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Fedotova MV, Chuev GN. The Three-Dimensional Reference Interaction Site Model Approach as a Promising Tool for Studying Hydrated Viruses and Their Complexes with Ligands. Int J Mol Sci 2024; 25:3697. [PMID: 38612508 PMCID: PMC11011341 DOI: 10.3390/ijms25073697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024] Open
Abstract
Viruses are the most numerous biological form living in any ecosystem. Viral diseases affect not only people but also representatives of fauna and flora. The latest pandemic has shown how important it is for the scientific community to respond quickly to the challenge, including critically assessing the viral threat and developing appropriate measures to counter this threat. Scientists around the world are making enormous efforts to solve these problems. In silico methods, which allow quite rapid obtention of, in many cases, accurate information in this field, are effective tools for the description of various aspects of virus activity, including virus-host cell interactions, and, thus, can provide a molecular insight into the mechanism of virus functioning. The three-dimensional reference interaction site model (3D-RISM) seems to be one of the most effective and inexpensive methods to compute hydrated viruses, since the method allows us to provide efficient calculations of hydrated viruses, remaining all molecular details of the liquid environment and virus structure. The pandemic challenge has resulted in a fast increase in the number of 3D-RISM calculations devoted to hydrated viruses. To provide readers with a summary of this literature, we present a systematic overview of the 3D-RISM calculations, covering the period since 2010. We discuss various biophysical aspects of the 3D-RISM results and demonstrate capabilities, limitations, achievements, and prospects of the method using examples of viruses such as influenza, hepatitis, and SARS-CoV-2 viruses.
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Affiliation(s)
- Marina V. Fedotova
- G.A. Krestov Institute of Solution Chemistry, The Russian Academy of Sciences, Akademicheskaya St., 1, 153045 Ivanovo, Russia
| | - Gennady N. Chuev
- Institute of Theoretical and Experimental Biophysics, The Russian Academy of Sciences, Institutskaya St., 142290 Pushchino, Russia
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Alshammari SO. Marine Brown Algae-Derived Compounds as Potential Inhibitors of Japanese Encephalitis Virus RNA-Dependent RNA Polymerase. Mar Drugs 2024; 22:92. [PMID: 38393063 PMCID: PMC10890675 DOI: 10.3390/md22020092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/07/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024] Open
Abstract
The Japanese encephalitis virus (JEV) is a mosquito-borne flavivirus that primarily affects people in Asia and seriously threatens public health. Considering the rising occurrence rates and lack of targeted antiviral treatments, it is essential to comprehend and tackle obstacles related to JEV in order to lessen its influence on world health. This investigation explores compounds derived from marine brown algae (Phaeophyceae) as potential inhibitors of JEV RNA-dependent RNA polymerase (RdRp), a critical enzyme in the virus's replication cycle. Employing the computational virtual screen approach, four compounds, i.e., CMNPD16749, CMNPD2606, CMNPD27817, and CMNPD23662, with favorable binding energies ranging from -15.7 Kcal/mol to -13.9 kcal/mol were identified. Subsequently, through molecular docking analysis, the interactions responsible for the binding stability between the target protein and hit molecules compared to the reference molecule Galidesvir were studied. Further, through extensive molecular dynamic (MD) simulation studies at 200 ns, it was confirmed that each docked complex showed acceptable dynamic stability compared to the reference molecule. These findings were further validated using MM/PBSA free binding energy calculations, PCA analysis and free energy landscape construction. These computational findings suggested that the brown algae-derived compounds may act as an antiviral drug against JEV infection and lay a crucial foundation for future experimental studies against JEV.
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Affiliation(s)
- Saud O Alshammari
- Department of Pharmacognosy and Alternative Medicine, Faculty of Pharmacy, Northern Border University, Rafha 76321, Saudi Arabia
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3
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Aghamali M, Kazemi A, Asgharzadeh M, Kafil HS. COVID-19, HIV, and Cryptococcal Meningitis Coinfections with Abnormal Laboratory Findings. Case Rep Pulmonol 2023; 2023:2868290. [PMID: 38034910 PMCID: PMC10684319 DOI: 10.1155/2023/2868290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 08/10/2023] [Accepted: 10/20/2023] [Indexed: 12/02/2023] Open
Abstract
Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first introduced in China in 2019, and it has rapidly spread all around the world. Cryptococcus neoformans is the leading cause of fungal meningitis in human immunodeficiency virus- (HIV-) infected patients. A variety of laboratory tests have been introduced for rapid diagnosis of meningitis. Methods Here, we report a case of coinfection with COVID-19 and cryptococcal meningitis in a HIV-positive patient with abnormal laboratory findings. In this case, COVID-19 was positive by polymerase chain reaction (PCR) and computerized tomography (CT) scan diagnosis. Cryptococcal antigen testing of CSF was negative, whereas India ink staining and cerebrospinal fluid (CSF) culture confirmed the presence of C. neoformans. Results Although the patient was in a critical stage of illness, serum and CSF levels of procalcitonin were abnormally low, within normal limits. On the other hand, although initial lumbar puncture had showed elevated protein level, the repeat CSFs presented remarkably reduced protein levels. Our findings indicate that despite COVID-19 infection, procalcitonin level may remain normal in HIV-associated cryptococcal meningitis, and findings of an apparently normal procalcitonin level should not exclude the possibility of infection. Also, antigen testing may present false-negative result, and it should not be the sole laboratory method for diagnosis of infectious meningitis. Consequently, CSF culture and staining is recommended, even when antigen testing of organism is negative and CSF profile is unremarkable. Conclusion Laboratory information should be combined with a good understanding of clinical manifestations of patient to determine if meningitis is present and confirmed COVID-19 should not ignore possibility of other infections for consideration.
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Affiliation(s)
- Mina Aghamali
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Abdolhassan Kazemi
- Department of Parasitology, Faculty of Medicine, Medical Philosophy and History Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Asgharzadeh
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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Zmudzinski M, Rut W, Olech K, Granda J, Giurg M, Burda-Grabowska M, Kaleta R, Zgarbova M, Kasprzyk R, Zhang L, Sun X, Lv Z, Nayak D, Kesik-Brodacka M, Olsen SK, Weber J, Hilgenfeld R, Jemielity J, Drag M. Ebselen derivatives inhibit SARS-CoV-2 replication by inhibition of its essential proteins: PL pro and M pro proteases, and nsp14 guanine N7-methyltransferase. Sci Rep 2023; 13:9161. [PMID: 37280236 DOI: 10.1038/s41598-023-35907-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/25/2023] [Indexed: 06/08/2023] Open
Abstract
Proteases encoded by SARS-CoV-2 constitute a promising target for new therapies against COVID-19. SARS-CoV-2 main protease (Mpro, 3CLpro) and papain-like protease (PLpro) are responsible for viral polyprotein cleavage-a process crucial for viral survival and replication. Recently it was shown that 2-phenylbenzisoselenazol-3(2H)-one (ebselen), an organoselenium anti-inflammatory small-molecule drug, is a potent, covalent inhibitor of both the proteases and its potency was evaluated in enzymatic and antiviral assays. In this study, we screened a collection of 34 ebselen and ebselen diselenide derivatives for SARS-CoV-2 PLpro and Mpro inhibitors. Our studies revealed that ebselen derivatives are potent inhibitors of both the proteases. We identified three PLpro and four Mpro inhibitors superior to ebselen. Independently, ebselen was shown to inhibit the N7-methyltransferase activity of SARS-CoV-2 nsp14 protein involved in viral RNA cap modification. Hence, selected compounds were also evaluated as nsp14 inhibitors. In the second part of our work, we employed 11 ebselen analogues-bis(2-carbamoylaryl)phenyl diselenides-in biological assays to evaluate their anti-SARS-CoV-2 activity in Vero E6 cells. We present their antiviral and cytoprotective activity and also low cytotoxicity. Our work shows that ebselen, its derivatives, and diselenide analogues constitute a promising platform for development of new antivirals targeting the SARS-CoV-2 virus.
