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Martin J, Michaelis M, Petrović S, Lehnen AC, Müllers Y, Wendler P, Möller HM, Hartlieb M, Glebe U. Application of Sortase-Mediated Ligation for the Synthesis of Block Copolymers and Protein-Polymer Conjugates. Macromol Biosci 2024:e2400316. [PMID: 39360589 DOI: 10.1002/mabi.202400316] [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: 07/05/2024] [Revised: 09/18/2024] [Indexed: 10/04/2024]
Abstract
Sortase-mediated ligation (SML) has become a powerful tool for site-specific protein modification. However, sortase A (SrtA) suffers from low catalytic efficiency and mediates an equilibrium reaction. Therefore, ligations with large macromolecules may be challenging. Here, the synthesis of polymeric building blocks for sortase-mediated ligation constituting peptide-polymers with either the recognition sequence for sortase A (LPX1TGX2) or its nucleophilic counterpart (Gx) is demonstrated. The peptide-polymers are synthesized by solid-phase peptide synthesis followed by photo-iniferter (PI) reversible addition-fragmentation chain-transfer (RAFT) polymerization of various monomers. The building blocks are subsequently utilized to investigate possibilities and limitations when using macromolecules in SML. In particular, diblock copolymers are obtained even when using the orthogonal building blocks in equimolar ratio by exploiting a technique to shift the reaction equilibrium. However, ligations of two polymers can not be achieved when the degree of polymerization exceeds 100. Subsequently, C-terminal protein-polymer conjugates are synthesized. Several polymers are utilized that can replace the omnipresent polyethylene glycol (PEG) in future therapeutics. The conjugation is exemplified with a nanobody that is known for efficient neutralization of SARS-CoV-2. The study demonstrates a universal approach to polymer-LPX1TGX2 and Gx-polymer building blocks and gives insight into their application in SML.
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Affiliation(s)
- Johannes Martin
- Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam-Golm, Germany
- Fraunhofer Institute for Applied Polymer Research IAP, Geiselbergstr. 69, 14476, Potsdam-Golm, Germany
| | - Marcus Michaelis
- Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam-Golm, Germany
| | - Saša Petrović
- Department of Biochemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam-Golm, Germany
| | - Anne-Catherine Lehnen
- Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam-Golm, Germany
- Fraunhofer Institute for Applied Polymer Research IAP, Geiselbergstr. 69, 14476, Potsdam-Golm, Germany
| | - Yannic Müllers
- Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam-Golm, Germany
- Fraunhofer Institute for Applied Polymer Research IAP, Geiselbergstr. 69, 14476, Potsdam-Golm, Germany
| | - Petra Wendler
- Department of Biochemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam-Golm, Germany
| | - Heiko M Möller
- Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam-Golm, Germany
| | - Matthias Hartlieb
- Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam-Golm, Germany
- Fraunhofer Institute for Applied Polymer Research IAP, Geiselbergstr. 69, 14476, Potsdam-Golm, Germany
| | - Ulrich Glebe
- Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam-Golm, Germany
- Fraunhofer Institute for Applied Polymer Research IAP, Geiselbergstr. 69, 14476, Potsdam-Golm, Germany
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2
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Singh V, Bhutkar M, Choudhary S, Nehul S, Kumar R, Singla J, Kumar P, Tomar S. Structure-guided mutations in CDRs for enhancing the affinity of neutralizing SARS-CoV-2 nanobody. Biochem Biophys Res Commun 2024; 734:150746. [PMID: 39366179 DOI: 10.1016/j.bbrc.2024.150746] [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: 06/01/2024] [Revised: 09/05/2024] [Accepted: 09/24/2024] [Indexed: 10/06/2024]
Abstract
The optimization of antibodies to attain the desired levels of affinity and specificity holds great promise for the development of next generation therapeutics. This study delves into the refinement and engineering of complementarity-determining regions (CDRs) through in silico affinity maturation followed by binding validation using isothermal titration calorimetry (ITC) and pseudovirus-based neutralization assays. Specifically, it focuses on engineering CDRs targeting the epitopes of receptor-binding domain (RBD) of the spike protein of SARS-CoV-2. A structure-guided virtual library of 112 single mutations in CDRs was generated and screened against RBD to select the potential affinity-enhancing mutations. Protein-protein docking analysis identified 32 single mutants of which nine mutants were selected for molecular dynamics (MD) simulations. Subsequently, biophysical ITC studies provided insights into binding affinity, and consistent with in silico findings, six mutations that demonstrated better binding affinity than native nanobody were further tested in vitro for neutralization activity against SARS-CoV-2 pseudovirus. Leu106Thr mutant was found to be most effective in virus-neutralization with IC50 values of ∼0.03 μM, as compared to the native nanobody (IC50 ∼0.77 μM). Thus, in this study, the developed computational pipeline guided by structure-aided interface profiles and thermodynamic analysis holds promise for the streamlined development of antibody-based therapeutic interventions against emerging variants of SARS-CoV-2 and other infectious pathogens.
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Affiliation(s)
- Vishakha Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Mandar Bhutkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Shweta Choudhary
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Sanketkumar Nehul
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Rajesh Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Jitin Singla
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India; Department of Computer Science and Engineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India.
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3
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Alfadhli A, Bates TA, Barklis RL, Romanaggi C, Tafesse FG, Barklis E. A nanobody interaction with SARS-COV-2 Spike allows the versatile targeting of lentivirus vectors. J Virol 2024; 98:e0079524. [PMID: 39207135 PMCID: PMC11406891 DOI: 10.1128/jvi.00795-24] [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: 05/06/2024] [Accepted: 07/25/2024] [Indexed: 09/04/2024] Open
Abstract
While investigating methods to target gene delivery vectors to specific cell types, we examined the potential of using a nanobody against the SARS-CoV-2 Spike protein receptor-binding domain to direct lentivirus infection of Spike-expressing cells. Using four different approaches, we found that lentiviruses with surface-exposed nanobody domains selectively infect Spike-expressing cells. Targeting is dependent on the fusion function of the Spike protein, and conforms to a model in which nanobody binding to the Spike protein triggers the Spike fusion machinery. The nanobody-Spike interaction also is capable of directing cell-cell fusion and the selective infection of nanobody-expressing cells by Spike-pseudotyped lentivirus vectors. Significantly, cells infected with SARS-CoV-2 are efficiently and selectively infected by lentivirus vectors pseudotyped with a chimeric nanobody protein. Our results suggest that cells infected by any virus that forms syncytia may be targeted for gene delivery by using an appropriate nanobody or virus receptor mimic. Vectors modified in this fashion may prove useful in the delivery of immunomodulators to infected foci to mitigate the effects of viral infections.IMPORTANCEWe have discovered that lentiviruses decorated on their surfaces with a nanobody against the SARS-CoV-2 Spike protein selectively infect Spike-expressing cells. Infection is dependent on the specificity of the nanobody and the fusion function of the Spike protein and conforms to a reverse fusion model, in which nanobody binding to Spike triggers the Spike fusion machinery. The nanobody-Spike interaction also can drive cell-cell fusion and infection of nanobody-expressing cells with viruses carrying the Spike protein. Importantly, cells infected with SARS-CoV-2 are selectively infected with nanobody-decorated lentiviruses. These results suggest that cells infected by any virus that expresses an active receptor-binding fusion protein may be targeted by vectors for delivery of cargoes to mitigate infections.
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Affiliation(s)
- Ayna Alfadhli
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Timothy A Bates
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Robin Lid Barklis
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon, USA
| | - CeAnn Romanaggi
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Fikadu G Tafesse
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Eric Barklis
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon, USA
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4
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Porebski B, Christ W, Corman A, Haraldsson M, Barz M, Lidemalm L, Häggblad M, Ilmain J, Wright SC, Murga M, Schlegel J, Jarvius M, Lapins M, Sezgin E, Bhabha G, Lauschke VM, Carreras-Puigvert J, Lafarga M, Klingström J, Hühn D, Fernandez-Capetillo O. Discovery of a novel inhibitor of macropinocytosis with antiviral activity. Mol Ther 2024; 32:3012-3024. [PMID: 38956870 PMCID: PMC11403221 DOI: 10.1016/j.ymthe.2024.06.038] [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: 02/16/2024] [Revised: 06/04/2024] [Accepted: 06/28/2024] [Indexed: 07/04/2024] Open
Abstract
Several viruses hijack various forms of endocytosis in order to infect host cells. Here, we report the discovery of a molecule with antiviral properties that we named virapinib, which limits viral entry by macropinocytosis. The identification of virapinib derives from a chemical screen using high-throughput microscopy, where we identified chemical entities capable of preventing infection with a pseudotype virus expressing the spike (S) protein from SARS-CoV-2. Subsequent experiments confirmed the capacity of virapinib to inhibit infection by SARS-CoV-2, as well as by additional viruses, such as mpox virus and TBEV. Mechanistic analyses revealed that the compound inhibited macropinocytosis, limiting this entry route for the viruses. Importantly, virapinib has no significant toxicity to host cells. In summary, we present the discovery of a molecule that inhibits macropinocytosis, thereby limiting the infectivity of viruses that use this entry route such as SARS-CoV2.
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Affiliation(s)
- Bartlomiej Porebski
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
| | - Wanda Christ
- Center of Infectious Medicine, Department of Medicine, Karolinska Institutet, 141-86 Huddinge, Sweden
| | - Alba Corman
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
| | - Martin Haraldsson
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Myriam Barz
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
| | - Louise Lidemalm
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
| | - Maria Häggblad
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
| | - Juliana Ilmain
- Grossman School of Medicine, New York University, New York, NY 10016, USA
| | - Shane C Wright
- Department of Physiology and Pharmacology, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Matilde Murga
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Jan Schlegel
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Malin Jarvius
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Box 591, SE-751 24 Uppsala, Sweden; Chemical Biology Consortium Sweden, Science for Life Laboratory, Department of Pharmaceutical Biosciences, Uppsala University, Box 591, SE-751 24 Uppsala, Sweden
| | - Maris Lapins
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Box 591, SE-751 24 Uppsala, Sweden
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Gira Bhabha
- Grossman School of Medicine, New York University, New York, NY 10016, USA
| | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, S-171 77 Stockholm, Sweden; Margarete Fischer-Bosch Institute of Clinical Pharmacology, D-70376 Stuttgart, Germany; University of Tuebingen, 72074 Tuebingen, Germany
| | - Jordi Carreras-Puigvert
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Box 591, SE-751 24 Uppsala, Sweden; Chemical Biology Consortium Sweden, Science for Life Laboratory, Department of Pharmaceutical Biosciences, Uppsala University, Box 591, SE-751 24 Uppsala, Sweden
| | - Miguel Lafarga
- Departament of Anatomy and Cellular Biology, Neurodegenerative Diseases Network (CIBERNED), University of Cantabria-IDIVAL, 39011 Santander, Spain
| | - Jonas Klingström
- Center of Infectious Medicine, Department of Medicine, Karolinska Institutet, 141-86 Huddinge, Sweden; Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden
| | - Daniela Hühn
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
| | - Oscar Fernandez-Capetillo
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden; Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain.
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5
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Lagoutte P, Bourhis JM, Mariano N, Gueguen-Chaignon V, Vandroux D, Moali C, Vadon-Le Goff S. Mono- and Bi-specific Nanobodies Targeting the CUB Domains of PCPE-1 Reduce the Proteolytic Processing of Fibrillar Procollagens. J Mol Biol 2024; 436:168667. [PMID: 38901640 DOI: 10.1016/j.jmb.2024.168667] [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: 04/03/2024] [Revised: 06/13/2024] [Accepted: 06/13/2024] [Indexed: 06/22/2024]
Abstract
The excessive deposition of fibrillar collagens is a hallmark of fibrosis. Collagen fibril formation requires proteolytic maturations by Procollagen N- and C-proteinases (PNPs and PCPs) to remove the N- and C-propeptides which maintain procollagens in the soluble form. Procollagen C-Proteinase Enhancer-1 (PCPE-1, a glycoprotein composed of two CUB domains and one NTR domain) is a regulatory protein that activates the C-terminal processing of procollagens by the main PCPs. It is often up-regulated in fibrotic diseases and represents a promising target for the development of novel anti-fibrotic strategies. Here, our objective was to develop the first antagonists of PCPE-1, based on the nanobody scaffold. Using both an in vivo selection through the immunization of a llama and an in vitro selection with a synthetic library, we generated 18 nanobodies directed against the CUB domains of PCPE1, which carry its enhancing activity. Among them, I5 from the immune library and H4 from the synthetic library have a high affinity for PCPE-1 and inhibit its interaction with procollagens. The crystal structure of the complex formed by PCPE-1, H4 and I5 showed that they have distinct epitopes and enabled the design of a biparatopic fusion, the diabody diab-D1. Diab-D1 has a sub-nanomolar affinity for PCPE-1 and is a potent antagonist of its activity, preventing the stimulation of procollagen cleavage in vitro. Moreover, Diab-D1 is also effective in reducing the proteolytic maturation of procollagen I in cultures of human dermal fibroblasts and hence holds great promise as a tool to modulate collagen deposition in fibrotic conditions.
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Affiliation(s)
- Priscillia Lagoutte
- Universite Claude Bernard Lyon 1, CNRS, Tissue Biology and Therapeutic Engineering Laboratory, LBTI, UMR5305, F-69367 Lyon, France
| | - Jean-Marie Bourhis
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, F-38000 Grenoble, France
| | - Natacha Mariano
- Universite Claude Bernard Lyon 1, CNRS, Tissue Biology and Therapeutic Engineering Laboratory, LBTI, UMR5305, F-69367 Lyon, France
| | - Virginie Gueguen-Chaignon
- Protein Science Facility, SFR BioSciences, Univ Lyon, CNRS UAR3444, Inserm US8, ENS de Lyon, F-69367 Lyon, France
| | | | - Catherine Moali
- Universite Claude Bernard Lyon 1, CNRS, Tissue Biology and Therapeutic Engineering Laboratory, LBTI, UMR5305, F-69367 Lyon, France
| | - Sandrine Vadon-Le Goff
- Universite Claude Bernard Lyon 1, CNRS, Tissue Biology and Therapeutic Engineering Laboratory, LBTI, UMR5305, F-69367 Lyon, France.
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6
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He L, Wu Q, Zhang Z, Chen L, Yu K, Li L, Jia Q, Wang Y, Ni J, Wang C, Li Q, Zhai X, Zhao J, Liu Y, Fan R, Li YP. Development of Broad-Spectrum Nanobodies for the Therapy and Diagnosis of SARS-CoV-2 and Its Multiple Variants. Mol Pharm 2024; 21:3866-3879. [PMID: 38920116 DOI: 10.1021/acs.molpharmaceut.4c00165] [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: 06/27/2024]
Abstract
The continuous evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evaded the efficacy of previously developed antibodies and vaccines, thus remaining a significant global public health threat. Therefore, it is imperative to develop additional antibodies that are capable of neutralizing emerging variants. Nanobodies, as the smallest functional single-domain antibodies, exhibit enhanced stability and penetration ability, enabling them to recognize numerous concealed epitopes that are inaccessible to conventional antibodies. Herein, we constructed an immune library based on the immunization of alpaca with the S1 subunit of the SARS-CoV-2 spike protein, from which two nanobodies, Nb1 and Nb2, were selected using phage display technology for further characterization. Both nanobodies, with the binding residues residing within the receptor-binding domain (RBD) region of the spike, exhibited high affinity toward the S1 subunit. Moreover, they displayed cross-neutralizing activity against both wild-type SARS-CoV-2 and 10 ο variants, including BA.1, BA.2, BA.3, BA.5, BA.2.75, BF.7, BQ.1, EG.5.1, XBB.1.5, and JN.1. Molecular modeling and dynamics simulations predicted that both nanobodies interacted with the viral RBD through their complementarity determining region 1 (CDR1) and CDR2. These two nanobodies are novel tools for the development of therapeutic and diagnostic countermeasures targeting SARS-CoV-2 variants and potentially emerging coronaviruses.
