1
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Zure D, David Kuo HW, Drizo A. Insights of phytoremediation mechanisms for viruses based on in-vitro, in-vivo and in-silico assessments of selected herbal plants. CHEMOSPHERE 2024; 351:141101. [PMID: 38171396 DOI: 10.1016/j.chemosphere.2023.141101] [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: 10/06/2023] [Revised: 12/24/2023] [Accepted: 12/31/2023] [Indexed: 01/05/2024]
Abstract
Waterborne pathogenic viruses present unrelenting challenges to the global health and wastewater treatment industry. Phytoremediation offers promising solutions for wastewater treatment through plant-based technologies. This study investigated antiviral mechanisms in-vivo using bacteriophages MS2 and T4 as surrogates for effective herbs screened in-vitro from three embryophytes (Ocimum basilicum, Mentha sp., Plectranthus amboinicus), two macrophytes (Eichhornia crassipes, Pistia stratiotes) and a perennial grass (Cyperus rotundas). In-silico virtual screening predicted antiviral phytochemicals for further antiviral potency assessment. Results suggested in-vitro antiviral activities of embryophytes and macrophytes were higher (43-62%) than grass (21-26%). O. basilicum (OB, 57-62%) and P. stratiotes (PS, 59-60%) exhibited the highest antiviral activities. In-vivo tests showed notable virus reduction (>60%) in culture solution, attributed to rhizofiltration (66-74%) and phytoinactivation/phytodegradation (63-84%). In-silico analysis identified rutin as a primary antiviral phytochemical for MS2 (-9.7 kcal/mol) and T4 (-10.9 kcal/mol), correlating with dose-response inactivation (∼58-62%). In-vivo tests suggested additional phytocompounds may contribute to viral inactivation, presenting new opportunities for herb-based wastewater treatment solutions. Consequently, this study not only demonstrates the antiviral capabilities of OB and PS but also introduces an innovative approach for addressing viral contaminants in water.
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Affiliation(s)
- Diaiti Zure
- Department of Environmental Science and Engineering
| | | | - Aleksandra Drizo
- Sustainable Science and Management Program, Tunghai University, Taiwan
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2
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Malá Z, Vojta M, Loskot J, Sleha R, Ježek B, Zelenka J. Analysis of SARS-CoV-2 interactions with the Vero cell lines by scanning electron microscopy. J Biol Phys 2023; 49:383-392. [PMID: 37389665 PMCID: PMC10397163 DOI: 10.1007/s10867-023-09638-y] [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: 08/31/2022] [Accepted: 06/03/2023] [Indexed: 07/01/2023] Open
Abstract
In this study, scanning electron microscopy (SEM) was used to study the cell structure of SARS-CoV-2 infected cells. Our measurements revealed infection remodeling caused by infection, including the emergence of new specialized areas where viral morphogenesis occurs at the cell membrane. Intercellular extensions for viral cell surfing have also been observed. Our results expand knowledge of SARS-CoV-2 interactions with cells, its spread from cell to cell, and their size distribution. Our findings suggest that SEM is a useful microscopic method for intracellular ultrastructure analysis of cells exhibiting specific surface modifications that could also be applied to studying other important biological processes.
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Affiliation(s)
- Zuzana Malá
- Department of Physics, Faculty of Science, University of Hradec Králové, Rokitanského 62, Hradec Králové, 500 03, Czech Republic.
| | - Marek Vojta
- Department of Physics, Faculty of Science, University of Hradec Králové, Rokitanského 62, Hradec Králové, 500 03, Czech Republic
| | - Jan Loskot
- Department of Physics, Faculty of Science, University of Hradec Králové, Rokitanského 62, Hradec Králové, 500 03, Czech Republic
| | - Radek Sleha
- Department of Epidemiology, University of Defencein Brno, Třebešská, 1575, 500 02, Czech Republic
| | - Bruno Ježek
- Department of Informatics and Quantitative Methods, University of Hradec Králové, Rokitanského 62, Hradec Králové, 500 03, Czech Republic
| | - Josef Zelenka
- Department of Recreology and Tourism, University of Hradec Králové, Rokitanského 62, Hradec Králové, 500 03, Czech Republic
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3
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Hristova SH, Zhivkov AM. Omicron Coronavirus: pH-Dependent Electrostatic Potential and Energy of Association of Spike Protein to ACE2 Receptor. Viruses 2023; 15:1752. [PMID: 37632094 PMCID: PMC10460073 DOI: 10.3390/v15081752] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
The association of the S-protein of the SARS-CoV-2 beta coronavirus to ACE2 receptors of the human epithelial cells determines its contagiousness and pathogenicity. We computed the pH-dependent electric potential on the surface of the interacting globular proteins and pH-dependent Gibbs free energy at the association of the wild-type strain and the omicron variant. The calculated isoelectric points of the ACE2 receptor (pI 5.4) and the S-protein in trimeric form (pI 7.3, wild type), (pI 7.8, omicron variant), experimentally verified by isoelectric focusing, show that at pH 6-7, the S1-ACE2 association is conditioned by electrostatic attraction of the oppositely charged receptor and viral protein. The comparison of the local electrostatic potentials of the omicron variant and the wild-type strain shows that the point mutations alter the electrostatic potential in a relatively small area on the surface of the receptor-binding domain (RBD) of the S1 subunit. The appearance of seven charge-changing point mutations in RBD (equivalent to three additional positive charges) leads to a stronger S1-ACE2 association at pH 5.5 (typical for the respiratory tract) and a weaker one at pH 7.4 (characteristic of the blood plasma); this reveals the reason for the higher contagiousness but lower pathogenicity of the omicron variant in comparison to the wild-type strain.
