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Chrestia JF, Oliveira AS, Mulholland AJ, Gallagher T, Bermúdez I, Bouzat C. A Functional Interaction Between Y674-R685 Region of the SARS-CoV-2 Spike Protein and the Human α7 Nicotinic Receptor. Mol Neurobiol 2022; 59:6076-6090. [PMID: 35859025 PMCID: PMC9299415 DOI: 10.1007/s12035-022-02947-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/28/2022] [Indexed: 11/15/2022]
Abstract
The α7 nicotinic acetylcholine receptor (nAChR) is present in neuronal and non-neuronal cells and has anti-inflammatory actions. Molecular dynamics simulations suggested that α7 nAChR interacts with a region of the SARS-CoV-2 spike protein (S), and a potential contribution of nAChRs to COVID-19 pathophysiology has been proposed. We applied whole-cell and single-channel recordings to determine whether a peptide corresponding to the Y674-R685 region of the S protein can directly affect α7 nAChR function. The S fragment exerts a dual effect on α7. It activates α7 nAChRs in the presence of positive allosteric modulators, in line with our previous molecular dynamics simulations showing favourable binding of this accessible region of the S protein to the nAChR agonist binding site. The S fragment also exerts a negative modulation of α7, which is evidenced by a profound concentration-dependent decrease in the durations of openings and activation episodes of potentiated channels and in the amplitude of macroscopic responses elicited by ACh. Our study identifies a potential functional interaction between α7 nAChR and a region of the S protein, thus providing molecular foundations for further exploring the involvement of nAChRs in COVID-19 pathophysiology.
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Affiliation(s)
- Juan Facundo Chrestia
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), Camino La Carrindanga Km 7-8000, Bahía Blanca, Argentina
| | - Ana Sofia Oliveira
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | | | - Isabel Bermúdez
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK.
| | - Cecilia Bouzat
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), Camino La Carrindanga Km 7-8000, Bahía Blanca, Argentina.
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52
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Ligiero CBP, Fernandes TS, D'Amato DL, Gaspar FV, Duarte PS, Strauch MA, Fonseca JG, Meirelles LGR, Bento da Silva P, Azevedo RB, Aparecida de Souza Martins G, Archanjo BS, Buarque CD, Machado G, Percebom AM, Ronconi CM. Influence of particle size on the SARS-CoV-2 spike protein detection using IgG-capped gold nanoparticles and dynamic light scattering. Mater Today Chem 2022; 25:100924. [PMID: 35475288 PMCID: PMC9023328 DOI: 10.1016/j.mtchem.2022.100924] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/27/2022] [Accepted: 03/29/2022] [Indexed: 05/03/2023]
Abstract
Due to the unprecedented and ongoing nature of the coronavirus outbreak, the development of rapid immunoassays to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its highly contagious variants is an important and challenging task. Here, we report the development of polyclonal antibody-functionalized spherical gold nanoparticle biosensors as well as the influence of the nanoparticle sizes on the immunoassay response to detect the SARS-CoV-2 spike protein by dynamic light scattering. By monitoring the increment in the hydrodynamic diameter (ΔDH) by dynamic light scattering measurements in the antigen-antibody interaction, SARS-CoV-2 S-protein can be detected in only 5 min. The larger the nanoparticles, the larger ΔDH in the presence of spike protein. From adsorption isotherm, the calculated binding constant (K D ) was 83 nM and the estimated limit of detection was 13 ng/mL (30 pM). The biosensor was stable up to 90 days at 4 °C. Therefore, the biosensor developed in this work could be potentially applied as a fast and sensible immunoassay to detect SARS-CoV-2 infection in patient samples.
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Affiliation(s)
- C B P Ligiero
- Departamento de Química Inorgânica, Universidade Federal Fluminense (UFF), Campus Do Valonguinho, Outeiro de São João Batista, S/n, 24020-141, Niterói, RJ, Brazil
| | - T S Fernandes
- Departamento de Química Inorgânica, Universidade Federal Fluminense (UFF), Campus Do Valonguinho, Outeiro de São João Batista, S/n, 24020-141, Niterói, RJ, Brazil
| | - D L D'Amato
- Departamento de Química Inorgânica, Universidade Federal Fluminense (UFF), Campus Do Valonguinho, Outeiro de São João Batista, S/n, 24020-141, Niterói, RJ, Brazil
| | - F V Gaspar
- Departamento de Química Inorgânica, Universidade Federal Fluminense (UFF), Campus Do Valonguinho, Outeiro de São João Batista, S/n, 24020-141, Niterói, RJ, Brazil
- Departamento de Química, Pontifícia Universidade Católica Do Rio de Janeiro (PUC-Rio), Rio de Janeiro, RJ, 22451-900, Brazil
| | - P S Duarte
- Departamento de Química, Pontifícia Universidade Católica Do Rio de Janeiro (PUC-Rio), Rio de Janeiro, RJ, 22451-900, Brazil
| | - M A Strauch
- Gerência de Desenvolvimento Tecnológico, Instituto Vital Brazil, Niterói, RJ, 24230-410, Brazil
| | - J G Fonseca
- Gerência de Desenvolvimento Tecnológico, Instituto Vital Brazil, Niterói, RJ, 24230-410, Brazil
| | - L G R Meirelles
- Fazenda Instituto Vital Brazil, Niterói, RJ, 24230-410, Brazil
| | - P Bento da Silva
- Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, 70910-900, Brazil
| | - R B Azevedo
- Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, 70910-900, Brazil
| | - G Aparecida de Souza Martins
- Programa de Pós-graduação Em Ciência e Tecnologia de Alimentos, Universidade Federal Do Tocantins, 77001-090, Brazil
| | - B S Archanjo
- Divisão de Metrologia de Materiais, Instituto Nacional de Metrologia, Qualidade e Tecnologia (Inmetro), Duque de Caxias, RJ, 25250-020, Brazil
| | - C D Buarque
- Departamento de Química, Pontifícia Universidade Católica Do Rio de Janeiro (PUC-Rio), Rio de Janeiro, RJ, 22451-900, Brazil
| | - G Machado
- Centro de Tecnologias Estratégicas Do Nordeste, Av. Prof. Luiz Freire 01, Recife, Pernambuco, 50740-540, Brazil
| | - A M Percebom
- Departamento de Química, Pontifícia Universidade Católica Do Rio de Janeiro (PUC-Rio), Rio de Janeiro, RJ, 22451-900, Brazil
| | - C M Ronconi
- Departamento de Química Inorgânica, Universidade Federal Fluminense (UFF), Campus Do Valonguinho, Outeiro de São João Batista, S/n, 24020-141, Niterói, RJ, Brazil
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Beaudoin CA, Pandurangan AP, Kim SY, Hamaia SW, Huang CL, Blundell TL, Vedithi SC, Jackson AP. In silico analysis of mutations near S1/S2 cleavage site in SARS-CoV-2 spike protein reveals increased propensity of glycosylation in Omicron strain. J Med Virol 2022; 94:4181-4192. [PMID: 35575289 PMCID: PMC9348480 DOI: 10.1002/jmv.27845] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 11/06/2022]
Abstract
Cleavage of the severe respiratory syndrome coronavirus-2 (SARS-CoV-2) spike protein has been demonstrated to contribute to viral-cell fusion and syncytia formation. Studies have shown that variants of concern (VOC) and variants of interest (VOI) show differing membrane fusion capacity. Mutations near cleavage motifs, such as the S1/S2 and S2' sites, may alter interactions with host proteases and, thus, the potential for fusion. The biochemical basis for the differences in interactions with host proteases for the VOC/VOI spike proteins has not yet been explored. Using sequence and structure-based bioinformatics, mutations near the VOC/VOI spike protein cleavage sites were inspected for their structural effects. All mutations found at the S1/S2 sites were predicted to increase affinity to the furin protease but not TMPRSS2. Mutations at the spike residue P681 in several strains, such P681R in the Delta strain, resulted in the disruption of a proline-directed kinase phosphorylation motif at the S1/S2 site, which may lessen the impact of phosphorylation for these variants. However, the unique N679K mutation in the Omicron strain was found to increase the propensity for O-linked glycosylation at the S1/S2 cleavage site, which may prevent recognition by proteases. Such glycosylation in the Omicron strain may hinder entry at the cell surface and, thus, decrease syncytia formation and induce cell entry through the endocytic pathway as has been shown in previous studies. Further experimental work is needed to confirm the effect of mutations and posttranslational modifications on SARS-CoV-2 spike protein cleavage sites.
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Affiliation(s)
| | - Arun P. Pandurangan
- Department of Biochemistry, Sanger BuildingUniversity of CambridgeCambridgeUnited Kingdom
| | - So Yeon Kim
- Department of Biochemistry, Sanger BuildingUniversity of CambridgeCambridgeUnited Kingdom
| | - Samir W. Hamaia
- Department of Biochemistry, Hopkins BuildingUniversity of CambridgeCambridgeUnited Kingdom
| | - Christopher L.‐H. Huang
- Department of Biochemistry, Hopkins BuildingUniversity of CambridgeCambridgeUnited Kingdom
- Physiological LaboratoryUniversity of CambridgeCambridgeUnited Kingdom
| | - Tom L. Blundell
- Department of Biochemistry, Sanger BuildingUniversity of CambridgeCambridgeUnited Kingdom
| | | | - Antony P. Jackson
- Department of Biochemistry, Hopkins BuildingUniversity of CambridgeCambridgeUnited Kingdom
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Müller L, Kannenberg J, Biemann R, Hönemann M, Ackermann G, Jassoy C. Comparison of the measured values of quantitative SARS-CoV-2 spike antibody assays. J Clin Virol 2022; 155:105269. [PMID: 36029637 PMCID: PMC9388276 DOI: 10.1016/j.jcv.2022.105269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/05/2022] [Accepted: 08/17/2022] [Indexed: 01/15/2023]
Abstract
Background The concentration of antibodies against the SARS-CoV-2 spike protein is frequently being measured for clinical and epidemiological purposes. The aim of this study was to examine whether the results of different quantitative SARS-CoV-2 spike antibody assays are comparable. Material and methods The Siemens SARS-CoV-2 IgG, Abbott SARS-CoV-2 IgG II Quant, Roche ElecsysT Anti-SARS-CoV-2 S, and Euroimmun Anti-SARS-CoV-2-QuantiVac assay were compared with 110 sera from patients 6-9 months after SARS-CoV-2 infection and the WHO First International SARS-CoV-2 antibody standard 20/136. The antibody values were converted into WHO binding antibody units (BAU)/ml. The diagnostic sensitivity of the assays was determined and the antibody values were compared. Results The diagnostic sensitivity ranged from 57.3% (Euroimmun) to 100% (Roche). The antibody concentration values of different assays correlated with Pearson coefficients of correlation between 0.729 and 0.953. The geometric mean antibody values of the Abbott, Siemens and Euroimmun assay varied by a factor of 1.1-1.2. The geometric mean antibody values of the Roche assay were 2.4-2.8 times higher than those from the other assays. The assays yielded varying results with the WHO International antibody standard. Conclusions The quantitative SARS-CoV-2 antibody assays from Abbott, Siemens, Roche and Euroimmun correlate strongly but differ in the antibody concentrations. Therefore, the same assay should be used when testing patients repeatedly. In addition, the name of the assay used and the manufacturer should be indicated along with the test results.
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Affiliation(s)
- Lars Müller
- Institute for Medical Microbiology and Virology, University Hospital and Medical Faculty, University of Leipzig, Johannisallee 30, Leipzig 04103, Germany
| | - Judith Kannenberg
- Institute for Medical Microbiology and Virology, University Hospital and Medical Faculty, University of Leipzig, Johannisallee 30, Leipzig 04103, Germany
| | - Ronald Biemann
- Institute for Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital and Medical Faculty, University of Leipzig, Germany
| | - Mario Hönemann
- Institute for Medical Microbiology and Virology, University Hospital and Medical Faculty, University of Leipzig, Johannisallee 30, Leipzig 04103, Germany
| | | | - Christian Jassoy
- Institute for Medical Microbiology and Virology, University Hospital and Medical Faculty, University of Leipzig, Johannisallee 30, Leipzig 04103, Germany.
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55
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Caputo E, Mandrich L. Structural and Phylogenetic Analysis of SARS-CoV-2 Spike Glycoprotein from the Most Widespread Variants. Life (Basel) 2022; 12:life12081245. [PMID: 36013424 PMCID: PMC9410480 DOI: 10.3390/life12081245] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 11/16/2022]
Abstract
The SARS-CoV-2 pandemic, reported for the first time at the end of 2019 in the city of Wuhan (China), has spread worldwide in three years; it lead to the infection of more than 500 million people and about six million dead. SARS-CoV-2 has proved to be very dangerous for human health. Therefore, several efforts have been made in studying this virus. In a short time, about one year, the mechanisms of SARS-CoV-2 infection and duplication and its physiological effect on human have been pointed out. Moreover, different vaccines against it have been developed and commercialized. To date, more than 11 billion doses have been inoculated all over the world. Since the beginning of the pandemic, SARS-CoV-2 has evolved; it has done so by accumulating mutations in the genome, generating new virus versions showing different characteristics, and which have replaced the pre-existing variants. In general, it has been observed that the new variants show an increased infectivity and cause milder symptoms. The latest isolated Omicron variants contain more than 50 mutations in the whole genome and show an infectivity 10-folds higher compared to the wild-type strain. Here, we analyse the SARS-CoV-2 variants from a phylogenetic point of view and hypothesize a future scenario for SARS-CoV-2, by following its evolution to date.
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Affiliation(s)
- Emilia Caputo
- Institute of Genetics and Biophysics-IGB-CNR, “A. Buzzati-Traverso”, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Luigi Mandrich
- Research Institute on Terrestrial Ecosystems-IRET-CNR, Via Pietro Castellino 111, 80131 Naples, Italy
- Correspondence:
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56
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Prout A, Rustandi RR, Tubbs C, Winters MA, McKenna P, Vlasak J. Functional profiling of Covid 19 vaccine candidate by flow virometry. Vaccine 2022; 40:5529-5536. [PMID: 35985887 PMCID: PMC9359933 DOI: 10.1016/j.vaccine.2022.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 05/20/2022] [Accepted: 08/03/2022] [Indexed: 11/29/2022]
Abstract
Vaccine development is a complex process, starting with selection of a promising immunogen in the discovery phase, followed by process development in the preclinical phase, and later by clinical trials in tandem with process improvements and scale up. A large suite of analytical techniques is required to gain understanding of the vaccine candidate so that a relevant immunogen is selected and subsequently manufactured consistently throughout the lifespan of the product. For viral vaccines, successful immunogen production is contingent on its maintained antigenicity and/or infectivity, as well as the ability to characterize these qualities within the context of the process, formulation, and clinical performance. In this report we show the utility of flow virometry during preclinical development of a Covid 19 vaccine candidate based on SARS-CoV-2 spike (S) protein expressed on vesicular stomatitis virus (VSV). Using a panel of monoclonal antibodies, we were able to detect the S protein on the surface of the recombinant VSV virus, monitor the expression levels, detect differences in the antigen based on S protein sequence and after virus inactivation, and monitor S protein stability. Collectively, flow virometry provided important data that helped to guide preclinical development of this vaccine candidate.
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Affiliation(s)
- Ashley Prout
- Vaccine Analytical Research and Development, Merck & Co., Inc., West Point, PA, USA
| | - Richard R Rustandi
- Vaccine Analytical Research and Development, Merck & Co., Inc., West Point, PA, USA
| | - Christopher Tubbs
- Vaccine Analytical Research and Development, Merck & Co., Inc., West Point, PA, USA
| | - Michael A Winters
- Vaccine Process Research and Development, Merck & Co., Inc., West Point, PA, USA
| | - Philip McKenna
- Infectious Diseases-Vaccines, Merck & Co., Inc., West Point, PA, USA
| | - Josef Vlasak
- Vaccine Analytical Research and Development, Merck & Co., Inc., West Point, PA, USA.
