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Agüero B, Berrios F, Pardo-Roa C, Ariyama N, Bennett B, Medina RA, Neira V. First detection of Omicron variant BA.4.1 lineage in dogs, Chile. Vet Q 2024; 44:1-10. [PMID: 38174799 PMCID: PMC10769545 DOI: 10.1080/01652176.2023.2298089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/16/2023] [Indexed: 01/05/2024] Open
Abstract
SARS-CoV-2's rapid global spread caused the declaration of COVID-19 as a pandemic in March 2020. Alongside humans, domestic dogs and cats are also susceptible to infection. However, limited reports on pet infections in Chile prompted a comprehensive study to address this knowledge gap. Between March 2021 and March 2023, the study assessed 65 pets (26 dogs and 39 cats) from 33 COVID-19+ households alongside 700 nasal swabs from animals in households with unknown COVID-19 status. Using RT-PCR, nasal, fecal, and environmental samples were analyzed for the virus. In COVID-19+ households, 6.06% tested positive for SARS-CoV-2, belonging to 3 dogs, indicating human-to-pet transmission. Pets from households with unknown COVID-19 status tested negative for the virus. We obtained 2 SARS-CoV-2 genomes from animals, that belonged to Omicron BA.4.1 variant, marking the first report of pets infected with this lineage globally. Phylogenetic analysis showed these sequences clustered with human sequences collected in Chile during the same period when the BA.4.1 variant was prevalent in the country. The prevalence of SARS-CoV-2 in Chilean pets was relatively low, likely due to the country's high human vaccination rate. Our study highlights the importance of upholding and strengthening human vaccination strategies to mitigate the risk of interspecies transmission. It underscores the critical role of the One Health approach in addressing emerging zoonotic diseases, calling for further research on infection dynamics and risk factors for a comprehensive understanding.
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Affiliation(s)
- B. Agüero
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Universidad de Chile, Santiago, Chile
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - F. Berrios
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - C. Pardo-Roa
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Child and Adolescent Health, School of Nursing, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - N. Ariyama
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Universidad de Chile, Santiago, Chile
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - B. Bennett
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - RA. Medina
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - V. Neira
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
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Sitjar J, Liao JD, Lee H, Tsai HP, Wang JR. Innovative and versatile surface-enhanced Raman spectroscopy-inspired approaches for viral detection leading to clinical applications: A review. Anal Chim Acta 2024; 1325:342917. [PMID: 39244310 DOI: 10.1016/j.aca.2024.342917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 09/09/2024]
Abstract
The evolution of analytical techniques has opened the possibilities of accurate analyte detection through a straightforward method and short acquisition time, leading towards their applicability to identify medical conditions. Surface-enhanced Raman spectroscopy (SERS) has long been proven effective for rapid detection and relies on SERS spectra that are unique to each specific analyte. However, the complexity of viruses poses challenges to SERS and hinders further progress in its practical applications. The principle of SERS revolves around the interaction among substrate, analyte, and Raman laser, but most studies only emphasize the substrate, especially label-free methods, and the synergy among these factors is often ignored. Therefore, issues related to reproducibility and consistency of results, which are crucial for medical diagnosis and are the main highlights of this review, can be understood and largely addressed when considering these interactions. Viruses are composed of multiple surface components and can be detected by label-free SERS, but the presence of non-target molecules in clinical samples interferes with the detection process. Appropriate spectral data processing workflow also plays an important role in the interpretation of results. Furthermore, integrating machine learning into data processing can account for changes brought about by the presence of non-target molecules when analyzing spectral features to accurately group the data, for example, whether the sample corresponds to a positive or negative patient, and whether a virus variant or multiple viruses are present in the sample. Subsequently, advances in interdisciplinary fields can bring SERS closer to practical applications.
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Affiliation(s)
- Jaya Sitjar
- Engineered Materials for Biomedical Applications Laboratory, Department of Materials Science and Engineering, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Jiunn-Der Liao
- Engineered Materials for Biomedical Applications Laboratory, Department of Materials Science and Engineering, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Han Lee
- Engineered Materials for Biomedical Applications Laboratory, Department of Materials Science and Engineering, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Huey-Pin Tsai
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 704, Taiwan; Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Jen-Ren Wang
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 704, Taiwan; Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan.
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3
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Jhanwar A, Sharma D, Das U. Unraveling the structural and functional dimensions of SARS-CoV2 proteins in the context of COVID-19 pathogenesis and therapeutics. Int J Biol Macromol 2024; 278:134850. [PMID: 39168210 DOI: 10.1016/j.ijbiomac.2024.134850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 08/14/2024] [Accepted: 08/16/2024] [Indexed: 08/23/2024]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) has emerged as the causative agent behind the global pandemic of Coronavirus Disease 2019 (COVID-19). As the scientific community strives to comprehend the intricate workings of this virus, a fundamental aspect lies in deciphering the myriad proteins it expresses. This knowledge is pivotal in unraveling the complexities of the viral machinery and devising targeted therapeutic interventions. The proteomic landscape of SARS-CoV2 encompasses structural, non-structural, and open-reading frame proteins, each playing crucial roles in viral replication, host interactions, and the pathogenesis of COVID-19. This comprehensive review aims to provide an updated and detailed examination of the structural and functional attributes of SARS-CoV2 proteins. By exploring the intricate molecular architecture, we have highlighted the significance of these proteins in viral biology. Insights into their roles and interplay contribute to a deeper understanding of the virus's mechanisms, thereby paving the way for the development of effective therapeutic strategies. As the global scientific community strives to combat the ongoing pandemic, this synthesis of knowledge on SARS-CoV2 proteins serves as a valuable resource, fostering informed approaches toward mitigating the impact of COVID-19 and advancing the frontier of antiviral research.
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Affiliation(s)
- Aniruddh Jhanwar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Dipika Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Uddipan Das
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
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4
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Ghaemi S, Abdoli A, Karimi H, Saadatpour F, Arefian E. The impact of host microRNAs on the development of conserved mutations of SARS-CoV-2. Sci Rep 2024; 14:22091. [PMID: 39333651 PMCID: PMC11437047 DOI: 10.1038/s41598-024-70974-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 08/22/2024] [Indexed: 09/29/2024] Open
Abstract
SARS-CoV-2, the virus responsible for the COVID-19 pandemic, has undergone various genetic alterations due to evolutionary pressures exerted by host cells, including intracellular antiviral mechanisms such as targeting by human microRNAs (miRNAs). This study investigates the impact of miRNAs hsa-miR-3132 and hsa-miR-4650 on the viral genome. Sequence alignment revealed conserved mutations in the binding sites of these miRNAs in adapted strains compared to the original Wuhan-Hu-1 strain, leading to their deletion. Despite modest expression of these miRNAs in SARS-CoV-2 target tissues, their efficacy against mutant strains is reduced due to the loss of binding sites. Structural analysis indicates that the mutant genome is more stable than the Wuhan-Hu-1 genome. Luciferase and virus titration assays demonstrate that hsa-miR-3132 and hsa-miR-4650 effectively target the Nsp3 gene in the Wuhan-Hu-1 strain but not in mutant strains lacking their binding sites. These findings suggest that the observed mutations help the virus evade selective pressure from human miRNAs, contributing to its adaptation.
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Affiliation(s)
- Shokoofeh Ghaemi
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Asghar Abdoli
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
- Amirabad Virology Laboratory, Vaccine Unit, Tehran, 1413693341, Iran
| | - Hesam Karimi
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Fatemeh Saadatpour
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Ehsan Arefian
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran.
- Stem Cells Technology and Tissue Regeneration Department, School of Biology, College of Science, University of Tehran, Tehran, Iran.
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Shrwani KJ, Mahallawi WH, Mohana AI, Algaissi A, Dhayhi N, Sharwani NJ, Gadour E, Aldossari SM, Asiri H, Kameli N, Asiri AY, Asiri AM, Sherwani AJ, Cunliffe N, Zhang Q. Mucosal immunity in upper and lower respiratory tract to MERS-CoV. Front Immunol 2024; 15:1358885. [PMID: 39281686 PMCID: PMC11392799 DOI: 10.3389/fimmu.2024.1358885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 07/15/2024] [Indexed: 09/18/2024] Open
Abstract
Introduction Middle East respiratory syndrome coronavirus (MERS-CoV) has emerged as a deadly pathogen with a mortality rate of up to 36.2%. MERS-CoV can cause severe respiratory tract disease and multiorgan failure. Therefore, therapeutic vaccines are urgently needed. This intensive review explores the human immune responses and their immunological mechanisms during MERS-CoV infection in the mucosa of the upper and lower respiratory tracts (URT and LRT, respectively). Objective The aim of this study is to provide a valuable, informative, and critical summary of the protective immune mechanisms against MERS-CoV infection in the URT/LRT for the purpose of preventing and controlling MERS-CoV disease and designing effective therapeutic vaccines. Methods In this review, we focus on the immune potential of the respiratory tract following MERS-CoV infection. We searched PubMed, Embase, Web of Science, Cochrane, Scopus, and Google Scholar using the following terms: "MERS-CoV", "B cells", "T cells", "cytokines", "chemokines", "cytotoxic", and "upper and lower respiratory tracts". Results We found and included 152 studies in this review. We report that the cellular innate immune response, including macrophages, dendritic cells, and natural killer cells, produces antiviral substances such as interferons and interleukins to prevent the virus from spreading. In the adaptive and humoral immune responses, CD4+ helper T cells, CD8+ cytotoxic T cells, B cells, and plasma cells protect against MERS-CoV infection in URT and LRT. Conclusion The human nasopharynx-associated lymphoid tissue (NALT) and bronchus-associated lymphoid tissue (BALT) could successfully limit the spread of several respiratory pathogens. However, in the case of MERS-CoV infection, limited research has been conducted in humans with regard to immunopathogenesis and mucosal immune responses due to the lack of relevant tissues. A better understanding of the immune mechanisms of the URT and LRT is vital for the design and development of effective MERS-CoV vaccines.
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Affiliation(s)
- Khalid J Shrwani
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Public Health Authority, Saudi Center for Disease Prevention and Control (SCDC), Jazan, Saudi Arabia
| | - Waleed H Mahallawi
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, Taibah University, Madinah, Saudi Arabia
| | - Abdulrhman I Mohana
- Department of Antimicrobial Resistance, Public Health Authority, Riyadh, Saudi Arabia
| | - Abdullah Algaissi
- Department of Medical Laboratory Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
- Emerging and Endemic Infectious Diseases Research Unit, Health Sciences Research Center, Jazan University, Jazan, Saudi Arabia
| | - Nabil Dhayhi
- Department of Pediatrics, King Fahad Central Hospital, Ministry of Health, Gizan, Saudi Arabia
| | - Nouf J Sharwani
- Department of Surgery, Mohammed bin Nasser Hospital, Ministry of Health, Gizan, Saudi Arabia
| | - Eyad Gadour
- Department of Gastroenterology and Hepatology, King Abdulaziz National Guard Hospital, Ahsa, Saudi Arabia
- Department of Medicine, Faculty of Medicine, Zamzam University College, Khartoum, Sudan
| | - Saeed M Aldossari
- Medical Laboratory Technology Department, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Hasan Asiri
- Medical Laboratory Department, Prince Mohammed bin Abdulaziz Hospital, Riyadh, Saudi Arabia
| | - Nader Kameli
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Ayad Y Asiri
- Intensive Care Unit Department, Al Inma Medical Group, Al Hayat National Hospital, Ministry of Health, Riyadh, Saudi Arabia
| | - Abdullah M Asiri
- Preventive Medicine Assistant Deputyship, Ministry of Health, Riyadh, Saudi Arabia
| | - Alaa J Sherwani
- Department of Pediatrics, Abu-Arish General Hospital, Ministry of Health, Gizan, Saudi Arabia
| | - Nigel Cunliffe
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Qibo Zhang
- Academic and Research Departments, Section of Immunology, School of Biosciences, University of Surrey, Surrey, United Kingdom
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Gaiya DD, Muhammad A, Musa JS, Auta R, Dadah AJ, Bello RO, Hassan M, Eke SS, Odihi RI, Sankey M. In silico analysis of balsaminol as anti-viral agents targeting SARS-CoV-2 main protease, spike receptor binding domain and papain-like protease receptors. In Silico Pharmacol 2024; 12:75. [PMID: 39155972 PMCID: PMC11329488 DOI: 10.1007/s40203-024-00241-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 07/13/2024] [Indexed: 08/20/2024] Open
Abstract
Plant-derived phytochemicals from medicinal plants are becoming increasingly attractive natural sources of antimicrobial and antiviral agents due to their therapeutic value, mechanism of action, level of toxicity and bioavailability. The continued emergence of more immune-evasive strains and the rate of resistance to current antiviral drugs have created a need to identify new antiviral agents against SARS-CoV-2. This study investigated the antiviral potential of balsaminol, a bioactive compound from Momordica balsamina, and its inhibitory activities against SARS-CoV-2 receptor proteins. In this study, three Food and Drug Administration (FDA) COVID-19 approved drugs namely; nirmatrelvir, ritonavir and remdesivir were used as positive control. Molecular docking was performed to determine the predominant binding mode (most negative Gibbs free energy of binding/ΔG) and inhibitory activity of balsaminol against SARS-CoV-2 receptor proteins. The pharmacokinetics, toxicity, physicochemical and drug-like properties of balsaminol were evaluated to determine its potential as an active oral drug candidate as well as its non-toxicity in humans. The results show that balsaminol E has the highest binding affinity to the SARS CoV-2 papain-like protease (7CMD) with a free binding energy of - 8.7 kcal/mol, followed by balsaminol A interacting with the spike receptor binding domain (6VW1) with - 8.5 kcal/mol and balsaminol C had a binding energy of - 8.1 kcal/mol with the main protease (6LU7) comparable to the standard drugs namely ritonavir, nirmatrelvir and remdesivir. However, the ADMET and drug-like profile of balsaminol F favours it as a better potential drug candidate and inhibitor of the docked SARS-CoV-2 receptor proteins. Further preclinical studies are therefore recommended. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-024-00241-0.
