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Krismer L, Schöppe H, Rauch S, Bante D, Sprenger B, Naschberger A, Costacurta F, Fürst A, Sauerwein A, Rupp B, Kaserer T, von Laer D, Heilmann E. Study of key residues in MERS-CoV and SARS-CoV-2 main proteases for resistance against clinically applied inhibitors nirmatrelvir and ensitrelvir. NPJ VIRUSES 2024; 2:23. [PMID: 38933182 PMCID: PMC11196219 DOI: 10.1038/s44298-024-00028-2] [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: 01/21/2024] [Accepted: 03/14/2024] [Indexed: 06/28/2024]
Abstract
The Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is an epidemic, zoonotically emerging pathogen initially reported in Saudi Arabia in 2012. MERS-CoV has the potential to mutate or recombine with other coronaviruses, thus acquiring the ability to efficiently spread among humans and become pandemic. Its high mortality rate of up to 35% and the absence of effective targeted therapies call for the development of antiviral drugs for this pathogen. Since the beginning of the SARS-CoV-2 pandemic, extensive research has focused on identifying protease inhibitors for the treatment of SARS-CoV-2. Our intention was therefore to assess whether these protease inhibitors are viable options for combating MERS-CoV. To that end, we used previously established protease assays to quantify inhibition of SARS-CoV-2, MERS-CoV and other main proteases. Nirmatrelvir inhibited several of these proteases, whereas ensitrelvir was less broadly active. To simulate nirmatrelvir's clinical use against MERS-CoV and subsequent resistance development, we applied a safe, surrogate virus-based system. Using the surrogate virus, we previously selected hallmark mutations of SARS-CoV-2-Mpro, such as T21I, M49L, S144A, E166A/K/V and L167F. In the current study, we selected a pool of MERS-CoV-Mpro mutants, characterized the resistance and modelled the steric effect of catalytic site mutants S142G, S142R, S147Y and A171S.
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Affiliation(s)
- Laura Krismer
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020 Austria
| | - Helge Schöppe
- Institute of Pharmacy/Pharmaceutical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, 6020 Austria
| | - Stefanie Rauch
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020 Austria
| | - David Bante
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020 Austria
| | - Bernhard Sprenger
- Institute of Biochemistry, University of Innsbruck, CMBI – Center for Molecular Biosciences Innsbruck, Innsbruck, 6020 Austria
| | - Andreas Naschberger
- Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology KAUST, Thuwal, Saudi Arabia
| | | | - Anna Fürst
- Institute of Molecular Immunology, Technical University of Munich, Munich, 81675 Germany
| | - Anna Sauerwein
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020 Austria
| | - Bernhard Rupp
- Division of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, 6020 Austria
| | - Teresa Kaserer
- Institute of Pharmacy/Pharmaceutical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, 6020 Austria
| | - Dorothee von Laer
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020 Austria
| | - Emmanuel Heilmann
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020 Austria
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Gattan HS, Mahmoud Alawi M, Bajrai LH, Alandijany TA, Alsaady IM, El-Daly MM, Dwivedi VD, Azhar EI. A Multifaceted Computational Approach to Understanding the MERS-CoV Main Protease and Brown Algae Compounds' Interaction. Mar Drugs 2023; 21:626. [PMID: 38132947 PMCID: PMC10744363 DOI: 10.3390/md21120626] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 11/22/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023] Open
Abstract
Middle East Respiratory Syndrome (MERS) is a viral respiratory disease caused b a special type of coronavirus called MERS-CoV. In the search for effective substances against the MERS-CoV main protease, we looked into compounds from brown algae, known for their medicinal benefits. From a set of 1212 such compounds, our computer-based screening highlighted four-CMNPD27819, CMNPD1843, CMNPD4184, and CMNPD3156. These showed good potential in how they might attach to the MERS-CoV protease, comparable to a known inhibitor. We confirmed these results with multiple computer tests. Studies on the dynamics and steadiness of these compounds with the MERS-CoV protease were performed using molecular dynamics (MD) simulations. Metrics like RMSD and RMSF showed their stability. We also studied how these compounds and the protease interact in detail. An analysis technique, PCA, showed changes in atomic positions over time. Overall, our computer studies suggest brown algae compounds could be valuable in fighting MERS. However, experimental validation is needed to prove their real-world effectiveness.
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Affiliation(s)
- Hattan S. Gattan
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia; (H.S.G.); (M.M.A.); (L.H.B.); (T.A.A.); (M.M.E.-D.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Maha Mahmoud Alawi
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia; (H.S.G.); (M.M.A.); (L.H.B.); (T.A.A.); (M.M.E.-D.)
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Infection Control & Environmental Health Unit, King Abdulaziz University Hospital, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Leena H. Bajrai
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia; (H.S.G.); (M.M.A.); (L.H.B.); (T.A.A.); (M.M.E.-D.)
- Biochemistry Department, Faculty of Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Thamir A. Alandijany
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia; (H.S.G.); (M.M.A.); (L.H.B.); (T.A.A.); (M.M.E.-D.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Isra M. Alsaady
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia; (H.S.G.); (M.M.A.); (L.H.B.); (T.A.A.); (M.M.E.-D.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Mai M. El-Daly
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia; (H.S.G.); (M.M.A.); (L.H.B.); (T.A.A.); (M.M.E.-D.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Vivek Dhar Dwivedi
- Center for Global Health Research, Saveetha Institute of Medical and Technical Sciences, Saveetha Medical College and Hospitals, Saveetha University, Chennai 605102, India
- Bioinformatics Research Division, Quanta Calculus, Greater Noida 201310, India
| | - Esam I. Azhar
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia; (H.S.G.); (M.M.A.); (L.H.B.); (T.A.A.); (M.M.E.-D.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
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Sokouti B. A review on in silico virtual screening methods in COVID-19 using anticancer drugs and other natural/chemical inhibitors. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2023; 4:994-1026. [PMID: 38023988 PMCID: PMC10651357 DOI: 10.37349/etat.2023.00177] [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: 12/30/2022] [Accepted: 05/22/2023] [Indexed: 12/01/2023] Open
Abstract
The present coronavirus disease 2019 (COVID-19) pandemic scenario has posed a difficulty for cancer treatment. Even under ideal conditions, malignancies like small cell lung cancer (SCLC) are challenging to treat because of their fast development and early metastases. The treatment of these patients must not be jeopardized, and they must be protected as much as possible from the continuous spread of the COVID-19 infection. Initially identified in December 2019 in Wuhan, China, the contagious coronavirus illness 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Finding inhibitors against the druggable targets of SARS-CoV-2 has been a significant focus of research efforts across the globe. The primary motivation for using molecular modeling tools against SARS-CoV-2 was to identify candidates for use as therapeutic targets from a pharmacological database. In the published study, scientists used a combination of medication repurposing and virtual drug screening methodologies to target many structures of SARS-CoV-2. This virus plays an essential part in the maturation and replication of other viruses. In addition, the total binding free energy and molecular dynamics (MD) modeling findings showed that the dynamics of various medications and substances were stable; some of them have been tested experimentally against SARS-CoV-2. Different virtual screening (VS) methods have been discussed as potential means by which the evaluated medications that show strong binding to the active site might be repurposed for use against SARS-CoV-2.
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Affiliation(s)
- Babak Sokouti
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz 5165665813, Iran
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AL-Taee HSR, Sekhi AA, Gharban HAJ, Biati HMA. Serological identification of MERS-CoV in camels of Wasit province, Iraq. Open Vet J 2023; 13:1283-1289. [PMID: 38027406 PMCID: PMC10658013 DOI: 10.5455/ovj.2023.v13.i10.7] [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: 07/17/2023] [Accepted: 09/11/2023] [Indexed: 12/01/2023] Open
Abstract
Background Since the first human case of Middle East Respiratory Syndrome (MERS) caused by Coronavirus (MERS-CoV) in 2012, several evidence bases have shown one-humped camels as the main reservoir host, from which infection is transmitted to humans. Aim Serological investigation of MERS in dromedary camels in Wasit province (Iraq), detection severity of infection, and association to some risk factors. Methods A total of 455 dromedary camels were selected randomly from two main districts in Wasit province, Iraq, during January and April (2023). Sera of all study camels were examined by enzyme-linked immunosorbent assay (ELISA), and titers of positive study animals were categorized according to their severity. Results Serological testing yielded 37.58% positive animals for MERS infection. According to the severity of positive ODs (titer), a total of 53.22%, 30.99%, 12.28%, and 3.51% showed mild, moderate, strong, and very strong infections, respectively. Regarding risk factors, significant elevation in seropositivity was seen in camels of >3-6 and >6 years old and reduced in camels of £3 years old with an elevated risk of MERS with increased age. Regionally, seropositivity and relative risk were increased in the camels of Shaykh Sa'd when compared with Al-Numaniyah. Regarding sex, no significant variation was detected between seropositive females and males; however, male camels appeared at higher risk than females. Association between the severity of MERS infection and risk factors revealed that there was a significant increase in mild and moderate infections in female camels of >6 years old; whereas strong and very strong infections were seen in male camels of 33-6 years old. Mild and very strong infections were recorded in Shaykh Sa'd; while moderate and strong infections in Al-Numaniyah. Conclusion The study indicated a longstanding existence of MERS-CoV in camels of Wasit province; therefore, recent infections or active viral excretion are required for confirmation by molecular approaches.
