1
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Guerra D, Radić L, Brinkkemper M, Poniman M, van der Maas L, Torres JL, Ward AB, Sliepen K, Schinkel J, Sanders RW, van Gils MJ, Beaumont T. Broadening sarbecovirus neutralization with bispecific antibodies combining distinct conserved targets on the receptor binding domain. Hum Vaccin Immunother 2024; 20:2388344. [PMID: 39165108 PMCID: PMC11340772 DOI: 10.1080/21645515.2024.2388344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 07/05/2024] [Accepted: 08/01/2024] [Indexed: 08/22/2024] Open
Abstract
Monoclonal neutralizing antibodies (mAbs) are considered an important prophylactic against SARS-CoV-2 infection in at-risk populations and a strategy to counteract future sarbecovirus-induced disease. However, most mAbs isolated so far neutralize only a few sarbecovirus strains. Therefore, there is a growing interest in bispecific antibodies (bsAbs) which can simultaneously target different spike epitopes and thereby increase neutralizing breadth and prevent viral escape. Here, we generate and characterize a panel of 30 novel broadly reactive bsAbs using an efficient controlled Fab-arm exchange protocol. We specifically combine some of the broadest mAbs described so far, which target conserved epitopes on the receptor binding domain (RBD). Several bsAbs show superior cross-binding and neutralization compared to the parental mAbs and cocktails against sarbecoviruses from diverse clades, including recent SARS-CoV-2 variants. BsAbs which include mAb COVA2-02 are among the most potent and broad combinations. As a result, we study the unknown epitope of COVA2-02 and show that this mAb targets a distinct conserved region at the base of the RBD, which could be of interest when designing next-generation bsAb constructs to contribute to a better pandemic preparedness.
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Affiliation(s)
- Denise Guerra
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
| | - Laura Radić
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
| | - Mitch Brinkkemper
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
| | - Meliawati Poniman
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
| | - Lara van der Maas
- Department of Structural Biology and Computational Biology, The Scripps Research Institute, La Jolla, USA
| | - Jonathan L. Torres
- Department of Structural Biology and Computational Biology, The Scripps Research Institute, La Jolla, USA
| | - Andrew B. Ward
- Department of Structural Biology and Computational Biology, The Scripps Research Institute, La Jolla, USA
| | - Kwinten Sliepen
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
| | - Janke Schinkel
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
| | - Rogier W. Sanders
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, USA
| | - Marit J. van Gils
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
| | - Tim Beaumont
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
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2
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Helin T, Palviainen M, Lemponen M, Maaninka K, Siljander P, Joutsi-Korhonen L. Increased circulating platelet-derived extracellular vesicles in severe COVID-19 disease. Platelets 2024; 35:2313362. [PMID: 38380806 DOI: 10.1080/09537104.2024.2313362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/27/2024] [Indexed: 02/22/2024]
Abstract
Coagulation disturbances are major contributors to COVID-19 pathogenicity, but limited data exist on the involvement of extracellular vesicles (EVs) and residual cells (RCs). Fifty hospitalized COVID-19 patients stratified by their D-dimer levels into high (>1.5 mg/L, n = 15) or low (≤1.5 mg/l, n = 35) and 10 healthy controls were assessed for medium-sized EVs (mEVs; 200-1000 nm) and large EVs/RCs (1000-4000 nm) by high sensitivity flow cytometry. EVs were analyzed for CD61, CD235a, CD45, and CD31, commonly used to detect platelets, red blood cells, leukocytes or endothelial cells, respectively, whilst phosphatidyl serine EVs/RCs were detected by lactadherin-binding implicating procoagulant catalytic surface. Small EV detection (sEVs; 50-200 nm) and CD41a (platelet integrin) colocalization with general EV markers CD9, CD63, and CD81 were performed by single particle interferometric reflectance imaging sensor. Patients with increased D-dimer exhibited the highest number of RCs and sEVs irrespective of cell origin (p < .05). Platelet activation, reflected by increased CD61+ and lactadherin+ mEV and RC levels, associated with coagulation disturbances. Patients with low D-dimer could be discriminated from controls by tetraspanin signatures of the CD41a+ sEVs, suggesting the changes in the circulating platelet sEV subpopulations may offer added prognostic value during COVID progression.
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Affiliation(s)
- Tuukka Helin
- HUS Diagnostics Centre, HUSLAB Clinical Chemistry, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Mari Palviainen
- EV group, Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, and CURED, Drug Research Program, Faculty of Pharmacy, Division of Pharmaceutical Biosciences, University of Helsinki, Helsinki, Finland
- EV core, Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Marja Lemponen
- HUS Diagnostics Centre, HUSLAB Clinical Chemistry, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Katariina Maaninka
- EV group, Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, and CURED, Drug Research Program, Faculty of Pharmacy, Division of Pharmaceutical Biosciences, University of Helsinki, Helsinki, Finland
- EV core, Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Pia Siljander
- EV group, Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, and CURED, Drug Research Program, Faculty of Pharmacy, Division of Pharmaceutical Biosciences, University of Helsinki, Helsinki, Finland
- EV core, Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Lotta Joutsi-Korhonen
- HUS Diagnostics Centre, HUSLAB Clinical Chemistry, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
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3
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Hasan M, He Z, Jia M, Leung ACF, Natarajan K, Xu W, Yap S, Zhou F, Chen S, Su H, Zhu K, Su H. Dynamic expedition of leading mutations in SARS-CoV-2 spike glycoproteins. Comput Struct Biotechnol J 2024; 23:2407-2417. [PMID: 38882678 PMCID: PMC11176665 DOI: 10.1016/j.csbj.2024.05.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 05/21/2024] [Accepted: 05/21/2024] [Indexed: 06/18/2024] Open
Abstract
The continuous evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which caused the recent pandemic, has generated countless new variants with varying fitness. Mutations of the spike glycoprotein play a particularly vital role in shaping its evolutionary trajectory, as they have the capability to alter its infectivity and antigenicity. We present a time-resolved statistical method, Dynamic Expedition of Leading Mutations (deLemus), to analyze the evolutionary dynamics of the SARS-CoV-2 spike glycoprotein. The proposed L -index of the deLemus method is effective in quantifying the mutation strength of each amino acid site and outlining evolutionarily significant sites, allowing the comprehensive characterization of the evolutionary mutation pattern of the spike glycoprotein.
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Affiliation(s)
- Muhammad Hasan
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Zhouyi He
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Mengqi Jia
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Alvin C F Leung
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | | | - Wentao Xu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Shanqi Yap
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Feng Zhou
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Shihong Chen
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Hailei Su
- Bengbu Hospital of Traditional Chinese Medicine, 4339 Huai-shang Road, Anhui 233080, China
| | - Kaicheng Zhu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Haibin Su
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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4
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Sun H, Xia L, Li J, Zhang Y, Zhang G, Huang P, Wang X, Cui Y, Fang T, Fan P, Zhou Q, Chi X, Yu C. A novel bispecific antibody targeting two overlapping epitopes in RBD improves neutralizing potency and breadth against SARS-CoV-2. Emerg Microbes Infect 2024; 13:2373307. [PMID: 38953857 PMCID: PMC11249148 DOI: 10.1080/22221751.2024.2373307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 06/22/2024] [Indexed: 07/04/2024]
Abstract
SARS-CoV-2 has been evolving into a large number of variants, including the highly pathogenic Delta variant, and the currently prevalent Omicron subvariants with extensive evasion capability, which raises an urgent need to develop new broad-spectrum neutralizing antibodies. Herein, we engineer two IgG-(scFv)2 form bispecific antibodies with overlapping epitopes (bsAb1) or non-overlapping epitopes (bsAb2). Both bsAbs are significantly superior to the parental monoclonal antibodies in terms of their antigen-binding and virus-neutralizing activities against all tested circulating SARS-CoV-2 variants including currently dominant JN.1. The bsAb1 can efficiently neutralize all variants insensitive to parental monoclonal antibodies or the cocktail with IC50 lower than 20 ng/mL, even slightly better than bsAb2. Furthermore, the cryo-EM structures of bsAb1 in complex with the Omicron spike protein revealed that bsAb1 with overlapping epitopes effectively locked the S protein, which accounts for its conserved neutralization against Omicron variants. The bispecific antibody strategy engineered from overlapping epitopes provides a novel solution for dealing with viral immune evasion.
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Affiliation(s)
- Hancong Sun
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Lingyun Xia
- Center for Infectious Disease Research, Research Center for Industries of the Future, Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Institute of Biology, Westlake Institute for Advanced Study, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, People’s Republic of China
| | - Jianhua Li
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Province, Hangzhou, Zhejiang Province, People’s Republic of China
| | - Yuanyuan Zhang
- Center for Infectious Disease Research, Research Center for Industries of the Future, Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Institute of Biology, Westlake Institute for Advanced Study, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, People’s Republic of China
| | - Guanying Zhang
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Ping Huang
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Xingxing Wang
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Province, Hangzhou, Zhejiang Province, People’s Republic of China
| | - Yue Cui
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Ting Fang
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Pengfei Fan
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Qiang Zhou
- Center for Infectious Disease Research, Research Center for Industries of the Future, Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Institute of Biology, Westlake Institute for Advanced Study, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, People’s Republic of China
| | - Xiangyang Chi
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Changming Yu
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
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5
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Baig MMFA, Wong LY, Wu H. Development of mRNA nano-vaccines for COVID-19 prevention and its biochemical interactions with various disease conditions and age groups. J Drug Target 2024; 32:21-32. [PMID: 38010097 DOI: 10.1080/1061186x.2023.2288996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 11/18/2023] [Indexed: 11/29/2023]
Abstract
This review has focused on the development of mRNA nano-vaccine and the biochemical interactions of anti-COVID-19 mRNA vaccines with various disease conditions and age groups. It studied five major groups of individuals with different disease conditions and ages, including allergic background, infarction background, adolescent, and adult (youngsters), pregnant women, and elderly. All five groups had been reported to have background-related adverse effects. Allergic background individuals were observed to have higher chances of experiencing allergic reactions and even anaphylaxis. Individuals with an infarction background had a higher risk of vaccine-induced diseases, e.g. pneumonitis and interstitial lung diseases. Pregnant women were seen to suffer from obstetric and gynecological adverse effects after receiving vaccinations. However, interestingly, the elderly individuals (> 65 years old) had experienced milder and less frequent adverse effects compared to the adolescent (<19 and >9 years old) and young adulthood (19-39 years old), or middle adulthood (40-59 years old) age groups, while middle to late adolescent (14-17 years old) was the riskiest age group to vaccine-induced cardiovascular manifestations.
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Affiliation(s)
- Mirza Muhammad Faran Ashraf Baig
- Department of Chemistry and the Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Lok Yin Wong
- Department of Chemistry and the Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Hongkai Wu
- Department of Chemistry and the Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration, The Hong Kong University of Science and Technology, Hong Kong, China
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6
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Chakraborty A, Ghosh R, Barik S, Mohapatra SS, Biswas A, Chowdhuri S. Deciphering inhibitory activity of marine algae Ecklonia cava phlorotannins against SARS CoV-2 main protease: A coupled in-silico docking and molecular dynamics simulation study. Gene 2024; 926:148620. [PMID: 38821329 DOI: 10.1016/j.gene.2024.148620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/21/2024] [Accepted: 05/28/2024] [Indexed: 06/02/2024]
Abstract
The onset of COVID-19 due to the SARS CoV-2 virus has spurred an urgent need for potent therapeutics and vaccines to combat this global pandemic. The main protease (Mpro) of the virus, crucial in its replication, has become a focal point in developing anti-COVID-19 drugs. The cysteine protease Mpro in SARS CoV-2 bears a significant resemblance to the same protease found in SARS CoV-1. Previous research highlighted phlorotannins derived from Ecklonia cava, an edible marine algae, as inhibitors of SARS CoV-1 Mpro activity. However, it remains unclear whether these marine-derived phlorotannins also exert a similar inhibitory effect on SARS CoV-2 Mpro. To unravel this, our study utilized diverse in-silico methodologies. We explored the pharmacological potential of various phlorotannins (phloroglucinol, triphloretol-A, eckol, 2-phloroeckol, 7-phloroeckol, fucodiphloroethol G, dieckol, and phlorofucofuroeckol-A) and assessed their binding efficacies alongside established Mpro inhibitors (N3 and lopinavir) through molecular docking studies. Among these compounds, five phlorotannins (eckol, 2-phloroeckol, 7-phloroeckol, dieckol, and phlorofucofuroeckol-A) exhibited potent binding affinities comparable to or surpassing N3 and lopinavir, interacting especially with the catalytic residues His41 and Cys145 of Mpro. Moreover, molecular dynamics simulations revealed that these five Mpro-phlorotannin complexes displayed enhanced stability and maintained comparable or slightly reduced compactness. They exhibited reduced conformational changes and increased expansion relative to the Mpro-N3 and/or Mpro-lopinavir complex. Our MM-GBSA analysis further supported these findings. Overall, our investigation highlights the potential of these five phlorotannins in inhibiting the proteolytic function of SARS CoV-2 Mpro, offering promise for anti-COVID-19 drug development.
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Affiliation(s)
- Ayon Chakraborty
- University Institute of Biotechnology, University Centre for Research & Development, Chandigarh University, Mohali, India
| | - Rajesh Ghosh
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Subhashree Barik
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | | | - Ashis Biswas
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India.
| | - Snehasis Chowdhuri
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India.
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7
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Wang Q, Wang X, Ding J, Huang L, Wang Z. Structural insight of cell surface sugars in viral infection and human milk glycans as natural antiviral substance. Int J Biol Macromol 2024; 277:133867. [PMID: 39009265 DOI: 10.1016/j.ijbiomac.2024.133867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/24/2024] [Accepted: 07/11/2024] [Indexed: 07/17/2024]
Abstract
Viral infections are caused by the adhesion of viruses to host cell receptors, including sialylated glycans, glycosaminoglycans, and human blood group antigens (HBGAs). Atomic-level structural information on the interactions between viral particles or proteins with glycans can be determined to provide precise targets for designing antiviral drugs. Milk glycans, existing as free oligosaccharides or glycoconjugates, have attracted increasing attention; milk glycans protect infants against infectious diseases, particularly poorly manageable viral infections. Furthermore, several glycans containing structurally distinct sialic acid/fucose/sulfate modifications in human milk acting as a "receptor decoy" and serving as the natural antiviral library, could interrupt virus-receptor interaction in the first line of defense for viral infection. This review highlights the basis of virus-glycan interactions, presents specific glycan receptor binding by gastroenterovirus viruses, including norovirus, enteroviruses, and the breakthroughs in the studies on the antiviral properties of human milk glycans, and also elucidates the role of glycans in respiratory viruses infection. In addition, recent advances in methods for performing virus/viral protein-glycan interactions were reported. Finally, we discuss the prospects and challenges of the studies on the clinical application of human milk glycan for viral interventions.
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Affiliation(s)
- Qingling Wang
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China
| | - Xiaoqin Wang
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China
| | - Jieqiong Ding
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China
| | - Linjuan Huang
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China.
| | - Zhongfu Wang
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China.