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Affiliation(s)
- Daniel Danladi Gaiya
- Biology Unit, Air Force Institute of Technology, Nigerian Air Force Base, P.M.B 2104, Kaduna, Nigeria
| | - Aliyu Muhammad
- Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, P.M.B. 1045, Samaru Zaria, Nigeria
| | - Joy Sim Musa
- Department of Chemistry, Faculty of Physical Sciences, Ahmadu Bello University, P.M.B. 1045, Samaru Zaria, Nigeria
| | - Richard Auta
- Department of Biochemistry, Faculty of Life Sciences, Kaduna State University, Tafawa Balewa Way, P.M.B. 2339, Kaduna, Nigeria
| | - Anthony John Dadah
- Department of Microbiology, Faculty of Life Sciences, Kaduna State University, Tafawa Balewa Way, P.M.B. 2339, Kaduna, Nigeria
| | | | - Madinat Hassan
- Biology Unit, Air Force Institute of Technology, Nigerian Air Force Base, P.M.B 2104, Kaduna, Nigeria
| | - Samuel Sunday Eke
- Biology Unit, Air Force Institute of Technology, Nigerian Air Force Base, P.M.B 2104, Kaduna, Nigeria
| | - Rebecca Imoo Odihi
- Department of Biological Science, Nigerian Defence Academy, Kaduna, Nigeria
| | - Musa Sankey
- Department of Chemistry, Kaduna State College of Education, Gidan Waya, Kaduna, Nigeria
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Chakravarty S, Varghese M, Fan S, Taylor RT, Chakravarti R, Chattopadhyay S. IRF3 inhibits inflammatory signaling pathways in macrophages to prevent viral pathogenesis. SCIENCE ADVANCES 2024; 10:eadn2858. [PMID: 39121222 PMCID: PMC11313863 DOI: 10.1126/sciadv.adn2858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 07/05/2024] [Indexed: 08/11/2024]
Abstract
Viral inflammation contributes to pathogenesis and mortality during respiratory virus infections. IRF3, a critical component of innate antiviral immune responses, interacts with pro-inflammatory transcription factor NF-κB, and inhibits its activity. This mechanism helps suppress inflammatory gene expression in virus-infected cells and mice. We evaluated the cells responsible for IRF3-mediated suppression of viral inflammation using newly engineered conditional Irf3Δ/Δ mice. Irf3Δ/Δ mice, upon respiratory virus infection, showed increased susceptibility and mortality. Irf3 deficiency caused enhanced inflammatory gene expression, lung inflammation, immunopathology, and damage, accompanied by increased infiltration of pro-inflammatory macrophages. Deletion of Irf3 in macrophages (Irf3MKO) displayed, similar to Irf3Δ/Δ mice, increased inflammatory responses, macrophage infiltration, lung damage, and lethality, indicating that IRF3 in these cells suppressed lung inflammation. RNA-seq analyses revealed enhanced NF-κB-dependent gene expression along with activation of inflammatory signaling pathways in infected Irf3MKO lungs. Targeted analyses revealed activated MAPK signaling in Irf3MKO lungs. Therefore, IRF3 inhibited inflammatory signaling pathways in macrophages to prevent viral inflammation and pathogenesis.
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Affiliation(s)
- Sukanya Chakravarty
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Science, Toledo, OH, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Merina Varghese
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Science, Toledo, OH, USA
| | - Shumin Fan
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Science, Toledo, OH, USA
| | - Roger Travis Taylor
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Science, Toledo, OH, USA
| | - Ritu Chakravarti
- Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Science, Toledo, OH, USA
| | - Saurabh Chattopadhyay
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Science, Toledo, OH, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine, Lexington, KY, USA
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Jung-Rodriguez E, Barbault F, Bignon E, Monari A. Molecular Bases and Specificity behind the Activation of the Immune System OAS/RNAse L Pathway by Viral RNA. Viruses 2024; 16:1246. [PMID: 39205220 PMCID: PMC11359028 DOI: 10.3390/v16081246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 07/31/2024] [Accepted: 08/01/2024] [Indexed: 09/04/2024] Open
Abstract
The first line of defense against invading pathogens usually relies on innate immune systems. In this context, the recognition of exogenous RNA structures is primordial to fight, notably, against RNA viruses. One of the most efficient immune response pathways is based on the sensing of RNA double helical motifs by the oligoadenylate synthase (OAS) proteins, which in turn triggers the activity of RNase L and, thus, cleaves cellular and viral RNA. In this contribution, by using long-range molecular dynamics simulations, complemented with enhanced sampling techniques, we elucidate the structural features leading to the activation of OAS by interaction with a model double-strand RNA oligomer mimicking a viral RNA. We characterize the allosteric regulation induced by the nucleic acid leading to the population of the active form of the protein. Furthermore, we also identify the free energy profile connected to the active vs. inactive conformational transitions in the presence and absence of RNA. Finally, the role of two RNA mutations, identified as able to downregulate OAS activation, in shaping the protein/nucleic acid interface and the conformational landscape of OAS is also analyzed.
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Affiliation(s)
- Emma Jung-Rodriguez
- Université Paris Cité and CNR, ITODYS, F-75006 Paris, France; (E.J.-R.); (F.B.)
| | - Florent Barbault
- Université Paris Cité and CNR, ITODYS, F-75006 Paris, France; (E.J.-R.); (F.B.)
| | - Emmanuelle Bignon
- Université de Lorraine and CNRS, LPCT UMR 7019, F-54000 Nancy, France;
| | - Antonio Monari
- Université Paris Cité and CNR, ITODYS, F-75006 Paris, France; (E.J.-R.); (F.B.)
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9
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Nguyen H, Nguyen HL, Li MS. Binding of SARS-CoV-2 Nonstructural Protein 1 to 40S Ribosome Inhibits mRNA Translation. J Phys Chem B 2024; 128:7033-7042. [PMID: 39007765 DOI: 10.1021/acs.jpcb.4c01391] [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: 07/16/2024]
Abstract
Experimental evidence has established that SARS-CoV-2 NSP1 acts as a factor that restricts cellular gene expression and impedes mRNA translation within the ribosome's 40S subunit. However, the precise molecular mechanisms underlying this phenomenon have remained elusive. To elucidate this issue, we employed a combination of all-atom steered molecular dynamics and coarse-grained alchemical simulations to explore the binding affinity of mRNA to the 40S ribosome, both in the presence and absence of SARS-CoV-2 NSP1. Our investigations revealed that the binding of SARS-CoV-2 NSP1 to the 40S ribosome leads to a significant enhancement in the binding affinity of mRNA. This observation, which aligns with experimental findings, strongly suggests that SARS-CoV-2 NSP1 has the capability to inhibit mRNA translation. Furthermore, we identified electrostatic interactions between mRNA and the 40S ribosome as the primary driving force behind mRNA translation. Notably, water molecules were found to play a pivotal role in stabilizing the mRNA-40S ribosome complex, underscoring their significance in this process. We successfully pinpointed the specific SARS-CoV-2 NSP1 residues that play a critical role in triggering the translation arrest.
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Affiliation(s)
- Hung Nguyen
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Hoang Linh Nguyen
- Institute of Fundamental and Applied Sciences, Duy Tan University, Ho Chi Minh City 700000, Vietnam
- Faculty of Environmental and Natural Sciences, Duy Tan University, Da Nang City 550000, Vietnam
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland
- Quang Trung Software City, Life Science Lab, Institute for Computational Science and Technology, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 729110, Vietnam
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10
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Nawaz T, Tajammal A, Qurashi AW, Nisa MU, Binjawhar DN, Iqbal M. Synthesis, antibacterial, antibiofilm, and docking studies of chalcones against multidrug resistance pathogens. Heliyon 2024; 10:e30618. [PMID: 39044977 PMCID: PMC11263648 DOI: 10.1016/j.heliyon.2024.e30618] [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: 12/01/2023] [Revised: 04/22/2024] [Accepted: 04/30/2024] [Indexed: 07/25/2024] Open
Abstract
The escalating threat of drug-resistant microbes underscores the urgent need for novel antimicrobial agents. In response, considerable research effort has been directed towards developing innovative frameworks and strategies to address this challenge. Chalcones, known for their broad-spectrum biological activities, have emerged as promising candidates for combating drug resistance. In this study, a series of 2'-Hydroxychalcones (5a, 5b, 5c, and 5d) with varying electron withdrawing and donating groups were synthesized via Claisen Schmidt condensation. FT-IR, 1H NMR, and 13C NMR analyses were employed to confirm the structure of the synthesized compounds. Subsequent evaluation of the synthesized compounds revealed their potential as antibacterial and antibiofilm agents. Notably, compounds 5a and 5d exhibited potent antibacterial activity against multidrug-resistant (MDR) bacteria E. coli, P. aeruginosa, K. pneumoniae, and S. aureus, surpassing the reference drug Ciprofloxacin (30 μg/mL) and other synthesized compounds. Compound 5d showed a notable 19.5 mm zone of inhibition against K. pneumoniae. Furthermore, 5a (at a concentration of 30 μg) and 5d (at a concentration of 50 μg) exhibited statistically significant (P > 0.05) biofilm inhibition efficacy compared to Ciprofloxacin (30 μg/mL). The synthesized chalcones 5a-5d were also docked via PachDock molecular docking software for Glucosamine-6-phosphate (GlcN-6-P) synthase inhibition and showed that ligand 5a exhibited outstanding results with score 4238 and ACE value -160.89 kcal/mol, consistent with the observed antibacterial activity. These findings underscore the potential of chalcones, particularly 5a and 5d, as promising candidates for the development of new antimicrobial agents targeting drug-resistant microbes and biofilm formation.
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Affiliation(s)
- Tariq Nawaz
- Department of Chemistry, Lahore Garrison University, Pakistan
| | - Affifa Tajammal
- Department of Chemistry, Lahore Garrison University, Pakistan
| | | | - Mehr-un Nisa
- Department of Chemistry, The University of Lahore, 1-km Defence Road, Lahore, Pakistan
| | - Dalal Nasser Binjawhar
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Munawar Iqbal
- School of Chemistry, University of the Punjab, Lahore 54590, Pakistan
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Abla N, Almond LM, Bonner JJ, Richardson N, Wells TNC, Möhrle JJ. PBPK-led assessment of antimalarial drugs as candidates for Covid-19: Simulating concentrations at the site of action to inform repurposing strategies. Clin Transl Sci 2024; 17:e13865. [PMID: 39020517 PMCID: PMC11254780 DOI: 10.1111/cts.13865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 07/19/2024] Open
Abstract
The urgent need for safe, efficacious, and accessible drug treatments to treat coronavirus disease 2019 (COVID-19) prompted a global effort to evaluate drug repurposing opportunities. Pyronaridine and amodiaquine are both components of approved antimalarials with in vitro activity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In vitro activity does not always translate to clinical efficacy across a therapeutic dose range. This study applied available, verified, physiologically based pharmacokinetic (PBPK) models for pyronaridine, amodiaquine, and its active metabolite N-desethylamodiaquine (DEAQ) to predict drug concentrations in lung tissue relative to plasma or blood in the default healthy virtual population. Lung exposures were compared to published data across the reported range of in vitro EC50 values against SARS-CoV-2. In the multicompartment permeability-limited PBPK model, the predicted total Cmax in lung mass for pyronaridine was 34.2 μM on Day 3, 30.5-fold greater than in blood (1.12 μM) and for amodiaquine was 0.530 μM, 8.83-fold greater than in plasma (0.060 μM). In the perfusion-limited PBPK model, the DEAQ predicted total Cmax on Day 3 in lung mass (30.2 μM) was 21.4-fold greater than for plasma (1.41 μM). Based on the available in vitro data, predicted drug concentrations in lung tissue for pyronaridine and DEAQ, but not amodiaquine, appeared sufficient to inhibit SARS-CoV-2 replication. Simulations indicated standard dosing regimens of pyronaridine-artesunate and artesunate-amodiaquine have potential to treat COVID-19. These findings informed repurposing strategies to select the most relevant compounds for clinical investigation in COVID-19. Clinical data for model verification may become available from ongoing clinical studies.
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Affiliation(s)
- Nada Abla
- MMV Medicines for Malaria VentureGenevaSwitzerland
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12
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Sulistyani LD, Julia V, Soeprapto A, Swari RP, Rosmanato F, Haryanto B, Cahyarini C, Panjaitan R, Maharani DA. The effects of mouth rinsing and gargling with mouthwash containing povidone-iodine and hydrogen peroxide on the cycle threshold value of Severe Acute Respiratory Syndrome Coronavirus 2: A randomized controlled trial of asymptomatic and mildly symptomatic patients. F1000Res 2024; 11:1238. [PMID: 38988895 PMCID: PMC11234079 DOI: 10.12688/f1000research.110843.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/23/2024] [Indexed: 07/12/2024] Open
Abstract
Background Coronavirus disease 2019 can spread rapidly. Surgery in the oral cavity poses a high risk of transmission of severe acute respiratory syndrome coronavirus 2. The American Dental Association and the Centers for Disease Control and Prevention recommend the use of mouthwash containing 1.5% hydrogen peroxide (H 2O 2) or 0.2% povidone iodine (PI) to reduce the viral load in the upper respiratory tract and decrease the risk of transmission. The aim of the present study was to analyze the effect of mouth rinsing and gargling with mouthwash containing 1% PI, 0.5% PI, 3% H 2O 2, or 1.5% H 2O 2 and water on the cycle threshold (CT) value obtained by real-time reverse transcription polymerase chain reaction (RT-PCR). Methods This study is a randomized single blind controlled clinical trial which has been registered in the International Standard Randomized Controlled Trial Number (ISRCTN) registry on the 3 rd February 2022 (Registration number: ISRCTN18356379). In total, 69 subjects recruited from Persahabatan General Hospital who met the inclusion criteria were randomly assigned to one of four treatment groups or the control group. The subjects were instructed to gargle with 15 mL of mouthwash for 30 s in the oral cavity followed by 30 s in the back of the throat, three times per day for 5 days. CT values were collected on postprocedural days 1, 3, and 5. Results The results of the Friedman test significantly differed among the groups (n=15). The CT values increased from baseline (day 0) to postprocedural days 1, 3, and 5. Conclusions Mouth rinsing and gargling with mouthwash containing 1% PI, 0.5% PI, 3% H 2O 2, or 1.5% H 2O 2 and water increased the CT value.