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Affiliation(s)
- Hala S. R. AL-Taee
- Department of Microbiology, College of Veterinary Medicine, University of Wasit, Wasit, Iraq
| | - Azhar Ali Sekhi
- Department of Microbiology, College of Medicine, University of Al-Qadisiyah, Al-Qadisiyah, Iraq
| | - Hasanain A. J. Gharban
- Department of Internal and Preventive Veterinary Medicine, College of Veterinary Medicine, University of Wasit, Wasit, Iraq
| | - Hussien M. A. Biati
- Department of Medical Microbiology, College of Medicine, University of Wasit, Wasit, Iraq
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Wang D, Chen Y, Xiang S, Hu H, Zhan Y, Yu Y, Zhang J, Wu P, Liu FY, Kai T, Ding P. Recent advances in immunoassay technologies for the detection of human coronavirus infections. Front Cell Infect Microbiol 2023; 12:1040248. [PMID: 36683684 PMCID: PMC9845787 DOI: 10.3389/fcimb.2022.1040248] [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: 09/09/2022] [Accepted: 11/30/2022] [Indexed: 01/05/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the seventh coronavirus (CoV) that has spread in humans and has become a global pandemic since late 2019. Efficient and accurate laboratory diagnostic methods are one of the crucial means to control the development of the current pandemic and to prevent potential future outbreaks. Although real-time reverse transcription-polymerase chain reaction (rRT-PCR) is the preferred laboratory method recommended by the World Health Organization (WHO) for diagnosing and screening SARS-CoV-2 infection, the versatile immunoassays still play an important role for pandemic control. They can be used not only as supplemental tools to identify cases missed by rRT-PCR, but also for first-line screening tests in areas with limited medical resources. Moreover, they are also indispensable tools for retrospective epidemiological surveys and the evaluation of the effectiveness of vaccination. In this review, we summarize the mainstream immunoassay methods for human coronaviruses (HCoVs) and address their benefits, limitations, and applications. Then, technical strategies based on bioinformatics and advanced biosensors were proposed to improve the performance of these methods. Finally, future suggestions and possibilities that can lead to higher sensitivity and specificity are provided for further research.
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Affiliation(s)
- Danqi Wang
- Xiang Ya School of Public Health, Central South University, Changsha, Hunan, China
| | - Yuejun Chen
- Breast Surgery Department I, Hunan Cancer Hospital, Changsha, Hunan, China
| | - Shan Xiang
- Xiang Ya School of Public Health, Central South University, Changsha, Hunan, China
| | - Huiting Hu
- Breast Surgery Department I, Hunan Cancer Hospital, Changsha, Hunan, China
| | - Yujuan Zhan
- Xiang Ya School of Public Health, Central South University, Changsha, Hunan, China
| | - Ying Yu
- Xiang Ya School of Public Health, Central South University, Changsha, Hunan, China
| | - Jingwen Zhang
- Xiang Ya School of Public Health, Central South University, Changsha, Hunan, China
| | - Pian Wu
- Xiang Ya School of Public Health, Central South University, Changsha, Hunan, China
| | - Fei Yue Liu
- Department of Economics and Management, ChangSha University, Changsha, Hunan, China
| | - Tianhan Kai
- Xiang Ya School of Public Health, Central South University, Changsha, Hunan, China
| | - Ping Ding
- Xiang Ya School of Public Health, Central South University, Changsha, Hunan, China
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Hurtado-Tamayo J, Requena-Platek R, Enjuanes L, Bello-Perez M, Sola I. Contribution to pathogenesis of accessory proteins of deadly human coronaviruses. Front Cell Infect Microbiol 2023; 13:1166839. [PMID: 37197199 PMCID: PMC10183600 DOI: 10.3389/fcimb.2023.1166839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/11/2023] [Indexed: 05/19/2023] Open
Abstract
Coronaviruses (CoVs) are enveloped and positive-stranded RNA viruses with a large genome (∼ 30kb). CoVs include essential genes, such as the replicase and four genes coding for structural proteins (S, M, N and E), and genes encoding accessory proteins, which are variable in number, sequence and function among different CoVs. Accessory proteins are non-essential for virus replication, but are frequently involved in virus-host interactions associated with virulence. The scientific literature on CoV accessory proteins includes information analyzing the effect of deleting or mutating accessory genes in the context of viral infection, which requires the engineering of CoV genomes using reverse genetics systems. However, a considerable number of publications analyze gene function by overexpressing the protein in the absence of other viral proteins. This ectopic expression provides relevant information, although does not acknowledge the complex interplay of proteins during virus infection. A critical review of the literature may be helpful to interpret apparent discrepancies in the conclusions obtained by different experimental approaches. This review summarizes the current knowledge on human CoV accessory proteins, with an emphasis on their contribution to virus-host interactions and pathogenesis. This knowledge may help the search for antiviral drugs and vaccine development, still needed for some highly pathogenic human CoVs.
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Affiliation(s)
| | | | | | | | - Isabel Sola
- *Correspondence: Melissa Bello-Perez, ; Isabel Sola,
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Dzuvor CKO, Tettey EL, Danquah MK. Aptamers as promising nanotheranostic tools in the COVID-19 pandemic era. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2022; 14:e1785. [PMID: 35238490 PMCID: PMC9111085 DOI: 10.1002/wnan.1785] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/02/2022] [Accepted: 02/07/2022] [Indexed: 12/13/2022]
Abstract
The emergence of SARS‐COV‐2, the causative agent of new coronavirus disease (COVID‐19) has become a pandemic threat. Early and precise detection of the virus is vital for effective diagnosis and treatment. Various testing kits and assays, including nucleic acid detection methods, antigen tests, serological tests, and enzyme‐linked immunosorbent assay (ELISA), have been implemented or are being explored to detect the virus and/or characterize cellular and antibody responses to the infection. However, these approaches have inherent drawbacks such as nonspecificity, high cost, are characterized by long turnaround times for test results, and can be labor‐intensive. Also, the circulating SARS‐COV‐2 variant of concerns, reduced antibody sensitivity and/or neutralization, and possible antibody‐dependent enhancement (ADE) have warranted the search for alternative potent therapeutics. Aptamers, which are single‐stranded oligonucleotides, generated artificially by SELEX (Evolution of Ligands by Exponential Enrichment) may offer the capacity to generate high‐affinity neutralizers and/or bioprobes for monitoring relevant SARS‐COV‐2 and COVID‐19 biomarkers. This article reviews and discusses the prospects of implementing aptamers for rapid point‐of‐care detection and treatment of SARS‐COV‐2. We highlight other SARS‐COV‐2 targets (N protein, spike protein stem‐helix), SELEX augmented with competition assays and in silico technologies for rapid discovery and isolation of theranostic aptamers against COVID‐19 and future pandemics. It further provides an overview on site‐specific bioconjugation approaches, customizable molecular scaffolding strategies, and nanotechnology platforms to engineer these aptamers into ultrapotent blockers, multivalent therapeutics, and vaccines to boost both humoral and cellular immunity against the virus. This article is categorized under:Therapeutic Approaches and Drug Discovery > Emerging Technologies Diagnostic Tools > Biosensing Therapeutic Approaches and Drug Discovery > Nanomedicine for Infectious Disease Therapeutic Approaches and Drug Discovery > Nanomedicine for Respiratory Disease
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Affiliation(s)
- Christian K O Dzuvor
- Bioengineering Laboratory, Department of Chemical and Biological Engineering, Monash University, Clayton, Victoria, Australia
| | | | - Michael K Danquah
- Department of Chemical Engineering, University of Tennessee, Chattanooga, Tennessee, USA
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Chourasia R, Padhi S, Phukon LC, Abedin MM, Sirohi R, Singh SP, Rai AK. Peptide candidates for the development of therapeutics and vaccines against β-coronavirus infection. Bioengineered 2022; 13:9435-9454. [PMID: 35387556 PMCID: PMC9161909 DOI: 10.1080/21655979.2022.2060453] [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] [Indexed: 01/18/2023] Open
Abstract
Betacoronaviruses (β-CoVs) have caused major viral outbreaks in the last two decades in the world. The mutation and recombination abilities in β-CoVs resulted in zoonotic diseases in humans. Proteins responsible for viral attachment and replication are highly conserved in β-CoVs. These conserved proteins have been extensively studied as targets for preventing infection and the spread of β-CoVs. Peptides are among the most promising candidates for developing vaccines and therapeutics against viral pathogens. The immunostimulatory and viral inhibitory potential of natural and synthetic peptides has been extensively studied since the SARS-CoV outbreak. Food-derived peptides demonstrating high antiviral activity can be used to develop effective therapeutics against β-CoVs. Specificity, tolerability, and customizability of peptides can be explored to develop potent drugs against β-CoVs. However, the proteolytic susceptibility and low bioavailability of peptides pose challenges for the development of therapeutics. This review illustrates the potential role of peptides in eliciting an adaptive immune response and inhibiting different stages of the β-CoV life cycle. Further, the challenges and future directions associated with developing peptide-based therapeutics and vaccines against existing and future β-CoV pathogens have been discussed.