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Affiliation(s)
- Lei He
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China
- China Animal Disease Control Center, Beijing 102618, China
| | - Qian Wu
- Institute of Human Virology, Department of Pathogen Biology and Biosecurity, and Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Zhaoyong Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Lingling Chen
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China
- China Animal Disease Control Center, Beijing 102618, China
| | - Kuai Yu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Leibin Li
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China
- China Animal Disease Control Center, Beijing 102618, China
| | - Qiong Jia
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China
| | - Yanqun Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Jianqiang Ni
- China Animal Disease Control Center, Beijing 102618, China
| | - Chuanbin Wang
- China Animal Disease Control Center, Beijing 102618, China
| | - Qi Li
- China Animal Disease Control Center, Beijing 102618, China
| | - Xinyan Zhai
- China Animal Disease Control Center, Beijing 102618, China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Yuliang Liu
- China Animal Disease Control Center, Beijing 102618, China
| | - Ruiwen Fan
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China
| | - Yi-Ping Li
- Institute of Human Virology, Department of Pathogen Biology and Biosecurity, and Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
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7
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Ma S, Zhang D, Wang Q, Zhu L, Wu X, Ye S, Wang Y. Structure defining of ultrapotent neutralizing nanobodies against MERS-CoV with novel epitopes on receptor binding domain. PLoS Pathog 2024; 20:e1012438. [PMID: 39141662 PMCID: PMC11324105 DOI: 10.1371/journal.ppat.1012438] [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: 05/16/2024] [Accepted: 07/22/2024] [Indexed: 08/16/2024] Open
Abstract
The Middle East Respiratory Syndrome Coronavirus (MERS-CoV) causes severe and fatal acute respiratory disease in humans. High fatality rates and continued infectiousness remain a pressing concern for global health preparedness. Antibodies targeted at the receptor-binding domain (RBD) are major countermeasures against human viral infection. Here, we report four potent nanobodies against MERS-CoV, which are isolated from alpaca, and especially the potency of Nb14 is highest in the pseudotyped virus assay. Structural studies show that Nb14 framework regions (FRs) are mainly involved in interactions targeting a novel epitope, which is entirely distinct from all previously reported antibodies, and disrupt the protein-carbohydrate interaction between residue W535 of RBD and hDPP4 N229-linked carbohydrate moiety (hDPP4-N229-glycan). Different from Nb14, Nb9 targets the cryptic face of RBD, which is distinctive from the hDPP4 binding site and the Nb14 epitope, and it induces the β5-β6 loop to inflect towards a shallow groove of the RBD and dampens the accommodation of a short helix of hDPP4. The particularly striking epitopes endow the two Nbs administrate synergistically in the pseudotyped MERS-CoV assays. These results not only character unprecedented epitopes for antibody recognition but also provide promising agents for prophylaxis and therapy of MERS-CoV infection.
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Affiliation(s)
- Sen Ma
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, P.R. China
| | - Doudou Zhang
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, P.R. China
| | - Qiwei Wang
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, P.R. China
| | - Linjing Zhu
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, P.R. China
| | - Xilin Wu
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, P.R. China
| | - Sheng Ye
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, P.R. China
| | - Yaxin Wang
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, P.R. China
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8
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Sun L, Chen B, Liu X, Zhu Y, Zhang G, Liang X, Xing L, Xu W, Jiang S, Wang X. Alpaca-derived nanobody targeting the hydrophobic pocket of the HIV-1 gp41 NHR broadly neutralizes HIV-1 by blocking six-helix bundle formation. CURRENT RESEARCH IN MICROBIAL SCIENCES 2024; 7:100263. [PMID: 39176008 PMCID: PMC11339056 DOI: 10.1016/j.crmicr.2024.100263] [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] [Indexed: 08/24/2024] Open
Abstract
The highly conserved hydrophobic pocket region of HIV-1 gp41 NHR triple-stranded coiled coil is crucial for the binding of CHR to NHR to form a six-helix bundle (6-HB). This pocket is only exposed instantaneously during fusion, making it an ideal target for antibody drug design. However, IgG molecule is too big to enter the pocket during the fusion process. Therefore, to overcome the steric hindrance and kinetic obstacles caused by the formation of gp41 pre-hairpin fusion intermediate, we obtained nanobodies (Nbs) targeting NHR by immunizing alpaca with an NHR-trimer mimic. Specifically, we identified a Nb, Nb-172, that exhibited potent and broadly neutralizing activity against HIV-1 pseudoviruses, HIV-1 primary isolates, and T20-resistant HIV-1 strains. In addition, the combinatorial use of mD1.22 and Nb-172 exhibited synergism in inhibiting HIV-1 infection inactivating cell-free virions. Nb-172 can competitively bind to the hydrophobic pocket of gp41 NHR to inhibit 6-HB formation. These findings suggest that Nb-172 merits further investigation as a potential therapeutic for HIV-1 infection.
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Affiliation(s)
- Lujia Sun
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai, China
| | - Bo Chen
- Chengdu NBbiolab. CO., LTD, SME Incubation Park, 319 Qingpi Avenue, Chengdu, China
| | - Xianbo Liu
- Chengdu NBbiolab. CO., LTD, SME Incubation Park, 319 Qingpi Avenue, Chengdu, China
| | - Yun Zhu
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Guangxu Zhang
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai, China
| | - Xiaoxing Liang
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai, China
| | - Lixiao Xing
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai, China
| | - Wei Xu
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai, China
| | - Shibo Jiang
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai, China
| | - Xinling Wang
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai, China
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9
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Haynes JR, Whitmore CA, Behof WJ, Landman CA, Ong HH, Feld AP, Suero IC, Greer CB, Gore JC, Wijesinghe P, Matsubara JA, Wadzinski BE, Spiller BW, Pham W. Targeting soluble amyloid-beta oligomers with a novel nanobody. Sci Rep 2024; 14:16086. [PMID: 38992064 PMCID: PMC11239946 DOI: 10.1038/s41598-024-66970-6] [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: 02/09/2024] [Accepted: 07/05/2024] [Indexed: 07/13/2024] Open
Abstract
The classical amyloid cascade hypothesis postulates that the aggregation of amyloid plaques and the accumulation of intracellular hyperphosphorylated Tau tangles, together, lead to profound neuronal death. However, emerging research has demonstrated that soluble amyloid-β oligomers (SAβOs) accumulate early, prior to amyloid plaque formation. SAβOs induce memory impairment and disrupt cognitive function independent of amyloid-β plaques, and even in the absence of plaque formation. This work describes the development and characterization of a novel anti-SAβO (E3) nanobody generated from an alpaca immunized with SAβO. In-vitro assays and in-vivo studies using 5XFAD mice indicate that the fluorescein (FAM)-labeled E3 nanobody recognizes both SAβOs and amyloid-β plaques. The E3 nanobody traverses across the blood-brain barrier and binds to amyloid species in the brain of 5XFAD mice. Imaging of mouse brains reveals that SAβO and amyloid-β plaques are not only different in size, shape, and morphology, but also have a distinct spatial distribution in the brain. SAβOs are associated with neurons, while amyloid plaques reside in the extracellular matrix. The results of this study demonstrate that the SAβO nanobody can serve as a diagnostic agent with potential theragnostic applications in Alzheimer's disease.
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Affiliation(s)
- Justin R Haynes
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Clayton A Whitmore
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - William J Behof
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Charlotte A Landman
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Henry H Ong
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Andrew P Feld
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Isabelle C Suero
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Celeste B Greer
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, 37232, USA
| | - John C Gore
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, 37232, USA
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37235, USA
- Vanderbilt Ingram Cancer Center, Nashville, TN, 37232, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Printha Wijesinghe
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, BC, V5Z3N9, Canada
| | - Joanne A Matsubara
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, BC, V5Z3N9, Canada
| | - Brian E Wadzinski
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA.
- Vanderbilt Ingram Cancer Center, Nashville, TN, 37232, USA.
| | - Benjamin W Spiller
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA.
- Vanderbilt Center for Structural Biology, Vanderbilt University, Nashville, TN, 37235, USA.
| | - Wellington Pham
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, 37232, USA.
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37235, USA.
- Vanderbilt Ingram Cancer Center, Nashville, TN, 37232, USA.
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 37232, USA.
- Vanderbilt Institute of Nanoscale Science and Engineering, Vanderbilt University, Nashville, TN, 37235, USA.
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, 37212, USA.
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10
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Thalén NB, Karlander M, Lundqvist M, Persson H, Hofström C, Turunen SP, Godzwon M, Volk AL, Malm M, Ohlin M, Rockberg J. Mammalian cell display with automated oligo design and library assembly allows for rapid residue level conformational epitope mapping. Commun Biol 2024; 7:805. [PMID: 38961245 PMCID: PMC11222437 DOI: 10.1038/s42003-024-06508-8] [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: 11/29/2023] [Accepted: 06/25/2024] [Indexed: 07/05/2024] Open
Abstract
Precise epitope determination of therapeutic antibodies is of great value as it allows for further comprehension of mechanism of action, therapeutic responsiveness prediction, avoidance of unwanted cross reactivity, and vaccine design. The golden standard for discontinuous epitope determination is the laborious X-ray crystallography method. Here, we present a combinatorial method for rapid mapping of discontinuous epitopes by mammalian antigen display, eliminating the need for protein expression and purification. The method is facilitated by automated workflows and tailored software for antigen analysis and oligonucleotide design. These oligos are used in automated mutagenesis to generate an antigen receptor library displayed on mammalian cells for direct binding analysis by flow cytometry. Through automated analysis of 33930 primers an optimized single condition cloning reaction was defined allowing for mutation of all surface-exposed residues of the receptor binding domain of SARS-CoV-2. All variants were functionally expressed, and two reference binders validated the method. Furthermore, epitopes of three novel therapeutic antibodies were successfully determined followed by evaluation of binding also towards SARS-CoV-2 Omicron BA.2. We find the method to be highly relevant for rapid construction of antigen libraries and determination of antibody epitopes, especially for the development of therapeutic interventions against novel pathogens.
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Affiliation(s)
- Niklas Berndt Thalén
- Department Protein science, KTH-Royal Institute of Technology, Stockholm, SE-106 91, Sweden
| | - Maximilian Karlander
- Department Protein science, KTH-Royal Institute of Technology, Stockholm, SE-106 91, Sweden
| | - Magnus Lundqvist
- Department Protein science, KTH-Royal Institute of Technology, Stockholm, SE-106 91, Sweden
| | - Helena Persson
- Science for Life Laboratory, Drug Discovery and Development Platform & School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Camilla Hofström
- Science for Life Laboratory, Drug Discovery and Development Platform & School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - S Pauliina Turunen
- Science for Life Laboratory, Drug Discovery and Development Platform & School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden
| | | | - Anna-Luisa Volk
- Department Protein science, KTH-Royal Institute of Technology, Stockholm, SE-106 91, Sweden
| | - Magdalena Malm
- Department Protein science, KTH-Royal Institute of Technology, Stockholm, SE-106 91, Sweden
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Johan Rockberg
- Department Protein science, KTH-Royal Institute of Technology, Stockholm, SE-106 91, Sweden.
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11
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Hwang J, Jang IY, Bae E, Choi J, Kim JH, Lee SB, Kim JH, Lee JP, Jang HY, Kim HT, Lim JW, Yeom M, Jang E, Kim SE, Jeong HH, Kim JW, Seong SY, Song D, Na W. H1N1 nanobody development and therapeutic efficacy verification in H1N1-challenged mice. Biomed Pharmacother 2024; 176:116781. [PMID: 38805966 DOI: 10.1016/j.biopha.2024.116781] [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: 03/11/2024] [Revised: 05/08/2024] [Accepted: 05/17/2024] [Indexed: 05/30/2024] Open
Abstract
Influenza A virus causes numerous deaths and infections worldwide annually. Therefore, we have considered nanobodies as a potential treatment for patients with severe cases of influenza. We developed a nanobody that was expected to have protective efficacy against the A/California/04/2009 (CA/04; pandemic 2009 flu strain) and evaluated its therapeutic efficacy against CA/04 in mice experiments. This nanobody was derived from the immunization of the alpaca, and the inactivated CA/04 virus was used as an immunogen. We successfully generated a nanobody library through bio-panning, phage ELISA, and Bio-layer interferometry. Moreover, we confirmed that administering nanobodies after lethal doses of CA/04 reduced viral replication in the lungs and influenza-induced clinical signs in mice. These research findings will help to develop nanobodies as viral therapeutics for CA/04 and other infectious viruses.
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Affiliation(s)
- Jaehyun Hwang
- College of Veterinary Medicine, Chonnam National University, Gwangju 61186, Republic of Korea; Dental Research Institute, School of Dentistry, Seoul National University, Seoul 03080, Republic of Korea
| | - In-Young Jang
- Shaperon R&D center, Shaperon, Inc., Seoul 06373, Republic of Korea
| | - Eunseo Bae
- College of Veterinary Medicine, Chonnam National University, Gwangju 61186, Republic of Korea; Dental Research Institute, School of Dentistry, Seoul National University, Seoul 03080, Republic of Korea
| | - Jaeseok Choi
- College of Veterinary Medicine, Chonnam National University, Gwangju 61186, Republic of Korea; Dental Research Institute, School of Dentistry, Seoul National University, Seoul 03080, Republic of Korea
| | - Jeong Hwan Kim
- Shaperon R&D center, Shaperon, Inc., Seoul 06373, Republic of Korea
| | - Sang Beum Lee
- Shaperon R&D center, Shaperon, Inc., Seoul 06373, Republic of Korea
| | - Jong Hyun Kim
- Shaperon R&D center, Shaperon, Inc., Seoul 06373, Republic of Korea
| | - Jae Pil Lee
- Shaperon R&D center, Shaperon, Inc., Seoul 06373, Republic of Korea
| | - Ho Young Jang
- Shaperon R&D center, Shaperon, Inc., Seoul 06373, Republic of Korea
| | - Hyoung Tae Kim
- Shaperon R&D center, Shaperon, Inc., Seoul 06373, Republic of Korea
| | - Jong-Woo Lim
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Minjoo Yeom
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Eunhee Jang
- Research Center, HuVet bio, Inc., Seoul 05836, Republic of Korea
| | - Seong-Eun Kim
- Research Center, HuVet bio, Inc., Seoul 05836, Republic of Korea
| | - Hyoung Hwa Jeong
- Research Center, HuVet bio, Inc., Seoul 05836, Republic of Korea
| | - Jung Woo Kim
- Research Center, HuVet bio, Inc., Seoul 05836, Republic of Korea
| | - Seung-Yong Seong
- Shaperon R&D center, Shaperon, Inc., Seoul 06373, Republic of Korea.
| | - Daesub Song
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea.
| | - Woonsung Na
- Dental Research Institute, School of Dentistry, Seoul National University, Seoul 03080, Republic of Korea; Department of Oral Microbiology and Immunology, School of Dentistry, Seoul National University, Seoul 03080, Republic of Korea.