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Affiliation(s)
- Mikolaj Zmudzinski
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland.
| | - Wioletta Rut
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Kamila Olech
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Jarosław Granda
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Mirosław Giurg
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Małgorzata Burda-Grabowska
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Rafał Kaleta
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Michala Zgarbova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nám. 2, 16610, Prague, Czech Republic
| | - Renata Kasprzyk
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
| | - Linlin Zhang
- Institute of Molecular Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Xinyuanyuan Sun
- Institute of Molecular Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Zongyang Lv
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Digant Nayak
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | | | - Shaun K Olsen
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Jan Weber
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nám. 2, 16610, Prague, Czech Republic
| | - Rolf Hilgenfeld
- Institute of Molecular Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, 23562, Lübeck, Germany
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland.
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Bafandeh S, Khodadadi E, Ganbarov K, Asgharzadeh M, Köse Ş, Samadi Kafil H. Natural Products as a Potential Source of Promising Therapeutics for COVID-19 and Viral Diseases. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2023; 2023:5525165. [PMID: 37096202 PMCID: PMC10122587 DOI: 10.1155/2023/5525165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/19/2023] [Accepted: 03/24/2023] [Indexed: 04/26/2023]
Abstract
Background A global pandemic has recently been observed due to the new coronavirus disease, caused by SARS-CoV-2. Since there are currently no antiviral medicines to combat the highly contagious and lethal COVID-19 infection, identifying natural sources that can either be viricidal or boost the immune system and aid in the fight against the disease can be an essential therapeutic support. Methods This review was conducted based on published papers related to the herbal therapy of COVID-19 by search on databases including PubMed and Scopus with herbal, COVID-19, SARS-CoV-2, and therapy keywords. Results To combat this condition, people may benefit from the therapeutic properties of medicinal plants, such as increasing their immune system or providing an antiviral impact. As a result, SARS-CoV-2 infection death rates can be reduced. Various traditional medicinal plants and their bioactive components, such as COVID-19, are summarized in this article to assist in gathering and debating techniques for combating microbial diseases in general and boosting our immune system in particular. Conclusion The immune system benefits from natural products and many of these play a role in activating antibody creation, maturation of immune cells, and stimulation of innate and adaptive immune responses. The lack of particular antivirals for SARS-CoV-2 means that apitherapy might be a viable option for reducing the hazards associated with COVID-19 in the absence of specific antivirals.
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Affiliation(s)
- Soheila Bafandeh
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ehsaneh Khodadadi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Khudaverdi Ganbarov
- Research Laboratory of Microbiology and Virology, Baku State University, Baku, Azerbaijan
| | - Mohammad Asgharzadeh
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Şükran Köse
- Department of Infectious Diseases and Clinical Microbiology, Dokuz Eylül Üniversitesi, Izmir, Turkey
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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Kashi P, Pakdel F, Barhaghi MHS, Rezaee MA, Taghizadeh S, Sadeghi J, Yousefi M, Ghotaslou R, Asgharzadeh M, Gholizadeh P, Kafil HS. Genetic diversity of Mycobacterium tuberculosis isolates from northwest of Iran during COVID-19 era. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2023; 24:3. [PMID: 37519898 PMCID: PMC9829222 DOI: 10.1186/s43042-023-00383-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 12/31/2022] [Indexed: 01/11/2023] Open
Abstract
Background Tuberculosis (TB) is considered one of the most infectious diseases in the world. In this study, we intended to examine the epidemiology of tuberculosis by MIRU-VNTR to define the changes that occur in the transmission of tuberculosis in the region during the COVID-19 era. A total of 120 Mycobacterium tuberculosis isolates were collected from sputum samples of patients referred to East Azerbaijan Center TB from December 2020 to August 2021. Demographic information such as age, sex, place of birth, previous TB history, and relevant medical data was collected. The proportion method was performed for drug susceptibility testing, and the PCR-based MIRU-VNTR method was applied to identify molecular epidemiology relationships. Results The isolates were collected from 78 male (65%) and 39 female (32.5%) Iranian patients and 3 (2.5%) Azerbaijani patients. Ninety-three distinct patterns were identified including 15 clustered patterns and 36 unique patterns. The largest cluster was composed of seven isolates. Furthermore, one cluster with 5 members, four clusters with 3 members, and nine clusters with 2 members. In MIRU-VNTR typing, 75 clusters belonged to the Tabriz region and just 3 to the Republic of Azerbaijan. All isolates were sensitive to rifampin, isoniazid, and ethambutol. Conclusions Results of the current study showed COVID-19 pandemic had a direct effect on the transmission and diagnosis of tuberculosis. Less diagnosis and less clustering can indicate public controls and hygiene, and the use of masks had a direct effect on the transmission and diagnosis of tuberculosis. However, misidentification and less focus on other respiratory infections are expected during the pandemic. Studies on the co-infection of COVID-19 and tuberculosis and the role of mask and sanitization against TB are strongly recommended.
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Affiliation(s)
- Peyvand Kashi
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Farzaneh Pakdel
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | | | - Sepehr Taghizadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Javid Sadeghi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Yousefi
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Reza Ghotaslou
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Asgharzadeh
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Pourya Gholizadeh
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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Köse S, Mandiracioglu A, Özbel Y, Zeyrek S, Dereli Akdeniz D, Kafil HS. Covid-19 vaccination acceptance and hesitancy among the Turkish adult population. GMS HYGIENE AND INFECTION CONTROL 2023; 18:Doc01. [PMID: 36875330 PMCID: PMC9978452 DOI: 10.3205/dgkh000427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Objective The aim of this study was to determine the acceptance of Covid-19 vaccine among the Turkish adult population. Methods A total of 2023 persons participated in this cross-sectional study between October 2020 and January 2021. The questionnaire, which was delivered via social media, was filled out by the participants over "Google Forms". Results Questionnaire results showed that 68.7% of the participants might agree to vaccinated against COVID-19. According to univariate analysis, the age group of 50-59, urban residents, healthcare workers, non-smokers, and those with chronic diseases, those who were vaccinated against influenza, pneumonia, and tetanus were all willing to be vaccinated against COVID-19. Conclusions It is very important to determine a community's willingness to be vaccinated against COVID-19 so that interventions can be made to solve related problems. Risk of exposure and importance of Prevention play a critical role in vaccination acceptance.
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Affiliation(s)
- Sükran Köse
- Department of Infectious Diseases and Clinical Microbiology, Dokuz Eylül Üniversitesi, İzmir, Turkey
| | - Aliye Mandiracioglu
- Ege University Faculty of Medicine, Department of Parasitology, Bornova, İzmir, Turkey
| | - Yusuf Özbel
- Ege University Faculty of Medicine, Department of Public Health, Bornova, İzmir, Turkey
| | - Seheray Zeyrek
- Department of Infectious Diseases and Clinical Microbiology, Dokuz Eylül Üniversitesi, İzmir, Turkey
| | - Didem Dereli Akdeniz
- Department of Endochronology, Faculty of Medicine, Bakirçay University, Izmir, Turkey
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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In Silico Analysis of Bacteriocins from Lactic Acid Bacteria Against SARS-CoV-2. Probiotics Antimicrob Proteins 2023; 15:17-29. [PMID: 34837166 PMCID: PMC8626284 DOI: 10.1007/s12602-021-09879-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2021] [Indexed: 01/18/2023]
Abstract
The COVID-19 pandemic caused by a novel coronavirus (SARS-CoV-2) is a serious health concern in the twenty-first century for scientists, health workers, and all humans. The absence of specific biotherapeutics requires new strategies to prevent the spread and prophylaxis of the novel virus and its variants. The SARS-CoV-2 virus shows pathogenesis by entering the host cells via spike protein and Angiotensin-Converting Enzyme 2 receptor protein. Thus, the present study aims to compute the binding energies between a wide range of bacteriocins with receptor-binding domain (RBD) on spike proteins of wild type (WT) and beta variant (lineage B.1.351). Molecular docking analyses were performed to evaluate binding energies. Upon achieving the best bio-peptides with the highest docking scores, further molecular dynamics (MD) simulations were performed to validate the structure and interaction stability. Protein-protein docking of the chosen 22 biopeptides with WT-RBD showed docking scores lower than -7.9 kcal/mol. Pediocin PA-1 and salivaricin P showed the lowest (best) docking scores of - 12 kcal/mol. Pediocin PA-1, salivaricin B, and salivaricin P showed a remarkable increase in the double mutant's predicted binding affinity with -13.8 kcal/mol, -13.0 kcal/mol, and -12.5 kcal/mol, respectively. Also, a better predicted binding affinity of pediocin PA-1 and salivaricin B against triple mutant was observed compared to the WT. Thus, pediocin PA-1 binds stronger to mutants of the RBD, particularly to double and triple mutants. Salivaricin B showed a better predicted binding affinity towards triple mutant compared to WT, showing that it might be another bacteriocin with potential activity against the SARS-CoV-2 beta variant. Overall, pediocin PA-1, salivaricin P, and salivaricin B are the most promising candidates for inhibiting SARS-CoV-2 (including lineage B.1.351) entrance into the human cells. These bacteriocins derived from lactic acid bacteria hold promising potential for paving an alternative way for treatment and prophylaxis of WT and beta variants.
