151
|
Giron CC, Laaksonen A, Barroso da Silva FL. Differences between Omicron SARS-CoV-2 RBD and other variants in their ability to interact with cell receptors and monoclonal antibodies. J Biomol Struct Dyn 2023; 41:5707-5727. [PMID: 35815535 DOI: 10.1080/07391102.2022.2095305] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/23/2022] [Indexed: 12/23/2022]
Abstract
SARS-CoV-2 remains a health threat with the continuous emergence of new variants. This work aims to expand the knowledge about the SARS-CoV-2 receptor-binding domain (RBD) interactions with cell receptors and monoclonal antibodies (mAbs). By using constant-pH Monte Carlo simulations, the free energy of interactions between the RBD from different variants and several partners (Angiotensin-Converting Enzyme-2 (ACE2) polymorphisms and various mAbs) were predicted. Computed RBD-ACE2-binding affinities were higher for two ACE2 polymorphisms (rs142984500 and rs4646116) typically found in Europeans which indicates a genetic susceptibility. This is amplified for Omicron (BA.1) and its sublineages BA.2 and BA.3. The antibody landscape was computationally investigated with the largest set of mAbs so far in the literature. From the 32 studied binders, groups of mAbs were identified from weak to strong binding affinities (e.g. S2K146). These mAbs with strong binding capacity and especially their combination are amenable to experimentation and clinical trials because of their high predicted binding affinities and possible neutralization potential for current known virus mutations and a universal coronavirus.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Carolina Corrêa Giron
- Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
- Universidade Federal do Triângulo Mineiro, Hospital de Clínicas, Uberaba, MG, Brazil
| | - Aatto Laaksonen
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
- State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, Nanjing, PR China
- Centre of Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry, Iasi, Romania
- Department of Engineering Sciences and Mathematics, Division of Energy Science, Luleå University of Technology, Luleå, Sweden
- Department of Chemical and Geological Sciences, University of Cagliari, Monserrato, Italy
| | - Fernando Luís Barroso da Silva
- Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| |
Collapse
|
152
|
D'Arminio N, Giordano D, Scafuri B, Facchiano A, Marabotti A. Standardizing macromolecular structure files: further efforts are needed. Trends Biochem Sci 2023; 48:590-596. [PMID: 37031054 DOI: 10.1016/j.tibs.2023.03.002] [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: 11/16/2022] [Revised: 02/25/2023] [Accepted: 03/14/2023] [Indexed: 04/10/2023]
Abstract
Investigating large datasets of biological information by automatic procedures may offer chances of progress in knowledge. Recently, tremendous improvements in structural biology have allowed the number of structures in the Protein Data Bank (PDB) archive to increase rapidly, in particular those for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-associated proteins. However, their automatic analysis can be hampered by the nonuniform descriptors used by authors in some records of the PDB and PDBx/mmCIF files. In this opinion article we highlight the difficulties encountered in automating the analysis of hundreds of structures, suggesting that further standardization of the description of these molecular entities and of their attributes, generalized to the macromolecular structures contained in the PDB, might generate files more suitable for automatized analyses of a large number of structures.
Collapse
Affiliation(s)
- Nancy D'Arminio
- Department of Chemistry and Biology 'A. Zambelli', University of Salerno, Fisciano, (SA), Italy
| | - Deborah Giordano
- National Research Council, Institute of Food Science, Avellino, Italy
| | - Bernardina Scafuri
- Department of Chemistry and Biology 'A. Zambelli', University of Salerno, Fisciano, (SA), Italy
| | - Angelo Facchiano
- National Research Council, Institute of Food Science, Avellino, Italy.
| | - Anna Marabotti
- Department of Chemistry and Biology 'A. Zambelli', University of Salerno, Fisciano, (SA), Italy.
| |
Collapse
|
153
|
Ma C, Liu C, Xiong Q, Gu M, Shi L, Wang C, Si J, Tong F, Liu P, Huang M, Yan H. Broad host tropism of ACE2-using MERS-related coronaviruses and determinants restricting viral recognition. Cell Discov 2023; 9:57. [PMID: 37321999 DOI: 10.1038/s41421-023-00566-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 05/14/2023] [Indexed: 06/17/2023] Open
Abstract
Recently, two Middle East respiratory syndrome coronavirus (MERS-CoV) closely related to bat merbecoviruses, NeoCoV and PDF-2180, were discovered to use angiotensin-converting enzyme 2 (ACE2) for entry. The two viruses cannot use human ACE2 efficiently, and their host range and cross-species transmissibility across a wide range of mammalian species remain unclear. Herein, we characterized the species-specific receptor preference of these viruses by testing ACE2 orthologues from 49 bats and 53 non-bat mammals through receptor-binding domain (RBD)-binding and pseudovirus entry assays. Results based on bat ACE2 orthologues revealed that the two viruses were unable to use most, but not all, ACE2 from Yinpterochiropteran bats (Yin-bats), which is distinct from NL63 and SARS-CoV-2. Besides, both viruses exhibited broad receptor recognition spectra across non-bat mammals. Genetic and structural analyses of bat ACE2 orthologues highlighted four crucial host range determinants, all confirmed by subsequent functional assays in human and bat cells. Notably, residue 305, participating in a critical viral receptor interaction, plays a crucial role in host tropism determination, particularly in non-bat mammals. Furthermore, NeoCoV and PDF-2180 mutants with enhanced human ACE2 recognition expanded the potential host range, especially by enhancing their interaction with an evolutionarily conserved hydrophobic pocket. Our results elucidate the molecular basis for the species-specific ACE2 usage of MERS-related viruses and shed light on their zoonotic risks.
Collapse
Affiliation(s)
- Chengbao Ma
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Chen Liu
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Qing Xiong
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Mengxue Gu
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Lulu Shi
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Chunli Wang
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Junyu Si
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Fei Tong
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Peng Liu
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Meiling Huang
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Huan Yan
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China.
| |
Collapse
|
154
|
Shehzadi K, Saba A, Yu M, Liang J. Structure-Based Drug Design of RdRp Inhibitors against SARS-CoV-2. Top Curr Chem (Cham) 2023; 381:22. [PMID: 37318607 DOI: 10.1007/s41061-023-00432-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a worldwide pandemic since 2019, spreading rapidly and posing a significant threat to human health and life. With over 6 billion confirmed cases of the virus, the need for effective therapeutic drugs has become more urgent than ever before. RNA-dependent RNA polymerase (RdRp) is crucial in viral replication and transcription, catalysing viral RNA synthesis and serving as a promising therapeutic target for developing antiviral drugs. In this article, we explore the inhibition of RdRp as a potential treatment for viral diseases, analysing the structural information of RdRp in virus proliferation and summarizing the reported inhibitors' pharmacophore features and structure-activity relationship profiles. We hope that the information provided by this review will aid in structure-based drug design and aid in the global fight against SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Kiran Shehzadi
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China
| | - Afsheen Saba
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China
| | - Mingjia Yu
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China.
| | - Jianhua Liang
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China.
- Yangtze Delta Region Academy of Beijing Institute of Technology, Jiaxing, 314019, China.
| |
Collapse
|
155
|
Zaher K, Basingab F, Alrahimi J, Basahel K, Aldahlawi A. Gender Differences in Response to COVID-19 Infection and Vaccination. Biomedicines 2023; 11:1677. [PMID: 37371774 DOI: 10.3390/biomedicines11061677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Since COVID-19 first appeared, a number of follow-up events have taken place. In an effort to find a solution to this catastrophe, a great deal of study and analysis has been conducted. Because of the high morbidity and exceptionally large losses, scientists are being pushed to conduct more research and find vaccination and treatments. The virus has a wide range of effects, one of which is how it affects sexual activity in both men and women. The impact of the cardiovascular system and susceptibility to embolism, lung stress, and infection heightens the probability of hospitalization in the intensive care unit for pregnant women who have contracted COVID-19. There is no evidence of infection being passed from mother to child. In the current review, the role of COVID-19 infection and vaccination on male and female sexual activity, hormones, and the menstrual cycle for females, as well as on male sex hormones and sexual activity during infection and after vaccination, are being investigated. There are no reports of the virus being isolated from the semen of an infected patient or recently recovered patients. A recent investigation on the influence of the virus on gender susceptibility to sexual organs and function has been uncovered throughout this study.
Collapse
Affiliation(s)
- Kawther Zaher
- Immunology Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Fatemah Basingab
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah 21859, Saudi Arabia
- Immunology Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Jehan Alrahimi
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah 21859, Saudi Arabia
- Immunology Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Kholood Basahel
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah 21859, Saudi Arabia
- Immunology Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Alia Aldahlawi
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah 21859, Saudi Arabia
- Immunology Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| |
Collapse
|
156
|
Chen P, Wu M, He Y, Jiang B, He ML. Metabolic alterations upon SARS-CoV-2 infection and potential therapeutic targets against coronavirus infection. Signal Transduct Target Ther 2023; 8:237. [PMID: 37286535 DOI: 10.1038/s41392-023-01510-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 04/18/2023] [Accepted: 05/19/2023] [Indexed: 06/09/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) caused by coronavirus SARS-CoV-2 infection has become a global pandemic due to the high viral transmissibility and pathogenesis, bringing enormous burden to our society. Most patients infected by SARS-CoV-2 are asymptomatic or have mild symptoms. Although only a small proportion of patients progressed to severe COVID-19 with symptoms including acute respiratory distress syndrome (ARDS), disseminated coagulopathy, and cardiovascular disorders, severe COVID-19 is accompanied by high mortality rates with near 7 million deaths. Nowadays, effective therapeutic patterns for severe COVID-19 are still lacking. It has been extensively reported that host metabolism plays essential roles in various physiological processes during virus infection. Many viruses manipulate host metabolism to avoid immunity, facilitate their own replication, or to initiate pathological response. Targeting the interaction between SARS-CoV-2 and host metabolism holds promise for developing therapeutic strategies. In this review, we summarize and discuss recent studies dedicated to uncovering the role of host metabolism during the life cycle of SARS-CoV-2 in aspects of entry, replication, assembly, and pathogenesis with an emphasis on glucose metabolism and lipid metabolism. Microbiota and long COVID-19 are also discussed. Ultimately, we recapitulate metabolism-modulating drugs repurposed for COVID-19 including statins, ASM inhibitors, NSAIDs, Montelukast, omega-3 fatty acids, 2-DG, and metformin.
Collapse
Affiliation(s)
- Peiran Chen
- Department of Biomedical Sciences, City University of Hong Kong, HKSAR, Hong Kong, China
| | - Mandi Wu
- Department of Biomedical Sciences, City University of Hong Kong, HKSAR, Hong Kong, China
| | - Yaqing He
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, Guangdong, China
| | - Binghua Jiang
- Cell Signaling and Proteomic Center, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Ming-Liang He
- Department of Biomedical Sciences, City University of Hong Kong, HKSAR, Hong Kong, China.
| |
Collapse
|
157
|
Li F, Fang T, Guo F, Zhao Z, Zhang J. Comprehensive Understanding of the Kinetic Behaviors of Main Protease from SARS-CoV-2 and SARS-CoV: New Data and Comparison to Published Parameters. Molecules 2023; 28:4605. [PMID: 37375160 DOI: 10.3390/molecules28124605] [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: 04/09/2023] [Revised: 05/15/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
The main protease (Mpro) is a promising drug target for inhibiting the coronavirus due to its conserved properties and lack of homologous genes in humans. However, previous studies on Mpro's kinetic parameters have been confusing, hindering the selection of accurate inhibitors. Therefore, obtaining a clear view of Mpro's kinetic parameters is necessary. In our study, we investigated the kinetic behaviors of Mpro from SARS-CoV-2 and SARS-CoV using both FRET-based cleavage assay and the LC-MS method, respectively. Our findings indicate that the FRET-based cleavage assay could be used for preliminary screening of Mpro inhibitors, while the LC-MS method should be applied to select the effective inhibitors with higher reliability. Furthermore, we constructed the active site mutants (H41A and C145A) and measured the kinetic parameters to gain a deeper understanding of the atomic-level enzyme efficiency reduction compared to the wild type. Overall, our study provides valuable insights for inhibitor screening and design by offering a comprehensive understanding of Mpro's kinetic behaviors.
Collapse
Affiliation(s)
- Fangya Li
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Tingting Fang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Feng Guo
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Zipeng Zhao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Jianyu Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| |
Collapse
|
158
|
Moustafa RI, Faraag AHI, El-Shenawy R, Agwa MM, Elsayed H. Harnessing immunoinformatics for developing a multiple-epitope peptide-based vaccination approach against SARS-CoV-2 spike protein. Saudi J Biol Sci 2023; 30:103661. [PMID: 37163156 PMCID: PMC10141799 DOI: 10.1016/j.sjbs.2023.103661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/30/2023] [Accepted: 04/21/2023] [Indexed: 05/11/2023] Open
Abstract
COVID-19 has spread to over 200 countries with variable severity and mortality rates. Computational analysis is a valuable tool for developing B-cell and T-cell epitope-based vaccines. In this study, by harnessing immunoinformatics tools, we designed a multiple-epitope vaccine to protect against COVID-19. The candidate epitopes were designed from highly conserved regions of the SARS-CoV-2 spike (S) glycoprotein. The consensus amino acids sequence of ten SARS-CoV-2 variants including Gamma, Beta, Epsilon, Delta, Alpha, Kappa, Iota, Lambda, Mu, and Omicron was involved. Applying the multiple sequence alignment plugin and the antigenic prediction tools of Geneious prime 2021, ten predicted variants were identified and consensus S-protein sequences were used to predict the antigenic part. According to ElliPro analysis of S-protein B-cell prediction, we explored 22 continuous linear epitopes with high scores ranging from 0.879 to 0.522. First, we reported five promising epitopes: BE1 1115-1192, BE2 481-563, BE3 287-313, BE4 62-75, and BE5 112-131 with antigenicity scores of 0.879, 0.86, 0.813, 0.779, and 0.765, respectively, while only nine discontinuous epitopes scored between 0.971 and 0.511. Next, we identified 194 Major Histocompatibility Complex (MHC) - I and 156 MHC - II epitopes with antigenic characteristics. These spike-specific peptide-epitopes with characteristically high immunogenic and antigenic scores have the potential as a SARS-CoV-2 multiple-epitope peptide-based vaccination strategy. Nevertheless, further experimental investigations are needed to test for the vaccine efficacy and efficiency.
Collapse
Affiliation(s)
- Rehab I Moustafa
- Department of Microbial Biotechnology, Biotechnology Research Institute, National Research Centre, Egypt
| | - Ahmed H I Faraag
- Botany and Microbiology Department, Faculty of Science, Helwan University, Egypt
- School of Biotechnology, Badr University in Cairo, Egypt
| | | | - Mona M Agwa
- Department of Chemistry of Natural and Microbial Products, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Egypt
| | - Hassan Elsayed
- Department of Microbial Biotechnology, Biotechnology Research Institute, National Research Centre, Egypt
| |
Collapse
|
159
|
Jaisinghani P, Kumar R. Obesity and Viral Infections. Gastroenterol Clin North Am 2023; 52:393-402. [PMID: 37197881 DOI: 10.1016/j.gtc.2023.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The 2019 novel coronavirus disease (COVID-19) triggered a rapidly expanding global pandemic. The presence of obesity in patients with COVID-19 has been established as a risk factor for disease severity, hospital admission, and mortality. Thus, it is imperative those living with obesity be vaccinated against COVID-19. Although there is a timeframe COVID-19 vaccines are efficacious in those living with obesity, more studies need to be conducted to ensure that those long-lasting protection is maintained, as obesity has implications on the immune system.