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12
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Sluchanko NN, Shcheblyakov DV, Varfolomeeva LA, Favorskaya IA, Dolzhikova IV, Korobkova AI, Alekseeva IA, Esmagambetov IB, Derkaev AA, Prokofiev VV, Zorkov ID, Logunov DY, Gintsburg AL, Popov VO, Boyko KM. Structural Basis for Evasion of New SARS-CoV-2 Variants from the Potent Virus-Neutralizing Nanobody Targeting the S-Protein Receptor-Binding Domain. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:1260-1272. [PMID: 39218023 DOI: 10.1134/s0006297924070083] [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: 05/16/2024] [Revised: 06/04/2024] [Accepted: 06/06/2024] [Indexed: 09/04/2024]
Abstract
COVID-19 has caused millions of deaths and many times more infections worldwide, emphasizing the unpreparedness of the global health system in the face of new infections and the key role for vaccines and therapeutics, including virus-neutralizing antibodies, in prevention and containment of the disease. Continuous evolution of the SARS-CoV-2 coronavirus has been causing its new variants to evade the action of the immune system, which highlighted the importance of detailed knowledge of the epitopes of already selected potent virus-neutralizing antibodies. A single-chain antibody ("nanobody") targeting the SARS-CoV-2 receptor-binding domain (RBD), clone P2C5, had exhibited robust virus-neutralizing activity against all SARS-CoV-2 variants and, being a major component of the anti-COVID-19 formulation "GamCoviMab", had successfully passed Phase I of clinical trials. However, after the emergence of the Delta and XBB variants, a decrease in the neutralizing activity of this nanobody was observed. Here we report on the successful crystal structure determination of the RBD:P2C5 complex at 3.1 Å, which revealed the intricate protein-protein interface, sterically occluding full ACE2 receptor binding by the P2C5-neutralized RBD. Moreover, the structure revealed the developed RBD:P2C5 interface centered around residues Leu452 and Phe490, thereby explaining the evasion of the Delta or Omicron XBB, but not Omicron B.1.1.529 variant, as a result of the single L452R or F490S mutations, respectively, from the action of P2C5. The structure obtained is expected to foster nanobody engineering in order to rescue neutralization activity and will facilitate epitope mapping for other neutralizing nanobodies by competition assays.
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Affiliation(s)
- Nikolai N Sluchanko
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071, Russia.
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N. F. Gamaleya, Ministry of Health of the Russian Federation, Moscow, 123098, Russia
| | - Dmitry V Shcheblyakov
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N. F. Gamaleya, Ministry of Health of the Russian Federation, Moscow, 123098, Russia.
| | - Larisa A Varfolomeeva
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071, Russia
| | - Irina A Favorskaya
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N. F. Gamaleya, Ministry of Health of the Russian Federation, Moscow, 123098, Russia
| | - Inna V Dolzhikova
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N. F. Gamaleya, Ministry of Health of the Russian Federation, Moscow, 123098, Russia
| | - Anastasia I Korobkova
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N. F. Gamaleya, Ministry of Health of the Russian Federation, Moscow, 123098, Russia
| | - Irina A Alekseeva
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N. F. Gamaleya, Ministry of Health of the Russian Federation, Moscow, 123098, Russia
| | - Ilias B Esmagambetov
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N. F. Gamaleya, Ministry of Health of the Russian Federation, Moscow, 123098, Russia
| | - Artem A Derkaev
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N. F. Gamaleya, Ministry of Health of the Russian Federation, Moscow, 123098, Russia
| | - Vladimir V Prokofiev
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N. F. Gamaleya, Ministry of Health of the Russian Federation, Moscow, 123098, Russia
| | - Ilya D Zorkov
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N. F. Gamaleya, Ministry of Health of the Russian Federation, Moscow, 123098, Russia
| | - Denis Y Logunov
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N. F. Gamaleya, Ministry of Health of the Russian Federation, Moscow, 123098, Russia
| | - Alexander L Gintsburg
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N. F. Gamaleya, Ministry of Health of the Russian Federation, Moscow, 123098, Russia
| | - Vladimir O Popov
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071, Russia
| | - Konstantin M Boyko
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071, Russia.
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N. F. Gamaleya, Ministry of Health of the Russian Federation, Moscow, 123098, Russia
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13
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Sheward DJ, Pushparaj P, Das H, Greaney AJ, Kim C, Kim S, Hanke L, Hyllner E, Dyrdak R, Lee J, Dopico XC, Dosenovic P, Peacock TP, McInerney GM, Albert J, Corcoran M, Bloom JD, Murrell B, Karlsson Hedestam GB, Hällberg BM. Structural basis of broad SARS-CoV-2 cross-neutralization by affinity-matured public antibodies. Cell Rep Med 2024; 5:101577. [PMID: 38761799 PMCID: PMC11228396 DOI: 10.1016/j.xcrm.2024.101577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 12/15/2023] [Accepted: 04/24/2024] [Indexed: 05/20/2024]
Abstract
Descendants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant now account for almost all SARS-CoV-2 infections. The Omicron variant and its sublineages have spike glycoproteins that are highly diverged from the pandemic founder and first-generation vaccine strain, resulting in significant evasion from monoclonal antibody therapeutics and vaccines. Understanding how commonly elicited antibodies can broaden to cross-neutralize escape variants is crucial. We isolate IGHV3-53, using "public" monoclonal antibodies (mAbs) from an individual 7 months post infection with the ancestral virus and identify antibodies that exhibit potent and broad cross-neutralization, extending to the BA.1, BA.2, and BA.4/BA.5 sublineages of Omicron. Deep mutational scanning reveals these mAbs' high resistance to viral escape. Structural analysis via cryoelectron microscopy of a representative broadly neutralizing antibody, CAB-A17, in complex with the Omicron BA.1 spike highlights the structural underpinnings of this broad neutralization. By reintroducing somatic hypermutations into a germline-reverted CAB-A17, we delineate the role of affinity maturation in the development of cross-neutralization by a public class of antibodies.
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Affiliation(s)
- Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Division of Medical Virology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Pradeepa Pushparaj
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Hrishikesh Das
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Allison J Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Changil Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Sungyong Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Erik Hyllner
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Robert Dyrdak
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jimin Lee
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Xaquin Castro Dopico
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Pia Dosenovic
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
| | - Gerald M McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| | | | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden; Centre for Structural Systems Biology (CSSB) and Karolinska Institutet VR-RÅC, Notkestraße 85, 22607 Hamburg, Germany.
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14
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Budylowski P, Chau SLL, Banerjee A, Guvenc F, Samson R, Hu Q, Fiddes L, Seifried L, Chao G, Buchholz M, Estacio A, Cheatley PL, Pavenski K, Patriquin CJ, Liu Y, Sheikh-Mohamed S, Crasta K, Yue F, Pasic MD, Mossman K, Gingras AC, Gommerman JL, Ehrhardt GRA, Mubareka S, Ostrowski M. A Significant Contribution of the Classical Pathway of Complement in SARS-CoV-2 Neutralization of Convalescent and Vaccinee Sera. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:1922-1931. [PMID: 38683124 DOI: 10.4049/jimmunol.2300320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 04/09/2024] [Indexed: 05/01/2024]
Abstract
Although high titers of neutralizing Abs in human serum are associated with protection from reinfection by SARS-CoV-2, there is considerable heterogeneity in human serum-neutralizing Abs against SARS-CoV-2 during convalescence between individuals. Standard human serum live virus neutralization assays require inactivation of serum/plasma prior to testing. In this study, we report that the SARS-CoV-2 neutralization titers of human convalescent sera were relatively consistent across all disease states except for severe COVID-19, which yielded significantly higher neutralization titers. Furthermore, we show that heat inactivation of human serum significantly lowered neutralization activity in a live virus SARS-CoV-2 neutralization assay. Heat inactivation of human convalescent serum was shown to inactivate complement proteins, and the contribution of complement in SARS-CoV-2 neutralization was often >50% of the neutralizing activity of human sera without heat inactivation and could account for neutralizing activity when standard titers were zero after heat inactivation. This effect was also observed in COVID-19 vaccinees and could be abolished in individuals who were undergoing treatment with therapeutic anti-complement Abs. Complement activity was mainly dependent on the classical pathway with little contributions from mannose-binding lectin and alternative pathways. Our study demonstrates the importance of the complement pathway in significantly increasing viral neutralization activity against SARS-CoV-2 in spike seropositive individuals.
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Affiliation(s)
- Patrick Budylowski
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Serena L L Chau
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Arinjay Banerjee
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Furkan Guvenc
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Reuben Samson
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Queenie Hu
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Lindsey Fiddes
- Microscopy Imaging Lab, University of Toronto, Toronto, Ontario, Canada
| | - Laurie Seifried
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Gary Chao
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Megan Buchholz
- Apheresis Unit, Kidney and Metabolism Program, St Michael's Hospital, Unity Health, Toronto, Ontario, Canada
| | - Antonio Estacio
- Keenan Research Centre for Biomedical Science of St Michael's Hospital, Unity Health, Toronto, Ontario, Canada
| | - Patti Lou Cheatley
- Apheresis Unit, Kidney and Metabolism Program, St Michael's Hospital, Unity Health, Toronto, Ontario, Canada
| | - Katerina Pavenski
- Apheresis Unit, Kidney and Metabolism Program, St Michael's Hospital, Unity Health, Toronto, Ontario, Canada
- Department of Laboratory Medicine, St Michael's Hospital, Unity Health, Toronto, Ontario, Canada
| | - Christopher J Patriquin
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Division of Medical Oncology and Hematology, Department of Medicine, University Health Network, Toronto, Ontario, Canada
| | - Yanling Liu
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | | | - Kimberly Crasta
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - FengYun Yue
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Maria D Pasic
- Department of Immunology, Unity Health Toronto, Toronto, Ontario, Canada
| | - Karen Mossman
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | | | - Götz R A Ehrhardt
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Samira Mubareka
- Sunnybrook Research Institute, Sunnybrook Hospital, Toronto, Ontario, Canada
| | - Mario Ostrowski
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
- Keenan Research Centre for Biomedical Science of St Michael's Hospital, Unity Health, Toronto, Ontario, Canada
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15
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Adair A, Tan LL, Feng J, Girkin J, Bryant N, Wang M, Mordant F, Chan LJ, Bartlett NW, Subbarao K, Pymm P, Tham WH. Human coronavirus OC43 nanobody neutralizes virus and protects mice from infection. J Virol 2024; 98:e0053124. [PMID: 38709106 PMCID: PMC11237593 DOI: 10.1128/jvi.00531-24] [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: 03/27/2024] [Accepted: 03/29/2024] [Indexed: 05/07/2024] Open
Abstract
Human coronavirus (hCoV) OC43 is endemic to global populations and usually causes asymptomatic or mild upper respiratory tract illness. Here, we demonstrate the neutralization efficacy of isolated nanobodies from alpacas immunized with the S1B and S1C domain of the hCoV-OC43 spike glycoprotein. A total of 40 nanobodies bound to recombinant OC43 protein with affinities ranging from 1 to 149 nM. Two nanobodies WNb 293 and WNb 294 neutralized virus at 0.21 and 1.79 nM, respectively. Intranasal and intraperitoneal delivery of WNb 293 fused to an Fc domain significantly reduced nasal viral load in a mouse model of hCoV-OC43 infection. Using X-ray crystallography, we observed that WNb 293 bound to an epitope on the OC43 S1B domain, distal from the sialoglycan-binding site involved in host cell entry. This result suggests that neutralization mechanism of this nanobody does not involve disruption of glycan binding. Our work provides characterization of nanobodies against hCoV-OC43 that blocks virus entry and reduces viral loads in vivo and may contribute to future nanobody-based therapies for hCoV-OC43 infections. IMPORTANCE The pandemic potential presented by coronaviruses has been demonstrated by the ongoing COVID-19 pandemic and previous epidemics caused by severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus. Outside of these major pathogenic coronaviruses, there are four endemic coronaviruses that infect humans: hCoV-OC43, hCoV-229E, hCoV-HKU1, and hCoV-NL63. We identified a collection of nanobodies against human coronavirus OC43 (hCoV-OC43) and found that two high-affinity nanobodies potently neutralized hCoV-OC43 at low nanomolar concentrations. Prophylactic administration of one neutralizing nanobody reduced viral loads in mice infected with hCoV-OC43, showing the potential for nanobody-based therapies for hCoV-OC43 infections.
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Affiliation(s)
- Amy Adair
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Li Lynn Tan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Jackson Feng
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jason Girkin
- />College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Infection Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Nathan Bryant
- />College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Infection Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Mingyang Wang
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Francesca Mordant
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Li-Jin Chan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Nathan W. Bartlett
- />College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Infection Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Kanta Subbarao
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Phillip Pymm
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Wai-Hong Tham
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
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16
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Alfadhli A, Bates TA, Barklis RL, Romanaggi C, Tafesse FG, Barklis E. A Nanobody Interaction with SARS-CoV-2 Spike Allows the Versatile Targeting of Lentivirus Vectors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597774. [PMID: 38895228 PMCID: PMC11185593 DOI: 10.1101/2024.06.06.597774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
While investigating methods to target gene delivery vectors to specific cell types, we examined the potential of using a nanobody against the SARS-CoV-2 Spike protein receptor binding domain to direct lentivirus infection of Spike-expressing cells. Using three different approaches, we found that lentiviruses with surface-exposed nanobody domains selectively infect Spike-expressing cells. The targeting is dependent on the fusion function of Spike, and conforms to a model in which nanobody binding to the Spike protein triggers the Spike fusion machinery. The nanobody-Spike interaction also is capable of directing cell-cell fusion, and the selective infection of nanobody-expressing cells by Spike-pseudotyped lentivirus vectors. Significantly, cells infected with SARS-CoV-2 are efficiently and selectively infected by lentivirus vectors pseudotyped with a chimeric nanobody protein. Our results suggest that cells infected by any virus that forms syncytia may be targeted for gene delivery using an appropriate nanobody or virus receptor mimic. Vectors modified in this fashion may prove useful in the delivery of immunomodulators to infected foci to mitigate the effects of viral infections. IMPORTANCE We have discovered that lentiviruses decorated on their surfaces with a nanobody against the SARS-CoV-2 Spike protein selectively infect Spike-expressing cells. Infection is dependent on the specificity of the nanobody and the fusion function of the Spike protein, and conforms to a reverse fusion model, in which nanobody binding to Spike triggers the Spike fusion machinery. The nanobody-Spike interaction also can drive cell-cell fusion, and infection of nanobody-expressing cells with viruses carrying the Spike protein. Importantly, cells infected with SARS-CoV-2 are selectively infected with nanobody-decorated lentiviruses. These results suggest that cells infected by any virus that expresses an active receptor-binding fusion protein may be targeted by vectors for delivery of cargoes to mitigate infections.
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17
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Cornish K, Huo J, Jones L, Sharma P, Thrush JW, Abdelkarim S, Kipar A, Ramadurai S, Weckener M, Mikolajek H, Liu S, Buckle I, Bentley E, Kirby A, Han X, Laidlaw SM, Hill M, Eyssen L, Norman C, Le Bas A, Clarke J, James W, Stewart JP, Carroll M, Naismith JH, Owens RJ. Structural and functional characterization of nanobodies that neutralize Omicron variants of SARS-CoV-2. Open Biol 2024; 14:230252. [PMID: 38835241 DOI: 10.1098/rsob.230252] [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: 07/30/2023] [Accepted: 03/22/2024] [Indexed: 06/06/2024] Open
Abstract
The Omicron strains of SARS-CoV-2 pose a significant challenge to the development of effective antibody-based treatments as immune evasion has compromised most available immune therapeutics. Therefore, in the 'arms race' with the virus, there is a continuing need to identify new biologics for the prevention or treatment of SARS-CoV-2 infections. Here, we report the isolation of nanobodies that bind to the Omicron BA.1 spike protein by screening nanobody phage display libraries previously generated from llamas immunized with either the Wuhan or Beta spike proteins. The structure and binding properties of three of these nanobodies (A8, H6 and B5-5) have been characterized in detail providing insight into their binding epitopes on the Omicron spike protein. Trimeric versions of H6 and B5-5 neutralized the SARS-CoV-2 variant of concern BA.5 both in vitro and in the hamster model of COVID-19 following nasal administration. Thus, either alone or in combination could serve as starting points for the development of new anti-viral immunotherapeutics.