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Affiliation(s)
- Lilies Dwi Sulistyani
- Oral and Maxillofacial Surgery, Faculty of Dentistry, Universitas Indonesia, Central Jakarta, DKI Jakarta, 10430, Indonesia
| | - Vera Julia
- Oral and Maxillofacial Surgery, Faculty of Dentistry, Universitas Indonesia, Central Jakarta, DKI Jakarta, 10430, Indonesia
| | - Andrianto Soeprapto
- Oral and Maxillofacial Surgery, Faculty of Dentistry, Universitas Indonesia, Central Jakarta, DKI Jakarta, 10430, Indonesia
| | - Rumartha Putri Swari
- Oral and Maxillofacial Surgery, Faculty of Dentistry, Universitas Indonesia, Central Jakarta, DKI Jakarta, 10430, Indonesia
| | - Febriadi Rosmanato
- Oral and Maxillofacial Surgery, Faculty of Dentistry, Universitas Indonesia, Central Jakarta, DKI Jakarta, 10430, Indonesia
| | - Budi Haryanto
- Clinical Microbiology, Persahabatan Central General Hospital, East Jakarta, DKI Jakarta, 13230, Indonesia
| | - Cahyarini Cahyarini
- Clinical Microbiology, Persahabatan Central General Hospital, East Jakarta, DKI Jakarta, 13230, Indonesia
| | - Rinaldi Panjaitan
- Clinical Microbiology, Persahabatan Central General Hospital, East Jakarta, DKI Jakarta, 13230, Indonesia
| | - Diah Ayu Maharani
- Department of Preventive and Public Health Dentistry, Faculty of Dentistry, Universitas Indonesia, Central Jakarta, DKI Jakarta, 10430, Indonesia
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13
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Raheem MA, Rahim MA, Gul I, Reyad-Ul-Ferdous M, Zhang CY, Yu D, Pandey V, Du K, Wang R, Han S, Han Y, Qin P. COVID-19: Post infection implications in different age groups, mechanism, diagnosis, effective prevention, treatment, and recommendations. Life Sci 2024:122861. [PMID: 38925222 DOI: 10.1016/j.lfs.2024.122861] [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: 11/22/2023] [Revised: 05/28/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024]
Abstract
SARS-CoV-2 is a highly contagious pathogen that predominantly caused the COVID-19 pandemic. The persistent effects of COVID-19 are defined as an inflammatory or host response to the virus that begins four weeks after initial infection and persists for an undetermined length of time. Chronic effects are more harmful than acute ones thus, this review explored the long-term effects of the virus on various human organs, including the pulmonary, cardiovascular, and neurological, reproductive, gastrointestinal, musculoskeletal, endocrine, and lymphoid systems and found that SARS-CoV-2 adversely affects these organs of older adults. Regarding diagnosis, the RT-PCR is a gold standard method of diagnosing COVID-19; however, it requires specialized equipment and personnel for performing assays and a long time for results production. Therefore, to overcome these limitations, artificial intelligence employed in imaging and microfluidics technologies is the most promising in diagnosing COVID-19. Pharmacological and non-pharmacological strategies are the most effective treatment for reducing the persistent impacts of COVID-19 by providing immunity to post-COVID-19 patients by reducing cytokine release syndrome, improving the T cell response, and increasing the circulation of activated natural killer and CD8 T cells in blood and tissues, which ultimately reduces fever, nausea, fatigue, and muscle weakness and pain. Vaccines such as inactivated viral, live attenuated viral, protein subunit, viral vectored, mRNA, DNA, or nanoparticle vaccines significantly reduce the adverse long-term virus effects in post-COVID-19 patients; however, no vaccine was reported to provide lifetime protection against COVID-19; consequently, protective measures such as physical separation, mask use, and hand cleansing are promising strategies. This review provides a comprehensive knowledge of the persistent effects of COVID-19 on people of varying ages, as well as diagnosis, treatment, vaccination, and future preventative measures against the spread of SARS-CoV-2.
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Affiliation(s)
- Muhammad Akmal Raheem
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, PR China
| | - Muhammad Ajwad Rahim
- College of Animal Science and Technology, Ahnui Agricultural University, Hefei, PR China
| | - Ijaz Gul
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, PR China
| | - Md Reyad-Ul-Ferdous
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, PR China
| | - Can Yang Zhang
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, PR China
| | - Dongmei Yu
- School of Mechanical, Electrical & Information Engineering, Shandong University
| | - Vijay Pandey
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, PR China
| | - Ke Du
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
| | - Runming Wang
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, PR China
| | - Sanyang Han
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, PR China
| | - Yuxing Han
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, PR China
| | - Peiwu Qin
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, PR China.
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14
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Bailón-Cuenca JA, Cortés-Sarabia K, Legorreta-Soberanis J, Alvarado-Castro VM, Juárez-Baltazar U, Sánchez-Gervacio BM, Vences-Velázquez A, Leyva-Vázquez MA, Del Moral-Hernández O, Illades-Aguiar B. Detection of IgG antibodies against the receptor binding domain of the spike protein and nucleocapsid of SARS-CoV-2 at university students from Southern Mexico: a cross-sectional study. BMC Infect Dis 2024; 24:584. [PMID: 38867165 PMCID: PMC11170790 DOI: 10.1186/s12879-024-09435-5] [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: 12/04/2023] [Accepted: 05/27/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND Natural infection and vaccination against SARS-CoV-2 is associated with the development of immunity against the structural proteins of the virus. Specifically, the two most immunogenic are the S (spike) and N (nucleocapsid) proteins. Seroprevalence studies performed in university students provide information to estimate the number of infected patients (symptomatic or asymptomatic) and generate knowledge about the viral spread, vaccine efficacy, and epidemiological control. Which, the aim of this study was to evaluate IgG antibodies against the S and N proteins of SARS-CoV-2 at university students from Southern Mexico. METHODS A total of 1418 serum samples were collected from eighteen work centers of the Autonomous University of Guerrero. Antibodies were detected by Indirect ELISA using as antigen peptides derived from the S and N proteins. RESULTS We reported a total seroprevalence of 39.9% anti-S/N (positive to both antigens), 14.1% anti-S and 0.5% anti-N. The highest seroprevalence was reported in the work centers from Costa Grande, Acapulco and Centro. Seroprevalence was associated with age, COVID-19, contact with infected patients, and vaccination. CONCLUSION University students could play an essential role in disseminating SARS-CoV-2. We reported a seroprevalence of 54.5% against the S and N proteins, which could be due to the high population rate and cultural resistance to safety measures against COVID-19 in the different regions of the state.
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Affiliation(s)
- Jesús Adolfo Bailón-Cuenca
- Laboratorio de Inmunobiología y Diagnóstico Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo, Guerrero, México
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo, Guerrero, México
| | - Karen Cortés-Sarabia
- Laboratorio de Inmunobiología y Diagnóstico Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo, Guerrero, México
| | - José Legorreta-Soberanis
- Centro de Investigación de Enfermedades Tropicales, Universidad Autónoma de Guerrero, Acapulco, Guerrero, México
| | | | - Ulises Juárez-Baltazar
- Laboratorio de Inmunobiología y Diagnóstico Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo, Guerrero, México
| | | | - Amalia Vences-Velázquez
- Laboratorio de Inmunobiología y Diagnóstico Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo, Guerrero, México
| | - Marco Antonio Leyva-Vázquez
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo, Guerrero, México
| | - Oscar Del Moral-Hernández
- Laboratorio de Virología, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero. Chilpancingo de los Bravo, Guerrero, México.
| | - Berenice Illades-Aguiar
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo, Guerrero, México.
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15
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Carvajal JJ, García-Castillo V, Cuellar SV, Campillay-Véliz CP, Salazar-Ardiles C, Avellaneda AM, Muñoz CA, Retamal-Díaz A, Bueno SM, González PA, Kalergis AM, Lay MK. New insights into the pathogenesis of SARS-CoV-2 during and after the COVID-19 pandemic. Front Immunol 2024; 15:1363572. [PMID: 38911850 PMCID: PMC11190347 DOI: 10.3389/fimmu.2024.1363572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 04/24/2024] [Indexed: 06/25/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the respiratory distress condition known as COVID-19. This disease broadly affects several physiological systems, including the gastrointestinal, renal, and central nervous (CNS) systems, significantly influencing the patient's overall quality of life. Additionally, numerous risk factors have been suggested, including gender, body weight, age, metabolic status, renal health, preexisting cardiomyopathies, and inflammatory conditions. Despite advances in understanding the genome and pathophysiological ramifications of COVID-19, its precise origins remain elusive. SARS-CoV-2 interacts with a receptor-binding domain within angiotensin-converting enzyme 2 (ACE2). This receptor is expressed in various organs of different species, including humans, with different abundance. Although COVID-19 has multiorgan manifestations, the main pathologies occur in the lung, including pulmonary fibrosis, respiratory failure, pulmonary embolism, and secondary bacterial pneumonia. In the post-COVID-19 period, different sequelae may occur, which may have various causes, including the direct action of the virus, alteration of the immune response, and metabolic alterations during infection, among others. Recognizing the serious adverse health effects associated with COVID-19, it becomes imperative to comprehensively elucidate and discuss the existing evidence surrounding this viral infection, including those related to the pathophysiological effects of the disease and the subsequent consequences. This review aims to contribute to a comprehensive understanding of the impact of COVID-19 and its long-term effects on human health.
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Affiliation(s)
- Jonatan J. Carvajal
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
| | - Valeria García-Castillo
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
| | - Shelsy V. Cuellar
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
| | | | - Camila Salazar-Ardiles
- Center for Research in Physiology and Altitude Medicine (FIMEDALT), Biomedical Department, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
| | - Andrea M. Avellaneda
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
- Department of Basic Sciences, Faculty of Sciences, Universidad Santo Tomás, Antofagasta, Chile
| | - Christian A. Muñoz
- Research Center in Immunology and Biomedical Biotechnology of Antofagasta (CIIBBA), University of Antofagasta, Antofagasta, Chile
- Department of Medical Technology, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
- Millennium Institute on Immunology and Immunotherapy, Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, Department of Medical Technology, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
| | - Angello Retamal-Díaz
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
- Research Center in Immunology and Biomedical Biotechnology of Antofagasta (CIIBBA), University of Antofagasta, Antofagasta, Chile
- Millennium Institute on Immunology and Immunotherapy, Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, Department of Medical Technology, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
| | - Susan M. Bueno
- Millennium Institute on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pablo A. González
- Millennium Institute on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alexis M. Kalergis
- Millennium Institute on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Margarita K. Lay
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
- Research Center in Immunology and Biomedical Biotechnology of Antofagasta (CIIBBA), University of Antofagasta, Antofagasta, Chile
- Millennium Institute on Immunology and Immunotherapy, Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, Department of Medical Technology, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
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16
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Ali MA, Sheikh H, Yaseen M, Faruqe MO, Ullah I, Kumar N, Bhat MA, Mollah MNH. Exploring the Therapeutic Potential of Petiveria alliacea L. Phytochemicals: A Computational Study on Inhibiting SARS-CoV-2's Main Protease (Mpro). Molecules 2024; 29:2524. [PMID: 38893400 PMCID: PMC11173994 DOI: 10.3390/molecules29112524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 06/21/2024] Open
Abstract
The outbreak of SARS-CoV-2, also known as the COVID-19 pandemic, is still a critical risk factor for both human life and the global economy. Although, several promising therapies have been introduced in the literature to inhibit SARS-CoV-2, most of them are synthetic drugs that may have some adverse effects on the human body. Therefore, the main objective of this study was to carry out an in-silico investigation into the medicinal properties of Petiveria alliacea L. (P. alliacea L.)-mediated phytocompounds for the treatment of SARS-CoV-2 infections since phytochemicals have fewer adverse effects compared to synthetic drugs. To explore potential phytocompounds from P. alliacea L. as candidate drug molecules, we selected the infection-causing main protease (Mpro) of SARS-CoV-2 as the receptor protein. The molecular docking analysis of these receptor proteins with the different phytocompounds of P. alliacea L. was performed using AutoDock Vina. Then, we selected the three top-ranked phytocompounds (myricitrin, engeletin, and astilbin) as the candidate drug molecules based on their highest binding affinity scores of -8.9, -8.7 and -8.3 (Kcal/mol), respectively. Then, a 100 ns molecular dynamics (MD) simulation study was performed for their complexes with Mpro using YASARA software, computed RMSD, RMSF, PCA, DCCM, MM/PBSA, and free energy landscape (FEL), and found their almost stable binding performance. In addition, biological activity, ADME/T, DFT, and drug-likeness analyses exhibited the suitable pharmacokinetics properties of the selected phytocompounds. Therefore, the results of this study might be a useful resource for formulating a safe treatment plan for SARS-CoV-2 infections after experimental validation in wet-lab and clinical trials.
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Affiliation(s)
- Md. Ahad Ali
- Bioinformatics Laboratory, Department of Statistics, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh;
- Department of Chemistry, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Humaira Sheikh
- Department of Chemistry, Faculty of Science, Bangabandhu Sheikh Mujibur Rahman Science & Technology University, Gopalganj 8100, Bangladesh;
| | - Muhammad Yaseen
- Institute of Chemical Sciences, University of Swat, Main Campus, Charbagh 19130, Pakistan;
| | - Md Omar Faruqe
- Department of Computer Science and Engineering, Faculty of Engineering, University of Rajshahi, Rajshahi 6205, Bangladesh;
| | - Ihsan Ullah
- Institute of Chemical Sciences, University of Swat, Main Campus, Charbagh 19130, Pakistan;
| | - Neeraj Kumar
- Department of Pharmaceutical Chemistry, Bhupal Nobles’ College of Pharmacy, Udaipur 313001, Rajasthan, India;
| | - Mashooq Ahmad Bhat
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Md. Nurul Haque Mollah
- Bioinformatics Laboratory, Department of Statistics, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh;
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17
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Nazir MS, Ahmad M, Aslam S, Rafiq A, Al-Hussain SA, Zaki MEA. A Comprehensive Update of Anti-COVID-19 Activity of Heterocyclic Compounds. Drug Des Devel Ther 2024; 18:1547-1571. [PMID: 38737333 PMCID: PMC11088867 DOI: 10.2147/dddt.s450499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/24/2024] [Indexed: 05/14/2024] Open
Abstract
The Coronavirus disease 2019 (COVID-19) pandemic is one of the most considerable health problems across the world. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the major causative agent of COVID-19. The severe symptoms of this deadly disease include shortness of breath, fever, cough, loss of smell, and a broad spectrum of other health issues such as diarrhea, pneumonia, bronchitis, septic shock, and multiple organ failure. Currently, there are no medications available for coronavirus patients, except symptom-relieving drugs. Therefore, SARS-CoV-2 requires the development of effective drugs and specific treatments. Heterocycles are important constituents of more than 85% of the physiologically active pharmaceutical drugs on the market now. Several FDA-approved drugs have been reported including molnupiravir, remdesivir, ritonavir, oseltamivir, favipiravir, chloroquine, and hydroxychloroquine for the cure of COVID-19. In this study, we discuss potent anti-SARS-CoV-2 heterocyclic compounds that have been synthesized over the past few years. These compounds included; indole, piperidine, pyrazine, pyrimidine, pyrrole, piperazine, quinazoline, oxazole, quinoline, isoxazole, thiazole, quinoxaline, pyrazole, azafluorene, imidazole, thiadiazole, triazole, coumarin, chromene, and benzodioxole. Both in vitro and in silico studies were performed to determine the potential of these heterocyclic compounds in the fight against various SARS-CoV-2 proteins.
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Affiliation(s)
| | - Matloob Ahmad
- Department of Chemistry, Government College University, Faisalabad, Pakistan
| | - Sana Aslam
- Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Ayesha Rafiq
- Department of Chemistry, Government College University, Faisalabad, Pakistan
| | - Sami A Al-Hussain
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Magdi E A Zaki
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
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18
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Nagahawatta DP, Liyanage NM, Jayawardena TU, Jayawardhana HHACK, Jeong SH, Kwon HJ, Jeon YJ. Role of marine natural products in the development of antiviral agents against SARS-CoV-2: potential and prospects. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:280-297. [PMID: 38827130 PMCID: PMC11136918 DOI: 10.1007/s42995-023-00215-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 10/17/2023] [Indexed: 06/04/2024]
Abstract
A novel coronavirus, known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has surfaced and caused global concern owing to its ferocity. SARS-CoV-2 is the causative agent of coronavirus disease 2019; however, it was only discovered at the end of the year and was considered a pandemic by the World Health Organization. Therefore, the development of novel potent inhibitors against SARS-CoV-2 and future outbreaks is urgently required. Numerous naturally occurring bioactive substances have been studied in the clinical setting for diverse disorders. The intricate infection and replication mechanism of SARS-CoV-2 offers diverse therapeutic drug targets for developing antiviral medicines by employing natural products that are safer than synthetic compounds. Marine natural products (MNPs) have received increased attention in the development of novel drugs owing to their high diversity and availability. Therefore, this review article investigates the infection and replication mechanisms, including the function of the SARS-CoV-2 genome and structure. Furthermore, we highlighted anti-SARS-CoV-2 therapeutic intervention efforts utilizing MNPs and predicted SARS-CoV-2 inhibitor design. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00215-9.