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Sharma S, Sharma A, Bhattacharyya D, Chauhan RS. Computational identification of potential inhibitory compounds in Indian medicinal and aromatic plant species against major pathogenicity determinants of SARS-CoV-2. J Biomol Struct Dyn 2022; 40:14096-14114. [PMID: 34766880 DOI: 10.1080/07391102.2021.2000500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
SARS-CoV-2 (COVID-19) viral pandemic has been reported across 223 countries and territories. Globalized vaccination programs alongside administration of repurposed drugs will assumingly confer a stronger and longer individual specific immune protection. However, considering possible recurrence of the disease via new variants, a conveniently deliverable phytopharmaceutical drug might be the best option for COVID-19 treatment. In the current study, the efforts have been made to identify potential leads for inhalation therapy as nasal swabs have been reported to transfer viral load prominently. In that direction, 2363 Essential oil (EOs) compounds from Indian medicinal and aromatic plants were screened through docking analysis and potential candidates were shortlisted that can interfere with viral pathogenicity. The main protease (Mpro) of SARS-CoV-2 interacted closely with jatamansin (JM), 6,7-dehydroferruginol (FG) and beta-sitosterol (BS), while Papain-like Protease (PLpro) with friedelane-3-one (F3O) and lantadene D (LD) independently. Reduced Lantadene A (LAR) exhibited preferable interaction with RNA-dependent-RNA-polymerase (RdRp) whereas Lantadene A (LA) with RdRp and spike-glycoprotein (SG-pro) both target proteins. When compared against highest binding affinity conformations of well-known inhibitors of targets, these prioritized compounds conferred superior or comparable SARS-CoV-2 protein inhibition. Additionally, promising results were noted from pharmacokinetics prediction for all shortlisted compounds. Besides, molecular dynamics simulation for 100 ns in two replicates and binding free energy analysis revealed the stability of complexes with optimum compactness. To the best of our knowledge, the current investigation is a unique initial attempt whereby EO compounds have been computationally screened, irrespective of their known medicinal properties to fight COVID-19 infection.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shilpa Sharma
- Department of Biotechnology, School of Engineering & Applied Sciences, Bennett University, Uttar Pradesh, India
| | - Ashish Sharma
- Department of Biotechnology, School of Engineering & Applied Sciences, Bennett University, Uttar Pradesh, India
| | - Dipto Bhattacharyya
- Department of Biotechnology, School of Engineering & Applied Sciences, Bennett University, Uttar Pradesh, India
| | - Rajinder S Chauhan
- Department of Biotechnology, School of Engineering & Applied Sciences, Bennett University, Uttar Pradesh, India
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Sabzchi-Dehkharghani H, Samadi Kafil H, Majnooni-Heris A, Akbarzadeh A, Naderi-Ahranjani R, Fakherifard A, Mosaferi M, Gilani N, Noury M, Eydi P, Sayyari Sis S, Toghyanian N, Yegani R. Investigation of SARS-CoV-2 RNA contamination in water supply resources of Tabriz metropolitan during a peak of COVID-19 pandemic. SUSTAINABLE WATER RESOURCES MANAGEMENT 2022; 9:21. [PMID: 36570697 PMCID: PMC9759279 DOI: 10.1007/s40899-022-00809-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
It is crucial to have access to clean water resources during the COVID-19 pandemic for hygiene, since virus infection through wastewater leaks in metropolitan areas can be a threat. Accurate monitoring of urban water resources during the pandemic seems to be the only way to confirm safe and infected resources. Here, in this study, the amount of Severe Acute Respiratory Syndrome Coronavirus 2's Ribonucleic Acid (SARS-CoV-2 RNA) in the Tabriz urban water network located in the northwest of Iran was investigated by an extensive sampling of the city's water sources at a severe peak of the COVID-19 pandemic. The sampling process comprised a range of water sources, including wells, qanats, water treatment facilities, dams, and reservoirs. For each sample, a combination of polyethylene glycol (PEG) and sodium chloride (NaCl) was used for concentration and a laboratory RNA-based method was conducted for quantification. Before applying the extraction and quantification procedure to real samples, the proposed concentration method was verified with synthetic serum samples for the first time. After the concentration, RNA extraction was done by the BehPrep extraction column method, and Reverse Transcription Polymerase Chain Reaction (RT-PCR) detection of the virus was done by Covitech COVID-19 RT-PCR kit. In none of the water supply resources, SARS-COV-2 RNA has been detected except in a sample grabbed from a well adjacent to an urban wastewater discharge point downstream. The results of molecular analysis for the positive sample showed that the CT value and concentration of the virus genome were equal to 32.57 and 5720 copies/L, respectively. Quantitative analysis of real samples shows that the city's water network was safe at the time of the study. However, given that the positive sample was exposed to wastewater leakage, periodic sampling from wells and qanats is suggested during the pandemic until it can be proven that the leakage to these water sources is impossible.
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Affiliation(s)
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | | | - Rana Naderi-Ahranjani
- Membrane Technology Research Center, Faculty of Chemical Engineering, Sahand University of Technology, PO. BOX 51335/1996, Tabriz, Iran
| | - Ahmad Fakherifard
- Department of Water Engineering, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Mohammad Mosaferi
- Health and Environment Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Neda Gilani
- Department of Statistics and Epidemiology, Faculty of Health, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mojtaba Noury
- Iranian Water Resources Management Company, Tehran, Iran
| | - Parisa Eydi
- Membrane Technology Research Center, Faculty of Chemical Engineering, Sahand University of Technology, PO. BOX 51335/1996, Tabriz, Iran
| | - Sajjad Sayyari Sis
- Membrane Technology Research Center, Faculty of Chemical Engineering, Sahand University of Technology, PO. BOX 51335/1996, Tabriz, Iran
| | | | - Reza Yegani
- Membrane Technology Research Center, Faculty of Chemical Engineering, Sahand University of Technology, PO. BOX 51335/1996, Tabriz, Iran
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Lei S, Chen X, Wu J, Duan X, Men K. Small molecules in the treatment of COVID-19. Signal Transduct Target Ther 2022; 7:387. [PMID: 36464706 PMCID: PMC9719906 DOI: 10.1038/s41392-022-01249-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 12/11/2022] Open
Abstract
The outbreak of COVID-19 has become a global crisis, and brought severe disruptions to societies and economies. Until now, effective therapeutics against COVID-19 are in high demand. Along with our improved understanding of the structure, function, and pathogenic process of SARS-CoV-2, many small molecules with potential anti-COVID-19 effects have been developed. So far, several antiviral strategies were explored. Besides directly inhibition of viral proteins such as RdRp and Mpro, interference of host enzymes including ACE2 and proteases, and blocking relevant immunoregulatory pathways represented by JAK/STAT, BTK, NF-κB, and NLRP3 pathways, are regarded feasible in drug development. The development of small molecules to treat COVID-19 has been achieved by several strategies, including computer-aided lead compound design and screening, natural product discovery, drug repurposing, and combination therapy. Several small molecules representative by remdesivir and paxlovid have been proved or authorized emergency use in many countries. And many candidates have entered clinical-trial stage. Nevertheless, due to the epidemiological features and variability issues of SARS-CoV-2, it is necessary to continue exploring novel strategies against COVID-19. This review discusses the current findings in the development of small molecules for COVID-19 treatment. Moreover, their detailed mechanism of action, chemical structures, and preclinical and clinical efficacies are discussed.