Collapse
Affiliation(s)
- Priya Jaisinghani
- Division of Endocrinology, Diabetes and Metabolism, New York University Grossman School of Medicine, New York, NY, USA.
| | - Rekha Kumar
- Division of Endocrinology, New York-Presbyterian Hospital and Weill Cornell Medical Center, New York, NY, USA
| |
Collapse
|
160
|
Wang Y, Li P, Lavrijsen M, Rottier RJ, den Hoed CM, Bruno MJ, Kamar N, Peppelenbosch MP, de Vries AC, Pan Q. Immunosuppressants exert differential effects on pan-coronavirus infection and distinct combinatory antiviral activity with molnupiravir and nirmatrelvir. United European Gastroenterol J 2023; 11:431-447. [PMID: 37226653 PMCID: PMC10256998 DOI: 10.1002/ueg2.12417] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/18/2023] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND Immunocompromised populations, such as organ transplant recipients and patients with inflammatory bowel disease (IBD) receiving immunosuppressive/immunomodulatory medications, may be more susceptible to coronavirus infections. However, little is known about how immunosuppressants affect coronavirus replication and their combinational effects with antiviral drugs. OBJECTIVE This study aims to profile the effects of immunosuppressants and the combination of immunosuppressants with oral antiviral drugs molnupiravir and nirmatrelvir on pan-coronavirus infection in cell and human airway organoids (hAOs) culture models. METHODS Different coronaviruses (including wild type, delta and omicron variants of SARS-CoV-2, and NL63, 229E and OC43 seasonal coronaviruses) were used in lung cell lines and hAOs models. The effects of immunosuppressants were tested. RESULTS Dexamethasone and 5-aminosalicylic acid moderately stimulated the replication of different coronaviruses. Mycophenolic acid (MPA), 6-thioguanine (6-TG), tofacitinib and filgotinib treatment dose-dependently inhibited viral replication of all tested coronaviruses in both cell lines and hAOs. The half maximum effective concentration (EC50) of tofacitinib against SARS-CoV-2 was 0.62 μM and the half maximum cytotoxic concentration (CC50) was above 30 μM, which resulted in a selective index (SI) of about 50. The anti-coronavirus effect of the JAK inhibitors tofacitinib and filgotinib is dependent on the inhibition of STAT3 phosphorylation. Combinations of MPA, 6-TG, tofacitinib, and filgotinib with the oral antiviral drugs molnupiravir or nirmatrelvir exerted an additive or synergistic antiviral activity. CONCLUSIONS Different immunosuppressants have distinct effects on coronavirus replication, with 6-TG, MPA, tofacitinib and filgotinib possessing pan-coronavirus antiviral activity. The combinations of MPA, 6-TG, tofacitinib and filgotinib with antiviral drugs exerted an additive or synergistic antiviral activity. Thus, these findings provide an important reference for optimal management of immunocompromised patients infected with coronaviruses.
Collapse
Affiliation(s)
- Yining Wang
- Department of Gastroenterology and HepatologyErasmus MC‐University Medical CenterRotterdamThe Netherlands
| | - Pengfei Li
- Department of Gastroenterology and HepatologyErasmus MC‐University Medical CenterRotterdamThe Netherlands
| | - Marla Lavrijsen
- Department of Gastroenterology and HepatologyErasmus MC‐University Medical CenterRotterdamThe Netherlands
| | - Robbert J. Rottier
- Department of Pediatric SurgeryErasmus MC‐Sophia Children's HospitalRotterdamThe Netherlands
- Department of Cell BiologyErasmus MC‐University Medical CenterRotterdamThe Netherlands
| | - Caroline M. den Hoed
- Department of Gastroenterology and HepatologyErasmus MC‐University Medical CenterRotterdamThe Netherlands
- Erasmus MC Transplant InstituteErasmus MC‐University Medical CenterRotterdamThe Netherlands
| | - Marco J. Bruno
- Department of Gastroenterology and HepatologyErasmus MC‐University Medical CenterRotterdamThe Netherlands
| | - Nassim Kamar
- Department of NephrologyDialysis and Organ TransplantationCHU RangueilINSERM UMR 1291Toulouse Institute for Infectious and Inflammatory Disease (Infinity)University Paul SabatierToulouseFrance
| | - Maikel P. Peppelenbosch
- Department of Gastroenterology and HepatologyErasmus MC‐University Medical CenterRotterdamThe Netherlands
| | - Annemarie C. de Vries
- Department of Gastroenterology and HepatologyErasmus MC‐University Medical CenterRotterdamThe Netherlands
| | - Qiuwei Pan
- Department of Gastroenterology and HepatologyErasmus MC‐University Medical CenterRotterdamThe Netherlands
- Erasmus MC Transplant InstituteErasmus MC‐University Medical CenterRotterdamThe Netherlands
| |
Collapse
|
161
|
Raman K, Rajagopal K, Ramesh B, Nallasivan PK, Raja MKMM, Jupudi S, Byran G, Khan SL, Bin Emran T. Drug target of natural products and COVID-19: how far has science progressed? Ann Med Surg (Lond) 2023; 85:2731-2742. [PMID: 37363478 PMCID: PMC10289732 DOI: 10.1097/ms9.0000000000000703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 04/10/2023] [Indexed: 06/28/2023] Open
Abstract
The new coronavirus [severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)] that caused a viral disease with a high risk of mortality (coronavirus disease 2019) was found toward the end of 2019. This was a significant acute respiratory syndrome. In a brief period, this virus spread throughout the entire planet, causing tremendous loss of life and economic damage. The process of developing new treatments takes time, and there are presently no recognized specific treatments to treat this infection. The most promising participants, who subsequently developed into prospective leads, were dropped from the clinical research in their latter phases. Medication that has previously acquired permission may only be repurposed for use for various medical reasons following a thorough investigation for safety and effectiveness. Because there are now no effective treatments available, natural products are being used haphazardly as antiviral medications and immunity boosters. The fundamental statement that most natural compounds have powerful antiviral action does not apply to SARS-CoV-2. Middle East respiratory syndrome coronavirus and severe acute respiratory syndrome coronavirus infections are inhibited by natural treatments. According to an in silico study, the virus' nonstructural proteins, including PLpro, Mpro, and RdRp, as well as structural proteins like the spike (S) protein, have been shown to have a strong affinity for several natural products and to be inhibited by them. The virus also suggests that it is a valid candidate for therapeutic research since it utilizes the intracellular angiotensin-converting enzyme 2 receptor of the host cell. In this study, interesting targets for SARS-CoV-2 medication development are explored, as well as the antiviral properties of some well-known natural compounds.
Collapse
Affiliation(s)
- Kannan Raman
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy (JSS Academy of Higher Education & Research), Ooty, The Nilgiris, Tamil Nadu India
| | - Kalirajan Rajagopal
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy (JSS Academy of Higher Education & Research), Ooty, The Nilgiris, Tamil Nadu India
| | - B. Ramesh
- Kakatiya Government College, Hanumakonda, Telangana India
| | - P. Kumar Nallasivan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Karpagam Academy of Higher Education, Coimbatore India
| | - M. K. Mohan M. Raja
- Parul Institute of Pharmacy and Research, Parul University, Vadodara, Gujarat India
| | - Srikanth Jupudi
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy (JSS Academy of Higher Education & Research), Ooty, The Nilgiris, Tamil Nadu India
| | - Gowramma Byran
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy (JSS Academy of Higher Education & Research), Ooty, The Nilgiris, Tamil Nadu India
| | - Sharuk L. Khan
- Department of Pharmaceutical Chemistry, N.B.S. Institute of Pharmacy, Ausa, Maharashtra, India
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, Bangladesh
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| |
Collapse
|
162
|
Fan S, Wang H, Wu D, Liu L. Pharmaceutical approaches for COVID-19: An update on current therapeutic opportunities. ACTA PHARMACEUTICA (ZAGREB, CROATIA) 2023; 73:157-173. [PMID: 37307372 DOI: 10.2478/acph-2023-0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/18/2022] [Indexed: 06/14/2023]
Abstract
SARS-CoV-2, a newly discovered coronavirus, has been linked to the COVID-19 pandemic and is currently an important public health issue. Despite all the work done to date around the world, there is still no viable treatment for COVID-19. This study examined the most recent evidence on the efficacy and safety of several therapeutic options available including natural substances, synthetic drugs and vaccines in the treatment of COVID-19. Various natural compounds such as sarsapogenin, lycorine, biscoclaurine, vitamin B12, glycyrrhizic acid, riboflavin, resveratrol and kaempferol, various vaccines and drugs such as AZD1222, mRNA-1273, BNT162b2, Sputnik V, and remdesivir, lopinavir, favipiravir, darunavir, oseltamivir, and umifenovir, resp., have been discussed comprehensively. We attempted to provide exhaustive information regarding the various prospective therapeutic approaches available in order to assist researchers and physicians in treating COVID-19 patients.
Collapse
Affiliation(s)
- Sijia Fan
- 1Department of Intensive Care Unit, South China Hospital, Health Science Center Shenzhen University Guangdong, Shenzhen 518116, P. R. China
| | - Hongling Wang
- 2Department of Cardiothoracic Surgery 940th Hospital of Joint Logistic Support Force of PLA, Lanzhou, Gansu, 730050, P. R. China
| | - Dean Wu
- 3Department of Respiratory Medicine, The Third People's Hospital of Gansu Province Lanzhou University, Lanzhou, Gansu 730050, P. R. China
| | - Lu Liu
- 4The First Pulmonary and Critical Care Medicine, The Fourth Affiliated Hospital of China Medical University, Shenyang Liaoning, 110032, P. R. China
| |
Collapse
|
163
|
Romani A, Sergi D, Zauli E, Voltan R, Lodi G, Vaccarezza M, Caruso L, Previati M, Zauli G. Nutrients, herbal bioactive derivatives and commensal microbiota as tools to lower the risk of SARS-CoV-2 infection. Front Nutr 2023; 10:1152254. [PMID: 37324739 PMCID: PMC10267353 DOI: 10.3389/fnut.2023.1152254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/15/2023] [Indexed: 06/17/2023] Open
Abstract
The SARS-CoV-2 outbreak has infected a vast population across the world, causing more than 664 million cases and 6.7 million deaths by January 2023. Vaccination has been effective in reducing the most critical aftermath of this infection, but some issues are still present regarding re-infection prevention, effectiveness against variants, vaccine hesitancy and worldwide accessibility. Moreover, although several old and new antiviral drugs have been tested, we still lack robust and specific treatment modalities. It appears of utmost importance, facing this continuously growing pandemic, to focus on alternative practices grounded on firm scientific bases. In this article, we aim to outline a rigorous scientific background and propose complementary nutritional tools useful toward containment, and ultimately control, of SARS-CoV-2 infection. In particular, we review the mechanisms of viral entry and discuss the role of polyunsaturated fatty acids derived from α-linolenic acid and other nutrients in preventing the interaction of SARS-CoV-2 with its entry gateways. In a similar way, we analyze in detail the role of herbal-derived pharmacological compounds and specific microbial strains or microbial-derived polypeptides in the prevention of SARS-CoV-2 entry. In addition, we highlight the role of probiotics, nutrients and herbal-derived compounds in stimulating the immunity response.
Collapse
Affiliation(s)
- Arianna Romani
- Department of Environmental and Prevention Sciences and LTTA Centre, University of Ferrara, Ferrara, Italy
| | - Domenico Sergi
- Department of Translational Medicine and LTTA Centre, University of Ferrara, Ferrara, Italy
| | - Enrico Zauli
- Department of Translational Medicine and LTTA Centre, University of Ferrara, Ferrara, Italy
| | - Rebecca Voltan
- Department of Environmental and Prevention Sciences and LTTA Centre, University of Ferrara, Ferrara, Italy
| | - Giada Lodi
- Department of Environmental and Prevention Sciences and LTTA Centre, University of Ferrara, Ferrara, Italy
| | - Mauro Vaccarezza
- Curtin Medical School & Curtin Health Innovation Research Institute (CHIRI), Faculty of Health Sciences, Curtin University, Perth, WA, Australia
| | - Lorenzo Caruso
- Department of Environmental and Prevention Sciences and LTTA Centre, University of Ferrara, Ferrara, Italy
| | - Maurizio Previati
- Department of Translational Medicine and LTTA Centre, University of Ferrara, Ferrara, Italy
| | - Giorgio Zauli
- Research Department, King Khaled Eye Specialistic Hospital, Riyadh, Saudi Arabia
| |
Collapse
|
164
|
Rahimian K, Arefian E, Mahdavi B, Mahmanzar M, Kuehu D, Deng Y. SARS2Mutant: SARS-CoV-2 amino-acid mutation atlas database. NAR Genom Bioinform 2023; 5:lqad037. [PMID: 37101659 PMCID: PMC10124966 DOI: 10.1093/nargab/lqad037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 02/27/2023] [Accepted: 04/18/2023] [Indexed: 04/28/2023] Open
Abstract
The coronavirus disease 19 (COVID-19) is a highly pathogenic viral infection of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), resulted in the global pandemic of 2020. A lack of therapeutic and preventive strategies has quickly posed significant threats to world health. A comprehensive understanding of SARS-CoV-2 evolution and natural selection, how it impacts host interaction, and phenotype symptoms is vital to develop effective strategies against the virus. The SARS2Mutant database (http://sars2mutant.com/) was developed to provide valuable insights based on millions of high-quality, high-coverage SARS-CoV-2 complete protein sequences. Users of this database have the ability to search for information on three amino acid substitution mutation strategies based on gene name, geographical zone, or comparative analysis. Each strategy is presented in five distinct formats which includes: (i) mutated sample frequencies, (ii) heat maps of mutated amino acid positions, (iii) mutation survivals, (iv) natural selections and (v) details of substituted amino acids, including their names, positions, and frequencies. GISAID is a primary database of genomics sequencies of influenza viruses updated daily. SARS2Mutant is a secondary database developed to discover mutation and conserved regions from the primary data to assist with design for targeted vaccine, primer, and drug discoveries.