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Affiliation(s)
- Katy Cornish
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
| | - Jiandong Huo
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford , Oxford, UK
| | - Luke Jones
- Nuffield Department of Medicine, Pandemic Sciences Institute, University of Oxford , Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford , Oxford, UK
| | - Parul Sharma
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool , Liverpool, UK
| | - Joseph W Thrush
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
| | - Sahar Abdelkarim
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
| | - Anja Kipar
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool , Liverpool, UK
- Vetsuisse Faculty, Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, University of Zurich , Zurich, Switzerland
| | - Siva Ramadurai
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
| | - Miriam Weckener
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
| | | | - Sai Liu
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford , Oxford, UK
| | - Imogen Buckle
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
| | - Eleanor Bentley
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool , Liverpool, UK
| | - Adam Kirby
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool , Liverpool, UK
| | - Ximeng Han
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool , Liverpool, UK
| | - Stephen M Laidlaw
- Nuffield Department of Medicine, Pandemic Sciences Institute, University of Oxford , Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford , Oxford, UK
| | - Michelle Hill
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford , Oxford, UK
| | - Lauren Eyssen
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
| | - Chelsea Norman
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
| | - Audrey Le Bas
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
| | - John Clarke
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
| | - William James
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford , Oxford, UK
| | - James P Stewart
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool , Liverpool, UK
| | - Miles Carroll
- Nuffield Department of Medicine, Pandemic Sciences Institute, University of Oxford , Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford , Oxford, UK
| | - James H Naismith
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford , Oxford, UK
| | - Raymond J Owens
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford , Oxford, UK
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18
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Rizk SS, Moustafa DM, ElBanna SA, Nour El-Din HT, Attia AS. Nanobodies in the fight against infectious diseases: repurposing nature's tiny weapons. World J Microbiol Biotechnol 2024; 40:209. [PMID: 38771414 PMCID: PMC11108896 DOI: 10.1007/s11274-024-03990-4] [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: 02/20/2024] [Accepted: 04/15/2024] [Indexed: 05/22/2024]
Abstract
Nanobodies are the smallest known antigen-binding molecules to date. Their small size, good tissue penetration, high stability and solubility, ease of expression, refolding ability, and negligible immunogenicity in the human body have granted them excellence over conventional antibodies. Those exceptional attributes of nanobodies make them promising candidates for various applications in biotechnology, medicine, protein engineering, structural biology, food, and agriculture. This review presents an overview of their structure, development methods, advantages, possible challenges, and applications with special emphasis on infectious diseases-related ones. A showcase of how nanobodies can be harnessed for applications including neutralization of viruses and combating antibiotic-resistant bacteria is detailed. Overall, the impact of nanobodies in vaccine design, rapid diagnostics, and targeted therapies, besides exploring their role in deciphering microbial structures and virulence mechanisms are highlighted. Indeed, nanobodies are reshaping the future of infectious disease prevention and treatment.
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Affiliation(s)
- Soha S Rizk
- Microbiology and Immunology Postgraduate Program, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Dina M Moustafa
- Department of Medical Sciences, Faculty of Dentistry, The British University in Egypt, El Sherouk City, Cairo, 11837, Egypt
| | - Shahira A ElBanna
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Hanzada T Nour El-Din
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Ahmed S Attia
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt.
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19
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De Greve H, Fioravanti A. Single domain antibodies from camelids in the treatment of microbial infections. Front Immunol 2024; 15:1334829. [PMID: 38827746 PMCID: PMC11140111 DOI: 10.3389/fimmu.2024.1334829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 04/29/2024] [Indexed: 06/04/2024] Open
Abstract
Infectious diseases continue to pose significant global health challenges. In addition to the enduring burdens of ailments like malaria and HIV, the emergence of nosocomial outbreaks driven by antibiotic-resistant pathogens underscores the ongoing threats. Furthermore, recent infectious disease crises, exemplified by the Ebola and SARS-CoV-2 outbreaks, have intensified the pursuit of more effective and efficient diagnostic and therapeutic solutions. Among the promising options, antibodies have garnered significant attention due to their favorable structural characteristics and versatile applications. Notably, nanobodies (Nbs), the smallest functional single-domain antibodies of heavy-chain only antibodies produced by camelids, exhibit remarkable capabilities in stable antigen binding. They offer unique advantages such as ease of expression and modification and enhanced stability, as well as improved hydrophilicity compared to conventional antibody fragments (antigen-binding fragments (Fab) or single-chain variable fragments (scFv)) that can aggregate due to their low solubility. Nanobodies directly target antigen epitopes or can be engineered into multivalent Nbs and Nb-fusion proteins, expanding their therapeutic potential. This review is dedicated to charting the progress in Nb research, particularly those derived from camelids, and highlighting their diverse applications in treating infectious diseases, spanning both human and animal contexts.
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Affiliation(s)
- Henri De Greve
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Antonella Fioravanti
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- VIB-VUB Center for Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium
- Fondazione ParSeC – Parco delle Scienze e della Cultura, Prato, Italy
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20
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Hills FR, Eruera AR, Hodgkinson-Bean J, Jorge F, Easingwood R, Brown SHJ, Bouwer JC, Li YP, Burga LN, Bostina M. Variation in structural motifs within SARS-related coronavirus spike proteins. PLoS Pathog 2024; 20:e1012158. [PMID: 38805567 PMCID: PMC11236199 DOI: 10.1371/journal.ppat.1012158] [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: 02/05/2024] [Revised: 07/10/2024] [Accepted: 03/28/2024] [Indexed: 05/30/2024] Open
Abstract
SARS-CoV-2 is the third known coronavirus (CoV) that has crossed the animal-human barrier in the last two decades. However, little structural information exists related to the close genetic species within the SARS-related coronaviruses. Here, we present three novel SARS-related CoV spike protein structures solved by single particle cryo-electron microscopy analysis derived from bat (bat SL-CoV WIV1) and civet (cCoV-SZ3, cCoV-007) hosts. We report complex glycan trees that decorate the glycoproteins and density for water molecules which facilitated modeling of the water molecule coordination networks within structurally important regions. We note structural conservation of the fatty acid binding pocket and presence of a linoleic acid molecule which are associated with stabilization of the receptor binding domains in the "down" conformation. Additionally, the N-terminal biliverdin binding pocket is occupied by a density in all the structures. Finally, we analyzed structural differences in a loop of the receptor binding motif between coronaviruses known to infect humans and the animal coronaviruses described in this study, which regulate binding to the human angiotensin converting enzyme 2 receptor. This study offers a structural framework to evaluate the close relatives of SARS-CoV-2, the ability to inform pandemic prevention, and aid in the development of pan-neutralizing treatments.
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Affiliation(s)
- Francesca R. Hills
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Alice-Roza Eruera
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - James Hodgkinson-Bean
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Fátima Jorge
- Otago Microscopy and Nano Imaging Unit, University of Otago, Dunedin, New Zealand
| | - Richard Easingwood
- Otago Microscopy and Nano Imaging Unit, University of Otago, Dunedin, New Zealand
| | - Simon H. J. Brown
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, University of Wollongong, Wollongong, New South Wales, Australia
| | - James C. Bouwer
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, University of Wollongong, Wollongong, New South Wales, Australia
| | - Yi-Ping Li
- Institute of Human Virology and Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Laura N. Burga
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Mihnea Bostina
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Otago Microscopy and Nano Imaging Unit, University of Otago, Dunedin, New Zealand
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21
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Hannula L, Kuivanen S, Lasham J, Kant R, Kareinen L, Bogacheva M, Strandin T, Sironen T, Hepojoki J, Sharma V, Saviranta P, Kipar A, Vapalahti O, Huiskonen JT, Rissanen I. Nanobody engineering for SARS-CoV-2 neutralization and detection. Microbiol Spectr 2024; 12:e0419922. [PMID: 38363137 PMCID: PMC10986514 DOI: 10.1128/spectrum.04199-22] [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: 10/17/2022] [Accepted: 01/03/2024] [Indexed: 02/17/2024] Open
Abstract
In response to the ongoing COVID-19 pandemic, the quest for coronavirus inhibitors has inspired research on a variety of small proteins beyond conventional antibodies, including robust single-domain antibody fragments, i.e., "nanobodies." Here, we explore the potential of nanobody engineering in the development of antivirals and diagnostic tools. Through fusion of nanobody domains that target distinct binding sites, we engineered multimodular nanobody constructs that neutralize wild-type SARS-CoV-2 and the Alpha and Delta variants at high potency, with IC50 values as low as 50 pM. Despite simultaneous binding to distinct epitopes, Beta and Omicron variants were more resistant to neutralization by the multimodular nanobodies, which highlights the importance of accounting for antigenic drift in the design of biologics. To further explore the applications of nanobody engineering in outbreak management, we present an assay based on fusions of nanobodies with fragments of NanoLuc luciferase that can detect sub-nanomolar quantities of the SARS-CoV-2 spike protein in a single step. Our work showcases the potential of nanobody engineering to combat emerging infectious diseases. IMPORTANCE Nanobodies, small protein binders derived from the camelid antibody, are highly potent inhibitors of respiratory viruses that offer several advantages over conventional antibodies as candidates for specific therapies, including high stability and low production costs. In this work, we leverage the unique properties of nanobodies and apply them as building blocks for new therapeutic and diagnostic tools. We report ultra-potent SARS-CoV-2 inhibition by engineered nanobodies comprising multiple modules in structure-guided combinations and develop nanobodies that carry signal molecules, allowing rapid detection of the SARS-CoV-2 spike protein. Our results highlight the potential of engineered nanobodies in the development of effective countermeasures, both therapeutic and diagnostic, to manage outbreaks of emerging viruses.
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Affiliation(s)
- Liina Hannula
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Suvi Kuivanen
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jonathan Lasham
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Ravi Kant
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Tropical Parasitology, Institute of Maritime and Tropical Medicine, Medical University of Gdansk, Gdynia, Poland
| | - Lauri Kareinen
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Mariia Bogacheva
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Tomas Strandin
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Tarja Sironen
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Jussi Hepojoki
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Vivek Sharma
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Petri Saviranta
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | - Anja Kipar
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Olli Vapalahti
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- HUSLAB, Helsinki University Hospital, Helsinki, Finland
| | - Juha T. Huiskonen
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Ilona Rissanen
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
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22
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Yang ML, Yuan TZ, Chan KY, Ding L, Han Z, Franco H, Holliday C, Kannan S, Davidson E, Doranz BJ, Chandran K, Miller EH, Plante JA, Weaver SC, Cho E, Kailasan S, Marsalek L, Giang H, Abdiche Y, Sato AK. A VHH single-domain platform enabling discovery and development of monospecific antibodies and modular neutralizing bispecifics against SARS-CoV-2 variants. Antib Ther 2024; 7:164-176. [PMID: 38933534 PMCID: PMC11200683 DOI: 10.1093/abt/tbae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 04/21/2024] [Accepted: 05/03/2024] [Indexed: 06/28/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve, escape coronavirus disease 2019 therapeutics and vaccines, and jeopardize public health. To combat SARS-CoV-2 antigenic escape, we developed a rapid, high-throughput pipeline to discover monospecific VHH antibodies and iteratively develop VHH-Fc-VHH bispecifics capable of neutralizing emerging SARS-CoV-2 variants. By panning VHH single-domain phage libraries against ancestral or beta spike proteins, we discovered high-affinity VHH antibodies with unique target epitopes. Combining two VHHs into a tetravalent bispecific construct conferred broad neutralization activity against multiple variants and was more resistant to antigenic escape than the monospecific antibody alone. Following the rise of the Omicron variant, a VHH in the original bispecific construct was replaced with another VHH discovered against the Omicron BA.1 receptor binding domain; the resulting bispecific exhibited neutralization against both BA.1 and BA.5 sublineage variants. A heavy chain-only tetravalent VHH-Fc-VHH bispecific platform derived from humanized synthetic libraries held a myriad of unique advantages: (i) synthetic preconstructed libraries minimized risk of liabilities and maximized discovery speed, (ii) VHH scaffolds allowed for a modular "plug-and-play" format that could be rapidly iterated upon as variants of concern arose, (iii) natural dimerization of single VHH-Fc-VHH polypeptides allowed for straightforward bispecific production and purification methods, and (iv) multivalent approaches enhanced avidity boosting effects and neutralization potency, and conferred more robust resistance to antigenic escape than monovalent approaches against specific variants. This iterative platform of rapid VHH discovery combined with modular bispecific design holds promise for long-term viral control efforts.
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Affiliation(s)
- Marisa L Yang
- Biopharma Department, Twist Bioscience, South San Francisco, CA 94080, United States
| | - Tom Z Yuan
- Biopharma Department, Twist Bioscience, South San Francisco, CA 94080, United States
| | - Kara Y Chan
- Biopharma Department, Twist Bioscience, South San Francisco, CA 94080, United States
| | - Lin Ding
- Biopharma Department, Twist Bioscience, South San Francisco, CA 94080, United States
| | - Zhen Han
- Biopharma Department, Twist Bioscience, South San Francisco, CA 94080, United States
| | - Hector Franco
- Biopharma Department, Twist Bioscience, South San Francisco, CA 94080, United States
| | - Carson Holliday
- Biopharma Department, Twist Bioscience, South San Francisco, CA 94080, United States
| | - Shruthi Kannan
- Integral Molecular, Philadelphia, PA 19104, United States
| | - Edgar Davidson
- Integral Molecular, Philadelphia, PA 19104, United States
| | | | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, United States
| | - Emily Happy Miller
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, United States
| | - Jessica A Plante
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX 77555, United States
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, United States
| | - Scott C Weaver
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX 77555, United States
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, United States
| | - Eunice Cho
- Integrated Biotherapeutics, Rockville, MD 20850, United States
| | - Shweta Kailasan
- Integrated Biotherapeutics, Rockville, MD 20850, United States
| | | | - Hoa Giang
- Biopharma Department, Twist Bioscience, South San Francisco, CA 94080, United States
| | - Yasmina Abdiche
- Revelar Biotherapeutics, Inc., Bethesda, MD 20817, United States
| | - Aaron K Sato
- Biopharma Department, Twist Bioscience, South San Francisco, CA 94080, United States
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23
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Merwaiss F, Lozano‐Sanchez E, Zulaica J, Rusu L, Vazquez‐Vilar M, Orzáez D, Rodrigo G, Geller R, Daròs J. Plant virus-derived nanoparticles decorated with genetically encoded SARS-CoV-2 nanobodies display enhanced neutralizing activity. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:876-891. [PMID: 37966715 PMCID: PMC10955499 DOI: 10.1111/pbi.14230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/16/2023]
Abstract
Viral nanoparticles (VNPs) are a new class of virus-based formulations that can be used as building blocks to implement a variety of functions of potential interest in biotechnology and nanomedicine. Viral coat proteins (CP) that exhibit self-assembly properties are particularly appropriate for displaying antigens and antibodies, by generating multivalent VNPs with therapeutic and diagnostic potential. Here, we developed genetically encoded multivalent VNPs derived from two filamentous plant viruses, potato virus X (PVX) and tobacco etch virus (TEV), which were efficiently and inexpensively produced in the biofactory Nicotiana benthamiana plant. PVX and TEV-derived VNPs were decorated with two different nanobodies recognizing two different regions of the receptor-binding domain (RBD) of the SARS-CoV-2 Spike protein. The addition of different picornavirus 2A ribosomal skipping peptides between the nanobody and the CP allowed for modulating the degree of VNP decoration. Nanobody-decorated VNPs purified from N. benthamiana tissues successfully recognized the RBD antigen in enzyme-linked immunosorbent assays and showed efficient neutralization activity against pseudoviruses carrying the Spike protein. Interestingly, multivalent PVX and TEV-derived VNPs exhibited a neutralizing activity approximately one order of magnitude higher than the corresponding nanobody in a dimeric format. These properties, combined with the ability to produce VNP cocktails in the same N. benthamiana plant based on synergistic infection of the parent PVX and TEV, make these green nanomaterials an attractive alternative to standard antibodies for multiple applications in diagnosis and therapeutics.