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Affiliation(s)
- Rounak Chourasia
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Regional Centre, Tadong- 737102, India
| | - Srichandan Padhi
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Regional Centre, Tadong- 737102, India
| | - Loreni Chiring Phukon
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Regional Centre, Tadong- 737102, India
| | - Md Minhajul Abedin
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Regional Centre, Tadong- 737102, India
| | - Ranjana Sirohi
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, 02841, Republic of Korea
| | - Sudhir P Singh
- Centre of Innovative and Applied Bioprocessing (DBT-CIAB), Sector-81, S.A.S. Nagar, Mohali- 140306, India
| | - Amit Kumar Rai
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Regional Centre, Tadong- 737102, India.,Institute of Bioresources and Sustainable Development (DBT-IBSD), Mizoram Node, Aizawl, India
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Kandeel M, Kim J, Fayez M, Kitade Y, Kwon HJ. Antiviral drug discovery by targeting the SARS-CoV-2 polyprotein processing by inhibition of the main protease. PeerJ 2022; 10:e12929. [PMID: 35186496 PMCID: PMC8833224 DOI: 10.7717/peerj.12929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 01/21/2022] [Indexed: 01/11/2023] Open
Abstract
The spread of SARS-CoV-2, the causative agent for COVID-19, has led to a global and deadly pandemic. To date, few drugs have been approved for treating SARS-CoV-2 infections. In this study, a structure-based approach was adopted using the SARS-CoV-2 main protease (Mpro) and a carefully selected dataset of 37,060 compounds comprising Mpro and antiviral protein-specific libraries. The compounds passed two-step docking filtration, starting with standard precision (SP) followed by extra precision (XP) runs. Fourteen compounds with the highest XP docking scores were examined by 20 ns molecular dynamics simulations (MDs). Based on backbone route mean square deviations (RMSD) and molecular mechanics/generalized Born surface area (MM/GBSA) binding energy, four drugs were selected for comprehensive MDs analysis at 100 ns. Results indicated that birinapant, atazanavir, and ritonavir potently bound and stabilized SARS-CoV-2 Mpro structure. Binding energies higher than -102 kcal/mol, RMSD values <0.22 nm, formation of several hydrogen bonds with Mpro, favourable electrostatic contributions, and low radii of gyration were among the estimated factors contributing to the strength of the binding of these three compounds with Mpro. The top two compounds, atazanavir and birinapant, were tested for their ability to prevent SARS-CoV-2 plaque formation. At 10 µM of birinapant concentration, antiviral tests against SARS-CoV-2 demonstrated a 37% reduction of virus multiplication. Antiviral assays demonstrated that birinapant has high anti-SARS-CoV-2 activity in the low micromolar range, with an IC50 value of 18 ± 3.6 µM. Therefore, birinapant is a candidate for further investigation to determine whether it is a feasible therapy option.
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Affiliation(s)
- Mahmoud Kandeel
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-hofuf, Al-ahsa, Saudi Arabia,Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelshikh University, Kafrelshikh, Egypt
| | - Jinsoo Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, South Korea
| | - Mahmoud Fayez
- Al-Ahsa Veterinary Diagnostic Laboratory, Ministry of Agriculture, Al-Ahsa, Saudi Arabia,Veterinary Serum and Vaccine Institute, Cairo, Dokki, Egypt
| | - Yukio Kitade
- Department of Applied Chemistry, Faculty of Engineering, Aichi Institute of Technology, Toyota, Japan
| | - Hyung-Joo Kwon
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, South Korea
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Mohamed N, Hamad MA, Ghaleb AH, Esmat G, Elsabahy M. Applications of nanoengineered therapeutics and vaccines: special emphasis on COVID-19. IMMUNOMODULATORY EFFECTS OF NANOMATERIALS 2022. [PMCID: PMC9212255 DOI: 10.1016/b978-0-323-90604-3.00003-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nanomedicine provides innovative strategies that had significantly improved drug and gene delivery and allowed control over the engineering of therapeutics, diagnostics, vaccines, and other medical devices, for a diversity of medical applications. This review focuses on the current attempts to develop potent nanoengineered vaccines and therapeutics against coronaviruses, and the recent fabrication strategies and design principles to control acute infections from the escalating SARS-CoV-2 pandemic. Nanomedical approaches provide versatile platforms that can be utilized to enhance the overall potency, safety, and stability of vaccines, thus augmenting the desired immune response. Their modulable conformational features of size, shape, surface charge, antigen display, and composition allow for precise tuning and optimization of the nanoconstructs for the management of a variety of diseases and pathological conditions. The ability to control the release of their encapsulated cargoes and the possibility of surface decoration with various moieties support the construction of multifunctional nanomaterials that ultimately boost and prolong the immune response elicited and/or therapeutic effects, selectively at the diseased tissues and target sites.
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Filipe HAL, Fiuza SM, Henriques CA, Antunes FE. Antiviral and antibacterial activity of hand sanitizer and surface disinfectant formulations. Int J Pharm 2021; 609:121139. [PMID: 34592397 DOI: 10.1016/j.ijpharm.2021.121139] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 09/13/2021] [Accepted: 09/24/2021] [Indexed: 01/04/2023]
Abstract
Emergent diseases caused by viral and bacterial infections have proven to be a current and future challenge. The occurrence of these diseases is usually accompanied by the lack of vaccines and dedicated therapies leaving prevention as the best strategy to adopt. In that context, and apart from confinement and physical distancing measures, an increase in hygiene actions, namely hand and surface cleaning and disinfection can reduce the infection spread originated from our day-to-day routines. However, during crisis situations the high disinfectants demand can very likely lead to having them running out of stock. This impels many individuals and companies to produce their own disinfectants. Here, we explore the main components of a disinfection formulation, both for hand-rub and surface cleaning. Alcohol and non-alcohol based formulations are described, including the possibility to fine tune the properties of the final product in order to increase public acceptance while maintaining product efficacy. The action mechanisms of the main active principles are also described conjugating information from experimental and theoretical data. Overall, the main aspects to develop a disinfectant formulation are addressed, as well as their function, helping formulation developers to better understand the impact of their choices.
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Affiliation(s)
- Hugo A L Filipe
- Coimbra Chemistry Centre, Dept. of Chemistry, University of Coimbra, Rua Larga, 3004-535, Coimbra, Portugal; CPIRN-IPG-Center of Potential and Innovation of Natural Resources, Polytechnic Institute of Guarda, 6300-559 Guarda, Portugal.
| | - Sónia M Fiuza
- Science351, IPN (Edifício C) Rua Pedro Nunes, 3030-199 Coimbra, Portugal
| | - César A Henriques
- EcoXperience, HIESE, Quinta Vale do Espinhal, 3230-343 Penela, Portugal
| | - Filipe E Antunes
- Coimbra Chemistry Centre, Dept. of Chemistry, University of Coimbra, Rua Larga, 3004-535, Coimbra, Portugal
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12
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Du N, Ye F, Sun J, Liu K. Stimuli-Responsive Natural Proteins and Their Applications. Chembiochem 2021; 23:e202100416. [PMID: 34773331 DOI: 10.1002/cbic.202100416] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 11/12/2021] [Indexed: 01/02/2023]
Abstract
Natural proteins are essential biomacromolecules that fulfill versatile functions in the living organism, such as their usage as cytoskeleton, nutriment transporter, homeostasis controller, catalyzer, or immune guarder. Due to the excellent mechanical properties and good biocompatibility/biodegradability, natural protein-based biomaterials are well equipped for prospective applications in various fields. Among these natural proteins, stimuli-responsive proteins can be reversibly and precisely manipulated on demand, rendering the protein-based biomaterials promising candidates for numerous applications, including disease detection, drug delivery, bio-sensing, and regenerative medicine. Therefore, we present some typical natural proteins with diverse physical stimuli-responsive properties, including temperature, light, force, electrical, and magnetic sensing in this review. The structure-function mechanism of these proteins is discussed in detail. Finally, we give a summary and perspective for the development of stimuli-responsive proteins.