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Affiliation(s)
- D. P. Nagahawatta
- Department of Marine Life Sciences, Jeju National University, Jeju, 690-756 Republic of Korea
| | - N. M. Liyanage
- Department of Marine Life Sciences, Jeju National University, Jeju, 690-756 Republic of Korea
| | - Thilina U. Jayawardena
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, QC G8Z 4M3 Canada
| | | | - Seong-Hun Jeong
- Functional Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Hyung-Jun Kwon
- Functional Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - You-Jin Jeon
- Department of Marine Life Sciences, Jeju National University, Jeju, 690-756 Republic of Korea
- Marine Science Institute, Jeju National University, Jeju, 63333 Republic of Korea
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19
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Vajdi M, Karimi A, Hassanizadeh S, Farhangi MA, Bagherniya M, Askari G, Roufogalis BD, Davies NM, Sahebkar A. Effect of polyphenols against complications of COVID-19: current evidence and potential efficacy. Pharmacol Rep 2024; 76:307-327. [PMID: 38498260 DOI: 10.1007/s43440-024-00585-6] [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: 09/23/2023] [Revised: 03/01/2024] [Accepted: 03/03/2024] [Indexed: 03/20/2024]
Abstract
The COVID-19 pandemic that started in 2019 and resulted in significant morbidity and mortality continues to be a significant global health challenge, characterized by inflammation, oxidative stress, and immune system dysfunction.. Developing therapies for preventing or treating COVID-19 remains an important goal for pharmacology and drug development research. Polyphenols are effective against various viral infections and can be extracted and isolated from plants without losing their therapeutic potential. Researchers have developed methods for separating and isolating polyphenols from complex matrices. Polyphenols are effective in treating common viral infections, including COVID-19, and can also boost immunity. Polyphenolic-based antiviral medications can mitigate SARS-CoV-2 enzymes vital to virus replication and infection. Individual polyphenolic triterpenoids, flavonoids, anthraquinonoids, and tannins may also inhibit the SARS-CoV-2 protease. Polyphenol pharmacophore structures identified to date can explain their action and lead to the design of novel anti-COVID-19 compounds. Polyphenol-containing mixtures offer the advantages of a well-recognized safety profile with few known severe side effects. However, studies to date are limited, and further animal studies and randomized controlled trials are needed in future studies. The purpose of this study was to review and present the latest findings on the therapeutic impact of plant-derived polyphenols on COVID-19 infection and its complications. Exploring alternative approaches to traditional therapies could aid in developing novel drugs and remedies against coronavirus infection.
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Affiliation(s)
- Mahdi Vajdi
- Department of Community Nutrition, School of Nutrition and Food Science, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Arash Karimi
- Traditional Medicine and Hydrotherapy Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Shirin Hassanizadeh
- Department of Community Nutrition, School of Nutrition and Food Science, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mahdieh Abbasalizad Farhangi
- Department of Community Nutrition, Faculty of Nutrition and Food Science, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Bagherniya
- Department of Community Nutrition, Food Security Research Center, School of Nutrition and Food Science, Isfahan University of Medical Sciences, Isfahan, Iran
- Anesthesia and Critical Care Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Gholamreza Askari
- Department of Community Nutrition, Food Security Research Center, School of Nutrition and Food Science, Isfahan University of Medical Sciences, Isfahan, Iran
- Anesthesia and Critical Care Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Basil D Roufogalis
- Discipline of Pharmacology, School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
- NICM Health Research Institute, Western Sydney University, Penrith, NSW, Australia
| | - Neal M Davies
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
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20
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Liu C, Xue RY, Li GC, Zhang Y, Wu WY, Liu JY, Feng R, Jin Z, Deng Y, Jin ZL, Cheng H, Mao L, Zou QM, Li HB. pGM-CSF as an adjuvant in DNA vaccination against SARS-CoV-2. Int J Biol Macromol 2024; 264:130660. [PMID: 38460634 DOI: 10.1016/j.ijbiomac.2024.130660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/19/2024] [Accepted: 03/04/2024] [Indexed: 03/11/2024]
Abstract
The emergence of SARS-CoV-2 presents a significant global public health dilemma. Vaccination has long been recognized as the most effective means of preventing the spread of infectious diseases. DNA vaccines have attracted attention due to their safety profile, cost-effectiveness, and ease of production. This study aims to assess the efficacy of plasmid-encoding GM-CSF (pGM-CSF) as an adjuvant to augment the specific humoral and cellular immune response elicited by DNA vaccines based on the receptor-binding domain (RBD) antigen. Compared to the use of plasmid-encoded RBD (pRBD) alone, mice that were immunized with a combination of pRBD and pGM-CSF exhibited significantly elevated levels of RBD-specific antibody titers in serum, BALF, and nasal wash. Furthermore, these mice generated more potent neutralization antibodies against both the wild-type and Omicron pseudovirus, as well as the ancestral virus. In addition, pGM-CSF enhanced pRBD-induced CD4+ and CD8+ T cell responses and promoted central memory T cells storage in the spleen. At the same time, tissue-resident memory T (Trm) cells in the lung also increased significantly, and higher levels of specific responses were maintained 60 days post the final immunization. pGM-CSF may play an adjuvant role by promoting antigen expression, immune cells recruitment and GC B cell responses. In conclusion, pGM-CSF may be an effective adjuvant candidate for the DNA vaccines against SARS-CoV-2.
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Affiliation(s)
- Chang Liu
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University (Army Medical University), Chongqing 400038, PR China; Department of Pharmacy, Chinese People's Liberation Army Unit 32265, Guangzhou 510310, PR China
| | - Ruo-Yi Xue
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University (Army Medical University), Chongqing 400038, PR China
| | - Guo-Cheng Li
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University (Army Medical University), Chongqing 400038, PR China
| | - Yi Zhang
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University (Army Medical University), Chongqing 400038, PR China
| | - Wei-Yi Wu
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University (Army Medical University), Chongqing 400038, PR China
| | - Jing-Yi Liu
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University (Army Medical University), Chongqing 400038, PR China
| | - Rang Feng
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University (Army Medical University), Chongqing 400038, PR China
| | - Zhe Jin
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University (Army Medical University), Chongqing 400038, PR China
| | - Yan Deng
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University (Army Medical University), Chongqing 400038, PR China
| | - Zi-Li Jin
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University (Army Medical University), Chongqing 400038, PR China
| | - Hao Cheng
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University (Army Medical University), Chongqing 400038, PR China
| | - Ling Mao
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University (Army Medical University), Chongqing 400038, PR China
| | - Quan-Ming Zou
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University (Army Medical University), Chongqing 400038, PR China.
| | - Hai-Bo Li
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University (Army Medical University), Chongqing 400038, PR China.
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21
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Ogando-Rivas E, Castillo P, Yang C, Trivedi V, Zhang D, Pohl-Guimarães F, Liu R, Barpujari A, Candelario KM, Mendez-Gomez H, Sayour EJ, Mitchell DA. Expanded specific T cells to hypomutated regions of the SARS-CoV-2 using mRNA electroporated antigen-presenting cells. Mol Ther Methods Clin Dev 2024; 32:101192. [PMID: 38327807 PMCID: PMC10847775 DOI: 10.1016/j.omtm.2024.101192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 01/18/2024] [Indexed: 02/09/2024]
Abstract
The COVID-19 pandemic has caused about seven million deaths worldwide. Preventative vaccines have been developed including Spike gp mRNA-based vaccines that provide protection to immunocompetent patients. However, patients with primary immunodeficiencies, patients with cancer, or hematopoietic stem cell transplant recipients are not able to mount robust immune responses against current vaccine approaches. We propose to target structural SARS-CoV-2 antigens (i.e., Spike gp, Membrane, Nucleocapsid, and Envelope) using circulating human antigen-presenting cells electroporated with full length SARS-CoV-2 structural protein-encoding mRNAs to activate and expand specific T cells. Based on the Th1-type cytokine and cytolytic enzyme secretion upon antigen rechallenge, we were able to generate SARS-CoV-2 specific T cells in up to 70% of unexposed unvaccinated healthy donors (HDs) after 3 subsequent stimulations and in 100% of recovered patients (RPs) after 2 stimulations. By means of SARS-CoV-2 specific TCRβ repertoire analysis, T cells specific to Spike gp-derived hypomutated regions were identified in HDs and RPs despite viral genomic evolution. Hence, we demonstrated that SARS-CoV-2 mRNA-loaded antigen-presenting cells are effective activating and expanding COVID19-specific T cells. This approach represents an alternative to patients who are not able to mount adaptive immune responses to current COVID-19 vaccines with potential protection across new variants that have conserved genetic regions.
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Affiliation(s)
- Elizabeth Ogando-Rivas
- UF Brain Tumor Immunotherapy Program, Preston A. Wells Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, University of Florida, Gainesville, FL, USA
| | - Paul Castillo
- UF Division of Pediatric Hematology Oncology, Department of Pediatrics, University of Florida, Gainesville, FL, USA
| | - Changlin Yang
- UF Brain Tumor Immunotherapy Program, Preston A. Wells Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, University of Florida, Gainesville, FL, USA
| | - Vrunda Trivedi
- UF Brain Tumor Immunotherapy Program, Preston A. Wells Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, University of Florida, Gainesville, FL, USA
| | - Dingpeng Zhang
- UF Brain Tumor Immunotherapy Program, Preston A. Wells Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, University of Florida, Gainesville, FL, USA
| | - Fernanda Pohl-Guimarães
- UF Brain Tumor Immunotherapy Program, Preston A. Wells Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, University of Florida, Gainesville, FL, USA
| | - Ruixuan Liu
- UF Brain Tumor Immunotherapy Program, Preston A. Wells Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, University of Florida, Gainesville, FL, USA
| | - Arnav Barpujari
- UF Division of Pediatric Hematology Oncology, Department of Pediatrics, University of Florida, Gainesville, FL, USA
| | - Kate M. Candelario
- UF Brain Tumor Immunotherapy Program, Preston A. Wells Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, University of Florida, Gainesville, FL, USA
| | - Hector Mendez-Gomez
- UF Brain Tumor Immunotherapy Program, Preston A. Wells Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, University of Florida, Gainesville, FL, USA
| | - Elias J. Sayour
- UF Brain Tumor Immunotherapy Program, Preston A. Wells Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, University of Florida, Gainesville, FL, USA
- UF Division of Pediatric Hematology Oncology, Department of Pediatrics, University of Florida, Gainesville, FL, USA
| | - Duane A. Mitchell
- UF Brain Tumor Immunotherapy Program, Preston A. Wells Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, University of Florida, Gainesville, FL, USA
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22
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Feinstein P. Rapid Degradation of the Human ACE2 Receptor Upon Binding and Internalization of SARS-Cov-2-Spike-RBD Protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583884. [PMID: 38496410 PMCID: PMC10942428 DOI: 10.1101/2024.03.07.583884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
It is widely accepted that the SARS-CoV-2 betacoronavirus infects humans through binding the human Angiotensin Receptor 2 (ACE2) that lines the nasal cavity and lungs, followed by import into a cell utilizing the Transmembrane Protease, Serine 2 (TMPRSS2) cofactor. ACE2 binding is mediated by an approximately 200-residue portion of the SARS-CoV-2 extracellular spike protein, the receptor binding domain (RBD). Robust interactions are shown using a novel cell-based assay between an RBD membrane tethered-GFP fusion protein and the membrane bound ACE2-Cherry fusion protein. Several observations were not predicted including, quick and sustained interactions leading to internalization of RBD fusion protein into the ACE2 cells and rapid downregulation of the ACE2-Cherry fluorescence. Targeted mutation in the RBD disulfide Loop 4 led to a loss of internalization for several variants tested. However, a secreted RBD did not cause ACE2 downregulation of ACE2-Cherry fluorescence. Thus, the membrane associated form of RBD found on the viral coat may have long-term system wide consequences on ACE2 expressing cells.
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Affiliation(s)
- Paul Feinstein
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY 10065
- The Graduate Center Programs in Biochemistry, Biology and CUNY Neuroscience Collaborative, 365 5th Ave, New York, NY 10016
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23
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Hassan SS, Bhattacharya T, Nawn D, Jha I, Basu P, Redwan EM, Lundstrom K, Barh D, Andrade BS, Tambuwala MM, Aljabali AA, Hromić-Jahjefendić A, Baetas-da-Cruz W, Serrano-Aroca Á, Uversky VN. SARS-CoV-2 NSP14 governs mutational instability and assists in making new SARS-CoV-2 variants. Comput Biol Med 2024; 170:107899. [PMID: 38232455 DOI: 10.1016/j.compbiomed.2023.107899] [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: 09/26/2023] [Revised: 12/03/2023] [Accepted: 12/23/2023] [Indexed: 01/19/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the rapidly evolving RNA virus behind the COVID-19 pandemic, has spawned numerous variants since its 2019 emergence. The multifunctional Nonstructural protein 14 (NSP14) enzyme, possessing exonuclease and messenger RNA (mRNA) capping capabilities, serves as a key player. Notably, single and co-occurring mutations within NSP14 significantly influence replication fidelity and drive variant diversification. This study comprehensively examines 120 co-mutations, 68 unique mutations, and 160 conserved residues across NSP14 homologs, shedding light on their implications for phylogenetic patterns, pathogenicity, and residue interactions. Quantitative physicochemical analysis categorizes 3953 NSP14 variants into three clusters, revealing genetic diversity. This research underscoresthe dynamic nature of SARS-CoV-2 evolution, primarily governed by NSP14 mutations. Understanding these genetic dynamics provides valuable insights for therapeutic and vaccine development.