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57
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Han J, Lee SL, Kim J, Seo G, Lee YW. SARS-CoV-2 spike protein detection using slightly tapered no-core fiber-based optical transducer. Mikrochim Acta 2022; 189:321. [PMID: 35932379 PMCID: PMC9362518 DOI: 10.1007/s00604-022-05413-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/08/2022] [Indexed: 12/01/2022]
Abstract
The label-free detection of SARS-CoV-2 spike protein is demonstrated by using slightly tapered no-core fiber (ST-NCF) functionalized with ACE2. In the fabricated sensor head, abrupt changes in the mode-field diameter at the interfaces between single-mode fiber and no-core fiber excite multi-guided modes and facilitate multi-mode interference (MMI). Its slightly tapered region causes the MMI to be more sensitive to the refractive index (RI) modulation of the surrounding medium. The transmission minimum of the MMI spectrum was selected as a sensor indicator. The sensor surface was functionalized with ACE2 bioreceptors through the pretreatment process. The ACE2-immobilized ST-NCF sensor head was exposed to the samples of SARS-CoV-2 spike protein with concentrations ranging from 1 to 104 ng/mL. With increasing sample concentration, we observed that the indicator dip moved towards a longer wavelength region. The observed spectral shifts are attributed to localized RI modulations at the sensor surface, which are induced by selective bioaffinity binding between ACE2 and SARS-CoV-2 spike protein. Also, we confirmed the capability of the sensor head as an effective and simple optical probe for detecting antigen protein samples by applying saliva solution used as a measurement buffer. Moreover, we compared its detection sensitivity to SARS-CoV-2 and MERS-CoV spike protein to examine its cross-reactivity. In particular, we proved the reproducibility of the bioassay protocol adopted here by employing the ST-NCF sensor head reconstructed with ACE2. Our ST-NCF transducer is expected to be beneficially utilized as a low-cost and portable biosensing platform for the rapid detection of SARS-CoV-2 spike protein.
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Affiliation(s)
- Jinsil Han
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan, 48513, Republic of Korea
| | - Seul-Lee Lee
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan, 48513, Republic of Korea
| | - Jihoon Kim
- School of Electrical Engineering, Pukyong National University, Busan, 48513, Republic of Korea
| | - Giwan Seo
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea. .,Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea.
| | - Yong Wook Lee
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan, 48513, Republic of Korea. .,School of Electrical Engineering, Pukyong National University, Busan, 48513, Republic of Korea.
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Verkhivker G, Agajanian S, Kassab R, Krishnan K. Integrating Conformational Dynamics and Perturbation-Based Network Modeling for Mutational Profiling of Binding and Allostery in the SARS-CoV-2 Spike Variant Complexes with Antibodies: Balancing Local and Global Determinants of Mutational Escape Mechanisms. Biomolecules 2022; 12:964. [PMID: 35883520 DOI: 10.3390/biom12070964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 02/05/2023] Open
Abstract
In this study, we combined all-atom MD simulations, the ensemble-based mutational scanning of protein stability and binding, and perturbation-based network profiling of allosteric interactions in the SARS-CoV-2 spike complexes with a panel of cross-reactive and ultra-potent single antibodies (B1-182.1 and A23-58.1) as well as antibody combinations (A19-61.1/B1-182.1 and A19-46.1/B1-182.1). Using this approach, we quantify the local and global effects of mutations in the complexes, identify protein stability centers, characterize binding energy hotspots, and predict the allosteric control points of long-range interactions and communications. Conformational dynamics and distance fluctuation analysis revealed the antibody-specific signatures of protein stability and flexibility of the spike complexes that can affect the pattern of mutational escape. A network-based perturbation approach for mutational profiling of allosteric residue potentials revealed how antibody binding can modulate allosteric interactions and identified allosteric control points that can form vulnerable sites for mutational escape. The results show that the protein stability and binding energetics of the SARS-CoV-2 spike complexes with the panel of ultrapotent antibodies are tolerant to the effect of Omicron mutations, which may be related to their neutralization efficiency. By employing an integrated analysis of conformational dynamics, binding energetics, and allosteric interactions, we found that the antibodies that neutralize the Omicron spike variant mediate the dominant binding energy hotpots in the conserved stability centers and allosteric control points in which mutations may be restricted by the requirements of the protein folding stability and binding to the host receptor. This study suggested a mechanism in which the patterns of escape mutants for the ultrapotent antibodies may not be solely determined by the binding interaction changes but are associated with the balance and tradeoffs of multiple local and global factors, including protein stability, binding affinity, and long-range interactions.
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Lykhmus O, Kalashnyk O, Koval L, Krynina O, Komisarenko S, Skok M. Immunization with 674-685 fragment of SARS-Cov-2 spike protein induces neuroinflammation and impairs episodic memory of mice. Biochem Biophys Res Commun 2022; 622:57-63. [PMID: 35843095 PMCID: PMC9263688 DOI: 10.1016/j.bbrc.2022.07.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/06/2022] [Indexed: 11/02/2022]
Abstract
COVID-19 is accompanied by strong inflammatory reaction and is often followed by long-term cognitive disorders. The fragment 674-685 of SARS-Cov-2 spike protein was shown to interact with α7 nicotinic acetylcholine receptor involved in regulating both inflammatory reactions and cognitive functions. Here we show that mice immunized with the peptide corresponding to 674-685 fragment of SARS-Cov-2 spike protein conjugated to hemocyanin (KLH-674-685) demonstrate decreased level of α7 nicotinic acetylcholine receptors, increased levels of IL-1β and TNFα in the brain and impairment of episodic memory. Choline injections prevented α7 nicotinic receptor decline and memory loss. Mice injected with immunoglobulins obtained from the blood of (KLH-674-685)-immunized mice also demonstrated episodic memory decline. These data allow suggesting that post-COVID memory impairment in humans is related to SARS-Cov-2 spike protein-specific immune reaction. The mechanisms of such effect are being discussed.
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Affiliation(s)
- Olena Lykhmus
- Palladin Institute of Biochemistry, NAS of Ukraine, 9, Leontovycha str., 01054, Kyiv, Ukraine.
| | - Olena Kalashnyk
- Palladin Institute of Biochemistry, NAS of Ukraine, 9, Leontovycha str., 01054, Kyiv, Ukraine.
| | - Lyudmyla Koval
- Palladin Institute of Biochemistry, NAS of Ukraine, 9, Leontovycha str., 01054, Kyiv, Ukraine.
| | - Olga Krynina
- Palladin Institute of Biochemistry, NAS of Ukraine, 9, Leontovycha str., 01054, Kyiv, Ukraine.
| | - Serhiy Komisarenko
- Palladin Institute of Biochemistry, NAS of Ukraine, 9, Leontovycha str., 01054, Kyiv, Ukraine.
| | - Maryna Skok
- Palladin Institute of Biochemistry, NAS of Ukraine, 9, Leontovycha str., 01054, Kyiv, Ukraine.
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Atalis A, Keenum MC, Pandey B, Beach A, Pradhan P, Vantucci C, O'Farrell L, Noel R, Jain R, Hosten J, Smith C, Kramer L, Jimenez A, Ochoa MA, Frey D, Roy K. Nanoparticle-delivered TLR4 and RIG-I agonists enhance immune response to SARS-CoV-2 subunit vaccine. J Control Release 2022; 347:476-488. [PMID: 35577151 PMCID: PMC9121740 DOI: 10.1016/j.jconrel.2022.05.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/04/2022] [Accepted: 05/10/2022] [Indexed: 01/25/2023]
Abstract
Despite success in vaccinating populations against SARS-CoV-2, concerns about immunity duration, continued efficacy against emerging variants, protection from infection and transmission, and worldwide vaccine availability remain. Molecular adjuvants targeting pattern recognition receptors (PRRs) on antigen-presenting cells (APCs) could improve and broaden the efficacy and durability of vaccine responses. Native SARS-CoV-2 infection stimulates various PRRs, including toll-like receptors (TLRs) and retinoic acid-inducible gene I (RIG-I)-like receptors. We hypothesized that targeting PRRs using molecular adjuvants on nanoparticles (NPs) along with a stabilized spike protein antigen could stimulate broad and efficient immune responses. Adjuvants targeting TLR4 (MPLA), TLR7/8 (R848), TLR9 (CpG), and RIG-I (PUUC) delivered on degradable polymer NPs were combined with the S1 subunit of spike protein and assessed in vitro with isogeneic mixed lymphocyte reactions (isoMLRs). For in vivo studies, the adjuvant-NPs were combined with stabilized spike protein or spike-conjugated NPs and assessed using a two-dose intranasal or intramuscular vaccination model in mice. Combination adjuvant-NPs simultaneously targeting TLR and RIG-I receptors (MPLA+PUUC, CpG+PUUC, and R848+PUUC) differentially induced T cell proliferation and increased proinflammatory cytokine secretion by APCs in vitro. When delivered intranasally, MPLA+PUUC NPs enhanced CD4+CD44+ activated memory T cell responses against spike protein in the lungs while MPLA NPs increased anti-spike IgA in the bronchoalveolar (BAL) fluid and IgG in the blood. Following intramuscular delivery, PUUC NPs induced strong humoral immune responses, characterized by increases in anti-spike IgG in the blood and germinal center B cell populations (GL7+ and BCL6+ B cells) in the draining lymph nodes (dLNs). MPLA+PUUC NPs further boosted spike protein-neutralizing antibody titers and T follicular helper cell populations in the dLNs. These results suggest that protein subunit vaccines with particle-delivered molecular adjuvants targeting TLR4 and RIG-I could lead to robust and unique route-specific adaptive immune responses against SARS-CoV-2.
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Affiliation(s)
- Alexandra Atalis
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Mark C Keenum
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Bhawana Pandey
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Alexander Beach
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Pallab Pradhan
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA; Marcus Center for Therapeutic Cell Characterization and Manufacturing, Georgia Institute of Technology, Atlanta, GA, USA; The Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Casey Vantucci
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Laura O'Farrell
- Physiological Research Laboratory, Georgia Institute of Technology, Atlanta, GA, USA
| | - Richard Noel
- Physiological Research Laboratory, Georgia Institute of Technology, Atlanta, GA, USA
| | - Ritika Jain
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Justin Hosten
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Clinton Smith
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Liana Kramer
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Angela Jimenez
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Miguel Armenta Ochoa
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - David Frey
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Krishnendu Roy
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA; Marcus Center for Therapeutic Cell Characterization and Manufacturing, Georgia Institute of Technology, Atlanta, GA, USA; The Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA.
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61
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Fujimoto D, Fukuya M, Terao S, Irei I, Akiyama T, Watanabe A, Yasuda Y, Yoshioka D, Takada K, Hayakawa S, Moriya T. Sputum characteristics of patients with severe COVID-19: report of two cases with immunocytochemical detection of SARS-CoV-2 spike protein. Med Mol Morphol 2022; 55:316-322. [PMID: 35716257 PMCID: PMC9206128 DOI: 10.1007/s00795-022-00326-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/31/2022] [Indexed: 11/16/2022]
Abstract
Patients with SARS-CoV-2 infection and with severe COVID-19 often have multiple coinfections, and their treatment is challenging. Here, we performed cytology analysis on sputum samples from two patients with severe COVID-19. The specimens were prepared using the rubbing method and stained with Papanicolaou stain. In both cases, several cells with frosted nuclei were observed, and the cytological findings per 100 cells were evaluated. The infected cells were mononuclear to multinuclear, showing chromatin aggregation at the nuclear margins, intranuclear inclusion bodies, eosinophilic cytoplasmic inclusion bodies, and mutual pressure exclusion of the nuclei. Immunocytochemical staining revealed that the cells were positive for AE1/AE3 and negative for CD68 expression, indicating their epithelial origin. Furthermore, infected cells with frosted nuclei were positive for surfactant protein A (SP-A) in Case 2, suggesting infection of type II alveolar pneumocytes or Clara cells. Moreover, in Case 2, the infected cells were positive for herpes simplex virus (HSV) I + II and SARS-CoV-2 spike protein, confirming double infection in these cells. In conclusion, sputum cytology is an important tool for determining the diversity of viral infection, and additional immunocytochemistry can be used for definitive diagnosis.
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Affiliation(s)
- Daichi Fujimoto
- Department of Pathology, Kawasaki Medical School Hospital, Kurashiki, Okayama, 701-0192, Japan
| | - Minako Fukuya
- Department of Pathology, Kawasaki Medical School Hospital, Kurashiki, Okayama, 701-0192, Japan
| | - Sachie Terao
- Department of Pathology, Kawasaki Medical School Hospital, Kurashiki, Okayama, 701-0192, Japan
| | - Isao Irei
- Department of Pathology, Kawasaki Medical School Hospital, Kurashiki, Okayama, 701-0192, Japan.,Department of Pathology, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama, 701-0192, Japan
| | - Takashi Akiyama
- Department of Pathology, Kawasaki Medical School Hospital, Kurashiki, Okayama, 701-0192, Japan.,Department of Pathology, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama, 701-0192, Japan
| | - Anna Watanabe
- Department of Respiratory Medicine, Kawasaki Medical School, Kurashiki, Okayama, 701-0192, Japan
| | - Yuri Yasuda
- Department of Respiratory Medicine, Kawasaki Medical School, Kurashiki, Okayama, 701-0192, Japan
| | - Daisuke Yoshioka
- Department of Respiratory Medicine, Kawasaki Medical School, Kurashiki, Okayama, 701-0192, Japan
| | - Kazuhide Takada
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Itabashi, Tokyo, 173-8610, Japan
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Itabashi, Tokyo, 173-8610, Japan
| | - Takuya Moriya
- Department of Pathology, Kawasaki Medical School Hospital, Kurashiki, Okayama, 701-0192, Japan. .,Department of Pathology, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama, 701-0192, Japan.
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62
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Thuy PX, Bao TDD, Moon EY. Ursodeoxycholic acid ameliorates cell migration retarded by the SARS-CoV-2 spike protein in BEAS-2B human bronchial epithelial cells. Biomed Pharmacother 2022; 150:113021. [PMID: 35658221 PMCID: PMC9035373 DOI: 10.1016/j.biopha.2022.113021] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/07/2022] [Accepted: 04/20/2022] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) is caused by severe acute -respiratory syndrome coronavirus 2 (SARS- CoV-2) through interaction of the spike protein (SP) with the receptor-binding domain (RBD) and its receptor, angiotensin converting enzyme 2(ACE2). Repair mechanisms induced following virus infection can restore the protective barrier through wound healing. Then, cells from the epithelial basal layer repopulate the damaged area, followed by cell proliferation and differentiation, as well as changes in gene expression. METHODS Using Beas-2B cells and SP, we investigated whether ursodeoxycholic acid (UDCA) contributes to restoration of the bronchial epithelial layer. ACE2 expression was measured by RT-PCR and Western blotting. SP-ACE2 interaction was analyzed by flow cytometry and visualized through immunostaining. Cell migration was assessed using single cell path tracking and wound healing assay. RESULTS Upon ACE2 overexpression in HeLa, HEK293T, and Beas-2B cells following the transfection of pCMV-ACE2 plasmid DNA, SP binding on each cell was increased in the ACE2 overexpression group compared to pCMV-transfected control cells. SP treatment delayed the migration of BEAS-2B cells compared to the control. SP also reduced cell migration, even under ACE2 overexpression; SP binding was greater in ACE2-overexpressed cells than control cells. UDCA interfered significantly with the binding of SP to ACE2 under our experimental conditions. UDCA also restored the inhibitory migration of Beas-2B cells induced by SP treatment. CONCLSION Our data demonstrate that UDCA can contribute to the inhibition of abnormal airway epithelial cell migration. These results suggest that UDCA can enhance the repair mechanism, to prevent damage caused by SP-ACE2 interaction and enhance restoration of the epithelial basal layer.
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Affiliation(s)
- Pham Xuan Thuy
- Department of Integrated Bioscience and Biotechnology, Seoul 05006, Republic of Korea
| | - Tran Duc Duy Bao
- Department of Integrated Bioscience and Biotechnology, Seoul 05006, Republic of Korea
| | - Eun-Yi Moon
- Department of Integrated Bioscience and Biotechnology, Seoul 05006, Republic of Korea.