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Affiliation(s)
- Na Du
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325001, P. R. China.,State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
| | - Fangfu Ye
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325001, P. R. China
| | - Jing Sun
- Institute of Organic Chemistry, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Kai Liu
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China.,Department of Chemistry, Tsinghua University, Beijing, 100084, P. R. China
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13
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Das A, Roy S, Swarnakar S, Chatterjee N. Understanding the immunological aspects of SARS-CoV-2 causing COVID-19 pandemic: A therapeutic approach. Clin Immunol 2021; 231:108804. [PMID: 34303849 PMCID: PMC8378842 DOI: 10.1016/j.clim.2021.108804] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 05/03/2021] [Accepted: 07/20/2021] [Indexed: 12/28/2022]
Abstract
In December 2019, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), a novel variant of coronavirus has emerged from Wuhan in China and has created havoc impulses across the world with a larger number of fatalities. At the same time, studies are on roll to discover potent vaccine against it or repurposing of approved drugs which are widely adopted are under trial to eradicate the SARS-CoV-2 causing COVID-19 pandemic. Reports have also shown that there are asymptomatic carriers of COVID-19 disease who can transmit the disease to others too. However, the first line defense of the viral attack is body's strong and well-coordinated immune response producing excessive inflammatory innate reaction, thus impaired adaptive host immune defense which lead to death upon the malfunctioning. Considerable works are going on to establish the relation between immune parameters and viral replication that, might alter both the innate and adaptive immune system of COVID-19 patient by up riding a massive cytokines and chemokines secretion. This review mainly gives an account on how SARS-CoV-2 interacts with our immune system and how does our immune system responds to it, along with that drugs which are being used or can be used in fighting COVID-19 disease. The curative therapies as treatment for it have also been addressed in the perspective of adaptive immunity of the patients.
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Affiliation(s)
- Ananya Das
- Department of Receptor Biology and Tumor Metastasis, Chittaranjan National Cancer Institute, Kolkata, India
| | - Sraddhya Roy
- Department of Receptor Biology and Tumor Metastasis, Chittaranjan National Cancer Institute, Kolkata, India
| | - Snehasikta Swarnakar
- Department of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India.
| | - Nabanita Chatterjee
- Department of Receptor Biology and Tumor Metastasis, Chittaranjan National Cancer Institute, Kolkata, India.
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14
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Guo Q, Li M, Wang C, Guo J, Jiang X, Tan J, Wu S, Wang P, Xiao T, Zhou M, Fang Z, Xiao Y, Zhu H. Predicting hosts based on early SARS-CoV-2 samples and analyzing the 2020 pandemic. Sci Rep 2021; 11:17422. [PMID: 34465838 PMCID: PMC8408148 DOI: 10.1038/s41598-021-96903-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 08/18/2021] [Indexed: 11/16/2022] Open
Abstract
The SARS-CoV-2 pandemic has raised concerns in the identification of the hosts of the virus since the early stages of the outbreak. To address this problem, we proposed a deep learning method, DeepHoF, based on extracting viral genomic features automatically, to predict the host likelihood scores on five host types, including plant, germ, invertebrate, non-human vertebrate and human, for novel viruses. DeepHoF made up for the lack of an accurate tool, reaching a satisfactory AUC of 0.975 in the five-classification, and could make a reliable prediction for the novel viruses without close neighbors in phylogeny. Additionally, to fill the gap in the efficient inference of host species for SARS-CoV-2 using existing tools, we conducted a deep analysis on the host likelihood profile calculated by DeepHoF. Using the isolates sequenced in the earliest stage of the COVID-19 pandemic, we inferred that minks, bats, dogs and cats were potential hosts of SARS-CoV-2, while minks might be one of the most noteworthy hosts. Several genes of SARS-CoV-2 demonstrated their significance in determining the host range. Furthermore, a large-scale genome analysis, based on DeepHoF's computation for the later pandemic in 2020, disclosed the uniformity of host range among SARS-CoV-2 samples and the strong association of SARS-CoV-2 between humans and minks.
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Affiliation(s)
- Qian Guo
- State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
- Center for Quantitative Biology, Peking University, Beijing, 100871, China
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
| | - Mo Li
- Peking University-Tsinghua University-National Institute of Biological Sciences (PTN) Joint PhD Program, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Chunhui Wang
- Peking University-Tsinghua University-National Institute of Biological Sciences (PTN) Joint PhD Program, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jinyuan Guo
- State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
| | - Xiaoqing Jiang
- State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
- Center for Quantitative Biology, Peking University, Beijing, 100871, China
- Institute of Medical Technology, Peking University Health Science Center, Beijing, 100191, China
| | - Jie Tan
- State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
| | - Shufang Wu
- State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
- Center for Quantitative Biology, Peking University, Beijing, 100871, China
| | - Peihong Wang
- State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
| | - Tingting Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Man Zhou
- State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
- Center for Quantitative Biology, Peking University, Beijing, 100871, China
| | - Zhencheng Fang
- State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
- Center for Quantitative Biology, Peking University, Beijing, 100871, China
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310006, China.
| | - Huaiqiu Zhu
- State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China.
- Center for Quantitative Biology, Peking University, Beijing, 100871, China.
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA.
- Institute of Medical Technology, Peking University Health Science Center, Beijing, 100191, China.
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15
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Zhu L, Gao T, Fu Y, Han X, Yue J, Liu Y, Liu H, Dong Q, Yang W, Hu Y, Jin Y, Li P, Liu X, Cao C. The MERS-CoV N Protein Regulates Host Cytokinesis and Protein Translation via Interaction With EF1A. Front Microbiol 2021; 12:551602. [PMID: 34248858 PMCID: PMC8261062 DOI: 10.3389/fmicb.2021.551602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 04/14/2021] [Indexed: 01/19/2023] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV), a pathogen causing severe respiratory disease in humans that emerged in June 2012, is a novel beta coronavirus similar to severe acute respiratory syndrome coronavirus (SARS-CoV). In this study, immunoprecipitation and proximity ligation assays revealed that the nucleocapsid (N) protein of MERS-CoV interacted with human translation elongation factor 1A (EF1A), an essential component of the translation system with important roles in protein translation, cytokinesis, and filamentous actin (F-actin) bundling. The C-terminal motif (residues 359–363) of the N protein was the crucial domain involved in this interaction. The interaction between the MERS-CoV N protein and EF1A resulted in cytokinesis inhibition due to the formation of inactive F-actin bundles, as observed in an in vitro actin polymerization assay and in MERS-CoV-infected cells. Furthermore, the translation of a CoV-like reporter mRNA carrying the MERS-CoV 5′UTR was significantly potentiated by the N protein, indicating that a similar process may contribute to EF1A-associated viral protein translation. This study highlights the crucial role of EF1A in MERS-CoV infection and provides new insights into the pathogenesis of coronavirus infections.