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Affiliation(s)
- Svetlana H. Hristova
- Department of Medical Physics and Biophysics, Medical Faculty, Medical University—Sofia, Zdrave Str. 2, 1431 Sofia, Bulgaria;
| | - Alexandar M. Zhivkov
- Institute of Physical Chemistry, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., bl. 11, 1113 Sofia, Bulgaria
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4
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Appadurai R, Koneru JK, Bonomi M, Robustelli P, Srivastava A. Clustering Heterogeneous Conformational Ensembles of Intrinsically Disordered Proteins with t-Distributed Stochastic Neighbor Embedding. J Chem Theory Comput 2023; 19:4711-4727. [PMID: 37338049 PMCID: PMC11108026 DOI: 10.1021/acs.jctc.3c00224] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Intrinsically disordered proteins (IDPs) populate a range of conformations that are best described by a heterogeneous ensemble. Grouping an IDP ensemble into "structurally similar" clusters for visualization, interpretation, and analysis purposes is a much-desired but formidable task, as the conformational space of IDPs is inherently high-dimensional and reduction techniques often result in ambiguous classifications. Here, we employ the t-distributed stochastic neighbor embedding (t-SNE) technique to generate homogeneous clusters of IDP conformations from the full heterogeneous ensemble. We illustrate the utility of t-SNE by clustering conformations of two disordered proteins, Aβ42, and α-synuclein, in their APO states and when bound to small molecule ligands. Our results shed light on ordered substates within disordered ensembles and provide structural and mechanistic insights into binding modes that confer specificity and affinity in IDP ligand binding. t-SNE projections preserve the local neighborhood information, provide interpretable visualizations of the conformational heterogeneity within each ensemble, and enable the quantification of cluster populations and their relative shifts upon ligand binding. Our approach provides a new framework for detailed investigations of the thermodynamics and kinetics of IDP ligand binding and will aid rational drug design for IDPs.
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Affiliation(s)
- Rajeswari Appadurai
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | | | - Massimiliano Bonomi
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry. CNRS UMR 3528, C3BI, CNRS USR 3756, Institut Pasteur, Paris, France
| | - Paul Robustelli
- Dartmouth College, Department of Chemistry, Hanover, NH, 03755, USA
| | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
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5
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Jugler C, Sun H, Nguyen K, Palt R, Felder M, Steinkellner H, Chen Q. A novel plant-made monoclonal antibody enhances the synergetic potency of an antibody cocktail against the SARS-CoV-2 Omicron variant. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:549-559. [PMID: 36403203 PMCID: PMC9946148 DOI: 10.1111/pbi.13970] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/06/2022] [Accepted: 11/12/2022] [Indexed: 06/01/2023]
Abstract
This study describes a novel, neutralizing monoclonal antibody (mAb), 11D7, discovered by mouse immunization and hybridoma generation, against the parental Wuhan-Hu-1 RBD of SARS-CoV-2. We further developed this mAb into a chimeric human IgG and recombinantly expressed it in plants to produce a mAb with human-like, highly homogenous N-linked glycans that has potential to impart greater potency and safety as a therapeutic. The epitope of 11D7 was mapped by competitive binding with well-characterized mAbs, suggesting that it is a Class 4 RBD-binding mAb that binds to the RBD outside the ACE2 binding site. Of note, 11D7 maintains recognition against the B.1.1.529 (Omicron) RBD, as well neutralizing activity. We also provide evidence that this novel mAb may be useful in providing additional synergy to established antibody cocktails, such as Evusheld™ containing the antibodies tixagevimab and cilgavimab, against the Omicron variant. Taken together, 11D7 is a unique mAb that neutralizes SARS-CoV-2 through a mechanism that is not typical among developed therapeutic mAbs and by being produced in ΔXFT Nicotiana benthamiana plants, highlights the potential of plants to be an economic and safety-friendly alternative platform for generating mAbs to address the evolving SARS-CoV-2 crisis.
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Affiliation(s)
- Collin Jugler
- The Biodesign InstituteArizona State UniversityTempeArizonaUSA
- School of Life SciencesArizona State UniversityTempeArizonaUSA
| | - Haiyan Sun
- The Biodesign InstituteArizona State UniversityTempeArizonaUSA
| | - Katherine Nguyen
- School of Molecular SciencesArizona State UniversityTempeArizonaUSA
| | - Roman Palt
- Department of Applied Genetics and Cell BiologyUniversity of Natural Resources and Life SciencesViennaAustria
| | | | - Herta Steinkellner
- Department of Applied Genetics and Cell BiologyUniversity of Natural Resources and Life SciencesViennaAustria
| | - Qiang Chen
- The Biodesign InstituteArizona State UniversityTempeArizonaUSA
- School of Life SciencesArizona State UniversityTempeArizonaUSA
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6
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Du J, Wu G, Chen Q, Yu C, Xu G, Liu A, Wang L. Fingerprinting trimeric SARS-CoV-2 RBD by capillary isoelectric focusing with whole-column imaging detection. Anal Biochem 2023; 663:115034. [PMID: 36586502 PMCID: PMC9794521 DOI: 10.1016/j.ab.2022.115034] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/20/2022] [Accepted: 12/27/2022] [Indexed: 12/29/2022]
Abstract
Because the spike (S) protein of the severe acute respiratory syndrome coronavirus (SARS-CoV) is the immunodominant antigen, the S protein and its receptor-binding domain (RBD) are both targets currently to be genetically engineered for designing the broad-spectrum vaccine. In theory, the expressed protein exists as a set of variants that are roughly the same but slightly different, which depends on the protein expression system. The variants can be phenotypically manifested as charge heterogeneity. Here, we attempted to depict the charge heterogeneity of the trimeric SARS-CoV-2 RBD by using capillary isoelectric focusing with whole-column imaging detection (cIEF-WCID). In its nature form, the electropherogram fingerprints of the trimeric RBD were presented under optimized experimental conditions. The peaks of matrix buffers can be fully distinguishable from peaks of trimeric RBD. The isoelectric point (pI) was determined to be within a range of 6.67-9.54 covering the theoretical pI of 9.02. The fingerprints of three batches of trimeric RBDs are completely the same, with the intra-batch and batch-to-batch relative standard deviations (RSDs) of both pI values and area percentage of each peak no more than 1.0%, indicating that the production process is stable and this method can be used to surveillance the batch-to-batch consistency. The fingerprint remained unchanged after incubating at 37 °C for 7 d and oxidizing by 0.015% H2O2. In addition, the fingerprint was destroyed when adjusting the pH value to higher than 10.0 but still stable when the pH was lower than 4.0. In summary, the cIEF-WCID fingerprint can be used for the identification, batch-to-batch consistency evaluation, and stability study of the trimeric SARS-CoV-2 RBD, as part of a quality control strategy during the potential vaccine production.