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63
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Maniscalco GT, Ferrara AL, Liotti A, Manzo V, Di Battista ME, Salvatore S, Graziano D, Viola A, Amato G, Moreggia O, Di Giulio Cesare D, Alfieri G, Di Iorio W, Della Rocca G, Andreone V, De Rosa V. Long term persistence of SARS-CoV-2 humoral response in multiple sclerosis subjects. Mult Scler Relat Disord 2022; 62:103800. [PMID: 35462168 PMCID: PMC9005241 DOI: 10.1016/j.msard.2022.103800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 03/18/2022] [Accepted: 04/08/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND & OBJECTIVES The persistence of the severe acute respiratory syndrome coronavirus (SARS-CoV)-2 pandemic, partly due to the appearance of highly infectious variants, has made booster vaccinations necessary for vulnerable groups. Here, we present data regarding the decline of the SARS-CoV-2 BNT162b2 mRNA vaccine-induced humoral immune response in a monocentric cohort of MS patients. METHODS 96 MS patients undergoing eight different DMTs, all without previous SARS-CoV-2 infection, were evaluated for anti-Spike IgG levels, 21 days (T1) and 5-6 months (T2) after the second SARS-CoV-2 BNT162b2 mRNA vaccine dose. The anti-Spike IgG titre from MS subjects was compared with 21 age- and sex-matched healthy controls (HC). RESULTS When compared with SARS-CoV-2 IgG levels at T2 in HC, we observed comparable levels in interferon-β 1a-, dimethyl fumarate-, teriflunomide- and natalizumab-treated MS subjects, but an impaired humoral response in MS subjects undergoing glatiramer acetate-, cladribine-, fingolimod- and ocrelizumab-treatments. Moreover, comparison between SARS-CoV-2 IgG Spike titre at T1 and T2 revealed a faster decline of the humoral response in patients undergoing dimethyl fumarate-, interferon-β 1a- and glatiramer acetate-therapies, while those receiving teriflunomide and natalizumab showed higher persistence compared to healthy controls. CONCLUSION The prominent decline in humoral response in MS subjects undergoing dimethyl fumarate-, interferon-β 1a- and glatiramer acetate-therapies should be considered when formulating booster regimens as these subjects would benefit of early booster vaccinations.
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Affiliation(s)
- Giorgia Teresa Maniscalco
- Neurological Clinic and Stroke Unit, "A. Cardarelli" Hospital, Via A. Cardarelli 9, Naples 80131, Italy; Multiple Sclerosis Center, "A. Cardarelli" Hospital, Via A. Cardarelli 9, Naples 80131, Italy.
| | - Anne Lise Ferrara
- Institute of Experimental Endocrinology and Oncology (IEOS-CNR), Via S. Pansini 5, Naples 80131, Italy; Department of Translational Medical Science and Center for Basic and Clinical Immunology Research (CISI), University of Naples "Federico II", Via S. Pansini 5, Naples 80131, Italy
| | - Antonietta Liotti
- Institute of Experimental Endocrinology and Oncology (IEOS-CNR), Via S. Pansini 5, Naples 80131, Italy.
| | - Valentino Manzo
- Neurological Clinic and Stroke Unit, "A. Cardarelli" Hospital, Via A. Cardarelli 9, Naples 80131, Italy.
| | - Maria Elena Di Battista
- Neurological Clinic and Stroke Unit, "A. Cardarelli" Hospital, Via A. Cardarelli 9, Naples 80131, Italy; Multiple Sclerosis Center, "A. Cardarelli" Hospital, Via A. Cardarelli 9, Naples 80131, Italy.
| | - Simona Salvatore
- Neurological Clinic and Stroke Unit, "A. Cardarelli" Hospital, Via A. Cardarelli 9, Naples 80131, Italy; Multiple Sclerosis Center, "A. Cardarelli" Hospital, Via A. Cardarelli 9, Naples 80131, Italy.
| | - Daniela Graziano
- Unit of Trasfusional Medicine, SIMT, "A. Cardarelli" Hospital, Via A. Cardarelli 9, Naples 80131, Italy.
| | - Assunta Viola
- Molecular Biology Laboratory, Hematology and Transplantation CSE, "A. Cardarelli" Hospital, Via A. Cardarelli 9, Naples 80131, Italy.
| | - Gerardino Amato
- Clinical Pathology and Microbiology Laboratory "A. Cardarelli" Hospital, Via A. Cardarelli 9, Naples 80131, Italy.
| | - Ornella Moreggia
- Multiple Sclerosis Center, "A. Cardarelli" Hospital, Via A. Cardarelli 9, Naples 80131, Italy
| | | | - Gennaro Alfieri
- Neurological Clinic and Stroke Unit, "A. Cardarelli" Hospital, Via A. Cardarelli 9, Naples 80131, Italy.
| | - Walter Di Iorio
- Neurological Clinic and Stroke Unit, "A. Cardarelli" Hospital, Via A. Cardarelli 9, Naples 80131, Italy.
| | - Gennaro Della Rocca
- Neurological Clinic and Stroke Unit, "A. Cardarelli" Hospital, Via A. Cardarelli 9, Naples 80131, Italy.
| | - Vincenzo Andreone
- Neurological Clinic and Stroke Unit, "A. Cardarelli" Hospital, Via A. Cardarelli 9, Naples 80131, Italy.
| | - Veronica De Rosa
- Institute of Experimental Endocrinology and Oncology (IEOS-CNR), Via S. Pansini 5, Naples 80131, Italy.
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64
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Tamayo-Velasco Á, Peñarrubia-Ponce MJ, Álvarez FJ, de la Fuente I, Pérez-González S, Andaluz-Ojeda D. ABO Blood System and COVID-19 Susceptibility: Anti-A and Anti-B Antibodies Are the Key Points. Front Med (Lausanne) 2022; 9:882477. [PMID: 35547235 PMCID: PMC9081929 DOI: 10.3389/fmed.2022.882477] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 03/18/2022] [Indexed: 12/11/2022] Open
Abstract
The implication of the ABO blood group in COVID-19 disease was formulated early, at the beginning of the COVID-19 pandemic more than 2 years ago. It has now been established that the A blood group is associated with more susceptibility and severe symptoms of COVID-19, while the O blood group shows protection against viral infection. In this review, we summarize the underlying pathophysiology of ABO blood groups and COVID-19 to explain the molecular aspects behind the protective mechanism in the O blood group. A or B antigens are not associated with a different risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection than that of other antigens. In this case, the cornerstone is natural anti-A and anti-B antibodies from the ABO system. They are capable of interfering with the S protein (SARS-CoV-2) and angiotensin-converting enzyme 2 (ACE2; host cell receptor), thereby conferring protection to patients with sufficient antibodies (O blood group). Indeed, the titers of natural antibodies and the IgG isotype (specific to the O blood group) may be determinants of susceptibility and severity. Moreover, older adults are associated with a higher risk of bad outcomes due to the lack of antibodies and the upregulation of ACE2 expression during senescence. A better understanding of the role of the molecular mechanism of ABO blood groups in COVID-19 facilitates better prognostic stratification of the disease. Furthermore, it could represent an opportunity for new therapeutic strategies.
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Affiliation(s)
- Álvaro Tamayo-Velasco
- Haematology and Hemotherapy Service, University Clinical Hospital, Valladolid, Spain.,BioCritic. Group for Biomedical Research in Critical Care Medicine, Valladolid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Francisco Javier Álvarez
- BioCritic. Group for Biomedical Research in Critical Care Medicine, Valladolid, Spain.,Pharmacological Big Data Laboratory, Pharmacology, Faculty of Medicine, University of Valladolid, Valladolid, Spain
| | - Ignacio de la Fuente
- Haematology and Hemotherapy Service, University Clinical Hospital, Valladolid, Spain
| | - Sonia Pérez-González
- Haematology and Hemotherapy Service, University Clinical Hospital, Valladolid, Spain
| | - David Andaluz-Ojeda
- Intensive Care Service, Hospital Universitario Sanchinarro, HM Hospitales, Madrid, Spain
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65
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Stebbings R, Jones C, Cotton P, Armour G, Maguire S, Skellett V, Tang CM, Goodman J, Brady T, Takahashi V, Daunt A, Lapointe JM, Cohen TS. SARS-CoV-2 Spike Protein Expression In Vitro and Hematologic Effects in Mice Vaccinated With AZD1222 (ChAdOx1 nCoV-19). Front Immunol 2022; 13:836492. [PMID: 35493482 PMCID: PMC9039667 DOI: 10.3389/fimmu.2022.836492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/14/2022] [Indexed: 01/17/2023] Open
Abstract
Severe COVID-19 can be associated with a prothrombotic state, increasing risk of morbidity and mortality. The SARS-CoV-2 spike glycoprotein is purported to directly promote platelet activation via the S1 subunit and is cleaved from host cells during infection. High plasma concentrations of S1 subunit are associated with disease progression and respiratory failure during severe COVID-19. There is limited evidence on whether COVID-19 vaccine-induced spike protein is similarly cleaved and on the immediate effects of vaccination on host immune responses or hematology parameters. We investigated vaccine-induced S1 subunit cleavage and effects on hematology parameters using AZD1222 (ChAdOx1 nCoV-19), a simian, replication-deficient adenovirus-vectored COVID-19 vaccine. We observed S1 subunit cleavage in vitro following AZD1222 transduction of HEK293x cells. S1 subunit cleavage also occurred in vivo and was detectable in sera 12 hours post intramuscular immunization (1x1010 viral particles) in CD-1 mice. Soluble S1 protein levels decreased within 3 days and were no longer detectable 7–14 days post immunization. Intravenous immunization (1x109 viral particles) produced higher soluble S1 protein levels with similar expression kinetics. Spike protein was undetectable by immunohistochemistry 14 days post intramuscular immunization. Intramuscular immunization resulted in transiently lower platelet (12 hours) and white blood cell (12–24 hours) counts relative to vehicle. Similarly, intravenous immunization resulted in lower platelet (24–72 hours) and white blood cell (12–24 hours) counts, and increased neutrophil (2 hours) counts. The responses observed with either route of immunization represent transient hematologic changes and correspond to expected innate immune responses to adenoviral infection.
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Affiliation(s)
- Richard Stebbings
- Oncology Safety, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Melbourn, United Kingdom
| | - Christopher Jones
- Integrated Bioanalysis, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Peter Cotton
- Research and Development, BioPharmaceuticals R&D, AstraZeneca, Macclesfield, United Kingdom
| | - Gillian Armour
- Regulatory Toxicology and Safety Pharmacology, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Melbourn, United Kingdom
| | - Shaun Maguire
- Regulatory Toxicology and Safety Pharmacology, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Melbourn, United Kingdom
| | - Vicky Skellett
- Integrated Bioanalysis, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Chi-Man Tang
- Integrated Bioanalysis, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Joanne Goodman
- Integrated Bioanalysis, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Tyler Brady
- Translational Medicine, Vaccines & Immune Therapies, BioPharmaceuticals Medical, AstraZeneca, Gaithersburg, MD, United States
| | - Virginia Takahashi
- Microbiome Discovery, Vaccines & Immune Therapies, BioPharmaceuticals Medical, AstraZeneca, Gaithersburg, MD, United States
| | - Andrew Daunt
- Labcorp Early Development Laboratories Limited, Harrogate, United Kingdom
| | - Jean-Martin Lapointe
- Oncology Safety Pathology, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Taylor S Cohen
- Microbiome Discovery, Vaccines & Immune Therapies, BioPharmaceuticals Medical, AstraZeneca, Gaithersburg, MD, United States
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66
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Verkhivker G, Agajanian S, Kassab R, Krishnan K. Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations. Int J Mol Sci 2022; 23:4376. [PMID: 35457196 PMCID: PMC9032413 DOI: 10.3390/ijms23084376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 02/01/2023] Open
Abstract
In this study, we combine all-atom MD simulations and comprehensive mutational scanning of S-RBD complexes with the angiotensin-converting enzyme 2 (ACE2) host receptor in the native form as well as the S-RBD Delta and Omicron variants to (a) examine the differences in the dynamic signatures of the S-RBD complexes and (b) identify the critical binding hotspots and sensitivity of the mutational positions. We also examined the differences in allosteric interactions and communications in the S-RBD complexes for the Delta and Omicron variants. Through the perturbation-based scanning of the allosteric propensities of the SARS-CoV-2 S-RBD residues and dynamics-based network centrality and community analyses, we characterize the global mediating centers in the complexes and the nature of local stabilizing communities. We show that a constellation of mutational sites (G496S, Q498R, N501Y and Y505H) correspond to key binding energy hotspots and also contribute decisively to the key interfacial communities that mediate allosteric communications between S-RBD and ACE2. These Omicron mutations are responsible for both favorable local binding interactions and long-range allosteric interactions, providing key functional centers that mediate the high transmissibility of the virus. At the same time, our results show that other mutational sites could provide a "flexible shield" surrounding the stable community network, thereby allowing the Omicron virus to modulate immune evasion at different epitopes, while protecting the integrity of binding and allosteric interactions in the RBD-ACE2 complexes. This study suggests that the SARS-CoV-2 S protein may exploit the plasticity of the RBD to generate escape mutants, while engaging a small group of functional hotspots to mediate efficient local binding interactions and long-range allosteric communications with ACE2.
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Affiliation(s)
- Gennady Verkhivker
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (S.A.); (R.K.); (K.K.)
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
| | - Steve Agajanian
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (S.A.); (R.K.); (K.K.)
| | - Ryan Kassab
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (S.A.); (R.K.); (K.K.)
| | - Keerthi Krishnan
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (S.A.); (R.K.); (K.K.)
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67
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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68
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Díaz-Troyano N, Gabriel-Medina P, Weber S, Klammer M, Barquín-DelPino R, Castillo-Ribelles L, Esteban A, Hernández-González M, Ferrer-Costa R, Pumarola T, Rodríguez-Frías F. Soluble Angiotensin-Converting Enzyme 2 as a Prognostic Biomarker for Disease Progression in Patients Infected with SARS-CoV-2. Diagnostics (Basel) 2022; 12:diagnostics12040886. [PMID: 35453934 PMCID: PMC9031748 DOI: 10.3390/diagnostics12040886] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/25/2022] [Accepted: 03/31/2022] [Indexed: 02/07/2023] Open
Abstract
Predicting disease severity in patients infected with SARS-CoV-2 is difficult. Soluble angiotensin-converting enzyme 2 (sACE2) arises from the shedding of membrane ACE2 (mACE2), which is a receptor for SARS-CoV-2 spike protein. We evaluated the predictive value of sACE2 compared with known biomarkers of inflammation and tissue damage (CRP, GDF-15, IL-6, and sFlt-1) in 850 patients with and without SARS-CoV-2 with different clinical outcomes. For univariate analyses, median differences between biomarker levels were calculated for the following patient groups (classified by clinical outcome): RT-PCR-confirmed SARS-CoV-2 positive (Groups 1−4); RT-PCR-confirmed SARS-CoV-2 negative following previous SARS-CoV-2 infection (Groups 5 and 6); and ‘SARS-CoV-2 unexposed’ patients (Group 7). Median levels of CRP, GDF-15, IL-6, and sFlt-1 were significantly higher in hospitalized patients with SARS-CoV-2 compared with discharged patients (all p < 0.001), whereas levels of sACE2 were significantly lower (p < 0.001). ROC curve analysis of sACE2 provided cut-offs for predicting hospital admission (≤0.05 ng/mL (positive predictive value: 89.1%) and ≥0.42 ng/mL (negative predictive value: 84.0%)). These findings support further investigation of sACE2, as a single biomarker or as part of a panel, to predict hospitalization risk and disease severity in patients with SARS-CoV-2 infection.
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Affiliation(s)
- Noelia Díaz-Troyano
- Biochemistry Department (Clinical Laboratories), Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (N.D.-T.); (P.G.-M.); (R.B.-D.); (L.C.-R.); (A.E.); (R.F.-C.)
- Vall d’Hebron Research Institute, 08035 Barcelona, Spain; (M.H.-G.); (T.P.)
- Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Pablo Gabriel-Medina
- Biochemistry Department (Clinical Laboratories), Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (N.D.-T.); (P.G.-M.); (R.B.-D.); (L.C.-R.); (A.E.); (R.F.-C.)
- Vall d’Hebron Research Institute, 08035 Barcelona, Spain; (M.H.-G.); (T.P.)
- Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Stephen Weber
- Roche Diagnostics GmbH, 82377 Penzberg, Germany; (S.W.); (M.K.)
| | - Martin Klammer
- Roche Diagnostics GmbH, 82377 Penzberg, Germany; (S.W.); (M.K.)
| | - Raquel Barquín-DelPino
- Biochemistry Department (Clinical Laboratories), Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (N.D.-T.); (P.G.-M.); (R.B.-D.); (L.C.-R.); (A.E.); (R.F.-C.)
- Vall d’Hebron Research Institute, 08035 Barcelona, Spain; (M.H.-G.); (T.P.)
| | - Laura Castillo-Ribelles
- Biochemistry Department (Clinical Laboratories), Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (N.D.-T.); (P.G.-M.); (R.B.-D.); (L.C.-R.); (A.E.); (R.F.-C.)
- Vall d’Hebron Research Institute, 08035 Barcelona, Spain; (M.H.-G.); (T.P.)
- Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Angels Esteban
- Biochemistry Department (Clinical Laboratories), Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (N.D.-T.); (P.G.-M.); (R.B.-D.); (L.C.-R.); (A.E.); (R.F.-C.)
| | - Manuel Hernández-González
- Vall d’Hebron Research Institute, 08035 Barcelona, Spain; (M.H.-G.); (T.P.)
- Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- Immunology Department (Clinical Laboratories), Vall d’Hebron University Hospital, 08035 Barcelona, Spain
| | - Roser Ferrer-Costa
- Biochemistry Department (Clinical Laboratories), Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (N.D.-T.); (P.G.-M.); (R.B.-D.); (L.C.-R.); (A.E.); (R.F.-C.)
- Vall d’Hebron Research Institute, 08035 Barcelona, Spain; (M.H.-G.); (T.P.)
| | - Tomas Pumarola
- Vall d’Hebron Research Institute, 08035 Barcelona, Spain; (M.H.-G.); (T.P.)
- Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- Microbiology Department (Clinical Laboratories), Vall d’Hebron University Hospital, 08035 Barcelona, Spain
| | - Francisco Rodríguez-Frías
- Biochemistry Department (Clinical Laboratories), Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (N.D.-T.); (P.G.-M.); (R.B.-D.); (L.C.-R.); (A.E.); (R.F.-C.)
- Vall d’Hebron Research Institute, 08035 Barcelona, Spain; (M.H.-G.); (T.P.)
- Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- Correspondence:
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Kar P, Saleh-E-In MM, Jaishee N, Anandraj A, Kormuth E, Vellingiri B, Angione C, Rahman PKSM, Pillay S, Sen A, Naidoo D, Roy A, Choi YE. Computational profiling of natural compounds as promising inhibitors against the spike proteins of SARS-CoV-2 wild-type and the variants of concern, viral cell-entry process, and cytokine storm in COVID-19. J Cell Biochem 2022; 123:964-986. [PMID: 35342986 DOI: 10.1002/jcb.30243] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 12/16/2022]
Abstract
The continuous spread and evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the rapid surge in infection cases in the coronavirus disease 2019 (COVID-19) evoke a dire need for effective therapeutics. In this study, we explored the inhibitory potential of a library of 605 phytocompounds, selected from Indian medicinal plants with reported antiviral and anti-inflammatory activities, against the receptor-binding domain of spike proteins of the SARS-CoV-2 wild-type and the variants of concern, including variants B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), B.1.617.2 (Delta), and B.1.1.529 (Omicron). Our approach was based on extensive molecular docking, assessment of drug-likeness, and robust molecular dynamics simulations. We also identified promising inhibitory candidates against the host (human) proteins associated with SARS-CoV-2 spike activation and attachment, namely, ACE2 receptor, proteases TMPRSS2 and CTSL, and the endocytic regulator AAK1. In addition, we screened promising inhibitory compounds against the human proinflammatory cytokines- IL-6, IL-1β, TNF-α, and IFN-γ, that are associated with the adverse cytokine storm in COVID-19 patients. Our analysis returned an encouraging list of promising inhibitory candidates that includes: abietatriene against the spike proteins of the SARS-CoV-2 wild-type and the variants of concern; taraxerol against the human ACE2, CTSL and TNF-α; β-amyrin against the human TMPRSS2; cynaroside against the human AAK1 and IL-1β; and friedelin against the human IL-6 and IFN-γ. Our findings provide substantial evidence for the inhibitory potential of these compounds and encourage further in vitro and in vivo studies to validate their use as safe and effective therapeutics against COVID-19.
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Affiliation(s)
- Pallab Kar
- Molecular Cytogenetics Laboratory, Department of Botany, University of North Bengal, Siliguri, West Bengal, India
| | - Md Moshfekus Saleh-E-In
- Division of Forest Resources, College of Forest and Environmental Sciences, Kangwon National University, Chunchon, South Korea
| | - Nishika Jaishee
- Faculty of Natural Sciences, Mangosuthu University of Technology, Durban, South Africa
| | - Akash Anandraj
- Centre for Algal Biotechnology, Faculty of Natural Sciences, Mangosuthu University of Technology, Durban, South Africa
| | - Emil Kormuth
- Faculty of Natural Sciences, Mangosuthu University of Technology, Durban, South Africa
| | - Balachandar Vellingiri
- Human Molecular Cytogenetics and Stem Cell Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Claudio Angione
- School of Computing, Engineering and Digital Technologies, Teesside University, Middlesbrough, UK.,Centre for Digital Innovation, Teesside University, Middlesbrough, UK.,National Horizons Centre, Teesside University, Darlington, UK
| | | | | | - Arnab Sen
- Molecular Cytogenetics Laboratory, Department of Botany, University of North Bengal, Siliguri, West Bengal, India
| | - Devashan Naidoo
- Centre for Algal Biotechnology, Faculty of Natural Sciences, Mangosuthu University of Technology, Durban, South Africa
| | - Ayan Roy
- Department of Biotechnology, Lovely Professional University, Phagwara, Punjab, India
| | - Yong E Choi
- Division of Forest Resources, College of Forest and Environmental Sciences, Kangwon National University, Chunchon, South Korea
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Wang J, Luo J, Wen Z, Wang X, Shuai L, Zhong G, Wang C, Sun Z, Chen W, Ge J, Liu R, Wang X, Bu Z. Alpha-Soluble NSF Attachment Protein Prevents the Cleavage of the SARS-CoV-2 Spike Protein by Functioning as an Interferon-Upregulated Furin Inhibitor. mBio 2022; 13:e0244321. [PMID: 35012335 DOI: 10.1128/mbio.02443-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Loss of the furin cleavage motif in the SARS-CoV-2 spike protein reduces the virulence and transmission of SARS-CoV-2, suggesting that furin is an attractive antiviral drug target. However, lack of understanding of the regulation of furin activity has largely limited the development of furin-based therapeutic strategies. Here, we find that alpha-soluble NSF attachment protein (α-SNAP), an indispensable component of vesicle trafficking machinery, inhibits the cleavage of SARS-CoV-2 spike protein and other furin-dependent virus glycoproteins. SARS-CoV-2 infection increases the expression of α-SNAP, and overexpression of α-SNAP reduces SARS-CoV-2 infection in cells. We further reveal that α-SNAP is an interferon-upregulated furin inhibitor that inhibits furin function by interacting with its P domain. Our study demonstrates that α-SNAP, in addition to its role in vesicle trafficking, plays an important role in the host defense against furin-dependent virus infection and therefore could be a target for the development of therapeutic options for COVID-19. IMPORTANCE Some key mutations of SARS-CoV-2 spike protein, such as D614G and P681R mutations, increase the transmission or pathogenicity by enhancing the cleavage efficacy of spike protein by furin. Loss of the furin cleavage motif of SARS-CoV-2 spike protein reduces the virulence and transmission, suggesting that furin is an attractive antiviral drug target. However, lack of understanding of the regulation of furin activity has largely limited the development of furin-based therapeutic strategies. Here, we found that in addition to its canonical role in vesicle trafficking, alpha-soluble NSF attachment protein (α-SNAP) plays an important role in the host defense against furin-dependent virus infection. we identified that α-SNAP is a novel interferon-upregulated furin inhibitor and inhibits the cleavage of SARS-CoV-2 spike protein and other furin-dependent virus glycoproteins by interacting with P domain of furin. Our study demonstrates that α-SNAP could be a target for the development of therapeutic options for COVID-19.
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Verkhivker G. Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. Int J Mol Sci 2022; 23:2172. [PMID: 35216287 DOI: 10.3390/ijms23042172] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/13/2022] [Accepted: 02/14/2022] [Indexed: 02/04/2023] Open
Abstract
Structural and biochemical studies have recently revealed a range of rationally engineered nanobodies with efficient neutralizing capacity against the SARS-CoV-2 virus and resilience against mutational escape. In this study, we performed a comprehensive computational analysis of the SARS-CoV-2 spike trimer complexes with single nanobodies Nb6, VHH E, and complex with VHH E/VHH V nanobody combination. We combined coarse-grained and all-atom molecular simulations and collective dynamics analysis with binding free energy scanning, perturbation-response scanning, and network centrality analysis to examine mechanisms of nanobody-induced allosteric modulation and cooperativity in the SARS-CoV-2 spike trimer complexes with these nanobodies. By quantifying energetic and allosteric determinants of the SARS-CoV-2 spike protein binding with nanobodies, we also examined nanobody-induced modulation of escaping mutations and the effect of the Omicron variant on nanobody binding. The mutational scanning analysis supported the notion that E484A mutation can have a significant detrimental effect on nanobody binding and result in Omicron-induced escape from nanobody neutralization. Our findings showed that SARS-CoV-2 spike protein might exploit the plasticity of specific allosteric hotspots to generate escape mutants that alter response to binding without compromising activity. The network analysis supported these findings showing that VHH E/VHH V nanobody binding can induce long-range couplings between the cryptic binding epitope and ACE2-binding site through a broader ensemble of communication paths that is less dependent on specific mediating centers and therefore may be less sensitive to mutational perturbations of functional residues. The results suggest that binding affinity and long-range communications of the SARS-CoV-2 complexes with nanobodies can be determined by structurally stable regulatory centers and conformationally adaptable hotspots that are allosterically coupled and collectively control resilience to mutational escape.
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Ayankojo AG, Boroznjak R, Reut J, Öpik A, Syritski V. Molecularly imprinted polymer based electrochemical sensor for quantitative detection of SARS-CoV-2 spike protein. Sens Actuators B Chem 2022; 353:131160. [PMID: 34866797 PMCID: PMC8626155 DOI: 10.1016/j.snb.2021.131160] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 11/24/2021] [Accepted: 11/24/2021] [Indexed: 05/05/2023]
Abstract
The continued spread of the coronavirus disease and prevalence of the global pandemic is exacerbated by the increase in the number of asymptomatic individuals who unknowingly spread the SARS-CoV-2 virus. Although remarkable progress is being achieved at curtailing further rampage of the disease, there is still the demand for simple and rapid diagnostic tools for early detection of the COVID-19 infection and the following isolation. We report the fabrication of an electrochemical sensor based on a molecularly imprinted polymer synthetic receptor for the quantitative detection of SARS-CoV-2 spike protein subunit S1 (ncovS1), by harnessing the covalent interaction between 1,2-diols of the highly glycosylated protein and the boronic acid group of 3-aminophenylboronic acid (APBA). The sensor displays a satisfactory performance with a reaction time of 15 min and is capable of detecting ncovS1 both in phosphate buffered saline and patient's nasopharyngeal samples with LOD values of 15 fM and 64 fM, respectively. Moreover, the sensor is compatible with portable potentiostats thus allowing on-site measurements thereby holding a great potential as a point-of-care testing platform for rapid and early diagnosis of COVID-19 patients.
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Affiliation(s)
- Akinrinade George Ayankojo
- Department of Materials and Environmental Technology, Tallinn University of Technology, Ehitajate tee 5, 19086 Tallinn, Estonia
| | - Roman Boroznjak
- Department of Materials and Environmental Technology, Tallinn University of Technology, Ehitajate tee 5, 19086 Tallinn, Estonia
| | - Jekaterina Reut
- Department of Materials and Environmental Technology, Tallinn University of Technology, Ehitajate tee 5, 19086 Tallinn, Estonia
| | - Andres Öpik
- Department of Materials and Environmental Technology, Tallinn University of Technology, Ehitajate tee 5, 19086 Tallinn, Estonia
| | - Vitali Syritski
- Department of Materials and Environmental Technology, Tallinn University of Technology, Ehitajate tee 5, 19086 Tallinn, Estonia
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Maniscalco GT, Manzo V, Ferrara AL, Perrella A, Di Battista M, Salvatore S, Graziano D, Viola A, Amato G, Moreggia O, Di Giulio Cesare D, Barbato S, Servillo G, Longo K, Di Giovanni M, Scarpati B, Muggianu SM, Longo G, Russo G, Andreone V, De Rosa V. Interferon Beta-1a treatment promotes SARS-CoV-2 mRNA vaccine response in multiple sclerosis subjects. Mult Scler Relat Disord 2022; 58:103455. [PMID: 34929455 PMCID: PMC8683261 DOI: 10.1016/j.msard.2021.103455] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/22/2021] [Accepted: 12/03/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND Several concerns exist on the immunogenicity of SARS-CoV-2 vaccines in multiple sclerosis (MS) subjects due to their immunomodulating disease modifying therapies (DMTs). Here we report a comparison of the humoral response to BNT162b2-mRNA coronavirus (COVID)-19 vaccine and the immunological phenotype in a cohort of 125 MS subjects undergoing different DMTs, with no history of SARS-CoV-2 infection. METHODS We collected serum and blood samples at the first day of vaccine (T0) and 21 days after the second vaccine dose (T1) from 125 MS subjects, undergoing eight different DMTs. Sera were tested using the Elecsys anti-SARS-CoV-2-IgG assay for the detection of IgG antibodies to SARS-CoV-2 spike protein. The anti-spike IgG titres from MS subjects were compared with 24 age- and sex-matched healthy controls (HC). Percentage and absolute number of B and T lymphocytes were evaluated by cytofluorimetric analysis in the same study cohort. RESULTS When compared with SARS-CoV-2 IgG levels in HC (n = 24, median 1089 (IQR 652.5-1625) U/mL), we observed an increased secretion of SARS-CoV-2 IgG in interferon-beta 1a (IFN)-treated MS subjects (n = 22, median 1916 (IQR 1024-2879) U/mL) and an impaired humoral response in MS subjects undergoing cladribine (CLAD) (n = 10, median 396.9 (IQR 37.52-790.9) U/mL), fingolimod (FTY) (n = 19, median 7.9 (IQR 4.8-147.6) U/mL) and ocrelizumab (OCRE) (n = 15, median 0.67 (IQR 0.4-5.9) U/mL) treatment. Moreover, analysis of geometric mean titre ratio (GMTR) between different DMT's groups of MS subjects revealed that, when compared with IFN-treated MS subjects, intrinsic antibody production was impaired in teriflunomide (TERI)-, natalizumab (NAT)-, CLAD-, FTY- and OCRE-, while preserved in DMF- and GA-treated MS subjects. CONCLUSION Humoral response to BNT162b2-mRNA-vaccine was increased in IFN-treated MS subjects while clearly blunted in those under CLAD, FTY and OCRE treatment. This suggests that the DMTs could have a key role in the protection from SARS-CoV-2 related disease and complication in MS subjects, underlying a novel aspect that should be considered in the selection of the most appropriate therapy under COVID-19 pandemic.