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Affiliation(s)
- Lin Zhu
- Beijing Institute of Biotechnology, Army Institute of Military Medical Sciences, Academy of Military Sciences, Beijing, China.,Institute of Physical Science and Information Technology, Anhui University, Hefei, China
| | - Ting Gao
- Beijing Institute of Biotechnology, Army Institute of Military Medical Sciences, Academy of Military Sciences, Beijing, China
| | - Yangbo Fu
- Beijing Institute of Biotechnology, Army Institute of Military Medical Sciences, Academy of Military Sciences, Beijing, China
| | - Xiujing Han
- Department of Clinical Laboratory, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Junjie Yue
- Beijing Institute of Biotechnology, Army Institute of Military Medical Sciences, Academy of Military Sciences, Beijing, China
| | - Yaoning Liu
- Institute of Physical Science and Information Technology, Anhui University, Hefei, China
| | - Hainan Liu
- Beijing Institute of Biotechnology, Army Institute of Military Medical Sciences, Academy of Military Sciences, Beijing, China
| | - Qincai Dong
- Beijing Institute of Biotechnology, Army Institute of Military Medical Sciences, Academy of Military Sciences, Beijing, China
| | - Weihong Yang
- Institute of Physical Science and Information Technology, Anhui University, Hefei, China
| | - Yong Hu
- Beijing Institute of Biotechnology, Army Institute of Military Medical Sciences, Academy of Military Sciences, Beijing, China
| | - Yanwen Jin
- Beijing Institute of Biotechnology, Army Institute of Military Medical Sciences, Academy of Military Sciences, Beijing, China
| | - Ping Li
- Beijing Institute of Biotechnology, Army Institute of Military Medical Sciences, Academy of Military Sciences, Beijing, China
| | - Xuan Liu
- Beijing Institute of Biotechnology, Army Institute of Military Medical Sciences, Academy of Military Sciences, Beijing, China
| | - Cheng Cao
- Beijing Institute of Biotechnology, Army Institute of Military Medical Sciences, Academy of Military Sciences, Beijing, China
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16
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Attia YA, El-Saadony MT, Swelum AA, Qattan SYA, Al-Qurashi AD, Asiry KA, Shafi ME, Elbestawy AR, Gado AR, Khafaga AF, Hussein EOS, Ba-Awadh H, Tiwari R, Dhama K, Alhussaini B, Alyileili SR, El-Tarabily KA, Abd El-Hack ME. COVID-19: pathogenesis, advances in treatment and vaccine development and environmental impact-an updated review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:22241-22264. [PMID: 33733422 PMCID: PMC7969349 DOI: 10.1007/s11356-021-13018-1] [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: 12/26/2020] [Accepted: 02/15/2021] [Indexed: 05/08/2023]
Abstract
Diseases negatively impact the environment, causing many health risks and the spread of pollution and hazards. A novel coronavirus, severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) has led to a recent respiratory syndrome epidemic in humans. In December 2019, the sudden emergence of this new coronavirus and the subsequent severe disease it causes created a serious global health threat and hazards. This is in contrast to the two aforementioned coronaviruses, SARS-CoV-2 (in 2002) and middle east respiratory syndrome coronavirus MERS-CoV (in 2012), which were much more easily contained. The World Health Organization (WHO) dubbed this contagious respiratory disease an "epidemic outbreak" in March 2020. More than 80 companies and research institutions worldwide are working together, in cooperation with many governmental agencies, to develop an effective vaccine. To date, six authorized vaccines have been registered. Up till now, no approved drugs and drug scientists are racing from development to clinical trials to find new drugs for COVID-19. Wild animals, such as snakes, bats, and pangolins are the main sources of coronaviruses, as determined by the sequence homology between MERS-CoV and viruses in these animals. Human infection is caused by inhalation of respiratory droplets. To date, the only available treatment protocol for COVID-19 is based on the prevalent clinical signs. This review aims to summarize the current information regarding the origin, evolution, genomic organization, epidemiology, and molecular and cellular characteristics of SARS-CoV-2 as well as the diagnostic and treatment approaches for COVID-19 and its impact on global health, environment, and economy.
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Affiliation(s)
- Youssef A Attia
- Agriculture Department, Faculty of Environmental Sciences, King Abdulaziz University, P.O. Box 80208, Jeddah, 21589, Saudi Arabia.
- The Strategic Center to Kingdom Vision Realization, King Abdulaziz University, Jeddah, Saudi Arabia.
- Animal and Poultry Production Department, Faculty of Agriculture, Damanhour University, Damanhour, Egypt.
| | - Mohamed T El-Saadony
- Department of Agricultural Microbiology, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
| | - Ayman A Swelum
- Department of Animal Production, College of Food and Agriculture Sciences, King Saud University, Riyadh, 11451, Saudi Arabia.
- Department of Theriogenology, Faculty of Veterinary Medicine, Zagazig University, Sharkia, Zagazig, 44519, Egypt.
| | - Shaza Y A Qattan
- Department of Biological Sciences, Microbiology, King Abdulaziz University, P.O. Box 80203, Jeddah, 21589, Saudi Arabia
| | - Adel D Al-Qurashi
- Agriculture Department, Faculty of Environmental Sciences, King Abdulaziz University, P.O. Box 80208, Jeddah, 21589, Saudi Arabia
| | - Khalid A Asiry
- Agriculture Department, Faculty of Environmental Sciences, King Abdulaziz University, P.O. Box 80208, Jeddah, 21589, Saudi Arabia
| | - Manal E Shafi
- Department of Biological Sciences, Zoology, King Abdulaziz University, P.O. Box 80203, Jeddah, 21589, Saudi Arabia
| | - Ahmed R Elbestawy
- Poultry and Fish Diseases Department, Faculty of Veterinary Medicine, Damanhour University, Damanhur, 22511, Egypt
| | - Ahmed R Gado
- Poultry and Fish Diseases Department, Faculty of Veterinary Medicine, Damanhour University, Damanhur, 22511, Egypt
| | - Asmaa F Khafaga
- Department of Pathology, Faculty of Veterinary Medicine, Alexandria University, Edfina, Alexandria, 22758, Egypt
| | - Elsayed O S Hussein
- Department of Animal Production, College of Food and Agriculture Sciences, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Hani Ba-Awadh
- Department of Animal Production, College of Food and Agriculture Sciences, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, Uttar Pradesh Pandit Deen Dayal Upadhyaya Pashu Chikitsa Vigyan Vishwavidyalaya Evam Go Anusandhan Sansthan (DUVASU), Mathura, 281001, India
| | - Kuldeep Dhama
- Division of Pathology, Indian Veterinary Research Institute (IVRI), Izatnagar-243, Bareilly, Uttar Pradesh, 122, India
| | - Bakr Alhussaini
- Department of Pediatric, Faculty of Medicine, King Abdualziz University, Jeddah, Saudi Arabia
| | - Salem R Alyileili
- Department of Integrative Agriculture, College of Food and Agriculture, United Arab Emirates University, 15551, Al-Ain, United Arab Emirates
| | - Khaled A El-Tarabily
- Department of Biology, College of Science, United Arab Emirates University, 15551, Al-Ain, United Arab Emirates.
- Harry Butler Institute, Murdoch University, Murdoch, Western Australia, 6150, Australia.
| | - Mohamed E Abd El-Hack
- Department of Poultry, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
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17
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Protein Intrinsic Disorder and Evolvability of MERS-CoV. Biomolecules 2021; 11:biom11040608. [PMID: 33923962 PMCID: PMC8074149 DOI: 10.3390/biom11040608] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 12/31/2022] Open
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18
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Alshehri MA, Manee MM, Alqahtani FH, Al-Shomrani BM, Uversky VN. On the Prevalence and Potential Functionality of an Intrinsic Disorder in the MERS-CoV Proteome. Viruses 2021; 13:v13020339. [PMID: 33671602 PMCID: PMC7926987 DOI: 10.3390/v13020339] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 02/12/2021] [Accepted: 02/13/2021] [Indexed: 12/14/2022] Open
Abstract
Middle East respiratory syndrome is a severe respiratory illness caused by an infectious coronavirus. This virus is associated with a high mortality rate, but there is as of yet no effective vaccine or antibody available for human immunity/treatment. Drug design relies on understanding the 3D structures of viral proteins; however, arriving at such understanding is difficult for intrinsically disordered proteins, whose disorder-dependent functions are key to the virus’s biology. Disorder is suggested to provide viral proteins with highly flexible structures and diverse functions that are utilized when invading host organisms and adjusting to new habitats. To date, the functional roles of intrinsically disordered proteins in the mechanisms of MERS-CoV pathogenesis, transmission, and treatment remain unclear. In this study, we performed structural analysis to evaluate the abundance of intrinsic disorder in the MERS-CoV proteome and in individual proteins derived from the MERS-CoV genome. Moreover, we detected disordered protein binding regions, namely, molecular recognition features and short linear motifs. Studying disordered proteins/regions in MERS-CoV could contribute to unlocking the complex riddles of viral infection, exploitation strategies, and drug development approaches in the near future by making it possible to target these important (yet challenging) unstructured regions.
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Affiliation(s)
- Manal A. Alshehri
- National Center for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia; (M.A.A.); (M.M.M.); (F.H.A.)
| | - Manee M. Manee
- National Center for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia; (M.A.A.); (M.M.M.); (F.H.A.)
| | - Fahad H. Alqahtani
- National Center for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia; (M.A.A.); (M.M.M.); (F.H.A.)
| | - Badr M. Al-Shomrani
- National Center for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia; (M.A.A.); (M.M.M.); (F.H.A.)