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Affiliation(s)
- Jialiang Du
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Division of Monoclonal Antibody Products, National Institutes for Food and Drug Control, Beijing, 102629, China
| | - Gang Wu
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Division of Monoclonal Antibody Products, National Institutes for Food and Drug Control, Beijing, 102629, China
| | - Quanyao Chen
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Division of Monoclonal Antibody Products, National Institutes for Food and Drug Control, Beijing, 102629, China,School of Pharmacy, Yantai University, Yantai, 264005, China
| | - Chuanfei Yu
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Division of Monoclonal Antibody Products, National Institutes for Food and Drug Control, Beijing, 102629, China
| | - Gangling Xu
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Division of Monoclonal Antibody Products, National Institutes for Food and Drug Control, Beijing, 102629, China
| | - Anhui Liu
- School of Pharmacy, Yantai University, Yantai, 264005, China
| | - Lan Wang
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Division of Monoclonal Antibody Products, National Institutes for Food and Drug Control, Beijing, 102629, China.
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7
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Lee M, Major M, Hong H. Distinct Conformations of SARS-CoV-2 Omicron Spike Protein and Its Interaction with ACE2 and Antibody. Int J Mol Sci 2023; 24:3774. [PMID: 36835186 PMCID: PMC9967551 DOI: 10.3390/ijms24043774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Since November 2021, Omicron has been the dominant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant that causes the coronavirus disease 2019 (COVID-19) and has continuously impacted human health. Omicron sublineages are still increasing and cause increased transmission and infection rates. The additional 15 mutations on the receptor binding domain (RBD) of Omicron spike proteins change the protein conformation, enabling the Omicron variant to evade neutralizing antibodies. For this reason, many efforts have been made to design new antigenic variants to induce effective antibodies in SARS-CoV-2 vaccine development. However, understanding the different states of Omicron spike proteins with and without external molecules has not yet been addressed. In this review, we analyze the structures of the spike protein in the presence and absence of angiotensin-converting enzyme 2 (ACE2) and antibodies. Compared to previously determined structures for the wildtype spike protein and other variants such as alpha, beta, delta, and gamma, the Omicron spike protein adopts a partially open form. The open-form spike protein with one RBD up is dominant, followed by the open-form spike protein with two RBD up, and the closed-form spike protein with the RBD down. It is suggested that the competition between antibodies and ACE2 induces interactions between adjacent RBDs of the spike protein, which lead to a partially open form of the Omicron spike protein. The comprehensive structural information of Omicron spike proteins could be helpful for the efficient design of vaccines against the Omicron variant.
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Affiliation(s)
- Myeongsang Lee
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Marian Major
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Huixiao Hong
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
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8
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Mishra S, Kundu N, Pramanick I, Kumar A, Chattopadhyay K, Dutta S. Structural insights into thermostable direct hemolysin of Vibrio parahaemolyticus using single-particle cryo-EM. Proteins 2023; 91:137-146. [PMID: 36000388 DOI: 10.1002/prot.26416] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 08/09/2022] [Accepted: 08/12/2022] [Indexed: 01/07/2023]
Abstract
Thermostable direct hemolysin (TDH) is a ~19 kDa, hemolytic pore-forming toxin from the gram-negative marine bacterium Vibrio parahaemolyticus, one of the causative agents of seafood-borne acute gastroenteritis and septicemia. Previous studies have established that TDH exists as a tetrameric assembly in physiological state; however, there is limited knowledge regarding the molecular arrangement of its disordered N-terminal region (NTR)-the absence of which has been shown to compromise TDH's hemolytic and cytotoxic abilities. In our current study, we have employed single-particle cryo-electron microscopy to resolve the solution-state structures of wild-type TDH and a TDH construct with deletion of the NTR (NTD), in order to investigate structural aspects of NTR on the overall tetrameric architecture. We observed that both TDH and NTD electron density maps, resolved at global resolutions of 4.5 and 4.2 Å, respectively, showed good correlation in their respective oligomeric architecture. Additionally, we were able to locate extra densities near the pore opening of TDH which might correspond to the disordered NTR. Surprisingly, under cryogenic conditions, we were also able to observe novel supramolecular assemblies of TDH tetramers, which we were able to resolve to 4.3 Å. We further investigated the tetrameric and inter-tetrameric interaction interfaces to elaborate upon the key residues involved in both TDH tetramers and TDH super assemblies. Our current structural study will aid in understanding the mechanistic aspects of this pore-forming toxin and the role of its disordered NTR in membrane interaction.
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Affiliation(s)
- Suman Mishra
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Nidhi Kundu
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab, India
| | - Ishika Pramanick
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Anil Kumar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Kausik Chattopadhyay
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab, India
| | - Somnath Dutta
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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9
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Li ZL, Buck M. Computational analysis of interior mutations of SARS-CoV-2 Spike protein suggest a balance of protein stability and S2: S1 separation propensity. Comput Struct Biotechnol J 2022; 20:6078-6086. [PMID: 36373151 PMCID: PMC9638846 DOI: 10.1016/j.csbj.2022.10.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
SARS-CoV-2 variants often include surface mutations in the Spike protein that are important for viruses to recognize host receptors and evade antibody neutralization. The Spike protein also has mutations in the interior of the protein likely to affect the Spike protein S1 - S2 subunit's separation propensity, the most important of which is the D614G mutation. Remarkably, the Omicron variant contains a large number of internal mutations at the S2: S1 interface, which have not been investigated yet. In this study, we examined the effects of such interfacial mutations on the S2: S1 and subunit domain interactions and on the subunit's dissociation process. We found that the interaction with S2 is mainly contributed by the three encapsulation domains, named INT, ED1 and ED2 of S1, which are sandwiched between the S1 RBD and N-terminal NTD domain. We found that D614 is the strongest contributor for the S2: S1 interaction which is greatly weakened by the D614G mutation. Surprisingly, we found that, mutations T547K, H655Y, N764K, N856K, N969K, L981F in the Omicron variant largely enhance the S2: ED1 interaction, partially compensating the loss of S2: ED2 interaction due to the D614G mutation. Lastly, these results, together with biological considerations, allow us to suggest that in addition to the binding strength of between the RBD and ACE2, the stability of the Spike protein and the propensity of Spike protein S2: S1 separation are critical factors which likely exist in a balance for a particular infectivity and pathogenicity of the virus.