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8
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Sarkar M, Madabhavi I. COVID-19 mutations: An overview. World J Methodol 2024; 14:89761. [DOI: 10.5662/wjm.v14.i3.89761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 02/07/2024] [Accepted: 04/17/2024] [Indexed: 06/25/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) belongs to the genus Beta coronavirus and the family of Coronaviridae. It is a positive-sense, non-segmented single-strand RNA virus. Four common types of human coronaviruses circulate globally, particularly in the fall and winter seasons. They are responsible for 10%-30% of all mild upper respiratory tract infections in adults. These are 229E, NL63 of the Alfacoronaviridae family, OC43, and HKU1 of the Betacoronaviridae family. However, there are three highly pathogenic human coronaviruses: SARS-CoV-2, Middle East respiratory syndrome coronavirus, and the latest pandemic caused by the SARS-CoV-2 infection. All viruses, including SARS-CoV-2, have the inherent tendency to evolve. SARS-CoV-2 is still evolving in humans. Additionally, due to the development of herd immunity, prior infection, use of medication, vaccination, and antibodies, the viruses are facing immune pressure. During the replication process and due to immune pressure, the virus may undergo mutations. Several SARS-CoV-2 variants, including the variants of concern (VOCs), such as B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617/B.1.617.2 (Delta), P.1 (Gamma), and B.1.1.529 (Omicron) have been reported from various parts of the world. These VOCs contain several important mutations; some of them are on the spike proteins. These mutations may lead to enhanced infectivity, transmissibility, and decreased neutralization efficacy by monoclonal antibodies, convalescent sera, or vaccines. Mutations may also lead to a failure of detection by molecular diagnostic tests, leading to a delayed diagnosis, increased community spread, and delayed treatment. We searched PubMed, EMBASE, Covariant, the Stanford variant Database, and the CINAHL from December 2019 to February 2023 using the following search terms: VOC, SARS-CoV-2, Omicron, mutations in SARS-CoV-2, etc. This review discusses the various mutations and their impact on infectivity, transmissibility, and neutralization efficacy.
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Affiliation(s)
- Malay Sarkar
- Department of Pulmonary Medicine, Indira Gandhi Medical College, Shimla 171001, Himachal Pradesh, India
| | - Irappa Madabhavi
- Department of Medical and Pediatric Oncology and Hematology, J N Medical College, and KAHER, Belagavi, Karnataka 590010, India
- Department of Medical and Pediatric Oncology and Hematology, Kerudi Cancer Hospital, Bagalkot, Karnataka 587103, India
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9
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Jiang B, Yang Y, Zhao R, Chen D, Wang Y, Liu J, Long F, Chen R, Hao R. A multifunctional evanescent wave biosensor for the universal assay of SARS-CoV-2 variants and affinity analysis of coronavirus spike protein-hACE2 interactions. Biosens Bioelectron 2024; 260:116426. [PMID: 38815461 DOI: 10.1016/j.bios.2024.116426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/12/2024] [Accepted: 05/23/2024] [Indexed: 06/01/2024]
Abstract
The conventional detection model of passive adaptation to pathogen mutations, i.e., developing assays using corresponding antibodies or nucleic acid probes, is difficult to address frequent outbreaks of emerging infectious diseases. In particular, adaptive mutations observed in coronaviruses, which increase the affinity of the spike protein with the human cellular receptor hACE2, play pivotal roles in the transmission and immune evasion of coronaviruses. Herein, we developed a multifunctional optical fiber evanescent wave biosensor for the universal assay of coronavirus and affinity analysis of the spike protein interacting with hACE2, namely, My-SPACE. By competitively binding with Cy5.5-hACE2 between coronavirus spike proteins in mobile buffer and that modified on optical fibers from the SARS-CoV-2 wild type, My-SPACE could automatically detect SARS-CoV-2 and its variants within 10 min. My-SPACE demonstrated greater sensitivity and faster results than ELISA for SARS-CoV-2 variants, achieving 100% specificity and 94.10% sensitivity in detecting the Omicron variant in 18 clinical samples. Moreover, the interaction between hACE2 and the coronavirus spike protein was accurately characterized across SARS-CoV-2 mutants, SARS-CoV and hCoV-NL63. The accuracy of the affinity determined by My-SPACE was verified by SPR. This approach enables preliminary assessment of the transmissibility and hazards of emerging coronaviruses. The sensor fibers of My-SPACE can be reused more than 40 times, and the device is compact and easy to use; moreover, it is available as a rapid and cost-effective on-site detection tool adapted to coronavirus variability and as an effective assessment platform for early warning of coronavirus transmission risk.
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Affiliation(s)
- Bo Jiang
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing, China
| | - Yi Yang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Rongtao Zhao
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Dan Chen
- School of Environment and Natural Resources, Renmin University of China, Beijing, China
| | - Yule Wang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Junwen Liu
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing, China
| | - Feng Long
- School of Environment and Natural Resources, Renmin University of China, Beijing, China.
| | - Rui Chen
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing, China.
| | - Rongzhang Hao
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing, China.
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10
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Singh P, Pahari P, Mukherjee S, Karmakar S, Hoffmann M, Mandal T, Das DK. SARS-CoV-2 spike fusion peptide trans interaction with phosphatidylserine lipid triggers membrane fusion for viral entry. mBio 2024; 15:e0107724. [PMID: 39115315 DOI: 10.1128/mbio.01077-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 06/30/2024] [Indexed: 09/12/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike is the fusion machine for host cell entry. Still, the mechanism by which spike protein interacts with the target lipid membrane to facilitate membrane fusion during entry is not fully understood. Here, using steady-state membrane fusion and single-molecule fluorescence resonance energy transfer imaging of spike trimers on the surface of SARS-CoV-2 pseudovirion, we directly show that spike protein interacts with phosphatidylserine (PS) lipid in the target membrane for mediating fusion. We observed that the fusion peptide of the spike S2 domain interacts with the PS lipid of the target membrane. Low pH and Ca2+ trigger the spike conformational change and bring fusion peptide in close proximity to the PS lipid of the membrane. The binding of the spike with PS lipid of its viral membrane (cis interaction) impedes the fusion activation. PS on the target membrane promotes spike binding via trans interaction, prevents the cis interaction, and accelerates fusion. Sequestering or absence of PS lipid abrogates the spike-mediated fusion process and restricts SARS-CoV-2 infectivity. We found that PS-dependent interaction for fusion is conserved across all the SARS-CoV-2 spike variants of concern (D614G, Alpha, Beta, Delta, and Omicron). Our study suggests that PS lipid is indispensable for SARS-CoV-2 spike-mediated virus and target membrane fusion for entry, and restricting PS interaction with spike inhibits the SARS-CoV-2 spike-mediated entry. Therefore, PS is an important cofactor and acts as a molecular beacon in the target membrane for SARS-CoV-2 entry. IMPORTANCE The role of lipids in the host cell target membrane for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) entry is not clear. We do not know whether SARS-CoV-2 spike protein has any specificity in terms of lipid for membrane fusion reaction. Here, using in vitro reconstitution of membrane fusion assay and single-molecule fluorescence resonance energy transfer imaging of SARS-CoV-2 spike trimers on the surface of the virion, we have demonstrated that phosphatidylserine (PS) lipid plays a key role in SARS-CoV-2 spike-mediated membrane fusion reaction for entry. Membrane-externalized PS lipid strongly promotes spike-mediated membrane fusion and COVID-19 infection. Blocking externalized PS lipid with PS-binding protein or in the absence of PS, SARS-CoV-2 spike-mediated fusion is strongly inhibited. Therefore, PS is an important target for restricting viral entry and intervening spike, and PS interaction presents new targets for COVID-19 interventions.
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Affiliation(s)
- Puspangana Singh
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, India
| | - Purba Pahari
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, India
| | - Srija Mukherjee
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, India
| | - Sharmistha Karmakar
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland, USA
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center-Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg August University, Göttingen, Germany
| | - Taraknath Mandal
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, India
| | - Dibyendu Kumar Das
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, India
- Center for Engineering in Medicine, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, India
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11
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Wang S, Li W, Wang Z, Yang W, Li E, Xia X, Yan F, Chiu S. Emerging and reemerging infectious diseases: global trends and new strategies for their prevention and control. Signal Transduct Target Ther 2024; 9:223. [PMID: 39256346 DOI: 10.1038/s41392-024-01917-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 06/13/2024] [Accepted: 07/05/2024] [Indexed: 09/12/2024] Open
Abstract
To adequately prepare for potential hazards caused by emerging and reemerging infectious diseases, the WHO has issued a list of high-priority pathogens that are likely to cause future outbreaks and for which research and development (R&D) efforts are dedicated, known as paramount R&D blueprints. Within R&D efforts, the goal is to obtain effective prophylactic and therapeutic approaches, which depends on a comprehensive knowledge of the etiology, epidemiology, and pathogenesis of these diseases. In this process, the accessibility of animal models is a priority bottleneck because it plays a key role in bridging the gap between in-depth understanding and control efforts for infectious diseases. Here, we reviewed preclinical animal models for high priority disease in terms of their ability to simulate human infections, including both natural susceptibility models, artificially engineered models, and surrogate models. In addition, we have thoroughly reviewed the current landscape of vaccines, antibodies, and small molecule drugs, particularly hopeful candidates in the advanced stages of these infectious diseases. More importantly, focusing on global trends and novel technologies, several aspects of the prevention and control of infectious disease were discussed in detail, including but not limited to gaps in currently available animal models and medical responses, better immune correlates of protection established in animal models and humans, further understanding of disease mechanisms, and the role of artificial intelligence in guiding or supplementing the development of animal models, vaccines, and drugs. Overall, this review described pioneering approaches and sophisticated techniques involved in the study of the epidemiology, pathogenesis, prevention, and clinical theatment of WHO high-priority pathogens and proposed potential directions. Technological advances in these aspects would consolidate the line of defense, thus ensuring a timely response to WHO high priority pathogens.
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Affiliation(s)
- Shen Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130000, China
| | - Wujian Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130000, China
- College of Veterinary Medicine, Jilin University, Changchun, Jilin, China
| | - Zhenshan Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130000, China
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, Jilin, China
| | - Wanying Yang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130000, China
| | - Entao Li
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, China
- Key Laboratory of Anhui Province for Emerging and Reemerging Infectious Diseases, Hefei, 230027, Anhui, China
| | - Xianzhu Xia
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130000, China
| | - Feihu Yan
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130000, China.
| | - Sandra Chiu
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, China.
- Key Laboratory of Anhui Province for Emerging and Reemerging Infectious Diseases, Hefei, 230027, Anhui, China.
- Department of Laboratory Medicine, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
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12
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Chen E, Xi L. Cardiovascular adverse effects of antiviral therapies for COVID-19: Evidence and plausible mechanisms. Acta Pharmacol Sin 2024:10.1038/s41401-024-01382-w. [PMID: 39251859 DOI: 10.1038/s41401-024-01382-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 08/15/2024] [Indexed: 09/11/2024] Open
Abstract
Antiviral therapeutics have made a critical contribution in mitigating the symptoms and clinical outcomes of the coronavirus disease of 2019 (COVID-19), in which a single-stranded RNA viral pathogen, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causes multi-organ injuries. Several antivirals were widely prescribed to treat COVID-19, either through the emergency use authorization (EUA) by the governmental regulatory agencies (i.e., remdesivir, paxlovid, molnupiravir, and the SARS-CoV-2-targeted monoclonal antibodies - tixagevimab and cilgavimab), as well as the repurposed use of the existing antiviral or antimalarial drugs (e.g., hydroxychloroquine, chloroquine, and ivermectin). Despite their efficacy in ameliorating COVID-19 symptoms, some adverse side-effects of the antivirals were also reported during the COVID-19 pandemic. Our current review has aimed to gather and extrapolate the recently published information concerning cardiovascular adverse effects caused by each of the antivirals. We also provide further discussion on the potential cellular mechanisms underlying the cardiovascular adverse effects of the selected antiviral drugs, which should be carefully considered when evaluating risk factors in managing patients with COVID-19 or similar infectious diseases. It is foreseeable that future antiviral drug development assisted with the newest artificial intelligence platform may improve the accuracy to predict the structures of biomolecules of antivirals and therefore to mitigate their associated cardiovascular adversities.
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Affiliation(s)
- Eileen Chen
- Virginia Commonwealth University School of Medicine (M.D. Class 2027), Richmond, VA, 23298, USA
| | - Lei Xi
- Pauley Heart Center, Division of Cardiology, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, 23298-0204, USA.
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13
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Des Soye BJ, Melani RD, Hollas MAR, Duan J, Patrie SM, Fisher TD, Mattamana BB, Daud A, Pinelli DF, Ladner DP, Kelleher NL, Forte E. Characterization of the Antibody Response to SARS-CoV-2 Infection in COVID-19 Transplant versus Nontransplant Recipients by Ig-MS. J Proteome Res 2024; 23:3944-3957. [PMID: 39146476 DOI: 10.1021/acs.jproteome.4c00285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Solid organ transplant recipients with immunosuppressant regimens to prevent rejection are less able to mount effective immune responses to pathogenic infection. Here, we apply a recently reported mass spectrometry-based serological approach known as Ig-MS to characterize immune responses against infection with SARS-CoV-2 in cohorts of transplant recipients and immunocompetent controls, both at a single early time point following COVID-19 diagnosis as well as over the course of one-month postdiagnosis. We found that the antibody repertoires generated by transplant recipients against SARS-CoV-2 do not differ significantly compared to immunocompetent individuals with regard to repertoire titer, clonality, or glycan composition. Importantly, our study is the first to characterize the evolution of antibody glycan profiles in transplant recipients with COVID-19 disease, presenting evidence that the evolution of glycan composition in these immunocompromised individuals is similar to that in immunocompetent people.
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Affiliation(s)
- Benjamin J Des Soye
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Rafael D Melani
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael A R Hollas
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Jiana Duan
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Steven M Patrie
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Troy D Fisher
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Basil Baby Mattamana
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Amna Daud
- Department of Surgery, Feinberg School of Medicine, Comprehensive Transplant Center, Northwestern University, Chicago, Illinois 60611, United States
| | - David F Pinelli
- Department of Surgery, Feinberg School of Medicine, Comprehensive Transplant Center, Northwestern University, Chicago, Illinois 60611, United States
| | - Daniela P Ladner
- Department of Surgery, Feinberg School of Medicine, Comprehensive Transplant Center, Northwestern University, Chicago, Illinois 60611, United States
| | - Neil L Kelleher
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Eleonora Forte
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
- Department of Surgery, Feinberg School of Medicine, Comprehensive Transplant Center, Northwestern University, Chicago, Illinois 60611, United States
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14
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Wee J, Chen J, Wei GW. Preventing future zoonosis: SARS-CoV-2 mutations enhance human-animal cross-transmission. Comput Biol Med 2024; 182:109101. [PMID: 39243518 DOI: 10.1016/j.compbiomed.2024.109101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 08/13/2024] [Accepted: 08/31/2024] [Indexed: 09/09/2024]
Abstract
The COVID-19 pandemic has driven substantial evolution of the SARS-CoV-2 virus, yielding subvariants that exhibit enhanced infectiousness in humans. However, this adaptive advantage may not universally extend to zoonotic transmission. In this work, we hypothesize that viral adaptations favoring animal hosts do not necessarily correlate with increased human infectivity. In addition, we consider the potential for gain-of-function mutations that could facilitate the virus's rapid evolution in humans following adaptation in animal hosts. Specifically, we identify the SARS-CoV-2 receptor-binding domain (RBD) mutations that enhance human-animal cross-transmission. To this end, we construct a multitask deep learning model, MT-TopLap trained on multiple deep mutational scanning datasets, to accurately predict the binding free energy changes upon mutation for the RBD to ACE2 of various species, including humans, cats, bats, deer, and hamsters. By analyzing these changes, we identified key RBD mutations such as Q498H in SARS-CoV-2 and R493K in the BA.2 variant that are likely to increase the potential for human-animal cross-transmission.
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Affiliation(s)
- JunJie Wee
- Department of Mathematics, Michigan State University, East Lansing, MI 48824, USA
| | - Jiahui Chen
- Department of Mathematical Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Guo-Wei Wei
- Department of Mathematics, Michigan State University, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI 48824, USA.
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15
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Cui W, Duan Y, Gao Y, Wang W, Yang H. Structural review of SARS-CoV-2 antiviral targets. Structure 2024; 32:1301-1321. [PMID: 39241763 DOI: 10.1016/j.str.2024.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/25/2024] [Accepted: 08/06/2024] [Indexed: 09/09/2024]
Abstract
The coronavirus disease 2019 (COVID-19), the disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), represents the most disastrous infectious disease pandemic of the past century. As a member of the Betacoronavirus genus, the SARS-CoV-2 genome encodes a total of 29 proteins. The spike protein, RNA-dependent RNA polymerase, and proteases play crucial roles in the virus replication process and are promising targets for drug development. In recent years, structural studies of these viral proteins and of their complexes with antibodies and inhibitors have provided valuable insights into their functions and laid a solid foundation for drug development. In this review, we summarize the structural features of these proteins and discuss recent progress in research regarding therapeutic development, highlighting mechanistically representative molecules and those that have already been approved or are under clinical investigation.
