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Hu L, Sun J, Wang Y, Tan D, Cao Z, Gao L, Guan Y, Jia X, Mao J. A Review of Inactivated COVID-19 Vaccine Development in China: Focusing on Safety and Efficacy in Special Populations. Vaccines (Basel) 2023; 11:1045. [PMID: 37376434 DOI: 10.3390/vaccines11061045] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/27/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been widespread globally, and vaccination is critical for preventing further spread or resurgence of the outbreak. Inactivated vaccines made from whole inactivated SARS-CoV-2 virus particles generated in Vero cells are currently the most widely used COVID-19 vaccines, with China being the largest producer of inactivated vaccines. As a result, the focus of this review is on inactivated vaccines, with a multidimensional analysis of the development process, platforms, safety, and efficacy in special populations. Overall, inactivated vaccines are a safe option, and we hope that the review will serve as a foundation for further development of COVID-19 vaccines, thus strengthening the defense against the pandemic caused by SARS-CoV-2.
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Affiliation(s)
- Lidan Hu
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310030, China
| | - Jingmiao Sun
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310030, China
| | - Yan Wang
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310030, China
| | - Danny Tan
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310030, China
| | - Zhongkai Cao
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310030, China
| | - Langping Gao
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310030, China
| | - Yuelin Guan
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310030, China
| | - Xiuwei Jia
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310030, China
| | - Jianhua Mao
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310030, China
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Zhang H, Liang B, Sang X, An J, Huang Z. Discovery of Potential Inhibitors of SARS-CoV-2 Main Protease by a Transfer Learning Method. Viruses 2023; 15:v15040891. [PMID: 37112871 PMCID: PMC10143255 DOI: 10.3390/v15040891] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 remains a global public health threat and has prompted the development of antiviral therapies. Artificial intelligence may be one of the strategies to facilitate drug development for emerging and re-emerging diseases. The main protease (Mpro) of SARS-CoV-2 is an attractive drug target due to its essential role in the virus life cycle and high conservation among SARS-CoVs. In this study, we used a data augmentation method to boost transfer learning model performance in screening for potential inhibitors of SARS-CoV-2 Mpro. This method appeared to outperform graph convolution neural network, random forest and Chemprop on an external test set. The fine-tuned model was used to screen for a natural compound library and a de novo generated compound library. By combination with other in silico analysis methods, a total of 27 compounds were selected for experimental validation of anti-Mpro activities. Among all the selected hits, two compounds (gyssypol acetic acid and hyperoside) displayed inhibitory effects against Mpro with IC50 values of 67.6 μM and 235.8 μM, respectively. The results obtained in this study may suggest an effective strategy of discovering potential therapeutic leads for SARS-CoV-2 and other coronaviruses.
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Dutta R, Makhaik S, Zhao P, Cruz KG, Park KW, Liu H, Andrew TL, Hardy JA, Thayumanavan S. Colorimetric Cotton Swab for Viral Protease Detection. Anal Chem 2022; 94:12699-12705. [PMID: 36054755 DOI: 10.1021/acs.analchem.2c02033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reporting the activity of a specific viral protease remains an acute need for rapid point-of-care detection strategies that can distinguish active infection from a resolved infection. In this work, we present a simple colorimetric approach for reporting the activity of a specific viral protease through direct color conversion on a cotton swab, which has the potential to be extended to detect the corresponding virus. We use SARS-CoV-2 viral protease as a proof-of-concept model system. We use 4-aminomalachite green (4-AMG) as the base chromophore structure to design a CoV2-AMG reporter, which is selective toward the SARS-CoV-2 Mpro but does not produce any observable color change in the presence of other viral proteases. The color change is observable by the naked eye, as well as smartphone imaging, which affords a lower limit of detection. The simplicity and generalizability of the method could be instrumental in combating future viral outbreaks.
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Mukherjee MD, Kumar A, Solanki PR, Verma D, Yadav AK, Chaudhary N, Kumar P. Recent Advances in Understanding SARS-CoV-2 Infection and Updates on
Potential Diagnostic and Therapeutics for COVID-19. CORONAVIRUSES 2022; 3. [DOI: 10.2174/2666796703666220302143102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/09/2021] [Accepted: 12/13/2021] [Indexed: 09/25/2023]
Abstract
Abstract:
A more focused approach is needed to understand the SARS-CoV-2 virulence, structure, and
genomics to devise more effective diagnostic and treatment interventions as this virus can evade the immune
attack and causes life-threatening complications such as cytokine storm. The spread of the virus is
still amplifying and causing thousands of new cases worldwide. It is essential to review current diagnostics
and treatment approaches to pave the way to correct or modify our current practices to make more
effective interventions against COVID-19. COVID-19 vaccine development has moved at a breakneck
pace since the outbreak began, utilizing practically all possible platforms or tactics to ensure the success
of vaccines. A total of 42 vaccine candidates have already entered clinical trials, including promising
results from numerous vaccine candidates in phase 1 or phase 2 trials. Further, many existing drugs are
being explored on broad-spectrum antiviral medications for their use in clinical recovery against COVID-
19. The present review attempts to re-examine the SARS-CoV-2 structure, its viral life cycle, clinical
symptoms and pathogenesis, mode of transmission, diagnostics, and treatment strategies that may be useful
for resorting to more effective approaches for controlling COVID-19. Various antiviral drugs and
vaccination strategies with their strengths and weaknesses are also discussed in the paper to augment our
understanding of COVID-19 management.