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Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur, 721140, West Bengal, India.
| | - Tanishta Bhattacharya
- Department of Biological Sciences, Indian Institute of Science Education and Research, Berhampur, IISER Berhampur Transit campus (Govt. ITI Building), Engg. School Junction, Berhampur, 760010, Odisha, India.
| | - Debaleena Nawn
- Indian Research Institute for Integrated Medicine (IRIIM), Unsani, Howrah, 711302, West Bengal, India.
| | - Ishana Jha
- Department of Bioinformatics, Pondicherry University, Chinna Kalapet, Kalapet, Puducherry 605014, India.
| | - Pallab Basu
- School of Physics, University of the Witwatersrand, Johannesburg, Braamfontein 2000, 721140, South Africa; Adjunct Faculty, Woxsen School of Sciences, Woxsen University, Telangana, 500 033, India.
| | - Elrashdy M Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications, New Borg EL-Arab, 21934, Alexandria, Egypt.
| | | | - Debmalya Barh
- Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, 721172, India; Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Brazil.
| | - Bruno Silva Andrade
- Laboratory of Bioinformatics and Computational Chemistry, Department of Biological Sciences, State University of Southwest of Bahia (UESB), Jequié 45083-900, Brazil.
| | - Murtaza M Tambuwala
- Lincoln Medical School, University of Lincoln, Brayford Pool Campus, Lincoln LN6 7TS, UK; College of Pharmacy, Ras Al Khaimah Medical and Health Sciences University, Ras Al Khaimah, United Arab Emirates.
| | - Alaa A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Yarmouk University, Irbid 21163, Jordan.
| | - Altijana Hromić-Jahjefendić
- Department of Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, International University of Sarajevo, Hrasnicka cesta 15, 71000 Sarajevo, Bosnia and Herzegovina.
| | - Wagner Baetas-da-Cruz
- Centre for Experimental Surgery, Translational Laboratory in Molecular Physiology, College of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia San Vicente Mártir, c/Guillem de Castro 94, 46001 Valencia, Spain.
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
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24
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Tramonti C, Graziani F, Pasqualone E, Ricci E, Moncini C, Lombardi B. Outpatient rehabilitation in post-acute COVID-19 patients: a combined progressive treatment protocol. Disabil Rehabil 2024:1-11. [PMID: 38407196 DOI: 10.1080/09638288.2024.2316797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 02/06/2024] [Indexed: 02/27/2024]
Abstract
PURPOSE to investigate the effectiveness of a 4-week combined progressive program on functional abilities, disability status and quality of life (QoL) in COVID-19 recovered patients. MATERIALS & METHODS 18 COVID-19 recovered patients performed a combined rehabilitation treatment accounting for 12 sessions, including both respiratory and motor training sessions. A careful monitoring of exercise intensity, duration and progression to tailor complexity evolution on patients' competencies was carried out. Patients were monitored with different functional scales and self-reported questionnaires before (T0) and after (T1) rehabilitation. RESULTS 6-Minutes Walk Test, Timed Up and Go Test and Short Physical Performance Battery significantly improved, while Physiological Cost Index presented a significant reduction after rehabilitation. Moreover, Barthel Index significantly improved and patients presented significantly increased upper and lower limbs strength at T1. Furthermore, mMRC Dyspnoea Scale presented a significant reduction after training. Finally, physical and psychological well-being scales improved according to Short-Form 36; while, self-reported questionnaires related to mood and depression showed no significant modification after rehabilitation. CONCLUSIONS results evidenced the efficacy of the combined progressive intervention in COVID-19 recovered patients. The specific customization on patients' needs and the careful exercise monitoring promoted improvements on functional abilities and disability status, with positive impact on QoL.
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Affiliation(s)
- Caterina Tramonti
- Department of Physical and Rehabilitation Medicine, Firenze, Italy
- Levante Ligure Rehabilitation Center, Fondazione Don C. Gnocchi Onlus, La Spezia, Italy
| | | | | | - Eleonora Ricci
- Department of Physical and Rehabilitation Medicine, Firenze, Italy
| | - Cristina Moncini
- Department of Physical and Rehabilitation Medicine, Firenze, Italy
| | - Bruna Lombardi
- Department of Physical and Rehabilitation Medicine, Firenze, Italy
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25
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Sulimov AV, Ilin IS, Tashchilova AS, Kondakova OA, Kutov DC, Sulimov VB. Docking and other computing tools in drug design against SARS-CoV-2. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2024; 35:91-136. [PMID: 38353209 DOI: 10.1080/1062936x.2024.2306336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/10/2024] [Indexed: 02/16/2024]
Abstract
The use of computer simulation methods has become an indispensable component in identifying drugs against the SARS-CoV-2 coronavirus. There is a huge body of literature on application of molecular modelling to predict inhibitors against target proteins of SARS-CoV-2. To keep our review clear and readable, we limited ourselves primarily to works that use computational methods to find inhibitors and test the predicted compounds experimentally either in target protein assays or in cell culture with live SARS-CoV-2. Some works containing results of experimental discovery of corresponding inhibitors without using computer modelling are included as examples of a success. Also, some computational works without experimental confirmations are also included if they attract our attention either by simulation methods or by databases used. This review collects studies that use various molecular modelling methods: docking, molecular dynamics, quantum mechanics, machine learning, and others. Most of these studies are based on docking, and other methods are used mainly for post-processing to select the best compounds among those found through docking. Simulation methods are presented concisely, information is also provided on databases of organic compounds that can be useful for virtual screening, and the review itself is structured in accordance with coronavirus target proteins.
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Affiliation(s)
- A V Sulimov
- Dimonta Ltd., Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - I S Ilin
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - A S Tashchilova
- Dimonta Ltd., Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - O A Kondakova
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - D C Kutov
- Dimonta Ltd., Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - V B Sulimov
- Dimonta Ltd., Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
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26
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Kumar SA, Selvaa Kumar C, Dsouza N. Bitter taste receptors establish a stable binding affinity with the SARS-CoV-2-spike 1 protein akin to ACE2. J Biomol Struct Dyn 2024:1-14. [PMID: 38189335 DOI: 10.1080/07391102.2023.2300128] [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: 03/18/2023] [Accepted: 12/23/2023] [Indexed: 01/09/2024]
Abstract
COVID-19 is caused by the highly contagious SARS-CoV-2 virus, which originated in Wuhan, China, resulting in the highest worldwide mortality rate. Gustatory dysfunction is common among individuals infected with the Wild-type Wuhan strain. However, there are no reported cases of gustatory dysfunction among patients infected with the mutant delta variant. The reason behind this remains elusive to date. This in-silico-based study aims to unravel this clinical factor by evaluating the overall binding affinity of predominant bitter taste receptors associated with gustatory function (T2R-4, 10, 14, 19, 31, 38, 43, and 46) with the Receptor Binding Domain (RBD) of spike 1 (S1) protein of Wuhan (Wild)/delta-SARS-CoV-2 (mut1-T478K; mut2-E484K) variants. Based on docking and MM/PBSA free binding energy scores, the Wild RBD showed a stronger interaction with T2R-46 compared to the ACE2 protein. However, both delta variant mutants (mut1 and mut2) could not establish a stronger binding affinity with bitter taste receptor proteins, except for T2R-43 against mut1. In conclusion, the delta variants could not establish a better binding affinity with bitter taste receptors, contradicting the Wild variant that determines the severity of gustatory dysfunction among patients exposed to the delta and Wild SARS-CoV-2 variants. The study's inference also proposes T2R-46 as an alternate binding receptor target for RBD-S1 of Wild SARS-CoV-2, augmenting its virulence in all functional organs with compromised α-gustducin interaction and bitter sensitization. This in-silico-based study needs further wet-lab-based validation for a better understanding of the role of T2R-46-based viral entry in the human host.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Senthil Arun Kumar
- Department of Biotechnology, Parul Institute of Technology, Parul University, Vadodara, Gujarat, India
| | - C Selvaa Kumar
- School of Biotechnology and Bioinformatics, D. Y. Patil Deemed to Be University, Sector-15, CBD Belapur, Navi Mumbai, India
| | - Norine Dsouza
- Department of Biotechnology, St. Xavier's College, Mumbai, India
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27
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Najimi N, Kadi C, Elmtili N, Seghrouchni F, Bakri Y. Unravelling humoral immunity in SARS-CoV-2: Insights from infection and vaccination. Hum Antibodies 2024; 32:85-106. [PMID: 38758995 DOI: 10.3233/hab-230017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2024]
Abstract
Following infection and vaccination against SARS-CoV-2, humoral components of the adaptive immune system play a key role in protecting the host. Specifically, B cells generate high-affinity antibodies against various antigens of the virus. In this review, we discuss the mechanisms of immunity initiation through both natural infection and vaccination, shedding light on the activation of B cell subsets in response to SARS-CoV-2 infection and vaccination. The innate immune system serves as the initial line of primary and nonspecific defence against viruses. However, within several days following infection or a vaccine dose, a virus-specific immune response is initiated, primarily by B cells that produce antibodies. These antibodies contribute to the resolution of the disease. Subsequently, these B cells transition into memory B cells, which play a crucial role in providing long-term immunity against the virus. CD4+ T helper cells initiate a cascade, leading to B cell somatic hypermutation, germinal center memory B cells, and the production of neutralizing antibodies. B-cell dysfunction can worsen disease severity and reduce vaccine efficacy. Notably, individuals with B cell immunodeficiency show lower IL-6 production. Furthermore, this review delves into several aspects of immune responses, such as hybrid immunity, which has shown promise in boosting broad-spectrum protection. Cross-reactive immunity is under scrutiny as well, as pre-existing antibodies can offer protection against the disease. We also decipher breakthrough infection mechanisms, especially with the novel variants of the virus. Finally, we discuss some potential therapeutic solutions regarding B cells including convalescent plasma therapy, B-1 cells, B regulatory cell (Breg) modulation, and the use of neutralizing monoclonal antibodies in combating the infection. Ongoing research is crucial to grasp population immunity trends and assess the potential need for booster doses in maintaining effective immune responses against potential viral threats.
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Affiliation(s)
- Nouhaila Najimi
- Laboratory of Human Pathologies Biology and Center of Genomic of Human Pathologies Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
- Mohammed VI Center for Research and Innovation, Rabat, Morocco
- Mohammed VI University of Sciences and Health, Casablanca, Morocco
| | - Chaimae Kadi
- Mohammed VI Center for Research and Innovation, Rabat, Morocco
- Mohammed VI University of Sciences and Health, Casablanca, Morocco
- Laboratory of Biology and Health, Faculty of Sciences of Tétouan, Abdelmalek Essaâdi University, Tétouan, Morocco
| | - Noureddine Elmtili
- Laboratory of Biology and Health, Faculty of Sciences of Tétouan, Abdelmalek Essaâdi University, Tétouan, Morocco
| | - Fouad Seghrouchni
- Mohammed VI Center for Research and Innovation, Rabat, Morocco
- Mohammed VI University of Sciences and Health, Casablanca, Morocco
| | - Youssef Bakri
- Laboratory of Human Pathologies Biology and Center of Genomic of Human Pathologies Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
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Chavda V, Yadav D, Parmar H, Brahmbhatt R, Patel B, Madhwani K, Jain M, Song M, Patel S. A Narrative Overview of Coronavirus Infection: Clinical Signs and Symptoms, Viral Entry and Replication, Treatment Modalities, and Management. Curr Top Med Chem 2024; 24:1883-1916. [PMID: 38859776 DOI: 10.2174/0115680266296095240529114058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 04/18/2024] [Accepted: 04/26/2024] [Indexed: 06/12/2024]
Abstract
The global pandemic known as coronavirus disease (COVID-19) is causing morbidity and mortality on a daily basis. The severe acute respiratory syndrome coronavirus-2 (SARS-CoV- -2) virus has been around since December 2019 and has infected a high number of patients due to its idiopathic pathophysiology and rapid transmission. COVID-19 is now deemed a newly identified "syndrome" condition since it causes a variety of unpleasant symptoms and systemic side effects following the pandemic. Simultaneously, it always becomes potentially hazardous when new variants develop during evolution. Its random viral etiology prevents accurate and suitable therapy. Despite the fact that multiple preclinical and research studies have been conducted to combat this lethal virus, and various therapeutic targets have been identified, the precise course of therapy remains uncertain. However, just a few drugs have shown efficacy in treating this viral infection in its early stages. Currently, several medicines and vaccinations have been licensed following clinical trial research, and many countries are competing to find the most potent and effective immunizations against this highly transmissible illness. For this narrative review, we used PubMed, Google Scholar, and Scopus to obtain epidemiological data, pre-clinical and clinical trial outcomes, and recent therapeutic alternatives for treating COVID-19 viral infection. In this study, we discussed the disease's origin, etiology, transmission, current advances in clinical diagnostic technologies, different new therapeutic targets, pathophysiology, and future therapy options for this devastating virus. Finally, this review delves further into the hype surrounding the SARS-CoV-2 illness, as well as present and potential COVID-19 therapies.
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Affiliation(s)
- Vishal Chavda
- Department of Pathology, Stanford School of Medicine, Stanford University Medical Center, Palo Alto94305, CA, USA
- Department of Medicine, Multispeciality, Trauma and ICCU Center, Sardar Hospital, Ahmedabad, 382352, Gujarat, India
| | - Dhananjay Yadav
- Department of Life Science, Yeungnam University, South Korea
| | - Harisinh Parmar
- Department of Neurosurgery, Krishna institute of medical sciences, Karad, Maharashtra, India
| | - Raxit Brahmbhatt
- Department of Medicine, Multispeciality, Trauma and ICCU Center, Sardar Hospital, Ahmedabad, 382352, Gujarat, India
| | - Bipin Patel
- Department of Medicine, Multispeciality, Trauma and ICCU Center, Sardar Hospital, Ahmedabad, 382352, Gujarat, India
| | - Kajal Madhwani
- Department of Life Science, University of Westminster, London, W1B 2HW, United Kingdom
| | - Meenu Jain
- Gajra Raja Medical College, Gwalior, 474009, Madhya Pradesh, India
| | - Minseok Song
- Department of Life Science, Yeungnam University, South Korea
| | - Snehal Patel
- Department of Pharmacology, Nirma University, Ahmedabad, 382481, Gujarat, India
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Li K, Huntwork RHC, Horn GQ, Abraha M, Hastie KM, Li H, Rayaprolu V, Olmedillas E, Feeney E, Cronin K, Schendel SL, Heise M, Bedinger D, Mattocks MD, Baric RS, Alam SM, Ollmann Saphire E, Tomaras GD, Dennison SM. Cryptic-site-specific antibodies to the SARS-CoV-2 receptor binding domain can retain functional binding affinity to spike variants. J Virol 2023; 97:e0107023. [PMID: 38019013 PMCID: PMC10746274 DOI: 10.1128/jvi.01070-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/05/2023] [Indexed: 11/30/2023] Open
Abstract
IMPORTANCE Multiple SARS-CoV-2 variants of concern have emerged and caused a significant number of infections and deaths worldwide. These variants of concern contain mutations that might significantly affect antigen-targeting by antibodies. It is therefore important to further understand how antibody binding and neutralization are affected by the mutations in SARS-CoV-2 variants. We highlighted how antibody epitope specificity can influence antibody binding to SARS-CoV-2 spike protein variants and neutralization of SARS-CoV-2 variants. We showed that weakened spike binding and neutralization of Beta (B.1.351) and Omicron (BA.1) variants compared to wildtype are not universal among the panel of antibodies and identified antibodies of a specific binding footprint exhibiting consistent enhancement of spike binding and retained neutralization to Beta variant. These data and analysis can inform how antigen-targeting by antibodies might evolve during a pandemic and prepare for potential future sarbecovirus outbreaks.