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Affiliation(s)
- Giorgia Teresa Maniscalco
- Neurological Clinic and Stroke Unit, "A. Cardarelli" Hospital, Via A. Cardarelli 9, 80131, Naples, Italy; Multiple Sclerosis Center, "A. Cardarelli" Hospital, Via A. Cardarelli 9, 80131, Naples, Italy.
| | - Valentino Manzo
- Neurological Clinic and Stroke Unit, "A. Cardarelli" Hospital, Via A. Cardarelli 9, 80131, Naples, Italy.
| | - Anne Lise Ferrara
- Institute of Endocrinology and Experimental Oncology (IEOS-CNR), Via S. Pansini 5, 80131, Naples, Italy; Department of Translational Medical Science and Center for Basic and Clinical Immunology Research (CISI), University of Naples "Federico II", Via S. Pansini 5, Naples 80131, Italy.
| | - Alessandro Perrella
- Infectious Disease of Healthcare Direction, "A. Cardarelli" Hospital, Via A. Cardarelli 9, 80131, Naples, Italy.
| | - Mariaelena Di Battista
- Neurological Clinic and Stroke Unit, "A. Cardarelli" Hospital, Via A. Cardarelli 9, 80131, Naples, Italy; Multiple Sclerosis Center, "A. Cardarelli" Hospital, Via A. Cardarelli 9, 80131, Naples, Italy.
| | - Simona Salvatore
- Neurological Clinic and Stroke Unit, "A. Cardarelli" Hospital, Via A. Cardarelli 9, 80131, Naples, Italy; Multiple Sclerosis Center, "A. Cardarelli" Hospital, Via A. Cardarelli 9, 80131, Naples, Italy.
| | - Daniela Graziano
- Unit of Transfusional Medicine, SIMT, "A. Cardarelli" Hospital, Via A. Cardarelli 9, 80131, Naples, Italy.
| | - Assunta Viola
- Molecular Biology Laboratory, Hematology and Transplantation CSE, "A. Cardarelli" Hospital, Via A. Cardarelli 9, 80131, Naples, Italy.
| | - Gerardino Amato
- Clinical Pathology and Microbiology Laboratory "A. Cardarelli" Hospital, Via A. Cardarelli 9, 80131, Naples, Italy.
| | - Ornella Moreggia
- Multiple Sclerosis Center, "A. Cardarelli" Hospital, Via A. Cardarelli 9, 80131, Naples, Italy.
| | | | - Stefano Barbato
- Neurological Clinic and Stroke Unit, "A. Cardarelli" Hospital, Via A. Cardarelli 9, 80131, Naples, Italy.
| | - Giovanna Servillo
- Neurological Clinic and Stroke Unit, "A. Cardarelli" Hospital, Via A. Cardarelli 9, 80131, Naples, Italy.
| | - Katia Longo
- Neurological Clinic and Stroke Unit, "A. Cardarelli" Hospital, Via A. Cardarelli 9, 80131, Naples, Italy.
| | - Mario Di Giovanni
- Neurological Clinic and Stroke Unit, "A. Cardarelli" Hospital, Via A. Cardarelli 9, 80131, Naples, Italy.
| | - Barbara Scarpati
- Unit of Transfusional Medicine, SIMT, "A. Cardarelli" Hospital, Via A. Cardarelli 9, 80131, Naples, Italy.
| | - Simona Maria Muggianu
- Molecular Biology Laboratory, Hematology and Transplantation CSE, "A. Cardarelli" Hospital, Via A. Cardarelli 9, 80131, Naples, Italy.
| | - Giuseppe Longo
- General Direction "A. Cardarelli" Hospital, Via A. Cardarelli 9, 80131, Naples, Italy.
| | - Giuseppe Russo
- Infectious Disease of Healthcare Direction, "A. Cardarelli" Hospital, Via A. Cardarelli 9, 80131, Naples, Italy.
| | - Vincenzo Andreone
- Neurological Clinic and Stroke Unit, "A. Cardarelli" Hospital, Via A. Cardarelli 9, 80131, Naples, Italy.
| | - Veronica De Rosa
- Institute of Endocrinology and Experimental Oncology (IEOS-CNR), Via S. Pansini 5, 80131, Naples, Italy.
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Zhao J, Zhao F, Li H, Xiong Y, Cai S, Wang C, Chen Y, Han N, Yang R. Magnet-assisted electrochemical immunosensor based on surface-clean Pd-Au nanosheets for sensitive detection of SARS-CoV-2 spike protein. Electrochim Acta 2022; 404:139766. [PMID: 34961798 PMCID: PMC8696018 DOI: 10.1016/j.electacta.2021.139766] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 12/13/2021] [Accepted: 12/17/2021] [Indexed: 12/18/2022]
Abstract
Tracking and monitoring of low concentrations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can effectively control asymptomatic transmission of current coronavirus disease 2019 (COVID-19) in the early stages of infection. Here, we highlight an electrochemical immunosensor for sensitive detection of SARS-CoV-2 antigen marker spike protein. The surface-clean Pd-Au nanosheets as a substrate for efficient sensing and signal output have been synthesized. The morphology, chemical states and excellent stable electrochemical properties of this surface-clean heterostructures have been studied. Functionalized superparamagnetic nanoparticles (MNPs) were introduced as sample separators and signal amplifiers. This biosensor was tested in phosphate buffered saline (PBS) and nasopharyngeal samples. The results showed that the sensor has a wide linear dynamic range (0.01 ng mL−1 to 1000 ng mL−1) with a low detection limit (0.0072 ng mL−1), which achieved stable and sensitive detection of the spike protein. Therefore, this immunosensing method provides a promising electrochemical measurement tool, which can furnish ideas for early screening and the reasonable optimization of detection methods of SARS-CoV-2.
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Affiliation(s)
- Jialin Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Center of Materials Science and Optoelectronics Engineering, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, University of Chinese Academy of Sciences, No.11 ZhongGuanCun BeiYiTiao, Beijing 100190, China.,Sino-Danish College, Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fu Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Center of Materials Science and Optoelectronics Engineering, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, University of Chinese Academy of Sciences, No.11 ZhongGuanCun BeiYiTiao, Beijing 100190, China
| | - Haolin Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Center of Materials Science and Optoelectronics Engineering, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, University of Chinese Academy of Sciences, No.11 ZhongGuanCun BeiYiTiao, Beijing 100190, China.,Sino-Danish College, Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Youlin Xiong
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Center of Materials Science and Optoelectronics Engineering, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, University of Chinese Academy of Sciences, No.11 ZhongGuanCun BeiYiTiao, Beijing 100190, China
| | - Shuangfei Cai
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Center of Materials Science and Optoelectronics Engineering, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, University of Chinese Academy of Sciences, No.11 ZhongGuanCun BeiYiTiao, Beijing 100190, China
| | - Chen Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Center of Materials Science and Optoelectronics Engineering, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, University of Chinese Academy of Sciences, No.11 ZhongGuanCun BeiYiTiao, Beijing 100190, China
| | - Yunfa Chen
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
| | - Ning Han
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
| | - Rong Yang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Center of Materials Science and Optoelectronics Engineering, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, University of Chinese Academy of Sciences, No.11 ZhongGuanCun BeiYiTiao, Beijing 100190, China.,Sino-Danish College, Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing 100049, China
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Verkhivker G. Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. Int J Mol Sci 2022; 23:ijms23031646. [PMID: 35163572 PMCID: PMC8836237 DOI: 10.3390/ijms23031646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/22/2022] [Accepted: 01/29/2022] [Indexed: 02/01/2023] Open
Abstract
Structural and functional studies of the SARS-CoV-2 spike proteins have recently determined distinct functional states of the B.1.1.7 and B.1.351 spike variants, providing a molecular framework for understanding the mechanisms that link the effect of mutations with the enhanced virus infectivity and transmissibility. A detailed dynamic and energetic analysis of these variants was undertaken in the present work to quantify the effects of different mutations on functional conformational changes and stability of the SARS-CoV-2 spike protein. We employed the efficient and accurate coarse-grained (CG) simulations of multiple functional states of the D614G mutant, B.1.1.7 and B.1.351 spike variants to characterize conformational dynamics of the SARS-CoV-2 spike proteins and identify dynamic signatures of the functional regions that regulate transitions between the closed and open forms. By combining molecular simulations with full atomistic reconstruction of the trajectories and the ensemble-based mutational frustration analysis, we characterized how the intrinsic flexibility of specific spike regions can control functional conformational changes required for binding with the host-cell receptor. Using the residue-based mutational scanning of protein stability, we determined protein stability hotspots and identified potential energetic drivers favoring the receptor-accessible open spike states for the B.1.1.7 and B.1.351 spike variants. The results suggested that modulation of the energetic frustration at the inter-protomer interfaces can serve as a mechanism for allosteric couplings between mutational sites and the inter-protomer hinges of functional motions. The proposed mechanism of mutation-induced energetic frustration may result in greater adaptability and the emergence of multiple conformational states in the open form. This study suggested that SARS-CoV-2 B.1.1.7 and B.1.351 variants may leverage the intrinsic plasticity of functional regions in the spike protein for mutation-induced modulation of protein dynamics and allosteric regulation to control binding with the host cell receptor.
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Affiliation(s)
- Gennady Verkhivker
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; ; Tel.: +17-14-516-4586
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
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76
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Marchetti C, Vaglietti S, Rizzo F, Di Nardo G, Colnaghi L, Ghirardi M, Fiumara F. Heptad stereotypy, S/Q layering, and remote origin of the SARS-CoV-2 fusion core. Virus Evol 2022; 7:veab097. [PMID: 35039783 PMCID: PMC8754743 DOI: 10.1093/ve/veab097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 10/24/2021] [Accepted: 11/23/2021] [Indexed: 11/13/2022] Open
Abstract
The fusion of the SARS-CoV-2 virus with cells, a key event in the pathogenesis of Covid-19, depends on the assembly of a six-helix fusion core (FC) formed by portions of the spike protein heptad repeats (HRs) 1 and 2. Despite the critical role in regulating infectivity, its distinctive features, origin, and evolution are scarcely understood. Thus, we undertook a structure-guided positional and compositional analysis of the SARS-CoV-2 FC, in comparison with FCs of related viruses, tracing its origin and ongoing evolution. We found that clustered amino acid substitutions within HR1, distinguishing SARS-CoV-2 from SARS-CoV-1, enhance local heptad stereotypy and increase sharply the FC serine-to-glutamine (S/Q) ratio, determining a neat alternate layering of S-rich and Q-rich subdomains along the post-fusion structure. Strikingly, SARS-CoV-2 ranks among viruses with the highest FC S/Q ratio, together with highly syncytiogenic respiratory pathogens (RSV, NDV), whereas MERS-Cov, HIV, and Ebola viruses display low ratios, and this feature reflects onto S/Q segregation and H-bonding patterns. Our evolutionary analyses revealed that the SARS-CoV-2 FC occurs in other SARS-CoV-1-like Sarbecoviruses identified since 2005 in Hong Kong and adjacent regions, tracing its origin to >50 years ago with a recombination-driven spread. Finally, current mutational trends show that the FC is varying especially in the FC1 evolutionary hotspot. These findings establish a novel analytical framework illuminating the sequence/structure evolution of the SARS-CoV-2 FC, tracing its long history within Sarbecoviruses, and may help rationalize the evolution of the fusion machinery in emerging pathogens and the design of novel therapeutic fusion inhibitors.
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Affiliation(s)
- Chiara Marchetti
- Rita Levi Montalcini Department of Neuroscience, University of Torino, Corso Raffaello 30, Torino 10125, Italy
| | - Serena Vaglietti
- Rita Levi Montalcini Department of Neuroscience, University of Torino, Corso Raffaello 30, Torino 10125, Italy
| | - Francesca Rizzo
- Istituto Zooprofilattico Sperimentale (IZS) del Piemonte, Liguria e Valle d'Aosta, Via Bologna 148, Torino 10148, Italy
| | - Giovanna Di Nardo
- Department of Life Sciences and Systems Biology (DBIOS), University of Torino, Via Accademia Albertina 13, Torino 10123, Italy
| | - Luca Colnaghi
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Via Olgettina 60, Milano 20132, Italy
| | - Mirella Ghirardi
- Rita Levi Montalcini Department of Neuroscience, University of Torino, Corso Raffaello 30, Torino 10125, Italy
| | - Ferdinando Fiumara
- Rita Levi Montalcini Department of Neuroscience, University of Torino, Corso Raffaello 30, Torino 10125, Italy
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Verta R, Grange C, Skovronova R, Tanzi A, Peruzzi L, Deregibus MC, Camussi G, Bussolati B. Generation of Spike-Extracellular Vesicles (S-EVs) as a Tool to Mimic SARS-CoV-2 Interaction with Host Cells. Cells 2022; 11:146. [PMID: 35011708 PMCID: PMC8750506 DOI: 10.3390/cells11010146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/20/2021] [Accepted: 12/30/2021] [Indexed: 01/08/2023] Open
Abstract
Extracellular vesicles (EVs) and viruses share common features: size, structure, biogenesis and uptake. In order to generate EVs expressing the SARS-CoV-2 spike protein on their surface (S-EVs), we collected EVs from SARS-CoV-2 spike expressing human embryonic kidney (HEK-293T) cells by stable transfection with a vector coding for the S1 and S2 subunits. S-EVs were characterized using nanoparticle tracking analysis, ExoView and super-resolution microscopy. We obtained a population of EVs of 50 to 200 nm in size. Spike expressing EVs represented around 40% of the total EV population and co-expressed spike protein with tetraspanins on the surfaces of EVs. We subsequently used ACE2-positive endothelial and bronchial epithelial cells for assessing the internalization of labeled S-EVs using a cytofluorimetric analysis. Internalization of S-EVs was higher than that of control EVs from non-transfected cells. Moreover, S-EV uptake was significantly decreased by anti-ACE2 antibody pre-treatment. Furthermore, colchicine, a drug currently used in clinical trials, significantly reduced S-EV entry into the cells. S-EVs represent a simple, safe, and scalable model to study host-virus interactions and the mechanisms of novel therapeutic drugs.
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Affiliation(s)
- Roberta Verta
- Department of Molecular Biotechnology and Health Sciences, University of Turin, 10126 Turin, Italy; (R.V.); (R.S.); (A.T.)
| | - Cristina Grange
- Department of Medical Science, University of Turin, 10126 Turin, Italy; (C.G.); (G.C.)
| | - Renata Skovronova
- Department of Molecular Biotechnology and Health Sciences, University of Turin, 10126 Turin, Italy; (R.V.); (R.S.); (A.T.)
| | - Adele Tanzi
- Department of Molecular Biotechnology and Health Sciences, University of Turin, 10126 Turin, Italy; (R.V.); (R.S.); (A.T.)
| | - Licia Peruzzi
- Pediatric Nephrology Unit, Regina Margherita Children’s Hospital, Città della Salute e della Scienza di Torino, 10126 Turin, Italy;
| | - Maria Chiara Deregibus
- 2i3T Business Incubator and Technology Transfer, University of Turin, 10126 Turin, Italy;
| | - Giovanni Camussi
- Department of Medical Science, University of Turin, 10126 Turin, Italy; (C.G.); (G.C.)
| | - Benedetta Bussolati
- Department of Molecular Biotechnology and Health Sciences, University of Turin, 10126 Turin, Italy; (R.V.); (R.S.); (A.T.)
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78
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Chen M, Cui D, Zhao Z, Kang D, Li Z, Albawardi S, Alsageer S, Alamri F, Alhazmi A, Amer MR, Zhou C. Highly sensitive, scalable, and rapid SARS-CoV-2 biosensor based on In 2O 3 nanoribbon transistors and phosphatase. Nano Res 2022; 15:5510-5516. [PMID: 35371413 PMCID: PMC8959552 DOI: 10.1007/s12274-022-4190-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 05/06/2023]
Abstract
UNLABELLED Developing convenient and accurate SARS-CoV-2 antigen test and serology test is crucial in curbing the global COVID-19 pandemic. In this work, we report an improved indium oxide (In2O3) nanoribbon field-effect transistor (FET) biosensor platform detecting both SARS-CoV-2 antigen and antibody. Our FET biosensors, which were fabricated using a scalable and cost-efficient lithography-free process utilizing shadow masks, consist of an In2O3 channel and a newly developed stable enzyme reporter. During the biosensing process, the phosphatase enzymatic reaction generated pH change of the solution, which was then detected and converted to electrical signal by our In2O3 FETs. The biosensors applied phosphatase as enzyme reporter, which has a much better stability than the widely used urease in FET based biosensors. As proof-of-principle studies, we demonstrate the detection of SARS-CoV-2 spike protein in both phosphate-buffered saline (PBS) buffer and universal transport medium (UTM) (limit of detection [LoD]: 100 fg/mL). Following the SARS-CoV-2 antigen tests, we developed and characterized additional sensors aimed at SARS-CoV-2 IgG antibodies, which is important to trace past infection and vaccination. Our spike protein IgG antibody tests exhibit excellent detection limits in both PBS and human whole blood ((LoD): 1 pg/mL). Our biosensors display similar detection performance in different mediums, demonstrating that our biosensor approach is not limited by Debye screening from salts and can selectively detect biomarkers in physiological fluids. The newly selected enzyme for our platform performs much better performance and longer shelf life which will lead our biosensor platform to be capable for real clinical diagnosis usage. ELECTRONIC SUPPLEMENTARY MATERIAL Supplementary material (materials and methods for device fabrication, functionalization of In2O3 devices, photographs of the liquid gate measurement setup, mobilities of the nine devices labeled in Fig. 1(b), family curves of I DS-V DS with the liquid gate setup and current change after bubbling the substrate solution (current vs. time curve for S1 antigen detection)) is available in the online version of this article at 10.1007/s12274-022-4190-0.