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Affiliation(s)
- Wen Cui
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China
| | - Yinkai Duan
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yan Gao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201203, China
| | - Wei Wang
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China.
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201203, China.
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16
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Mifsud JCO, Lytras S, Oliver MR, Toon K, Costa VA, Holmes EC, Grove J. Mapping glycoprotein structure reveals Flaviviridae evolutionary history. Nature 2024:10.1038/s41586-024-07899-8. [PMID: 39232167 DOI: 10.1038/s41586-024-07899-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 08/01/2024] [Indexed: 09/06/2024]
Abstract
Viral glycoproteins drive membrane fusion in enveloped viruses and determine host range, tissue tropism and pathogenesis1. Despite their importance, there is a fragmentary understanding of glycoproteins within the Flaviviridae2, a large virus family that include pathogens such as hepatitis C, dengue and Zika viruses, and numerous other human, animal and emergent viruses. For many flaviviruses the glycoproteins have not yet been identified, for others, such as the hepaciviruses, the molecular mechanisms of membrane fusion remain uncharacterized3. Here we combine phylogenetic analyses with protein structure prediction to survey glycoproteins across the entire Flaviviridae. We find class II fusion systems, homologous to the Orthoflavivirus E glycoprotein in most species, including highly divergent jingmenviruses and large genome flaviviruses. However, the E1E2 glycoproteins of the hepaciviruses, pegiviruses and pestiviruses are structurally distinct, may represent a novel class of fusion mechanism, and are strictly associated with infection of vertebrate hosts. By mapping glycoprotein distribution onto the underlying phylogeny, we reveal a complex evolutionary history marked by the capture of bacterial genes and potentially inter-genus recombination. These insights, made possible through protein structure prediction, refine our understanding of viral fusion mechanisms and reveal the events that have shaped the diverse virology and ecology of the Flaviviridae.
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Affiliation(s)
- Jonathon C O Mifsud
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Spyros Lytras
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Michael R Oliver
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Kamilla Toon
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Vincenzo A Costa
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
| | - Joe Grove
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK.
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17
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García-Arribas AB, Ibáñez-Freire P, Carlero D, Palacios-Alonso P, Cantero-Reviejo M, Ares P, López-Polín G, Yan H, Wang Y, Sarkar S, Chhowalla M, Oksanen HM, Martín-Benito J, de Pablo PJ, Delgado-Buscalioni R. Broad Adaptability of Coronavirus Adhesion Revealed from the Complementary Surface Affinity of Membrane and Spikes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2404186. [PMID: 39231361 DOI: 10.1002/advs.202404186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 07/21/2024] [Indexed: 09/06/2024]
Abstract
Coronavirus stands for a large family of viruses characterized by protruding spikes surrounding a lipidic membrane adorned with proteins. The present study explores the adhesion of transmissible gastroenteritis coronavirus (TGEV) particles on a variety of reference solid surfaces that emulate typical virus-surface interactions. Atomic force microscopy informs about trapping effectivity and the shape of the virus envelope on each surface, revealing that the deformation of TGEV particles spans from 20% to 50% in diameter. Given this large deformation range, experimental Langmuir isotherms convey an unexpectedly moderate variation in the adsorption-free energy, indicating a viral adhesion adaptability which goes beyond the membrane. The combination of an extended Helfrich theory and coarse-grained simulations reveals that, in fact, the envelope and the spikes present complementary adsorption affinities. While strong membrane-surface interaction lead to highly deformed TGEV particles, surfaces with strong spike attraction yield smaller deformations with similar or even larger adsorption-free energies.
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Affiliation(s)
- Aritz B García-Arribas
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Pablo Ibáñez-Freire
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Diego Carlero
- Departamento de Estructura de Macromoléculas, Centro Nacional de Biotecnología CSIC, Madrid, 28049, Spain
| | - Pablo Palacios-Alonso
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Miguel Cantero-Reviejo
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Pablo Ares
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Guillermo López-Polín
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Han Yan
- Department of Materials Science and Metallurgy, University of Cambridge, Cambridge, CB3 0FS, UK
| | - Yan Wang
- Department of Materials Science and Metallurgy, University of Cambridge, Cambridge, CB3 0FS, UK
| | - Soumya Sarkar
- Department of Materials Science and Metallurgy, University of Cambridge, Cambridge, CB3 0FS, UK
| | - Manish Chhowalla
- Department of Materials Science and Metallurgy, University of Cambridge, Cambridge, CB3 0FS, UK
| | - Hanna M Oksanen
- Faculty of Biological and Environmental Sciences, Vijkki Biocenter, University of Helsinki, Helsinki, 00014, Finland
| | - Jaime Martín-Benito
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Pedro J de Pablo
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, 28049, Spain
- Instituto de Física de la Materia Condensada IFIMAC, Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Rafael Delgado-Buscalioni
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, 28049, Spain
- Instituto de Física de la Materia Condensada IFIMAC, Universidad Autónoma de Madrid, Madrid, 28049, Spain
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18
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Lee J, Kim B, Woo HM, Kim JW, Jung I, Park SW, Kim YS, Na JH, Jung ST. Enhanced Omicron Variant Neutralization by a Human Antibody Tailored to Wild-Type and Delta-Variant SARS-CoV-2 RBDs. Mol Pharm 2024; 21:4336-4346. [PMID: 39058261 DOI: 10.1021/acs.molpharmaceut.4c00297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
Given the previous SARS-CoV-2 pandemic and the inherent unpredictability of viral antigenic drift and shift, preemptive development of diverse neutralizing antibodies targeting a broad spectrum of epitopes is essential to ensure immediate therapeutic and prophylactic interventions during emerging outbreaks. In this study, we present a monoclonal antibody engineered for cross-reactivity to both wild-type and Delta RBDs, which, surprisingly, demonstrates enhanced neutralizing activity against the Omicron variant despite a significant number of mutations. Using an Escherichia coli inner membrane display of a human naïve antibody library, we identified antibodies specific to the wild-type SARS-CoV-2 receptor binding domain (RBD). Subsequent directed evolution via yeast surface display yielded JS18.1, an antibody with high binding affinity for both the Delta and Kappa RBDs, as well as enhanced binding to other RBDs (wild-type, Alpha, Beta, Gamma, Kappa, and Mu). Notably, JS18.1 (engineered for wild-type and Delta RBDs) exhibits enhanced neutralizing capability against the Omicron variant and binds to RBDs noncompetitively with ACE2, distinguishing it from other previously reported antibodies. This underscores the potential of pre-existing antibodies to neutralize emerging SARS-CoV-2 strains and offers insights into strategies to combat emerging viruses.
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Affiliation(s)
- Jisun Lee
- Department of Biomedical Sciences, Graduate School, Korea University, Seoul 02841, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Bomi Kim
- Department of Biomedical Sciences, Graduate School, Korea University, Seoul 02841, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Hye-Min Woo
- Division of Emerging Virus and Vector Research, Center for Emerging Virus Research, National Institute of Health, Korea Centers for Disease Control and Prevention Agency, Osong, Cheongju 28159, Republic of Korea
| | - Jun-Won Kim
- Division of Emerging Virus and Vector Research, Center for Emerging Virus Research, National Institute of Health, Korea Centers for Disease Control and Prevention Agency, Osong, Cheongju 28159, Republic of Korea
| | - Inji Jung
- Department of Biomedical Sciences, Graduate School, Korea University, Seoul 02841, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Seong-Wook Park
- Department of Molecular Science and Technology, Ajou University, Suwon, Gyeonggi-do 16499, Republic of Korea
| | - Yong-Sung Kim
- Department of Molecular Science and Technology, Ajou University, Suwon, Gyeonggi-do 16499, Republic of Korea
- Department of Allergy and Clinical Immunology, Ajou University Medical School, Suwon, Gyeonggi-do 16499, Republic of Korea
| | - Jung-Hyun Na
- School of Biopharmaceutical and Medical Sciences, Sungshin Women's University, Seoul 01133, Republic of Korea
| | - Sang Taek Jung
- Department of Biomedical Sciences, Graduate School, Korea University, Seoul 02841, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea
- Biomedical Research Center, Korea University Anam Hospital, Seoul 02841, Republic of Korea
- Institute of Human Genetics, Korea University College of Medicine, Seoul 02841, Republic of Korea
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19
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Hung HC, Tan BF, Lin WS, Wu SC. Glycan masking of NTD loops with a chimeric RBD of the spike protein as a vaccine design strategy against emerging SARS-CoV-2 Omicron variants. J Med Virol 2024; 96:e29893. [PMID: 39192804 DOI: 10.1002/jmv.29893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 07/12/2024] [Accepted: 08/19/2024] [Indexed: 08/29/2024]
Abstract
The N-terminal domain (NTD) of the SARS-CoV-2 S protein comprises five exposed protruding loops. Deletions, insertions, and substitutions within these NTD loops play a significant role in viral evolution and contribute to immune evasion. We reported previously that introducing the glycan masking mutation R158N/Y160T in the NTD loop led to increased titers of neutralizing antibodies against the SARS-CoV-2 Wuhan-Hu-01 strain, as well as the Alpha, Beta, and Delta variants. In this study, we conducted further investigations on 10 additional glycan-masking sites in the NTD loops. Our findings indicate that the introduction of glycan masking mutations, specifically N87/G89T, H146N/N148T, N185/K187T, and V213N/D215T significantly enhanced neutralizing antibody titers against the Delta variant. The combination of dual glycan-masking mutations R158N/Y160T+V213N/D215T and R158N/Y160T+G219N results in a shift toward the Omicron BA.1. Furthermore, the introduction of the Omicron receptor binding domain (RBD) alongside these two dual glycan masking mutations of Wuhan-Hu-1 and XBB.1 NTD sequences resulted in a noticeable shift in antigenic distances, aligning with the Omicron BA.4/5, BA.2.75.2, BQ.1.1, and XBB.1 subvariants on the antigenic map. This strategic combination, which involves the dual glycan masking mutations R158N/Y160T+V213N/D215T and R158N/Y160T+G219N in the NTD loops, along with the domain swap incorporating the Omicron RBD, emerges as a promising vaccine design strategy for the continuous development of next-generation SARS-CoV-2 vaccines.
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Affiliation(s)
- Hao-Chan Hung
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - Boon-Fatt Tan
- Department of Pediatrics, National Taiwan University Hospital, Hsin-Chu Branch, Hsinchu, Taiwan
| | - Wei-Shuo Lin
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - Suh-Chin Wu
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
- Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan
- Adimmune Corporation, Taichung, Taiwan
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20
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Srivastava PK, Klomhaus AM, Rafique A, Desai PS, Daniels LB, Yancy CW, Yang EH, Fonarow GC, Parikh RV. Guideline-directed medical therapy prescribing patterns and in-hospital outcomes among heart failure patients during COVID-19. AMERICAN HEART JOURNAL PLUS : CARDIOLOGY RESEARCH AND PRACTICE 2024; 45:100440. [PMID: 39220717 PMCID: PMC11363726 DOI: 10.1016/j.ahjo.2024.100440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 07/30/2024] [Accepted: 07/31/2024] [Indexed: 09/04/2024]
Abstract
Study objective The association of prior to admission guideline-directed medical therapy (GDMT) use in patients hospitalized with Heart Failure with Reduced Ejection Fraction (HFrEF, ejection fraction ≤40 %) and Coronavirus Disease 2019 (COVID-19) with in-hospital outcomes has not been well studied. Design/setting/participants/interventions/outcome measures Using the American Heart Association's Get With The Guidelines Heart Failure Registry, we identified HFrEF patients presenting with acute decompensated heart failure (ADHF) and compared rates of GDMT prescription between those presenting prior to and during the pandemic. In a subgroup of patients with a concomitant COVID-19 diagnosis, we evaluated the association of prior to admission GDMT use with in-hospital mortality and severe COVID-19. Results 23,899 patients were admitted with HFrEF during the pandemic (2/16/20-3/24/21) and 26,459 patients were admitted in the year prior (2/16/19-2/15/20). In this overall cohort, prior to admission ACEI/ARB/ARNI (45.6 % vs 48.1 %, p < 0.0001) and BB (56.9 % vs 62.4 %, p < 0.0001) use was lower among admitted HFrEF patients during the pandemic when compared to the year prior. Rates of ACEI/ARB/ARNI, MRA, and triple therapy (ACE/ARB/ARNI + BB + MRA) prescription at discharge were higher during the pandemic compared to the year prior. Among a subgroup of those with HFrEF and COVID-19 (n = 333), prior to admission GDMT use was not associated with in-hospital mortality or severe COVID-19. Conclusion We found no association between prior to admission GDMT use and in-hospital mortality or severe COVID-19 among HFrEF patients admitted with ADHF and COVID-19. GDMT prescription at discharge for HFrEF patients overall has remained either similar or improved during the pandemic.
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Affiliation(s)
- Pratyaksh K. Srivastava
- Division of Cardiology, Ronald Reagan UCLA Medical Center, Los Angeles, CA, United States of America
| | - Alexandra M. Klomhaus
- Department of Medicine, Statistics Core, UCLA, Los Angeles, CA, United States of America
| | - Asim Rafique
- Division of Cardiology, Ronald Reagan UCLA Medical Center, Los Angeles, CA, United States of America
| | - Pooja S. Desai
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Lori B. Daniels
- Division of Cardiovascular Medicine, UC San Diego, La Jolla, CA, United States of America
| | - Clyde W. Yancy
- Division of Cardiology, Northwestern University School of Medicine, Chicago, IL, United States of America
| | - Eric H. Yang
- Division of Cardiology, Ronald Reagan UCLA Medical Center, Los Angeles, CA, United States of America
| | - Gregg C. Fonarow
- Division of Cardiology, Ronald Reagan UCLA Medical Center, Los Angeles, CA, United States of America
| | - Rushi V. Parikh
- Division of Cardiology, Ronald Reagan UCLA Medical Center, Los Angeles, CA, United States of America
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21
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Liang Z, Wang J, Zhang H, Gao L, Xu J, Li P, Yang J, Fu X, Duan H, Liu J, Liu T, Ma W, Wu K. Peptide S4 is an entry inhibitor of SARS-CoV-2 infection. Virology 2024; 597:110149. [PMID: 38917689 DOI: 10.1016/j.virol.2024.110149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 06/07/2024] [Accepted: 06/18/2024] [Indexed: 06/27/2024]
Abstract
Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a significant socioeconomic burden, and combating COVID-19 is imperative. Blocking the SARS-CoV-2 RBD-ACE2 interaction is a promising therapeutic approach for viral infections, as SARS-CoV-2 binds to the ACE2 receptors of host cells via the RBD of spike proteins to infiltrate these cells. We used computer-aided drug design technology and cellular experiments to screen for peptide S4 with high affinity and specificity for the human ACE2 receptor through structural analysis of SARS-CoV-2 and ACE2 interactions. Cellular experiments revealed that peptide S4 effectively inhibited SARS-CoV-2 and HCoV-NL63 viruses from infecting host cells and was safe for cells at effective concentrations. Based on these findings, peptide S4 may be a potential pharmaceutical agent for clinical application in the treatment of the ongoing SARS-CoV-2 pandemic.
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Affiliation(s)
- Zhiyu Liang
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China; Department of Microbiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Jiamei Wang
- Department of Microbiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Huan Zhang
- Guangdong Center for Disease Control and Prevention, Guangdong, China
| | - Lixia Gao
- Department of Microbiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Jun Xu
- College of Pharmacy, Jinan University, Guangzhou, China
| | - Peiran Li
- Department of Microbiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Jie Yang
- Department of Microbiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Xinting Fu
- Department of Microbiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Han Duan
- Department of Microbiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Jiayan Liu
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China; Institute of Antibody Engineering, School of Laboratory Medicine & Biotechnology, Southern Medical University, Guangzhou, China
| | - Tiancai Liu
- Institute of Antibody Engineering, School of Laboratory Medicine & Biotechnology, Southern Medical University, Guangzhou, China
| | - Weifeng Ma
- Department of Microbiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China.
| | - Kun Wu
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China.