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Affiliation(s)
- Sibei Lei
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041 People’s Republic of China
| | - Xiaohua Chen
- grid.54549.390000 0004 0369 4060Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072 China
| | - Jieping Wu
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041 People’s Republic of China
| | - Xingmei Duan
- grid.54549.390000 0004 0369 4060Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072 China
| | - Ke Men
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041 People’s Republic of China
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12
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Gandhi Y, Mishra SK, Rawat H, Grewal J, Kumar R, Shakya SK, Jain VK, Babu G, Singh A, Singh R, Acharya R, Kumar V. Phytomedicines explored under in vitro and in silico studies against coronavirus: An opportunity to develop traditional medicines. SOUTH AFRICAN JOURNAL OF BOTANY : OFFICIAL JOURNAL OF THE SOUTH AFRICAN ASSOCIATION OF BOTANISTS = SUID-AFRIKAANSE TYDSKRIF VIR PLANTKUNDE : AMPTELIKE TYDSKRIF VAN DIE SUID-AFRIKAANSE GENOOTSKAP VAN PLANTKUNDIGES 2022; 151:451-483. [PMID: 35530267 PMCID: PMC9057940 DOI: 10.1016/j.sajb.2022.04.053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 04/07/2022] [Accepted: 04/29/2022] [Indexed: 05/21/2023]
Abstract
The widespread COVID-19 pandemic, caused by novel coronavirus SARS-CoV-2, has emanated as one of the most life-threatening transmissible diseases. Currently, the repurposed drugs such as remdesivir, azithromycine, chloroquine, and hydroxychloroquine are being employed in the management of COVID-19 but their adverse effects are a matter of concern. In this regard, alternative treatment options i.e., traditional medicine, medicinal plants, and their phytochemicals, which exhibit significant therapeutic efficacy and show a low toxicity profile, are being explored. The current review aims at unraveling the promising medicinal plants, phytochemicals, and traditional medicines against SARS-CoV-2 to discover phytomedicines for the management of COVID-19 on the basis of their potent antiviral activities against coronaviruses, as demonstrated in various biochemical and computational chemical biology studies. The review consists of integrative and updated information on the potential traditional medicines against COVID-19 and will facilitate researchers to develop traditional medicines for the management of COVID-19.
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Affiliation(s)
- Yashika Gandhi
- Department of Chemistry, Central Ayurveda Research Institute Jhansi, Uttar Pradesh, 284003, India
| | - Sujeet K Mishra
- Department of Chemistry, Central Ayurveda Research Institute Jhansi, Uttar Pradesh, 284003, India
| | - Hemant Rawat
- Department of Chemistry, Central Ayurveda Research Institute Jhansi, Uttar Pradesh, 284003, India
| | - Jyotika Grewal
- Department of Chemistry, Central Ayurveda Research Institute Jhansi, Uttar Pradesh, 284003, India
| | - Ravi Kumar
- Department of Chemistry, Central Ayurveda Research Institute Jhansi, Uttar Pradesh, 284003, India
| | - Santosh K Shakya
- Department of Chemistry, Central Ayurveda Research Institute Jhansi, Uttar Pradesh, 284003, India
| | - Vipin Kumar Jain
- Department of Chemistry, Central Ayurveda Research Institute Jhansi, Uttar Pradesh, 284003, India
| | - G Babu
- Department of Ayurveda, Central Ayurveda Research Institute Jhansi, Uttar Pradesh, 284003, India
| | - Arjun Singh
- Central Council for Research in Ayurvedic Sciences, New Delhi, 110058, India
| | - Ravindra Singh
- Central Council for Research in Ayurvedic Sciences, New Delhi, 110058, India
| | - Rabinarayan Acharya
- Central Council for Research in Ayurvedic Sciences, New Delhi, 110058, India
| | - Vijay Kumar
- Department of Chemistry, Central Ayurveda Research Institute Jhansi, Uttar Pradesh, 284003, India
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13
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Asadi Faezi N, Mehramouz B, Taghizadeh S, Pagliano P, Kafil HS. Acute hepatitis (Non Hepa A-E) of unknown origin among pediatrics. LE INFEZIONI IN MEDICINA 2022; 30:353-361. [PMID: 36148173 PMCID: PMC9448315 DOI: 10.53854/liim-3003-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 07/14/2022] [Indexed: 06/16/2023]
Abstract
Several clusters and individual cases of acute hepatitis have been reported in the US, Europe and recently in Asia and Central America since October 2021. A laboratory investigation of the common viral hepatitis agents (HAV, HBV, HCV, HDV and HEV) yielded negative results prompting the use of the term "acute non HepA-E hepatitis" to describe this condition. As of 24 June of 2022, WHO have reported 920 probable cases of severe acute hepatitis of unknown origin among pediatrics in 33 countries in five WHO regions. Since the previous reports on 27 May 2022, 270 new probable cases have been increased, including from four new countries, some of whom were also found to be positive for SARS-CoV-2. All the patients showed symptoms such as vomiting, diarrhea, jaundice, and abdominal pain. The patients' liver enzymes were remarkably increased. No connection with SARS-CoV-2 or its vaccine has been found so far. However, the suspected cause is adenovirus, including its genomic variations, because its pathogenesis and laboratory investigations have been positively linked. Until further evidence emerges, hygiene precautions could be helpful to prevent its spread.
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Affiliation(s)
- Nasim Asadi Faezi
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Bahareh Mehramouz
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sepehr Taghizadeh
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Hossein Samadi Kafil
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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14
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Hsu JN, Chen JS, Lin SM, Hong JY, Chen YJ, Jeng US, Luo SY, Hou MH. Targeting the N-Terminus Domain of the Coronavirus Nucleocapsid Protein Induces Abnormal Oligomerization via Allosteric Modulation. Front Mol Biosci 2022; 9:871499. [PMID: 35517857 PMCID: PMC9061996 DOI: 10.3389/fmolb.2022.871499] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/17/2022] [Indexed: 12/20/2022] Open
Abstract
Epidemics caused by coronaviruses (CoVs), namely the severe acute respiratory syndrome (SARS) (2003), Middle East respiratory syndrome (MERS) (2012), and coronavirus disease 2019 (COVID-19) (2019), have triggered a global public health emergency. Drug development against CoVs is inherently arduous. The nucleocapsid (N) protein forms an oligomer and facilitates binding with the viral RNA genome, which is critical in the life cycle of the virus. In the current study, we found a potential allosteric site (Site 1) using PARS, an online allosteric site predictor, in the CoV N-N-terminal RNA-binding domain (NTD) to modulate the N protein conformation. We identified 5-hydroxyindole as the lead via molecular docking to target Site 1. We designed and synthesized four 5-hydroxyindole derivatives, named P4-1 to P4-4, based on the pose of 5-hydroxyindole in the docking model complex. Small-angle X-ray scattering (SAXS) data indicate that two 5-hydroxyindole compounds with higher hydrophobic R-groups mediate the binding between N-NTD and N-C-terminal dimerization domain (CTD) and elicit high-order oligomerization of the whole N protein. Furthermore, the crystal structures suggested that these two compounds act on this novel cavity and create a flat surface with higher hydrophobicity, which may mediate the interaction between N-NTD and N-CTD. Taken together, we discovered an allosteric binding pocket targeting small molecules that induces abnormal aggregation of the CoV N protein. These novel concepts will facilitate protein-protein interaction (PPI)-based drug design against various CoVs.