Collapse
Affiliation(s)
- Karim Rahimian
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Ehsan Arefian
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Bahar Mahdavi
- Department of Computer Science, Tarbiat Modares University, Tehran, Iran
| | - Mohammadamin Mahmanzar
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Donna Lee Kuehu
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Youping Deng
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| |
Collapse
|
165
|
Hoffman T, Kolstad L, Akaberi D, Järhult JD, Rönnberg B, Lundkvist Å. Reduced Binding between Omicron B.1.1.529 and the Human ACE2 Receptor in a Surrogate Virus Neutralization Test for SARS-CoV-2. Viruses 2023; 15:1280. [PMID: 37376580 DOI: 10.3390/v15061280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
The current gold standard assay for detecting neutralizing antibodies (NAbs) against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the conventional virus neutralization test (cVNT), which requires infectious virus and a biosafety level 3 laboratory. Here, we report the development of a SARS-CoV-2 surrogate virus neutralization test (sVNT) that, with Luminex technology, detects NAbs. The assay was designed to mimic the virus-host interaction and is based on antibody blockage between the human angiotensin-converting enzyme 2 (hACE2) receptor and the spike (S) protein of the Wuhan, Delta, and Omicron (B.1.1.529) variants of SARS-CoV-2. The sVNT proved to have a 100% correlation with a SARS-CoV-2 cVNT regarding qualitative results. Binding between the hACE2 receptor and the S1 domain of the B.1.1.529 lineage of the Omicron variant was not observed in the assay but between the receptor and an S1 + S2 trimer and the receptor binding domain (RBD) in a reduced manner, suggesting less efficient receptor binding for the B.1.1.529 Omicron variant. The results indicate that the SARS-CoV-2 sVNT is a suitable tool for both the research community and the public health service, as it may serve as an efficient diagnostic alternative to the cVNT.
Collapse
Affiliation(s)
- Tove Hoffman
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center (ZSC), Uppsala University, 752 37 Uppsala, Sweden
| | - Linda Kolstad
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center (ZSC), Uppsala University, 752 37 Uppsala, Sweden
| | - Dario Akaberi
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center (ZSC), Uppsala University, 752 37 Uppsala, Sweden
| | - Josef D Järhult
- Department of Medical Sciences, Zoonosis Science Center (ZSC), Uppsala University, 751 85 Uppsala, Sweden
| | - Bengt Rönnberg
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center (ZSC), Uppsala University, 752 37 Uppsala, Sweden
| | - Åke Lundkvist
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center (ZSC), Uppsala University, 752 37 Uppsala, Sweden
| |
Collapse
|
166
|
Kaewchim K, Glab-ampai K, Mahasongkram K, Saenlom T, Thepsawat W, Chulanetra M, Choowongkomon K, Sookrung N, Chaicumpa W. Neutralizing and Enhancing Epitopes of the SARS-CoV-2 Receptor-Binding Domain (RBD) Identified by Nanobodies. Viruses 2023; 15:1252. [PMID: 37376552 PMCID: PMC10301551 DOI: 10.3390/v15061252] [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: 04/11/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
Engineered nanobodies (VHs) to the SARS-CoV-2 receptor-binding domain (RBD) were generated using phage display technology. A recombinant Wuhan RBD served as bait in phage panning to fish out nanobody-displaying phages from a VH/VHH phage display library. Sixteen phage-infected E. coli clones produced nanobodies with 81.79-98.96% framework similarity to human antibodies; thus, they may be regarded as human nanobodies. Nanobodies of E. coli clones 114 and 278 neutralized SARS-CoV-2 infectivity in a dose-dependent manner; nanobodies of clones 103 and 105 enhanced the virus's infectivity by increasing the cytopathic effect (CPE) in an infected Vero E6 monolayer. These four nanobodies also bound to recombinant Delta and Omicron RBDs and native SARS-CoV-2 spike proteins. The neutralizing VH114 epitope contains the previously reported VYAWN motif (Wuhan RBD residues 350-354). The linear epitope of neutralizing VH278 at Wuhan RBD 319RVQPTESIVRFPNITN334 is novel. In this study, for the first time, we report SARS-CoV-2 RBD-enhancing epitopes, i.e., a linear VH103 epitope at RBD residues 359NCVADVSVLYNSAPFFTFKCYG380, and the VH105 epitope, most likely conformational and formed by residues in three RBD regions that are spatially juxtaposed upon the protein folding. Data obtained in this way are useful for the rational design of subunit SARS-CoV-2 vaccines that should be devoid of enhancing epitopes. VH114 and VH278 should be tested further for clinical use against COVID-19.
Collapse
Affiliation(s)
- Kanasap Kaewchim
- Graduate Program in Immunology, Department of Immunology, Faculty of Medicine Siriraj Hospital, Bangkok 10700, Thailand;
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Bangkok 10700, Thailand; (K.G.-a.); (K.M.); (T.S.); (W.T.); (M.C.); (N.S.)
| | - Kittirat Glab-ampai
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Bangkok 10700, Thailand; (K.G.-a.); (K.M.); (T.S.); (W.T.); (M.C.); (N.S.)
| | - Kodchakorn Mahasongkram
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Bangkok 10700, Thailand; (K.G.-a.); (K.M.); (T.S.); (W.T.); (M.C.); (N.S.)
| | - Thanatsaran Saenlom
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Bangkok 10700, Thailand; (K.G.-a.); (K.M.); (T.S.); (W.T.); (M.C.); (N.S.)
| | - Watayagorn Thepsawat
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Bangkok 10700, Thailand; (K.G.-a.); (K.M.); (T.S.); (W.T.); (M.C.); (N.S.)
| | - Monrat Chulanetra
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Bangkok 10700, Thailand; (K.G.-a.); (K.M.); (T.S.); (W.T.); (M.C.); (N.S.)
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Sciences, Kasetsart University, Bangkok 10900, Thailand;
| | - Nitat Sookrung
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Bangkok 10700, Thailand; (K.G.-a.); (K.M.); (T.S.); (W.T.); (M.C.); (N.S.)
- Biomedical Research Incubator Unit, Department of Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Wanpen Chaicumpa
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Bangkok 10700, Thailand; (K.G.-a.); (K.M.); (T.S.); (W.T.); (M.C.); (N.S.)
| |
Collapse
|
167
|
Rozak H, Nihonyanagi S, Myalitsin A, Roy S, Ahmed M, Tahara T, Rzeznicka II. Adsorption of SARS-CoV-2 Spike (N501Y) RBD to Human Angiotensin-Converting Enzyme 2 at a Lipid/Water Interface. J Phys Chem B 2023; 127:4406-4414. [PMID: 37171105 DOI: 10.1021/acs.jpcb.3c00832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The receptor binding domain (RBD) of spike proteins plays a crucial role in the process of severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) attachment to the human angiotensin-converting enzyme 2 (ACE2). The N501Y mutation and later mutations introduced extra positive charges on the spike RBD and resulted in higher transmissibility, likely due to stronger binding with the highly negatively charged ACE2. Consequently, many studies have been devoted to understanding the molecular mechanism of spike protein binding with the ACE2 receptor. Most of the theoretical studies, however, have been done on isolated proteins. ACE2 is a transmembrane protein; thus, it is important to understand the interaction of spike proteins with ACE2 in a lipid matrix. In this study, the adsorption of ACE2 and spike (N501Y) RBD at a lipid/water interface was studied using the heterodyne-detected vibrational sum frequency generation (HD-VSFG) technique. The technique is a non-linear optical spectroscopy which measures vibrational spectra of molecules at an interface and provides information on their structure and orientation. It is found that ACE2 is effectively adsorbed at the positively charged 1,2-dipalmitoyl-3-trimethylammonium-propane (DPTAP) lipid monolayer via electrostatic interactions. The adsorption of ACE2 at the DPTAP monolayer causes a reorganization of interfacial water (D2O) from the D-down to the D-up orientation, indicating that the originally positively charged DPTAP interface becomes negatively charged due to ACE2 adsorption. The negatively charged interface (DPTAP/ACE2) allows further adsorption of positively charged spike RBD. HD-VSFG spectra in the amide I region show differences for spike (N501Y) RBD adsorbed at D2O, DPTAP, and DPTAP/ACE2 interfaces. A red shift observed for the spectra of spike RBD/DPTAP suggests that spike RBD oligomers are formed upon contact with DPTAP lipids.
Collapse
Affiliation(s)
- Harison Rozak
- College of Engineering, Shibaura Institute of Technology, Saitama City, Saitama 337-8570, Japan
| | - Satoshi Nihonyanagi
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Anton Myalitsin
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- ANVOS Analytics Co., 4-168 Motomachi, Naka-ku, Yokohama, Kanagawa 231-0861, Japan
| | - Subhadip Roy
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Mohammed Ahmed
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Izabela I Rzeznicka
- College of Engineering, Shibaura Institute of Technology, Saitama City, Saitama 337-8570, Japan
| |
Collapse
|
168
|
Shahab M, Akter S, Sarkar MMH, Banu TA, Goswami B, Chowdhury SF, Naser SR, Habib MA, Shaikh AA, Saki M, Zheng G, Khan MS. Computational design of medicinal compounds to inhibit RBD-hACE2 interaction in the Omicron variant: unveiling a vulnerable target site. INFORMATICS IN MEDICINE UNLOCKED 2023; 40:101281. [PMID: 37265644 PMCID: PMC10210851 DOI: 10.1016/j.imu.2023.101281] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/22/2023] [Accepted: 05/22/2023] [Indexed: 06/03/2023] Open
Abstract
The COVID-19 pandemic, caused by SARS-CoV-2, has globally affected both human health and economy. Several variants with a high potential for reinfection and the ability to evade immunity were detected shortly after the initial reported case of COVID-19. A total of 30 mutations in the spike protein (S) have been reported in the SARS-CoV-2 (BA.2) variant in India and South Africa, while half of these mutations are in the receptor-binding domain and have spread rapidly throughout the world. Drug repurposing offers potential advantages over the discovery of novel drugs, and one is that it can be delivered quickly without lengthy assessments and time-consuming clinical trials. In this study, computational drug design, such as pharmacophore-based virtual screening and MD simulation has been concentrated, in order to find a novel small molecular inhibitor that prevents hACE2 from binding to the receptor binding domain (RBD). three medicinal compound databases: North-East African, North African, and East African were screened and carried out a multi-step screening approach that identified three compounds, which are thymoquinol 2-O-beta-glucopyranoside (C1), lanneaflavonol (C2), and naringenin-4'-methoxy-7-O-Alpha-L-rhamnoside (C3), with excellent anti-viral properties against the RBD of the omicron variant. Furthermore, PAIN assay interference, computation bioactivity prediction, binding free energy, and dissociation constant were used to validate the top hits, which indicated good antiviral activity. The three compounds that were found may be useful against COVID-19, though more research is required. These findings could aid the development of novel therapeutic drugs against the emerging Omicron variant of SARS-CoV-2.
Collapse
Affiliation(s)
- Muhammad Shahab
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Shahina Akter
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | | | - Tanjina Akhtar Banu
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Barna Goswami
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | | | - Showti Raheel Naser
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Md Ahashan Habib
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Aftab Ali Shaikh
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Morteza Saki
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Guojun Zheng
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Md Salim Khan
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| |
Collapse
|
169
|
Wuo M, Dugan AE, Halim M, Hauser BM, Feldman J, Caradonna TM, Zhang S, Pepi LE, Atyeo C, Fischinger S, Alter G, Garcia-Beltran WF, Azadi P, Hung D, Schmidt AG, Kiessling LL. Lectin Fingerprinting Distinguishes Antibody Neutralization in SARS-CoV-2. ACS CENTRAL SCIENCE 2023; 9:947-956. [PMID: 37252360 PMCID: PMC10214521 DOI: 10.1021/acscentsci.2c01471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Indexed: 05/31/2023]
Abstract
Enveloped viruses co-opt host glycosylation pathways to decorate their surface proteins. As viruses evolve, emerging strains can modify their glycosylation patterns to influence host interactions and subvert immune recognition. Still, changes in viral glycosylation or their impact on antibody protection cannot be predicted from genomic sequences alone. Using the highly glycosylated SARS-CoV-2 Spike protein as a model system, we present a lectin fingerprinting method that rapidly reports on changes in variant glycosylation state, which are linked to antibody neutralization. In the presence of antibodies or convalescent and vaccinated patient sera, unique lectin fingerprints emerge that distinguish neutralizing versus non-neutralizing antibodies. This information could not be inferred from direct binding interactions between antibodies and the Spike receptor-binding domain (RBD) binding data alone. Comparative glycoproteomics of the Spike RBD of wild-type (Wuhan-Hu-1) and Delta (B.1.617.2) variants reveal O-glycosylation differences as a key determinant of immune recognition differences. These data underscore the interplay between viral glycosylation and immune recognition and reveal lectin fingerprinting to be a rapid, sensitive, and high-throughput assay to distinguish the neutralization potential of antibodies that target critical viral glycoproteins.
Collapse
Affiliation(s)
- Michael
G. Wuo
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Amanda E. Dugan
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Melanie Halim
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Blake M. Hauser
- Ragon
Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
| | - Jared Feldman
- Ragon
Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
| | - Timothy M. Caradonna
- Ragon
Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
| | - Shuting Zhang
- The
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department
of Molecular Biology and Center for Computational and Integrative
Biology, Massachusetts General Hospital, Boston, Massachusetts 02139, United States
- Department
of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Lauren E. Pepi
- Complex
Carbohydrate Research Center, University
of Georgia, Athens, Georgia 30602, United States
| | - Caroline Atyeo
- Ragon
Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
| | - Stephanie Fischinger
- Ragon
Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
| | - Galit Alter
- Ragon
Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
| | | | - Parastoo Azadi
- Complex
Carbohydrate Research Center, University
of Georgia, Athens, Georgia 30602, United States
| | - Deb Hung
- The
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department
of Molecular Biology and Center for Computational and Integrative
Biology, Massachusetts General Hospital, Boston, Massachusetts 02139, United States
- Department
of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Aaron G. Schmidt
- Ragon
Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
- Department
of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Laura L. Kiessling
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
- The
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Koch
Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
170
|
Oh J, Park U, Kim J, Jeon K, Kim C, Cho NH, Choi YS. Enhancing immune protection against MERS-CoV: the synergistic effect of proteolytic cleavage sites and the fusion peptide and RBD domain targeting VLP immunization. Front Immunol 2023; 14:1201136. [PMID: 37275866 PMCID: PMC10235442 DOI: 10.3389/fimmu.2023.1201136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/09/2023] [Indexed: 06/07/2023] Open
Abstract
Introduction The Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is a zoonotic infectious virus that has caused significant outbreaks in the Middle East and beyond. Due to a highly mortality rate, easy transmission, and rapid spread of the MERS-CoV, it remains as a significant public health treat. There is currently no licensed vaccine available to protect against MERS-CoV. Methods In this study, we investigated whether the proteolytic cleavage sites and fusion peptide domain of the MERS-CoV spike (S) protein could be a vaccine target to elicit the MERS-CoV S protein-specific antibody responses and confer immune protection against MERS-CoV infection. Our results demonstrate that immunization of the proteolytic cleavage sites and the fusion peptide domain using virus-like particle (VLP) induced the MERS-CoV S protein-specific IgG antibodies with capacity to neutralize pseudotyped MERS-CoV infection in vitro. Moreover, proteolytic cleavage sites and the fusion peptide VLP immunization showed a synergistic effect on the immune protection against MERS-CoV infection elicited by immunization with VLP expressing the receptor binding domain (RBD) of the S protein. Additionally, immune evasion of MERS-CoV RBD variants from anti-RBD sera was significantly controlled by anti-proteolytic cleavage sites and the fusion peptide sera. Conclusion and discussion Our study demonstrates the potential of VLP immunization targeting the proteolytic cleavage sites and the fusion peptide and RBD domains of the MERS-CoV S protein for the development of effective treatments and vaccines against MERS-CoV and related variants.