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Affiliation(s)
- Kan Li
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, USA
- Department of Surgery, Duke University, Durham, North Carolina, USA
| | - Richard H. C. Huntwork
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, USA
- Department of Surgery, Duke University, Durham, North Carolina, USA
| | - Gillian Q. Horn
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, USA
- Department of Surgery, Duke University, Durham, North Carolina, USA
| | - Milite Abraha
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, USA
- Department of Surgery, Duke University, Durham, North Carolina, USA
| | - Kathryn M. Hastie
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Haoyang Li
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Vamseedhar Rayaprolu
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Eduardo Olmedillas
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Elizabeth Feeney
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, USA
- Department of Surgery, Duke University, Durham, North Carolina, USA
| | - Kenneth Cronin
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
| | - Sharon L. Schendel
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Mark Heise
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA
| | | | - Melissa D. Mattocks
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Ralph S. Baric
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - S. Munir Alam
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
- Department of Pathology, Duke University, Durham, North Carolina, USA
| | - Erica Ollmann Saphire
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Georgia D. Tomaras
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, USA
- Department of Surgery, Duke University, Durham, North Carolina, USA
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, USA
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - S. Moses Dennison
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, USA
- Department of Surgery, Duke University, Durham, North Carolina, USA
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Samsunder N, Devnarain N, Sivro A, Kharsany ABM. The Performance of Diagnostic Tests for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in the South African Population: A Scoping Review. Trop Med Infect Dis 2023; 8:514. [PMID: 38133446 PMCID: PMC10748306 DOI: 10.3390/tropicalmed8120514] [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: 10/16/2023] [Revised: 11/29/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023] Open
Abstract
To determine the performance and reliability of diagnostic tests for the identification of SARS-CoV-2 infection in South Africa, we conducted a scoping review to identify published studies undertaken in the English language from March 2020 to August 2022 that evaluated the performance of antigen- and antibody-based diagnostic tests for SARS-CoV-2 in South Africa. We identified 17 relevant peer-reviewed articles; six reported on SARS-CoV-2 gene and/or antigen detection whilst 11 reported on antibody detection. Of the SARS-CoV-2 gene and/or antigen-based tests, sensitivity ranged from 40% to 100%, whilst for the antibody-based tests, sensitivity ranged from 13% to 100%. All tests evaluated were highly dependent on the stage of infection and the timing of sample collection. This scoping review demonstrated that no single SARS-CoV-2 gene and/or antigen- or antibody-based assay was sufficiently sensitive and specific simultaneously. The sensitivity of the tests was highly dependent on the timing of sample collection with respect to SARS-CoV-2 infection. In the case of SARS-CoV-2 gene and/or antigen detection, the earlier the collection of samples, the greater the sensitivity, while antibody detection tests showed better sensitivity using samples from later stages of infection.
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Affiliation(s)
- Natasha Samsunder
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa; (N.S.); (N.D.); (A.S.)
| | - Nikita Devnarain
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa; (N.S.); (N.D.); (A.S.)
- School of Health Science, University of KwaZulu-Natal, Durban 4013, South Africa
| | - Aida Sivro
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa; (N.S.); (N.D.); (A.S.)
- Department of Medical Microbiology, University of KwaZulu-Natal, Durban 4013, South Africa
- JC Wilt Infectious Disease Research Centre, National Microbiology laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3L5, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Ayesha B. M. Kharsany
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa; (N.S.); (N.D.); (A.S.)
- Department of Medical Microbiology, University of KwaZulu-Natal, Durban 4013, South Africa
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31
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Li X, Song Y. Structure and function of SARS-CoV and SARS-CoV-2 main proteases and their inhibition: A comprehensive review. Eur J Med Chem 2023; 260:115772. [PMID: 37659195 PMCID: PMC10529944 DOI: 10.1016/j.ejmech.2023.115772] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/24/2023] [Accepted: 08/26/2023] [Indexed: 09/04/2023]
Abstract
Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) identified in 2003 infected ∼8000 people in 26 countries with 800 deaths, which was soon contained and eradicated by syndromic surveillance and enhanced quarantine. A closely related coronavirus SARS-CoV-2, the causative agent of COVID-19 identified in 2019, has been dramatically more contagious and catastrophic. It has infected and caused various flu-like symptoms of billions of people in >200 countries, including >6 million people died of or with the virus. Despite the availability of several vaccines and antiviral drugs against SARS-CoV-2, finding new therapeutics is needed because of viral evolution and a possible emerging coronavirus in the future. The main protease (Mpro) of these coronaviruses plays important roles in their life cycle and is essential for the viral replication. This article represents a comprehensive review of the function, structure and inhibition of SARS-CoV and -CoV-2 Mpro, including structure-activity relationships, protein-inhibitor interactions and clinical trial status.
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Affiliation(s)
- Xin Li
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
| | - Yongcheng Song
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
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32
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Afzal S, Abdul Manap AS, Attiq A, Albokhadaim I, Kandeel M, Alhojaily SM. From imbalance to impairment: the central role of reactive oxygen species in oxidative stress-induced disorders and therapeutic exploration. Front Pharmacol 2023; 14:1269581. [PMID: 37927596 PMCID: PMC10622810 DOI: 10.3389/fphar.2023.1269581] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 10/02/2023] [Indexed: 11/07/2023] Open
Abstract
Increased production and buildup of reactive oxygen species (ROS) can lead to various health issues, including metabolic problems, cancers, and neurological conditions. Our bodies counteract ROS with biological antioxidants such as SOD, CAT, and GPx, which help prevent cellular damage. However, if there is an imbalance between ROS and these antioxidants, it can result in oxidative stress. This can cause genetic and epigenetic changes at the molecular level. This review delves into how ROS plays a role in disorders caused by oxidative stress. We also look at animal models used for researching ROS pathways. This study offers insights into the mechanism, pathology, epigenetic changes, and animal models to assist in drug development and disease understanding.
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Affiliation(s)
- Sheryar Afzal
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Aimi Syamima Abdul Manap
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Ali Attiq
- Discipline of Pharmacology, School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden, Malaysia
| | - Ibrahim Albokhadaim
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Mahmoud Kandeel
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia
- Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Sameer M. Alhojaily
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia
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33
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Bodakuntla S, Kuhn CC, Biertümpfel C, Mizuno N. Cryo-electron microscopy in the fight against COVID-19-mechanism of virus entry. Front Mol Biosci 2023; 10:1252529. [PMID: 37867557 PMCID: PMC10587472 DOI: 10.3389/fmolb.2023.1252529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/20/2023] [Indexed: 10/24/2023] Open
Abstract
Cryogenic electron microscopy (cryo-EM) and electron tomography (cryo-ET) have become a critical tool for studying viral particles. Cryo-EM has enhanced our understanding of viral assembly and replication processes at a molecular resolution. Meanwhile, in situ cryo-ET has been used to investigate how viruses attach to and invade host cells. These advances have significantly contributed to our knowledge of viral biology. Particularly, prompt elucidations of structures of the SARS-CoV-2 spike protein and its variants have directly impacted the development of vaccines and therapeutic measures. This review discusses the progress made by cryo-EM based technologies in comprehending the severe acute respiratory syndrome coronavirus-2 (SARS-Cov-2), the virus responsible for the devastating global COVID-19 pandemic in 2020 with focus on the SARS-CoV-2 spike protein and the mechanisms of the virus entry and replication.
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Affiliation(s)
- Satish Bodakuntla
- Laboratory of Structural Cell Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Christopher Cyrus Kuhn
- Laboratory of Structural Cell Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Christian Biertümpfel
- Laboratory of Structural Cell Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Naoko Mizuno
- Laboratory of Structural Cell Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, United States
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34
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Zheng W, Zhou Z, Guo X, Zuo X, Zhang J, An Y, Zheng H, Yue Y, Wang G, Wang F. Efferocytosis and Respiratory Disease. Int J Mol Sci 2023; 24:14871. [PMID: 37834319 PMCID: PMC10573909 DOI: 10.3390/ijms241914871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/26/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
Cells are the smallest units that make up living organisms, which constantly undergo the processes of proliferation, differentiation, senescence and death. Dead cells need to be removed in time to maintain the homeostasis of the organism and keep it healthy. This process is called efferocytosis. If the process fails, this may cause different types of diseases. More and more evidence suggests that a faulty efferocytosis process is closely related to the pathological processes of respiratory diseases. In this review, we will first introduce the process and the related mechanisms of efferocytosis of the macrophage. Secondly, we will propose some methods that can regulate the function of efferocytosis at different stages of the process. Next, we will discuss the role of efferocytosis in different lung diseases and the related treatment approaches. Finally, we will summarize the drugs that have been applied in clinical practice that can act upon efferocytosis, in order to provide new ideas for the treatment of lung diseases.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Guoqiang Wang
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (W.Z.); (Z.Z.); (X.G.); (X.Z.); (J.Z.); (Y.A.); (H.Z.); (Y.Y.)
| | - Fang Wang
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (W.Z.); (Z.Z.); (X.G.); (X.Z.); (J.Z.); (Y.A.); (H.Z.); (Y.Y.)
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35
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Perez-Romero CA, Mendoza-Maldonado L, Tonda A, Coz E, Tabeling P, Vanhomwegen J, MacSharry J, Szafran J, Bobadilla-Morales L, Corona-Rivera A, Claassen E, Garssen J, Kraneveld AD, Lopez-Rincon A. An Innovative AI-based primer design tool for precise and accurate detection of SARS-CoV-2 variants of concern. Sci Rep 2023; 13:15782. [PMID: 37737287 PMCID: PMC10516913 DOI: 10.1038/s41598-023-42348-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 09/08/2023] [Indexed: 09/23/2023] Open
Abstract
As the COVID-19 pandemic winds down, it leaves behind the serious concern that future, even more disruptive pandemics may eventually surface. One of the crucial steps in handling the SARS-CoV-2 pandemic was being able to detect the presence of the virus in an accurate and timely manner, to then develop policies counteracting the spread. Nevertheless, as the pandemic evolved, new variants with potentially dangerous mutations appeared. Faced by these developments, it becomes clear that there is a need for fast and reliable techniques to create highly specific molecular tests, able to uniquely identify VOCs. Using an automated pipeline built around evolutionary algorithms, we designed primer sets for SARS-CoV-2 (main lineage) and for VOC, B.1.1.7 (Alpha) and B.1.1.529 (Omicron). Starting from sequences openly available in the GISAID repository, our pipeline was able to deliver the primer sets for the main lineage and each variant in a matter of hours. Preliminary in-silico validation showed that the sequences in the primer sets featured high accuracy. A pilot test in a laboratory setting confirmed the results: the developed primers were favorably compared against existing commercial versions for the main lineage, and the specific versions for the VOCs B.1.1.7 and B.1.1.529 were clinically tested successfully.
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Affiliation(s)
- Carmina Angelica Perez-Romero
- Departamento de Investigación, Universidad Central de Queretaro (UNICEQ), Av. 5 de Febrero 1602, San Pablo, Santiago de Querétaro, 76130, Qro., Mexico
| | - Lucero Mendoza-Maldonado
- Hospital Civil de Guadalajara "Dr. Juan I. Menchaca", Salvador Quevedo y Zubieta 750, Independencia Oriente, C.P. 44340, Guadalajara, Jalisco, México
| | - Alberto Tonda
- UMR 518 MIA Paris-Saclay, INRAE, AgroParisTech, Université Paris-Saclay, 91120, Palaiseau, France
| | - Etienne Coz
- CBI, ESPCI Paris, Université PSL, CNRS, 75005, Paris, France
| | | | | | - John MacSharry
- School of Microbiology and School of Medicine, University College Cork, College Rd, University College, Cork, Ireland
| | - Joanna Szafran
- School of Microbiology and School of Medicine, University College Cork, College Rd, University College, Cork, Ireland
| | - Lucina Bobadilla-Morales
- Hospital Civil de Guadalajara "Dr. Juan I. Menchaca", Salvador Quevedo y Zubieta 750, Independencia Oriente, C.P. 44340, Guadalajara, Jalisco, México
| | - Alfredo Corona-Rivera
- Hospital Civil de Guadalajara "Dr. Juan I. Menchaca", Salvador Quevedo y Zubieta 750, Independencia Oriente, C.P. 44340, Guadalajara, Jalisco, México
| | - Eric Claassen
- Athena Institute, Vrije Universiteit, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Johan Garssen
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
- Department Immunology, Danone Nutricia research, Uppsalalaan 12, 3584 CT, Utrecht, The Netherlands
| | - Aletta D Kraneveld
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Alejandro Lopez-Rincon
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands.
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands.
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36
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Wongnak R, Brindha S, Yoshizue T, Onchaiya S, Mizutani K, Kuroda Y. E. coli production of a multi-disulfide bonded SARS-CoV-2 Omicron BA.5 RBD exhibiting native-like biochemical and biophysical properties. Biophys Physicobiol 2023; 20:e200036. [PMID: 38344033 PMCID: PMC10850476 DOI: 10.2142/biophysico.bppb-v20.0036] [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: 07/27/2023] [Accepted: 09/19/2023] [Indexed: 03/27/2024] Open
Abstract
Low-cost bacterial production of the receptor binding domain (RBD) of the SARS-CoV-2 Omicron spike protein holds significant potential in expediting the development of therapeutics against COVID-19. However, RBD contains eight cysteines forming four disulfide bonds, and expression in E. coli using standard protocols produces insoluble RBD forming non-native disulfide bonds. Here, we expressed RBD in E. coli T7 SHuffle with high aeration, which enhanced disulfide formation in the cytoplasm and reshuffling of non-native disulfide bonds, and at a low temperature of 16°C, which stabilized the native conformation and thus the formation of the native disulfide bonds. The yield of RBD was as high as 3 mg per 200 mL culture. We analyzed the conformational and biophysical properties of our E. coli-expressed RBD. First, the RP-HPLC elution profile indicated a single peak, suggesting that RBD was folded with a single disulfide bond pairing pattern. Next, circular dichroism analysis indicated a secondary structure content very close to that computed from the crystal structure. RBD's thermal denaturation monitored by CD was cooperative, strongly indicating a well-folded protein structure. Moreover, limited proteolysis showed that RBD was nearly as stable as RNase A, and the formation of native disulfide bonds was confirmed by LC-MS analysis. Furthermore, BLI analysis indicated a strong binding of RBD with the hACE2 with a dissociation constant of 0.83 nM, confirming the folded nature of RBD. Altogether, these results demonstrate that our E. coli-expression system can provide a large amount of highly purified RBD with correct disulfide bonds and native-like biochemical and biophysical properties.