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Affiliation(s)
- Mingrui Chen
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089 USA
| | - Dingzhou Cui
- Ming Hsieh Department of Electrical Engineering, University of Southern California, Los Angeles, California 90089 USA
| | - Zhiyuan Zhao
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089 USA
| | - Di Kang
- eDNA Biotech, Pasadena, California 91107 USA
| | - Zhen Li
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089 USA
| | - Shahad Albawardi
- Center of Excellence for Green Nanotechnologies, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Shahla Alsageer
- Center of Excellence for Green Nanotechnologies, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Faisal Alamri
- Center of Excellence for Green Nanotechnologies, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Abrar Alhazmi
- Center of Excellence for Green Nanotechnologies, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Moh. R. Amer
- Center of Excellence for Green Nanotechnologies, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
- Department of Electrical Engineering, 420 Westwood Plaza, 5412 Boelter Hall, University of California, Los Angeles, Los Angeles, California 90095 USA
| | - Chongwu Zhou
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089 USA
- Ming Hsieh Department of Electrical Engineering, University of Southern California, Los Angeles, California 90089 USA
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79
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Abdi Ghavidel A, Rojhannezhad M, Kazemi B, Bandehpour M. Effectiveness of Coronavirus Vaccines against Syndrome Coronavirus 2 (SARS-CoV-2) and Its New Variants. Iran J Allergy Asthma Immunol 2021; 20:647-671. [PMID: 34920649 DOI: 10.18502/ijaai.v20i6.8016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 07/06/2021] [Indexed: 06/14/2023]
Abstract
The widespread outbreak of coronavirus disease 2019 in late 2019 caused many people worldwide to die or suffer from certain clinical complications even after the recovery. The virus has many social and economic adverse effects. Studies on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have specified that spike, surface glycoprotein antigen, is considered as a major target to stimulate the immune system. This glycoprotein binds to the angiotensin-converting enzyme 2 on the surface of human cells especially lung epithelial cells and facilitates the virus entry. Therefore, the immune response stimulated by vaccination targeting this antigen may cause immunity against the whole virus. Currently, many companies are working on SARS-CoV-2 vaccines. They include 'traditional' vaccines like attenuated or inactivated virus platforms as well as the brand-new generations of vaccines such as viral vector-based, subunit, nucleic acid-based, and virus-like particle vaccines. Certainly, each vaccine platform presents several advantages and disadvantages affecting its efficacy and safety which is the main topic of this paper.
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Affiliation(s)
- Afshin Abdi Ghavidel
- Student Research Committee, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mahbubeh Rojhannezhad
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Bahram Kazemi
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mojgan Bandehpour
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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80
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Kuznetsov A, Arukuusk P, Härk H, Juronen E, Ustav M, Langel Ü, Järv J. ACE2 Peptide Fragment Interaction with Different S1 Protein Sites. Int J Pept Res Ther 2021; 28:7. [PMID: 34867130 PMCID: PMC8634746 DOI: 10.1007/s10989-021-10324-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2021] [Indexed: 11/25/2022]
Abstract
We study the effect of the peptide QAKTFLDKFNHEAEDLFYQ on the kinetics of the SARS-CoV-2 spike protein S1 binding to angiotensin-converting enzyme 2 (ACE2), with the aim to characterize the interaction mechanism of the SARS-CoV2 virus with its host cell. This peptide corresponds to the sequence 24–42 of the ACE2 α1 domain, which marks the binding site for the S1 protein. The kinetics of S1-ACE2 complex formation was measured in the presence of various concentrations of the peptide using bio-layer interferometry. Formation of the S1-ACE2 complex was inhibited by the peptide in cases where it was preincubated with S1 protein before the binding experiment. The kinetic analysis of S1-ACE2 complex dissociation revealed that preincubation stabilized this complex, and this effect was dependent on the peptide concentration as well as the preincubation time. The results point to the formation of the ternary complex of S1 with ACE2 and the peptide. This is possible in the presence of another binding site for the S1 protein beside the receptor-binding domain for ACE2, which binds the peptide QAKTFLDKFNHEAEDLFYQ. Therefore, we conducted computational mapping of the S1 protein surface, revealing two additional binding sites located at some distance from the main receptor-binding domain on S1. We suggest the possibility to predict and test the short protein derived peptides for development of novel strategies in inhibiting virus infections.
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Affiliation(s)
| | - Piret Arukuusk
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Heleri Härk
- Institute of Technology, University of Tartu, Tartu, Estonia
| | | | - Mart Ustav
- Institute of Technology, University of Tartu, Tartu, Estonia.,Icosagen Cell Factory OÜ, Tartu, Estonia
| | - Ülo Langel
- Institute of Technology, University of Tartu, Tartu, Estonia.,Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Jaak Järv
- Institute of Chemistry, University of Tartu, Tartu, Estonia
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81
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Chen P, Wang J, Xu X, Li Y, Zhu Y, Li X, Li M, Hao P. Molecular dynamic simulation analysis of SARS-CoV-2 spike mutations and evaluation of ACE2 from pets and wild animals for infection risk. Comput Biol Chem 2021; 96:107613. [PMID: 34896769 PMCID: PMC8634692 DOI: 10.1016/j.compbiolchem.2021.107613] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 11/29/2021] [Indexed: 12/28/2022]
Abstract
Coronavirus Disease 2019 (COVID-19) is an ongoing global health emergency that has caused tremendous stress and loss of life worldwide. The viral spike glycoprotein is a critical molecule mediating transmission of SARS-CoV-2 by interacting with human ACE2. However, through the course of the pandemics, there has not been a thorough analysis of the spike protein mutations, and on how these mutants influence the transmission of SARS-CoV-2. Besides, cases of SARS-CoV-2 infection among pets and wild animals have been reported, so the susceptibility of these animals requires great attention to investigate, as they may also link to the renewed question of a possible intermediate host for SARS-CoV-2 before it was transmitted to humans. With over 226,000 SARS-CoV-2 sequences obtained, we found 1573 missense mutations in the spike gene, and 226 of them were within the receptor-binding domain (RBD) region that directly interacts with human ACE2. Modeling the interactions between SARS-CoV-2 spike mutants and ACE2 molecules showed that most of the 74 missense mutations in the RBD region of the interaction interface had little impact on spike binding to ACE2, whereas several within the spike RBD increased the binding affinity toward human ACE2 thus making the virus likely more contagious. On the other hand, modeling the interactions between animal ACE2 molecules and SARS-CoV-2 spike revealed that many pets and wild animals' ACE2 had a variable binding ability. Particularly, ACE2 of bamboo rat had stronger binding to SARS-CoV-2 spike protein, whereas that of mole, vole, Mus pahari, palm civet, and pangolin had a weaker binding compared to human ACE2. Our results provide structural insights into the impact on interactions of the SARS-CoV-2 spike mutants to human ACE2, and shed light on SARS-CoV-2 transmission in pets and wild animals, and possible clues to the intermediate host(s) for SARS-CoV-2.
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Affiliation(s)
- Ping Chen
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China; Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jingfang Wang
- Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xintian Xu
- Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yuping Li
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - Yan Zhu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Science, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xuan Li
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Science, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China.
| | - Ming Li
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China.
| | - Pei Hao
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China; Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100039, China.
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82
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Beaudoin CA, Hamaia SW, Huang CLH, Blundell TL, Jackson AP. Can the SARS-CoV-2 Spike Protein Bind Integrins Independent of the RGD Sequence? Front Cell Infect Microbiol 2021; 11:765300. [PMID: 34869067 PMCID: PMC8637727 DOI: 10.3389/fcimb.2021.765300] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/25/2021] [Indexed: 12/20/2022] Open
Abstract
The RGD motif in the Severe Acute Syndrome Coronavirus 2 (SARS-CoV-2) spike protein has been predicted to bind RGD-recognizing integrins. Recent studies have shown that the spike protein does, indeed, interact with αVβ3 and α5β1 integrins, both of which bind to RGD-containing ligands. However, computational studies have suggested that binding between the spike RGD motif and integrins is not favourable, even when unfolding occurs after conformational changes induced by binding to the canonical host entry receptor, angiotensin-converting enzyme 2 (ACE2). Furthermore, non-RGD-binding integrins, such as αx, have been suggested to interact with the SARS-CoV-2 spike protein. Other viral pathogens, such as rotaviruses, have been recorded to bind integrins in an RGD-independent manner to initiate host cell entry. Thus, in order to consider the potential for the SARS-CoV-2 spike protein to bind integrins independent of the RGD sequence, we investigate several factors related to the involvement of integrins in SARS-CoV-2 infection. First, we review changes in integrin expression during SARS-CoV-2 infection to identify which integrins might be of interest. Then, all known non-RGD integrin-binding motifs are collected and mapped to the spike protein receptor-binding domain and analyzed for their 3D availability. Several integrin-binding motifs are shown to exhibit high sequence similarity with solvent accessible regions of the spike receptor-binding domain. Comparisons of these motifs with other betacoronavirus spike proteins, such as SARS-CoV and RaTG13, reveal that some have recently evolved while others are more conserved throughout phylogenetically similar betacoronaviruses. Interestingly, all of the potential integrin-binding motifs, including the RGD sequence, are conserved in one of the known pangolin coronavirus strains. Of note, the most recently recorded mutations in the spike protein receptor-binding domain were found outside of the putative integrin-binding sequences, although several mutations formed inside and close to one motif, in particular, may potentially enhance binding. These data suggest that the SARS-CoV-2 spike protein may interact with integrins independent of the RGD sequence and may help further explain how SARS-CoV-2 and other viruses can evolve to bind to integrins.
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Affiliation(s)
- Christopher A Beaudoin
- Department of Biochemistry, Sanger Building, University of Cambridge, Cambridge, United Kingdom
| | - Samir W Hamaia
- Department of Biochemistry, Hopkins Building, University of Cambridge, Cambridge, United Kingdom
| | - Christopher L-H Huang
- Department of Biochemistry, Hopkins Building, University of Cambridge, Cambridge, United Kingdom
- Physiological Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Tom L Blundell
- Department of Biochemistry, Sanger Building, University of Cambridge, Cambridge, United Kingdom
| | - Antony P Jackson
- Department of Biochemistry, Hopkins Building, University of Cambridge, Cambridge, United Kingdom
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83
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Piccinini E, Allegretto JA, Scotto J, Cantillo AL, Fenoy GE, Marmisollé WA, Azzaroni O. Surface Engineering of Graphene through Heterobifunctional Supramolecular-Covalent Scaffolds for Rapid COVID-19 Biomarker Detection. ACS Appl Mater Interfaces 2021; 13:43696-43707. [PMID: 34470205 DOI: 10.1021/acsami.1c12142] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Graphene is a two-dimensional semiconducting material whose application for diagnostics has been a real game-changer in terms of sensitivity and response time, variables of paramount importance to stop the COVID-19 spreading. Nevertheless, strategies for the modification of docking recognition and antifouling elements to obtain covalent-like stability without the disruption of the graphene band structure are still needed. In this work, we conducted surface engineering of graphene through heterofunctional supramolecular-covalent scaffolds based on vinylsulfonated-polyamines (PA-VS). In these scaffolds, one side binds graphene through multivalent π-π interactions with pyrene groups, and the other side presents vinylsulfonated pending groups that can be used for covalent binding. The construction of PA-VS scaffolds was demonstrated by spectroscopic ellipsometry, Raman spectroscopy, and contact angle measurements. The covalent binding of -SH, -NH2, or -OH groups was confirmed, and it evidenced great chemical versatility. After field-effect studies, we found that the PA-VS-based scaffolds do not disrupt the semiconducting properties of graphene. Moreover, the scaffolds were covalently modified with poly(ethylene glycol) (PEG), which improved the resistance to nonspecific proteins by almost 7-fold compared to the widely used PEG-monopyrene approach. The attachment of recognition elements to PA-VS was optimized for concanavalin A (ConA), a model lectin with a high affinity to glycans. Lastly, the platform was implemented for the rapid, sensitive, and regenerable recognition of SARS-CoV-2 spike protein and human ferritin in lab-made samples. Those two are the target molecules of major importance for the rapid detection and monitoring of COVID-19-positive patients. For that purpose, monoclonal antibodies (mAbs) were bound to the scaffolds, resulting in a surface coverage of 436 ± 30 ng/cm2. KD affinity constants of 48.4 and 2.54 nM were obtained by surface plasmon resonance (SPR) spectroscopy for SARS-CoV-2 spike protein and human ferritin binding on these supramolecular scaffolds, respectively.
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Affiliation(s)
- Esteban Piccinini
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET, CC 16 Suc. 4, La Plata B1904DPI, Argentina
| | - Juan A Allegretto
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET, CC 16 Suc. 4, La Plata B1904DPI, Argentina
| | - Juliana Scotto
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET, CC 16 Suc. 4, La Plata B1904DPI, Argentina
| | - Agustín L Cantillo
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET, CC 16 Suc. 4, La Plata B1904DPI, Argentina
- GISENS BIOTECH, Ciudad Autónoma de Buenos Aires 1195, Argentina
| | - Gonzalo E Fenoy
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET, CC 16 Suc. 4, La Plata B1904DPI, Argentina
| | - Waldemar A Marmisollé
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET, CC 16 Suc. 4, La Plata B1904DPI, Argentina
| | - Omar Azzaroni
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET, CC 16 Suc. 4, La Plata B1904DPI, Argentina
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84
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Tian F, Tong B, Sun L, Shi S, Zheng B, Wang Z, Dong X, Zheng P. N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. eLife 2021; 10:e69091. [PMID: 34414884 PMCID: PMC8455130 DOI: 10.7554/elife.69091] [Citation(s) in RCA: 196] [Impact Index Per Article: 65.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 08/19/2021] [Indexed: 12/18/2022] Open
Abstract
SARS-CoV-2 has been spreading around the world for the past year. Recently, several variants such as B.1.1.7 (alpha), B.1.351 (beta), and P.1 (gamma), which share a key mutation N501Y on the receptor-binding domain (RBD), appear to be more infectious to humans. To understand the underlying mechanism, we used a cell surface-binding assay, a kinetics study, a single-molecule technique, and a computational method to investigate the interaction between these RBD (mutations) and ACE2. Remarkably, RBD with the N501Y mutation exhibited a considerably stronger interaction, with a faster association rate and a slower dissociation rate. Atomic force microscopy (AFM)-based single-molecule force microscopy (SMFS) consistently quantified the interaction strength of RBD with the mutation as having increased binding probability and requiring increased unbinding force. Molecular dynamics simulations of RBD-ACE2 complexes indicated that the N501Y mutation introduced additional π-π and π-cation interactions that could explain the changes observed by force microscopy. Taken together, these results suggest that the reinforced RBD-ACE2 interaction that results from the N501Y mutation in the RBD should play an essential role in the higher rate of transmission of SARS-CoV-2 variants, and that future mutations in the RBD of the virus should be under surveillance.
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Affiliation(s)
- Fang Tian
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing UniversityNanjingChina
| | - Bei Tong
- Institute of Botany, Jiangsu Province and Chinese Academy of SciencesNanjingChina
| | - Liang Sun
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing UniversityNanjingChina
| | - Shengchao Shi
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing UniversityNanjingChina
| | - Bin Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing UniversityNanjingChina
| | - Zibin Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing UniversityNanjingChina
| | - Xianchi Dong
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing UniversityNanjingChina
- Engineering Research Center of Protein and Peptide Medicine, Ministry of EducationNanjingChina
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing UniversityNanjingChina
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85
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Souaid K, Oulès B, Sohier P, Deschamps L, Aractingi S, Dupin N. Type I Interferon Signature in Chilblains Following SARS-CoV-2 mRNA Vaccine: A Case Report. Acta Derm Venereol 2021; 101:adv00589. [PMID: 34396420 PMCID: PMC9455332 DOI: 10.2340/00015555-3888] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Karim Souaid
- Department of Dermatology, Hôpital Cochin, AP-HP, AP-HP Centre-Université de Paris, 89 rue d'Assas, FR-75006 Paris, France
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86
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Wu CT, Lidsky PV, Xiao Y, Lee IT, Cheng R, Nakayama T, Jiang S, Demeter J, Bevacqua RJ, Chang CA, Whitener RL, Stalder AK, Zhu B, Chen H, Goltsev Y, Tzankov A, Nayak JV, Nolan GP, Matter MS, Andino R, Jackson PK. SARS-CoV-2 infects human pancreatic β cells and elicits β cell impairment. Cell Metab 2021; 33:1565-1576.e5. [PMID: 34081912 PMCID: PMC8130512 DOI: 10.1016/j.cmet.2021.05.013] [Citation(s) in RCA: 185] [Impact Index Per Article: 61.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 04/01/2021] [Accepted: 05/07/2021] [Indexed: 01/08/2023]
Abstract
Emerging evidence points toward an intricate relationship between the pandemic of coronavirus disease 2019 (COVID-19) and diabetes. While preexisting diabetes is associated with severe COVID-19, it is unclear whether COVID-19 severity is a cause or consequence of diabetes. To mechanistically link COVID-19 to diabetes, we tested whether insulin-producing pancreatic β cells can be infected by SARS-CoV-2 and cause β cell depletion. We found that the SARS-CoV-2 receptor, ACE2, and related entry factors (TMPRSS2, NRP1, and TRFC) are expressed in β cells, with selectively high expression of NRP1. We discovered that SARS-CoV-2 infects human pancreatic β cells in patients who succumbed to COVID-19 and selectively infects human islet β cells in vitro. We demonstrated that SARS-CoV-2 infection attenuates pancreatic insulin levels and secretion and induces β cell apoptosis, each rescued by NRP1 inhibition. Phosphoproteomic pathway analysis of infected islets indicates apoptotic β cell signaling, similar to that observed in type 1 diabetes (T1D). In summary, our study shows SARS-CoV-2 can directly induce β cell killing.