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Affiliation(s)
- Jia-Ning Hsu
- Institute of Genomics and Bioinformatics and Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Jyun-Siao Chen
- Department of Chemistry, National Chung Hsing University, Taichung, Taiwan
| | - Shan-Meng Lin
- Institute of Genomics and Bioinformatics and Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Jhen-Yi Hong
- Institute of Genomics and Bioinformatics and Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Yi-Jheng Chen
- Department of Chemistry, National Chung Hsing University, Taichung, Taiwan
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center, Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Shun-Yuan Luo
- Department of Chemistry, National Chung Hsing University, Taichung, Taiwan
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics and Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
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15
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Velázquez-Enríquez JM, Ramírez-Hernández AA, Navarro LMS, Reyes-Avendaño I, González-García K, Jiménez-Martínez C, Castro-Sánchez L, Sánchez-Chino XM, Vásquez-Garzón VR, Baltiérrez-Hoyos R. Proteomic Analysis Reveals Differential Expression Profiles in Idiopathic Pulmonary Fibrosis Cell Lines. Int J Mol Sci 2022; 23:ijms23095032. [PMID: 35563422 PMCID: PMC9105114 DOI: 10.3390/ijms23095032] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/18/2022] [Accepted: 04/28/2022] [Indexed: 02/04/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, irreversible lung disorder of unknown cause. This disease is characterized by profibrotic activation of resident pulmonary fibroblasts resulting in aberrant deposition of extracellular matrix (ECM) proteins. However, although much is known about the pathophysiology of IPF, the cellular and molecular processes that occur and allow aberrant fibroblast activation remain an unmet need. To explore the differentially expressed proteins (DEPs) associated with aberrant activation of these fibroblasts, we used the IPF lung fibroblast cell lines LL97A (IPF-1) and LL29 (IPF-2), compared to the normal lung fibroblast cell line CCD19Lu (NL-1). Protein samples were quantified and identified using a label-free quantitative proteomic analysis approach by liquid chromatography-tandem mass spectrometry (LC-MS/MS). DEPs were identified after pairwise comparison, including all experimental groups. Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG), and Protein–Protein Interaction (PPI) network construction were used to interpret the proteomic data. Eighty proteins expressed exclusively in the IPF-1 and IPF-2 clusters were identified. In addition, 19 proteins were identified up-regulated in IPF-1 and 10 in IPF-2; 10 proteins were down-regulated in IPF-1 and 2 in IPF-2 when compared to the NL-1 proteome. Using the search tool for retrieval of interacting genes/proteins (STRING) software, a PPI network was constructed between the DEPs and the 80 proteins expressed exclusively in the IPF-2 and IPF-1 clusters, containing 115 nodes and 136 edges. The 10 hub proteins present in the IPP network were identified using the CytoHubba plugin of the Cytoscape software. GO and KEGG pathway analyses showed that the hub proteins were mainly related to cell adhesion, integrin binding, and hematopoietic cell lineage. Our results provide relevant information on DEPs present in IPF lung fibroblast cell lines when compared to the normal lung fibroblast cell line that could play a key role during IPF pathogenesis.
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Affiliation(s)
- Juan Manuel Velázquez-Enríquez
- Laboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma “Benito Juárez” de Oaxaca, Oaxaca 68120, Mexico; (J.M.V.-E.); (A.A.R.-H.); (I.R.-A.); (K.G.-G.)
| | - Alma Aurora Ramírez-Hernández
- Laboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma “Benito Juárez” de Oaxaca, Oaxaca 68120, Mexico; (J.M.V.-E.); (A.A.R.-H.); (I.R.-A.); (K.G.-G.)
| | | | - Itayetzi Reyes-Avendaño
- Laboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma “Benito Juárez” de Oaxaca, Oaxaca 68120, Mexico; (J.M.V.-E.); (A.A.R.-H.); (I.R.-A.); (K.G.-G.)
| | - Karina González-García
- Laboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma “Benito Juárez” de Oaxaca, Oaxaca 68120, Mexico; (J.M.V.-E.); (A.A.R.-H.); (I.R.-A.); (K.G.-G.)
| | - Cristian Jiménez-Martínez
- Departamento de Ingeniería Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Unidad Profesional Adolfo López Mateos, Zacatenco, Av. Wilfrido Massieu Esq. Cda. Miguel Stampa S/N, Alcaldía Gustavo A. Madero, Mexico City 07738, Mexico;
| | - Luis Castro-Sánchez
- Conacyt-Centro Universitario de Investigaciones Biomédicas “CUIB”, Universidad de Colima, Colima 28045, Mexico;
| | - Xariss Miryam Sánchez-Chino
- Catedra-Conacyt, Departamento de Salud El Colegio de La Frontera Sur, Unidad Villahermosa, Tabasco 86280, Mexico;
| | | | - Rafael Baltiérrez-Hoyos
- Conacyt-Facultad de Medicina y Cirugía, Universidad Autónoma “Benito Juárez” de Oaxaca, Oaxaca 68120, Mexico;
- Correspondence:
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16
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Mukherjee PK, Efferth T, Das B, Kar A, Ghosh S, Singha S, Debnath P, Sharma N, Bhardwaj PK, Haldar PK. Role of medicinal plants in inhibiting SARS-CoV-2 and in the management of post-COVID-19 complications. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 98:153930. [PMID: 35114450 PMCID: PMC8730822 DOI: 10.1016/j.phymed.2022.153930] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 12/30/2021] [Accepted: 01/03/2022] [Indexed: 05/07/2023]
Abstract
BACKGROUND The worldwide corona virus disease outbreak, generally known as COVID-19 pandemic outbreak resulted in a major health crisis globally. The morbidity and transmission modality of COVID-19 appear more severe and uncontrollable. The respiratory failure and following cardiovascular complications are the main pathophysiology of this deadly disease. Several therapeutic strategies are put forward for the development of safe and effective treatment against SARS-CoV-2 virus from the pharmacological view point but till date there are no specific treatment regimen developed for this viral infection. PURPOSE The present review emphasizes the role of herbs and herbs-derived secondary metabolites in inhibiting SARS-CoV-2 virus and also for the management of post-COVID-19 related complications. This approach will foster and ensure the safeguards of using medicinal plant resources to support the healthcare system. Plant-derived phytochemicals have already been reported to prevent the viral infection and to overcome the post-COVID complications like parkinsonism, kidney and heart failure, liver and lungs injury and mental problems. In this review, we explored mechanistic approaches of herbal medicines and their phytocomponenets as antiviral and post-COVID complications by modulating the immunological and inflammatory states. STUDY DESIGN Studies related to diagnosis and treatment guidelines issued for COVID-19 by different traditional system of medicine were included. The information was gathered from pharmacological or non-pharmacological interventions approaches. The gathered information sorted based on therapeutic application of herbs and their components against SARSCoV-2 and COVID-19 related complications. METHODS A systemic search of published literature was conducted from 2003 to 2021 using different literature database like Google Scholar, PubMed, Science Direct, Scopus and Web of Science to emphasize relevant articles on medicinal plants against SARS-CoV-2 viral infection and Post-COVID related complications. RESULTS Collected published literature from 2003 onwards yielded with total 625 articles, from more than 18 countries. Among these 625 articles, more than 95 medicinal plants and 25 active phytomolecules belong to 48 plant families. Reports on the therapeutic activity of the medicinal plants belong to the Lamiaceae family (11 reports), which was found to be maximum reported from 4 different countries including India, China, Australia, and Morocco. Other reports on the medicinal plant of Asteraceae (7 reports), Fabaceae (8 reports), Piperaceae (3 reports), Zingiberaceae (3 reports), Ranunculaceae (3 reports), Meliaceae (4 reports) were found, which can be explored for the development of safe and efficacious products targeting COVID-19. CONCLUSION Keeping in mind that the natural alternatives are in the priority for the management and prevention of the COVID-19, the present review may help to develop an alternative approach for the management of COVID-19 viral infection and post-COVID complications from a mechanistic point of view.