Collapse
Affiliation(s)
- Jeein Oh
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Uni Park
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Juhyung Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyeongseok Jeon
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Chulwoo Kim
- Deparatment of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of Korea
| | - Nam-Hyuk Cho
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Seoul National University Bundang Hospital, Seongnam, Gyeonggi-do, Republic of Korea
| | - Youn Soo Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Transplantation Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| |
Collapse
|
171
|
Morita R, Kubota-Koketsu R, Lu X, Sasaki T, Nakayama EE, Liu YC, Okuzaki D, Motooka D, Wing JB, Fujikawa Y, Ichida Y, Amo K, Goto T, Hara J, Shirano M, Yamasaki S, Shioda T. COVID-19 relapse associated with SARS-CoV-2 evasion from CD4 + T-cell recognition in an agammaglobulinemia patient. iScience 2023; 26:106685. [PMID: 37124420 PMCID: PMC10116114 DOI: 10.1016/j.isci.2023.106685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 03/27/2023] [Accepted: 04/12/2023] [Indexed: 05/02/2023] Open
Abstract
A 25-year-old patient with a primary immunodeficiency lacking immunoglobulin production experienced a relapse after a 239-day period of persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Viral genetic sequencing demonstrated that SARS-CoV-2 had evolved during the infection period, with at least five mutations associated with host cellular immune recognition. Among them, the T32I mutation in ORF3a was found to evade recognition by CD4+ T cells. The virus found after relapse showed an increased proliferative capacity in vitro. SARS-CoV-2 may have evolved to evade recognition by CD4+ T cells and increased in its proliferative capacity during the persistent infection, likely leading to relapse. These mutations may further affect viral clearance in hosts with similar types of human leukocyte antigens. The early elimination of SARS-CoV-2 in immunocompromised patients is therefore important not only to improve the condition of patients but also to prevent the emergence of mutants that threaten public health.
Collapse
Affiliation(s)
- Ryo Morita
- Department of Infectious Diseases, Osaka City General Hospital, Osaka 534-0021, Japan
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Ritsuko Kubota-Koketsu
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Xiuyuan Lu
- Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Tadahiro Sasaki
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Emi E Nakayama
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Yu-Chen Liu
- Laboratory of Human Immunology (Single Cell Genomics), Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Daisuke Okuzaki
- Laboratory of Human Immunology (Single Cell Genomics), Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - James Badger Wing
- Laboratory of Human Immunology (Single Cell Immunology), Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Yasunori Fujikawa
- Department of Medical Laboratory, Osaka City General Hospital, Osaka 534-0021, Japan
| | - Yuji Ichida
- Department of Pharmacy, Osaka City General Hospital, Osaka 534-0021, Japan
| | - Kiyoko Amo
- Department of Pediatric Emergency Medicine, Osaka City General Hospital, Osaka 534-0021, Japan
| | - Tetsushi Goto
- Department of Infectious Diseases, Osaka City General Hospital, Osaka 534-0021, Japan
| | - Junichi Hara
- Department of Pediatric Hematology and Oncology, Osaka City General Hospital, Osaka 534-0021, Japan
| | - Michinori Shirano
- Department of Infectious Diseases, Osaka City General Hospital, Osaka 534-0021, Japan
| | - Sho Yamasaki
- Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Tatsuo Shioda
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| |
Collapse
|
172
|
Halma MTJ, Plothe C, Marik P, Lawrie TA. Strategies for the Management of Spike Protein-Related Pathology. Microorganisms 2023; 11:1308. [PMID: 37317282 PMCID: PMC10222799 DOI: 10.3390/microorganisms11051308] [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: 03/16/2023] [Revised: 05/04/2023] [Accepted: 05/10/2023] [Indexed: 06/16/2023] Open
Abstract
In the wake of the COVID-19 crisis, a need has arisen to prevent and treat two related conditions, COVID-19 vaccine injury and long COVID-19, both of which can trace at least part of their aetiology to the spike protein, which can cause harm through several mechanisms. One significant mechanism of harm is vascular, and it is mediated by the spike protein, a common element of the COVID-19 illness, and it is related to receiving a COVID-19 vaccine. Given the significant number of people experiencing these two related conditions, it is imperative to develop treatment protocols, as well as to consider the diversity of people experiencing long COVID-19 and vaccine injury. This review summarizes the known treatment options for long COVID-19 and vaccine injury, their mechanisms, and their evidentiary basis.
Collapse
Affiliation(s)
| | - Christof Plothe
- Center for Biophysical Osteopathy, Am Wegweiser 27, 55232 Alzey, Germany
| | - Paul Marik
- Front Line COVID-19 Critical Care Alliance (FLCCC), 2001 L St. NW Suite 500, Washington, DC 20036, USA;
| | | |
Collapse
|
173
|
Su M, Zheng G, Xu X, Song H. Antigen epitopes of animal coronaviruses: a mini-review. ANIMAL DISEASES 2023; 3:14. [PMID: 37220551 PMCID: PMC10189233 DOI: 10.1186/s44149-023-00080-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 04/13/2023] [Indexed: 05/25/2023] Open
Abstract
Coronaviruses are widespread in nature and can infect mammals and poultry, making them a public health concern. Globally, prevention and control of emerging and re-emerging animal coronaviruses is a great challenge. The mechanisms of virus-mediated immune responses have important implications for research on virus prevention and control. The antigenic epitope is a chemical group capable of stimulating the production of antibodies or sensitized lymphocytes, playing an important role in antiviral immune responses. Thus, it can shed light on the development of diagnostic methods and novel vaccines. Here, we have reviewed advances in animal coronavirus antigenic epitope research, aiming to provide a reference for the prevention and control of animal and human coronaviruses. Supplementary Information The online version contains supplementary material available at 10.1186/s44149-023-00080-0.
Collapse
Affiliation(s)
- Mingjun Su
- Key Laboratory of Applied Technology On Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang, A&F University, 666 Wusu Street, Lin’an District, Hangzhou, 311300 Zhejiang Province China
| | - Guanghui Zheng
- Key Laboratory of Applied Technology On Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang, A&F University, 666 Wusu Street, Lin’an District, Hangzhou, 311300 Zhejiang Province China
| | - Xiangwen Xu
- Key Laboratory of Applied Technology On Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang, A&F University, 666 Wusu Street, Lin’an District, Hangzhou, 311300 Zhejiang Province China
| | - Houhui Song
- Key Laboratory of Applied Technology On Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang, A&F University, 666 Wusu Street, Lin’an District, Hangzhou, 311300 Zhejiang Province China
| |
Collapse
|
174
|
Ma Y, Li P, Hu Y, Qiu T, Wang L, Lu H, Lv K, Xu M, Zhuang J, Liu X, He S, He B, Liu S, Liu L, Wang Y, Yue X, Zhai Y, Luo W, Mai H, Kuang Y, Chen S, Ye F, Zhou N, Zhao W, Chen J, Chen S, Xiong X, Shi M, Pan JA, Chen YQ. Spike substitution T813S increases Sarbecovirus fusogenicity by enhancing the usage of TMPRSS2. PLoS Pathog 2023; 19:e1011123. [PMID: 37196033 DOI: 10.1371/journal.ppat.1011123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 05/30/2023] [Accepted: 04/24/2023] [Indexed: 05/19/2023] Open
Abstract
SARS-CoV Spike (S) protein shares considerable homology with SARS-CoV-2 S, especially in the conserved S2 subunit (S2). S protein mediates coronavirus receptor binding and membrane fusion, and the latter activity can greatly influence coronavirus infection. We observed that SARS-CoV S is less effective in inducing membrane fusion compared with SARS-CoV-2 S. We identify that S813T mutation is sufficient in S2 interfering with the cleavage of SARS-CoV-2 S by TMPRSS2, reducing spike fusogenicity and pseudoparticle entry. Conversely, the mutation of T813S in SARS-CoV S increased fusion ability and viral replication. Our data suggested that residue 813 in the S was critical for the proteolytic activation, and the change from threonine to Serine at 813 position might be an evolutionary feature adopted by SARS-2-related viruses. This finding deepened the understanding of Spike fusogenicity and could provide a new perspective for exploring Sarbecovirus' evolution.
Collapse
Affiliation(s)
- Yong Ma
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Pengbin Li
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Yunqi Hu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Tianyi Qiu
- Institute of Clinical Science, Zhongshan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lixiang Wang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Hongjie Lu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Kexin Lv
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Mengxin Xu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Jiaxin Zhuang
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Xue Liu
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Suhua He
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Bing He
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Shuning Liu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Lin Liu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Yuanyuan Wang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Xinyu Yue
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Yanmei Zhai
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Wanyu Luo
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Haoting Mai
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Yu Kuang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Shifeng Chen
- The 74(th) Group Army Hospital, Guangzhou, China
| | - Feng Ye
- The 74(th) Group Army Hospital, Guangzhou, China
| | - Na Zhou
- The 74(th) Group Army Hospital, Guangzhou, China
| | - Wenjing Zhao
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Jun Chen
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Shoudeng Chen
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Xiaoli Xiong
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Mang Shi
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Ji-An Pan
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Yao-Qing Chen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- National Medical Products Administration Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, Sun Yat-sen University, Guanzhou, China
| |
Collapse
|
175
|
Kakavandi S, Zare I, VaezJalali M, Dadashi M, Azarian M, Akbari A, Ramezani Farani M, Zalpoor H, Hajikhani B. Structural and non-structural proteins in SARS-CoV-2: potential aspects to COVID-19 treatment or prevention of progression of related diseases. Cell Commun Signal 2023; 21:110. [PMID: 37189112 DOI: 10.1186/s12964-023-01104-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 03/15/2023] [Indexed: 05/17/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by a new member of the Coronaviridae family known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). There are structural and non-structural proteins (NSPs) in the genome of this virus. S, M, H, and E proteins are structural proteins, and NSPs include accessory and replicase proteins. The structural and NSP components of SARS-CoV-2 play an important role in its infectivity, and some of them may be important in the pathogenesis of chronic diseases, including cancer, coagulation disorders, neurodegenerative disorders, and cardiovascular diseases. The SARS-CoV-2 proteins interact with targets such as angiotensin-converting enzyme 2 (ACE2) receptor. In addition, SARS-CoV-2 can stimulate pathological intracellular signaling pathways by triggering transcription factor hypoxia-inducible factor-1 (HIF-1), neuropilin-1 (NRP-1), CD147, and Eph receptors, which play important roles in the progression of neurodegenerative diseases like Alzheimer's disease, epilepsy, and multiple sclerosis, and multiple cancers such as glioblastoma, lung malignancies, and leukemias. Several compounds such as polyphenols, doxazosin, baricitinib, and ruxolitinib could inhibit these interactions. It has been demonstrated that the SARS-CoV-2 spike protein has a stronger affinity for human ACE2 than the spike protein of SARS-CoV, leading the current study to hypothesize that the newly produced variant Omicron receptor-binding domain (RBD) binds to human ACE2 more strongly than the primary strain. SARS and Middle East respiratory syndrome (MERS) viruses against structural and NSPs have become resistant to previous vaccines. Therefore, the review of recent studies and the performance of current vaccines and their effects on COVID-19 and related diseases has become a vital need to deal with the current conditions. This review examines the potential role of these SARS-CoV-2 proteins in the initiation of chronic diseases, and it is anticipated that these proteins could serve as components of an effective vaccine or treatment for COVID-19 and related diseases. Video Abstract.
Collapse
Affiliation(s)
- Sareh Kakavandi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Iman Zare
- Research and Development Department, Sina Medical Biochemistry Technologies Co. Ltd., Shiraz, 7178795844, Iran
| | - Maryam VaezJalali
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoud Dadashi
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
- Non-Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Maryam Azarian
- Department of Radiology, Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Abdullatif Akbari
- Shiraz Neuroscience Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Marzieh Ramezani Farani
- Department of Biological Sciences and Bioengineering, Nano Bio High-Tech Materials Research Center, Inha University, Incheon, 22212, Republic of Korea
| | - Hamidreza Zalpoor
- Shiraz Neuroscience Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran.
| | - Bahareh Hajikhani
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
176
|
Guo L, Lin S, Chen Z, Cao Y, He B, Lu G. Targetable elements in SARS-CoV-2 S2 subunit for the design of pan-coronavirus fusion inhibitors and vaccines. Signal Transduct Target Ther 2023; 8:197. [PMID: 37164987 PMCID: PMC10170451 DOI: 10.1038/s41392-023-01472-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 04/04/2023] [Accepted: 04/23/2023] [Indexed: 05/12/2023] Open
Abstract
The ongoing global pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused devastating impacts on the public health and the global economy. Rapid viral antigenic evolution has led to the continual generation of new variants. Of special note is the recently expanding Omicron subvariants that are capable of immune evasion from most of the existing neutralizing antibodies (nAbs). This has posed new challenges for the prevention and treatment of COVID-19. Therefore, exploring broad-spectrum antiviral agents to combat the emerging variants is imperative. In sharp contrast to the massive accumulation of mutations within the SARS-CoV-2 receptor-binding domain (RBD), the S2 fusion subunit has remained highly conserved among variants. Hence, S2-based therapeutics may provide effective cross-protection against new SARS-CoV-2 variants. Here, we summarize the most recently developed broad-spectrum fusion inhibitors (e.g., nAbs, peptides, proteins, and small-molecule compounds) and candidate vaccines targeting the conserved elements in SARS-CoV-2 S2 subunit. The main focus includes all the targetable S2 elements, namely, the fusion peptide, stem helix, and heptad repeats 1 and 2 (HR1-HR2) bundle. Moreover, we provide a detailed summary of the characteristics and action-mechanisms for each class of cross-reactive fusion inhibitors, which should guide and promote future design of S2-based inhibitors and vaccines against new coronaviruses.
Collapse
Affiliation(s)
- Liyan Guo
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Sheng Lin
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Zimin Chen
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yu Cao
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
- Disaster Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Bin He
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Guangwen Lu
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
| |
Collapse
|
177
|
Sipala F, Cavallaro G, Forte G, Satriano C, Giuffrida A, Fraix A, Spadaro A, Petralia S, Bonaccorso C, Fortuna CG, Ronsisvalle S. Different In Silico Approaches Using Heterocyclic Derivatives against the Binding between Different Lineages of SARS-CoV-2 and ACE2. Molecules 2023; 28:molecules28093908. [PMID: 37175318 PMCID: PMC10180195 DOI: 10.3390/molecules28093908] [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: 03/22/2023] [Revised: 04/24/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
Over the last few years, the study of the SARS-CoV-2 spike protein and its mutations has become essential in understanding how it interacts with human host receptors. Since the crystallized structure of the spike protein bound to the angiotensin-converting enzyme 2 (ACE2) receptor was released (PDB code 6M0J), in silico studies have been performed to understand the interactions between these two proteins. Specifically, in this study, heterocyclic compounds with different chemical characteristics were examined to highlight the possibility of interaction with the spike protein and the disruption of the interaction between ACE2 and the spike protein. Our results showed that these compounds interacted with the spike protein and interposed in the interaction zone with ACE2. Although further studies are needed, this work points to these heterocyclic push-pull compounds as possible agents capable of interacting with the spike protein, with the potential for the inhibition of spike protein-ACE2 binding.