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Affiliation(s)
- Fernando Merwaiss
- Instituto de Biología Molecular y Celular de PlantasConsejo Superior de Investigaciones Científicas – Universitat Politècnica de ValènciaValenciaSpain
| | - Enrique Lozano‐Sanchez
- Instituto de Biología Molecular y Celular de PlantasConsejo Superior de Investigaciones Científicas – Universitat Politècnica de ValènciaValenciaSpain
| | - João Zulaica
- Institute for Integrative Systems BiologyConsejo Superior de Investigaciones Científicas – Universitat de ValènciaPaternaSpain
| | - Luciana Rusu
- Institute for Integrative Systems BiologyConsejo Superior de Investigaciones Científicas – Universitat de ValènciaPaternaSpain
| | - Marta Vazquez‐Vilar
- Instituto de Biología Molecular y Celular de PlantasConsejo Superior de Investigaciones Científicas – Universitat Politècnica de ValènciaValenciaSpain
| | - Diego Orzáez
- Instituto de Biología Molecular y Celular de PlantasConsejo Superior de Investigaciones Científicas – Universitat Politècnica de ValènciaValenciaSpain
| | - Guillermo Rodrigo
- Institute for Integrative Systems BiologyConsejo Superior de Investigaciones Científicas – Universitat de ValènciaPaternaSpain
| | - Ron Geller
- Institute for Integrative Systems BiologyConsejo Superior de Investigaciones Científicas – Universitat de ValènciaPaternaSpain
| | - José‐Antonio Daròs
- Instituto de Biología Molecular y Celular de PlantasConsejo Superior de Investigaciones Científicas – Universitat Politècnica de ValènciaValenciaSpain
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Shang W, Hu X, Lin X, Li S, Xiong S, Huang B, Wang X. Iterative In Silico Screening for Optimizing Stable Conformation of Anti-SARS-CoV-2 Nanobodies. Pharmaceuticals (Basel) 2024; 17:424. [PMID: 38675386 PMCID: PMC11054880 DOI: 10.3390/ph17040424] [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: 03/01/2024] [Revised: 03/20/2024] [Accepted: 03/23/2024] [Indexed: 04/28/2024] Open
Abstract
Nanobodies (Nbs or VHHs) are single-domain antibodies (sdAbs) derived from camelid heavy-chain antibodies. Nbs have special and unique characteristics, such as small size, good tissue penetration, and cost-effective production, making Nbs a good candidate for the diagnosis and treatment of viruses and other pathologies. Identifying effective Nbs against COVID-19 would help us control this dangerous virus or other unknown variants in the future. Herein, we introduce an in silico screening strategy for optimizing stable conformation of anti-SARS-CoV-2 Nbs. Firstly, various complexes containing nanobodies were downloaded from the RCSB database, which were identified from immunized llamas. The primary docking between Nbs and the SARS-CoV-2 spike protein receptor-binding domain was performed through the ClusPro program, with the manual screening leaving the reasonable conformation to the next step. Then, the binding distances of atoms between the antigen-antibody interfaces were measured through the NeighborSearch algorithm. Finally, filtered nanobodies were acquired according to HADDOCK scores through HADDOCK docking the COVID-19 spike protein with nanobodies under restrictions of calculated molecular distance between active residues and antigenic epitopes less than 4.5 Å. In this way, those nanobodies with more reasonable conformation and stronger neutralizing efficacy were acquired. To validate the efficacy ranking of the nanobodies we obtained, we calculated the binding affinities (∆G) and dissociation constants (Kd) of all screened nanobodies using the PRODIGY web tool and predicted the stability changes induced by all possible point mutations in nanobodies using the MAESTROWeb server. Furthermore, we examined the performance of the relationship between nanobodies' ranking and their number of mutation-sensitive sites (Spearman correlation > 0.68); the results revealed a robust correlation, indicating that the superior nanobodies identified through our screening process exhibited fewer mutation hotspots and higher stability. This correlation analysis demonstrates the validity of our screening criteria, underscoring the suitability of these nanobodies for future development and practical implementation. In conclusion, this three-step screening strategy iteratively in silico greatly improved the accuracy of screening desired nanobodies compared to using only ClusPro docking or default HADDOCK docking settings. It provides new ideas for the screening of novel antibodies and computer-aided screening methods.
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Affiliation(s)
| | | | | | | | | | - Bingding Huang
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen 518118, China; (W.S.); (X.H.); (X.L.); (S.L.); (S.X.)
| | - Xin Wang
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen 518118, China; (W.S.); (X.H.); (X.L.); (S.L.); (S.X.)
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25
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Park KS, Park TI, Lee JE, Hwang SY, Choi A, Pack SP. Aptamers and Nanobodies as New Bioprobes for SARS-CoV-2 Diagnostic and Therapeutic System Applications. BIOSENSORS 2024; 14:146. [PMID: 38534253 DOI: 10.3390/bios14030146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/10/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024]
Abstract
The global challenges posed by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic have underscored the critical importance of innovative and efficient control systems for addressing future pandemics. The most effective way to control the pandemic is to rapidly suppress the spread of the virus through early detection using a rapid, accurate, and easy-to-use diagnostic platform. In biosensors that use bioprobes, the binding affinity of molecular recognition elements (MREs) is the primary factor determining the dynamic range of the sensing platform. Furthermore, the sensitivity relies mainly on bioprobe quality with sufficient functionality. This comprehensive review investigates aptamers and nanobodies recently developed as advanced MREs for SARS-CoV-2 diagnostic and therapeutic applications. These bioprobes might be integrated into organic bioelectronic materials and devices, with promising enhanced sensitivity and specificity. This review offers valuable insights into advancing biosensing technologies for infectious disease diagnosis and treatment using aptamers and nanobodies as new bioprobes.
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Affiliation(s)
- Ki Sung Park
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Tae-In Park
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Jae Eon Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Seo-Yeong Hwang
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Anna Choi
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Seung Pil Pack
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
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26
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Haynes JR, Whitmore CA, Behof WJ, Landman CA, Ong HH, Feld AP, Suero IC, Greer CB, Gore JC, Wijesinghe P, Matsubara JA, Wadzinski BE, Spiller BW, Pham W. TARGETING SOLUBLE AMYLOID-BETA OLIGOMERS WITH A NOVEL NANOBODY. RESEARCH SQUARE 2024:rs.3.rs-3944211. [PMID: 38559050 PMCID: PMC10980145 DOI: 10.21203/rs.3.rs-3944211/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The classical amyloid cascade hypothesis postulates that the aggregation of amyloid plaques and the accumulation of intracellular hyperphosphorylated Tau tangles, together, lead to profound neuronal death. However, emerging research has demonstrated that soluble amyloid-β oligomers (SAβOs) accumulate early, prior to amyloid plaque formation. SAβOs induce memory impairment and disrupt cognitive function independent of amyloid-β plaques, and even in the absence of plaque formation. This work describes the development and characterization of a novel anti-SAβO (E3) nanobody generated from an alpaca immunized with SAβO. In-vitro assays and in-vivo studies using 5XFAD mice indicate that the fluorescein (FAM)-labeled E3 nanobody recognizes both SAβOs and amyloid-β plaques. The E3 nanobody traverses across the blood-brain barrier and binds to amyloid species in the brain of 5XFAD mice. Imaging of mouse brains reveals that SAβO and amyloid-β plaques are not only different in size, shape, and morphology, but also have a distinct spatial distribution in the brain. SAβOs are associated with neurons, while amyloid plaques reside in the extracellular matrix. The results of this study demonstrate that the SAβO nanobody can serve as a diagnostic agent with potential theragnostic applications in Alzheimer's disease.
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Affiliation(s)
- Justin R. Haynes
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Clayton A. Whitmore
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - William J. Behof
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Charlotte A. Landman
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Henry H. Ong
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Andrew P. Feld
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Isabelle C. Suero
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Celeste B. Greer
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN 37232, USA
| | - John C. Gore
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN 37232, USA
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37235, USA
- Vanderbilt Ingram Cancer Center, Nashville, TN 37232, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Printha Wijesinghe
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, British Columbia, V5Z3N9, Canada
| | - Joanne A. Matsubara
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, British Columbia, V5Z3N9, Canada
| | - Brian E. Wadzinski
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA
- Vanderbilt Ingram Cancer Center, Nashville, TN 37232, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Benjamin W. Spiller
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37232, USA
- Vanderbilt Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Wellington Pham
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN 37232, USA
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37235, USA
- Vanderbilt Ingram Cancer Center, Nashville, TN 37232, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37232, USA
- Vanderbilt Institute of Nanoscale Science and Engineering, Vanderbilt University, Nashville, TN 37235, USA
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, TN 37212, USA
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27
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Zhang W, Wang H, Wu T, Gao X, Shang Y, Zhang Z, Liu X, Li Y. A SARS-CoV-2 Nanobody Displayed on the Surface of Human Ferritin with High Neutralization Activity. Int J Nanomedicine 2024; 19:2429-2440. [PMID: 38476285 PMCID: PMC10929646 DOI: 10.2147/ijn.s450829] [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: 12/04/2023] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
Purpose COVID-19 is rampant throughout the world, which has caused great damage to human lives and seriously hindered the development of the global economy. Aiming at the treatment of SARS-CoV-2, in this study, we proposed a novel fenobody strategy based on ferritin (Fe) self-assembly technology. Methods The neutralizing nanobody H11-D4 of SARS-CoV-2 fused to the C-terminus of end-modified human ferritin was expressed in E. coli and silkworm baculovirus expression systems. A large number of nanoparticles were successfully self-assembled in silkworms, while relatively few nanoparticles can be observed in the treated products from E. coli by electron microscopy. Subsequently, the fenobody's expression level and neutralizing activity were then evaluated. Results The results showed that the IC50 of H11-D4 and fenobody Fe-H11-D4 expressed in E. coli were 171.1 nmol L-1 and 20.87 nmol L-1, respectively. However, the IC50 of Fe-HD11-D4 expressed in silkworms was 1.46 nmol L-1 showing better neutralization activity. Conclusion Therefore, fenobodies can be well self-assembled in silkworm baculovirus expression system, and ferritin self-assembly technology can effectively improve nanobody neutralization activity.
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Affiliation(s)
- Wenrong Zhang
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
- College of Life Sciences, Capital Normal University, Beijing, People’s Republic of China
| | - Haining Wang
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Tong Wu
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Xintao Gao
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Yuting Shang
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Zhifang Zhang
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Xingjian Liu
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Yinü Li
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
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28
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Song T, Cooper L, Galván Achi J, Wang X, Dwivedy A, Rong L, Wang X. Polyvalent Nanobody Structure Designed for Boosting SARS-CoV-2 Inhibition. J Am Chem Soc 2024; 146:5894-5900. [PMID: 38408177 PMCID: PMC10965196 DOI: 10.1021/jacs.3c11760] [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] [Indexed: 02/28/2024]
Abstract
Coronavirus transmission and mutations have brought intensive challenges on pandemic control and disease treatment. Developing robust and versatile antiviral drugs for viral neutralization is highly desired. Here, we created a new polyvalent nanobody (Nb) structure that shows the effective inhibition of SARS-CoV-2 infections. Our polyvalent Nb structure, called "PNS", is achieved by first conjugating single-stranded DNA (ssDNA) and the receptor-binding domain (RBD)-targeting Nb with retained binding ability to SARS-CoV-2 spike protein and then coalescing the ssDNA-Nb conjugates around a gold nanoparticle (AuNP) via DNA hybridization with a desired Nb density that offers spatial pattern-matching with that of the Nb binding sites on the trimeric spike. The surface plasmon resonance (SPR) assays show that the PNS binds the SARS-CoV-2 trimeric spike proteins with a ∼1000-fold improvement in affinity than that of monomeric Nbs. Furthermore, our viral entry inhibition assays using the PNS against SARS-CoV-2 WA/2020 and two recent variants of interest (BQ1.1 and XBB) show an over 400-fold enhancement in viral inhibition compared to free Nbs. Our PNS strategy built on a new DNA-protein conjugation chemistry provides a facile approach to developing robust virus inhibitors by using a corresponding virus-targeting Nb with a desired Nb density.
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Affiliation(s)
- Tingjie Song
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Laura Cooper
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Jazmin Galván Achi
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Xiaojing Wang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Abhisek Dwivedy
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Lijun Rong
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Xing Wang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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Yaghoobizadeh F, Roayaei Ardakani M, Ranjbar MM, Khosravi M, Galehdari H. Development of a potent recombinant scFv antibody against the SARS-CoV-2 by in-depth bioinformatics study: Paving the way for vaccine/diagnostics development. Comput Biol Med 2024; 170:108091. [PMID: 38295473 DOI: 10.1016/j.compbiomed.2024.108091] [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: 05/09/2023] [Revised: 01/26/2024] [Accepted: 01/27/2024] [Indexed: 02/02/2024]
Abstract
BACKGROUND The SARS-CoV-2 has led to a worldwide disaster. Thus, developing prophylactics/therapeutics is required to overcome this public health issue. Among these, producing the anti-SARS-CoV-2 single-chain variable fragment (scFv) antibodies has attracted a significant attention. Accordingly, this study aims to address this question: Is it possible to bioinformatics-based design of a potent anti-SARS-CoV-2 scFv as an alternative to current production approaches? METHOD Using the complexed SARS-CoV-2 spike-antibodies, two sets analyses were performed: (1) B-cell epitopes (BCEs) prediction in the spike receptor-binding domain (RBD) region as a parameter for antibody screening; (2) the computational analysis of antibodies variable domains (VH/VL). Based on these primary screenings, and docking/binding affinity rating, one antibody was selected. The protein-protein interactions (PPIs) among the selected antibody-epitope complex were predicted and its epitope conservancy was also evaluated. Thereafter, some elements were added to the final scFv: (1) the PelB signal peptide; (2) a GSGGGGS linker to connect the VH-VL. Finally, this scFv was analyzed/optimized using various web servers. RESULTS Among the antibody library, only one met the various criteria for being an efficient scFv candidate. Moreover, no interaction was predicted between its paratope and RBD hot-spot residues of SARS-CoV-2 variants-of-Concern (VOCs). CONCLUSIONS Herein, a step-by-step bioinformatics platform has been introduced to bypass some barriers of traditional antibody production approaches. Based on existing literature, the current study is one of the pioneer works in the field of bioinformatics-based scFv production. This scFv may be a good candidate for diagnostics/therapeutics design against the SARS-CoV-2 as an emerging aggressive pathogen.
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Affiliation(s)
- Fatemeh Yaghoobizadeh
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Khouzestan, 6135783151, Iran.
| | - Mohammad Roayaei Ardakani
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Khouzestan, 6135783151, Iran.
| | | | - Mohammad Khosravi
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Khouzestan, 6135783151, Iran.
| | - Hamid Galehdari
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Khouzestan, 6135783151, Iran.
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30
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Winiger RR, Perez L. Therapeutic antibodies and alternative formats against SARS-CoV-2. Antiviral Res 2024; 223:105820. [PMID: 38307147 DOI: 10.1016/j.antiviral.2024.105820] [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: 10/30/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/04/2024]
Abstract
The COVID-19 pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) heavily burdened the entire world. Despite a prompt generation of vaccines and therapeutics to confront infection, the virus remains a threat. The ancestor viral strain has evolved into several variants of concern, with the Omicron variant now having many distinct sublineages. Consequently, most available antibodies targeting the spike went obsolete and thus new therapies or therapeutic formats are needed. In this review we focus on antibody targets, provide an overview of the therapeutic progress made so far, describe novel formats being explored, and lessons learned from therapeutic antibodies that can enhance pandemic preparedness.
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Affiliation(s)
- Rahel R Winiger
- University of Lausanne (UNIL), Lausanne University Hospital (CHUV), Service of Immunology and Allergy, and Center for Human Immunology Lausanne (CHIL), Switzerland.
| | - Laurent Perez
- University of Lausanne (UNIL), Lausanne University Hospital (CHUV), Service of Immunology and Allergy, and Center for Human Immunology Lausanne (CHIL), Switzerland.