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Affiliation(s)
- Zhen-lu Li
- School of Life Science, Tianjin University, Tianjin 300072, China
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Pharmacology, Department of Neurosciences, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
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10
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Khatri B, Pramanick I, Malladi SK, Rajmani RS, Kumar S, Ghosh P, Sengupta N, Rahisuddin R, Kumar N, Kumaran S, Ringe RP, Varadarajan R, Dutta S, Chatterjee J. A dimeric proteomimetic prevents SARS-CoV-2 infection by dimerizing the spike protein. Nat Chem Biol 2022; 18:1046-1055. [PMID: 35654847 PMCID: PMC9512702 DOI: 10.1038/s41589-022-01060-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 05/10/2022] [Indexed: 11/17/2022]
Abstract
Protein tertiary structure mimetics are valuable tools to target large protein-protein interaction interfaces. Here, we demonstrate a strategy for designing dimeric helix-hairpin motifs from a previously reported three-helix-bundle miniprotein that targets the receptor-binding domain (RBD) of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). Through truncation of the third helix and optimization of the interhelical loop residues of the miniprotein, we developed a thermostable dimeric helix-hairpin. The dimeric four-helix bundle competes with the human angiotensin-converting enzyme 2 (ACE2) in binding to RBD with 2:2 stoichiometry. Cryogenic-electron microscopy revealed the formation of dimeric spike ectodomain trimer by the four-helix bundle, where all the three RBDs from either spike protein are attached head-to-head in an open conformation, revealing a novel mechanism for virus neutralization. The proteomimetic protects hamsters from high dose viral challenge with replicative SARS-CoV-2 viruses, demonstrating the promise of this class of peptides that inhibit protein-protein interaction through target dimerization.
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Affiliation(s)
- Bhavesh Khatri
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bangalore, India
| | - Ishika Pramanick
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bangalore, India
| | | | - Raju S Rajmani
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bangalore, India
| | - Sahil Kumar
- Virology Unit, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Pritha Ghosh
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bangalore, India
| | - Nayanika Sengupta
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bangalore, India
| | - R Rahisuddin
- Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Narender Kumar
- Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - S Kumaran
- Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Rajesh P Ringe
- Virology Unit, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | | | - Somnath Dutta
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bangalore, India.
| | - Jayanta Chatterjee
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bangalore, India.
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11
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Pipitò L, Rujan R, Reynolds CA, Deganutti G. Molecular dynamics studies reveal structural and functional features of the SARS-CoV-2 spike protein. Bioessays 2022; 44:e2200060. [PMID: 35843871 PMCID: PMC9350306 DOI: 10.1002/bies.202200060] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 06/21/2022] [Accepted: 07/01/2022] [Indexed: 12/23/2022]
Abstract
The SARS-CoV-2 virus is responsible for the COVID-19 pandemic the world experience since 2019. The protein responsible for the first steps of cell invasion, the spike protein, has probably received the most attention in light of its central role during infection. Computational approaches are among the tools employed by the scientific community in the enormous effort to study this new affliction. One of these methods, namely molecular dynamics (MD), has been used to characterize the function of the spike protein at the atomic level and unveil its structural features from a dynamic perspective. In this review, we focus on these main findings, including spike protein flexibility, rare S protein conformational changes, cryptic epitopes, the role of glycans, drug repurposing, and the effect of spike protein variants.
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Affiliation(s)
- Ludovico Pipitò
- Centre for Sport, Exercise and Life Sciences (CSELS)Faculty of Health and Life SciencesCoventry UniversityCoventryUK
| | - Roxana‐Maria Rujan
- Centre for Sport, Exercise and Life Sciences (CSELS)Faculty of Health and Life SciencesCoventry UniversityCoventryUK
| | - Christopher A. Reynolds
- Centre for Sport, Exercise and Life Sciences (CSELS)Faculty of Health and Life SciencesCoventry UniversityCoventryUK
| | - Giuseppe Deganutti
- Centre for Sport, Exercise and Life Sciences (CSELS)Faculty of Health and Life SciencesCoventry UniversityCoventryUK
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12
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Bandyopadhyay P, Pramanick I, Biswas R, PS S, Sreedharan S, Singh S, Rajmani RS, Laxman S, Dutta S, Singh A. S-Adenosylmethionine-responsive cystathionine β-synthase modulates sulfur metabolism and redox balance in Mycobacterium tuberculosis. SCIENCE ADVANCES 2022; 8:eabo0097. [PMID: 35749503 PMCID: PMC9232105 DOI: 10.1126/sciadv.abo0097] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 05/09/2022] [Indexed: 05/10/2023]
Abstract
Methionine and cysteine metabolisms are important for the survival and pathogenesis of Mycobacterium tuberculosis (Mtb). The transsulfuration pathway converts methionine to cysteine and represents an important link between antioxidant and methylation metabolism in diverse organisms. Using a combination of biochemistry and cryo-electron microscopy, we characterized the first enzyme of the transsulfuration pathway, cystathionine β-synthase (MtbCbs) in Mtb. We demonstrated that MtbCbs is a heme-less, pyridoxal-5'-phosphate-containing enzyme, allosterically activated by S-adenosylmethionine (SAM). The atomic model of MtbCbs in its native and SAM-bound conformations revealed a unique mode of SAM-dependent allosteric activation. Further, SAM stabilized MtbCbs by sterically occluding proteasomal degradation, which was crucial for supporting methionine and redox metabolism in Mtb. Genetic deficiency of MtbCbs reduced Mtb survival upon homocysteine overload in vitro, inside macrophages, and in mice coinfected with HIV. Thus, the MtbCbs-SAM axis constitutes an important mechanism of coordinating sulfur metabolism in Mtb.