Collapse
Affiliation(s)
- Federica Sipala
- Department of Drug and Health Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Gianfranco Cavallaro
- Department of Chemical Science, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Giuseppe Forte
- Department of Drug and Health Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Cristina Satriano
- Department of Chemical Science, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Alessandro Giuffrida
- Department of Chemical Science, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Aurore Fraix
- Department of Drug and Health Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Angelo Spadaro
- Department of Drug and Health Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Salvatore Petralia
- Department of Drug and Health Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Carmela Bonaccorso
- Department of Chemical Science, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Cosimo Gianluca Fortuna
- Department of Chemical Science, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Simone Ronsisvalle
- Department of Drug and Health Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| |
Collapse
|
178
|
Yu X, Juraszek J, Rutten L, Bakkers MJG, Blokland S, Melchers JM, van den Broek NJF, Verwilligen AYW, Abeywickrema P, Vingerhoets J, Neefs JM, Bakhash SAM, Roychoudhury P, Greninger A, Sharma S, Langedijk JPM. Convergence of immune escape strategies highlights plasticity of SARS-CoV-2 spike. PLoS Pathog 2023; 19:e1011308. [PMID: 37126534 PMCID: PMC10174534 DOI: 10.1371/journal.ppat.1011308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 05/11/2023] [Accepted: 03/21/2023] [Indexed: 05/02/2023] Open
Abstract
The global spread of the SARS-CoV-2 virus has resulted in emergence of lineages which impact the effectiveness of immunotherapies and vaccines that are based on the early Wuhan isolate. All currently approved vaccines employ the spike protein S, as it is the target for neutralizing antibodies. Here we describe two SARS-CoV-2 isolates with unusually large deletions in the N-terminal domain (NTD) of the spike. Cryo-EM structural analysis shows that the deletions result in complete reshaping of the NTD supersite, an antigenically important region of the NTD. For both spike variants the remodeling of the NTD negatively affects binding of all tested NTD-specific antibodies in and outside of the NTD supersite. For one of the variants, we observed a P9L mediated shift of the signal peptide cleavage site resulting in the loss of a disulfide-bridge; a unique escape mechanism with high antigenic impact. Although the observed deletions and disulfide mutations are rare, similar modifications have become independently established in several other lineages, indicating a possibility to become more dominant in the future. The observed plasticity of the NTD foreshadows its broad potential for immune escape with the continued spread of SARS-CoV-2.
Collapse
Affiliation(s)
- Xiaodi Yu
- Structural & Protein Sciences, Janssen Research and Development, Spring House, Pennsylvania, United States of America
| | - Jarek Juraszek
- Janssen Vaccines & Prevention BV, Leiden, the Netherlands
| | - Lucy Rutten
- Janssen Vaccines & Prevention BV, Leiden, the Netherlands
| | | | - Sven Blokland
- Janssen Vaccines & Prevention BV, Leiden, the Netherlands
| | | | | | | | - Pravien Abeywickrema
- Structural & Protein Sciences, Janssen Research and Development, Spring House, Pennsylvania, United States of America
| | - Johan Vingerhoets
- Janssen Pharmaceutica N.V., Clinical Microbiology and Immunology, Beerse, Belgium
| | - Jean-Marc Neefs
- Janssen Pharmaceutica N.V., Discovery Sciences, Beerse, Belgium
| | - Shah A Mohamed Bakhash
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington, Seattle, Washington, United States of America
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington, Seattle, Washington, United States of America
| | - Alex Greninger
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington, Seattle, Washington, United States of America
| | - Sujata Sharma
- Structural & Protein Sciences, Janssen Research and Development, Spring House, Pennsylvania, United States of America
| | | |
Collapse
|
179
|
Tian WJ, Wang XJ. Broad-Spectrum Antivirals Derived from Natural Products. Viruses 2023; 15:v15051100. [PMID: 37243186 DOI: 10.3390/v15051100] [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: 03/09/2023] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
Scientific advances have led to the development and production of numerous vaccines and antiviral drugs, but viruses, including re-emerging and emerging viruses, such as SARS-CoV-2, remain a major threat to human health. Many antiviral agents are rarely used in clinical treatment, however, because of their inefficacy and resistance. The toxicity of natural products may be lower, and some natural products have multiple targets, which means less resistance. Therefore, natural products may be an effective means to solve virus infection in the future. New techniques and ideas are currently being developed for the design and screening of antiviral drugs thanks to recent revelations about virus replication mechanisms and the advancement of molecular docking technology. This review will summarize recently discovered antiviral drugs, mechanisms of action, and screening and design strategies for novel antiviral agents.
Collapse
Affiliation(s)
- Wen-Jun Tian
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, China Agricultural University, Beijing 100193, China
| | - Xiao-Jia Wang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, China Agricultural University, Beijing 100193, China
| |
Collapse
|
180
|
Chen TH, Chang CJ, Hung PH. Possible Pathogenesis and Prevention of Long COVID: SARS-CoV-2-Induced Mitochondrial Disorder. Int J Mol Sci 2023; 24:8034. [PMID: 37175745 PMCID: PMC10179190 DOI: 10.3390/ijms24098034] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/27/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
Patients who have recovered from coronavirus disease 2019 (COVID-19) infection may experience chronic fatigue when exercising, despite no obvious heart or lung abnormalities. The present lack of effective treatments makes managing long COVID a major challenge. One of the underlying mechanisms of long COVID may be mitochondrial dysfunction. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections can alter the mitochondria responsible for energy production in cells. This alteration leads to mitochondrial dysfunction which, in turn, increases oxidative stress. Ultimately, this results in a loss of mitochondrial integrity and cell death. Moreover, viral proteins can bind to mitochondrial complexes, disrupting mitochondrial function and causing the immune cells to over-react. This over-reaction leads to inflammation and potentially long COVID symptoms. It is important to note that the roles of mitochondrial damage and inflammatory responses caused by SARS-CoV-2 in the development of long COVID are still being elucidated. Targeting mitochondrial function may provide promising new clinical approaches for long-COVID patients; however, further studies are needed to evaluate the safety and efficacy of such approaches.
Collapse
Affiliation(s)
- Tsung-Hsien Chen
- Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi 60002, Taiwan;
| | - Chia-Jung Chang
- Division of Critical Care Medicine, Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi 60002, Taiwan
| | - Peir-Haur Hung
- Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi 60002, Taiwan;
- Department of Life and Health Science, Chia-Nan University of Pharmacy and Science, Tainan 717301, Taiwan
| |
Collapse
|
181
|
Rando HM, Lordan R, Kolla L, Sell E, Lee AJ, Wellhausen N, Naik A, Kamil JP, Gitter A, Greene CS. The Coming of Age of Nucleic Acid Vaccines during COVID-19. mSystems 2023; 8:e0092822. [PMID: 36861992 PMCID: PMC10134841 DOI: 10.1128/msystems.00928-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
In the 21st century, several emergent viruses have posed a global threat. Each pathogen has emphasized the value of rapid and scalable vaccine development programs. The ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has made the importance of such efforts especially clear. New biotechnological advances in vaccinology allow for recent advances that provide only the nucleic acid building blocks of an antigen, eliminating many safety concerns. During the COVID-19 pandemic, these DNA and RNA vaccines have facilitated the development and deployment of vaccines at an unprecedented pace. This success was attributable at least in part to broader shifts in scientific research relative to prior epidemics: the genome of SARS-CoV-2 was available as early as January 2020, facilitating global efforts in the development of DNA and RNA vaccines within 2 weeks of the international community becoming aware of the new viral threat. Additionally, these technologies that were previously only theoretical are not only safe but also highly efficacious. Although historically a slow process, the rapid development of vaccines during the COVID-19 crisis reveals a major shift in vaccine technologies. Here, we provide historical context for the emergence of these paradigm-shifting vaccines. We describe several DNA and RNA vaccines in terms of their efficacy, safety, and approval status. We also discuss patterns in worldwide distribution. The advances made since early 2020 provide an exceptional illustration of how rapidly vaccine development technology has advanced in the last 2 decades in particular and suggest a new era in vaccines against emerging pathogens. IMPORTANCE The SARS-CoV-2 pandemic has caused untold damage globally, presenting unusual demands on but also unique opportunities for vaccine development. The development, production, and distribution of vaccines are imperative to saving lives, preventing severe illness, and reducing the economic and social burdens caused by the COVID-19 pandemic. Although vaccine technologies that provide the DNA or RNA sequence of an antigen had never previously been approved for use in humans, they have played a major role in the management of SARS-CoV-2. In this review, we discuss the history of these vaccines and how they have been applied to SARS-CoV-2. Additionally, given that the evolution of new SARS-CoV-2 variants continues to present a significant challenge in 2022, these vaccines remain an important and evolving tool in the biomedical response to the pandemic.
Collapse
Affiliation(s)
- Halie M. Rando
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz School of Medicine, Aurora, Colorado, USA
- Center for Health AI, University of Colorado Anschutz School of Medicine, Aurora, Colorado, USA
- Department of Biomedical Informatics, University of Colorado Anschutz School of Medicine, Aurora, Colorado, USA
| | - Ronan Lordan
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Likhitha Kolla
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Elizabeth Sell
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Alexandra J. Lee
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nils Wellhausen
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Amruta Naik
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jeremy P. Kamil
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center Shreveport, Shreveport, Louisiana, USA
| | - COVID-19 Review Consortium
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz School of Medicine, Aurora, Colorado, USA
- Center for Health AI, University of Colorado Anschutz School of Medicine, Aurora, Colorado, USA
- Department of Biomedical Informatics, University of Colorado Anschutz School of Medicine, Aurora, Colorado, USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center Shreveport, Shreveport, Louisiana, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
- Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Philadelphia, Pennsylvania, USA
| | - Anthony Gitter
- Department of Biostatistics and Medical Informatics, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Casey S. Greene
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz School of Medicine, Aurora, Colorado, USA
- Center for Health AI, University of Colorado Anschutz School of Medicine, Aurora, Colorado, USA
- Department of Biomedical Informatics, University of Colorado Anschutz School of Medicine, Aurora, Colorado, USA
- Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Philadelphia, Pennsylvania, USA
| |
Collapse
|
182
|
Cheng A, Ren H, Ma Z, Alam N, Jia L, Liu E. Trends and characteristics of COVID-19 and cardiovascular disease related studies. Front Pharmacol 2023; 14:1105459. [PMID: 37180704 PMCID: PMC10166808 DOI: 10.3389/fphar.2023.1105459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 04/11/2023] [Indexed: 05/16/2023] Open
Abstract
Introduction: The new coronavirus has caused a pandemic that has infected hundreds of millions of people around the world since its outbreak. But the cardiovascular damage caused by the new coronavirus is unknown. We have analyzed the current global scenario and the general pattern of growth. After summarizing the known relationship between cardiovascular diseases and new coronary pneumonia, relevant articles are analyzed through bibliometrics and visualization. Methods: Following our pre-designed search strategy, we selected publications on COVID-19 and cardiovascular disease in the Web of Science database. In our relevant bibliometric visualization analysis, a total of 7,028 related articles in the WOS core database up to 20th October 2022 were summarized, and the most prolific authors, the most prolific countries, and the journals and institutions that published the most articles were summarized and quantitatively analyzed. Results: SARS-CoV-2 is more infectious than SARS-CoV-1 and has significant involvement in the cardiovascular system in addition to pulmonary manifestations, with a difference of 10.16% (20.26%/10.10%) in the incidence of cardiovascular diseases. The number of cases increases in winter and decreases slightly in summer with temperature changes, but the increase in cases tends to break out of seasonality across the region as mutant strains emerge. The co-occurrence analysis found that with the progress of the epidemic, the research keywords gradually shifted from ACE2 and inflammation to the treatment of myocarditis and complications, indicating that the research on the new crown epidemic has entered the stage of prevention and treatment of complications. Conclusion: When combined with the current global pandemic trend, how to improve prognosis and reduce human body damage could become a research focus. At the same time, timely detection, prevention, and discovery of new mutant strains have also become key tasks in the fight against the epidemic, and full preparations have been made to prevent the spread of the next wave of mutant strains, and still need to continue to pay attention to the differential performance of the variant "omicron."
Collapse
Affiliation(s)
| | | | | | | | - Linying Jia
- Laboratory Animal Centre, Xi’an Jiaotong University Health Science Centre, Xi’an, Shaanxi, China
| | | |
Collapse
|
183
|
Curreli F, Chau K, Tran TT, Nicolau I, Ahmed S, Das P, Hillyer CD, Premenko-Lanier M, Debnath AK. Discovery of Highly Potent Small Molecule Pan-Coronavirus Fusion Inhibitors. Viruses 2023; 15:v15041001. [PMID: 37112982 PMCID: PMC10141620 DOI: 10.3390/v15041001] [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: 03/28/2023] [Revised: 04/12/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
The unprecedented pandemic of COVID-19, caused by a novel coronavirus, SARS-CoV-2, and its highly transmissible variants, led to massive human suffering, death, and economic devastation worldwide. Recently, antibody-evasive SARS-CoV-2 subvariants, BQ and XBB, have been reported. Therefore, the continued development of novel drugs with pan-coronavirus inhibition is critical to treat and prevent infection of COVID-19 and any new pandemics that may emerge. We report the discovery of several highly potent small-molecule inhibitors. One of which, NBCoV63, showed low nM potency against SARS-CoV-2 (IC50: 55 nM), SARS-CoV-1 (IC50: 59 nM), and MERS-CoV (IC50: 75 nM) in pseudovirus-based assays with excellent selectivity indices (SI > 900), suggesting its pan-coronavirus inhibition. NBCoV63 showed equally effective antiviral potency against SARS-CoV-2 mutant (D614G) and several variants of concerns (VOCs) such as B.1.617.2 (Delta), B.1.1.529/BA.1 and BA.4/BA.5 (Omicron), and K417T/E484K/N501Y (Gamma). NBCoV63 also showed similar efficacy profiles to Remdesivir against authentic SARS-CoV-2 (Hong Kong strain) and two of its variants (Delta and Omicron), SARS-CoV-1, and MERS-CoV by plaque reduction in Calu-3 cells. Additionally, we show that NBCoV63 inhibits virus-mediated cell-to-cell fusion in a dose-dependent manner. Furthermore, the absorption, distribution, metabolism, and excretion (ADME) data of NBCoV63 demonstrated drug-like properties.