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22
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Araujo-Silva CA, Marinho PM, Marcos AAA, Branco AMC, Sakamoto V, Matuoka ML, Moraes NF, Tierno PFGMM, Mourad WM, Nascimento H, Burnier M, de Souza W, Belfort R. Postmortem Ultrastructural Analysis of the Retina from COVID-19 Deceased Patients. Ocul Immunol Inflamm 2024; 32:1314-1322. [PMID: 37552861 DOI: 10.1080/09273948.2023.2238817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/14/2023] [Accepted: 07/16/2023] [Indexed: 08/10/2023]
Abstract
PURPOSE COVID-19 (coronavirus disease 2019) is an infectious disease caused by SARS-CoV-2, first reported in 2019 in Wuhan, China. Among the common complications is a pro-inflammatory and hypercoagulative response that compromises the vasculature among various organs. METHODS In this report, we present the postmortem retinal findings of five patients observed by means of optical microscopy and transmission and scanning electron microscopy techniques. RESULTS Clinical manifestations such as retinal hemorrhages and exacerbated inflammatory infiltrate, altered ultra structure with swollen mitochondria and pyknotic cells in both layers of the retina were observed in all analyzed eyes. CONCLUSION Our data point to the fragility of this tissue in cases of severe COVID-19.
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Affiliation(s)
- Carlla A Araujo-Silva
- Laboratório de Ultraestrutura Celular Hertha Meyer, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens - INBEB, Rio de Janeiro, Brazil
- Centro Nacional de Biologia Estrutural e Bioimagens - CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paula M Marinho
- São Paulo Hospital, Paulista School of Medicine, Federal University of São Paulo, São Paulo, Brazil
- Instituto Paulista de Estudos e Pesquisas em Oftalmologia - IPEPO, São Paulo, Brazil
| | - Alléxya A A Marcos
- São Paulo Hospital, Paulista School of Medicine, Federal University of São Paulo, São Paulo, Brazil
- Instituto Paulista de Estudos e Pesquisas em Oftalmologia - IPEPO, São Paulo, Brazil
| | - Ana M C Branco
- São Paulo Hospital, Paulista School of Medicine, Federal University of São Paulo, São Paulo, Brazil
- Instituto Paulista de Estudos e Pesquisas em Oftalmologia - IPEPO, São Paulo, Brazil
| | - Victoria Sakamoto
- São Paulo Hospital, Paulista School of Medicine, Federal University of São Paulo, São Paulo, Brazil
| | - Mateus L Matuoka
- Hospital Municipal de Barueri Dr. Francisco Moran, São Paulo, Brazil
| | - Nara F Moraes
- Hospital Municipal de Barueri Dr. Francisco Moran, São Paulo, Brazil
| | | | - Walid M Mourad
- Instituto Paulista de Estudos e Pesquisas em Oftalmologia - IPEPO, São Paulo, Brazil
| | - Heloisa Nascimento
- São Paulo Hospital, Paulista School of Medicine, Federal University of São Paulo, São Paulo, Brazil
- Instituto Paulista de Estudos e Pesquisas em Oftalmologia - IPEPO, São Paulo, Brazil
- Hospital Municipal de Barueri Dr. Francisco Moran, São Paulo, Brazil
| | - Miguel Burnier
- Department of Ophthalmology, McGill University, Montreal, Quebec, Canada
| | - Wanderley de Souza
- Laboratório de Ultraestrutura Celular Hertha Meyer, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens - INBEB, Rio de Janeiro, Brazil
- Centro Nacional de Biologia Estrutural e Bioimagens - CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rubens Belfort
- São Paulo Hospital, Paulista School of Medicine, Federal University of São Paulo, São Paulo, Brazil
- Instituto Paulista de Estudos e Pesquisas em Oftalmologia - IPEPO, São Paulo, Brazil
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23
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Izadi A, Godzwon M, Söderlund Strand A, Schmidt T, Kumlien Georén S, Drosten C, Ohlin M, Nordenfelt P. Protective Non-neutralizing anti-N-terminal Domain mAb Maintains Fc-mediated Function against SARS-COV-2 Variants up to BA.2.86-JN.1 with Superfluous In Vivo Protection against JN.1 Due to Attenuated Virulence. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 213:678-689. [PMID: 39018495 PMCID: PMC11335326 DOI: 10.4049/jimmunol.2300675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 06/25/2024] [Indexed: 07/19/2024]
Abstract
Substantial evidence supports that Fc-mediated effector functions of anti-spike Abs contribute to anti-SARS-Cov-2 protection. We have previously shown that two non-neutralizing but opsonic mAbs targeting the receptor-binding domain and N-terminal domain (NTD), Ab81 and Ab94, respectively, are protective against lethal Wuhan SARS-CoV-2 infection in K18-hACE2 mice. In this article, we investigated whether these protective non-neutralizing Abs maintain Fc-mediated function and Ag binding against mutated SARS-CoV-2 variants. Ab81 and Ab94 retained their nanomolar affinity and Fc-mediated function toward Omicron and its subvariants, such as BA.2, BA.4, BA.5, XBB, XBB1.5, and BQ1.1. However, when encountering the more heavily mutated BA.2.86, Ab81 lost its function, whereas the 10 new mutations in the NTD did not affect Ab94. In vivo experiments with Ab94 in K18-hACE2 mice inoculated with a stringent dose of 100,000 PFU of the JN.1 variant revealed unexpected results. Surprisingly, this variant exhibited low disease manifestation in this animal model with no weight loss or death in the control group. Still, assessment of mice using a clinical scoring system showed better protection for Ab94-treated mice, indicating that Fc-mediated functions are still beneficial. Our work shows that a protective anti-receptor-binding domain non-neutralizing mAb lost reactivity when BA.2.86 emerged, whereas the anti-NTD mAb was still functional. Finally, this work adds new insight into the evolution of the SARS-CoV-2 virus by reporting that JN.1 is substantially less virulent in vivo than previous strains.
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Affiliation(s)
- Arman Izadi
- Department of Clinical Sciences Lund, Division of Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | | | - Anna Söderlund Strand
- Department of Laboratory Medicine, Clinical Microbiology, Skåne University Hospital Lund, Lund University, Lund, Sweden
| | - Tobias Schmidt
- Department of Clinical Sciences Lund, Division of Pediatrics, Faculty of Medicine, Lund University, Lund, Sweden
- Wallenberg Center for Molecular Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | | | - Christian Drosten
- German Center for Infection Research, Berlin, Germany
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden
- SciLifeLab Drug Discovery and Development, Lund University, Lund, Sweden
| | - Pontus Nordenfelt
- Department of Clinical Sciences Lund, Division of Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
- Department of Laboratory Medicine, Clinical Microbiology, Skåne University Hospital Lund, Lund University, Lund, Sweden
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24
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El-Maradny YA, Badawy MA, Mohamed KI, Ragab RF, Moharm HM, Abdallah NA, Elgammal EM, Rubio-Casillas A, Uversky VN, Redwan EM. Unraveling the role of the nucleocapsid protein in SARS-CoV-2 pathogenesis: From viral life cycle to vaccine development. Int J Biol Macromol 2024; 279:135201. [PMID: 39216563 DOI: 10.1016/j.ijbiomac.2024.135201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 08/24/2024] [Accepted: 08/28/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND The nucleocapsid protein (N protein) is the most abundant protein in SARS-CoV-2. Viral RNA and this protein are bound by electrostatic forces, forming cytoplasmic helical structures known as nucleocapsids. Subsequently, these nucleocapsids interact with the membrane (M) protein, facilitating virus budding into early secretory compartments. SCOPE OF REVIEW Exploring the role of the N protein in the SARS-CoV-2 life cycle, pathogenesis, post-sequelae consequences, and interaction with host immunity has enhanced our understanding of its function and potential strategies for preventing SARS-CoV-2 infection. MAJOR CONCLUSION This review provides an overview of the N protein's involvement in SARS-CoV-2 infectivity, highlighting its crucial role in the virus-host protein interaction and immune system modulation, which in turn influences viral spread. GENERAL SIGNIFICANCE Understanding these aspects identifies the N protein as a promising target for developing effective antiviral treatments and vaccines against SARS-CoV-2.
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Affiliation(s)
- Yousra A El-Maradny
- Pharmaceutical and Fermentation Industries Development Center, City of Scientific Research and Technological Applications (SRTA-City), New Borg EL-Arab, Alexandria 21934, Egypt; Microbiology and Immunology, Faculty of Pharmacy, Arab Academy for Science, Technology and Maritime Transport (AASTMT), El Alamein 51718, Egypt.
| | - Moustafa A Badawy
- Industrial Microbiology and Applied Chemistry program, Faculty of Science, Alexandria University, Egypt.
| | - Kareem I Mohamed
- Microbiology and Immunology, Faculty of Pharmacy, Arab Academy for Science, Technology and Maritime Transport (AASTMT), El Alamein 51718, Egypt.
| | - Renad F Ragab
- Microbiology and Immunology, Faculty of Pharmacy, Arab Academy for Science, Technology and Maritime Transport (AASTMT), El Alamein 51718, Egypt.
| | - Hamssa M Moharm
- Genetics, Biotechnology Department, Faculty of Agriculture, Alexandria University, Egypt.
| | - Nada A Abdallah
- Medicinal Plants Department, Faculty of Agriculture, Alexandria University, Egypt.
| | - Esraa M Elgammal
- Microbiology and Immunology, Faculty of Pharmacy, Arab Academy for Science, Technology and Maritime Transport (AASTMT), El Alamein 51718, Egypt.
| | - Alberto Rubio-Casillas
- Autlan Regional Hospital, Health Secretariat, Autlan, JAL 48900, Mexico; Biology Laboratory, Autlan Regional Preparatory School, University of Guadalajara, Autlan, JAL 48900, Mexico.
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
| | - Elrashdy M Redwan
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA-City), New Borg EL-Arab, 21934 Alexandria, Egypt.
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25
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Alfadhli A, Bates TA, Barklis RL, Romanaggi C, Tafesse FG, Barklis E. A nanobody interaction with SARS-COV-2 Spike allows the versatile targeting of lentivirus vectors. J Virol 2024:e0079524. [PMID: 39207135 DOI: 10.1128/jvi.00795-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 07/25/2024] [Indexed: 09/04/2024] Open
Abstract
While investigating methods to target gene delivery vectors to specific cell types, we examined the potential of using a nanobody against the SARS-CoV-2 Spike protein receptor-binding domain to direct lentivirus infection of Spike-expressing cells. Using four different approaches, we found that lentiviruses with surface-exposed nanobody domains selectively infect Spike-expressing cells. Targeting is dependent on the fusion function of the Spike protein, and conforms to a model in which nanobody binding to the Spike protein triggers the Spike fusion machinery. The nanobody-Spike interaction also is capable of directing cell-cell fusion and the selective infection of nanobody-expressing cells by Spike-pseudotyped lentivirus vectors. Significantly, cells infected with SARS-CoV-2 are efficiently and selectively infected by lentivirus vectors pseudotyped with a chimeric nanobody protein. Our results suggest that cells infected by any virus that forms syncytia may be targeted for gene delivery by using an appropriate nanobody or virus receptor mimic. Vectors modified in this fashion may prove useful in the delivery of immunomodulators to infected foci to mitigate the effects of viral infections.IMPORTANCEWe have discovered that lentiviruses decorated on their surfaces with a nanobody against the SARS-CoV-2 Spike protein selectively infect Spike-expressing cells. Infection is dependent on the specificity of the nanobody and the fusion function of the Spike protein and conforms to a reverse fusion model, in which nanobody binding to Spike triggers the Spike fusion machinery. The nanobody-Spike interaction also can drive cell-cell fusion and infection of nanobody-expressing cells with viruses carrying the Spike protein. Importantly, cells infected with SARS-CoV-2 are selectively infected with nanobody-decorated lentiviruses. These results suggest that cells infected by any virus that expresses an active receptor-binding fusion protein may be targeted by vectors for delivery of cargoes to mitigate infections.
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Affiliation(s)
- Ayna Alfadhli
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Timothy A Bates
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Robin Lid Barklis
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon, USA
| | - CeAnn Romanaggi
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Fikadu G Tafesse
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Eric Barklis
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon, USA
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26
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Vissapragada M, Addala S, Aggunna M, Sodasani M, Grandhi AVKS, Yedidi RS. Leveraging the potential of bacterial lateral gene transfer in boosting the efficacy of an edible probiotic prototype yogurt vaccine for COVID-19. Biochem Biophys Res Commun 2024; 734:150622. [PMID: 39216410 DOI: 10.1016/j.bbrc.2024.150622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2024] [Accepted: 08/28/2024] [Indexed: 09/04/2024]
Abstract
Administration of coronavirus disease-2019 (COVID-19) vaccines with appropriate booster doses through painful injections under clinical supervision was challenging during the recent COVID-19 pandemic. As an alternative solution, we designed a safer, edible probiotic yogurt vaccine prototype (YoVac) that can be orally consumed by circumventing painful injections and clinical supervision. We hypothesized that YoVac prepared using Lactobacillus carrying an antigen coding gene (donor) can transfer the same to other bacteria (recipients) in the human gut microbiome (hgMb) through lateral gene transfer (LGT) for boosted antigen levels potentially triggering a robust immune response. In this study we confirmed the in vitro LGT efficiency of a plasmid (pRBD-Ampr) containing severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) spike protein-receptor binding domain (RBD) coding gene along with an ampicillin-resistance gene (selection marker) from the probiotic Lactobacillus (donor) cultured from homemade yogurt to E. coli and Helicobacter pylori (recipients). Both the donor and recipient bacteria not only exhibited ampicillin-resistance from pRBD-Ampr but also expressed RBD protein. Furthermore, Lactobacillus isolated from YoVac consistently showed the expression of RBD protein over a period of one month confirming the shelf life of our prototype stored at 4 °C. Taken together, our in vitro results provide a preliminary basis for the potential in vivo transfer of RBD coding gene from YoVac to other bacterial species in the hgMb through LGT and may potentially boost the vaccine dosage by delegating them.
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Affiliation(s)
- Madhuri Vissapragada
- Department of Intramural Research Core, The Center for Advanced-Applied Biological Sciences & Entrepreneurship (TCABS-E), Visakhapatnam, 530003, A.P, India
| | - Santhinissi Addala
- Department of Intramural Research Core, The Center for Advanced-Applied Biological Sciences & Entrepreneurship (TCABS-E), Visakhapatnam, 530003, A.P, India
| | - Madhumita Aggunna
- Department of Intramural Research Core, The Center for Advanced-Applied Biological Sciences & Entrepreneurship (TCABS-E), Visakhapatnam, 530003, A.P, India
| | - Manikanta Sodasani
- Department of Intramural Research Core, The Center for Advanced-Applied Biological Sciences & Entrepreneurship (TCABS-E), Visakhapatnam, 530003, A.P, India
| | - Abhinav V K S Grandhi
- Department of Intramural Research Core, The Center for Advanced-Applied Biological Sciences & Entrepreneurship (TCABS-E), Visakhapatnam, 530003, A.P, India
| | - Ravikiran S Yedidi
- Department of Intramural Research Core, The Center for Advanced-Applied Biological Sciences & Entrepreneurship (TCABS-E), Visakhapatnam, 530003, A.P, India.