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31
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Chen F, Liu Z, Kang W, Jiang F, Yang X, Yin F, Zhou Z, Li Z. Single-domain antibodies against SARS-CoV-2 RBD from a two-stage phage screening of universal and focused synthetic libraries. BMC Infect Dis 2024; 24:199. [PMID: 38350843 PMCID: PMC10865538 DOI: 10.1186/s12879-024-09022-8] [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: 06/05/2023] [Accepted: 01/16/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) is an evolving global pandemic, and nanobodies, as well as other single-domain antibodies (sdAbs), have been recognized as a potential diagnostic and therapeutic tool for infectious diseases. High-throughput screening techniques such as phage display have been developed as an alternative to in vivo immunization for the discovery of antibody-like target-specific binders. METHODS We designed and constructed a highly diverse synthetic phage library sdAb-U (single-domain Antibody - Universal library ) based on a human framework. The SARS-CoV-2 receptor-binding domain (RBD) was expressed and purified. The universal library sdAb-U was panned against the RBD protein target for two rounds, followed by monoclonal phage ELISA (enzyme-linked immunosorbent assay) to identify RBD-specific binders (the first stage). High-affinity binders were sequenced and the obtained CDR1 and CDR2 sequences were combined with fully randomized CDR3 to construct a targeted (focused) phage library sdAb-RBD, for subsequent second-stage phage panning (also two rounds) and screening. Then, sequences with high single-to-background ratios in phage ELISA were selected for expression. The binding affinities of sdAbs to RBD were measured by an ELISA-based method. In addition, we conducted competition ELISA (using ACE2 ectodomain S19-D615) and SARS-CoV-2 pseudovirus neutralization assays for the high-affinity RBD-binding sdAb39. RESULTS Significant enrichments were observed in both the first-stage (universal library) and the second-stage (focused library) phage panning. Five RBD-specific binders were identified in the first stage with high ELISA signal-to-background ratios. In the second stage, we observed a much higher possibility of finding RBD-specific clones in phage ELISA. Among 45 selected RBD-positive sequences, we found eight sdAbs can be well expressed, and five of them show high-affinity to RBD (EC50 < 100nM). We finally found that sdAb39 (EC50 ~ 4nM) can compete with ACE2 for binding to RBD. CONCLUSION Overall, this two-stage strategy of synthetic phage display libraries enables rapid selection of SARS-CoV-2 RBD sdAb with potential therapeutic activity, and this two-stage strategy can potentially be used for rapid discovery of sdAbs against other targets.
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Affiliation(s)
- Fangfang Chen
- Department of Pharmacy, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Zhihong Liu
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, China
| | - Wei Kang
- NanoAI Biotech Co., Ltd, Pingshan District, Shenzhen, China
| | - Fan Jiang
- NanoAI Biotech Co., Ltd, Pingshan District, Shenzhen, China.
| | - Xixiao Yang
- Department of Pharmacy, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Feng Yin
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, China
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Ziyuan Zhou
- National Cancer Center, National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Zigang Li
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, China.
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China.
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Sun M, Wang C, Luo H, Chen Y, Qu G, Chen J, Li L, Zhang M, Xue Q. Development and characterization of a novel nanobody with SRMV neutralizing activity. Microb Cell Fact 2024; 23:45. [PMID: 38341572 PMCID: PMC10858559 DOI: 10.1186/s12934-024-02311-6] [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: 08/27/2023] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Peste des petits ruminants (PPR) is an acute, contact infectious disease caused by the small ruminant morbillivirus (SRMV), and its morbidity in goats and sheep can be up to 100% with significant mortality. Nanobody generated from camelid animals such as alpaca has attracted wide attention because of its unique advantages compared with conventional antibodies. The main objective of this study was to produce specific nanobodies against SRMV and identify its characteristics. To obtain the coding gene of SRMV-specific nanobodies, we first constructed an immune phage-displayed library from the VHH repertoire of alpaca that was immunized with SRMV-F and -H proteins. By using phage display technology, the target antigen-specific VHHs can be obtained after four consecutive rounds of biopanning. Results showed that the size of this VHH library was 2.26 × 1010 CFU/mL and the SRMV-F and -H specific phage particles were greatly enriched after four rounds of biopanning. The positive phage clones were selected and sequenced, and total of five independent different sequences of SRMV-specific nanobodies were identified. Subsequently, the DNA fragments of the five nanobodies were cloned into E. coli BL21(DE3), respectively, and three of them were successfully expressed and purified. Specificity and affinity towards inactivated SRMV of these purified nanobodies were then evaluated using the ELISA method. Results demonstrated that NbSRMV-1-1, NbSRMV-2-10, and NbSRMV-1-21 showed no cross-reactivity with other antigens, such as inactivated BTV, inactivated FMDV, His-tag labeled protein, and BSA. The ELISA titer of these three nanobodies against inactivated SRMV was up to 1:1000. However, only NbSRMV-1-21 displayed SRMV neutralizing activity at a maximum dilution of 1:4. The results indicate that the nanobodies against SRMV generated in this study could be useful in future applications. This study provided a novel antibody tool and laid a foundation for the treatment and detection of SRMV.
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Affiliation(s)
- Miao Sun
- Department of Viral Biologics, China Institute of Veterinary Drug Control, Beijing, China
| | - Changjiang Wang
- Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, China
| | - Huaye Luo
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Yanfei Chen
- Department of Viral Biologics, China Institute of Veterinary Drug Control, Beijing, China
| | - Guanggang Qu
- Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, China
| | - Jian Chen
- Department of Viral Biologics, China Institute of Veterinary Drug Control, Beijing, China
| | - Ling Li
- Department of Viral Biologics, China Institute of Veterinary Drug Control, Beijing, China
| | - Min Zhang
- Tech-Bank Food Corporation Limited, Nanjing, China
| | - Qinghong Xue
- Department of Viral Biologics, China Institute of Veterinary Drug Control, Beijing, China.
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Pavan MF, Bok M, Betanzos San Juan R, Malito JP, Marcoppido GA, Franco DR, Militelo DA, Schammas JM, Bari SE, Stone W, López K, Porier DL, Muller JA, Auguste AJ, Yuan L, Wigdorovitz A, Parreño VG, Ibañez LI. SARS-CoV-2 Specific Nanobodies Neutralize Different Variants of Concern and Reduce Virus Load in the Brain of h-ACE2 Transgenic Mice. Viruses 2024; 16:185. [PMID: 38399961 PMCID: PMC10892724 DOI: 10.3390/v16020185] [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: 12/21/2023] [Revised: 01/17/2024] [Accepted: 01/20/2024] [Indexed: 02/25/2024] Open
Abstract
Since the beginning of the COVID-19 pandemic, there has been a significant need to develop antivirals and vaccines to combat the disease. In this work, we developed llama-derived nanobodies (Nbs) directed against the receptor binding domain (RBD) and other domains of the Spike (S) protein of SARS-CoV-2. Most of the Nbs with neutralizing properties were directed to RBD and were able to block S-2P/ACE2 interaction. Three neutralizing Nbs recognized the N-terminal domain (NTD) of the S-2P protein. Intranasal administration of Nbs induced protection ranging from 40% to 80% after challenge with the WA1/2020 strain in k18-hACE2 transgenic mice. Interestingly, protection was associated with a significant reduction in virus replication in nasal turbinates and a reduction in virus load in the brain. Employing pseudovirus neutralization assays, we identified Nbs with neutralizing capacity against the Alpha, Beta, Delta, and Omicron variants, including a Nb capable of neutralizing all variants tested. Furthermore, cocktails of different Nbs performed better than individual Nbs at neutralizing two Omicron variants (B.1.529 and BA.2). Altogether, the data suggest the potential of SARS-CoV-2 specific Nbs for intranasal treatment of COVID-19 encephalitis.
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Affiliation(s)
- María Florencia Pavan
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires ZC 1428, Argentina; (M.F.P.); (D.A.M.); (S.E.B.)
| | - Marina Bok
- Incuinta, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires ZC 1686, Argentina; (M.B.); (J.P.M.); (A.W.)
- Instituto de Virología e Innovaciones Tecnológicas, Consejo Nacional de Investigaciones Científicas y Técnicas (IVIT-CONICET), Hurlingham, Buenos Aires ZC 1686, Argentina;
| | - Rafael Betanzos San Juan
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Departamento de Química Biológicas, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires ZC 1428, Argentina;
| | - Juan Pablo Malito
- Incuinta, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires ZC 1686, Argentina; (M.B.); (J.P.M.); (A.W.)
- Instituto de Virología e Innovaciones Tecnológicas, Consejo Nacional de Investigaciones Científicas y Técnicas (IVIT-CONICET), Hurlingham, Buenos Aires ZC 1686, Argentina;
| | - Gisela Ariana Marcoppido
- Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires ZC 1686, Argentina; (G.A.M.); (D.R.F.)
| | - Diego Rafael Franco
- Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires ZC 1686, Argentina; (G.A.M.); (D.R.F.)
| | - Daniela Ayelen Militelo
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires ZC 1428, Argentina; (M.F.P.); (D.A.M.); (S.E.B.)
| | - Juan Manuel Schammas
- Instituto de Virología e Innovaciones Tecnológicas, Consejo Nacional de Investigaciones Científicas y Técnicas (IVIT-CONICET), Hurlingham, Buenos Aires ZC 1686, Argentina;
| | - Sara Elizabeth Bari
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires ZC 1428, Argentina; (M.F.P.); (D.A.M.); (S.E.B.)
| | - William Stone
- Department of Entomology, College of Agriculture and Life Sciences, Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA; (W.S.); (K.L.); (D.L.P.); (J.A.M.); (A.J.A.)
| | - Krisangel López
- Department of Entomology, College of Agriculture and Life Sciences, Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA; (W.S.); (K.L.); (D.L.P.); (J.A.M.); (A.J.A.)
| | - Danielle LaBrie Porier
- Department of Entomology, College of Agriculture and Life Sciences, Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA; (W.S.); (K.L.); (D.L.P.); (J.A.M.); (A.J.A.)
| | - John Anthony Muller
- Department of Entomology, College of Agriculture and Life Sciences, Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA; (W.S.); (K.L.); (D.L.P.); (J.A.M.); (A.J.A.)
| | - Albert Jonathan Auguste
- Department of Entomology, College of Agriculture and Life Sciences, Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA; (W.S.); (K.L.); (D.L.P.); (J.A.M.); (A.J.A.)
- Center for Emerging, Zoonotic, and Arthropod-Borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA;
| | - Lijuan Yuan
- Center for Emerging, Zoonotic, and Arthropod-Borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA;
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Andrés Wigdorovitz
- Incuinta, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires ZC 1686, Argentina; (M.B.); (J.P.M.); (A.W.)
- Instituto de Virología e Innovaciones Tecnológicas, Consejo Nacional de Investigaciones Científicas y Técnicas (IVIT-CONICET), Hurlingham, Buenos Aires ZC 1686, Argentina;
| | - Viviana Gladys Parreño
- Incuinta, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires ZC 1686, Argentina; (M.B.); (J.P.M.); (A.W.)
- Instituto de Virología e Innovaciones Tecnológicas, Consejo Nacional de Investigaciones Científicas y Técnicas (IVIT-CONICET), Hurlingham, Buenos Aires ZC 1686, Argentina;
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Lorena Itat Ibañez
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires ZC 1428, Argentina; (M.F.P.); (D.A.M.); (S.E.B.)
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Babamohamadi M, Mohammadi N, Faryadi E, Haddadi M, Merati A, Ghobadinezhad F, Amirian R, Izadi Z, Hadjati J. Anti-CTLA-4 nanobody as a promising approach in cancer immunotherapy. Cell Death Dis 2024; 15:17. [PMID: 38191571 PMCID: PMC10774412 DOI: 10.1038/s41419-023-06391-x] [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: 06/21/2023] [Revised: 11/25/2023] [Accepted: 12/13/2023] [Indexed: 01/10/2024]
Abstract
Cancer is one of the most common diseases and causes of death worldwide. Since common treatment approaches do not yield acceptable results in many patients, developing innovative strategies for effective treatment is necessary. Immunotherapy is one of the promising approaches that has been highly regarded for preventing tumor recurrence and new metastases. Meanwhile, inhibiting immune checkpoints is one of the most attractive methods of cancer immunotherapy. Cytotoxic T lymphocyte-associated protein-4 (CTLA-4) is an essential immune molecule that plays a vital role in cell cycle modulation, regulation of T cell proliferation, and cytokine production. This molecule is classically expressed by stimulated T cells. Inhibition of overexpression of immune checkpoints such as CTLA-4 receptors has been confirmed as an effective strategy. In cancer immunotherapy, immune checkpoint-blocking drugs can be enhanced with nanobodies that target immune checkpoint molecules. Nanobodies are derived from the variable domain of heavy antibody chains. These small protein fragments have evolved entirely without a light chain and can be used as a powerful tool in imaging and treating diseases with their unique structure. They have a low molecular weight, which makes them smaller than conventional antibodies while still being able to bind to specific antigens. In addition to low molecular weight, specific binding to targets, resistance to temperature, pH, and enzymes, high ability to penetrate tumor tissues, and low toxicity make nanobodies an ideal approach to overcome the disadvantages of monoclonal antibody-based immunotherapy. In this article, while reviewing the cellular and molecular functions of CTLA-4, the structure and mechanisms of nanobodies' activity, and their delivery methods, we will explain the advantages and challenges of using nanobodies, emphasizing immunotherapy treatments based on anti-CTLA-4 nanobodies.
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Affiliation(s)
- Mehregan Babamohamadi
- Department of Biology, School of Natural Sciences, University of Tabriz, Tabriz, Iran
- Stem Cell and Regenerative Medicine Innovation Center, Tehran University of Medical Sciences, Tehran, Iran
- USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Nastaran Mohammadi
- USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Department of Immunology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Elham Faryadi
- USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Department of Immunology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Maryam Haddadi
- USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Department of Immunology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Amirhossein Merati
- USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Department of Medical Laboratory Sciences, School of Paramedical, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Farbod Ghobadinezhad
- USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Roshanak Amirian
- USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Zhila Izadi
- USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Jamshid Hadjati
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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Jiang X, Qin Q, Zhu H, Qian J, Huang Q. Structure-guided design of a trivalent nanobody cluster targeting SARS-CoV-2 spike protein. Int J Biol Macromol 2024; 256:128191. [PMID: 38000614 DOI: 10.1016/j.ijbiomac.2023.128191] [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: 09/24/2023] [Revised: 11/06/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023]
Abstract
Nanobodies are natural anti-SARS-CoV-2 drug candidates. Engineering multivalent nanobodies is an effective way to improve the functional binding affinity of natural nanobodies by simultaneously targeting multiple sites on viral proteins. However, multivalent nanobodies have usually been engineered by trial and error, and rational designs are still lacking. Here, we describe a structure-guided design of a self-assembled trivalent nanobody cluster targeting the SARS-CoV-2 spike protein. Using the nanobody Nb6 as a monovalent binder, we first selected a human-derived trimerization scaffold evaluated by molecular dynamics simulations, then selected an optimal linker according to the minimum distance between Nb6 and the trimerization scaffold, and finally successfully engineered a trivalent nanobody cluster called Tribody. Compared with the low-affinity monovalent counterpart (Nb6), Tribody showed much higher target binding affinity (KD < 1 pM) and thus had a 900-fold increase in antiviral neutralization against SARS-CoV-2 pseudovirus. We determined the cryo-EM structure of the Tribody-spike complex and confirmed that all three Nb6 binders of Tribody collectively bind to the three receptor-binding domains (RBDs) of the spike and lock them in a 3-RBD-down conformation, fully consistent with our structure-guided design. This study demonstrates that synthetic nanobody clusters with human-derived self-assembled scaffolds are potential protein drugs against SARS-CoV-2 coronaviruses.
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Affiliation(s)
- Xinyi Jiang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Qin Qin
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Haixia Zhu
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jiaqiang Qian
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Qiang Huang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai 200438, China; Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 201203, China.