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Affiliation(s)
- Chien-Ting Wu
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peter V Lidsky
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yinghong Xiao
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ivan T Lee
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA; Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Ran Cheng
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA, USA
| | - Tsuguhisa Nakayama
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA; Department of Otorhinolaryngology, Jikei University School of Medicine, Tokyo, Japan
| | - Sizun Jiang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Janos Demeter
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Romina J Bevacqua
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Charles A Chang
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Robert L Whitener
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anna K Stalder
- Institute of Pathology, University of Basel, Schönbeinstrasse 40, 4003 Basel, Switzerland
| | - Bokai Zhu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Han Chen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yury Goltsev
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexandar Tzankov
- Institute of Pathology, University of Basel, Schönbeinstrasse 40, 4003 Basel, Switzerland
| | - Jayakar V Nayak
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthias S Matter
- Institute of Pathology, University of Basel, Schönbeinstrasse 40, 4003 Basel, Switzerland.
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA.
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87
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Hsu JTA, Tien CF, Yu GY, Shen S, Lee YH, Hsu PC, Wang Y, Chao PK, Tsay HJ, Shie FS. The Effects of Aβ 1-42 Binding to the SARS-CoV-2 Spike Protein S1 Subunit and Angiotensin-Converting Enzyme 2. Int J Mol Sci 2021; 22:8226. [PMID: 34360989 PMCID: PMC8347908 DOI: 10.3390/ijms22158226] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 11/16/2022] Open
Abstract
Increasing evidence suggests that elderly people with dementia are vulnerable to the development of severe coronavirus disease 2019 (COVID-19). In Alzheimer's disease (AD), the major form of dementia, β-amyloid (Aβ) levels in the blood are increased; however, the impact of elevated Aβ levels on the progression of COVID-19 remains largely unknown. Here, our findings demonstrate that Aβ1-42, but not Aβ1-40, bound to various viral proteins with a preferentially high affinity for the spike protein S1 subunit (S1) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the viral receptor, angiotensin-converting enzyme 2 (ACE2). These bindings were mainly through the C-terminal residues of Aβ1-42. Furthermore, Aβ1-42 strengthened the binding of the S1 of SARS-CoV-2 to ACE2 and increased the viral entry and production of IL-6 in a SARS-CoV-2 pseudovirus infection model. Intriguingly, data from a surrogate mouse model with intravenous inoculation of Aβ1-42 show that the clearance of Aβ1-42 in the blood was dampened in the presence of the extracellular domain of the spike protein trimers of SARS-CoV-2, whose effects can be prevented by a novel anti-Aβ antibody. In conclusion, these findings suggest that the binding of Aβ1-42 to the S1 of SARS-CoV-2 and ACE2 may have a negative impact on the course and severity of SARS-CoV-2 infection. Further investigations are warranted to elucidate the underlying mechanisms and examine whether reducing the level of Aβ1-42 in the blood is beneficial to the fight against COVID-19 and AD.
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Affiliation(s)
- John Tsu-An Hsu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli County 35053, Taiwan;
| | - Chih-Feng Tien
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County 35053, Taiwan; (C.-F.T.); (G.-Y.Y.)
| | - Guann-Yi Yu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County 35053, Taiwan; (C.-F.T.); (G.-Y.Y.)
| | - Santai Shen
- Antaimmu BioMed Co., Ltd., Hsinchu 30078, Taiwan;
| | - Yi-Hsuan Lee
- Department and Institute of Physiology, National Yang-Ming University, Taipei 11221, Taiwan; (Y.-H.L.); (P.-C.H.)
- Department and Institute of Physiology, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Pei-Chien Hsu
- Department and Institute of Physiology, National Yang-Ming University, Taipei 11221, Taiwan; (Y.-H.L.); (P.-C.H.)
- Department and Institute of Physiology, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Yun Wang
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli County 35053, Taiwan; (Y.W.); (P.-K.C.)
| | - Po-Kuan Chao
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli County 35053, Taiwan; (Y.W.); (P.-K.C.)
| | - Huey-Jen Tsay
- Institute of Neuroscience, School of Life Science, National Yang-Ming University, Taipei 11221, Taiwan;
| | - Feng-Shiun Shie
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli County 35053, Taiwan; (Y.W.); (P.-K.C.)
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88
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Nguyen NHL, Kim S, Lindemann G, Berry V. COVID-19 Spike Protein Induced Phononic Modification in Antibody-Coupled Graphene for Viral Detection Application. ACS Nano 2021; 15:11743-11752. [PMID: 34128653 PMCID: PMC8231663 DOI: 10.1021/acsnano.1c02549] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/10/2021] [Indexed: 05/09/2023]
Abstract
With an incubation time of about 5 days, early diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical to control the spread of the coronavirus disease 2019 (COVID-19) that killed more than 3 million people in its first 1.5 years. Here, we report on the modification of the dopant density and the phononic energy of antibody-coupled graphene when it interfaces with SARS-CoV-2 spike protein. This graphene chemeo-phononic system was able to detect SARS-CoV-2 spike protein at the limit of detection of ∼3.75 and ∼1 fg/mL in artificial saliva and phosphate-buffered saline, respectively. It also exhibited selectivity over proteins in saliva and MERS-CoV spike protein. Since the change in graphene phononics is monitored instead of the phononic signature of the analyte, this optical platform can be replicated for other COVID variants and specific-binding-based biodetection applications.
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Affiliation(s)
- Ngoc Hoang Lan Nguyen
- Department of Chemical Engineering,
University of Illinois at Chicago, 929 W. Taylor Street,
Chicago, Illinois 60607, United States
| | - Sungjoon Kim
- Department of Chemical Engineering,
University of Illinois at Chicago, 929 W. Taylor Street,
Chicago, Illinois 60607, United States
| | - Garrett Lindemann
- Ramaco LLC, 1101 Sugarview
Drive, Sheridan, Wyoming 82801, United States
| | - Vikas Berry
- Department of Chemical Engineering,
University of Illinois at Chicago, 929 W. Taylor Street,
Chicago, Illinois 60607, United States
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89
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Fathi-Hafshejani P, Azam N, Wang L, Kuroda MA, Hamilton MC, Hasim S, Mahjouri-Samani M. Two-Dimensional-Material-Based Field-Effect Transistor Biosensor for Detecting COVID-19 Virus (SARS-CoV-2). ACS Nano 2021; 15:11461-11469. [PMID: 34181385 PMCID: PMC8265534 DOI: 10.1021/acsnano.1c01188] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 06/23/2021] [Indexed: 05/20/2023]
Abstract
The emergence of rapidly expanding infectious diseases such as coronavirus (COVID-19) demands effective biosensors that can promptly detect and recognize the pathogens. Field-effect transistors based on semiconducting two-dimensional (2D) materials (2D-FETs) have been identified as potential candidates for rapid and label-free sensing applications. This is because any perturbation of such atomically thin 2D channels can significantly impact their electronic transport properties. Here, we report the use of FET based on semiconducting transition metal dichalcogenide (TMDC) WSe2 as a promising biosensor for the rapid and sensitive detection of SARS-CoV-2 in vitro. The sensor is created by functionalizing the WSe2 monolayers with a monoclonal antibody against the SARS-CoV-2 spike protein and exhibits a detection limit of down to 25 fg/μL in 0.01X phosphate-buffered saline (PBS). Comprehensive theoretical and experimental studies, including density functional theory, atomic force microscopy, Raman and photoluminescence spectroscopies, and electronic transport properties, were performed to characterize and explain the device performance. The results demonstrate that TMDC-based 2D-FETs can potentially serve as sensitive and selective biosensors for the rapid detection of infectious diseases.
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Affiliation(s)
- Parvin Fathi-Hafshejani
- Department of Electrical and Computer Engineering,
Auburn University, Auburn, Alabama 36849, United
States
| | - Nurul Azam
- Department of Electrical and Computer Engineering,
Auburn University, Auburn, Alabama 36849, United
States
| | - Lu Wang
- Department of Physics, Auburn
University, Auburn, Alabama 36849, United States
| | - Marcelo A. Kuroda
- Department of Physics, Auburn
University, Auburn, Alabama 36849, United States
| | - Michael C. Hamilton
- Department of Electrical and Computer Engineering,
Auburn University, Auburn, Alabama 36849, United
States
| | - Sahar Hasim
- Department of Biology, Mercer
University, Macon, Georgia 31207, United States
| | - Masoud Mahjouri-Samani
- Department of Electrical and Computer Engineering,
Auburn University, Auburn, Alabama 36849, United
States
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90
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Kogan EA, Kukleva AD, Berezovskiy YS, Blagova OV, Zharkov NV, Ainetdinova DK, Demyashkin GA. [Clinical and morphological characteristics of SARS-CoV-2-related myocarditis proven by the presence of viral RNA and proteins in myocardial tissue]. Arkh Patol 2021; 83:5-13. [PMID: 34278755 DOI: 10.17116/patol2021830415] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
OBJECTIVE To investigate the clinical and morphological features of SARS-CoV-2-related myocarditis, by determining the presence of viral RNA and proteins in myocardial tissue. MATERIAL AND METHODS The study was conducted to examine the material of 32 autopsies with a confirmed diagnosis of myocarditis. There were data of a morphological study, including a standard histological study, as well as immunohistochemical determination of the surface markers CD45, CD3, CD20, and CD68 cells of an inflammatory infiltrate and virus proteins (SARS-CoV-2 nucleocapsid protein and spike protein). Positive and negative control tests were carried out. In addition, coronavirus RNA was detected in the myocardium using a polymerase chain reaction. RESULTS Polymerase chain reaction (PCR) revealed viral RNA in myocardial tissue. Viral proteins were identified in the macrophages of an inflammatory infiltrate and cardiomyocytes. CONCLUSION The findings may suggest that the virus persists in the myocardium and chronic myocarditis develops.
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Affiliation(s)
- E A Kogan
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of Russia, Moscow, Russia
| | - A D Kukleva
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of Russia, Moscow, Russia
| | | | - O V Blagova
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of Russia, Moscow, Russia
| | - N V Zharkov
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of Russia, Moscow, Russia
| | - D Kh Ainetdinova
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of Russia, Moscow, Russia
| | - G A Demyashkin
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of Russia, Moscow, Russia
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91
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Liv L, Çoban G, Nakiboğlu N, Kocagöz T. A rapid, ultrasensitive voltammetric biosensor for determining SARS-CoV-2 spike protein in real samples. Biosens Bioelectron 2021; 192:113497. [PMID: 34274624 PMCID: PMC8276568 DOI: 10.1016/j.bios.2021.113497] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 07/04/2021] [Accepted: 07/08/2021] [Indexed: 12/27/2022]
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic continues to threaten public health systems all around the world. In controlling the viral outbreak, early diagnosis of COVID-19 is pivotal. This article describes a novel method of voltammetrically determining severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein with a newly designed sensor involving bovine serum albumin, SARS-CoV-2 spike antibody and a functionalised graphene oxide modified glassy carbon electrode (BSA/AB/f-GO/GCE) or screen-printed electrode (BSA/AB/f-GO/SPE). The oxidation reaction based on the antibody–antigen protein interaction was evaluated as a response to SARS-CoV-2 spike protein at -200 mV and 1430 mV with the BSA/AB/f-GO/SPE and BSA/AB/f-GO/GCE, respectively. The developed sensors, BSA/AB/f-GO/SPE and BSA/AB/f-GO/GCE, could detect 1 ag/mL of virus spike protein in synthetic, saliva and oropharyngeal swab samples in 5 min and 35 min, and both sensors demonstrated a dynamic response to the SARS-CoV-2 spike protein between 1 ag/mL and 10 fg/mL. Real-time polymerase chain reaction (RT-PCR), rapid antigen test and the proposed method were applied to saliva samples. When compared to RT-PCR, it was observed that the developed method had a 92.5% specificity and 93.3% sensitivity. Moreover, BSA/AB/f-GO/SPE sensor achieved 91.7% accuracy compared to 66.7% accuracy of rapid antigen test kit in positive samples. In view of these findings, the developed sensor provides great potential for the diagnosing of COVID-19 in real samples.
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Affiliation(s)
- Lokman Liv
- Electrochemistry Laboratory, Chemistry Group, The Scientific and Technological Research Council of Turkey, National Metrology Institute, (TUBITAK UME), 41470, Gebze, Kocaeli, Turkey.
| | - Gizem Çoban
- Electrochemistry Laboratory, Chemistry Group, The Scientific and Technological Research Council of Turkey, National Metrology Institute, (TUBITAK UME), 41470, Gebze, Kocaeli, Turkey
| | - Nuri Nakiboğlu
- Department of Chemistry, Faculty of Arts and Sciences, Balıkesir University, 10145, Balıkesir, Turkey
| | - Tanıl Kocagöz
- Department of Medical Microbiology and Medical Biotechnology, Acibadem University, 34752, Istanbul, Turkey
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92
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Fu Z, Zeng W, Cai S, Li H, Ding J, Wang C, Chen Y, Han N, Yang R. Porous Au@Pt nanoparticles with superior peroxidase-like activity for colorimetric detection of spike protein of SARS-CoV-2. J Colloid Interface Sci 2021; 604:113-121. [PMID: 34265672 PMCID: PMC8256686 DOI: 10.1016/j.jcis.2021.06.170] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 06/18/2021] [Accepted: 06/30/2021] [Indexed: 10/28/2022]
Abstract
The development of colorimetric assays for rapid and accurate diagnosis of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is of practical importance for point-of-care (POC) testing. Here we report the colorimetric detection of spike (S1) protein of SARS-CoV-2 based on excellent peroxidase-like activity of Au@Pt nanoparticles, with merits of rapidness, easy operation, and high sensitivity. The Au@Pt NPs were fabricated by a facile seed-mediated growth approach, in which spherical Au NPs were premade as seeds, followed by the Pt growth on Au seeds, producing uniform, monodispersed and porous Au@Pt core-shell NPs. The as-obtained Au@Pt NPs showed a remarkable enhancement in the peroxidase-mimic catalysis, which well abided by the typical Michaelis-Menten theory. The enhanced catalysis of Au@Pt NPs was ascribed to the porous nanostructure and formed electron-rich Pt shells, which enabled the catalytic pathway to switch from hydroxyl radical generation to electron transfer process. On a basis of these findings, a colorimetric assay of spike (S1) protein of SARS-CoV-2 was established, with a linear detection range of 10-100 ng mL-1 of protein concentration and a low limit of detection (LOD) of 11 ng mL-1. The work presents a novel strategy for diagnosis of COVID-19 based on metallic nanozyme-catalysis.
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Affiliation(s)
- Zhao Fu
- CAS Key Lab for Biomedical Effects of Nanomaterials and Nanosafety, Center of Materials Science and Optoelectronics Engineering, CAS center for Excellence in Nanoscience, National Center for Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Weilun Zeng
- CAS Key Lab for Biomedical Effects of Nanomaterials and Nanosafety, Center of Materials Science and Optoelectronics Engineering, CAS center for Excellence in Nanoscience, National Center for Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing, China; Sino-Danish College, Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing, China
| | - Shuangfei Cai
- CAS Key Lab for Biomedical Effects of Nanomaterials and Nanosafety, Center of Materials Science and Optoelectronics Engineering, CAS center for Excellence in Nanoscience, National Center for Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing, China.
| | - Haolin Li
- CAS Key Lab for Biomedical Effects of Nanomaterials and Nanosafety, Center of Materials Science and Optoelectronics Engineering, CAS center for Excellence in Nanoscience, National Center for Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing, China; Sino-Danish College, Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing, China
| | - Jianwei Ding
- CAS Key Lab for Biomedical Effects of Nanomaterials and Nanosafety, Center of Materials Science and Optoelectronics Engineering, CAS center for Excellence in Nanoscience, National Center for Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Chen Wang
- CAS Key Lab for Biomedical Effects of Nanomaterials and Nanosafety, Center of Materials Science and Optoelectronics Engineering, CAS center for Excellence in Nanoscience, National Center for Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Yunfa Chen
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
| | - Ning Han
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
| | - Rong Yang
- CAS Key Lab for Biomedical Effects of Nanomaterials and Nanosafety, Center of Materials Science and Optoelectronics Engineering, CAS center for Excellence in Nanoscience, National Center for Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing, China; Sino-Danish College, Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing, China.