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27
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Sakurai Y, Okada S, Ozeki T, Yoshikawa R, Kinoshita T, Yasuda J. SARS-CoV-2 Omicron subvariants progressively adapt to human cells with altered host cell entry. mSphere 2024:e0033824. [PMID: 39191389 DOI: 10.1128/msphere.00338-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 07/26/2024] [Indexed: 08/29/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant exhibits high transmissibility with a strong immune escape ability and causes frequent large-scale global infections by producing predominant subvariants. Here, using human upper/lower airway and intestinal cells, we examined the previously dominant BA.1-BA.5 and BA.2.75 subvariants, together with the recently emerged XBB/BQ lineages, in comparison to the former Delta variant. We observed a tendency for each virus to demonstrate higher growth capability than the previously dominant subvariants. Unlike human bronchial and intestinal cells, nasal epithelial cells accommodated the efficient entry of certain Omicron subvariants, similar to the Delta variant. In contrast to the Delta's reliance on cell-surface transmembrane protease serine 2, all tested Omicron variants depended on endosomal cathepsin L. Moreover, S1/S2 cleavage of early Omicron spikes was less efficient, whereas recent viruses exhibit improved cleavage efficacy. Our results show that the Omicron variant progressively adapts to human cells through continuous endosome-mediated host cell entry.IMPORTANCESARS-CoV-2, the causative agent of coronavirus disease 2019, has evolved into a number of variants/subvariants, which have generated multiple global waves of infection. In order to monitor/predict virological features of emerging variants and determine appropriate strategies for anti-viral development, understanding conserved or altered features of evolving SARS-CoV-2 is important. In this study, we addressed previously or recently predominant Omicron subvariants and demonstrated the gradual adaptation to human cells. The host cell entry route, which was altered from the former Delta variant, was conserved among all tested Omicron subvariants. Collectively, this study revealed both changing and maintained features of SARS-CoV-2 during the Omicron variant evolution.
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Affiliation(s)
- Yasuteru Sakurai
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
- Department of Emerging Infectious Diseases, National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki, Japan
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Sayaka Okada
- Department of Emerging Infectious Diseases, National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki, Japan
| | - Takehiro Ozeki
- Department of Emerging Infectious Diseases, National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki, Japan
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Rokusuke Yoshikawa
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
- Department of Emerging Infectious Diseases, National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki, Japan
| | - Takaaki Kinoshita
- Department of Emerging Infectious Diseases, National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki, Japan
| | - Jiro Yasuda
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
- Department of Emerging Infectious Diseases, National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki, Japan
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
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Nuqui X, Casalino L, Zhou L, Shehata M, Wang A, Tse AL, Ojha AA, Kearns FL, Rosenfeld MA, Miller EH, Acreman CM, Ahn SH, Chandran K, McLellan JS, Amaro RE. Simulation-driven design of stabilized SARS-CoV-2 spike S2 immunogens. Nat Commun 2024; 15:7370. [PMID: 39191724 PMCID: PMC11350062 DOI: 10.1038/s41467-024-50976-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 07/25/2024] [Indexed: 08/29/2024] Open
Abstract
The full-length prefusion-stabilized SARS-CoV-2 spike (S) is the principal antigen of COVID-19 vaccines. Vaccine efficacy has been impacted by emerging variants of concern that accumulate most of the sequence modifications in the immunodominant S1 subunit. S2, in contrast, is the most evolutionarily conserved region of the spike and can elicit broadly neutralizing and protective antibodies. Yet, S2's usage as an alternative vaccine strategy is hampered by its general instability. Here, we use a simulation-driven approach to design S2-only immunogens stabilized in a closed prefusion conformation. Molecular simulations provide a mechanistic characterization of the S2 trimer's opening, informing the design of tryptophan substitutions that impart kinetic and thermodynamic stabilization. Structural characterization via cryo-EM shows the molecular basis of S2 stabilization in the closed prefusion conformation. Informed by molecular simulations and corroborated by experiments, we report an engineered S2 immunogen that exhibits increased protein expression, superior thermostability, and preserved immunogenicity against sarbecoviruses.
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Affiliation(s)
- Xandra Nuqui
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Lorenzo Casalino
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Ling Zhou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Mohamed Shehata
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Albert Wang
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Alexandra L Tse
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Anupam A Ojha
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Fiona L Kearns
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Mia A Rosenfeld
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Emily Happy Miller
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Medicine, Division of Infectious Diseases, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Cory M Acreman
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Surl-Hee Ahn
- Department of Chemical Engineering, University of California Davis, Davis, CA, USA
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA.
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA.
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Xin K, Ma X, Meng X, Zhang X, Yang W, Ma T, Zhou C, Wang J, Li G. Assessment of myocardial injury by SPECT myocardial perfusion imaging in patients with COVID-19 infection in a single center after lifting the restrictions in China. Ann Nucl Med 2024:10.1007/s12149-024-01970-0. [PMID: 39186242 DOI: 10.1007/s12149-024-01970-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Accepted: 08/12/2024] [Indexed: 08/27/2024]
Abstract
PURPOSE To assess myocardial injury using rest single photon emission computed tomography (SPECT) myocardial perfusion imaging (MPI) in patients with COVID-19 and to evaluate whether myocardial injury detected by rest MPI predict the prognosis of symptoms after 6 months follow-up. METHODS Patients suspected of myocarditis between December 2022 and March 2023, after the lifting of COVID-19 pandemic restrictions, and between December 2018 and March 2019, prior to the pandemic, were referred to our study. All patients underwent rest MPI. One hundred and sixty four patients with COVID-19 infection after the lifting of pandemic restrictions and 101 patients before the pandemic were included as the study and control groups, respectively. One hundred and fifty three patients of the study group and 83 of the control group presented symptoms when they initially visit to our department. Compare the parameters of myocardial injury detected by rest SPECT MPI between the two groups and then investigate the association between myocardial injury and symptom prognosis in symptomatic patients of both groups. RESULTS Total perfusion defect (TPD) (4.2% ± 3.3% vs. 2.3% ± 2.2%, P < 0.001), summed rest score (SRS) (5.3 ± 5.4 vs. 2.7 ± 2.0, P < 0.001), the proportion of patients with TPD > 4% (43.3% vs. 17.8%, P < 0.001), TPD > 10% (6.71% vs 0, P < 0.001), SRS > 4 (40.2% vs 15.8%, P < 0.001), SRS > 10 (12.8% vs 0, P < 0.001), the number of abnormal perfusion segments (3.9 ± 3.1 vs. 2.4 ± 1.7, P < 0.001) were all significantly higher in the study group. All the parameters of rest MPI were not associated with the prognosis of symptoms in symptomatic patients of both groups after 6 months follow-up. CONCLUSION Myocardial injury in COVID-19 patients could be assessed by rest SPECT MPI. The COVID-19 patients could exhibited a higher frequency and greater severity of myocardial injury than uninfected control patients. Myocardial injury assessed by rest MPI did not predict for the prognosis of symptoms in symptomatic patients of both COVID-19 patients and uninfected patients.
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Affiliation(s)
- Keke Xin
- Department of Nuclear Medicine, Xijing Hospital, Fourth Military Medical University, No. 127 Changle West Road, Xincheng District, Xi'an, Shaanxi, 710032, China
| | - Xinghong Ma
- Department of Nuclear Medicine, Air Force Medical Center, No. 30 Fucheng Road, Haidian District, Beijing, 100142, China
| | - Xiaoli Meng
- Department of Nuclear Medicine, Xijing Hospital, Fourth Military Medical University, No. 127 Changle West Road, Xincheng District, Xi'an, Shaanxi, 710032, China
| | - Xiao Zhang
- Department of Nuclear Medicine, Sanmenxia Central Hospital, Middle of Xiaoshan Road, Hubin District, Sanmenxia, Henan, 472000, China
| | - Weidong Yang
- Department of Nuclear Medicine, Xijing Hospital, Fourth Military Medical University, No. 127 Changle West Road, Xincheng District, Xi'an, Shaanxi, 710032, China
| | - Taoqi Ma
- Department of Nuclear Medicine, Xijing Hospital, Fourth Military Medical University, No. 127 Changle West Road, Xincheng District, Xi'an, Shaanxi, 710032, China
| | - Cheng Zhou
- Department of Nuclear Medicine, Xijing Hospital, Fourth Military Medical University, No. 127 Changle West Road, Xincheng District, Xi'an, Shaanxi, 710032, China
| | - Jing Wang
- Department of Nuclear Medicine, Xijing Hospital, Fourth Military Medical University, No. 127 Changle West Road, Xincheng District, Xi'an, Shaanxi, 710032, China.
| | - Guoquan Li
- Department of Nuclear Medicine, Xijing Hospital, Fourth Military Medical University, No. 127 Changle West Road, Xincheng District, Xi'an, Shaanxi, 710032, China.
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30
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Blazhynska M, Lagardère L, Liu C, Adjoua O, Ren P, Piquemal JP. Water-glycan interactions drive the SARS-CoV-2 spike dynamics: insights into glycan-gate control and camouflage mechanisms. Chem Sci 2024:d4sc04364b. [PMID: 39220162 PMCID: PMC11359970 DOI: 10.1039/d4sc04364b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024] Open
Abstract
To develop therapeutic strategies against COVID-19, we introduce a high-resolution all-atom polarizable model capturing many-body effects of protein, glycan, solvent, and membrane components in SARS-CoV-2 spike protein open and closed states. Employing μs-long molecular dynamics simulations powered by high-performance cloud-computing and unsupervised density-driven adaptive sampling, we investigated the differences in bulk-solvent-glycan and protein-solvent-glycan interfaces between these states. We unraveled a sophisticated solvent-glycan polarization interaction network involving the N165/N343 glycan-gate patterns that provide structural support for the open state and identified key water molecules that could potentially be targeted to destabilize this configuration. In the closed state, the reduced solvent polarization diminishes the overall N165/N343 dipoles, yet internal interactions and a reorganized sugar coat stabilize this state. Despite variations, our glycan-solvent accessibility analysis reveals the glycan shield capability to conserve constant interactions with the solvent, effectively camouflaging the virus from immune detection in both states. The presented insights advance our comprehension of viral pathogenesis at an atomic level, offering potential to combat COVID-19.
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Affiliation(s)
- Marharyta Blazhynska
- Laboratoire de Chimie Théorique, Sorbonne Université, UMR 7616 CNRS 75005 Paris France
| | - Louis Lagardère
- Laboratoire de Chimie Théorique, Sorbonne Université, UMR 7616 CNRS 75005 Paris France
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin Texas 78712 USA
- Qubit Pharmaceuticals 75014 Paris France
| | - Olivier Adjoua
- Laboratoire de Chimie Théorique, Sorbonne Université, UMR 7616 CNRS 75005 Paris France
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin Texas 78712 USA
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Université, UMR 7616 CNRS 75005 Paris France
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31
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Begum F, Chandra S, Mallik MH, Dey J, Tripathi PP, Ray U. A SARS-CoV-2 peptide antigen purified from bacteria and displayed in a high-density repetitive manner on a virus-like particle could generate anti-SARS-CoV-2 neutralizing antibodies unlike free peptide. Biochem Biophys Res Commun 2024; 739:150579. [PMID: 39205338 DOI: 10.1016/j.bbrc.2024.150579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 08/08/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024]
Abstract
SARS-CoV-2 is an enveloped virus. Proteins of the lipid based envelope are not rigidly arranged as compared to non-enveloped viruses lacking lipid based outer layer. Rigidly arranged multivalent display has been reported to be important for potent immune stimulation. We assembled himeric virus-like-particle (VLP) where the core of the particle is composed of the coat protein of Acinetobacter phage. Peptide-based antigen from receptor binding domain (RBD) of SARS-CoV-2 spike protein has been displayed on the coat based VLP matrix using spy-tag/spy-catcher split inteine conjugation system that allows spontaneous, irreversible isopeptide bond formation. Both the matrix as well as peptide have been purified from bacteria which is an easy platform for protein purification. We used the closed state of spike trimer for epitope mapping as this is the conformation of the spike that the immune system visualizes unlike the open state that appears when the virus tries to attach to receptor. Mice based immunization studies were used to test immunogenicity of the antigens. The work demonstrates that peptide-based antigens displayed in high densities can induce neutralizing antibody production unlike free peptide. Careful choice of peptides can deliver better candidates. Also, small size allows easy improvisation. Production in bacteria offers cheaper and robust purification option.
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Affiliation(s)
- Feroza Begum
- CSIR-Indian Institute of Chemical Biology, 4, Raja S.C., Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shreyashi Chandra
- CSIR-Indian Institute of Chemical Biology, 4, Raja S.C., Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Md Hasan Mallik
- CSIR-Indian Institute of Chemical Biology, 4, Raja S.C., Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Jhilik Dey
- CSIR-Indian Institute of Chemical Biology, 4, Raja S.C., Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Prem Prakash Tripathi
- CSIR-Indian Institute of Chemical Biology, 4, Raja S.C., Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Upasana Ray
- CSIR-Indian Institute of Chemical Biology, 4, Raja S.C., Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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32
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Huang Q, Zhou N, Peng J, Zeng X, Du L, Zhao Y, Luo X. Sensitivity-improved SERS detection of SARS-CoV-2 spike protein by Au NPs/COFs integrated with catalytic-hairpin-assembly amplification technology. Anal Chim Acta 2024; 1318:342924. [PMID: 39067931 DOI: 10.1016/j.aca.2024.342924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/26/2024] [Accepted: 06/28/2024] [Indexed: 07/30/2024]
Abstract
BACKGROUND The COVID-19 pandemic, caused by the novel coronavirus, has had a profound impact on global health and economies worldwide. This unprecedented crisis has affected individuals, communities, and nations in diverse manners. Developing simple and accurate diagnostic methods is an imperative task for frequent testing to mitigate the spread of the virus. Among these methods, SARS-CoV-2 antigen tests in clinical specimens have emerged as a promising diagnostic method for COVID-19 due to their sensitive and accurate detection of spike (S) protein, which plays a crucial role in viral infection initiation. RESULTS In this work, a dual-signal amplification surface enhanced Raman scattering (SERS)-based S protein biosensor was constructed based on Au NPs/COFs and enzyme-free catalytic hairpin assembly (CHA) amplification method. The approach relies on a released free DNA sequence (T), which is generated from the competition reaction between Aptamer/T and Aptamer/S protein, to trigger a CHA reaction. Due to the high binding affinity and selectivity between the S protein and its aptamer, CHA process was triggered with the maximum SERS tags (H2-conjugated Au@4-mercaptobenzonitrile@Ag) anchored onto Au NPs/COFs substrate surface. This SERS platform could detect the S protein at concentrations with high sensitivity (limit of detection = 3.0 × 10-16 g/mL), wide detection range (1 × 10-16 to 1 × 10-11 g/mL), acceptable reproducibility (relative standard deviation = 7.01 %) and excellent specificity. The biosensor was also employed to detect S protein in artificial human salivas. SIGNIFICANCE Thus, this study not only developed a novel Au NPs/COFs substrate exhibiting strong SERS enhancement ability and high reproducibility, but also proposed a promising dual-signal amplification SERS-based diagnostic method for COVID-19, holding immense potential for the detection of a wide range of antigens and infectious diseases in future applications.
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Affiliation(s)
- Qiuwen Huang
- School of Science, Xihua University, Chengdu, Sichuan, 610039, China
| | - Na Zhou
- School of Science, Xihua University, Chengdu, Sichuan, 610039, China; Food Microbiology, Key Laboratory of Sichuan Province, Xihua University, Chengdu, 610039, Sichuan, China
| | - Jiayi Peng
- School of Science, Xihua University, Chengdu, Sichuan, 610039, China
| | - Xuanjiang Zeng
- School of Science, Xihua University, Chengdu, Sichuan, 610039, China
| | - Lijuan Du
- School of Science, Xihua University, Chengdu, Sichuan, 610039, China
| | - Yan Zhao
- School of Science, Xihua University, Chengdu, Sichuan, 610039, China; Asymmetric Synthesis and Chiral Technology Key Laboratory of Sichuan Province, Chengdu, 610039, Sichuan, China.
| | - Xiaojun Luo
- School of Science, Xihua University, Chengdu, Sichuan, 610039, China; Asymmetric Synthesis and Chiral Technology Key Laboratory of Sichuan Province, Chengdu, 610039, Sichuan, China.