Collapse
Affiliation(s)
- Francesca Curreli
- Laboratory of Molecular Modeling and Drug Design, Lindsey F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA
| | - Kent Chau
- SRI Biosciences (A Division of SRI International), 333 Ravenswood Avenue, Menlo Park, CA 94025, USA
| | - Thanh-Thuy Tran
- SRI Biosciences (A Division of SRI International), 333 Ravenswood Avenue, Menlo Park, CA 94025, USA
| | - Isabella Nicolau
- Laboratory of Molecular Modeling and Drug Design, Lindsey F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA
| | - Shahad Ahmed
- Laboratory of Molecular Modeling and Drug Design, Lindsey F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA
| | - Pujita Das
- Laboratory of Molecular Modeling and Drug Design, Lindsey F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA
| | - Christopher D Hillyer
- Laboratory of Molecular Modeling and Drug Design, Lindsey F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA
| | - Mary Premenko-Lanier
- SRI Biosciences (A Division of SRI International), 333 Ravenswood Avenue, Menlo Park, CA 94025, USA
- Department of Basic Science, Samuel Merritt University, 3100 Telegraph Avenue, Oakland, CA 94609, USA
| | - Asim K Debnath
- Laboratory of Molecular Modeling and Drug Design, Lindsey F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA
| |
Collapse
|
184
|
Jin Y, Fayyaz A, Liaqat A, Khan A, Alshammari A, Wang Y, Gu RX, Wei DQ. Proteomics-based vaccine targets annotation and design of subunit and mRNA-based vaccines for Monkeypox virus (MPXV) against the recent outbreak. Comput Biol Med 2023; 159:106893. [PMID: 37116237 PMCID: PMC10083144 DOI: 10.1016/j.compbiomed.2023.106893] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/17/2023] [Accepted: 04/09/2023] [Indexed: 04/30/2023]
Abstract
Monkeypox Virus (MPXV) is a growing public health threat with increasing cases and fatalities globally. To date, no specific vaccine or small molecule therapeutic choices are available for the treatment of MPXV disease. In this work, we employed proteomics and structural vaccinology approaches to design mRNA and multi-epitopes-based vaccines (MVC) against MPXV. We first identified ten proteins from the whole proteome of MPXV as potential vaccine targets. We then employed structural vaccinology approaches to map potential epitopes of these proteins for B cell, cytotoxic T lymphocytes (CTL), and Helper T lymphocytes (HTL). Finally, 9 CTL, 6 B cell, and 5 HTL epitopes were joined together through suitable linkers to construct MVC (multi-epitope vaccine) and mRNA-based vaccines. Molecular docking, binding free energy calculation, and in silico cloning revealed robust interaction of the designed MVC with toll-like receptor 2 (TLR2) and efficient expression in E. Coli K12 strain. The immune simulation results revealed that the antigen titer after the injection reached to the maximum level on the 5th day and an abrupt decline in the antigen titer was observed upon the production of IgM, IgG and IgM + IgG, dendritic cells, IFN-gamma, and IL (interleukins), which suggested the potential of our designed vaccine candidate for inducing an immune response against MPXV.
Collapse
Affiliation(s)
- Yifan Jin
- College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Addeela Fayyaz
- Fatima Jinnah Medical University, Lahore, Punjab, Pakistan
| | - Ayesha Liaqat
- King Edward Medical University, Lahore, Punjab, Pakistan
| | - Abbas Khan
- College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China; Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Meixi, Nanyang, Henan, 473006, PR China
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh, 11451, Saudi Arabia.
| | - Yanjing Wang
- Engineering Research Center of Cell & Therapeutic Antibody, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, PR China.
| | - Ruo-Xu Gu
- College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China.
| | - Dong-Qing Wei
- College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China; Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Meixi, Nanyang, Henan, 473006, PR China; Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District, Shenzhen, Guangdong, 518055, PR China; Centre for Research in Molecular Modeling, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, H4B 1R6, Canada.
| |
Collapse
|
185
|
Chang CC, Algaissi A, Lai CC, Chang CK, Lin JS, Wang YS, Chang BH, Chang YC, Chen WT, Fan YQ, Peng BH, Chao CY, Tzeng SR, Liang PH, Sung WC, Hu AYC, Chang SC, Chang MF. Subunit vaccines with a saponin-based adjuvant boost humoral and cellular immunity to MERS coronavirus. Vaccine 2023; 41:3337-3346. [PMID: 37085450 PMCID: PMC10083212 DOI: 10.1016/j.vaccine.2023.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/15/2023] [Accepted: 04/03/2023] [Indexed: 04/23/2023]
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) outbreaks have constituted a public health issue with drastic mortality higher than 34%, necessitating the development of an effective vaccine. During MERS-CoV infection, the trimeric spike protein on the viral envelope is primarily responsible for attachment to host cellular receptor, dipeptidyl peptidase 4 (DPP4). With the goal of generating a protein-based prophylactic, we designed a subunit vaccine comprising the recombinant S1 protein with a trimerization motif (S1-Fd) and examined its immunogenicity and protective immune responses in combination with various adjuvants. We found that sera from immunized wild-type and human DPP4 transgenic mice contained S1-specific antibodies that can neutralize MERS-CoV infection in susceptible cells. Vaccination with S1-Fd protein in combination with a saponin-based QS-21 adjuvant provided long-term humoral as well as cellular immunity in mice. Our findings highlight the significance of the trimeric S1 protein in the development of MERS-CoV vaccines and offer a suitable adjuvant, QS-21, to induce robust and prolonged memory T cell response.
Collapse
Affiliation(s)
- Chi-Chieh Chang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Abdullah Algaissi
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX 77555, USA; Center for Biodefense and Emerging Disease, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Chia-Chun Lai
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County 35053, Taiwan; College of Life Science, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chun-Kai Chang
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei 100025, Taiwan
| | - Jr-Shiuan Lin
- Graduate Institute of Immunology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Yi-Shiang Wang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Bo-Hau Chang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Yu-Chiuan Chang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Wei-Ting Chen
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Yong-Qing Fan
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Bi-Hung Peng
- Department of Neurosciences, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Chih-Yu Chao
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Shiou-Ru Tzeng
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Pi-Hui Liang
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei 100025, Taiwan
| | - Wang-Chou Sung
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County 35053, Taiwan
| | - Alan Yung-Chih Hu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County 35053, Taiwan
| | - Shin C Chang
- Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Ming-Fu Chang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan.
| |
Collapse
|
186
|
Li W, Wang F, Li Y, Yan L, Liu L, Zhu W, Ma P, Shi X, Yang G. Potent NTD-Targeting Neutralizing Antibodies against SARS-CoV-2 Selected from a Synthetic Immune System. Vaccines (Basel) 2023; 11:vaccines11040771. [PMID: 37112683 PMCID: PMC10143083 DOI: 10.3390/vaccines11040771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/01/2023] [Accepted: 03/07/2023] [Indexed: 04/03/2023] Open
Abstract
The majority of neutralizing antibodies (NAbs) against SARS-CoV-2 recognize the receptor-binding domain (RBD) of the spike (S) protein. As an escaping strategy, the RBD of the virus is highly variable, evolving mutations to thwart a natural immune response or vaccination. Targeting non-RBD regions of the S protein thus provides a viable alternative to generating potential, robust NAbs. Using a pre-pandemic combinatorial antibody library of 1011, through an alternate negative and positive screening strategy, 11 non-RBD-targeting antibodies are identified. Amongst one NAb that binds specifically to the N-terminal domain of the S protein, SA3, shows mutually non-exclusive binding of the angiotensin-converting enzyme 2 receptor with the S protein. SA3 appears to be insensitive to the conformational change and to interact with both the “open” and “closed” configurations of the trimeric S protein. SA3 shows compatible neutralization as S-E6, an RBD-targeting NAb, against the wild type and variant of concern (VOC) B.1.351 (Beta) of the SARS-CoV-2 pseudo virus. More importantly, the combination of SA3 with S-E6 is synergistic and recovers from the 10-fold loss in neutralization efficacy against the VOC B.1.351 pseudo virus.
Collapse
Affiliation(s)
- Wenping Li
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (W.L.)
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Fulian Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (W.L.)
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Yu Li
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (W.L.)
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Lei Yan
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (W.L.)
| | - Lili Liu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (W.L.)
| | - Wei Zhu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (W.L.)
| | - Peixiang Ma
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedic Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200031, China
| | - Xiaojie Shi
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (W.L.)
- Correspondence: (X.S.); (G.Y.); Tel.: +86-21-20685030 (G.Y.)
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (W.L.)
- Correspondence: (X.S.); (G.Y.); Tel.: +86-21-20685030 (G.Y.)
| |
Collapse
|
187
|
Martins M, do Nascimento GM, Conforti A, Noll JCG, Impellizeri JA, Sanchez E, Wagner B, Lione L, Salvatori E, Pinto E, Compagnone M, Viscount B, Hayward J, Shorrock C, Aurisicchio L, Diel DG. A linear SARS-CoV-2 DNA vaccine candidate reduces virus shedding in ferrets. Arch Virol 2023; 168:124. [PMID: 36988739 PMCID: PMC10052258 DOI: 10.1007/s00705-023-05746-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/03/2023] [Indexed: 03/30/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), has caused more than 760 million cases and over 6.8 million deaths as of March 2023. Vaccination has been the main strategy used to contain the spread of the virus and to prevent hospitalizations and deaths. Currently, two mRNA-based vaccines and one adenovirus-vectored vaccine have been approved and are available for use in the U.S. population. The versatility, low cost, and rapid production of DNA vaccines provide important advantages over other platforms. Additionally, DNA vaccines efficiently induce both B- and T-cell responses by expressing the antigen within transfected host cells, and the antigen, after being processed into peptides, can associate with MHC class I or II of antigen-presenting cells (APCs) to stimulate different T cell responses. However, the efficiency of DNA vaccination needs to be improved for use in humans. Importantly, in vivo DNA delivery combined with electroporation (EP) has been used successfully in the field of veterinary oncology, resulting in high rates of response after electrochemotherapy. Here, we evaluate the safety, immunogenicity, and protective efficacy of a novel linear SARS-CoV-2 DNA vaccine candidate delivered by intramuscular injection followed by electroporation (Vet-ePorator™) in ferrets. The linear SARS-CoV-2 DNA vaccine candidate did not cause unexpected side effects. Additionally, the vaccine elicited neutralizing antibodies and T cell responses on day 42 post-immunization using a low dose of the linear DNA construct in a prime-boost regimen. Most importantly, vaccination significantly reduced shedding of infectious SARS-CoV-2 through oral and nasal secretions in a ferret model.
Collapse
Affiliation(s)
- Mathias Martins
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Gabriela M do Nascimento
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | | | - Jessica C G Noll
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | | | | | - Bettina Wagner
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | | | | | | | | | - Brian Viscount
- Applied DNA Sciences, Inc., New York, NY, USA
- LineaRx, Inc. , New York, NY, USA
| | - James Hayward
- Applied DNA Sciences, Inc., New York, NY, USA
- LineaRx, Inc. , New York, NY, USA
| | - Clay Shorrock
- Applied DNA Sciences, Inc., New York, NY, USA
- LineaRx, Inc. , New York, NY, USA
| | - Luigi Aurisicchio
- Takis Biotech, Rome, Italy
- Evvivax Biotech, Rome, Italy
- Neomatrix Biotech, Rome, Italy
| | - Diego G Diel
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
| |
Collapse
|
188
|
Saviano A, Brigida M, Petruzziello C, Zanza C, Candelli M, Morabito Loprete MR, Saleem F, Ojetti V. Intestinal Damage, Inflammation and Microbiota Alteration during COVID-19 Infection. Biomedicines 2023; 11:biomedicines11041014. [PMID: 37189632 DOI: 10.3390/biomedicines11041014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Background: The virus SARS-CoV-2 is responsible for respiratory disorders due to the fact that it mainly infects the respiratory tract using the Angiotensin-converting enzyme 2 (ACE2) receptors. ACE2 receptors are also highly expressed on intestinal cells, representing an important site of entry for the virus in the gut. Literature studies underlined that the virus infects and replicates in the gut epithelial cells, causing gastrointestinal symptoms such as diarrhea, abdominal pain, nausea/vomiting and anorexia. Moreover, the SARS-CoV-2 virus settles into the bloodstream, hyperactivating the platelets and cytokine storms and causing gut–blood barrier damage with an alteration of the gut microbiota, intestinal cell injury, intestinal vessel thrombosis leading to malabsorption, malnutrition, an increasing disease severity and mortality with short and long-period sequelae. Conclusion: This review summarizes the data on how SARS-CoV-2 effects on the gastrointestinal systems, including the mechanisms of inflammation, relationship with the gut microbiota, endoscopic patterns, and the role of fecal calprotectin, confirming the importance of the digestive system in clinical practice for the diagnosis and follow-up of SARS-CoV-2 infection.
Collapse
|
189
|
Yue H, Nowak RP, Overwijn D, Payne NC, Fischinger S, Atyeo C, Lam EC, St. Denis K, Brais LK, Konishi Y, Sklavenitis-Pistofidis R, Baden LR, Nilles EJ, Karlson EW, Yu XG, Li JZ, Woolley AE, Ghobrial IM, Meyerhardt JA, Balazs AB, Alter G, Mazitschek R, Fischer ES. Diagnostic TR-FRET assays for detection of antibodies in patient samples. CELL REPORTS METHODS 2023; 3:100421. [PMID: 37056371 PMCID: PMC10088089 DOI: 10.1016/j.crmeth.2023.100421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/15/2022] [Accepted: 02/14/2023] [Indexed: 02/22/2023]
Abstract
Serological assays are important diagnostic tools for surveying exposure to the pathogen, monitoring immune response post vaccination, and managing spread of the infectious agent among the population. Current serological laboratory assays are often limited because they require the use of specialized laboratory technology and/or work with a limited number of sample types. Here, we evaluate an alternative by developing time-resolved Förster resonance energy transfer (TR-FRET) homogeneous assays that exhibited exceptional versatility, scalability, and sensitivity and outperformed or matched currently used strategies in terms of sensitivity, specificity, and precision. We validated the performance of the assays measuring total immunoglobulin G (IgG) levels; antibodies against severe acute respiratory syndrome coronavirus (SARS-CoV) or Middle Eastern respiratory syndrome (MERS)-CoV spike (S) protein; and SARS-CoV-2 S and nucleocapsid (N) proteins and applied it to several large sample sets and real-world applications. We further established a TR-FRET-based ACE2-S competition assay to assess the neutralization propensity of the antibodies. Overall, these TR-FRET-based serological assays can be rapidly extended to other antigens and are compatible with commonly used plate readers.
