conclusions on specific structure-function relationships. To illustrate these points, we analyze some significant chemical tendencies of prominent S-protein mutations in the context of the available structures. In the discussion of new variants, we emphasize the selectivity of binding to ACE2 vs prominent antibodies rather than simply the antibody escape or ACE2 affinity separately. We note that larger chemical changes, in particular increased electrostatic charge or side-chain volume of exposed surface residues, are recurring in mutations of concern, plausibly related to adaptation to the negative surface potential of human ACE2. We also find indications that the fixated mutations of the S-protein in the main variants are less destabilizing than would be expected on average, possibly pointing toward a selection pressure on the S-protein. The richness of available structures for all of these situations provides an enormously valuable basis for future research into these structure-function relationships.
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Affiliation(s)
- Rukmankesh Mehra
- Department of Chemistry, Indian Institute
of Technology Bhilai, Sejbahar, Raipur 492015, Chhattisgarh,
India
| | - Kasper P. Kepp
- DTU Chemistry, Technical University of
Denmark, Building 206, 2800 Kongens Lyngby,
Denmark
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23
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Hardenbrook NJ, Zhang P. A structural view of the SARS-CoV-2 virus and its assembly. Curr Opin Virol 2021; 52:123-134. [PMID: 34915287 PMCID: PMC8642146 DOI: 10.1016/j.coviro.2021.11.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/11/2021] [Accepted: 11/22/2021] [Indexed: 12/15/2022]
Abstract
Structural biology plays a vital role in SARS-CoV-2 vaccine and treatment. High-resolution structures of SARS-CoV-2 proteins and complexes have been obtained. In situ structures of SARS-CoV-2 virus and its assembly are visualized by cryoET.
The SARS-CoV-2 pandemic that struck in 2019 has left the world crippled with hundreds of millions of cases and millions of people dead. During this time, we have seen unprecedented support and collaboration amongst scientists to respond to this deadly disease. Advances in the field of structural biology, in particular cryoEM and cryo-electron tomography, have allowed unprecedented structural analysis of SARS-CoV-2. Here, we review the structural work on the SARS-CoV-2 virus and viral components, as well as its cellular assembly process, highlighting some important structural findings that have made significant impact on the protection from and treatment of emerging viral infections.
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Affiliation(s)
- Nathan J Hardenbrook
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Peijun Zhang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK; Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK; Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, OX3 7BN, UK.
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24
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Tang Q, Owens RJ, Naismith JH. Structural Biology of Nanobodies against the Spike Protein of SARS-CoV-2. Viruses 2021; 13:v13112214. [PMID: 34835020 PMCID: PMC8625641 DOI: 10.3390/v13112214] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/27/2021] [Accepted: 10/30/2021] [Indexed: 12/28/2022] Open
Abstract
Nanobodies are 130 amino acid single-domain antibodies (VHH) derived from the unique heavy-chain-only subclass of Camelid immunogloblins. Their small molecular size, facile expression, high affinity and stability have combined to make them unique targeting reagents with numerous applications in the biomedical sciences. The first nanobody agent has now entered the clinic as a treatment against a blood disorder. The spread of the SARS-CoV-2 virus has seen the global scientific endeavour work to accelerate the development of technologies to try to defeat a pandemic that has now killed over four million people. In a remarkably short period of time, multiple studies have reported nanobodies directed against the viral Spike protein. Several agents have been tested in culture and demonstrate potent neutralisation of the virus or pseudovirus. A few agents have completed animal trials with very encouraging results showing their potential for treating infection. Here, we discuss the structural features that guide the nanobody recognition of the receptor binding domain of the Spike protein of SARS-CoV-2.
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Affiliation(s)
- Qilong Tang
- Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot OX11 0FA, UK;
- The Wellcome Centre for Human Genetics, Division of Structural Biology, University of Oxford, Headington, Oxford OX3 7BN, UK
| | - Raymond J. Owens
- Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot OX11 0FA, UK;
- The Wellcome Centre for Human Genetics, Division of Structural Biology, University of Oxford, Headington, Oxford OX3 7BN, UK
- Correspondence: (R.J.O.); (J.H.N.)
| | - James H. Naismith
- Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot OX11 0FA, UK;
- The Wellcome Centre for Human Genetics, Division of Structural Biology, University of Oxford, Headington, Oxford OX3 7BN, UK
- Correspondence: (R.J.O.); (J.H.N.)
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25
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Cryo-EM structure determination of small proteins by nanobody-binding scaffolds (Legobodies). Proc Natl Acad Sci U S A 2021; 118:2115001118. [PMID: 34620716 PMCID: PMC8521671 DOI: 10.1073/pnas.2115001118] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2021] [Indexed: 12/14/2022] Open
Abstract
We describe a general method that allows structure determination of small proteins by single-particle cryo-electron microscopy (cryo-EM). The method is based on the availability of a target-binding nanobody, which is then rigidly attached to two scaffolds: 1) a Fab fragment of an antibody directed against the nanobody and 2) a nanobody-binding protein A fragment fused to maltose binding protein and Fab-binding domains. The overall ensemble of ∼120 kDa, called Legobody, does not perturb the nanobody-target interaction, is easily recognizable in EM images due to its unique shape, and facilitates particle alignment in cryo-EM image processing. The utility of the method is demonstrated for the KDEL receptor, a 23-kDa membrane protein, resulting in a map at 3.2-Å overall resolution with density sufficient for de novo model building, and for the 22-kDa receptor-binding domain (RBD) of SARS-CoV-2 spike protein, resulting in a map at 3.6-Å resolution that allows analysis of the binding interface to the nanobody. The Legobody approach thus overcomes the current size limitations of cryo-EM analysis.
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26
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Jin D, Wei J, Sun J. Analysis of the molecular mechanism of SARS-CoV-2 antibodies. Biochem Biophys Res Commun 2021; 566:45-52. [PMID: 34116356 PMCID: PMC8179121 DOI: 10.1016/j.bbrc.2021.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/01/2021] [Indexed: 12/15/2022]
Abstract
A newly-emergent beta-coronavirus, SARS-CoV-2, rapidly has become a pandemic since 2020. It is a serious respiratory disease and caused more than 100 million of deaths in the world. WHO named it COVIA-19 and there is no effective targeted drug for it. The main treatment strategies include chemical medicine, traditional Chinese medicine (TCM) and biologics. Due to SARS-CoV-2 uses the spike proteins (S proteins) on its envelope to infect human cells, monoclonal antibodies that neutralize the S protein have become one of the hot research areas in the current research and treatment of SARS-CoV-2. In this study, we reviewed the antibodies that have been reported to have neutralizing activity against the SARS-CoV-2 infection. According to their different binding epitope regions in RBD or NTD, they are classified, and the mechanism of the representative antibodies in each category is discussed in depth, which provides potential foundation for future antibody and vaccine therapy and the development of antibody cocktails against SARS-CoV-2 mutants.
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MESH Headings
- Angiotensin-Converting Enzyme 2/chemistry
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/therapeutic use
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/therapeutic use
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- Antibodies, Viral/therapeutic use
- COVID-19/immunology
- COVID-19/therapy
- COVID-19/virology
- COVID-19 Vaccines/immunology
- Epitopes/immunology
- Humans
- Models, Molecular
- Neutralization Tests
- Pandemics
- Protein Interaction Domains and Motifs
- Receptors, Virus/chemistry
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Single-Domain Antibodies/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
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Affiliation(s)
- Dongfu Jin
- Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Jing Wei
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China.
| | - Jian Sun
- Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China; Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China.
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