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Qiao S, Wang X. Structural determinants of spike infectivity in bat SARS-like coronaviruses RsSHC014 and WIV1. J Virol 2024; 98:e0034224. [PMID: 39028202 PMCID: PMC11334503 DOI: 10.1128/jvi.00342-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/20/2024] Open
Abstract
The recurrent spillovers of coronaviruses (CoVs) have posed severe threats to public health and the global economy. Bat severe acute respiratory syndrome (SARS)-like CoVs RsSHC014 and WIV1, currently circulating in bat populations, are poised for human emergence. The trimeric spike (S) glycoprotein, responsible for receptor recognition and membrane fusion, plays a critical role in cross-species transmission and infection. Here, we determined the cryo-electron microscopy (EM) structures of the RsSHC014 S protein in the closed state at 2.9 Å, the WIV1 S protein in the closed state at 2.8 Å, and the intermediate state at 4.0 Å. In the intermediate state, one receptor-binding domain (RBD) is in the "down" position, while the other two RBDs exhibit poor density. We also resolved the complex structure of the WIV1 S protein bound to human ACE2 (hACE2) at 4.5 Å, which provides structural basis for the future emergence of WIV1 in humans. Through biochemical experiments, we found that despite strong binding affinities between the RBDs and both human and civet ACE2, the pseudoviruses of RsSHC014, but not WIV1, failed to infect 293T cells overexpressing either human or civet ACE2. Mutagenesis analysis revealed that the Y623H substitution, located in the SD2 region, significantly improved the cell entry efficiency of RsSHC014 pseudoviruses, which is likely accomplished by promoting the open conformation of spike glycoproteins. Our findings emphasize the necessity of both efficient RBD lifting and tight RBD-hACE2 binding for viral infection and underscore the significance of the 623 site of the spike glycoprotein for the infectivity of bat SARS-like CoVs. IMPORTANCE The bat SARS-like CoVs RsSHC014 and WIV1 can use hACE2 for cell entry without further adaptation, indicating their potential risk of emergence in human populations. The S glycoprotein, responsible for receptor recognition and membrane fusion, plays a crucial role in cross-species transmission and infection. In this study, we determined the cryo-EM structures of the S glycoproteins of RsSHC014 and WIV1. Detailed comparisons revealed dynamic structural variations within spike proteins. We also elucidated the complex structure of WIV1 S-hACE2, providing structural evidence for the potential emergence of WIV1 in humans. Although RsSHC014 and WIV1 had similar hACE2-binding affinities, they exhibited distinct pseudovirus cell entry behavior. Through mutagenesis and cryo-EM analysis, we revealed that besides the structural variations, the 623 site in the SD2 region is another important structural determinant of spike infectivity.
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Affiliation(s)
- Shuyuan Qiao
- The Ministry of Education Key Laboratory of Protein Science, Beijing, China
- Beijing Frontier Research Center for Biological Structure, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Xinquan Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing, China
- Beijing Frontier Research Center for Biological Structure, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
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34
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Yılmaz Çolak Ç. Bacterial Membrane Vesicles as a Novel Vaccine Platform against SARS-CoV-2. Curr Microbiol 2024; 81:317. [PMID: 39164527 DOI: 10.1007/s00284-024-03846-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 08/15/2024] [Indexed: 08/22/2024]
Abstract
Throughout history, infectious diseases have plagued humanity, with outbreaks occurring regularly worldwide. Not every outbreak affects people globally; however, in the case of Coronavirus Disease 2019 (COVID-19), caused by a novel coronavirus (SARS-CoV-2), it reached a pandemic level within a remarkably short period. Fortunately, advancements in medicine and biotechnology have facilitated swift responses to the disease, resulting in the development of therapeutics and vaccines. Nevertheless, the persistent spread of the virus and the emergence of new variants underscore the necessity for protective interventions, leading researchers to seek more effective vaccines. Despite the presence of various types of vaccines, including mRNA and inactivated vaccines against SARS-CoV-2, new platforms have been investigated since the pandemic, and research on bacterial membrane vesicles (BMVs) has demonstrated their potential as a novel COVID-19 vaccine platform. Researchers have explored different strategies for BMV-based COVID-19 vaccines, such as mixing the vesicles with antigenic components of the virus due to their adjuvant capacity or decorating the vesicles with the viral antigens to create adjuvanted delivery systems. These approaches have presented promising results in inducing robust immune responses, but obstacles such as reproducibility in obtaining and homogeneous characterization of BMVs remain in developing vesicle-based vaccines. Overall, the development of BMV-based vaccines represents a novel and promising strategy in the fight against COVID-19. Additional research and clinical trials are needed to further evaluate the potential of these vaccines to offer long-lasting protection against SARS-CoV-2 and its evolving variants.
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Affiliation(s)
- Çiğdem Yılmaz Çolak
- Life Sciences, Marmara Research Center, TUBITAK, Kocaeli, Türkiye.
- Molecular Biology and Genetics Department, Istanbul Technical University, Istanbul, Türkiye.
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35
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Jhanwar A, Sharma D, Das U. Unraveling the structural and functional dimensions of SARS-CoV2 proteins in the context of COVID-19 pathogenesis and therapeutics. Int J Biol Macromol 2024; 278:134850. [PMID: 39168210 DOI: 10.1016/j.ijbiomac.2024.134850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 08/14/2024] [Accepted: 08/16/2024] [Indexed: 08/23/2024]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) has emerged as the causative agent behind the global pandemic of Coronavirus Disease 2019 (COVID-19). As the scientific community strives to comprehend the intricate workings of this virus, a fundamental aspect lies in deciphering the myriad proteins it expresses. This knowledge is pivotal in unraveling the complexities of the viral machinery and devising targeted therapeutic interventions. The proteomic landscape of SARS-CoV2 encompasses structural, non-structural, and open-reading frame proteins, each playing crucial roles in viral replication, host interactions, and the pathogenesis of COVID-19. This comprehensive review aims to provide an updated and detailed examination of the structural and functional attributes of SARS-CoV2 proteins. By exploring the intricate molecular architecture, we have highlighted the significance of these proteins in viral biology. Insights into their roles and interplay contribute to a deeper understanding of the virus's mechanisms, thereby paving the way for the development of effective therapeutic strategies. As the global scientific community strives to combat the ongoing pandemic, this synthesis of knowledge on SARS-CoV2 proteins serves as a valuable resource, fostering informed approaches toward mitigating the impact of COVID-19 and advancing the frontier of antiviral research.
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Affiliation(s)
- Aniruddh Jhanwar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Dipika Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Uddipan Das
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
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36
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Otsuka Y, Zhang L, Mou H, Shumate J, Kitzmiller CE, Scampavia L, Bannister TD, Farzan M, Choe H, Spicer TP. Simultaneous screening for selective SARS-CoV-2, Lassa, and Machupo virus entry inhibitors. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100178. [PMID: 39159824 DOI: 10.1016/j.slasd.2024.100178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 08/05/2024] [Accepted: 08/07/2024] [Indexed: 08/21/2024]
Abstract
Emerging highly pathogenic viruses can pose profound impacts on global health, the economy, and society. To meet that challenge, the National Institute of Allergy and Infectious Diseases (NIAID) established nine Antiviral Drug Discovery (AViDD) centers for early-stage identification and validation of novel antiviral drug candidates against viruses with pandemic potential. As part of this initiative, we established paired entry assays that simultaneously screen for inhibitors specifically targeting SARS-CoV-2 (SARS2), Lassa virus (LASV) and Machupo virus (MACV) entry. To do so we employed a dual pseudotyped virus (PV) infection system allowing us to screen ∼650,000 compounds efficiently and cost-effectively. Adaptation of these paired assays into 1536 well-plate format for ultra-high throughput screening (uHTS) resulted in the largest screening ever conducted in our facility, with over 2.4 million wells completed. The paired infection system allowed us to detect two PV infections simultaneously: LASV + MACV, MACV + SARS2, and SARS2 + LASV. Each PV contains a different luciferase reporter gene which enabled us to measure the infection of each PV exclusively, albeit in the same well. Each PV was screened at least twice utilizing different reporters, which allowed us to select the inhibitors specific to a particular PV and to exclude those that hit off targets, including cellular components or the reporter proteins. All assays were robust with an average Z' value ranging from 0.5 to 0.8. The primary screening of ∼650,000 compounds resulted in 1812, 1506, and 2586 unique hits for LASV, MACV, and SARS2, respectively. The confirmation screening narrowed this list further to 60, 40, and 90 compounds that are unique to LASV, MACV, and SARS2, respectively. Of these compounds, 8, 35, and 50 compounds showed IC50 value < 10 μM, some of which have much greater potency and excellent antiviral activity profiles specific to LASV, MACV, and SARS2, and none are cytotoxic. These selected compounds are currently being studied for their mechanism of action and to improve their specificity and potency through chemical modification.
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Affiliation(s)
- Yuka Otsuka
- Department of Molecular Medicine, Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Lizhou Zhang
- Division of Infectious Diseases, Boston Children's Hospital, Boston, MA 02115, United States; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, United States
| | - Huihui Mou
- Division of Infectious Diseases, Boston Children's Hospital, Boston, MA 02115, United States; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, United States
| | - Justin Shumate
- Department of Molecular Medicine, Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Claire E Kitzmiller
- Division of Infectious Diseases, Boston Children's Hospital, Boston, MA 02115, United States
| | - Louis Scampavia
- Department of Molecular Medicine, Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Thomas D Bannister
- Department of Molecular Medicine, Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Michael Farzan
- Division of Infectious Diseases, Boston Children's Hospital, Boston, MA 02115, United States; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, United States
| | - Hyeryun Choe
- Division of Infectious Diseases, Boston Children's Hospital, Boston, MA 02115, United States; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, United States
| | - Timothy P Spicer
- Department of Molecular Medicine, Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, 130 Scripps Way, Jupiter, FL 33458, United States.
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Duyvesteyn HME, Dijokaite-Guraliuc A, Liu C, Supasa P, Kronsteiner B, Jeffery K, Stafford L, Klenerman P, Dunachie SJ, Mongkolsapaya J, Fry EE, Ren J, Stuart DI, Screaton GR. Concerted deletions eliminate a neutralizing supersite in SARS-CoV-2 BA.2.87.1 spike. Structure 2024:S0969-2126(24)00283-1. [PMID: 39173622 DOI: 10.1016/j.str.2024.07.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 07/01/2024] [Accepted: 07/29/2024] [Indexed: 08/24/2024]
Abstract
BA.2.87.1 represents a major shift in the BA.2 lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is unusual in having two lengthy deletions of polypeptide in the spike (S) protein, one of which removes a beta-strand. Here we investigate its neutralization by a variety of sera from infected and vaccinated individuals and determine its spike (S) ectodomain structure. The BA.2.87.1 receptor binding domain (RBD) is structurally conserved and the RBDs are tightly packed in an "all-down" conformation with a small rotation relative to the trimer axis as compared to the closest previously observed conformation. The N-terminal domain (NTD) maintains a remarkably similar structure overall; however, the rearrangements resulting from the deletions essentially destroy the so-called supersite epitope and eliminate one glycan site, while a mutation creates an additional glycan site, effectively shielding another NTD epitope. BA.2.87.1 is relatively easily neutralized but acquisition of additional mutations in the RBD could increase antibody escape allowing it to become a dominant sub-lineage.
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Affiliation(s)
- Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Centre for Human Genetics, Oxford, UK
| | - Aiste Dijokaite-Guraliuc
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chang Liu
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Piyada Supasa
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Barbara Kronsteiner
- NDM Centre For Global Health Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Katie Jeffery
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Lizzie Stafford
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Juthathip Mongkolsapaya
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand.
| | - Elizabeth E Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Centre for Human Genetics, Oxford, UK.
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Centre for Human Genetics, Oxford, UK.
| | - David I Stuart
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Centre for Human Genetics, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK.
| | - Gavin R Screaton
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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Arshad NF, Nordin FJ, Foong LC, In LLA, Teo MYM. Engineering receptor-binding domain and heptad repeat domains towards the development of multi-epitopes oral vaccines against SARS-CoV-2 variants. PLoS One 2024; 19:e0306111. [PMID: 39146295 PMCID: PMC11326571 DOI: 10.1371/journal.pone.0306111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 06/11/2024] [Indexed: 08/17/2024] Open
Abstract
The inability of existing vaccines to cope with the mutation rate has highlighted the need for effective preventative strategies for COVID-19. Through the secretion of immunoglobulin A, mucosal delivery of vaccines can effectively stimulate mucosal immunity for better protection against SARS-CoV-2 infection. In this study, various immunoinformatic tools were used to design a multi-epitope oral vaccine against SARS-CoV-2 based on its receptor-binding domain (RBD) and heptad repeat (HR) domains. T and B lymphocyte epitopes were initially predicted from the RBD and HR domains of SARS-CoV-2, and potential antigenic, immunogenic, non-allergenic, and non-toxic epitopes were identified. Epitopes that are highly conserved and have no significant similarity to human proteome were selected. The epitopes were joined with appropriate linkers, and an adjuvant was added to enhance the vaccine efficacy. The vaccine 3D structure constructs were docked with toll-like receptor 4 (TLR-4) and TLR1-TLR2, and the binding affinity was calculated. The designed multi-epitope vaccine construct (MEVC) consisted of 33 antigenic T and B lymphocyte epitopes. The results of molecular dockings and free binding energies confirmed that the MEVC effectively binds to TLR molecules, and the complexes were stable. The results suggested that the designed MEVC is a potentially safe and effective oral vaccine against SARS-CoV-2. This in silico study presents a novel approach for creating an oral multi-epitope vaccine against the rapidly evolving SARS-CoV-2 variants. These findings offer valuable insights for developing an effective strategy to combat COVID-19. Further preclinical and clinical studies are required to confirm the efficacy of the MEVC vaccine.
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Affiliation(s)
- Nur Farhanah Arshad
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia
| | - Fariza Juliana Nordin
- Department of Biological Sciences and Biotechnology, Faculty of Science & Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Lian Chee Foong
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lionel Lian Aun In
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia
| | - Michelle Yee Mun Teo
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia
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Bellavita R, Esposito S, Braccia S, Madrid L, Ortega P, D'Auria G, Zarrilli F, Amato F, Galdiero S, de la Mata J, Falcigno L, Falanga A. Targetable domains for the design of peptide-dendrimer inhibitors of SARS-CoV-2. Int J Pharm 2024; 661:124389. [PMID: 38942185 DOI: 10.1016/j.ijpharm.2024.124389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/06/2024] [Accepted: 06/24/2024] [Indexed: 06/30/2024]
Abstract
We have recently witnessed that considerable progresses have been made in the rapid detection and appropriate treatments of COVID-19, but still this virus remains one of the main targets of world research. Based on the knowledge of the complex mechanism of viral infection we designed peptide-dendrimer inhibitors of SARS-CoV-2with the aim to block cell infection through interfering with the host-pathogen interactions. We used two different strategies: i) the first one aims at hindering the virus anchorage to the human cell; ii) the second -strategy points to interfere with the mechanism of virus-cell membrane fusion. We propose the use of different nanosized carriers, formed by several carbosilane dendritic wedges to deliver two different peptides designed to inhibit host interaction or virus entry. The antiviral activity of the peptide-dendrimers, as well as of free peptides and free dendrimers was evaluated through the use of SARS-CoV-2 pseudotyped lentivirus. The results obtained show that peptides designed to block host-pathogen interaction represent a valuable strategy for viral inhibition.