- Correspondence: (B.M.A.-S.); (V.N.U.)
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd, MDC07, Tampa, FL 33612, USA
- Correspondence: (B.M.A.-S.); (V.N.U.)
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19
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Wong NA, Saier MH. The SARS-Coronavirus Infection Cycle: A Survey of Viral Membrane Proteins, Their Functional Interactions and Pathogenesis. Int J Mol Sci 2021; 22:1308. [PMID: 33525632 PMCID: PMC7865831 DOI: 10.3390/ijms22031308] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 02/07/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is a novel epidemic strain of Betacoronavirus that is responsible for the current viral pandemic, coronavirus disease 2019 (COVID-19), a global health crisis. Other epidemic Betacoronaviruses include the 2003 SARS-CoV-1 and the 2009 Middle East Respiratory Syndrome Coronavirus (MERS-CoV), the genomes of which, particularly that of SARS-CoV-1, are similar to that of the 2019 SARS-CoV-2. In this extensive review, we document the most recent information on Coronavirus proteins, with emphasis on the membrane proteins in the Coronaviridae family. We include information on their structures, functions, and participation in pathogenesis. While the shared proteins among the different coronaviruses may vary in structure and function, they all seem to be multifunctional, a common theme interconnecting these viruses. Many transmembrane proteins encoded within the SARS-CoV-2 genome play important roles in the infection cycle while others have functions yet to be understood. We compare the various structural and nonstructural proteins within the Coronaviridae family to elucidate potential overlaps and parallels in function, focusing primarily on the transmembrane proteins and their influences on host membrane arrangements, secretory pathways, cellular growth inhibition, cell death and immune responses during the viral replication cycle. We also offer bioinformatic analyses of potential viroporin activities of the membrane proteins and their sequence similarities to the Envelope (E) protein. In the last major part of the review, we discuss complement, stimulation of inflammation, and immune evasion/suppression that leads to CoV-derived severe disease and mortality. The overall pathogenesis and disease progression of CoVs is put into perspective by indicating several stages in the resulting infection process in which both host and antiviral therapies could be targeted to block the viral cycle. Lastly, we discuss the development of adaptive immunity against various structural proteins, indicating specific vulnerable regions in the proteins. We discuss current CoV vaccine development approaches with purified proteins, attenuated viruses and DNA vaccines.
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Affiliation(s)
- Nicholas A. Wong
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Milton H. Saier
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
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20
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Mishra GP, Panigrahi D. Computational studies of drugs for possible action against Covid-19 infections. ACTA ACUST UNITED AC 2020. [DOI: 10.22270/jddt.v10i6.4381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
SARS-Cov-2 has emerged highly contagious viral infections so far and posed a global threat with significant human casualties and severe economic losses. There is urgent demand to develop rational therapies to control the drastic spread of the virus. Although there is no specific regimens are available to combat this pandemic situation so far. An attempt was made to perform Insilco studies of drugs applicable to respiratory tract infections with crucial SARS-COV-2 main protease (M-pro) enzyme. Insilco docking study was performed with Molegro Virtual Docker 5.5 on number of available medications of different categories specified for respiratory tract infections.Result indicates that Azithromycin, Dexamethasone and Remdesivir are highly effective and mainly interacted with key amino acid residues with hydrogen bonds and displayed excellent docking score -133, -141 and -153 kcal/mole respectively.
This study advocates the possible use Azithromycin, Dexamethasone and Remdesivir drugs in combination to battle this pandemic condition. Further, this study will provide rationalized drugs and target for further in vitro and in vivo studies of SARS-CoV-2, new insights for those drugs currently ongoing clinical studies, and also possible new strategies for drug repositioning to treat SARS-CoV-2 infections.
Keywords: Viruses, SARS-COV-2, Covid-19, Drugs, Computational docking Studies, Drug Design
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21
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Chen J, Hu C, Chen L, Tang L, Zhu Y, Xu X, Chen L, Gao H, Lu X, Yu L, Dai X, Xiang C, Li L. Clinical Study of Mesenchymal Stem Cell Treatment for Acute Respiratory Distress Syndrome Induced by Epidemic Influenza A (H7N9) Infection: A Hint for COVID-19 Treatment. ENGINEERING (BEIJING, CHINA) 2020; 6:1153-1161. [PMID: 32292627 PMCID: PMC7102606 DOI: 10.1016/j.eng.2020.02.006] [Citation(s) in RCA: 157] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 02/21/2020] [Accepted: 02/22/2020] [Indexed: 05/19/2023]
Abstract
H7N9 viruses quickly spread between mammalian hosts and carry the risk of human-to-human transmission, as shown by the 2013 outbreak. Acute respiratory distress syndrome (ARDS), lung failure, and acute pneumonia are major lung diseases in H7N9 patients. Transplantation of mesenchymal stem cells (MSCs) is a promising choice for treating virus-induced pneumonia, and was used to treat H7N9-induced ARDS in 2013. The transplant of MSCs into patients with H7N9-induced ARDS was conducted at a single center through an open-label clinical trial. Based on the principles of voluntariness and informed consent, 44 patients with H7N9-induced ARDS were included as a control group, while 17 patients with H7N9-induced ARDS acted as an experimental group with allogeneic menstrual-blood-derived MSCs. It was notable that MSC transplantation significantly lowered the mortality of the experimental group, compared with the control group (17.6% died in the experimental group while 54.5% died in the control group). Furthermore, MSC transplantation did not result in harmful effects in the bodies of four of the patients who were part of the five-year follow-up period. Collectively, these results suggest that MSCs significantly improve the survival rate of H7N9-induced ARDS and provide a theoretical basis for the treatment of H7N9-induced ARDS in both preclinical research and clinical studies. Because H7N9 and the coronavirus disease 2019 (COVID-19) share similar complications (e.g., ARDS and lung failure) and corresponding multi-organ dysfunction, MSC-based therapy could be a possible alternative for treating COVID-19.
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Affiliation(s)
- Jiajia Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Chenxia Hu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Lijun Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Lingling Tang
- Shulan (Hangzhou)Hospital Affiliated to Zhejiang Shuren University Shulan International Medical College, Hangzhou 310022, China
| | - Yixin Zhu
- Shulan (Hangzhou)Hospital Affiliated to Zhejiang Shuren University Shulan International Medical College, Hangzhou 310022, China
| | - Xiaowei Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Lu Chen
- Innovative Precision Medicine (IPM) Group, Hangzhou 311215, China
| | - Hainv Gao
- Shulan (Hangzhou)Hospital Affiliated to Zhejiang Shuren University Shulan International Medical College, Hangzhou 310022, China
| | - Xiaoqing Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Liang Yu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Xiahong Dai
- Shulan (Hangzhou)Hospital Affiliated to Zhejiang Shuren University Shulan International Medical College, Hangzhou 310022, China
| | - Charlie Xiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
- Shulan (Hangzhou)Hospital Affiliated to Zhejiang Shuren University Shulan International Medical College, Hangzhou 310022, China
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22
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Kyriakopoulos AM, Papaefthymiou A, Georgilas N, Doulberis M, Kountouras J. The Potential Role of Super Spread Events in SARS-COV-2 Pandemic; a Narrative Review. ARCHIVES OF ACADEMIC EMERGENCY MEDICINE 2020; 8:e74. [PMID: 33134970 PMCID: PMC7587986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Coronaviruses, members of Coronaviridae family, cause extensive epidemics of vast diseases like severe acute respiratory syndrome (SARS) and Coronavirus Disease-19 (COVID-19) in animals and humans. Super spread events (SSEs) potentiate early outbreak of the disease and its constant spread in later stages. Viral recombination events within species and across hosts lead to natural selection based on advanced infectivity and resistance. In this review, the importance of containment of SSEs was investigated with emphasis on stopping COVID-19 spread and its socio-economic consequences. A comprehensive search was conducted among literature available in multiple electronic sources to find articles that addressed the "potential role of SSEs on severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) pandemic" and were published before 20th of August 2020. Overall, ninety-eight articles were found eligible and reviewed. Specific screening strategies within potential super spreading host groups can also help to efficiently manage severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) epidemics, in contrast to the partially effective general restriction measures. The effect of SSEs on previous SARS epidemics has been documented in detail. However, the respective potential impact of SSEs on SARS-COV-2 outbreak is composed and presented in the current review, thereby implying the warranted effort required for effective SSE preventive strategies, which may lead to overt global community health benefits. This is crucial for SARS-COV-2 pandemic containment as the vaccine(s) development process will take considerable time to safely establish its potential usefulness for future clinical usage.