Collapse
Affiliation(s)
- Hong Yue
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Radosław P. Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Daan Overwijn
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - N. Connor Payne
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Center for Systems Biology, Massachusetts General Hospital (MGH), Boston, MA 02114, USA
| | - Stephanie Fischinger
- Ragon Institute of MGH, Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA 02139, USA
| | - Caroline Atyeo
- Ragon Institute of MGH, Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA 02139, USA
| | - Evan C. Lam
- Ragon Institute of MGH, Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA 02139, USA
| | - Kerri St. Denis
- Ragon Institute of MGH, Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA 02139, USA
| | - Lauren K. Brais
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Yoshinobu Konishi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Romanos Sklavenitis-Pistofidis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lindsey R. Baden
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Eric J. Nilles
- Department of Emergency Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | | | - Xu G. Yu
- Ragon Institute of MGH, Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA 02139, USA
| | - Jonathan Z. Li
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Ann E. Woolley
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Irene M. Ghobrial
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Alejandro B. Balazs
- Ragon Institute of MGH, Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA 02139, USA
| | - Galit Alter
- Ragon Institute of MGH, Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA 02139, USA
| | - Ralph Mazitschek
- Center for Systems Biology, Massachusetts General Hospital (MGH), Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eric S. Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
190
|
Sigamani A, Mayo KH, Miller MC, Chen-Walden H, Reddy S, Platt D. An Oral Galectin Inhibitor in COVID-19—A Phase II Randomized Controlled Trial. Vaccines (Basel) 2023; 11:vaccines11040731. [PMID: 37112643 PMCID: PMC10140888 DOI: 10.3390/vaccines11040731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/14/2023] [Accepted: 03/20/2023] [Indexed: 03/29/2023] Open
Abstract
Background: SARS-CoV-2 vaccines play an important role in reducing disease severity, hospitalization, and death, although they failed to prevent the transmission of SARS-CoV-2 variants. Therefore, an effective inhibitor of galectin-3 (Gal-3) could be used to treat and prevent the transmission of COVID-19. ProLectin-M (PL-M), a Gal-3 antagonist, was shown to interact with Gal-3 and thereby prevent cellular entry of SARS-CoV-2 in previous studies. Aim: The present study aimed to further evaluate the therapeutic effect of PL-M tablets in 34 subjects with COVID-19. Methods: The efficacy of PL-M was evaluated in a randomized, double-blind, placebo-controlled clinical study in patients with mild to moderately severe COVID-19. Primary endpoints included changes in the absolute RT-PCR Ct values of the nucleocapsid and open reading frame (ORF) genes from baseline to days 3 and 7. The incidence of adverse events, changes in blood biochemistry, inflammatory biomarkers, and levels of antibodies against COVID-19 were also evaluated as part of the safety evaluation. Results: PL-M treatment significantly (p = 0.001) increased RT-PCR cycle counts for N and ORF genes on days 3 (Ct values 32.09 ± 2.39 and 30.69 ± 3.38, respectively) and 7 (Ct values 34.91 ± 0.39 and 34.85 ± 0.61, respectively) compared to a placebo treatment. On day 3, 14 subjects in the PL-M group had cycle counts for the N gene above the cut-off value of 29 (target cycle count 29), whereas on day 7, all subjects had cycle counts above the cut-off value. Ct values in placebo subjects were consistently less than 29, and no placebo subjects were RT-PCR-negative until day 7. Most of the symptoms disappeared completely after receiving PL-M treatment for 7 days in more patients compared to the placebo group. Conclusion: PL-M is safe and effective for clinical use in reducing viral loads and promoting rapid viral clearance in COVID-19 patients by inhibiting SARS-CoV-2 entry into cells through the inhibition of Gal-3.
Collapse
Affiliation(s)
- Alben Sigamani
- Carmel Research Consultancy Pvt. Ltd., Bengaluru 560025, Karnataka, India
- Correspondence: ; Tel.: +9188-8443-1444
| | - Kevin H. Mayo
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church Street, Minneapolis, MN 55455, USA
| | - Michelle C. Miller
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church Street, Minneapolis, MN 55455, USA
| | - Hana Chen-Walden
- Pharmalectin India Pvt. Ltd., Rangareddy 500039, Telangana, India
| | - Surendar Reddy
- Department of Pulmonology, ESIC Medical College and Hospital, Sanath Nagar, Hyderabad 500038, Telangana, India
| | - David Platt
- Pharmalectin India Pvt. Ltd., Rangareddy 500039, Telangana, India
| |
Collapse
|
191
|
Talukder P, Saha A, Roy S, Ghosh G, Roy DD, Barua S. Drugs for COVID-19 Treatment: A New Challenge. Appl Biochem Biotechnol 2023; 195:3653-3670. [PMID: 36961509 PMCID: PMC10037400 DOI: 10.1007/s12010-023-04439-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2023] [Indexed: 03/25/2023]
Abstract
COVID-19 infection is a new disease and our knowledge is limited; day in and day out more and more interesting yet diverse observations are reported by the different research groups from different corners of the world. So, there is an urgent requirement of the invention of some effective and efficient drugs that can carry out the end of the deadly viral infection. Throughout the world, there have been many efforts carried out in different labs to invent such a drug and also identifying any pre-existing drugs which can carry out the killing of the virus. In this review, an effort has been made to understand the potential drugs which can be used against the SARS-CoV-2 viral infection. Again, the strategies on the current and the future drug discovery mechanisms against the SARS-CoV-2 are also mentioned. The different drugs made and the drugs re-used and also the drugs which are in the making process in different research laboratories across the world are also mentioned. To combat this unexpected crisis, we still need some more efforts from the different scientific communities around the world for finding a cure against this viral infection and this is needed to be done for the prevention of more loss of human life.
Collapse
Affiliation(s)
- Pratik Talukder
- Department of Biotechnology, University of Engineering and Management, Kolkata University Area, Plot, Street Number 03, Action Area III, B/5, Newtown, Kolkata, West Bengal, 700156, India.
| | - Arunima Saha
- Department of Biotechnology, University of Engineering and Management, Kolkata University Area, Plot, Street Number 03, Action Area III, B/5, Newtown, Kolkata, West Bengal, 700156, India
| | - Sohini Roy
- Department of Biotechnology, University of Engineering and Management, Kolkata University Area, Plot, Street Number 03, Action Area III, B/5, Newtown, Kolkata, West Bengal, 700156, India
| | - Gargi Ghosh
- Department of Biotechnology, University of Engineering and Management, Kolkata University Area, Plot, Street Number 03, Action Area III, B/5, Newtown, Kolkata, West Bengal, 700156, India
| | - Debshikha Dutta Roy
- Department of Biotechnology, University of Engineering and Management, Kolkata University Area, Plot, Street Number 03, Action Area III, B/5, Newtown, Kolkata, West Bengal, 700156, India
| | - Snejuti Barua
- Department of Biotechnology, University of Engineering and Management, Kolkata University Area, Plot, Street Number 03, Action Area III, B/5, Newtown, Kolkata, West Bengal, 700156, India
| |
Collapse
|
192
|
Cheng Y, Zheng D, Zhang D, Guo D, Wang Y, Liu W, Liang L, Hu J, Luo T. Molecular recognition of SARS-CoV-2 spike protein with three essential partners: exploring possible immune escape mechanisms of viral mutants. J Mol Model 2023; 29:109. [PMID: 36964244 PMCID: PMC10038388 DOI: 10.1007/s00894-023-05509-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 03/10/2023] [Indexed: 03/26/2023]
Abstract
OBJECTIVE The COVID-19 epidemic is raging around the world, with the emergence of viral mutant strains such as Delta and Omicron, posing severe challenges to people's health and quality of life. A full understanding life cycle of the virus in host cells helps to reveal inactivation mechanism of antibody and provide inspiration for the development of a new-generation vaccines. METHODS In this work, molecular recognitions and conformational changes of SARS-CoV-2 spike protein mutants (i.e., Delta, Mu, and Omicron) and three essential partners (i.e., membrane receptor hACE2, protease TMPRSS2, and antibody C121) both were compared and analyzed using molecular simulations. RESULTS Water basin and binding free energy calculations both show that the three mutants possess higher affinity for hACE2 than WT, exhibiting stronger virus transmission. The descending order of cleavage ability by TMPRSS2 is Mu, Delta, Omicron, and WT, which is related to the new S1/S2 cutting site induced by transposition effect. The inefficient utilization of TMPRSS2 by Omicron is consistent with its primary entry into cells via the endosomal pathway. In addition, RBD-directed antibody C121 showed obvious resistance to Omicron, which may have originated from high fluctuation of approaching angles, high flexibility of I472-F490 loop, and reduced binding ability. CONCLUSIONS According to the overall characteristics of the three mutants, high infectivity, high immune escape, and low virulence may be the future evolutionary selection of SARS-CoV-2. In a word, this work not only proposes the possible resistance mechanism of SARS-CoV-2 mutants, but also provides theoretical guidance for the subsequent drug design against COVID-19 based on S protein structure.
Collapse
Affiliation(s)
- Yan Cheng
- Breast Disease Center, West China Hospital, Sichuan University, Cancer CenterChengdu, 610000, China
| | - Dan Zheng
- Breast Disease Center, West China Hospital, Sichuan University, Cancer CenterChengdu, 610000, China
| | - Derong Zhang
- School of Marxism, Chengdu Vocational & Technical College of Industry, Chengdu, China
| | - Du Guo
- Breast Disease Center, West China Hospital, Sichuan University, Cancer CenterChengdu, 610000, China
| | - Yueteng Wang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Wei Liu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Li Liang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Jianping Hu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Ting Luo
- Breast Disease Center, West China Hospital, Sichuan University, Cancer CenterChengdu, 610000, China.
| |
Collapse
|
193
|
Wang X, Guan F, Miller H, Byazrova MG, Cndotti F, Benlagha K, Camara NOS, Lei J, Filatov A, Liu C. The role of dendritic cells in COVID-19 infection. Emerg Microbes Infect 2023; 12:2195019. [PMID: 36946172 PMCID: PMC10171120 DOI: 10.1080/22221751.2023.2195019] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
The persistent pandemic of coronavirus disease in 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) currently poses a major infectious threat to public health around the world. COVID-19 is an infectious disease characterized by strong induction of inflammatory cytokines, progressive lung inflammation, and potential multiple organ dysfunction. SARS-CoV-2 infection is closely related to the innate immune system and adaptive immune system. Dendritic cells (DCs), as a "bridge" connecting innate immunity and adaptive immunity, play many important roles in viral diseases. In this review, we will pay special attention to the possible mechanism of dendritic cells in human viral transmission and clinical progression of diseases, as well as the reduction and dysfunction of DCs in severe SARS-CoV-2 infection, so as to understand the mechanism and immunological characteristics of SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Xuying Wang
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science Technology, Wuhan, Hubei, China
- Tongji Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Fei Guan
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science Technology, Wuhan, Hubei, China
| | - Heather Miller
- Cytek Biosciences, R&D Clinical Reagents, Fremont, CA, United States
| | - Maria G Byazrova
- Laboratory of Immunochemistry, National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, 115522, Moscow, Russia
| | - Fabio Cndotti
- Division of Immunology and Allergy, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Kamel Benlagha
- Institut de Recherche Saint-Louis, Université de Paris, Paris, France
| | - Niels Olsen Saraiva Camara
- Laboratory of Human Immunology, Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo - SP, Brazil
| | - Jiahui Lei
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science Technology, Wuhan, Hubei, China
| | - Alexander Filatov
- Laboratory of Immunochemistry, National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, 115522, Moscow, Russia
| | - Chaohong Liu
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science Technology, Wuhan, Hubei, China
| |
Collapse
|
194
|
Said KB, Alsolami A, Alshammari F, Alshammari KF, Alazmi M, Bhardwaj T, Najm MZ, Singh R, Kausar MA. Molecular evolutionary model based on phylogenetic and mutation analysis of SARS-CoV-2 spike protein sequences from Asian countries: A phylogenomic approach. INFORMATICS IN MEDICINE UNLOCKED 2023; 38:101221. [PMID: 36974160 PMCID: PMC10030443 DOI: 10.1016/j.imu.2023.101221] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 03/24/2023] Open
Abstract
The lethal pathogenic severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection has caused the COVID-19 pandemic, posing serious risks to people. The clove-like spike (S) protein that distinguishes coronaviruses from other viruses is important for viral pathogenicity, evolution, and transmission. The investigation of the unique structural mutations of the SARS-CoV-2 spike protein among 34 Asian countries, as well as the resulting phylogenetic relationship, provided critical information in understanding the pathogenesis. This can be utilized for the discovery of possible treatments and vaccine development. The current study analyzed and depicted phylogenetic and evolutionary models useful for understanding SARS-CoV-2 human-human transmission dynamics in Asian regions with shared land borders. Further, integrated bioinformatics analysis was performed to predict the pathogenic potential and stability of 53 mutational positions among 34 coronavirus strains. Mutations at positions N969K, D614G and S884F have deleterious effects on protein function. These findings are crucial because the Asian mutations could potentially provide a vaccine candidate with co-protection against all SARS-CoV-2 strains. This region is vulnerable because of the high population density and the volume of domestic and international travel for business and tourism. These discoveries would also aid in the development of plans for governments and the general populace to implement all required biocontainment protocols common to all countries.
Collapse
Affiliation(s)
- Kamaleldin B Said
- Department of Pathology and Microbiology, College of Medicine, University of Ha'il, Ha'il, 55476, Saudi Arabia
| | - Ahmed Alsolami
- Department of Internal Medicine, College of Medicine, University of Ha'il, Ha'il, 55476, Saudi Arabia
| | - Fawaz Alshammari
- Department of Dermatology, College of Medicine, University of Ha'il, Ha'il, 55476, Saudi Arabia
| | - Khalid Farhan Alshammari
- Department of Internal Medicine, College of Medicine at University of Ha'il, Ha'il, 2440, Saudi Arabia
| | - Meshari Alazmi
- Department of Information and Computer Science, College of Computer Science and Engineering, University of Ha'il, Ha'il, 81481, Saudi Arabia
| | - Tulika Bhardwaj
- Department of Agriculture, Food and Nutritional Sciences, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | | | - Rajeev Singh
- Department of Environmental Science, Jamia Millia Islamia (Central University), New Delhi, 110025, India
| | - Mohd Adnan Kausar
- Department of Biochemistry, College of Medicine, University of Ha'il, Ha'il, 2440, Saudi Arabia
| |
Collapse
|
195
|
Sarkar P, Banerjee S, Saha SA, Mitra P, Sarkar S. Genome surveillance of SARS-CoV-2 variants and their role in pathogenesis focusing on second wave of COVID-19 in India. Sci Rep 2023; 13:4692. [PMID: 36949118 PMCID: PMC10031706 DOI: 10.1038/s41598-023-30815-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/01/2023] [Indexed: 03/24/2023] Open
Abstract
India had witnessed unprecedented surge in SARS-CoV-2 infections and its dire consequences during the second wave of COVID-19, but the detailed report of the epidemiological based spatiotemporal incidences of the disease is missing. In the manuscript, we have applied various statistical approaches (correlation, hierarchical clustering) to decipher the pattern of pathogenesis of the circulating VoCs responsible for surge in the incidences. B.1.617.1 (Kappa) was the predominant VoC during the early phase of the second wave, whereas, Delta (B.1.617.2) or Delta-like (AY.x) VoC constitutes majority ([Formula: see text]%) of the cases during the peak of the second wave. The correlation plot of Delta/Delta-like lineage demonstrates inverse correlation with other lineages including B.1.617.1, B.1.1.7, B.1, B.1.36.29 and B.1.36. The spatiotemporal analysis shows that most of the Indian states were affected during the peak of the second wave due to the Delta surge, and fall under the same cluster. The second cluster populated mostly by north-eastern states and the islands of India were minimally affected. The presence of signature mutations (T478K, D950N, E156G) along with L452K, D614G and P681R within the spike protein of Delta or Delta-like might cause elevation in the host cell attachment, increased transmission and altered antigenicity which in due course of time has replaced the other circulating variants.The timely assessment of new VoCs including Delta-like will provide a rationale for updating the diagnostic, vaccine development by medical industries and decision making by various agencies including government, educational institutions, and corporate industries.