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Affiliation(s)
- Rosa Bellavita
- Department of Pharmacy, School of Medicine, University of Naples 'Federico II', Via Domenico Montesano 49, 80131 Naples, Italy
| | - Speranza Esposito
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, 80131 Naples, Italy; CEINGE Biotecnologie Avanzate Franco Salvatore, Scarl, 80131 Naples, Italy
| | - Simone Braccia
- Department of Pharmacy, School of Medicine, University of Naples 'Federico II', Via Domenico Montesano 49, 80131 Naples, Italy
| | - Laura Madrid
- Universidad de Alcalá, Department of Organic and Inorganic Chemistry, Faculty of Sciences, and Research Institute in Chemistry "Andrés M. del Río" (IQAR), Italy
| | - Paula Ortega
- Universidad de Alcalá, Department of Organic and Inorganic Chemistry, Faculty of Sciences, and Research Institute in Chemistry "Andrés M. del Río" (IQAR), Italy; CIBER de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, 28801 Alcalá de Henares, Spain; Institute Ramón y Cajal for Health Research (IRYCIS), 28034 Madrid, Spain
| | - Gabriella D'Auria
- Department of Pharmacy, School of Medicine, University of Naples 'Federico II', Via Domenico Montesano 49, 80131 Naples, Italy
| | - Federica Zarrilli
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, 80131 Naples, Italy; CEINGE Biotecnologie Avanzate Franco Salvatore, Scarl, 80131 Naples, Italy
| | - Felice Amato
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, 80131 Naples, Italy; CEINGE Biotecnologie Avanzate Franco Salvatore, Scarl, 80131 Naples, Italy
| | - Stefania Galdiero
- Department of Pharmacy, School of Medicine, University of Naples 'Federico II', Via Domenico Montesano 49, 80131 Naples, Italy
| | - Javier de la Mata
- Universidad de Alcalá, Department of Organic and Inorganic Chemistry, Faculty of Sciences, and Research Institute in Chemistry "Andrés M. del Río" (IQAR), Italy; CIBER de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, 28801 Alcalá de Henares, Spain; Institute Ramón y Cajal for Health Research (IRYCIS), 28034 Madrid, Spain.
| | - Lucia Falcigno
- Department of Pharmacy, School of Medicine, University of Naples 'Federico II', Via Domenico Montesano 49, 80131 Naples, Italy.
| | - Annarita Falanga
- Department of Agricultural Science, University of Naples 'Federico II', Via Università 100, Portici, 80055 Portici, Italy.
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Benlarbi M, Ding S, Bélanger É, Tauzin A, Poujol R, Medjahed H, El Ferri O, Bo Y, Bourassa C, Hussin J, Fafard J, Pazgier M, Levade I, Abrams C, Côté M, Finzi A. Temperature-dependent Spike-ACE2 interaction of Omicron subvariants is associated with viral transmission. mBio 2024; 15:e0090724. [PMID: 38953636 PMCID: PMC11323525 DOI: 10.1128/mbio.00907-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/27/2024] [Indexed: 07/04/2024] Open
Abstract
The continued evolution of severe acute respiratory syndrome 2 (SARS-CoV-2) requires persistent monitoring of its subvariants. Omicron subvariants are responsible for the vast majority of SARS-CoV-2 infections worldwide, with XBB and BA.2.86 sublineages representing more than 90% of circulating strains as of January 2024. To better understand parameters involved in viral transmission, we characterized the functional properties of Spike glycoproteins from BA.2.75, CH.1.1, DV.7.1, BA.4/5, BQ.1.1, XBB, XBB.1, XBB.1.16, XBB.1.5, FD.1.1, EG.5.1, HK.3, BA.2.86 and JN.1. We tested their capacity to evade plasma-mediated recognition and neutralization, binding to angiotensin-converting enzyme 2 (ACE2), their susceptibility to cold inactivation, Spike processing, as well as the impact of temperature on Spike-ACE2 interaction. We found that compared to the early wild-type (D614G) strain, most Omicron subvariants' Spike glycoproteins evolved to escape recognition and neutralization by plasma from individuals who received a fifth dose of bivalent (BA.1 or BA.4/5) mRNA vaccine and improve ACE2 binding, particularly at low temperatures. Moreover, BA.2.86 had the best affinity for ACE2 at all temperatures tested. We found that Omicron subvariants' Spike processing is associated with their susceptibility to cold inactivation. Intriguingly, we found that Spike-ACE2 binding at low temperature was significantly associated with growth rates of Omicron subvariants in humans. Overall, we report that Spikes from newly emerged Omicron subvariants are relatively more stable and resistant to plasma-mediated neutralization, present improved affinity for ACE2 which is associated, particularly at low temperatures, with their growth rates.IMPORTANCEThe persistent evolution of SARS-CoV-2 gave rise to a wide range of variants harboring new mutations in their Spike glycoproteins. Several factors have been associated with viral transmission and fitness such as plasma-neutralization escape and ACE2 interaction. To better understand whether additional factors could be of importance in SARS-CoV-2 variants' transmission, we characterize the functional properties of Spike glycoproteins from several Omicron subvariants. We found that the Spike glycoprotein of Omicron subvariants presents an improved escape from plasma-mediated recognition and neutralization, Spike processing, and ACE2 binding which was further improved at low temperature. Intriguingly, Spike-ACE2 interaction at low temperature is strongly associated with viral growth rate, as such, low temperatures could represent another parameter affecting viral transmission.
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Affiliation(s)
- Mehdi Benlarbi
- Centre de Recherche du CHUM, Montréal, Québec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
| | - Shilei Ding
- Centre de Recherche du CHUM, Montréal, Québec, Canada
| | - Étienne Bélanger
- Centre de Recherche du CHUM, Montréal, Québec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
| | - Alexandra Tauzin
- Centre de Recherche du CHUM, Montréal, Québec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
| | - Raphaël Poujol
- Montreal Heart Institute, Research Center, Montreal, Quebec, Canada
| | | | - Omar El Ferri
- Department of Biochemistry, Microbiology and Immunology, Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Ontario, Canada
| | - Yuxia Bo
- Department of Biochemistry, Microbiology and Immunology, Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Julie Hussin
- Montreal Heart Institute, Research Center, Montreal, Quebec, Canada
- Département de Médecine, Université de Montréal, Montréal, Québec, Canada
- Mila—Quebec AI institute, Montreal, Quebec, Canada
| | - Judith Fafard
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Marzena Pazgier
- Infectious Disease Division, Department of Medicine of Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Inès Levade
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Cameron Abrams
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Marceline Côté
- Department of Biochemistry, Microbiology and Immunology, Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Ontario, Canada
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montréal, Québec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
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Jitender, Vikram Kumar B, Singh S, Verma G, Kumar R, Mishra PM, Kumar S, Nagaraj SK, Nag J, Joy CM, Nikam B, Singh D, Pooja, Kalidas N, Singh S, Mumtaz, Bhardwaj AK, Mankotia DS, Ringe RP, Gupta N, Tripathi S, Mishra RPN. Mammalian cell expressed recombinant trimeric spike protein is a potent vaccine antigen and confers near-complete protection against SARS-CoV-2 infection in Hamster. Vaccine 2024; 42:126099. [PMID: 38981743 DOI: 10.1016/j.vaccine.2024.06.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 06/20/2024] [Accepted: 06/30/2024] [Indexed: 07/11/2024]
Abstract
Numerous vaccine candidates have emerged in the fight against SARS-CoV-2, yet the challenges posed by viral evolution and the evasion of vaccine-induced immunity persist. The development of broadly protective vaccines is essential in countering the threat posed by variants of concern (VoC) capable of eluding existing vaccine defenses. Among the diverse SARS-CoV-2 vaccine candidates, detailed characterization of those based on the expression of the entire spike protein in mammalian cells have been limited. In our study, we engineered a recombinant prefusion-stabilized trimeric spike protein antigen, IMT-CVAX, encoded by the IMT-C20 gene. This antigen was expressed utilizing a suspension mammalian cell line (CHO-S). The establishment of a stable cell line expressing IMT-CVAX involved the integration of the gene into the CHO genome, followed by the expression, purification, and characterization of the protein. To gauge the vaccine potential of adjuvanted IMT-CVAX, we conducted assessments in small animals. Analyses of blood collected from immunized animals included measurements of anti-spike IgG, SARS-CoV-2 neutralization, and responses from GC-B and Tfh cells. Furthermore, the protective efficacy of IMT-CVAX was evaluated using a Hamster challenge model. Our findings indicate that adjuvanted IMT-CVAX elicits an excellent immune response in both mice and hamsters. Notably, sera from animals immunized with IMT-CVAX effectively neutralize a diverse range of SARS-CoV-2 variants. Moreover, IMT-CVAX immunization conferred complete protection to hamsters against SARS-CoV-2 infection. In hACE2 transgenic mice, IMT-CVAX vaccination induced a robust response from GC-B and Tfh cells. Based on our preclinical model assessments, adjuvanted IMT-CVAX emerges as a highly efficacious vaccine candidate. This protein-subunit-based vaccine exhibits promise for clinical development, offering an affordable solution for both primary and heterologous immunization against SARS-CoV-2 variants.
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Affiliation(s)
- Jitender
- Vaccine & Biotherapeutics Research Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - B Vikram Kumar
- Vaccine & Biotherapeutics Research Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Sneha Singh
- Vaccine & Biotherapeutics Research Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Geetika Verma
- Vaccine & Biotherapeutics Research Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Reetesh Kumar
- Vaccine & Biotherapeutics Research Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Pranaya M Mishra
- Vaccine & Biotherapeutics Research Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Sahil Kumar
- Vaccine & Biotherapeutics Research Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Santhosh K Nagaraj
- Centre for Infectious Disease Research, Indian Institute of Science, Bengaluru, India
| | - Joydeep Nag
- Centre for Infectious Disease Research, Indian Institute of Science, Bengaluru, India
| | - Christy M Joy
- Centre for Infectious Disease Research, Indian Institute of Science, Bengaluru, India
| | | | | | - Pooja
- Vaccine & Biotherapeutics Research Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Nidhi Kalidas
- Vaccine & Biotherapeutics Research Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Shubham Singh
- Vaccine & Biotherapeutics Research Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Mumtaz
- Vaccine & Biotherapeutics Research Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Ashwani K Bhardwaj
- Vaccine & Biotherapeutics Research Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Dhananjay S Mankotia
- Vaccine & Biotherapeutics Research Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Rajesh P Ringe
- Vaccine & Biotherapeutics Research Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Nimesh Gupta
- National Institute of Immunology, New Delhi, India
| | - Shashank Tripathi
- Centre for Infectious Disease Research, Indian Institute of Science, Bengaluru, India; Microbiology & Cell Biology Department, Indian Institute of Science, Bengaluru, India
| | - Ravi P N Mishra
- Vaccine & Biotherapeutics Research Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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42
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Wu B, Liu Y, Zhang X, Luo D, Wang X, Qiao C, Liu J. A bibliometric insight into nanomaterials in vaccine: trends, collaborations, and future avenues. Front Immunol 2024; 15:1420216. [PMID: 39188723 PMCID: PMC11345159 DOI: 10.3389/fimmu.2024.1420216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 07/24/2024] [Indexed: 08/28/2024] Open
Abstract
Background The emergence of nanotechnology has injected new vigor into vaccine research. Nanovaccine research has witnessed exponential growth in recent years; yet, a comprehensive analysis of related publications has been notably absent. Objective This study utilizes bibliometric methodologies to reveal the evolution of themes and the distribution of nanovaccine research. Methods Using tools such as VOSviewer, CiteSpace, Scimago Graphica, Pajek, R-bibliometrix, and R packages for the bibliometric analysis and visualization of literature retrieved from the Web of Science database. Results Nanovaccine research commenced in 1981. The publication volume exponentially increased, notably in 2021. Leading contributors include the United States, the Chinese Academy of Sciences, the "Vaccine", and researcher Zhao Kai. Other significant contributors comprise China, the University of California, San Diego, Veronique Preat, the Journal of Controlled Release, and the National Natural Science Foundation of China. The USA functions as a central hub for international cooperation. Financial support plays a pivotal role in driving research advancements. Key themes in highly cited articles include vaccine carrier design, cancer vaccines, nanomaterial properties, and COVID-19 vaccines. Among 7402 keywords, the principal nanocarriers include Chitosan, virus-like particles, gold nanoparticles, PLGA, and lipid nanoparticles. Nanovaccine is primarily intended to address diseases including SARS-CoV-2, cancer, influenza, and HIV. Clustering analysis of co-citation networks identifies 9 primary clusters, vividly illustrating the evolution of research themes over different periods. Co-citation bursts indicate that cancer vaccines, COVID-19 vaccines, and mRNA vaccines are pivotal areas of focus for current and future research in nanovaccines. "candidate vaccines," "protein nanoparticle," "cationic lipids," "ionizable lipids," "machine learning," "long-term storage," "personalized cancer vaccines," "neoantigens," "outer membrane vesicles," "in situ nanovaccine," and "biomimetic nanotechnologies" stand out as research interest. Conclusions This analysis emphasizes the increasing scholarly interest in nanovaccine research and highlights pivotal recent research themes such as cancer and COVID-19 vaccines, with lipid nanoparticle-mRNA vaccines leading novel research directions.
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Affiliation(s)
- Beibei Wu
- Department of Information, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- Traditional Chinese Medicine (TCM) Big Data Innovation Lab of Beijing Office of Academic Research, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- Graduate School, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ye Liu
- Graduate School, Beijing University of Chinese Medicine, Beijing, China
| | - Xuexue Zhang
- Department of Information, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- Graduate School, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ding Luo
- Department of Information, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- Traditional Chinese Medicine (TCM) Big Data Innovation Lab of Beijing Office of Academic Research, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xuejie Wang
- Department of Information, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- Traditional Chinese Medicine (TCM) Big Data Innovation Lab of Beijing Office of Academic Research, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Chen Qiao
- Department of Information, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- Traditional Chinese Medicine (TCM) Big Data Innovation Lab of Beijing Office of Academic Research, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jian Liu
- Department of Information, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- Traditional Chinese Medicine (TCM) Big Data Innovation Lab of Beijing Office of Academic Research, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
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43
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Bosch A, Guzman HV, Pérez R. Adsorption-Driven Deformation and Footprints of the RBD Proteins in SARS-CoV-2 Variants on Biological and Inanimate Surfaces. J Chem Inf Model 2024; 64:5977-5990. [PMID: 39083670 PMCID: PMC11323246 DOI: 10.1021/acs.jcim.4c00460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 08/02/2024]
Abstract
Respiratory viruses, carried through airborne microdroplets, frequently adhere to surfaces, including plastics and metals. However, our understanding of the interactions between viruses and materials remains limited, particularly in scenarios involving polarizable surfaces. Here, we investigate the role of the receptor-binding domain (RBD) of the spike protein mutations on the adsorption of SARS-CoV-2 to hydrophobic and hydrophilic surfaces employing molecular simulations. To contextualize our findings, we contrast the interactions on inanimate surfaces with those on native biological interfaces, specifically the angiotensin-converting enzyme 2. Notably, we identify a 2-fold increase in structural deformations for the protein's receptor binding motif (RBM) onto inanimate surfaces, indicative of enhanced shock-absorbing mechanisms. Furthermore, the distribution of adsorbed amino acids (landing footprints) on the inanimate surface reveals a distinct regional asymmetry relative to the biological interface, with roughly half of the adsorbed amino acids arranged in opposite sites. In spite of the H-bonds formed at the hydrophilic substrate, the simulations consistently show a higher number of contacts and interfacial area with the hydrophobic surface, where the wild-type RBD adsorbs more strongly than the Delta or Omicron RBDs. In contrast, the adsorption of Delta and Omicron to hydrophilic surfaces was characterized by a distinctive hopping-pattern. The novel shock-absorbing mechanisms identified in the virus adsorption on inanimate surfaces show the embedded high-deformation capacity of the RBD without losing its secondary structure, which could lead to current experimental strategies in the design of virucidal surfaces.