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Affiliation(s)
- Anthony M. Kyriakopoulos
- Department of Research and Development, Nasco AD Biotechnology Laboratory, Piraeus 18536, Greece. ,Corresponding author: Anthony M. Kyriakopoulos; Department of Research and Development, Nasco AD Biotechnology Laboratory, 11 Sachtouri Str, Piraeus 18536, Greece. , Fax : 00309210818032
| | - Apostolis Papaefthymiou
- Department of Gastroenterology, University Hospital of Larisa, Larisa 41110, Greece.,Department of Internal Medicine, Second Medical Clinic, Ippokration Hospital, Aristotle University of Thessaloniki, Thessaloniki, 54642 Macedonia, Greece
| | - Nikolaos Georgilas
- Department of Nephrology, Agios Pavlos Hospital of Thessaloniki, Thessaloniki 55134, Macedonia, Greece
| | - Michael Doulberis
- Department of Internal Medicine, Second Medical Clinic, Ippokration Hospital, Aristotle University of Thessaloniki, Thessaloniki, 54642 Macedonia, Greece.,Division of Gastroenterology and Hepatology, University Medical Department Kantonsspital Aarau, Aarau 5001, Switzerland
| | - Jannis Kountouras
- Department of Internal Medicine, Second Medical Clinic, Ippokration Hospital, Aristotle University of Thessaloniki, Thessaloniki, 54642 Macedonia, Greece
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23
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Zhang N, Shang J, Li C, Zhou K, Du L. An overview of Middle East respiratory syndrome coronavirus vaccines in preclinical studies. Expert Rev Vaccines 2020; 19:817-829. [PMID: 32842811 DOI: 10.1080/14760584.2020.1813574] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
INTRODUCTION Middle East respiratory syndrome coronavirus (MERS-CoV) causes high mortality in humans. No vaccines are approved for use in humans; therefore, a consistent effort to develop safe and effective MERS vaccines is needed. AREAS COVERED This review describes the structure of MERS-CoV and the function of its proteins, summarizes MERS vaccine candidates under preclinical study (based on spike and non-spike structural proteins, inactivated virus, and live-attenuated virus), and highlights potential problems that could prevent these vaccines entering clinical trials. It provides guidance for the development of safe and effective MERS-CoV vaccines. EXPERT OPINION Although many MERS-CoV vaccines have been developed, most remain at the preclinical stage. Some vaccines demonstrate immunogenicity and efficacy in animal models, while others have potential adverse effects or low efficacy against high-dose or divergent virus strains. Novel strategies are needed to design safe and effective MERS vaccines to induce broad-spectrum immune responses and improve protective efficacy against multiple strains of MERS-CoV and MERS-like coronaviruses with pandemic potential. More funds should be invested to move vaccine candidates into human clinical trials.
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Affiliation(s)
- Naru Zhang
- Department of Clinical Medicine, School of Medicine, Zhejiang University City College , Hangzhou, China
| | - Jian Shang
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota , Saint Paul, MN, USA
| | - Chaoqun Li
- Department of Clinical Medicine, School of Medicine, Zhejiang University City College , Hangzhou, China
| | - Kehui Zhou
- Department of Clinical Medicine, School of Medicine, Zhejiang University City College , Hangzhou, China
| | - Lanying Du
- Lindsley F. Kimball Research Institute, New York Blood Center , New York, NY, USA
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24
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Benedetti F, Snyder GA, Giovanetti M, Angeletti S, Gallo RC, Ciccozzi M, Zella D. Emerging of a SARS-CoV-2 viral strain with a deletion in nsp1. J Transl Med 2020; 18:329. [PMID: 32867854 PMCID: PMC7457216 DOI: 10.1186/s12967-020-02507-5] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 08/26/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The new Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), which was first detected in Wuhan (China) in December of 2019 is responsible for the current global pandemic. Phylogenetic analysis revealed that it is similar to other betacoronaviruses, such as SARS-CoV and Middle-Eastern Respiratory Syndrome, MERS-CoV. Its genome is ∼ 30 kb in length and contains two large overlapping polyproteins, ORF1a and ORF1ab that encode for several structural and non-structural proteins. The non-structural protein 1 (nsp1) is arguably the most important pathogenic determinant, and previous studies on SARS-CoV indicate that it is both involved in viral replication and hampering the innate immune system response. Detailed experiments of site-specific mutagenesis and in vitro reconstitution studies determined that the mechanisms of action are mediated by (a) the presence of specific amino acid residues of nsp1 and (b) the interaction between the protein and the host's small ribosomal unit. In fact, substitution of certain amino acids resulted in reduction of its negative effects. METHODS A total of 17,928 genome sequences were obtained from the GISAID database (December 2019 to July 2020) from patients infected by SARS-CoV-2 from different areas around the world. Genomes alignment was performed using MAFFT (REFF) and the nsp1 genomic regions were identified using BioEdit and verified using BLAST. Nsp1 protein of SARS-CoV-2 with and without deletion have been subsequently modelled using I-TASSER. RESULTS We identified SARS-CoV-2 genome sequences, from several Countries, carrying a previously unknown deletion of 9 nucleotides in position 686-694, corresponding to the AA position 241-243 (KSF). This deletion was found in different geographical areas. Structural prediction modelling suggests an effect on the C-terminal tail structure. CONCLUSIONS Modelling analysis of a newly identified deletion of 3 amino acids (KSF) of SARS-CoV-2 nsp1 suggests that this deletion could affect the structure of the C-terminal region of the protein, important for regulation of viral replication and negative effect on host's gene expression. In addition, substitution of the two amino acids (KS) from nsp1 of SARS-CoV was previously reported to revert loss of interferon-alpha expression. The deletion that we describe indicates that SARS-CoV-2 is undergoing profound genomic changes. It is important to: (i) confirm the spreading of this particular viral strain, and potentially of strains with other deletions in the nsp1 protein, both in the population of asymptomatic and pauci-symptomatic subjects, and (ii) correlate these changes in nsp1 with potential decreased viral pathogenicity.
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Affiliation(s)
- Francesca Benedetti
- Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, USA.,Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, USA
| | - Greg A Snyder
- Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, USA.,Department of Microbiology and Immunology, University of Maryland, Baltimore, USA
| | - Marta Giovanetti
- Flavivirus Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Silvia Angeletti
- Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy
| | - Robert C Gallo
- Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, USA.,Department of Medicine, University of Biomedical Campus, Rome, Italy.,Global Virus Network, Baltimore, USA
| | - Massimo Ciccozzi
- Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy.
| | - Davide Zella
- Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, USA. .,Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, USA. .,Global Virus Network, Baltimore, USA.
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25
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Clinical study using mesenchymal stem cells for the treatment of patients with severe COVID-19. Front Med 2020; 14:664-673. [PMID: 32761491 PMCID: PMC7406954 DOI: 10.1007/s11684-020-0810-9] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 06/10/2020] [Indexed: 01/08/2023]
Abstract
The Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 was identified in December 2019. The symptoms include fever, cough, dyspnea, early symptom of sputum, and acute respiratory distress syndrome (ARDS). Mesenchymal stem cell (MSC) therapy is the immediate treatment used for patients with severe cases of COVID-19. Herein, we describe two confirmed cases of COVID-19 in Wuhan to explore the role of MSC in the treatment of COVID-19. MSC transplantation increases the immune indicators (including CD4 and lymphocytes) and decreases the inflammation indicators (interleukin-6 and C-reactive protein). High-flow nasal cannula can be used as an initial support strategy for patients with ARDS. With MSC transplantation, the fraction of inspired O2 (FiO2) of the two patients gradually decreased while the oxygen saturation (SaO2) and partial pressure of oxygen (PO2) improved. Additionally, the patients’ chest computed tomography showed that bilateral lung exudate lesions were adsorbed after MSC infusion. Results indicated that MSC transplantation provides clinical data on the treatment of COVID-19 and may serve as an alternative method for treating COVID-19, particularly in patients with ARDS.