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Mia ME, Howlader M, Akter F, Hossain MM. Preclinical and Clinical Investigations of Potential Drugs and Vaccines for COVID-19 Therapy: A Comprehensive Review With Recent Update. CLINICAL PATHOLOGY (THOUSAND OAKS, VENTURA COUNTY, CALIF.) 2024; 17:2632010X241263054. [PMID: 39070952 PMCID: PMC11282570 DOI: 10.1177/2632010x241263054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 06/03/2024] [Indexed: 07/30/2024]
Abstract
The COVID-19 pandemic-led worldwide healthcare crisis necessitates prompt societal, ecological, and medical efforts to stop or reduce the rising number of fatalities. Numerous mRNA based vaccines and vaccines for viral vectors have been licensed for use in emergencies which showed 90% to 95% efficacy in preventing SARS-CoV-2 infection. However, safety issues, vaccine reluctance, and skepticism remain major concerns for making mass vaccination a successful approach to treat COVID-19. Hence, alternative therapeutics is needed for eradicating the global burden of COVID-19 from developed and low-resource countries. Repurposing current medications and drug candidates could be a more viable option for treating SARS-CoV-2 as these therapies have previously passed a number of significant checkpoints for drug development and patient care. Besides vaccines, this review focused on the potential usage of alternative therapeutic agents including antiviral, antiparasitic, and antibacterial drugs, protease inhibitors, neuraminidase inhibitors, and monoclonal antibodies that are currently undergoing preclinical and clinical investigations to assess their effectiveness and safety in the treatment of COVID-19. Among the repurposed drugs, remdesivir is considered as the most promising agent, while favipiravir, molnupiravir, paxlovid, and lopinavir/ritonavir exhibited improved therapeutic effects in terms of elimination of viruses. However, the outcomes of treatment with oseltamivir, umifenovir, disulfiram, teicoplanin, and ivermectin were not significant. It is noteworthy that combining multiple drugs as therapy showcases impressive effectiveness in managing individuals with COVID-19. Tocilizumab is presently employed for the treatment of patients who exhibit COVID-19-related pneumonia. Numerous antiviral drugs such as galidesivir, griffithsin, and thapsigargin are under clinical trials which could be promising for treating COVID-19 individuals with severe symptoms. Supportive treatment for patients of COVID-19 may involve the use of corticosteroids, convalescent plasma, stem cells, pooled antibodies, vitamins, and natural substances. This study provides an updated progress in SARS-CoV-2 medications and a crucial guide for inventing novel interventions against COVID-19.
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Affiliation(s)
- Md. Easin Mia
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Mithu Howlader
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Farzana Akter
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Md. Murad Hossain
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
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Panda M, Kalita E, Singh S, Kumar K, Prajapati VK. Nanobody-peptide-conjugate (NPC) for passive immunotherapy against SARS-CoV-2 variants of concern (VoC): a prospective pan-coronavirus therapeutics. Mol Divers 2023; 27:2577-2603. [PMID: 36400898 PMCID: PMC9676808 DOI: 10.1007/s11030-022-10570-x] [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: 10/06/2022] [Accepted: 11/11/2022] [Indexed: 11/19/2022]
Abstract
The COVID-19 crisis, incited by the zoonotic SARS-CoV-2 virus, has quickly escalated into a catastrophic public health issue and a grave threat to humankind owing to the advent of mutant viruses. Multiple pharmaceutical therapies or biologics envision stopping the virus from spreading further; however, WHO has voiced concerns about the variants of concern (VoCs) inability to respond. Nanobodies are a new class of antibody mimics with binding affinity and specificity similar to classical mAbs, as well as the privileges of a small molecular weight, ease of entry into solid tissues, and binding cryptic epitopes of the antigen. Herein, we investigated multiple putative anti-SARS-CoV-2 nanobodies targeting the Receptor binding domain of the WHO-listed SARS-CoV-2 variants of concern using a comprehensive computational immunoinformatics methodology. With affinity maturation via alanine scanning mutagenesis, we remodeled an ultrapotent nanobody with substantial breadth and potency, exhibiting pico-molar binding affinities against all the VoCs. An antiviral peptide with specificity for ACE-2 receptors was affixed to make it multispecific and discourage viral entry. Collectively, we constructed a broad-spectrum therapeutic biparatopic nanobody-peptide conjugate (NPC) extending coverage to SARS-CoV-2 VoCs RBDs. We PEGylated the biparatopic construct with 20kD maleimide-terminated PEG (MAL-(PEG)n-OMe) to improve its clinical efficacy limiting rapid renal clearance, and performed in silico cloning to facilitate future experimental studies. Our findings suggest that combining biparatopic nanobody conjugate with standard treatment may be a promising bivariate tool for combating viral entry during COVID-19 illness.
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Affiliation(s)
- Mamta Panda
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, Rajasthan, 305817, India
| | - Elora Kalita
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, Rajasthan, 305817, India
| | - Satyendra Singh
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, Rajasthan, 305817, India
| | - Ketan Kumar
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, Rajasthan, 305817, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, Rajasthan, 305817, India.
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Wang WB, Ma YB, Lei ZH, Zhang XF, Li J, Li SS, Dong ZY, Liang Y, Li QM, Su JG. Identification of key mutations responsible for the enhancement of receptor-binding affinity and immune escape of SARS-CoV-2 Omicron variant. J Mol Graph Model 2023; 124:108540. [PMID: 37352723 PMCID: PMC10254043 DOI: 10.1016/j.jmgm.2023.108540] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/25/2023]
Abstract
The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has raised concerns worldwide due to its enhanced transmissibility and immune escapability. The first dominant Omicron BA.1 subvariant harbors more than 30 mutations in the spike protein from the prototype virus, of which 15 mutations are located at the receptor binding domain (RBD). These mutations in the RBD region attracted significant attention, which potentially enhance the binding of the receptor human angiotensin-converting enzyme 2 (hACE2) and decrease the potency of neutralizing antibodies/nanobodies. This study applied the molecular dynamics simulations combined with the molecular mechanics-generalized Born surface area (MMGBSA) method, to investigate the molecular mechanism behind the impact of the mutations acquired by Omicron on the binding affinity between RBD and hACE2. Our results indicate that five key mutations, i.e., N440K, T478K, E484A, Q493R, and G496S, contributed significantly to the enhancement of the binding affinity by increasing the electrostatic interactions of the RBD-hACE2 complex. Moreover, fourteen neutralizing antibodies/nanobodies complexed with RBD were used to explore the effects of the mutations in Omicron RBD on their binding affinities. The calculation results indicate that the key mutations E484A and Y505H reduce the binding affinities to RBD for most of the studied neutralizing antibodies/nanobodies, mainly attributed to the elimination of the original favorable gas-phase electrostatic and hydrophobic interactions between them, respectively. Our results provide valuable information for developing effective vaccines and antibody/nanobody drugs.
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Affiliation(s)
- Wei Bu Wang
- High Performance Computing Center, National Vaccine and Serum Institute (NVSI), Beijing, China; National Engineering Center for New Vaccine Research, Beijing, China
| | - Yi Bo Ma
- High Performance Computing Center, National Vaccine and Serum Institute (NVSI), Beijing, China; National Engineering Center for New Vaccine Research, Beijing, China
| | - Ze Hua Lei
- National Engineering Center for New Vaccine Research, Beijing, China; The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
| | - Xue Feng Zhang
- National Engineering Center for New Vaccine Research, Beijing, China; The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
| | - Jiao Li
- High Performance Computing Center, National Vaccine and Serum Institute (NVSI), Beijing, China; National Engineering Center for New Vaccine Research, Beijing, China
| | - Shan Shan Li
- High Performance Computing Center, National Vaccine and Serum Institute (NVSI), Beijing, China; National Engineering Center for New Vaccine Research, Beijing, China
| | - Ze Yuan Dong
- High Performance Computing Center, National Vaccine and Serum Institute (NVSI), Beijing, China; National Engineering Center for New Vaccine Research, Beijing, China
| | - Yu Liang
- National Engineering Center for New Vaccine Research, Beijing, China; The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
| | - Qi Ming Li
- National Engineering Center for New Vaccine Research, Beijing, China; The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China.
| | - Ji Guo Su
- High Performance Computing Center, National Vaccine and Serum Institute (NVSI), Beijing, China; National Engineering Center for New Vaccine Research, Beijing, China.
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Mohammad Faizal NDF, Ramli NA, Mat Rani NNI, Shaibie NA, Aarti, Poonsawas P, Sharma SK, Mohd Amin MCI. Leveraging immunoliposomes as nanocarriers against SARS-CoV-2 and its emerging variants. Asian J Pharm Sci 2023; 18:100855. [PMID: 38125653 PMCID: PMC10730353 DOI: 10.1016/j.ajps.2023.100855] [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: 06/03/2023] [Revised: 08/20/2023] [Accepted: 08/21/2023] [Indexed: 12/23/2023] Open
Abstract
The global COVID-19 pandemic arising from SARS-CoV-2 has impacted many lives, gaining interest worldwide ever since it was first identified in December 2019. Till 2023, 752 million cumulative cases and 6.8 million deaths were documented globally. COVID-19 has been rapidly evolving, affecting virus transmissibility and properties and contributing to increased disease severity. The Omicron is the most circulating variant of concern. Although success in its treatment has indicated progress in tackling the virus, limitations in delivering the current antiviral agents in battling emerging variants remain remarkable. With the latest advancements in nanotechnology for controlling infectious diseases, liposomes have the potential to counteract SARS-CoV-2 because of their ability to employ different targeting strategies, incorporating monoclonal antibodies for the active and passive targeting of infected patients. This review will present a concise summary of the possible strategies for utilizing immunoliposomes to improve current treatment against the occurrence of SARS-CoV-2 and its variants.
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Affiliation(s)
- Nur Dini Fatini Mohammad Faizal
- Centre for Drug Delivery Technology and Vaccine (CENTRIC), Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Kuala Lumpur 50300, Malaysia
| | - Nurul Afina Ramli
- Centre for Drug Delivery Technology and Vaccine (CENTRIC), Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Kuala Lumpur 50300, Malaysia
| | - Nur Najihah Izzati Mat Rani
- Faculty of Pharmacy, University Royal College of Medicine Perak (UniKL RCMP) No.3, Jalan Greentown, Ipoh 30450, Perak, Malaysia
| | - Nur Adania Shaibie
- Centre for Drug Delivery Technology and Vaccine (CENTRIC), Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Kuala Lumpur 50300, Malaysia
| | - Aarti
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | | | - Sunil K. Sharma
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Mohd Cairul Iqbal Mohd Amin
- Centre for Drug Delivery Technology and Vaccine (CENTRIC), Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Kuala Lumpur 50300, Malaysia
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Wu D, Cong J, Wei J, Hu J, Sun W, Ran W, Liao C, Zheng H, Ye L. A Naïve Phage Display Library-Derived Nanobody Neutralizes SARS-CoV-2 and Three Variants of Concern. Int J Nanomedicine 2023; 18:5781-5795. [PMID: 37869063 PMCID: PMC10588750 DOI: 10.2147/ijn.s427990] [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: 06/28/2023] [Accepted: 10/07/2023] [Indexed: 10/24/2023] Open
Abstract
Background The emergence of the coronavirus disease 2019 (COVID-19) pandemic and the new severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants of concern (VOCs) requires the continuous development of safe, effective, and affordable prevention and therapeutics. Nanobodies have demonstrated antiviral activity against a variety of viruses, providing a new candidate for the prevention and treatment of SARS-CoV-2 and its variants. Methods SARS-CoV-2 glycoprotein spike 1 subunit (S1) was selected as the target antigen for nanobody screening of a naïve phage display library. We obtained a nanobody, named Nb-H6, and then determined its affinity, inhibition, and stability by ELISA, Competitive ELISA, and Biolayer Interferometry (BLI). Infection assays of authentic and pseudotyped SARS-CoV-2 were performed to evaluate the neutralization of Nb-H6. The structure and mechanism of action were investigated by AlphaFold, docking, and residue mutation assays. Results We isolated and characterized a nanobody, Nb-H6, which exhibits a broad affinity for S1 and the receptor binding domain (RBD) of SARS-CoV-2, or Alpha (B.1.1.7), Delta (B.1.617.2), Lambda (C.37), and Omicron (BA.2 and BA.5), and blocks receptor angiotensin-converting enzyme 2 (ACE2) binding. Moreover, Nb-H6 can retain its binding capability after pH or thermal treatment and effectively neutralize both pseudotyped and authentic SARS-CoV-2, as well as VOC Alpha (B.1.1.7), Delta (B.1.617.2), and Omicron (BA.2 and BA.5) pseudoviruses. We also confirmed that Nb-H6 binds two distinct amino acid residues of the RBD, preventing SARS-CoV-2 from interacting with the host receptor. Conclusion Our study highlights a novel nanobody, Nb-H6, that may be useful therapeutically in SARS-CoV-2 and VOC outbreaks and pandemics. These findings also provide a molecular foundation for further studies into how nanobodies neutralize SARS-CoV-2 and variants and imply potential therapeutic targets for the treatment of COVID-19.
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Affiliation(s)
- Dandan Wu
- Department of Immunology, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, People’s Republic of China
| | - Junxiao Cong
- Department of Immunology, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, People’s Republic of China
| | - Jiali Wei
- Department of Immunology, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, People’s Republic of China
| | - Jing Hu
- Department of Immunology, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, People’s Republic of China
| | - Wenhao Sun
- Department of Immunology, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, People’s Republic of China
| | - Wei Ran
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Chenghui Liao
- Department of Immunology, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, People’s Republic of China
| | - Housheng Zheng
- Department of Immunology, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, People’s Republic of China
| | - Liang Ye
- Department of Immunology, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, People’s Republic of China
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Prado NDR, Brilhante-Da-Silva N, Sousa RMO, Morais MSDS, Roberto SA, Luiz MB, Assis LCD, Marinho ACM, Araujo LFLD, Pontes RDS, Stabeli RG, Fernandes CFC, Pereira SDS. Single-domain antibodies applied as antiviral immunotherapeutics. J Virol Methods 2023; 320:114787. [PMID: 37516366 DOI: 10.1016/j.jviromet.2023.114787] [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: 12/12/2022] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 07/31/2023]
Abstract
Viral infections have been the cause of high mortality rates throughout different periods in history. Over the last two decades, outbreaks caused by zoonotic diseases and transmitted by arboviruses have had a significant impact on human health. The emergence of viral infections in different parts of the world encourages the search for new inputs to fight pathologies of viral origin. Antibodies represent the predominant class of new drugs developed in recent years and approved for the treatment of various human diseases, including cancer, autoimmune and infectious diseases. A promising group of antibodies are single-domain antibodies derived from camelid heavy chain immunoglobulins, or VHHs, are biomolecules with nanometric dimensions and unique pharmaceutical and biophysical properties that can be used in the diagnosis and immunotherapy of viral infections. For viral neutralization to occur, VHHs can act in different stages of the viral cycle, including the actual inhibition of infection, to hindering viral replication or assembly. This review article addresses advances involving the use of VHHs in therapeutic propositions aimed to battle different viruses that affect human health.