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Affiliation(s)
- Parijat Bandyopadhyay
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka 560012, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Ishika Pramanick
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Rupam Biswas
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Sabarinath PS
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, Karnataka 560065, India
| | - Sreesa Sreedharan
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, Karnataka 560065, India
| | - Shalini Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka 560012, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Raju S. Rajmani
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, Karnataka 560065, India
| | - Somnath Dutta
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Amit Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka 560012, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, Karnataka 560012, India
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13
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Potential for a Plant-Made SARS-CoV-2 Neutralizing Monoclonal Antibody as a Synergetic Cocktail Component. Vaccines (Basel) 2022; 10:vaccines10050772. [PMID: 35632528 PMCID: PMC9145534 DOI: 10.3390/vaccines10050772] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/08/2022] [Accepted: 05/11/2022] [Indexed: 01/27/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a public health crisis over the last two years. Monoclonal antibody (mAb)-based therapeutics against the spike (S) protein have been shown to be effective treatments for SARS-CoV-2 infection, especially the original viral strain. However, the current mAbs produced in mammalian cells are expensive and might be unaffordable for many. Furthermore, the emergence of variants of concern demands the development of strategies to prevent mutant escape from mAb treatment. Using a cocktail of mAbs that bind to complementary neutralizing epitopes is one such strategy. In this study, we use Nicotiana benthamiana plants in an effort to expedite the development of efficacious and affordable antibody cocktails against SARS-CoV-2. We show that two mAbs can be highly expressed in plants and are correctly assembled into IgG molecules. Moreover, they retain target epitope recognition and, more importantly, neutralize multiple SARS-CoV-2 variants. We also show that one plant-made mAb has neutralizing synergy with other mAbs that we developed in hybridomas. This is the first report of a plant-made mAb to be assessed as a potential component of a SARS-CoV-2 neutralizing cocktail. This work may offer a strategy for using plants to quickly develop mAb cocktail-based therapeutics against emerging viral diseases with high efficacy and low costs.
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14
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Sakuma C, Nakagawa M, Tomioka Y, Maruyama T, Entzminger K, Fleming JK, Shibata T, Kurosawa Y, Okumura CJ, Arakawa T, Akuta T. Western blotting of native proteins from agarose gels. Biotechniques 2022; 72:207-218. [PMID: 35383476 DOI: 10.2144/btn-2022-0012] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We have developed a new Western blotting method of native proteins from agarose-based gel electrophoresis using a buffer at pH 6.1 containing basic histidine and acidic 2-(N-morpholino)ethanesulfonic acid. This gel electrophoresis successfully provided native structures for a variety of proteins and macromolecular complexes. This paper is focused on the Western blotting of native protein bands separated on agarose gels. Two blotting methods from agarose gel to PVDF membrane are introduced here, one by contact (diffusion) blotting and another by electroblotting after pre-treating the agarose gels with SDS. The contact blotting resulted in the transfer of native GFP, native human plexin domain containing protein 2 (PLXDC2) and native SARS-CoV-2 spike protein, which were detected by conformation-specific antibodies generated in-house.
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Affiliation(s)
- Chiaki Sakuma
- Research & Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki, 318-0004, Japan
| | - Masataka Nakagawa
- Research & Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki, 318-0004, Japan
| | - Yui Tomioka
- Research & Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki, 318-0004, Japan
| | - Toshiaki Maruyama
- Abwiz Bio Inc., 9823 Pacific Heights Blvd, suite J, San Diego, CA 9212, USA
| | - Kevin Entzminger
- Abwiz Bio Inc., 9823 Pacific Heights Blvd, suite J, San Diego, CA 9212, USA
| | - Jonathan K Fleming
- Abwiz Bio Inc., 9823 Pacific Heights Blvd, suite J, San Diego, CA 9212, USA
| | - Takashi Shibata
- Research & Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki, 318-0004, Japan
| | - Yasunori Kurosawa
- Research & Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki, 318-0004, Japan.,Abwiz Bio Inc., 9823 Pacific Heights Blvd, suite J, San Diego, CA 9212, USA
| | - C J Okumura
- Abwiz Bio Inc., 9823 Pacific Heights Blvd, suite J, San Diego, CA 9212, USA
| | - Tsutomu Arakawa
- Alliance Protein Laboratories, 13380 Pantera Rd, San Diego, CA 92130, USA
| | - Teruo Akuta
- Research & Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki, 318-0004, Japan
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15
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Dokainish HM, Re S, Mori T, Kobayashi C, Jung J, Sugita Y. The inherent flexibility of receptor binding domains in SARS-CoV-2 spike protein. eLife 2022; 11:e75720. [PMID: 35323112 PMCID: PMC8963885 DOI: 10.7554/elife.75720] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 03/15/2022] [Indexed: 12/17/2022] Open
Abstract
Spike (S) protein is the primary antigenic target for neutralization and vaccine development for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It decorates the virus surface and undergoes large motions of its receptor binding domains (RBDs) to enter the host cell. Here, we observe Down, one-Up, one-Open, and two-Up-like structures in enhanced molecular dynamics simulations, and characterize the transition pathways via inter-domain interactions. Transient salt-bridges between RBDA and RBDC and the interaction with glycan at N343B support RBDA motions from Down to one-Up. Reduced interactions between RBDA and RBDB in one-Up induce RBDB motions toward two-Up. The simulations overall agree with cryo-electron microscopy structure distributions and FRET experiments and provide hidden functional structures, namely, intermediates along Down-to-one-Up transition with druggable cryptic pockets as well as one-Open with a maximum exposed RBD. The inherent flexibility of S-protein thus provides essential information for antiviral drug rational design or vaccine development.