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Affiliation(s)
- Rawiwan Wongnak
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Subbaian Brindha
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8538, Japan
| | - Takahiro Yoshizue
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Sawaros Onchaiya
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Kenji Mizutani
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | - Yutaka Kuroda
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8538, Japan
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37
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Hajjo R, Momani E, Sabbah DA, Baker N, Tropsha A. Identifying a causal link between prolactin signaling pathways and COVID-19 vaccine-induced menstrual changes. NPJ Vaccines 2023; 8:129. [PMID: 37658087 PMCID: PMC10474200 DOI: 10.1038/s41541-023-00719-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 08/04/2023] [Indexed: 09/03/2023] Open
Abstract
COVID-19 vaccines have been instrumental tools in the fight against SARS-CoV-2 helping to reduce disease severity and mortality. At the same time, just like any other therapeutic, COVID-19 vaccines were associated with adverse events. Women have reported menstrual cycle irregularity after receiving COVID-19 vaccines, and this led to renewed fears concerning COVID-19 vaccines and their effects on fertility. Herein we devised an informatics workflow to explore the causal drivers of menstrual cycle irregularity in response to vaccination with mRNA COVID-19 vaccine BNT162b2. Our methods relied on gene expression analysis in response to vaccination, followed by network biology analysis to derive testable hypotheses regarding the causal links between BNT162b2 and menstrual cycle irregularity. Five high-confidence transcription factors were identified as causal drivers of BNT162b2-induced menstrual irregularity, namely: IRF1, STAT1, RelA (p65 NF-kB subunit), STAT2 and IRF3. Furthermore, some biomarkers of menstrual irregularity, including TNF, IL6R, IL6ST, LIF, BIRC3, FGF2, ARHGDIB, RPS3, RHOU, MIF, were identified as topological genes and predicted as causal drivers of menstrual irregularity. Our network-based mechanism reconstruction results indicated that BNT162b2 exerted biological effects similar to those resulting from prolactin signaling. However, these effects were short-lived and didn't raise concerns about long-term infertility issues. This approach can be applied to interrogate the functional links between drugs/vaccines and other side effects.
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Affiliation(s)
- Rima Hajjo
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130, Amman, 11733, Jordan.
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Jordan CDC, Amman, Jordan.
| | - Ensaf Momani
- Department of Basic Medical sciences, Faculty of Medicine, Al Balqa' Applied University, Al-Salt, Jordan
- Applied Science Research Center, Applied Science Private University, Amman, Jordan
| | - Dima A Sabbah
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130, Amman, 11733, Jordan
| | - Nancy Baker
- ParlezChem, 123 W Union St., Hillsborough, NC, 27278, USA
| | - Alexander Tropsha
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Islam MJ, Alom MS, Hossain MS, Ali MA, Akter S, Islam S, Ullah MO, Halim MA. Unraveling the impact of ORF3a Q57H mutation on SARS-CoV-2: insights from molecular dynamics. J Biomol Struct Dyn 2023:1-14. [PMID: 37649361 DOI: 10.1080/07391102.2023.2252908] [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: 11/14/2022] [Accepted: 08/22/2023] [Indexed: 09/01/2023]
Abstract
ORF3a is a conserved accessory protein of SARS-CoV-2, linked to viral infection and pathogenesis, with acquired mutations at various locations. Previous studies have shown that the occurrence of the Q57H mutation is higher in comparison to other positions in ORF3a. This mutation is known to induce conformational changes, yet the extent of structural alteration and its role in the viral adaptation process remain unknown. Here we performed molecular dynamics (MD) simulations of wt-ORF3a, Q57H, and Q57A mutants to analyze structural changes caused by mutations compared to the native protein. The MD analysis revealed that Q57H and Q57A mutants show significant structural changes in the dimer conformation than the wt-ORF3a. This dimer conformer narrows down the ion channel cavity, which reduces Na + or K + permeability leading to decrease the antigenic response that can help the virus to escape the host immune system. Non-bonding interaction analysis shows the Q57H mutant has more interacting residues, resulting in more stability within dimer conformation than the wt-ORF3a and Q57A. Moreover, both mutant dimers (Q57H and Q57A) form a novel salt-bridge interaction at the same position between A:Asp142 and B:Lys61, whereas such an interaction is absent in the wt-ORF3a dimer. We have also noticed that the TM3 domain's flexibility in Q57H is increased because of strong inter-domain interactions of TM1 and TM2 within the dimer conformation. These unusual interactions and flexibility of Q57H mutant can have significant impacts on the SARS-CoV-2 adaptations, virulence, transmission, and immune system evasion. Our findings are consistent with the previous experimental data and provided details information on the structural perturbation in ORF3a caused by mutations, which can help better understand the structural change at the molecular level as well as the reason for the high virulence properties of this variant.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Md Jahirul Islam
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Md Siddik Alom
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio, USA
- Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Md Shahadat Hossain
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Md Ackas Ali
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Georgia, USA
| | - Shaila Akter
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Shafiqul Islam
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - M Obayed Ullah
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Mohammad A Halim
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Georgia, USA
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Mabuka T, Ncube N, Ross M, Silaji A, Macharia W, Ndemera T, Lemeke T. The impact of non-pharmaceutical interventions on the first COVID-19 epidemic wave in South Africa. BMC Public Health 2023; 23:1492. [PMID: 37542267 PMCID: PMC10403893 DOI: 10.1186/s12889-023-16162-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 06/20/2023] [Indexed: 08/06/2023] Open
Abstract
OBJECTIVE In this study, we investigated the impact of COVID-19 NPIs in South Africa to understand their effectiveness in the reduction of transmission of COVID-19 in the South African population. This study also investigated the COVID-19 testing, reporting, hospitalised cases, excess deaths and COVID-19 modelling in the first wave of the COVID-19 epidemic in South Africa. METHODS A semi-reactive stochastic COVID-19 model, the ARI COVID-19 SEIR model, was used to investigate the impact of NPIs in South Africa to understand their effectiveness in the reduction of COVID-19 transmission in the South African population. COVID-19 testing, reporting, hospitalised cases and excess deaths in the first COVID-19 epidemic wave in South Africa were investigated using regressional analysis and descriptive statistics. FINDINGS The general trend in population movement in South African locations shows that the COVID-19 NPIs (National Lockdown Alert Levels 5,4,3,2) were approximately 30% more effective in reducing population movement concerning each increase by 1 Alert Level. The translated reduction in the effective SARS-CoV-2 daily contact number (β) was 6.12% to 36.1% concerning increasing Alert Levels. Due to the implemented NPIs, the effective SARS-CoV-2 daily contact number in the first COVID-19 epidemic wave in South Africa was reduced by 58.1-71.1% while the peak was delayed by 84 days. The estimated COVID-19 reproductive number was between 1.98 to 0.40. During South Africa's first COVID-19 epidemic wave, the mean COVID-19 admission status in South African hospitals was 58.5%, 95% CI [58.1-59.0] in the general ward, 13.4%, 95% CI [13.1-13.7] in the intensive care unit, 13.3%, 95% CI [12.6-14.0] on oxygen, 6.37%, 95% CI [6.23-6.51] in high care, 6.29%, 95% CI [6.02-6.55] on ventilator and 2.13%, 95% CI [1.87-2.43] in isolation ward respectively. The estimated mean South African COVID-19 patient discharge rate was 11.9 days per patient. While the estimated mean of the South African COVID-19 patient case fatality rate (CFR) in hospital and outside the hospital was 2.06%, 95% CI [1.86-2.25] (deaths per admitted patients) and 2.30%, 95% CI [1.12-3.83](deaths per severe and critical cases) respectively. The relatively high coefficient of variance in COVID-19 model outputs observed in this study shows the uncertainty in the accuracy of the reviewed COVID-19 models in predicting the severity of COVID-19. However, the reviewed COVID-19 models were accurate in predicting the progression of the first COVID-19 epidemic wave in South Africa. CONCLUSION The results from this study show that the COVID-19 NPI policies implemented by the Government of South Africa played a significant role in the reduction of COVID-19 active, hospitalised cases and deaths in South Africa's first COVID-19 epidemic wave. The results also show the use of COVID-19 modelling to understand the COVID-19 pandemic and the impact of regressor variables in an epidemic.
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Affiliation(s)
- Thabo Mabuka
- African COVID-19 Modelling Research Group (ACMRG), The Afrikan Research Initiative (ARI), Cape Town, South Africa.
| | - Nesisa Ncube
- African COVID-19 Modelling Research Group (ACMRG), The Afrikan Research Initiative (ARI), Cape Town, South Africa
| | - Michael Ross
- African COVID-19 Modelling Research Group (ACMRG), The Afrikan Research Initiative (ARI), Cape Town, South Africa
| | - Andrea Silaji
- African COVID-19 Modelling Research Group (ACMRG), The Afrikan Research Initiative (ARI), Cape Town, South Africa
| | - Willie Macharia
- African COVID-19 Modelling Research Group (ACMRG), The Afrikan Research Initiative (ARI), Cape Town, South Africa
| | - Tinashe Ndemera
- African COVID-19 Modelling Research Group (ACMRG), The Afrikan Research Initiative (ARI), Cape Town, South Africa
| | - Tlaleng Lemeke
- African COVID-19 Modelling Research Group (ACMRG), The Afrikan Research Initiative (ARI), Cape Town, South Africa
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Tomkinson S, Triscott C, Schenk E, Foey A. The Potential of Probiotics as Ingestible Adjuvants and Immune Modulators for Antiviral Immunity and Management of SARS-CoV-2 Infection and COVID-19. Pathogens 2023; 12:928. [PMID: 37513775 PMCID: PMC10384479 DOI: 10.3390/pathogens12070928] [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: 05/19/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023] Open
Abstract
Probiotic bacteria are able to modulate general antiviral responsiveness, including barrier functionality and innate and adaptive immune responses. The COVID-19 pandemic, resulting from SARS-CoV-2 infection, has created a need to control and treat this viral infection and its ensuing immunopathology with a variety of approaches; one such approach may involve the administration of probiotic bacteria. As with most viral infections, its pathological responses are not fully driven by the virus, but are significantly contributed to by the host's immune response to viral infection. The potential adoption of probiotics in the treatment of COVID-19 will have to appreciate the fine line between inducing antiviral immunity without over-provoking immune inflammatory responses resulting in host-derived immunopathological tissue damage. Additionally, the effect exerted on the immune system by SARS-CoV-2 evasion strategies will also have to be considered when developing a robust response to this virus. This review will introduce the immunopathology of COVID-19 and the immunomodulatory effects of probiotic strains, and through their effects on a range of respiratory pathogens (IAV, SARS-CoV, RSV), as well as SARS-CoV-2, will culminate in a focus on how these bacteria can potentially manipulate both infectivity and immune responsiveness via barrier functionality and both innate and adaptive immunity. In conclusion, the harnessing of induction and augmentation of antiviral immunity via probiotics may not only act as an ingestible adjuvant, boosting immune responsiveness to SARS-CoV-2 infection at the level of barrier integrity and innate and adaptive immunity, but also act prophylactically to prevent infection and enhance protection afforded by current vaccine regimens.
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Affiliation(s)
- Sophie Tomkinson
- School of Biomedical Sciences, Faculty of Health, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
| | - Cloe Triscott
- School of Biomedical Sciences, Faculty of Health, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
| | - Emily Schenk
- School of Biomedical Sciences, Faculty of Health, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
- Peninsula Medical School, Faculty of Health, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
| | - Andrew Foey
- School of Biomedical Sciences, Faculty of Health, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
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Razi O, Teixeira AM, Tartibian B, Zamani N, Knechtle B. Respiratory issues in patients with multiple sclerosis as a risk factor during SARS-CoV-2 infection: a potential role for exercise. Mol Cell Biochem 2023; 478:1533-1559. [PMID: 36411399 PMCID: PMC9684932 DOI: 10.1007/s11010-022-04610-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 11/04/2022] [Indexed: 11/23/2022]
Abstract
Coronavirus disease-2019 (COVID-19) is associated with cytokine storm and is characterized by acute respiratory distress syndrome (ARDS) and pneumonia problems. The respiratory system is a place of inappropriate activation of the immune system in people with multiple sclerosis (MS), and this may cause damage to the lung and worsen both MS and infections.The concerns for patients with multiple sclerosis are because of an enhance risk of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The MS patients pose challenges in this pandemic situation, because of the regulatory defect of autoreactivity of the immune system and neurological and respiratory tract symptoms. In this review, we first indicate respiratory issues associated with both diseases. Then, the main mechanisms inducing lung damages and also impairing the respiratory muscles in individuals with both diseases is discussed. At the end, the leading role of physical exercise on mitigating respiratory issues inducing mechanisms is meticulously evaluated.
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Affiliation(s)
- Omid Razi
- Department of Exercise Physiology, Faculty of Physical Education and Sport Sciences, Razi University, Kermanshah, Iran
| | - Ana Maria Teixeira
- Research Center for Sport and Physical Activity, Faculty of Sport Sciences and Physical Education, University of Coimbra, Coimbra, Portugal
| | - Bakhtyar Tartibian
- Department of Exercise Physiology, Faculty of Physical Education and Sports Sciences, Allameh Tabataba’i University, Tehran, Iran
| | - Nastaran Zamani
- Department of Biology, Faculty of Science, Payame-Noor University, Tehran, Iran
| | - Beat Knechtle
- Institute of Primary Care, University of Zurich, Zurich, Switzerland
- Medbase St. Gallen Am Vadianplatz, Vadianstrasse 26, 9001 St. Gallen, Switzerland
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Tajnur R, Rezwan R, Aziz A, Islam MS. An update on vaccine status and the role of nanomedicine against SARS-CoV-2: A narrative review. Health Sci Rep 2023; 6:e1377. [PMID: 37404449 PMCID: PMC10315735 DOI: 10.1002/hsr2.1377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 06/03/2023] [Accepted: 06/14/2023] [Indexed: 07/06/2023] Open
Abstract
Background and Aims Coronavirus disease 2019 (COVID-19), caused by the SARS-CoV-2 novel coronavirus, is a highly communicable disease that gave rise to the ongoing pandemic. Despite prompt action across many laboratories in many countries, effective management of this disease is still out of reach. The focus of this review is to describe various vaccination approaches and nanomedicine-based delivery systems against COVID-19. Methods The articles included in this study were searched and added from different electronic databases, including PubMed, Scopus, Cochrane, Embase, and preprint databases. Results Mass immunization with vaccines is currently at the forefront of COVID-19 infection control. Such vaccines are live attenuated vaccines, inactivated vaccines, nucleic acid-based vaccines, protein subunit vaccines, viral-vector vaccines, and virus-like particle platforms. However, many promising avenues are currently being explored in laboratory and clinical settings, including treatment options, prevention, diagnosis, and management of the disease. Soft nanoparticles like lipid nanoparticles (solid lipid nanoparticles (SLNPs), liposomes, nanostructured lipid carriers, nanoemulsions, and protein nanoparticles play an essential role in nanomedicine. Because of their unique and excellent properties, nanomedicines have potential applications in treating COVID-19 disease. Conclusions This review work provides an overview of the therapeutic aspects of COVID-19, including vaccination and the role of nanomedicines in the diagnosis, treatment, and prevention of COVID-19.