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Affiliation(s)
- Maumita D. Mukherjee
- Amity Institute of Applied Sciences, Amity University, Noida, Uttar Pradesh-201313, India
| | - Anil Kumar
- National Institute of Immunology, New Delhi-110067, India
| | - Pratima R. Solanki
- Nano-Bio Laboratory, Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi-110067, India
| | - Damini Verma
- Nano-Bio Laboratory, Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi-110067, India
- Amity Institute of Applied Sciences, Amity University, Noida, Uttar Pradesh-201313, India
| | - Amit K. Yadav
- Nano-Bio Laboratory, Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi-110067, India
| | - Navneet Chaudhary
- Department of Biotechnology,
Delhi Technological University, Delhi-110042, India
| | - Pramod Kumar
- Sri Aurobindo College, Delhi University, New Delhi-110017,
India
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5
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Fallahi MJ, Esmaeilzadeh Shahri N, Khodamoradi Z, Meymandi Nia M, Sehatpour F, Mahmoudi L. Case of possible encephalopathy following receiving the first dose of Iranian COVID‐19Vaccine; COVIran Barakat. Clin Case Rep 2022; 10:e05661. [PMID: 35425597 PMCID: PMC8989018 DOI: 10.1002/ccr3.5661] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/10/2022] [Accepted: 02/25/2022] [Indexed: 01/07/2023] Open
Abstract
We report a case of possible encephalopathy after receiving the first dose of Iran's COVIran Barekat vaccine. The patient had no history of neurological or mental illness. Clinical examinations and radiology reports were performed and differential diagnoses were analyzed by the treatment team. Finally, the possible association between vaccination and encephalopathy was concluded.
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Affiliation(s)
| | - Navid Esmaeilzadeh Shahri
- Department of Clinical Pharmacy School of Pharmacy Shiraz University of Medical Sciences Shiraz Iran
| | - Zohre Khodamoradi
- Department of internal medicine Shiraz University of Medical Sciences Shiraz Iran
| | | | - Faezeh Sehatpour
- Department of internal medicine Shiraz University of Medical Sciences Shiraz Iran
| | - Laleh Mahmoudi
- Department of Clinical Pharmacy School of Pharmacy Shiraz University of Medical Sciences Shiraz Iran
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Dokainish HM, Re S, Mori T, Kobayashi C, Jung J, Sugita Y. The inherent flexibility of receptor binding domains in SARS-CoV-2 spike protein. eLife 2022; 11:e75720. [PMID: 35323112 PMCID: PMC8963885 DOI: 10.7554/elife.75720] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 03/15/2022] [Indexed: 12/17/2022] Open
Abstract
Spike (S) protein is the primary antigenic target for neutralization and vaccine development for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It decorates the virus surface and undergoes large motions of its receptor binding domains (RBDs) to enter the host cell. Here, we observe Down, one-Up, one-Open, and two-Up-like structures in enhanced molecular dynamics simulations, and characterize the transition pathways via inter-domain interactions. Transient salt-bridges between RBDA and RBDC and the interaction with glycan at N343B support RBDA motions from Down to one-Up. Reduced interactions between RBDA and RBDB in one-Up induce RBDB motions toward two-Up. The simulations overall agree with cryo-electron microscopy structure distributions and FRET experiments and provide hidden functional structures, namely, intermediates along Down-to-one-Up transition with druggable cryptic pockets as well as one-Open with a maximum exposed RBD. The inherent flexibility of S-protein thus provides essential information for antiviral drug rational design or vaccine development.