Collapse
Affiliation(s)
- Poulomi Sarkar
- CSIR-Indian Institute of Chemical Biology (IICB), Calcutta, WB, 700032, India
- IICB-Translational Research Unit of Excellence, Cancer Biology and Inflammatory Disorder, Salt Lake, WB, 700091, India
| | - Sarthak Banerjee
- CSIR-Indian Institute of Chemical Biology (IICB), Calcutta, WB, 700032, India
- IICB-Translational Research Unit of Excellence, Cancer Biology and Inflammatory Disorder, Salt Lake, WB, 700091, India
| | - Sarbar Ali Saha
- CSIR-Indian Institute of Chemical Biology (IICB), Calcutta, WB, 700032, India
- IICB-Translational Research Unit of Excellence, Cancer Biology and Inflammatory Disorder, Salt Lake, WB, 700091, India
| | - Pralay Mitra
- Indian Institute of Technology (IIT) Kharagpur, Computer Science and Engineering, Kharagpur, WB, 721302, India
| | - Siddik Sarkar
- CSIR-Indian Institute of Chemical Biology (IICB), Calcutta, WB, 700032, India.
- IICB-Translational Research Unit of Excellence, Cancer Biology and Inflammatory Disorder, Salt Lake, WB, 700091, India.
| |
Collapse
|
196
|
Zhao Y, Wang CL, Gao ZY, Qiao HX, Wang WJ, Liu XY, Chuai X. Ferrets: A powerful model of SARS-CoV-2. Zool Res 2023; 44:323-330. [PMID: 36799224 PMCID: PMC10083223 DOI: 10.24272/j.issn.2095-8137.2022.351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/16/2023] [Indexed: 02/18/2023] Open
Abstract
The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in recent years not only caused a global pandemic but resulted in enormous social, economic, and health burdens worldwide. Despite considerable efforts to combat coronavirus disease 2019 (COVID-19), various SARS-CoV-2 variants have emerged, and their underlying mechanisms of pathogenicity remain largely unknown. Furthermore, effective therapeutic drugs are still under development. Thus, an ideal animal model is crucial for studying the pathogenesis of COVID-19 and for the preclinical evaluation of vaccines and antivirals against SARS-CoV-2 and variant infections. Currently, several animal models, including mice, hamsters, ferrets, and non-human primates (NHPs), have been established to study COVID-19. Among them, ferrets are naturally susceptible to SARS-CoV-2 infection and are considered suitable for COVID-19 study. Here, we summarize recent developments and application of SARS-CoV-2 ferret models in studies on pathogenesis, therapeutic agents, and vaccines, and provide a perspective on the role of these models in preventing COVID-19 spread.
Collapse
Affiliation(s)
- Yan Zhao
- Department of Pathogenic Biology, Hebei Medical University, Shijiazhuang, Hebei 050017, China
- Institute of Medicine and Healthy of Hebei Medical University, Shijiazhuang, Hebei 050017, China
| | - Chang-Le Wang
- Department of Pathogenic Biology, Hebei Medical University, Shijiazhuang, Hebei 050017, China
| | - Zhi-Yun Gao
- Department of Pathogenic Biology, Hebei Medical University, Shijiazhuang, Hebei 050017, China
- Institute of Medicine and Healthy of Hebei Medical University, Shijiazhuang, Hebei 050017, China
| | - Hong-Xiu Qiao
- Department of Pathogenic Biology, Hebei Medical University, Shijiazhuang, Hebei 050017, China
- Institute of Medicine and Healthy of Hebei Medical University, Shijiazhuang, Hebei 050017, China
| | - Wei-Jie Wang
- Department of Pathogenic Biology, Hebei Medical University, Shijiazhuang, Hebei 050017, China
- Institute of Medicine and Healthy of Hebei Medical University, Shijiazhuang, Hebei 050017, China
| | - Xin-Yan Liu
- Department of Oncology, Hebei Provincial Thoracic Hospital, Shijiazhuang, Hebei 050010, China
| | - Xia Chuai
- Department of Pathogenic Biology, Hebei Medical University, Shijiazhuang, Hebei 050017, China
- Institute of Medicine and Healthy of Hebei Medical University, Shijiazhuang, Hebei 050017, China. E-mail:
| |
Collapse
|
197
|
Zehr JD, Kosakovsky Pond SL, Millet JK, Olarte-Castillo XA, Lucaci AG, Shank SD, Ceres KM, Choi A, Whittaker GR, Goodman LB, Stanhope MJ. Natural selection differences detected in key protein domains between non-pathogenic and pathogenic feline coronavirus phenotypes. Virus Evol 2023; 9:vead019. [PMID: 37038392 PMCID: PMC10082545 DOI: 10.1093/ve/vead019] [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: 01/09/2023] [Revised: 02/14/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
Feline coronaviruses (FCoVs) commonly cause mild enteric infections in felines worldwide (termed feline enteric coronavirus [FECV]), with around 12 per cent developing into deadly feline infectious peritonitis (FIP; feline infectious peritonitis virus [FIPV]). Genomic differences between FECV and FIPV have been reported, yet the putative genotypic basis of the highly pathogenic phenotype remains unclear. Here, we used state-of-the-art molecular evolutionary genetic statistical techniques to identify and compare differences in natural selection pressure between FECV and FIPV sequences, as well as to identify FIPV- and FECV-specific signals of positive selection. We analyzed full-length FCoV protein coding genes thought to contain mutations associated with FIPV (Spike, ORF3abc, and ORF7ab). We identified two sites exhibiting differences in natural selection pressure between FECV and FIPV: one within the S1/S2 furin cleavage site (FCS) and the other within the fusion domain of Spike. We also found fifteen sites subject to positive selection associated with FIPV within Spike, eleven of which have not previously been suggested as possibly relevant to FIP development. These sites fall within Spike protein subdomains that participate in host cell receptor interaction, immune evasion, tropism shifts, host cellular entry, and viral escape. There were fourteen sites (twelve novel sites) within Spike under positive selection associated with the FECV phenotype, almost exclusively within the S1/S2 FCS and adjacent to C domain, along with a signal of relaxed selection in FIPV relative to FECV, suggesting that furin cleavage functionality may not be needed for FIPV. Positive selection inferred in ORF7b was associated with the FECV phenotype and included twenty-four positively selected sites, while ORF7b had signals of relaxed selection in FIPV. We found evidence of positive selection in ORF3c in FCoV-wide analyses, but no specific association with the FIPV or FECV phenotype. We hypothesize that some combination of mutations in FECV may contribute to FIP development, and that it is unlikely to be one singular 'switch' mutational event. This work expands our understanding of the complexities of FIP development and provides insights into how evolutionary forces may alter pathogenesis in coronavirus genomes.
Collapse
Affiliation(s)
- Jordan D Zehr
- Department of Biology, Temple University, Institute for Genomics and Evolutionary Medicine, Philadelphia, PA 19122, USA
| | - Sergei L Kosakovsky Pond
- Department of Biology, Temple University, Institute for Genomics and Evolutionary Medicine, Philadelphia, PA 19122, USA
| | - Jean K Millet
- Université Paris-Saclay, INRAE, UVSQ, Virologie et Immunologie Moléculaires, Jouy-en-Josas 78352, France
| | - Ximena A Olarte-Castillo
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
- James A. Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Alexander G Lucaci
- Department of Biology, Temple University, Institute for Genomics and Evolutionary Medicine, Philadelphia, PA 19122, USA
| | - Stephen D Shank
- Department of Biology, Temple University, Institute for Genomics and Evolutionary Medicine, Philadelphia, PA 19122, USA
| | - Kristina M Ceres
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Annette Choi
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Gary R Whittaker
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Laura B Goodman
- James A. Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Michael J Stanhope
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|
198
|
Maya C. Using PyMOL to Understand Why COVID-19 Vaccines Save Lives. JOURNAL OF CHEMICAL EDUCATION 2023; 100:1351-1356. [PMID: 36920160 PMCID: PMC9999942 DOI: 10.1021/acs.jchemed.2c00779] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 02/15/2023] [Indexed: 06/18/2023]
Abstract
Chemistry and biochemistry instructors must help students to develop the ability to visualize and manipulate 3D biomolecular structures and critically analyze them and their relationship to their functions. To do this, representative systems must be strategically selected to stimulate students' motivation. Since the World Health Organization declared a global pandemic caused by a new beta-coronavirus, called SARS-CoV-2 in early 2020, huge efforts are being taken by researchers to learn in depth how this virus works and a lot of scientific results are continuously reported. Many of them focus on the structural features of the viral spike glycoprotein and their relation with the vaccine development. This paper presents a series of workouts that deep into the structural characteristics of the spike protein S SARS-CoV-2 virus and the structural features involved in its infection process, using free online resources such as the PDB and the computer program PyMOL. This type of activity is intended to engage structural biology students in examining these macromolecules and others to help establish procedures for controlling COVID-19 and other future infectious diseases. PyMOL session files and student activities are provided.
Collapse
|
199
|
Calvaresi V, Wrobel AG, Toporowska J, Hammerschmid D, Doores KJ, Bradshaw RT, Parsons RB, Benton DJ, Roustan C, Reading E, Malim MH, Gamblin SJ, Politis A. Structural dynamics in the evolution of SARS-CoV-2 spike glycoprotein. Nat Commun 2023; 14:1421. [PMID: 36918534 PMCID: PMC10013288 DOI: 10.1038/s41467-023-36745-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 02/15/2023] [Indexed: 03/15/2023] Open
Abstract
SARS-CoV-2 spike glycoprotein mediates receptor binding and subsequent membrane fusion. It exists in a range of conformations, including a closed state unable to bind the ACE2 receptor, and an open state that does so but displays more exposed antigenic surface. Spikes of variants of concern (VOCs) acquired amino acid changes linked to increased virulence and immune evasion. Here, using HDX-MS, we identified changes in spike dynamics that we associate with the transition from closed to open conformations, to ACE2 binding, and to specific mutations in VOCs. We show that the RBD-associated subdomain plays a role in spike opening, whereas the NTD acts as a hotspot of conformational divergence of VOC spikes driving immune evasion. Alpha, beta and delta spikes assume predominantly open conformations and ACE2 binding increases the dynamics of their core helices, priming spikes for fusion. Conversely, substitutions in omicron spike lead to predominantly closed conformations, presumably enabling it to escape antibodies. At the same time, its core helices show characteristics of being pre-primed for fusion even in the absence of ACE2. These data inform on SARS-CoV-2 evolution and omicron variant emergence.
Collapse
Affiliation(s)
- Valeria Calvaresi
- Department of Chemistry, King's College London, SE1 1DB, London, UK.
| | - Antoni G Wrobel
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, NW1 1AT, London, UK.
| | | | | | - Katie J Doores
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, SE1 9RT, London, UK
| | | | | | - Donald J Benton
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, NW1 1AT, London, UK
| | - Chloë Roustan
- Structural Biology Science Technology Platform, The Francis Crick Institute, NW1 1AT, London, UK
| | - Eamonn Reading
- Department of Chemistry, King's College London, SE1 1DB, London, UK
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, SE1 9RT, London, UK
| | - Steve J Gamblin
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, NW1 1AT, London, UK
| | - Argyris Politis
- Department of Chemistry, King's College London, SE1 1DB, London, UK.
- Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, M13 9PT, Manchester, UK.
- Manchester Institute of Biotechnology, The University of Manchester, M1 7DN, Manchester, UK.
| |
Collapse
|
200
|
Vidal LEL, Figueira-Mansur J, Jurgilas PB, Argondizzo APC, Pestana CP, Martins FO, da Silva Junior HC, Miguez M, Loureiro BO, Marques CDFS, Trinta KS, da Silva LBR, de Mello MB, da Silva ED, Bastos RC, Esteves G. Process development and characterization of recombinant nucleocapsid protein for its application on COVID-19 diagnosis. Protein Expr Purif 2023; 207:106263. [PMID: 36921810 PMCID: PMC10012136 DOI: 10.1016/j.pep.2023.106263] [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: 02/03/2023] [Accepted: 03/10/2023] [Indexed: 03/15/2023]
Abstract
COVID-19 pandemic was caused by the severe acute respiratory syndrome coronavirus 2 (Sars-CoV-2). The nucleocapsid (N) protein from Sars-CoV-2 is a highly immunogenic antigen and responsible for genome packing. Serological assays are important tools to detect previous exposure to SARS-CoV-2, complement epidemiological studies, vaccine evaluation and also in COVID-19 surveillance. SARS-CoV-2 N (r2N) protein was produced in Escherichia coli, characterized, and the immunological performance was evaluated by enzyme-linked immunosorbent assay (ELISA) and beads-based array immunoassay. r2N protein oligomers were evidenced when it is associated to nucleic acid. Benzonase treatment reduced host nucleic acid associated to r2N protein, but crosslinking assay still demonstrates the presence of higher-order oligomers. Nevertheless, after RNase treatment the higher-order oligomers reduced, and dimer form increased, suggesting RNA contributes to the oligomer formation. Structural analysis revealed nucleic acid did not interfere with the thermal stability of the recombinant protein. Interestingly, nucleic acid was able to prevent r2N protein aggregation even with increasing temperature while the protein benzonase treated begin aggregation process above 55 °C. In immunological characterization, ELISA performed with 233 serum samples presented a sensitivity of 97.44% (95% Confidence Interval, CI, 91.04%, 99.69%) and a specificity of 98.71% (95% CI, 95.42%, 99.84%) while beads-based array immunoassay carried out with 217 samples showed 100% sensitivity and 98.6% specificity. The results exhibited an excellent immunological performance of r2N protein in serologic assays showing that, even in presence of nucleic acid, it can be used as a component of an immunoassay for the sensitive and specific detection of SARS-CoV-2 antibodies.
Collapse
Affiliation(s)
- Luãnna Elisa Liebscher Vidal
- Macromolecules Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil.
| | - Janaina Figueira-Mansur
- Recombinant Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Patrícia Barbosa Jurgilas
- Macromolecules Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Ana Paula Correa Argondizzo
- Recombinant Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Cristiane Pinheiro Pestana
- Recombinant Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Fernanda Otaviano Martins
- Recombinant Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Haroldo Cid da Silva Junior
- Immunological Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Mariana Miguez
- Recombinant Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Bernardo Oliveira Loureiro
- Diagnostic Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Christiane de Fátima Silva Marques
- Diagnostic Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Karen Soares Trinta
- Diagnostic Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Leila Botelho Rodrigues da Silva
- Diagnostic Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Marcelle Bral de Mello
- Diagnostic Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Edimilson Domingos da Silva
- Diagnostic Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Renata Chagas Bastos
- Macromolecules Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Gabriela Esteves
- Recombinant Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| |
Collapse
|