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Grants
- FLAGSHIP 2020 project Ministry of Education, Culture, Sports, Science and Technology
- 19K06532 Ministry of Education, Culture, Sports, Science and Technology
- Dynamic Structural Biology/Glycolipidologue Initiative/Biology of Intracellular Environments RIKEN
- Priority Issue on Post-K computer Ministry of Education, Culture, Sports, Science and Technology
- Program for Promoting Researches on the Supercomputer Fugaku Ministry of Education, Culture, Sports, Science and Technology
- JPMXP1020200101 Ministry of Education, Culture, Sports, Science and Technology
- JPMXP1020200201 Ministry of Education, Culture, Sports, Science and Technology
- 19H05645 Ministry of Education, Culture, Sports, Science and Technology
- 21H05249 Ministry of Education, Culture, Sports, Science and Technology
- 20K15737 Ministry of Education, Culture, Sports, Science and Technology
- 19K12229 Ministry of Education, Culture, Sports, Science and Technology
- 21H05157 Ministry of Education, Culture, Sports, Science and Technology
- hp200135 HPCI System Research project
- hp200153 HPCI System Research project
- hp200028 HPCI System Research project
- hp210107 HPCI System Research project
- hp210177 HPCI System Research project
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Affiliation(s)
- Hisham M Dokainish
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering ResearchWakoJapan
| | - Suyong Re
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and NutritionOsakaJapan
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics ResearchKobeJapan
| | - Takaharu Mori
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering ResearchWakoJapan
| | - Chigusa Kobayashi
- Computational Biophysics Research Team, RIKEN Center for Computational ScienceKobeJapan
| | - Jaewoon Jung
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering ResearchWakoJapan
- Computational Biophysics Research Team, RIKEN Center for Computational ScienceKobeJapan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering ResearchWakoJapan
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics ResearchKobeJapan
- Computational Biophysics Research Team, RIKEN Center for Computational ScienceKobeJapan
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16
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Dobrynin D, Polishchuk I, Portal L, Zlotver I, Sosnik A, Pokroy B. Adsorption of SARS CoV-2 spike proteins on various functionalized surfaces correlates with the high transmissibility of Delta and Omicron variants. Mater Today Bio 2022; 14:100265. [PMID: 35465145 PMCID: PMC9017064 DOI: 10.1016/j.mtbio.2022.100265] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/11/2022] [Accepted: 04/14/2022] [Indexed: 12/12/2022] Open
Abstract
The SARS-CoV-2 virus emerged at the end of 2019 and rapidly developed several mutated variants, specifically the Delta and Omicron, which demonstrate higher transmissibility and escalating infection cases worldwide. The dominant transmission pathway of this virus is via human-to-human contact and aerosols which once inhaled interact with the mucosal tissue, but another possible route is through contact with surfaces contaminated with SARS-CoV-2, often exhibiting long-term survival. Here we compare the adsorption capacities of the S1 and S2 subunits of the spike (S) protein from the original variant to that of the S1 subunit from the Delta and Omicron variants on self-assembled monolayers by Quartz Crystal Microbalance. The results clearly show a significant difference in adsorption capacity between the different variants, as well as between the S1 and S2 subunits. Overall, our study demonstrates that while the Omicron variant is able to adsorb much more successfully than the Delta, both variants show enhanced adsorption capacity than that of the original strain. We also examined the influence of pH conditions on the adsorption ability of the S1 subunit and found that adsorption was strongest at pH 7.4, which is the physiological pH. The main conclusion of this study is that there is a strong correlation between the adsorption capacity and the transmissibility of the various SARS-CoV-2 variants.
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Affiliation(s)
- Daniela Dobrynin
- Bio-Inspired Surface Engineering and Biomineralization Lab, Department of Materials Science and Engineering, Technion – Israel Institute of Technology, 32000, Haifa, Israel
| | - Iryna Polishchuk
- Bio-Inspired Surface Engineering and Biomineralization Lab, Department of Materials Science and Engineering, Technion – Israel Institute of Technology, 32000, Haifa, Israel
| | - Lotan Portal
- Bio-Inspired Surface Engineering and Biomineralization Lab, Department of Materials Science and Engineering, Technion – Israel Institute of Technology, 32000, Haifa, Israel
| | - Ivan Zlotver
- Laboratory of Pharmaceutical Nanomaterials Science, Department of Materials Science and Engineering, Technion – Israel Institute of Technology, 32000, Haifa, Israel
| | - Alejandro Sosnik
- Laboratory of Pharmaceutical Nanomaterials Science, Department of Materials Science and Engineering, Technion – Israel Institute of Technology, 32000, Haifa, Israel
| | - Boaz Pokroy
- Bio-Inspired Surface Engineering and Biomineralization Lab, Department of Materials Science and Engineering, Technion – Israel Institute of Technology, 32000, Haifa, Israel
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17
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Hwang YC, Lu RM, Su SC, Chiang PY, Ko SH, Ke FY, Liang KH, Hsieh TY, Wu HC. Monoclonal antibodies for COVID-19 therapy and SARS-CoV-2 detection. J Biomed Sci 2022; 29:1. [PMID: 34983527 PMCID: PMC8724751 DOI: 10.1186/s12929-021-00784-w] [Citation(s) in RCA: 131] [Impact Index Per Article: 65.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 12/20/2021] [Indexed: 02/07/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is an exceptional public health crisis that demands the timely creation of new therapeutics and viral detection. Owing to their high specificity and reliability, monoclonal antibodies (mAbs) have emerged as powerful tools to treat and detect numerous diseases. Hence, many researchers have begun to urgently develop Ab-based kits for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Ab drugs for use as COVID-19 therapeutic agents. The detailed structure of the SARS-CoV-2 spike protein is known, and since this protein is key for viral infection, its receptor-binding domain (RBD) has become a major target for therapeutic Ab development. Because SARS-CoV-2 is an RNA virus with a high mutation rate, especially under the selective pressure of aggressively deployed prophylactic vaccines and neutralizing Abs, the use of Ab cocktails is expected to be an important strategy for effective COVID-19 treatment. Moreover, SARS-CoV-2 infection may stimulate an overactive immune response, resulting in a cytokine storm that drives severe disease progression. Abs to combat cytokine storms have also been under intense development as treatments for COVID-19. In addition to their use as drugs, Abs are currently being utilized in SARS-CoV-2 detection tests, including antigen and immunoglobulin tests. Such Ab-based detection tests are crucial surveillance tools that can be used to prevent the spread of COVID-19. Herein, we highlight some key points regarding mAb-based detection tests and treatments for the COVID-19 pandemic.