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Grants
- FLAGSHIP 2020 project Ministry of Education, Culture, Sports, Science and Technology
- 19K06532 Ministry of Education, Culture, Sports, Science and Technology
- Dynamic Structural Biology/Glycolipidologue Initiative/Biology of Intracellular Environments RIKEN
- Priority Issue on Post-K computer Ministry of Education, Culture, Sports, Science and Technology
- Program for Promoting Researches on the Supercomputer Fugaku Ministry of Education, Culture, Sports, Science and Technology
- JPMXP1020200101 Ministry of Education, Culture, Sports, Science and Technology
- JPMXP1020200201 Ministry of Education, Culture, Sports, Science and Technology
- 19H05645 Ministry of Education, Culture, Sports, Science and Technology
- 21H05249 Ministry of Education, Culture, Sports, Science and Technology
- 20K15737 Ministry of Education, Culture, Sports, Science and Technology
- 19K12229 Ministry of Education, Culture, Sports, Science and Technology
- 21H05157 Ministry of Education, Culture, Sports, Science and Technology
- hp200135 HPCI System Research project
- hp200153 HPCI System Research project
- hp200028 HPCI System Research project
- hp210107 HPCI System Research project
- hp210177 HPCI System Research project
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Affiliation(s)
- Hisham M Dokainish
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering ResearchWakoJapan
| | - Suyong Re
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and NutritionOsakaJapan
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics ResearchKobeJapan
| | - Takaharu Mori
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering ResearchWakoJapan
| | - Chigusa Kobayashi
- Computational Biophysics Research Team, RIKEN Center for Computational ScienceKobeJapan
| | - Jaewoon Jung
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering ResearchWakoJapan
- Computational Biophysics Research Team, RIKEN Center for Computational ScienceKobeJapan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering ResearchWakoJapan
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics ResearchKobeJapan
- Computational Biophysics Research Team, RIKEN Center for Computational ScienceKobeJapan
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Yin J, Li C, Ye C, Ruan Z, Liang Y, Li Y, Wu J, Luo Z. Advances in the development of therapeutic strategies against COVID-19 and perspectives in the drug design for emerging SARS-CoV-2 variants. Comput Struct Biotechnol J 2022; 20:824-837. [PMID: 35126885 PMCID: PMC8802458 DOI: 10.1016/j.csbj.2022.01.026] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/18/2022] [Accepted: 01/27/2022] [Indexed: 12/15/2022] Open
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Hijikata A, Shionyu C, Nakae S, Shionyu M, Ota M, Kanaya S, Shirai T. Current status of structure-based drug repurposing against COVID-19 by targeting SARS-CoV-2 proteins. Biophys Physicobiol 2021; 18:226-240. [PMID: 34745807 PMCID: PMC8550875 DOI: 10.2142/biophysico.bppb-v18.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/30/2021] [Indexed: 01/31/2023] Open
Abstract
More than one and half years have passed, as of August 2021, since the COVID-19 caused by the novel coronavirus named SARS-CoV-2 emerged in 2019. While the recent success of vaccine developments likely reduces the severe cases, there is still a strong requirement of safety and effective therapeutic drugs for overcoming the unprecedented situation. Here we review the recent progress and the status of the drug discovery against COVID-19 with emphasizing a structure-based perspective. Structural data regarding the SARS-CoV-2 proteome has been rapidly accumulated in the Protein Data Bank, and up to 68% of the total amino acid residues encoded in the genome were covered by the structural data. Despite a global effort of in silico and in vitro screenings for drug repurposing, there is only a limited number of drugs had been successfully authorized by drug regulation organizations. Although many approved drugs and natural compounds, which exhibited antiviral activity in vitro, were considered potential drugs against COVID-19, a further multidisciplinary investigation is required for understanding the mechanisms underlying the antiviral effects of the drugs.
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Affiliation(s)
- Atsushi Hijikata
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan
| | - Clara Shionyu
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan
| | - Setsu Nakae
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan
| | - Masafumi Shionyu
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan
| | - Motonori Ota
- Department of Complex Systems Science, Graduate School of Informatics, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Shigehiko Kanaya
- Computational Biology Lab. Division of Information Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), Ikoma, Nara 630-0192, Japan
| | - Tsuyoshi Shirai
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan
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9
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Yaqinuddin A, Shafqat A, Kashir J, Alkattan K. Effect of SARS-CoV-2 Mutations on the Efficacy of Antibody Therapy and Response to Vaccines. Vaccines (Basel) 2021; 9:914. [PMID: 34452039 PMCID: PMC8402590 DOI: 10.3390/vaccines9080914] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/08/2021] [Accepted: 08/12/2021] [Indexed: 12/11/2022] Open
Abstract
SARS-CoV-2 causes severe acute respiratory syndrome, which has led to significant morbidity and mortality around the world. Since its emergence, extensive prophylactic and therapeutic countermeasures have been employed to successfully prevent the spread of COVID-19. Extensive work has been undertaken on using monoclonal antibody therapies, mass vaccination programs, and antiviral drugs to prevent and treat COVID-19. However, since antiviral drugs could take years to become widely available, immunotherapy and vaccines currently appear to be the most feasible option. In December 2020, the first vaccine against SARS-CoV-2 was approved by the World Health Organization (WHO) and, subsequently, many other vaccines were approved for use by different international regulators in different countries. Most monoclonal antibodies (mAbs) and vaccines target the SARS-CoV-2 surface spike (S) protein. Recently, mutant (or variant) SARS-CoV-2 strains with increased infectivity and virulence that evade protective host antibodies present either due to infection, antibody therapy, or vaccine administration have emerged. In this manuscript, we discuss the different monoclonal antibody and vaccine therapies available against COVID-19 and how the efficacy of these therapies is affected by the emergence of variants of SARS-CoV-2. We also discuss strategies that might help society cope with variants that could neutralize the effects of immunotherapy and escape the protective immunity conferred by vaccines.
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Affiliation(s)
- Ahmed Yaqinuddin
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (A.S.); (J.K.); (K.A.)
| | - Areez Shafqat
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (A.S.); (J.K.); (K.A.)
| | - Junaid Kashir
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (A.S.); (J.K.); (K.A.)
- Department of Comparative Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11533, Saudi Arabia
| | - Khaled Alkattan
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (A.S.); (J.K.); (K.A.)
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