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Affiliation(s)
- Antonio
M. Bosch
- Departamento
de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Horacio V. Guzman
- Departamento
de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Department
of Theoretical Physics, Jožef Stefan
Institute, SI-1000 Ljubljana, Slovenia
| | - Rubén Pérez
- Departamento
de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Condensed
Matter Physics Center (IFIMAC), Universidad
Autónoma de Madrid, E-28049 Madrid, Spain
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Yu W, Yi SZ, Jiang CY, Guan JW, Xue R, Zhang XX, Zeng T, Tang H, Chen W, Han B. Biosensor-based active ingredient recognition system for screening potential small molecular Severe acute respiratory syndrome coronavirus 2 entry blockers targeting the spike protein from Rugosa rose. Biomed Chromatogr 2024:e5987. [PMID: 39126351 DOI: 10.1002/bmc.5987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024]
Abstract
The traditional formulation Hanchuan zupa granules (HCZPs) have been widely used for controlling coronavirus disease 2019 (COVID-19). However, its active components remain unknown. Here, HCZP components targeting the spike receptor-binding domain (S-RBD) of SARS-CoV-2 were investigated using a surface plasmon resonance (SPR) biosensor-based active ingredient recognition system (SPR-AIRS). Recombinant S-RBD proteins were immobilized on the SPR chip by amine coupling for the prescreening of nine HCZP medicinal herbs. Ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) identified gallic acid (GA) and methyl gallate (MG) from Rosa rugosa as S-RBD ligands, with KD values of 2.69 and 0.95 μM, respectively, as shown by SPR. Molecular dynamics indicated that GA formed hydrogen bonds with G496, N501, and Y505 of S-RBD, and MG with G496 and Y505, inhibiting S-RBD binding to angiotensin-converting enzyme 2 (ACE2). SPR-based competition analysis verified that both compounds blocked S-RBD and ACE2 binding, and SPR demonstrated that GA and MG bound to ACE2 (KD = 5.10 and 4.05 μM, respectively), suggesting that they blocked the receptor and neutralized SARS-CoV-2. Infection with SARS-CoV-2 pseudovirus showed that GA and MG suppressed viral entry into 293T-ACE2 cells. These S-RBD inhibitors have potential for drug design, while the findings provide a reference on HCZP composition and its use for treating COVID-19.
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Affiliation(s)
- Wei Yu
- School of Pharmacy/Key Laboratory of Xinjiang Phytomedicine Resource and Utilization/School of Medical, Shihezi University, Shihezi, China
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China
| | - Sheng-Zhe Yi
- School of Pharmacy/Key Laboratory of Xinjiang Phytomedicine Resource and Utilization/School of Medical, Shihezi University, Shihezi, China
| | - Cheng-Yu Jiang
- School of Pharmacy/Key Laboratory of Xinjiang Phytomedicine Resource and Utilization/School of Medical, Shihezi University, Shihezi, China
| | - Jia-Wei Guan
- School of Pharmacy/Key Laboratory of Xinjiang Phytomedicine Resource and Utilization/School of Medical, Shihezi University, Shihezi, China
| | - Rui Xue
- School of Pharmacy/Key Laboratory of Xinjiang Phytomedicine Resource and Utilization/School of Medical, Shihezi University, Shihezi, China
| | - Xu-Xuan Zhang
- School of Pharmacy/Key Laboratory of Xinjiang Phytomedicine Resource and Utilization/School of Medical, Shihezi University, Shihezi, China
| | - Tao Zeng
- Corps Center for Food and Drug Evaluation and Verification, Xinjiang Production and Construction Corps Market Supervision Administration, Urumqi, China
| | - Hui Tang
- School of Pharmacy/Key Laboratory of Xinjiang Phytomedicine Resource and Utilization/School of Medical, Shihezi University, Shihezi, China
| | - Wen Chen
- School of Pharmacy/Key Laboratory of Xinjiang Phytomedicine Resource and Utilization/School of Medical, Shihezi University, Shihezi, China
| | - Bo Han
- School of Pharmacy/Key Laboratory of Xinjiang Phytomedicine Resource and Utilization/School of Medical, Shihezi University, Shihezi, China
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Lee J, Case JB, Park YJ, Ravichandran R, Asarnow D, Tortorici MA, Brown JT, Sanapala S, Carter L, Baker D, Diamond MS, Veesler D. A pan-variant miniprotein inhibitor protects against SARS-CoV-2 variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.08.606885. [PMID: 39149384 PMCID: PMC11326246 DOI: 10.1101/2024.08.08.606885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
The continued evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has compromised neutralizing antibody responses elicited by prior infection or vaccination and abolished the utility of most monoclonal antibody therapeutics. We previously described a computationally-designed, homotrimeric miniprotein inhibitor, designated TRI2-2, that protects mice against pre-Omicron SARS-CoV-2 variants. Here, we show that TRI2-2 exhibits pan neutralization of variants that evolved during the 4.5 years since the emergence of SARS-CoV-2 and protects mice against BQ.1.1, XBB.1.5 and BA.2.86 challenge when administered post-exposure by an intranasal route. The resistance of TRI2-2 to viral escape and its direct delivery to the upper airways rationalize a path toward clinical advancement.
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Affiliation(s)
- Jimin Lee
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - James Brett Case
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Rashmi Ravichandran
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Daniel Asarnow
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - Jack T. Brown
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Shilpa Sanapala
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Michael S. Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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46
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McCallum M, Park YJ, Stewart C, Sprouse KR, Addetia A, Brown J, Tortorici MA, Gibson C, Wong E, Ieven M, Telenti A, Veesler D. Human coronavirus HKU1 recognition of the TMPRSS2 host receptor. Cell 2024; 187:4231-4245.e13. [PMID: 38964328 DOI: 10.1016/j.cell.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 04/26/2024] [Accepted: 06/05/2024] [Indexed: 07/06/2024]
Abstract
The human coronavirus HKU1 spike (S) glycoprotein engages host cell surface sialoglycans and transmembrane protease serine 2 (TMPRSS2) to initiate infection. The molecular basis of HKU1 binding to TMPRSS2 and determinants of host receptor tropism remain elusive. We designed an active human TMPRSS2 construct enabling high-yield recombinant production in human cells of this key therapeutic target. We determined a cryo-electron microscopy structure of the HKU1 RBD bound to human TMPRSS2, providing a blueprint of the interactions supporting viral entry and explaining the specificity for TMPRSS2 among orthologous proteases. We identified TMPRSS2 orthologs from five mammalian orders promoting HKU1 S-mediated entry into cells along with key residues governing host receptor usage. Our data show that the TMPRSS2 binding motif is a site of vulnerability to neutralizing antibodies and suggest that HKU1 uses S conformational masking and glycan shielding to balance immune evasion and receptor engagement.
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Affiliation(s)
- Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Amin Addetia
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Jack Brown
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Cecily Gibson
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Emily Wong
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Margareta Ieven
- Laboratory of Clinical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | | | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA.
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Acúrcio RC, Kleiner R, Vaskovich-Koubi D, Carreira B, Liubomirski Y, Palma C, Yeheskel A, Yeini E, Viana AS, Ferreira V, Araújo C, Mor M, Freund NT, Bacharach E, Gonçalves J, Toister-Achituv M, Fabregue M, Matthieu S, Guerry C, Zarubica A, Aviel-Ronen S, Florindo HF, Satchi-Fainaro R. Intranasal Multiepitope PD-L1-siRNA-Based Nanovaccine: The Next-Gen COVID-19 Immunotherapy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2404159. [PMID: 39116324 DOI: 10.1002/advs.202404159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 07/28/2024] [Indexed: 08/10/2024]
Abstract
The first approved vaccines for human use against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are nanotechnology-based. Although they are modular, rapidly produced, and can reduce disease severity, the currently available vaccines are restricted in preventing infection, stressing the global demand for novel preventive vaccine technologies. Bearing this in mind, we set out to develop a flexible nanovaccine platform for nasal administration to induce mucosal immunity, which is fundamental for optimal protection against respiratory virus infection. The next-generation multiepitope nanovaccines co-deliver immunogenic peptides, selected by an immunoinformatic workflow, along with adjuvants and regulators of the PD-L1 expression. As a case study, we focused on SARS-CoV-2 peptides as relevant antigens to validate the approach. This platform can evoke both local and systemic cellular- and humoral-specific responses against SARS-CoV-2. This led to the secretion of immunoglobulin A (IgA), capable of neutralizing SARS-CoV-2, including variants of concern, following a heterologous immunization strategy. Considering the limitations of the required cold chain distribution for current nanotechnology-based vaccines, it is shown that the lyophilized nanovaccine is stable for long-term at room temperature and retains its in vivo efficacy upon reconstitution. This makes it particularly relevant for developing countries and offers a modular system adaptable to future viral threats.
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Affiliation(s)
- Rita C Acúrcio
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, 1649-003, Portugal
| | - Ron Kleiner
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Daniella Vaskovich-Koubi
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Bárbara Carreira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, 1649-003, Portugal
| | - Yulia Liubomirski
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Carolina Palma
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, 1649-003, Portugal
| | - Adva Yeheskel
- The Blavatnik Center for Drug Discovery, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Eilam Yeini
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Ana S Viana
- Center of Chemistry and Biochemistry, Faculty of Sciences, University of Lisbon, Lisbon, 1749-016, Portugal
| | - Vera Ferreira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, 1649-003, Portugal
| | - Carlos Araújo
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, 1649-003, Portugal
| | - Michael Mor
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Natalia T Freund
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Eran Bacharach
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - João Gonçalves
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, 1649-003, Portugal
| | - Mira Toister-Achituv
- Inter-Lab, a subsidiary of Merck KGaA, South Industrial Area, Yavne, 8122004, Israel
| | - Manon Fabregue
- Centre d'Immunophénomique, Aix Marseille Université, Inserm, CNRS, PHENOMIN, Marseille, 13284, France
| | - Solene Matthieu
- Centre d'Immunophénomique, Aix Marseille Université, Inserm, CNRS, PHENOMIN, Marseille, 13284, France
| | - Capucine Guerry
- Centre d'Immunophénomique, Aix Marseille Université, Inserm, CNRS, PHENOMIN, Marseille, 13284, France
| | - Ana Zarubica
- Centre d'Immunophénomique, Aix Marseille Université, Inserm, CNRS, PHENOMIN, Marseille, 13284, France
| | - Sarit Aviel-Ronen
- Adelson School of Medicine, Ariel University, Ariel, 4070000, Israel
| | - Helena F Florindo
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, 1649-003, Portugal
| | - Ronit Satchi-Fainaro
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel
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48
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Michaels TM, Essop MF, Joseph DE. Potential Effects of Hyperglycemia on SARS-CoV-2 Entry Mechanisms in Pancreatic Beta Cells. Viruses 2024; 16:1243. [PMID: 39205219 PMCID: PMC11358987 DOI: 10.3390/v16081243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 07/29/2024] [Accepted: 07/30/2024] [Indexed: 09/04/2024] Open
Abstract
The COVID-19 pandemic has revealed a bidirectional relationship between SARS-CoV-2 infection and diabetes mellitus. Existing evidence strongly suggests hyperglycemia as an independent risk factor for severe COVID-19, resulting in increased morbidity and mortality. Conversely, recent studies have reported new-onset diabetes following SARS-CoV-2 infection, hinting at a potential direct viral attack on pancreatic beta cells. In this review, we explore how hyperglycemia, a hallmark of diabetes, might influence SARS-CoV-2 entry and accessory proteins in pancreatic β-cells. We examine how the virus may enter and manipulate such cells, focusing on the role of the spike protein and its interaction with host receptors. Additionally, we analyze potential effects on endosomal processing and accessory proteins involved in viral infection. Our analysis suggests a complex interplay between hyperglycemia and SARS-CoV-2 in pancreatic β-cells. Understanding these mechanisms may help unlock urgent therapeutic strategies to mitigate the detrimental effects of COVID-19 in diabetic patients and unveil if the virus itself can trigger diabetes onset.
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Affiliation(s)
- Tara M. Michaels
- Centre for Cardio-Metabolic Research in Africa, Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch 7600, South Africa;
| | - M. Faadiel Essop
- Centre for Cardio-Metabolic Research in Africa, Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa;
| | - Danzil E. Joseph
- Centre for Cardio-Metabolic Research in Africa, Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch 7600, South Africa;
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49
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Parihar A, Vishwakarma P, Khan R. Miniaturized MXene-based electrochemical biosensors for virus detection. Bioelectrochemistry 2024; 158:108700. [PMID: 38582009 DOI: 10.1016/j.bioelechem.2024.108700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 03/29/2024] [Accepted: 03/31/2024] [Indexed: 04/08/2024]
Abstract
The timely control of infectious diseases can prevent the spread of infections and mitigate the significant socio-economic damage witnessed during recent pandemics. Diagnostic methods play a significant role in detecting highly contagious agents, such as viruses, to prevent further transmission. The emergence of advanced point-of-care techniques offers several advantages over conventional approaches for detecting infectious agents. These techniques are highly sensitive, rapid, can be miniaturized, and are cost-effective. Recently, MXene-based 2D nanocomposites have proven beneficial for fabricating electrochemical biosensors due to their suitable electrical, optical, and mechanical properties. This article covers electrochemical biosensors based on MXene nanocomposite for the detection of viruses, along with the associated challenges and future possibilities. Additionally, we highlight various conventional techniques for the detection of infectious agents, discussing their pros and cons. We delve into the challenges faced during the fabrication of MXene-based biosensors and explore future endeavors. It is anticipated that the information presented in this work will pave the way for the development of Point-of-Care (POC) devices capable of sensitive and selective virus detection, enhancing preparedness for ongoing and future pandemics.
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Affiliation(s)
- Arpana Parihar
- Industrial Waste Utilization, Nano and Biomaterials, CSIR-Advanced Materials and Processes Research Institute (AMPRI), Hoshangabad Road, Bhopal- 462026, MP, India
| | - Preeti Vishwakarma
- Department of Microbiology, Barkatullah University, Hoshangabad Road, Bhopal- 462026, MP, India
| | - Raju Khan
- Industrial Waste Utilization, Nano and Biomaterials, CSIR-Advanced Materials and Processes Research Institute (AMPRI), Hoshangabad Road, Bhopal- 462026, MP, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India.
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50
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Guenthoer J, Garrett ME, Lilly M, Depierreux DM, Ruiz F, Chi M, Stoddard CI, Chohan V, Yaffe ZA, Sung K, Ralph D, Chu HY, Matsen FA, Overbaugh J. The S2 subunit of spike encodes diverse targets for functional antibody responses to SARS-CoV-2. PLoS Pathog 2024; 20:e1012383. [PMID: 39093891 PMCID: PMC11324185 DOI: 10.1371/journal.ppat.1012383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 08/14/2024] [Accepted: 07/01/2024] [Indexed: 08/04/2024] Open
Abstract
The SARS-CoV-2 virus responsible for the COVID-19 global pandemic has exhibited a striking capacity for viral evolution that drives continued evasion from vaccine and infection-induced immune responses. Mutations in the receptor binding domain of the S1 subunit of the spike glycoprotein have led to considerable escape from antibody responses, reducing the efficacy of vaccines and monoclonal antibody (mAb) therapies. Therefore, there is a need to interrogate more constrained regions of spike, such as the S2 subdomain. Here, we present a collection of S2 mAbs from two SARS-CoV-2 convalescent individuals that target multiple regions in S2, including regions outside of those commonly reported. One of the S2 mAbs, C20.119, which bound to a highly conserved epitope in the fusion peptide, was able to broadly neutralize across SARS-CoV-2 variants, SARS-CoV-1, and closely related zoonotic sarbecoviruses. The majority of the mAbs were non-neutralizing; however, many of them could mediate antibody-dependent cellular cytotoxicity (ADCC) at levels similar to the S1-targeting mAb S309 that was previously authorized for treatment of SARS-CoV-2 infections. Several of the mAbs with ADCC function also bound to spike trimers from other human coronaviruses (HCoVs), such as MERS-CoV and HCoV-HKU1. Our findings suggest S2 mAbs can target diverse epitopes in S2, including functional mAbs with HCoV and sarbecovirus breadth that likely target functionally constrained regions of spike. These mAbs could be developed for potential future pandemics, while also providing insight into ideal epitopes for eliciting a broad HCoV response.
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Affiliation(s)
- Jamie Guenthoer
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Meghan E. Garrett
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Michelle Lilly
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Delphine M. Depierreux
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Felicitas Ruiz
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Margaret Chi
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Caitlin I. Stoddard
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Vrasha Chohan
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Zak A. Yaffe
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Kevin Sung
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Duncan Ralph
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Helen Y. Chu
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Frederick A. Matsen
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Seattle, Washington, United States of America
| | - Julie Overbaugh
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
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