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Affiliation(s)
- Pulok K Mukherjee
- Institute of Bioresources and Sustainable Development, Imphal-795001, India; School of Natural Product Studies, Department of Pharmaceutical Technology, Jadavpur University, Kolkata -700 032, India.
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz, Germany
| | - Bhaskar Das
- School of Natural Product Studies, Department of Pharmaceutical Technology, Jadavpur University, Kolkata -700 032, India
| | - Amit Kar
- Institute of Bioresources and Sustainable Development, Imphal-795001, India
| | - Suparna Ghosh
- School of Natural Product Studies, Department of Pharmaceutical Technology, Jadavpur University, Kolkata -700 032, India
| | - Seha Singha
- School of Natural Product Studies, Department of Pharmaceutical Technology, Jadavpur University, Kolkata -700 032, India
| | - Pradip Debnath
- School of Natural Product Studies, Department of Pharmaceutical Technology, Jadavpur University, Kolkata -700 032, India
| | - Nanaocha Sharma
- Institute of Bioresources and Sustainable Development, Imphal-795001, India
| | | | - Pallab Kanti Haldar
- School of Natural Product Studies, Department of Pharmaceutical Technology, Jadavpur University, Kolkata -700 032, India
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17
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In silico detection of potential inhibitors from vitamins and their derivatives compounds against SARS-CoV-2 main protease by using Molecular Docking, Molecular Dynamic simulation and ADMET profiling. J Mol Struct 2022; 1258:132652. [PMID: 35194243 PMCID: PMC8855669 DOI: 10.1016/j.molstruc.2022.132652] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 02/12/2022] [Accepted: 02/16/2022] [Indexed: 12/25/2022]
Abstract
COVID-19 is a new infectious disease caused by SARS-COV-2 virus of the coronavirus Family. The identification of drugs against this serious infection is a significant requirement due to the rapid rise in the positive cases and deaths around the world. With this concept, a molecular docking analysis for vitamins and their derivatives (28 molecules) with the active site of SARS-CoV-2 main protease was carried out. The results of molecular docking indicate that the structures with best binding energy in the binding site of the studied enzyme (lowest energy level) are observed for the compounds; Folacin, Riboflavin, and Phylloquinone oxide (Vitamin K1 oxide). A Molecular Dynamic simulation was carried out to study the binding stability for the selected vitamins with the active site of SARS-CoV-2 main protease enzyme. Molecular Dynamic shows that Phylloquinone oxide and Folacin are quite unstable in binding to SARS-CoV-2 main protease, while the Riboflavin is comparatively rigid. The higher fluctuations in Phylloquinone oxide and Folacin indicate that they may not fit very well into the binding site. As expected, the Phylloquinone oxide exhibits small number of H-bonds with protein and Folacin does not form a good interaction with protein. Riboflavin exhibits the highest number of Hydrogen bonds and forms consistent interactions with protein. Additionally, this molecule respect the conditions mentioned in Lipinski's rule and have acceptable ADMET proprieties which indicates that Riboflavin (Vitamin B2) could be interesting for the antiviral treatment of COVID-19.
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18
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KÜÇÜK BEYZANUR, ŞİMŞEK RAHİME, ERDEMLİ KÖSE SELİNAYBAŞAK, YİRÜN ANIL, Erkekoglu P. Adverse Effects of COVID-19 Treatments: A Special Focus on Susceptible Populations. J Environ Pathol Toxicol Oncol 2022; 41:45-64. [DOI: 10.1615/jenvironpatholtoxicoloncol.2022039271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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19
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Siminea N, Popescu V, Sanchez Martin JA, Florea D, Gavril G, Gheorghe AM, Iţcuş C, Kanhaiya K, Pacioglu O, Popa IL, Trandafir R, Tusa MI, Sidoroff M, Păun M, Czeizler E, Păun A, Petre I. Network analytics for drug repurposing in COVID-19. Brief Bioinform 2021; 23:6447433. [PMID: 34864885 PMCID: PMC8690228 DOI: 10.1093/bib/bbab490] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/06/2021] [Accepted: 10/25/2021] [Indexed: 01/08/2023] Open
Abstract
To better understand the potential of drug repurposing in COVID-19, we analyzed control strategies over essential host factors for SARS-CoV-2 infection. We constructed comprehensive directed protein–protein interaction (PPI) networks integrating the top-ranked host factors, the drug target proteins and directed PPI data. We analyzed the networks to identify drug targets and combinations thereof that offer efficient control over the host factors. We validated our findings against clinical studies data and bioinformatics studies. Our method offers a new insight into the molecular details of the disease and into potentially new therapy targets for it. Our approach for drug repurposing is significant beyond COVID-19 and may be applied also to other diseases.
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Affiliation(s)
- Nicoleta Siminea
- Bioinformatics, National Institute of Research and Development for Biological Sciences, 296 Splaiul Independenţei, 060031, Romania.,Faculty of Mathematics and Computer Science, University of Bucharest, 14 Academiei, 010014, Romania
| | - Victor Popescu
- Department of Information Technologies, Åbo Akademi University, 3 Tuomiokirkontori, 20500, Finland
| | - Jose Angel Sanchez Martin
- Department of Computer Science, Technical University of Madrid, 7 Calle Ramiro de Maeztu, 28040, Spain
| | - Daniela Florea
- Bioinformatics, National Institute of Research and Development for Biological Sciences, 296 Splaiul Independenţei, 060031, Romania
| | - Georgiana Gavril
- Bioinformatics, National Institute of Research and Development for Biological Sciences, 296 Splaiul Independenţei, 060031, Romania
| | - Ana-Maria Gheorghe
- Bioinformatics, National Institute of Research and Development for Biological Sciences, 296 Splaiul Independenţei, 060031, Romania
| | - Corina Iţcuş
- Bioinformatics, National Institute of Research and Development for Biological Sciences, 296 Splaiul Independenţei, 060031, Romania
| | - Krishna Kanhaiya
- Department of Information Technologies, Åbo Akademi University, 3 Tuomiokirkontori, 20500, Finland
| | - Octavian Pacioglu
- Bioinformatics, National Institute of Research and Development for Biological Sciences, 296 Splaiul Independenţei, 060031, Romania
| | - Ioana Laura Popa
- Bioinformatics, National Institute of Research and Development for Biological Sciences, 296 Splaiul Independenţei, 060031, Romania
| | - Romica Trandafir
- Bioinformatics, National Institute of Research and Development for Biological Sciences, 296 Splaiul Independenţei, 060031, Romania
| | - Maria Iris Tusa
- Bioinformatics, National Institute of Research and Development for Biological Sciences, 296 Splaiul Independenţei, 060031, Romania
| | - Manuela Sidoroff
- Bioinformatics, National Institute of Research and Development for Biological Sciences, 296 Splaiul Independenţei, 060031, Romania
| | - Mihaela Păun
- Bioinformatics, National Institute of Research and Development for Biological Sciences, 296 Splaiul Independenţei, 060031, Romania.,Faculty of Administration and Business, University of Bucharest, 4-12 Regina Elisabeta Boulevard, 030018, Romania
| | - Eugen Czeizler
- Department of Information Technologies, Åbo Akademi University, 3 Tuomiokirkontori, 20500, Finland.,Bioinformatics, National Institute of Research and Development for Biological Sciences, 296 Splaiul Independenţei, 060031, Romania
| | - Andrei Păun
- Bioinformatics, National Institute of Research and Development for Biological Sciences, 296 Splaiul Independenţei, 060031, Romania.,Faculty of Mathematics and Computer Science, University of Bucharest, 14 Academiei, 010014, Romania
| | - Ion Petre
- Department of Mathematics and Statistics, University of Turku, 5 Vesilinnantie, 20014, Finland.,Bioinformatics, National Institute of Research and Development for Biological Sciences, 296 Splaiul Independenţei, 060031, Romania
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20
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Zhao W, Xu G, Yu Z, Li J, Liu J. Identification of nut protein-derived peptides against SARS-CoV-2 spike protein and main protease. Comput Biol Med 2021; 138:104937. [PMID: 34655899 PMCID: PMC8503973 DOI: 10.1016/j.compbiomed.2021.104937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 10/08/2021] [Accepted: 10/09/2021] [Indexed: 12/22/2022]
Abstract
Recently, an outbreak of a novel coronavirus disease (COVID-19) has reached pandemic proportions, and there is an urgent need to develop nutritional supplements to assist with prevention, treatment, and recovery. In this study, SARS-CoV-2 inhibitory peptides were screened from nut proteins in silico, and binding affinities of the peptides to the SARS-CoV-2 main protease (Mpro) and the spike protein receptor-binding domain (RBD) were evaluated. Peptide NDQF from peanuts and peptide ASGCGDC from almonds were found to have a strong binding affinity for both targets of the coronavirus. The binding sites of the NDQF and ASGCGDC peptides are highly consistent with the Mpro inhibitor N3. In addition, NDQF and ASGCGDC exhibited an effective binding affinity for amino acid residues Tyr453 and Gln493 of the spike RBD. Molecular dynamics simulation further confirmed that the NDQF and ASGCGDC peptides could bind stably to the SARS-COV-2 Mpro and spike RBD. In summary, nut protein may be helpful as nutritional supplements for COVID-19 patients, and the screened peptides could be considered a potential lead compound for designing entry inhibitors against SARS-CoV-2.