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Affiliation(s)
- Nidiane Dantas Reis Prado
- Laboratório de Engenharia de Anticorpos, Fundação Oswaldo Cruz, FIOCRUZ, unidade Rondônia, Porto Velho, RO, Brazil
| | - Nairo Brilhante-Da-Silva
- Laboratório de Engenharia de Anticorpos, Fundação Oswaldo Cruz, FIOCRUZ, unidade Rondônia, Porto Velho, RO, Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, IOC, Rio de Janeiro, RJ, Brazil
| | - Rosa Maria Oliveira Sousa
- Laboratório de Engenharia de Anticorpos, Fundação Oswaldo Cruz, FIOCRUZ, unidade Rondônia, Porto Velho, RO, Brazil
| | | | - Sibele Andrade Roberto
- Plataforma Bi-institucional de Medicina Translacional, Fundação Oswaldo Cruz-USP, Ribeirão Preto, SP, Brazil
| | - Marcos Barros Luiz
- Instituto Federal de Rondônia Campus Guajará-Mirim, IFRO, Guajará-Mirim, RO, Brazil
| | - Livia Coelho de Assis
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, IOC, Rio de Janeiro, RJ, Brazil; Laboratório Multiusuário de Pesquisa e Desenvolvimento, Fundação Oswaldo Cruz, Fiocruz unidade Ceará, Eusebio, CE, Brazil
| | - Anna Carolina M Marinho
- Laboratório Multiusuário de Pesquisa e Desenvolvimento, Fundação Oswaldo Cruz, Fiocruz unidade Ceará, Eusebio, CE, Brazil; Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Ceará, Fortaleza, CE, Brazil
| | - Luiz Felipe Lemes de Araujo
- Plataforma Bi-institucional de Medicina Translacional, Fundação Oswaldo Cruz-USP, Ribeirão Preto, SP, Brazil; Programa de Pós-Graduação em Imunologia Básica e Aplicada, Universidade de São Paulo, USP, Ribeirão Preto, SP, Brazil
| | - Rafael de Souza Pontes
- Plataforma Bi-institucional de Medicina Translacional, Fundação Oswaldo Cruz-USP, Ribeirão Preto, SP, Brazil; Programa de Pós-Graduação em Imunologia Básica e Aplicada, Universidade de São Paulo, USP, Ribeirão Preto, SP, Brazil
| | - Rodrigo Guerino Stabeli
- Plataforma Bi-institucional de Medicina Translacional, Fundação Oswaldo Cruz-USP, Ribeirão Preto, SP, Brazil
| | - Carla Freire Celedonio Fernandes
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, IOC, Rio de Janeiro, RJ, Brazil; Laboratório Multiusuário de Pesquisa e Desenvolvimento, Fundação Oswaldo Cruz, Fiocruz unidade Ceará, Eusebio, CE, Brazil; Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Ceará, Fortaleza, CE, Brazil
| | - Soraya Dos Santos Pereira
- Laboratório de Engenharia de Anticorpos, Fundação Oswaldo Cruz, FIOCRUZ, unidade Rondônia, Porto Velho, RO, Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, IOC, Rio de Janeiro, RJ, Brazil; Programa de Pós-graduação em Biologia Experimental, Universidade Federal de Rondônia, UNIR, Porto Velho, RO, Brazil.
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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: 5] [Impact Index Per Article: 5.0] [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.
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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.
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Xu Y, Zheng R, Prasad A, Liu M, Wan Z, Zhou X, Porter RM, Sample M, Poppleton E, Procyk J, Liu H, Li Y, Wang S, Yan H, Sulc P, Stephanopoulos N. High-affinity binding to the SARS-CoV-2 spike trimer by a nanostructured, trivalent protein-DNA synthetic antibody. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558353. [PMID: 37790307 PMCID: PMC10542138 DOI: 10.1101/2023.09.18.558353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Multivalency enables nanostructures to bind molecular targets with high affinity. Although antibodies can be generated against a wide range of antigens, their shape and size cannot be tuned to match a given target. DNA nanotechnology provides an attractive approach for designing customized multivalent scaffolds due to the addressability and programmability of the nanostructure shape and size. Here, we design a nanoscale synthetic antibody ("nano-synbody") based on a three-helix bundle DNA nanostructure with one, two, or three identical arms terminating in a mini-binder protein that targets the SARS-CoV-2 spike protein. The nano-synbody was designed to match the valence and distance between the three receptor binding domains (RBDs) in the spike trimer, in order to enhance affinity. The protein-DNA nano-synbody shows tight binding to the wild-type, Delta, and several Omicron variants of the SARS-CoV-2 spike trimer, with affinity increasing as the number of arms increases from one to three. The effectiveness of the nano-synbody was also verified using a pseudovirus neutralization assay, with the three-arm nanostructure inhibiting two Omicron variants against which the structures with only one or two arms are ineffective. The structure of the three-arm nano-synbody bound to the Omicron variant spike trimer was solved by negative-stain transmission electron microscopy reconstruction, and shows the protein-DNA nanostructure with all three arms attached to the RBD domains, confirming the intended trivalent attachment. The ability to tune the size and shape of the nano-synbody, as well as its potential ability to attach two or more different binding ligands, will enable the high-affinity targeting of a range of proteins not possible with traditional antibodies.
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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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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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Zhang J, Koolmeister C, Han J, Filograna R, Hanke L, Àdori M, Sheward DJ, Teifel S, Gopalakrishna S, Shao Q, Liu Y, Zhu K, Harris RA, McInerney G, Murrell B, Aoun M, Bäckdahl L, Holmdahl R, Pekalski M, Wedell A, Engvall M, Wredenberg A, Karlsson Hedestam GB, Castro Dopico X, Rorbach J. Antigen receptor stimulation induces purifying selection against pathogenic mitochondrial tRNA mutations. JCI Insight 2023; 8:e167656. [PMID: 37681412 PMCID: PMC10544217 DOI: 10.1172/jci.insight.167656] [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: 12/06/2022] [Accepted: 07/27/2023] [Indexed: 09/09/2023] Open
Abstract
Pathogenic mutations in mitochondrial (mt) tRNA genes that compromise oxidative phosphorylation (OXPHOS) exhibit heteroplasmy and cause a range of multisyndromic conditions. Although mitochondrial disease patients are known to suffer from abnormal immune responses, how heteroplasmic mtDNA mutations affect the immune system at the molecular level is largely unknown. Here, in mice carrying pathogenic C5024T in mt-tRNAAla and in patients with mitochondrial encephalomyopathy, lactic acidosis, stroke-like episodes (MELAS) syndrome carrying A3243G in mt-tRNALeu, we found memory T and B cells to have lower pathogenic mtDNA mutation burdens than their antigen-inexperienced naive counterparts, including after vaccination. Pathogenic burden reduction was less pronounced in myeloid compared with lymphoid lineages, despite C5024T compromising macrophage OXPHOS capacity. Rapid dilution of the C5024T mutation in T and B cell cultures could be induced by antigen receptor-triggered proliferation and was accelerated by metabolic stress conditions. Furthermore, we found C5024T to dysregulate CD8+ T cell metabolic remodeling and IFN-γ production after activation. Together, our data illustrate that the generation of memory lymphocytes shapes the mtDNA landscape, wherein pathogenic variants dysregulate the immune response.
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Affiliation(s)
- Jingdian Zhang
- Department of Medical Biochemistry and Biophysics, and
- Max Planck Institute Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Camilla Koolmeister
- Department of Medical Biochemistry and Biophysics, and
- Max Planck Institute Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Jinming Han
- Applied Immunology and Immunotherapy, Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Roberta Filograna
- Department of Medical Biochemistry and Biophysics, and
- Max Planck Institute Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Monika Àdori
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Daniel J. Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Sina Teifel
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Shreekara Gopalakrishna
- Department of Medical Biochemistry and Biophysics, and
- Max Planck Institute Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Qiuya Shao
- Department of Medical Biochemistry and Biophysics, and
- Max Planck Institute Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Yong Liu
- Department of Medical Biochemistry and Biophysics, and
- Max Planck Institute Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Keying Zhu
- Applied Immunology and Immunotherapy, Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Robert A. Harris
- Applied Immunology and Immunotherapy, Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Gerald McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Mike Aoun
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Liselotte Bäckdahl
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Rikard Holmdahl
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Marcin Pekalski
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Anna Wedell
- Max Planck Institute Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Center for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Martin Engvall
- Center for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Wredenberg
- Department of Medical Biochemistry and Biophysics, and
- Max Planck Institute Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
- Center for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | | | - Xaquin Castro Dopico
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, and
- Max Planck Institute Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
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Liu M, Liang Z, Cheng ZJ, Liu L, Liu Q, Mai Y, Chen H, Lei B, Yu S, Chen H, Zheng P, Sun B. SARS-CoV-2 neutralising antibody therapies: Recent advances and future challenges. Rev Med Virol 2023; 33:e2464. [PMID: 37322826 DOI: 10.1002/rmv.2464] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 05/01/2023] [Accepted: 05/30/2023] [Indexed: 06/17/2023]
Abstract
The COVID-19 pandemic represents an unparalleled global public health crisis. Despite concerted research endeavours, the repertoire of effective treatment options remains limited. However, neutralising-antibody-based therapies hold promise across an array of practices, encompassing the prophylaxis and management of acute infectious diseases. Presently, numerous investigations into COVID-19-neutralising antibodies are underway around the world, with some studies reaching clinical application stages. The advent of COVID-19-neutralising antibodies signifies the dawn of an innovative and promising strategy for treatment against SARS-CoV-2 variants. Comprehensively, our objective is to amalgamate contemporary understanding concerning antibodies targeting various regions, including receptor-binding domain (RBD), non-RBD, host cell targets, and cross-neutralising antibodies. Furthermore, we critically examine the prevailing scientific literature supporting neutralising antibody-based interventions, and also delve into the functional evaluation of antibodies, with a particular focus on in vitro (vivo) assays. Lastly, we identify and consider several pertinent challenges inherent to the realm of COVID-19-neutralising antibody-based treatments, offering insights into potential future directions for research and development.
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Affiliation(s)
- Mingtao Liu
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhiman Liang
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhangkai J Cheng
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Li Liu
- Guangzhou Medical University, Guangzhou, China
| | - Qiwen Liu
- Guangzhou Medical University, Guangzhou, China
| | - Yiyin Mai
- Guangzhou Medical University, Guangzhou, China
| | | | - Baoying Lei
- Guangzhou Medical University, Guangzhou, China
| | - Shangwei Yu
- Guangzhou Medical University, Guangzhou, China
| | - Huihui Chen
- Guangzhou Medical University, Guangzhou, China
| | - Peiyan Zheng
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Baoqing Sun
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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Song S, Shi Q. Interface-Based Design of High-Affinity Affibody Ligands for the Purification of RBD from Spike Proteins. Molecules 2023; 28:6358. [PMID: 37687186 PMCID: PMC10489752 DOI: 10.3390/molecules28176358] [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: 07/25/2023] [Revised: 08/17/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
The outbreak of coronavirus disease 2019 (COVID-19) has sparked an urgent demand for advanced diagnosis and vaccination worldwide. The discovery of high-affinity ligands is of great significance for vaccine and diagnostic reagent manufacturing. Targeting the receptor binding domain (RBD) from the spike protein of severe acute respiratory syndrome-coronavirus 2, an interface at the outer surface of helices on the Z domain from protein A was introduced to construct a virtual library for the screening of ZRBD affibody ligands. Molecular docking was performed using HADDOCK software, and three potential ZRBD affibodies, ZRBD-02, ZRBD-04, and ZRBD-07, were obtained. Molecular dynamics (MD) simulation verified that the binding of ZRBD affibodies to RBD was driven by electrostatic interactions. Per-residue free energy decomposition analysis further substantiated that four residues with negative-charge characteristics on helix α1 of the Z domain participated in this process. Binding affinity analysis by microscale thermophoresis showed that ZRBD affibodies had high affinity for RBD binding, and the lowest dissociation constant was 36.3 nmol/L for ZRBD-07 among the three potential ZRBD affibodies. Herein, ZRBD-02 and ZRBD-07 affibodies were selected for chromatographic verifications after being coupled to thiol-activated Sepharose 6 Fast Flow (SepFF) gel. Chromatographic experiments showed that RBD could bind on both ZRBD SepFF gels and was eluted by 0.1 mol/L NaOH. Moreover, the ZRBD-07 SepFF gel had a higher affinity for RBD. This research provided a new idea for the design of affibody ligands and validated the potential of affibody ligands in the application of RBD purification from complex feedstock.
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Affiliation(s)
- Siyuan Song
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
| | - Qinghong Shi
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
- Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
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Kunz S, Durandy M, Seguin L, Feral CC. NANOBODY ® Molecule, a Giga Medical Tool in Nanodimensions. Int J Mol Sci 2023; 24:13229. [PMID: 37686035 PMCID: PMC10487883 DOI: 10.3390/ijms241713229] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
Although antibodies remain the most widely used tool for biomedical research, antibody technology is not flawless. Innovative alternatives, such as Nanobody® molecules, were developed to address the shortcomings of conventional antibodies. Nanobody® molecules are antigen-binding variable-domain fragments derived from the heavy-chain-only antibodies of camelids (VHH) and combine the advantageous properties of small molecules and monoclonal antibodies. Nanobody® molecules present a small size (~15 kDa, 4 nm long and 2.5 nm wide), high solubility, stability, specificity, and affinity, ease of cloning, and thermal and chemical resistance. Recombinant production in microorganisms is cost-effective, and VHH are also building blocks for multidomain constructs. These unique features led to numerous applications in fundamental research, diagnostics, and therapy. Nanobody® molecules are employed as biomarker probes and, when fused to radioisotopes or fluorophores, represent ideal non-invasive in vivo imaging agents. They can be used as neutralizing agents, receptor-ligand antagonists, or in targeted vehicle-based drug therapy. As early as 2018, the first Nanobody®, Cablivi (caplacizumab), a single-domain antibody (sdAb) drug developed by French pharmaceutical giant Sanofi for the treatment of adult patients with acquired thrombocytopenic purpura (aTTP), was launched. Nanobody® compounds are ideal tools for further development in clinics for diagnostic and therapeutic purposes.
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Affiliation(s)
- Sarah Kunz
- Université Côte d’Azur, CNRS UMR7284, INSERM U1081, IRCAN, 06107 Nice, France; (S.K.); (M.D.); (L.S.)
- Department of Oncology, Sanofi Research Center, 94400 Vitry-sur-Seine, France
| | - Manon Durandy
- Université Côte d’Azur, CNRS UMR7284, INSERM U1081, IRCAN, 06107 Nice, France; (S.K.); (M.D.); (L.S.)
| | - Laetitia Seguin
- Université Côte d’Azur, CNRS UMR7284, INSERM U1081, IRCAN, 06107 Nice, France; (S.K.); (M.D.); (L.S.)
| | - Chloe C. Feral
- Université Côte d’Azur, CNRS UMR7284, INSERM U1081, IRCAN, 06107 Nice, France; (S.K.); (M.D.); (L.S.)
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50
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Freeman SL, Oliveira ASF, Gallio AE, Rosa A, Simitakou MK, Arthur CJ, Mulholland AJ, Cherepanov P, Raven EL. Heme binding to the SARS-CoV-2 spike glycoprotein. J Biol Chem 2023; 299:105014. [PMID: 37414149 PMCID: PMC10416065 DOI: 10.1016/j.jbc.2023.105014] [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: 04/11/2023] [Revised: 06/12/2023] [Accepted: 07/01/2023] [Indexed: 07/08/2023] Open
Abstract
The target for humoral immunity, SARS-CoV-2 spike glycoprotein, has become the focus of vaccine research and development. Previous work demonstrated that the N-terminal domain (NTD) of SARS-CoV-2 spike binds biliverdin-a product of heme catabolism-causing a strong allosteric effect on the activity of a subset of neutralizing antibodies. Herein, we show that the spike glycoprotein is also able to bind heme (KD = 0.5 ± 0.2 μM). Molecular modeling indicated that the heme group fits well within the same pocket on the SARS-CoV-2 spike NTD. Lined by aromatic and hydrophobic residues (W104, V126, I129, F192, F194, I203, and L226), the pocket provides a suitable environment to stabilize the hydrophobic heme. Mutagenesis of N121 has a substantive effect on heme binding (KD = 3000 ± 220 μM), confirming the pocket as a major heme binding location of the viral glycoprotein. Coupled oxidation experiments in the presence of ascorbate indicated that the SARS-CoV-2 glycoprotein can catalyze the slow conversion of heme to biliverdin. The heme trapping and oxidation activities of the spike may allow the virus to reduce levels of free heme during infection to facilitate evasion of the adaptive and innate immunity.
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Affiliation(s)
- Samuel L Freeman
- School of Chemistry, Cantock's Close, University of Bristol, Bristol, United Kingdom
| | - A Sofia F Oliveira
- School of Chemistry, Cantock's Close, University of Bristol, Bristol, United Kingdom
| | - Andrea E Gallio
- School of Chemistry, Cantock's Close, University of Bristol, Bristol, United Kingdom
| | - Annachiara Rosa
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Maria K Simitakou
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Christopher J Arthur
- School of Chemistry, Cantock's Close, University of Bristol, Bristol, United Kingdom
| | - Adrian J Mulholland
- School of Chemistry, Cantock's Close, University of Bristol, Bristol, United Kingdom
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom; Department of Infectious Disease, St-Mary's Campus, Imperial College London, United Kingdom.
| | - Emma L Raven
- School of Chemistry, Cantock's Close, University of Bristol, Bristol, United Kingdom.
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