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Affiliation(s)
- Yu-Chyi Hwang
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Ruei-Min Lu
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529, Taiwan
| | - Shih-Chieh Su
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Pao-Yin Chiang
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529, Taiwan
| | - Shih-Han Ko
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529, Taiwan
| | - Feng-Yi Ke
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529, Taiwan
| | - Kang-Hao Liang
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529, Taiwan
| | - Tzung-Yang Hsieh
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Han-Chung Wu
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan.
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529, Taiwan.
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18
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Abstract
Cryogenic electron microscopy (cryo-EM) has revolutionized the field of structural biology, particularly in solving the structures of large protein complexes or cellular machineries that play important biological functions. This review focuses on the contribution and future potential of cryo-EM in related emerging applications-enzymatic mechanisms and dynamic processes. Work on these subjects can benefit greatly from the capability of cryo-EM to solve the structures of specific protein complexes in multiple conditions, including variations in the buffer condition, ligands, and temperature, and to capture multiple conformational states, conformational change intermediates, and reaction intermediates. These studies can expand the structural landscape of specific proteins or protein complexes in multiple dimensions and drive new advances in the fields of enzymology and dynamic processes. The advantages and complementarity of cryo-EM relative to X-ray crystallography and nuclear magnetic resonance with regard to these applications are also addressed. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; .,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Wen-Jin Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan;
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; .,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
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19
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Abdalla M, Eltayb WA, El-Arabey AA, Singh K, Jiang X. Molecular dynamic study of SARS-CoV-2 with various S protein mutations and their effect on thermodynamic properties. Comput Biol Med 2021; 141:105025. [PMID: 34772510 PMCID: PMC8576119 DOI: 10.1016/j.compbiomed.2021.105025] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/05/2021] [Accepted: 11/07/2021] [Indexed: 11/30/2022]
Abstract
Studying the structure of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein is important to understand the infection process. The S protein is necessary in completing the virus life cycle and is responsible for the appearance of new variants and drug and vaccine resistance. Understanding the structure and dynamics of biological macromolecules is essential for understanding how they function. In this work, we investigated the effects of mutations on S protein stability and solubility through molecular dynamic (MD) simulation in a 100 ns (ns) period. We screened four variants in addition to the wild type (WT). Results show that changes on MD simulation parameters of S protein indicate fluctuations and changes in the conformation, especially in the area between 300 and 600 amino acids (aa). This provides us an image of how the virus protein can reshape itself to adapt to any changes that occur in human angiotensin-converting enzyme 2 or drugs that can target the protein region. Our results also show that the Brazil variant has high fluctuations and unstable folding at some stages compared with other variants.
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Affiliation(s)
- Mohnad Abdalla
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 Cultural West Road, Shandong Province, 250012, PR China.
| | - Wafa Ali Eltayb
- Biotechnology Department, Faculty of Science and Technology, Shendi University, Shendi, Nher Anile, Sudan
| | - Amr Ahmed El-Arabey
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt
| | - Kamal Singh
- Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Xinyi Jiang
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 Cultural West Road, Shandong Province, 250012, PR China.
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20
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Mariotti S, Capocefalo A, Chiantore MV, Iacobino A, Teloni R, De Angelis ML, Gallinaro A, Pirillo MF, Borghi M, Canitano A, Michelini Z, Baggieri M, Marchi A, Bucci P, McKay PF, Acchioni C, Sandini S, Sgarbanti M, Tosini F, Di Virgilio A, Venturi G, Marino F, Esposito V, Di Bonito P, Magurano F, Cara A, Negri D, Nisini R. Isolation and Characterization of Mouse Monoclonal Antibodies That Neutralize SARS-CoV-2 and Its Variants of Concern Alpha, Beta, Gamma and Delta by Binding Conformational Epitopes of Glycosylated RBD With High Potency. Front Immunol 2021; 12:750386. [PMID: 34764961 PMCID: PMC8576447 DOI: 10.3389/fimmu.2021.750386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/11/2021] [Indexed: 01/14/2023] Open
Abstract
Antibodies targeting Receptor Binding Domain (RBD) of SARS-CoV-2 have been suggested to account for the majority of neutralizing activity in COVID-19 convalescent sera and several neutralizing antibodies (nAbs) have been isolated, characterized and proposed as emergency therapeutics in the form of monoclonal antibodies (mAbs). However, SARS-CoV-2 variants are rapidly spreading worldwide from the sites of initial identification. The variants of concern (VOC) B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma) and B.1.167.2 (Delta) showed mutations in the SARS-CoV-2 spike protein potentially able to cause escape from nAb responses with a consequent reduction of efficacy of vaccines and mAbs-based therapy. We produced the recombinant RBD (rRBD) of SARS-CoV-2 spike glycoprotein from the Wuhan-Hu 1 reference sequence in a mammalian system, for mice immunization to isolate new mAbs with neutralizing activity. Here we describe four mAbs that were able to bind the rRBD in Enzyme-Linked Immunosorbent Assay and the transmembrane full-length spike protein expressed in HEK293T cells by flow cytometry assay. Moreover, the mAbs recognized the RBD in supernatants of SARS-CoV-2 infected VERO E6 cells by Western Blot under non-reducing condition or in supernatants of cells infected with lentivirus pseudotyped for spike protein, by immunoprecipitation assay. Three out of four mAbs lost their binding efficiency to completely N-deglycosylated rRBD and none was able to bind the same recombinant protein expressed in Escherichia coli, suggesting that the epitopes recognized by three mAbs are generated by the conformational structure of the glycosylated native protein. Of particular relevance, three mAbs were able to inhibit Wuhan SARS-CoV-2 infection of VERO E6 cells in a plaque-reduction neutralization test and the Wuhan SARS-CoV-2 as well as the Alpha, Beta, Gamma and Delta VOC in a pseudoviruses-based neutralization test. These mAbs represent important additional tools for diagnosis and therapy of COVID-19 and may contribute to the understanding of the functional structure of SARS-CoV-2 RBD.