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Affiliation(s)
- Wenzhu Zhao
- College of Food Science and Engineering, Bohai University, Jinzhou, 121013, PR China
| | - Ge Xu
- College of Food Science and Engineering, Bohai University, Jinzhou, 121013, PR China
| | - Zhipeng Yu
- College of Food Science and Engineering, Bohai University, Jinzhou, 121013, PR China.
| | - Jianrong Li
- College of Food Science and Engineering, Bohai University, Jinzhou, 121013, PR China
| | - Jingbo Liu
- Lab of Nutrition and Functional Food, Jilin University, Changchun, 130062, PR China
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21
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Ozma MA, Khodadadi E, Rezaee MA, Asgharzadeh M, Aghazadeh M, Zeinalzadeh E, Ganbarov K, Kafil H. Bacterial proteomics and its application for pathogenesis studies. Curr Pharm Biotechnol 2021; 23:1245-1256. [PMID: 34503411 DOI: 10.2174/1389201022666210908153234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/12/2021] [Accepted: 06/13/2021] [Indexed: 01/09/2023]
Abstract
Bacteria build their structures by implementing several macromolecules such as proteins, polysaccharides, phospholipids, and nucleic acids, which leads to preserve their lives and play an essential role in their pathogenesis. There are two genomic and proteomic methods to study various macromolecules of bacteria, which are complementary methods and provide comprehensive information. Proteomic approaches are used to identify proteins and their cell applications. Furthermore, to study bacterial proteins, macromolecules are involved in the bacteria's structures and functions. These protein-based methods provide comprehensive information about the cells, such as the external structures, internal compositions, post-translational modifications, and mechanisms of particular actions such as biofilm formation, antibiotic resistance, and adaptation to the environment, which are helpful in promoting bacterial pathogenesis. These methods use various devices such as MALDI-TOF MS, LC-MS, and two-dimensional electrophoresis, which are valuable tools for studying different structural and functional proteins of the bacteria and their mechanisms of pathogenesis that causes rapid, easy, and accurate diagnosis of the infections.
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Affiliation(s)
- Mahdi Asghari Ozma
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Ehsaneh Khodadadi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | | | - Mohammad Asgharzadeh
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Mohammad Aghazadeh
- Microbiome and Health Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Elham Zeinalzadeh
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | | | - Hossein Kafil
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz 5166614711. Iran
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22
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Ünlü B, Simsek R, Köse SBE, Yirün A, Erkekoglu P. Neurological Effects of Sars-Cov-2 And Neurotoxicity of Antiviral Drugs Against Covid-19. Mini Rev Med Chem 2021; 22:213-231. [PMID: 34191697 DOI: 10.2174/1389557521666210629100630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 04/26/2021] [Accepted: 05/04/2021] [Indexed: 11/22/2022]
Abstract
Severe Acute Respiratory Syndrome (SARS) is caused by different SARS viruses. In 2020, novel coronavirus (SARS-CoV-2) led to an ongoing pandemic, known as "Coronavirus Disease 2019 (COVID-19)". The disease can spread among individuals through direct (via saliva, respiratory secretions or secretion droplets) or indirect (through contaminated objects or surfaces) contact. The pandemic has spread rapidly from Asia to Europe and later to America. It continues to affect all parts of the world at an increasing rate. There have been over 92 million confirmed cases of COVID-19 by mid-January 2021. The similarity of homological sequences between SARS-CoV-2 and other SARS-CoVs is high. In addition, clinical symptoms of SARS-CoV-2 and other SARS viruses show similarities. However, some COVID-19 cases show neurologic signs like headache, loss of smell, hiccups and encephalopathy. The drugs used in the palliative treatment of the disease also have some neurotoxic effects. Currently, there are approved vaccines for COVID-19. However, there is a need for specific therapeutics against COVID-19. This review will describe the neurological effects of SARS-CoV-2 and the neurotoxicity of COVID-19 drugs used in clinics. Drugs used in the treatment of COVID-19 will be evaluated by their mechanism of action and their toxicological effects.
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Affiliation(s)
- Büşra Ünlü
- TOBB University, Bioengineering Department, Ankara, Turkey
| | - Rahime Simsek
- Hacettepe University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Sıhhiye 06100, Ankara, Turkey
| | - Selinay Başak Erdemli Köse
- Hacettepe University, Faculty of Pharmacy, Department of Pharmaceutical Toxicology, Sıhhiye 06100, Ankara, Turkey
| | - Anıl Yirün
- Hacettepe University, Faculty of Pharmacy, Department of Pharmaceutical Toxicology, Sıhhiye 06100, Ankara, Turkey
| | - Pinar Erkekoglu
- Hacettepe University, Faculty of Pharmacy, Department of Pharmaceutical Toxicology, Sıhhiye 06100, Ankara, Turkey
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23
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Das A, Pandita D, Jain GK, Agarwal P, Grewal AS, Khar RK, Lather V. Role of phytoconstituents in the management of COVID-19. Chem Biol Interact 2021; 341:109449. [PMID: 33798507 PMCID: PMC8008820 DOI: 10.1016/j.cbi.2021.109449] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 03/07/2021] [Accepted: 03/21/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND COVID-19, a severe global pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has emerged as one of the most threatening transmissible disease. As a great threat to global public health, the development of treatment options has become vital, and a rush to find a cure has mobilized researchers globally from all areas. SCOPE AND APPROACH This review focuses on deciphering the potential of different secondary metabolites from medicinal plants as therapeutic options either as inhibitors of therapeutic targets of SARS-CoV-2 or as blockers of viral particles entry through host cell receptors. The use of medicinal plants containing specific phytomoieties could be seen in providing a safer and long-term solution for the population with lesser side effects. Key Findings and Conclusions: Considering the high cost and time-consuming drug discovery process, therapeutic repositioning of existing drugs was explored as treatment option in COVID-19, however several molecules have been retracted as therapeutics either due to no positive outcomes or the severe side effects. These effects call for exploring the alternate treatment options which are therapeutically effective as well as safe. Keeping this in mind, phytopharmaceuticals derived from medicinal plants could be explored as important resources in the development of COVID-19 treatment, as their role in the past for treatment of viral diseases like HIV, MERS-CoV, and influenza has been well reported. Considering this fact, different phytoconstituents such as flavonoids, alkaloids, tannins and glycosides etc. Possessing antiviral properties against coronaviruses and possessing potential against SARS-CoV-2 have been reviewed in the present work.