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26
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Ma J, Shi X, Xu W, Lv F, Wu J, Pan Q, Yang J, Yu J, Cao H, Li L. Development and validation of a risk stratification model for screening suspected cases of COVID-19 in China. Aging (Albany NY) 2020; 12:13882-13894. [PMID: 32727933 PMCID: PMC7425460 DOI: 10.18632/aging.103694] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 06/25/2020] [Indexed: 02/05/2023]
Abstract
How to quickly identify high-risk populations is critical to epidemic control. We developed and validated a risk prediction model for screening SARS-CoV-2 infection in suspected cases with an epidemiological history. A total of 1019 patients, ≥13 years of age, who had an epidemiological history were enrolled from fever clinics between January 2020 and February 2020. Among 103 (10.11%) cases of COVID-19 were confirmed. Multivariable analysis summarized four features associated with increased risk of SARS-CoV-2 infection, summarized in the mnemonic COVID-19-REAL: radiological evidence of pneumonia (1 point), eosinophils < 0.005 × 109/L (1 point), age ≥ 32 years (2 points), and leukocytes < 6.05 × 109 /L (1 point). The area under the ROC curve for the training group was 0.863 (95% CI, 0.813 - 0.912). A cut-off value of less than 3 points for COVID-19-REAL was assigned to define the low-risk population. Only 10 (2.70%) of 371 patients were proved to be SARS-CoV-2 positive, with a negative predictive value of 0.973. External validation was similar. This study provides a simple, practical, and robust screening model, COVID-19-REAL, able to identify populations at high risk for SARS-CoV-2 infection.
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Affiliation(s)
- Jing Ma
- Department of Laboratory Medicine, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Xiaowei Shi
- State Key Laboratory for The Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Weiming Xu
- Taizhou Enze Medical Center (Group) Enze Hospital, Taizhou 318050, China
| | - Feifei Lv
- Department of Laboratory Medicine, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Jian Wu
- State Key Laboratory for The Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Qiaoling Pan
- State Key Laboratory for The Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Jinfeng Yang
- State Key Laboratory for The Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Jiong Yu
- State Key Laboratory for The Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Hongcui Cao
- State Key Laboratory for The Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Lanjuan Li
- State Key Laboratory for The Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
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27
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Pourrajab F, Zare-Khormizi MR, Sheikhha MH. Molecular Basis for Pathogenicity of Human Coronaviruses. Infect Drug Resist 2020; 13:2385-2405. [PMID: 32765013 PMCID: PMC7381773 DOI: 10.2147/idr.s255156] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/24/2020] [Indexed: 12/11/2022] Open
Abstract
Over the past years, several zoonotic viruses have crossed the species barrier into humans and have been causing outbreaks of severe, and often fatal, respiratory illness. The 21st century has seen the worldwide spread of three recognized coronaviruses (CoVs) which can cause pneumonia and severe acute respiratory symptoms (SARSs), SARS, MERS, and recently SARS-CoV-2. Herein, it is raising concerns about the dissemination of another new and highly lethal pandemic outbreak. Preparing for a pandemic outbreak involves a great deal of awareness necessary to stop initial outbreaks, through recognizing the molecular mechanisms underlying virus transmission and pathogenicity. CoV spike protein S is the key determinant of host tropism and viral pathogenicity which can undergo variations and makes the CoV a highly pathogenic and diffusible virus capable of sustained human-to-human transmission and spread easily. The three mentioned CoVs exhibit some similarities in S protein whereby constitute a promising target for the development of prophylactics and therapeutics in the future.
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Affiliation(s)
- Fatemeh Pourrajab
- Nutrition and Food Security Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
- Department of Biochemistry and Molecular Biology, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | | | - Mohammad Hasan Sheikhha
- Biotechnology Research Center, International Campus, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
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28
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AlBalwi MA, Khan A, AlDrees M, Gk U, Manie B, Arabi Y, Alabdulkareem I, AlJohani S, Alghoribi M, AlAskar A, AlAjlan A, Hajeer A. Evolving sequence mutations in the Middle East Respiratory Syndrome Coronavirus (MERS-CoV). J Infect Public Health 2020; 13:1544-1550. [PMID: 32654959 PMCID: PMC7328614 DOI: 10.1016/j.jiph.2020.06.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 06/10/2020] [Accepted: 06/25/2020] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Middle East respiratory syndrome coronavirus (MERS-CoV) has continued to cause sporadic outbreaks of severe respiratory tract infection over the last 8 years. METHODS Complete genome sequencing using next-generation sequencing was performed for MERS-CoV isolates from cases that occurred in Riyadh between 2015 and 2019. Phylogenetic analysis and molecular mutational analysis were carried out to investigate disease severity. RESULTS A total of eight MERS-CoV isolates were subjected to complete genome sequencing. Phylogenetic analysis resulted in the assembly of 7/8 sequences within lineage 3 and one sequence within lineage 4 showing complex genomic recombination. The isolates contained a variety of unique amino acid substitutions in ORF1ab (41), the N protein (10), the S protein (9) and ORF4b (5). CONCLUSION Our study shows that MERS-CoV is evolving. The emergence of new variants carries the potential for increased virulence and could impose a challenge to the global health system. We recommend the sequencing every new MERS-CoV isolate to observe the changes in the virus and relate them to clinical outcomes.
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Affiliation(s)
- Mohammed Ali AlBalwi
- Department of Pathology & Laboratory Medicine, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia; King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia; King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.
| | - Anis Khan
- The University of Sydney, Sydney, Austria
| | - Mohammed AlDrees
- King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia; King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | | | | | - Yaseen Arabi
- King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia; King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia; Department of Intensive Care Unit, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Ibrahim Alabdulkareem
- Health Sciences Research Center, King Abdullah Bin Abdulaziz University Hospital, Prince Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Sameera AlJohani
- Department of Pathology & Laboratory Medicine, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia; King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia; King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Majed Alghoribi
- King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia; King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Ahmed AlAskar
- King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia; King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Abdulaziz AlAjlan
- Department of Pathology & Laboratory Medicine, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia; King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia; King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Ali Hajeer
- Department of Pathology & Laboratory Medicine, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia; King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia; King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
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29
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Yoshimoto FK. The Proteins of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS CoV-2 or n-COV19), the Cause of COVID-19. Protein J 2020; 39:198-216. [PMID: 32447571 PMCID: PMC7245191 DOI: 10.1007/s10930-020-09901-4] [Citation(s) in RCA: 336] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The devastating effects of the recent global pandemic (termed COVID-19 for "coronavirus disease 2019") caused by the severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) are paramount with new cases and deaths growing at an exponential rate. In order to provide a better understanding of SARS CoV-2, this article will review the proteins found in the SARS CoV-2 that caused this global pandemic.
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Affiliation(s)
- Francis K Yoshimoto
- Department of Chemistry, The University of Texas at San Antonio (UTSA), San Antonio, TX, 78249-0698, USA.
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30
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Kandeel M, Al-Nazawi M. Virtual screening and repurposing of FDA approved drugs against COVID-19 main protease. Life Sci 2020; 251:117627. [PMID: 32251634 PMCID: PMC7194560 DOI: 10.1016/j.lfs.2020.117627] [Citation(s) in RCA: 223] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/27/2020] [Accepted: 03/30/2020] [Indexed: 02/06/2023]
Abstract
Aims In December 2019, the Coronavirus disease-2019 (COVID-19) virus has emerged in Wuhan, China. In this research, the first resolved COVID-19 crystal structure (main protease) was targeted in a virtual screening study by of FDA approved drugs dataset. In addition, a knowledge gap in relations of COVID-19 with the previously known fatal Coronaviruses (CoVs) epidemics, SARS and MERS CoVs, was covered by investigation of sequence statistics and phylogenetics. Materials and methods Molecular modeling, virtual screening, docking, sequence comparison statistics and phylogenetics of the COVID-19 main protease were investigated. Key findings COVID-19 Mpro formed a phylogenetic group with SARS CoV that was distant from MERS CoV. The identity% was 96.061 and 51.61 for COVID-19/SARS and COVID-19/MERS CoV sequence comparisons, respectively. The top 20 drugs in the virtual screening studies comprised a broad-spectrum antiviral (ribavirin), anti-hepatitis B virus (telbivudine), two vitamins (vitamin B12 and nicotinamide) and other miscellaneous systemically acting drugs. Of special interest, ribavirin had been used in treating cases of SARS CoV. Significance The present study provided a comprehensive targeting of the first resolved COVID+19 structure of Mpro and found a suitable save drugs for repurposing against the viral Mpro. Ribavirin, telbivudine, vitamin B12 and nicotinamide can be combined and used for COVID treatment. This initiative relocates already marketed and approved safe drugs for potential use in COVID-treatment.
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Affiliation(s)
- Mahmoud Kandeel
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-hofuf, 31982, Al-ahsa, Saudi Arabia; Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelshikh University, Kafrelshikh 33516, Egypt.
| | - Mohammed Al-Nazawi
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-hofuf, 31982, Al-ahsa, Saudi Arabia
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