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Affiliation(s)
- Rabeya Tajnur
- Department of PharmacyASA University BangladeshDhakaBangladesh
| | - Refaya Rezwan
- Department of PharmacyState University of BangladeshDhakaBangladesh
- Department of Molecular and Translational ScienceMonash UniversityClaytonVictoriaAustralia
| | - Abdul Aziz
- Department of PharmacyState University of BangladeshDhakaBangladesh
| | - Mohammad Safiqul Islam
- Laboratory of Pharmacogenomics and Molecular Biology, Department of PharmacyNoakhali Science and Technology UniversityNoakhaliBangladesh
- Department of Pharmacy, Faculty of ScienceNoakhali Science and Technology UniversityNoakhaliBangladesh
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Moroni-Zentgraf P, Keller C, Eschenfelder CC, Walter Müller H, Sigmund R, Galeana-Cadena D, Márquez-García JE, Moncada-Morales A, Zúñiga JA. Salivette® Cortisol versus oropharyngeal swabbing for the detection of SARS-CoV-2 infection. Expert Rev Mol Diagn 2023; 23:1011-1014. [PMID: 37724431 DOI: 10.1080/14737159.2023.2260308] [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: 07/21/2023] [Accepted: 09/10/2023] [Indexed: 09/20/2023]
Abstract
BACKGROUND Detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by naso/oropharyngeal swabbing may expose health-care workers to the virus and is technically challenging. The Salivette® is an alternative saliva-collection device with an oral cotton swab containing citric acid to stimulate saliva production, which may have an unpleasant taste. We present a pilot study comparing the Salivette® Cortisol (SC), which uses a synthetic swab without citric acid, against oropharyngeal swabbing for the detection of SARS-CoV-2 by reverse transcription quantitative polymerase chain reaction (RT-qPCR). RESEARCH DESIGN AND METHODS Symptomatic SARS-CoV-2-positive patients were sampled at various timepoints. The number of patients positive/negative for SARS-CoV-2 in oropharyngeal swab and SC samples and the percentage of patients testing true positive/true negative for SARS-CoV-2 from SC samples were determined. Positivity was defined by RT-qPCR amplification of 2/3 target SARS-CoV-2 N, ORF1, and S gene sequences. RESULTS SC demonstrated 100% specificity, 52.2% sensitivity, and positive correlation with oropharyngeal swabbing for the detection of the SARS-CoV-2 S gene. In later-stage disease, lower viral load was observed in SC samples compared with oropharyngeal swabs. CONCLUSIONS The SC may be an alternative for SARS-CoV-2 detection where naso/oropharyngeal swabbing is not feasible/available. This technique also confirms observations that the detection of SARS-CoV-2 in the upper airway may vary due to viral load over the disease course. TRIAL REGISTRATION NCT04599959.
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Affiliation(s)
- Petra Moroni-Zentgraf
- Human Pharma Medicine, Boehringer Ingelheim Pharma GmbH & Co. KG, Ingelheim, Germany
| | - Christoph Keller
- HP Country Pharmacovigilance, Boehringer Ingelheim Pharma GmbH & Co. KG, Ingelheim, Germany
| | | | - Hanns Walter Müller
- Non-Clinical Statistics, Boehringer Ingelheim Pharma GmbH & Co. KG, Ingelheim, Germany
| | - Ralf Sigmund
- Biostatistics and Data Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - David Galeana-Cadena
- Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias Ismaesl Cosío Villegas, Mexico City, Mexico
| | - José Eduardo Márquez-García
- Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias Ismaesl Cosío Villegas, Mexico City, Mexico
| | - Angélica Moncada-Morales
- Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias Ismaesl Cosío Villegas, Mexico City, Mexico
| | - Joaquin A Zúñiga
- Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias Ismaesl Cosío Villegas, Mexico City, Mexico
- National Institute of Respiratory Diseases-Mexico (INER), Tecnologico de Monterrey, Escuale ade Medicina y Ciencias de las Salud, Monterrey, Mexico
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Pelucelli A, Peana M, Orzeł B, Piasta K, Gumienna-Kontecka E, Medici S, Zoroddu MA. Zn 2+ and Cu 2+ Interaction with the Recognition Interface of ACE2 for SARS-CoV-2 Spike Protein. Int J Mol Sci 2023; 24:ijms24119202. [PMID: 37298154 DOI: 10.3390/ijms24119202] [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: 05/03/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
The spike protein (S) of SARS-CoV-2 is able to bind to the human angiotensin-converting enzyme 2 (ACE2) receptor with a much higher affinity compared to other coronaviruses. The binding interface between the ACE2 receptor and the spike protein plays a critical role in the entry mechanism of the SARS-CoV-2 virus. There are specific amino acids involved in the interaction between the S protein and the ACE2 receptor. This specificity is critical for the virus to establish a systemic infection and cause COVID-19 disease. In the ACE2 receptor, the largest number of amino acids playing a crucial role in the mechanism of interaction and recognition with the S protein is located in the C-terminal part, which represents the main binding region between ACE2 and S. This fragment is abundant in coordination residues such as aspartates, glutamates, and histidine that could be targeted by metal ions. Zn2+ ions bind to the ACE2 receptor in its catalytic site and modulate its activity, but it could also contribute to the structural stability of the entire protein. The ability of the human ACE2 receptor to coordinate metal ions, such as Zn2+, in the same region where it binds to the S protein could have a crucial impact on the mechanism of recognition and interaction of ACE2-S, with consequences on their binding affinity that deserve to be investigated. To test this possibility, this study aims to characterize the coordination ability of Zn2+, and also Cu2+ for comparison, with selected peptide models of the ACE2 binding interface using spectroscopic and potentiometric techniques.
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Affiliation(s)
- Alessio Pelucelli
- Department of Chemical, Physical, Mathematical and Natural Sciences, University of Sassari, 07100 Sassari, Italy
| | - Massimiliano Peana
- Department of Chemical, Physical, Mathematical and Natural Sciences, University of Sassari, 07100 Sassari, Italy
| | - Bartosz Orzeł
- Faculty of Chemistry, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Karolina Piasta
- Faculty of Chemistry, University of Wroclaw, 50-383 Wroclaw, Poland
| | | | - Serenella Medici
- Department of Chemical, Physical, Mathematical and Natural Sciences, University of Sassari, 07100 Sassari, Italy
| | - Maria Antonietta Zoroddu
- Department of Chemical, Physical, Mathematical and Natural Sciences, University of Sassari, 07100 Sassari, Italy
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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 PMCID: PMC10183699 DOI: 10.1186/s12964-023-01104-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [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.
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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.
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Srivastava S, Singh S, Mishra AC, Lohia P, Dwivedi DK. Numerical Study of Titanium Dioxide and MXene Nanomaterial-Based Surface Plasmon Resonance Biosensor for Virus SARS-CoV-2 Detection. PLASMONICS (NORWELL, MASS.) 2023; 18:1-12. [PMID: 37360047 PMCID: PMC10171911 DOI: 10.1007/s11468-023-01874-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 04/28/2023] [Indexed: 06/28/2023]
Abstract
A novel surface plasmon resonance-based biosensor for SARS-CoV-2 virus is proposed in this article. The biosensor is a Kretschmann configuration-based structure that consists of CaF2 prism as base, at which silver (Ag), TiO2, and MXene nanolayers are used to enhance the performance. Theoretically, the performance parameters have been investigated by means of Fresnel equations and transfer matrix method (TMM). The TiO2 nanolayer not only prevents oxidation of Ag layer but also enhances the evanescent field in its vicinity. The sensor provides an ultrahigh angular sensitivity of 346°/RIU for the detection of SARS-CoV-2 virus. Some other performance parameters, including FWHM (full width at half maxima), detection accuracy (DA), limit of detection (LOD), and quality factor (QF) have also been calculated for proposed SPR biosensor with their optimized values 2.907°, 0.3439 deg-1, 1.445 × 10-5, and 118.99 RIU-1, respectively. The obtained results designate that the proposed surface plasmon resonance (SPR) based biosensor has notably enhanced angular sensitivity as compared to previous results reported in the literatures till date. This work may facilitate a significant biological sample sensing device for fast and accurate diagnosis at early stage of SARS-CoV-2 virus.
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Affiliation(s)
- Swati Srivastava
- Photonics and Photovoltaic Research Lab, Department of Physics and Material Science, Madan Mohan Malaviya University of Technology, Gorakhpur, 273010 India
| | - Sachin Singh
- Photonics and Photovoltaic Research Lab, Department of Physics and Material Science, Madan Mohan Malaviya University of Technology, Gorakhpur, 273010 India
| | - Adarsh Chandra Mishra
- Photonics and Photovoltaic Research Lab, Department of Physics and Material Science, Madan Mohan Malaviya University of Technology, Gorakhpur, 273010 India
| | - Pooja Lohia
- Department of Electronics and Communication Engineering, Madan Mohan Malaviya University of Technology, Gorakhpur, 273010 India
| | - D. K. Dwivedi
- Photonics and Photovoltaic Research Lab, Department of Physics and Material Science, Madan Mohan Malaviya University of Technology, Gorakhpur, 273010 India
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Taya SA, Daher MG, Almawgani AHM, Hindi AT, Zyoud SH, Colak I. Detection of Virus SARS-CoV-2 Using a Surface Plasmon Resonance Device Based on BiFeO 3-Graphene Layers. PLASMONICS (NORWELL, MASS.) 2023; 18:1-8. [PMID: 37360049 PMCID: PMC10170057 DOI: 10.1007/s11468-023-01867-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 04/24/2023] [Indexed: 06/28/2023]
Abstract
Coronavirus disease (COVID-19) pandemic outbreak is being investigated by severe respirational syndrome coronavirus-2 (SARS-CoV-2) as a global health issue. It is crucial to propose sensitive and rapid coronavirus detectors. Herein, we propose a biosensor based on surface plasmon resonance (SPRE) for the detection of SARS-CoV-2 virus. To achieve improved sensitivity, a BiFeO3 layer is inserted between a metal (Ag) thin film and a graphene layer in the proposed SPRE device so that it has the structure BK7 prism/ Ag/ BiFeO3/ graphene/ analyte. It has been demonstrated that a small variation in the refractive index of the analyte can cause a considerable shift in the resonance angle caused by the remarkable dielectric properties of the BiFeO3 layer, which include a high index of refraction and low loss. The proposed device has shown an extremely high sensitivity of 293 deg/RIU by optimizing the thicknesses of Ag, BiFeO3, and the number of graphene sheets. The proposed SPRE-based sensor is encouraging for use in various sectors of biosensing because of its high sensitivity.
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Affiliation(s)
- Sofyan A. Taya
- Physics Department, Islamic University of Gaza, P.O. Box 108, Gaza, Palestine
| | - Malek G. Daher
- Physics Department, Islamic University of Gaza, P.O. Box 108, Gaza, Palestine
| | - Abdulkarem H. M. Almawgani
- Electrical Engineering Department, College of Engineering, Najran University, Najran, Kingdom of Saudi Arabia
| | - Ayman Taher Hindi
- Electrical Engineering Department, College of Engineering, Najran University, Najran, Kingdom of Saudi Arabia
| | - Samer H. Zyoud
- Department of Mathematics and Sciences, Ajman University, Ajman, United Arab Emirates
| | - Ilhami Colak
- Department of Electrical and Electronics Engineering, Nisantasi University, Istanbul, Turkey
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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: 24] [Impact Index Per Article: 24.0] [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.
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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
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Meo C, Palma G, Bruzzese F, Budillon A, Napoli C, de Nigris F. Spontaneous cancer remission after COVID-19: insights from the pandemic and their relevance for cancer treatment. J Transl Med 2023; 21:273. [PMID: 37085802 PMCID: PMC10119533 DOI: 10.1186/s12967-023-04110-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/06/2023] [Indexed: 04/23/2023] Open
Abstract
Early in the COVID-19 pandemic, it emerged that the risk of severe outcomes was greater in patients with co-morbidities, including cancer. The huge effort undertaken to fight the pandemic, affects the management of cancer care, influencing their outcome. Despite the high fatality rate of COVID-19 disease in cancer patients, rare cases of temporary or prolonged clinical remission from cancers after SARS-CoV-2 infection have been reported. We have reviewed sixteen case reports of COVID-19 disease with spontaneous cancer reduction of progression. Fourteen cases of remission following viral infections and two after anti-SARS-CoV-2 vaccination. The immune response to COVID-19, may be implicated in both tumor regression, and progression. Specifically, we discuss potential mechanisms which include oncolytic and priming hypotheses, that may have contributed to the cancer regression in these cases and could be useful for future options in cancer treatment.
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Affiliation(s)
- Concetta Meo
- Department of Precision Medicine, School of Medicine, University of Campania "Luigi Vanvitelli", Via De Crecchio 7, 80138, Naples, Italy
| | - Giuseppe Palma
- S.S.D. Sperimentazione Animale, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Naples, Italy.
| | - Francesca Bruzzese
- S.S.D. Sperimentazione Animale, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Naples, Italy
| | - Alfredo Budillon
- Scientific Directorate - National Institute of Cancer - IRCCS - Fondazione G. Pascale, Naples, Italy
| | - Claudio Napoli
- Clinical Department of Internal Medicine and Specialistic Units, Division of Clinical Immunology and Immunohematology, Transfusion Medicine, and Transplant Immunology (SIMT), Azienda Universitaria Policlinico (AOU), 80138, Naples, Italy
- Advanced Medical and Surgical Science (DAMSS), School of Medicine, University of Campania "Luigi Vanvitelli", 80138, Naples, Italy
| | - Filomena de Nigris
- Department of Precision Medicine, School of Medicine, University of Campania "Luigi Vanvitelli", Via De Crecchio 7, 80138, Naples, Italy.
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Afifah AR, Liana P, Fertilita S, Salim NA, Verdiansah V, Hilda F, Amin CA, Umar TP. C-Reactive Protein as The Predictor of Mortality for COVID-19 Patients in Indonesia. INDONESIAN JOURNAL OF CLINICAL PATHOLOGY AND MEDICAL LABORATORY 2023; 29:180-184. [DOI: 10.24293/ijcpml.v29i2.1997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
Coronavirus Disease 2019 (COVID-19) confirmed cases and deaths continue to rise. When a virus infects the body, the immune system tries to eliminate the virus. C-Reactive Protein (CRP) is a substance produced in the body in response to infection and inflammation. The study aimed to determine the role of CRP in predicting COVID-19 patients’ mortality. From the 1st of March to the 31st of August 2020, data on patients confirmed with COVID-19 were collected from medical records. The correlation between CRP levels and patient mortality was determined using a Chi-Square test. A Receiver Operator Curve (ROC) analysis was used to determine the best CRP cut-off point, and a survival analysis was used to assess the patient outcome. This study included a total of 210 eligible patients. Survivors and non-survivors were divided into two groups of patients (159 patients and 51 patients, respectively). The CRP cut-off was 54 mg/L, with an AUC of 0.817 (p<0.001). C-reactive protein levels were related to COVID-19 patient mortality (p=0.000). According to the survival analysis, patients with CRP levels > 54 mg/L had a lower chance of 30-day survival (p=0.0001). This study presented that CRP levels can be used to predict mortality in COVID-19 patients.
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