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Affiliation(s)
- Sabrina Mariotti
- Dipartimento di Malattie infettive, Istituto Superiore di Sanità, Roma, Italy
| | - Antonio Capocefalo
- Dipartimento Sicurezza alimentare, nutrizione e sanità pubblica veterinaria, Istituto Superiore di Sanità, Roma, Italy
| | | | - Angelo Iacobino
- Dipartimento di Malattie infettive, Istituto Superiore di Sanità, Roma, Italy
| | - Raffaela Teloni
- Dipartimento di Malattie infettive, Istituto Superiore di Sanità, Roma, Italy
| | - Maria Laura De Angelis
- Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Roma, Italy
| | - Alessandra Gallinaro
- Centro nazionale per la salute globale, Istituto Superiore di Sanità, Roma, Italy
| | - Maria Franca Pirillo
- Centro nazionale per la salute globale, Istituto Superiore di Sanità, Roma, Italy
| | - Martina Borghi
- Dipartimento di Malattie infettive, Istituto Superiore di Sanità, Roma, Italy
| | - Andrea Canitano
- Centro nazionale per la salute globale, Istituto Superiore di Sanità, Roma, Italy
| | - Zuleika Michelini
- Centro nazionale per la salute globale, Istituto Superiore di Sanità, Roma, Italy
| | - Melissa Baggieri
- Dipartimento di Malattie infettive, Istituto Superiore di Sanità, Roma, Italy
| | - Antonella Marchi
- Dipartimento di Malattie infettive, Istituto Superiore di Sanità, Roma, Italy
| | - Paola Bucci
- Dipartimento di Malattie infettive, Istituto Superiore di Sanità, Roma, Italy
| | - Paul F. McKay
- Department of Infectious Disease, Imperial College, London, United Kingdom
| | - Chiara Acchioni
- Dipartimento di Malattie infettive, Istituto Superiore di Sanità, Roma, Italy
| | - Silvia Sandini
- Dipartimento di Malattie infettive, Istituto Superiore di Sanità, Roma, Italy
| | - Marco Sgarbanti
- Dipartimento di Malattie infettive, Istituto Superiore di Sanità, Roma, Italy
| | - Fabio Tosini
- Dipartimento di Malattie infettive, Istituto Superiore di Sanità, Roma, Italy
| | - Antonio Di Virgilio
- Centro per la sperimentazione ed il benessere animale, Istituto Superiore di Sanità, Roma, Italy
| | - Giulietta Venturi
- Dipartimento di Malattie infettive, Istituto Superiore di Sanità, Roma, Italy
| | - Francesco Marino
- Centro nazionale per il controllo e la valutazione dei farmaci, Istituto Superiore di Sanità, Roma, Italy
| | - Valeria Esposito
- Centro nazionale per il controllo e la valutazione dei farmaci, Istituto Superiore di Sanità, Roma, Italy
| | - Paola Di Bonito
- Dipartimento di Malattie infettive, Istituto Superiore di Sanità, Roma, Italy
| | - Fabio Magurano
- Dipartimento di Malattie infettive, Istituto Superiore di Sanità, Roma, Italy
| | - Andrea Cara
- Centro nazionale per la salute globale, Istituto Superiore di Sanità, Roma, Italy
| | - Donatella Negri
- Dipartimento di Malattie infettive, Istituto Superiore di Sanità, Roma, Italy
| | - Roberto Nisini
- Dipartimento di Malattie infettive, Istituto Superiore di Sanità, Roma, Italy
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21
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Lobo VR, Warwicker J. Predicted pH-dependent stability of SARS-CoV-2 spike protein trimer from interfacial acidic groups. Comput Struct Biotechnol J 2021; 19:5140-5148. [PMID: 34490059 PMCID: PMC8410215 DOI: 10.1016/j.csbj.2021.08.049] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 08/29/2021] [Accepted: 08/30/2021] [Indexed: 01/10/2023] Open
Abstract
Transition between receptor binding domain (RBD) up and down forms of the SARS-CoV-2 spike protein trimer is coupled to receptor binding and is one route by which variants can alter viral properties. It is becoming apparent that key roles in the transition are played by pH and a more compact closed form, termed locked. Calculations of pH-dependence are made for a large set of spike trimers, including locked form trimer structures that have recently become available. Several acidic sidechains become sufficiently buried in the locked form to give a predicted pH-dependence in the mild acidic range, with stabilisation of the locked form as pH reduces from 7.5 to 5, consistent with emerging characterisation by cryo-electron microscopy. The calculated pH effects in pre-fusion spike trimers are modulated mainly by aspartic acid residues, rather than the more familiar histidine role at mild acidic pH. These acidic sidechains are generally surface located and weakly interacting when not in a locked conformation. According to this model, their replacement (perhaps with asparagine) would remove the pH-dependent destabilisation of locked spike trimer conformations, and increase their recovery at neutral pH. This would provide an alternative or supplement to the insertion of disulphide linkages for stabilising spike protein trimers, with potential relevance for vaccine design.
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Affiliation(s)
- Vanessa R. Lobo
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Institute of Biotechnology, University of Manchester, M1 7DN, UK
| | - Jim Warwicker
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Institute of Biotechnology, University of Manchester, M1 7DN, UK
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