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93
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Huang J, Wang D, Shipman RD, Zhu Z, Liu Y, Li L. Simultaneous enrichment and separation of neutral and sialyl glycopeptides of SARS-CoV-2 spike protein enabled by dual-functionalized Ti-IMAC material. Anal Bioanal Chem 2021. [PMID: 34155551 DOI: 10.1007/s00216-021-03433-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/19/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents a serious threat to human health all over the world. The development of effective vaccines has been focusing on the spike (S) glycoprotein, which mediates viral invasion to human cells through its interaction with the angiotensin-converting enzyme 2 (ACE2) receptor. In this work, we perform analytical characterization of N- and O-linked glycosylation of the SARS-CoV-2 S glycoprotein. We explore the novel use of dual-functionalized titanium (IV)-immobilized metal affinity chromatography (Ti-IMAC) material for simultaneous enrichment and separation of neutral and sialyl glycopeptides of a recombinant SARS-CoV-2 S glycoprotein from HEK293 cells. This strategy helps eliminate signal suppression from neutral glycopeptides for the detection of sialyl glycopeptides and improves the glycoform coverage of the S protein. We profiled 19 of its 22 potential N-glycosylated sites with 398 unique glycoforms using the dual-functional Ti-IMAC approach, which exhibited improvement of coverage by 1.6-fold compared to the conventional hydrophilic interaction chromatography (HILIC) glycopeptide enrichment method. We also identified O-linked glycosylation site that was not found using the conventional HILIC approach. In addition, we reported on the identification of mannose-6-phosphate (M6P) glycosylation, which substantially expands the current knowledge of the spike protein's glycosylation landscape and enables future investigation into the influence of M6P glycosylation of the spike protein on its cell entry.
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94
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Correa Y, Waldie S, Thépaut M, Micciulla S, Moulin M, Fieschi F, Pichler H, Trevor Forsyth V, Haertlein M, Cárdenas M. SARS-CoV-2 spike protein removes lipids from model membranes and interferes with the capacity of high density lipoprotein to exchange lipids. J Colloid Interface Sci 2021; 602:732-739. [PMID: 34157514 PMCID: PMC8195693 DOI: 10.1016/j.jcis.2021.06.056] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 01/18/2023]
Abstract
Cholesterol has been shown to affect the extent of coronavirus binding and fusion to cellular membranes. The severity of Covid-19 infection is also known to be correlated with lipid disorders. Furthermore, the levels of both serum cholesterol and high-density lipoprotein (HDL) decrease with Covid-19 severity, with normal levels resuming once the infection has passed. Here we demonstrate that the SARS-CoV-2 spike (S) protein interferes with the function of lipoproteins, and that this is dependent on cholesterol. In particular, the ability of HDL to exchange lipids from model cellular membranes is altered when co-incubated with the spike protein. Additionally, the S protein removes lipids and cholesterol from model membranes. We propose that the S protein affects HDL function by removing lipids from it and remodelling its composition/structure.
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Affiliation(s)
- Yubexi Correa
- Biofilms - Research Center for Biointerfaces and Department of Biomedical Science, Faculty of Health and Society, Malmö University, 20506 Malmö, Sweden
| | - Sarah Waldie
- Biofilms - Research Center for Biointerfaces and Department of Biomedical Science, Faculty of Health and Society, Malmö University, 20506 Malmö, Sweden; Life Sciences Group, Institut Laue Langevin, Grenoble F-38042, France; Partnership for Structural Biology, Grenoble F-38042, France
| | - Michel Thépaut
- Univ. Grenoble Alpes, CNRS, CEA, IBS, 71 avenue des Martyrs, F-38000 Grenoble, France
| | - Samantha Micciulla
- Large Scale Structures, Institut Laue Langevin (ILL), Grenoble F-38042, France
| | - Martine Moulin
- Life Sciences Group, Institut Laue Langevin, Grenoble F-38042, France; Partnership for Structural Biology, Grenoble F-38042, France
| | - Franck Fieschi
- Partnership for Structural Biology, Grenoble F-38042, France; Univ. Grenoble Alpes, CNRS, CEA, IBS, 71 avenue des Martyrs, F-38000 Grenoble, France
| | - Harald Pichler
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria; Graz University of Technology, Institute of Molecular Biotechnology, NAWI Graz, BioTechMed Graz, Petersgasse 14, 8010 Graz, Austria
| | - V Trevor Forsyth
- Life Sciences Group, Institut Laue Langevin, Grenoble F-38042, France; Partnership for Structural Biology, Grenoble F-38042, France; Faculty of Natural Sciences, Keele University, Staffordshire ST5 5BG, UK.
| | - Michael Haertlein
- Life Sciences Group, Institut Laue Langevin, Grenoble F-38042, France; Partnership for Structural Biology, Grenoble F-38042, France.
| | - Marité Cárdenas
- Biofilms - Research Center for Biointerfaces and Department of Biomedical Science, Faculty of Health and Society, Malmö University, 20506 Malmö, Sweden.
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95
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Budge JD, Young RJ, Smales CM. Engineering of Chinese Hamster Ovary Cells With NDPK-A to Enhance DNA Nuclear Delivery Combined With EBNA1 Plasmid Maintenance Gives Improved Exogenous Transient Reporter, mAb and SARS-CoV-2 Spike Protein Expression. Front Bioeng Biotechnol 2021; 9:679448. [PMID: 34150735 PMCID: PMC8212061 DOI: 10.3389/fbioe.2021.679448] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/10/2021] [Indexed: 12/15/2022] Open
Abstract
Transient gene expression (TGE) in mammalian cells is a method of rapidly generating recombinant protein material for initial characterisation studies that does not require time-consuming processes associated with stable cell line construction. High TGE yields are heavily dependent on efficient delivery of plasmid DNA across both the plasma and nuclear membranes. Here, we harness the protein nucleoside diphosphate kinase (NDPK-A) that contains a nuclear localisation signal (NLS) to enhance DNA delivery into the nucleus of CHO cells. We show that co-expression of NDPK-A during transient expression results in improved transfection efficiency in CHO cells, presumably due to enhanced transportation of plasmid DNA into the nucleus via the nuclear pore complex. Furthermore, introduction of the Epstein Barr Nuclear Antigen-1 (EBNA-1), a protein that is capable of inducing extrachromosomal maintenance, when coupled with complementary oriP elements on a transient plasmid, was utilised to reduce the effect of plasmid dilution. Whilst there was attenuated growth upon introduction of the EBNA-1 system into CHO cells, when both NDPK-A nuclear import and EBNA-1 mediated technologies were employed together this resulted in enhanced transient recombinant protein yields superior to those generated using either approach independently, including when expressing the complex SARS-CoV-2 spike (S) glycoprotein.
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Affiliation(s)
- James D Budge
- Industrial Biotechnology Centre, School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Robert J Young
- R&D Cell Engineering Group, Lonza Biologics, Chesterford Research Park, Saffron Walden, United Kingdom
| | - Christopher Mark Smales
- Industrial Biotechnology Centre, School of Biosciences, University of Kent, Canterbury, United Kingdom
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96
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Singh A, Dhar R. A large-scale computational screen identifies strong potential inhibitors for disrupting SARS-CoV-2 S-protein and human ACE2 interaction. J Biomol Struct Dyn 2021; 40:9004-9017. [PMID: 33998954 PMCID: PMC8146306 DOI: 10.1080/07391102.2021.1921034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 04/19/2021] [Indexed: 02/07/2023]
Abstract
SARS-CoV-2 has infected millions of individuals across the globe and has killed over 2.7 million people. Even though vaccines against this virus have recently been introduced, the antibody generated in the process has been reported to decline quickly. This can reduce the efficacy of vaccines over time and can result in re-infections. Thus, drugs that are effective against COVID-19 can provide a second line of defence and can prevent occurrence of the severe form of the disease. The interaction between SARS-CoV2 S-protein and human ACE2 (hACE2) is essential for the infection of the virus. Thus, drugs that block this interaction could potentially inhibit SARS-CoV-2 infection into the host cells. To identify such drugs, we first analyzed the recently published crystal structure of S-protein-hACE2 complex and identified essential residues of both S-protein and hACE2 for this interaction. We used this knowledge to virtually dock a drug library containing 4115 drug molecules against S-protein for repurposing drugs that could inhibit binding of S-protein to hACE2. We identified several potential inhibitors based on their docking scores, pharmacological effects and ability to block residues of S protein required for interaction with hACE2. The top inhibitors included drugs used for the treatment of hepatitis C (velpatasvir, pibrentasvir) as well as several vitamin D derivatives. Several molecules obtained from our screen already have good experimental support in published literature. Thus, we believe that our results will facilitate the discovery of an effective drug against COVID-19. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Adarsh Singh
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Riddhiman Dhar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
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97
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Laurini E, Marson D, Aulic S, Fermeglia A, Pricl S. Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. ACS Nano 2021; 15:6929-6948. [PMID: 33733740 PMCID: PMC8009103 DOI: 10.1021/acsnano.0c10833] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The coronavirus disease-2019 (COVID-19) pandemic, caused by the pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), started in China during late 2019 and swiftly spread worldwide. Since COVID-19 emergence, many therapeutic regimens have been relentlessly explored, and although two vaccines have just received emergency use authorization by different governmental agencies, antiviral therapeutics based neutralizing antibodies and small-drug inhibitors can still be vital viable options to prevent and treat SARS-CoV-2 infections. The viral spike glycoprotein (S-protein) is the key molecular player that promotes human host cellular invasion via recognition of and binding to the angiotensin-converting enzyme 2 gene (ACE2). In this work, we report the results obtained by mutating in silico the 18 ACE2 residues and the 14 S-protein receptor binding domain (S-RBDCoV-2) residues that contribute to the receptor/viral protein binding interface. Specifically, each wild-type protein-protein interface residue was replaced by a hydrophobic (isoleucine), polar (serine and threonine), charged (aspartic acid/glutamic acid and lysine/arginine), and bulky (tryptophan) residue, respectively, in order to study the different effects exerted by nature, shape, and dimensions of the mutant amino acids on the structure and strength of the resulting binding interface. The computational results were next validated a posteriori against the corresponding experimental data, yielding an overall agreement of 92%. Interestingly, a non-negligible number of mis-sense variations were predicted to enhance ACE2/S-RBDCoV-2 binding, including the variants Q24T, T27D/K/W, D30E, H34S7T/K, E35D, Q42K, L79I/W, R357K, and R393K on ACE2 and L455D/W, F456K/W, Q493K, N501T, and Y505W on S-RBDCoV-2, respectively.
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Affiliation(s)
- Erik Laurini
- Molecular
Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, 34127 Trieste, Italy
| | - Domenico Marson
- Molecular
Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, 34127 Trieste, Italy
| | - Suzana Aulic
- Molecular
Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, 34127 Trieste, Italy
| | - Alice Fermeglia
- Molecular
Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, 34127 Trieste, Italy
| | - Sabrina Pricl
- Molecular
Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, 34127 Trieste, Italy
- Department
of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, 90-136 Lodz, Poland
- . Phone: +39
040 558 3750
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98
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Abstract
Viral envelope glycoproteins are an important structural component on the surfaces of enveloped viruses that direct virus binding and entry and also serve as targets for the host adaptive immune response. In this study, we investigate the mechanism of action of the MARCH family of cellular proteins that disrupt the trafficking and virion incorporation of viral glycoproteins across several virus families. An emerging class of cellular inhibitory proteins has been identified that targets viral glycoproteins. These include the membrane-associated RING-CH (MARCH) family of E3 ubiquitin ligases that, among other functions, downregulate cell surface proteins involved in adaptive immunity. The RING-CH domain of MARCH proteins is thought to function by catalyzing the ubiquitination of the cytoplasmic tails (CTs) of target proteins, leading to their degradation. MARCH proteins have recently been reported to target retroviral envelope glycoproteins (Env) and vesicular stomatitis virus G glycoprotein (VSV-G). However, the mechanism of antiviral activity remains poorly defined. Here we show that MARCH8 antagonizes the full-length forms of HIV-1 Env, VSV-G, Ebola virus glycoprotein (EboV-GP), and the spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), thereby impairing the infectivity of virions pseudotyped with these viral glycoproteins. This MARCH8-mediated targeting of viral glycoproteins requires the E3 ubiquitin ligase activity of the RING-CH domain. We observe that MARCH8 protein antagonism of VSV-G is CT dependent. In contrast, MARCH8-mediated targeting of HIV-1 Env, EboV-GP, and SARS-CoV-2 S protein by MARCH8 does not require the CT, suggesting a novel mechanism of MARCH-mediated antagonism of these viral glycoproteins. Confocal microscopy data demonstrate that MARCH8 traps the viral glycoproteins in an intracellular compartment. We observe that the endogenous expression of MARCH8 in several relevant human cell types is rapidly inducible by type I interferon. These results help to inform the mechanism by which MARCH proteins exert their antiviral activity and provide insights into the role of cellular inhibitory factors in antagonizing the biogenesis, trafficking, and virion incorporation of viral glycoproteins.
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Mai HK, Trieu NB, Long TH, Thanh HT, Luong ND, Huy LX, Nguyet LA, Man DNH, Anderson DE, Thanh TT, Chau NVV, Thwaites G, Wang LF, Van Tan L, Hung DT. Long-Term Humoral Immune Response in Persons with Asymptomatic or Mild SARS-CoV-2 Infection, Vietnam. Emerg Infect Dis 2021; 27:663-666. [PMID: 33496647 PMCID: PMC7853537 DOI: 10.3201/eid2702.204226] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Antibody response against nucleocapsid and spike proteins of SARS-CoV-2 in 11 persons with mild or asymptomatic infection rapidly increased after infection. At weeks 18–30 after diagnosis, all remained seropositive but spike protein–targeting antibody titers declined. These data may be useful for vaccine development.
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100
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Sekar PC, Rajasekaran R. Could Dermaseptin Analogue be a Competitive Inhibitor for ACE2 Towards Binding with Viral Spike Protein Causing COVID19?: Computational Investigation. Int J Pept Res Ther 2021;:1-14. [PMID: 33488318 DOI: 10.1007/s10989-020-10149-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2020] [Indexed: 12/12/2022]
Abstract
Initial phase of COVID-19 infection is associated with the binding of viral spike protein S1 receptor binding domain (RBD) with the host cell surface receptor, ACE2. Peptide inhibitors typically interact with spike proteins in order to block its interaction with ACE2, and this knowledge would promote the use of such peptides as therapeutic scaffolds. The present study examined the competitive inhibitor activity of a broad spectrum antimicrobial peptide, Dermaseptin-S4 (S4) and its analogues. Three structural S4 analogues viz., S4 (K4), S4 (K20) and S4 (K4K20) were modelled by substituting charged lysine for non-polar residues in S4 and subsequently, docked with S1. Further, the comparative analysis of inter-residue contacts and non-covalent intermolecular interactions among S1–S4 (K4), S1–S4 (K4K20) and S1–ACE2 complexes were carried out to explore their mode of binding with S1. Interestingly, S1–S4 (K4) established more inter-molecular interactions compared to S4 (K4K20) and S1–ACE2. In order to substantiate this study, the normal mode analysis (NMA) was conducted to show how the structural stability of the flexible loop region in S1 is affected by atomic displacements in unbound S1 and docked complexes. Markedly, the strong interactions consistently maintained by S1–S4 (K4) complex revealed their conformational transition over the harmonic motion period. Moreover, S1–S4 (K4) peptide complex showed a higher energy deformation profile compared to S1–S4 (K4K20), where the higher energy deformation suggests the rigidity of the docked complex and thus it’s harder deformability, which is also substantiated by molecular dynamics simulation. In conclusion, S1–S4 (K4) complex has definitely exhibited a functionally significant dynamics compared to S1–ACE2 complex; this peptide inhibitor, S4 (K4) will need to be considered as the best therapeutic scaffold to block SARS-CoV-2 infection.
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