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Affiliation(s)
- Amiya Das
- Amity Institute of Molecular Medicine & Stem Cell Research (AIMMSCR), Amity University Uttar Pradesh, Sector-125, Noida, 201313, India
| | - Deepti Pandita
- Department of Pharmaceutics, Delhi Pharmaceutical Sciences and Research University, Pushp Vihar, New Delhi, 110017, India.
| | - Gaurav Kumar Jain
- Department of Pharmaceutics, Delhi Pharmaceutical Sciences and Research University, Pushp Vihar, New Delhi, 110017, India
| | - Pallavi Agarwal
- Amity Institute of Molecular Medicine & Stem Cell Research (AIMMSCR), Amity University Uttar Pradesh, Sector-125, Noida, 201313, India
| | | | - Roop K. Khar
- BS Anangpuria Institute of Pharmacy, Faridabad, Haryana, India
| | - Viney Lather
- Amity Institute of Pharmacy, Amity University Uttar Pradesh, Sector-125, Noida, 201313, India.
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24
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Asadi Faezi N, Gholizadeh P, Sanogo M, Oumarou A, Mohamed MN, Cissoko Y, Saliou Sow M, Keita BS, Baye YAM, Pagliano P, Akouda P, Soufiane S, Iknane AA, Safiatou Diallo MO, Gansane Z, Ali Khan B, Köse Ş, Allahverdipour H, Ganvarov K, Soumaré M, Asgharzadeh M, Dao S, Samadi Kafil H. Peoples' attitude toward COVID-19 vaccine, acceptance, and social trust among African and Middle East countries. Health Promot Perspect 2021; 11:171-178. [PMID: 34195040 PMCID: PMC8233680 DOI: 10.34172/hpp.2021.21] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 05/08/2021] [Indexed: 12/13/2022] Open
Abstract
Background: To end the COVID-19 pandemic, a large part of the world must be immune to the virus by vaccination. Therefore, this study aimed to gauge intent to be vaccinated against COVID-19 among ordinary people and to identify attitudes towards vaccines and barriers for vaccine acceptance. Methods: The study population comprises 1880 people residing in different countries that answer a prepared questionnaire. The questionnaire topics are demographics, historical issues, participants’ attitudes and beliefs regarding vaccines, concerns, and vaccine hesitancy. Results: Attitudes and beliefs relating to vaccines in general, and the COVID-19 vaccine, were ascertained. Overall, 66.81% of the contributors would like to be vaccinated against COVID-19, while %33.19 did not intend to be vaccinated. Reasons for COVID-19 vaccine hesitancy included concern regarding vaccine side effects, fear of getting sick from the uptake of the vaccine, and the absence of accurate vaccine promotion news. Individuals with higher education believe that India (68.6%) produces the best vaccine (P <0.001), while healthcare workers think the Chinese vaccine (44.2%) is the best (P =0.020). Individuals with higher education have not been vaccinated, not be healthcare workers, and females were the most contributors to effective of the vaccine in reducing mortality from COVID-19 disease. Conclusion: Given the degree of hesitancy against COVID-19 vaccination, a multifaceted approach to facilitate vaccine uptake that includes vaccine education, behavioral change strategies, and health promotion, is paramount.
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Affiliation(s)
- Nasim Asadi Faezi
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Pourya Gholizadeh
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Moussa Sanogo
- Faculty of Pharmacy USTTB, Faculty of Medicine and Odonto Stomatology, University of Science, Technics and Technology of Bamako, Bamako, Mali
| | - Amadou Oumarou
- Faculte des sciences la santé de l universite Dan Dicko DanKoulodo de Maradi, Niger
| | - Maad Nasser Mohamed
- Service des maladies infectieuses et tropicales de l'hôpital général peltier, Djibouti
| | - Yacouba Cissoko
- Faculty of Medicine and Odonto Stomatology (FMOS), USTTB, University of Science, Technics and Technology of Bamako, Bamako, Mali
| | - Mamadou Saliou Sow
- Service des Maladies Infectieuses, Hôpital National Donka, CHU Conakry, Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Guinea
| | - Bakary Sayon Keita
- Department of Medicine and Medical Specialities/Infectious Disease Unit of Fousseyni Daou Hospital, Kayes, Mali
| | - Youssouf Ag Mohamed Baye
- Faculty of Medicine and Odonto Stomatology (FMOS), USTTB, University of Science, Technics and Technology of Bamako, Bamako, Mali.,Department of Medicine and Medical Specialities/Infectious Disease Unit of Fousseyni Daou Hospital, Kayes, Mali
| | | | | | | | - Akory Ag Iknane
- Faculty of Medicine and Odonto Stomatology (FMOS), USTTB, University of Science, Technics and Technology of Bamako, Bamako, Mali.,Institut National de Santé Publique, Bamako, Mali
| | - Mamadou Oury Safiatou Diallo
- Service des Maladies Infectieuses, Hôpital National Donka, CHU Conakry, Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Guinea
| | - Zakaria Gansane
- Burkinabé Observatory for Healthcare Quality and Safety, Ouagadougou, Burkina Faso
| | - Barkat Ali Khan
- Department of Pharmaceutics, Faculty of Pharmacy, Gomal University, Dera Ismail Khan, Pakistan
| | - Şükran Köse
- Department of Infectious Diseases and Clinical Microbiology, University of Health Sciences, Tepecik Training and Research Hospital, İzmir, Turkey
| | - Hamid Allahverdipour
- Research Center of Psychiatry and Behavioural Sciences and Department of Health Education and Promotion, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Mariam Soumaré
- Faculty of Medicine and Odonto Stomatology (FMOS), USTTB, University of Science, Technics and Technology of Bamako, Bamako, Mali
| | - Mohammad Asgharzadeh
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sounkalo Dao
- Faculty of Medicine and Odonto Stomatology (FMOS), USTTB, University of Science, Technics and Technology of Bamako, Bamako, Mali
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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25
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Al-Masaeed M, Alghawanmeh M, Al-Singlawi A, Alsababha R, Alqudah M. An Examination of COVID-19 Medications' Effectiveness in Managing and Treating COVID-19 Patients: A Comparative Review. Healthcare (Basel) 2021; 9:557. [PMID: 34068474 PMCID: PMC8151388 DOI: 10.3390/healthcare9050557] [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: 02/24/2021] [Revised: 04/25/2021] [Accepted: 05/03/2021] [Indexed: 12/23/2022] Open
Abstract
Background: The review seeks to shed light on the administered and recommended COVID-19 treatment medications through an evaluation of their efficacy. Methods: Data were collected from key databases, including Scopus, Medline, Google Scholar, and CINAHL. Other platforms included WHO and FDA publications. The review's literature search was guided by the WHO solidarity clinical trials for COVID-19 scope and trial-assessment parameters. Results: The findings indicate that the use of antiretroviral drugs as an early treatment for COVID-19 patients has been useful. It has reduced hospital time, hastened the clinical cure period, delayed and reduced the need for mechanical and invasive ventilation, and reduced mortality rates. The use of vitamins, minerals, and supplements has been linked to increased immunity and thus offering the body a fighting chance. Nevertheless, antibiotics do not correlate with improving patients' wellbeing and are highly discouraged from the developed clinical trials. Conclusions: The review demonstrates the need for additional clinical trials with a randomized, extensive sample base and over a more extended period to examine the potential side effects of the medications administered. Critically, the findings underscore the need for vaccination as the only viable medication to limit the SARS-CoV-2 virus spread.
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Affiliation(s)
- Mahmoud Al-Masaeed
- Faculty of Health and Medicine, University of Newcastle, Callaghan 2308, Australia;
| | | | | | - Rawan Alsababha
- School of nursing and Midwifery, Western Sydney University, Sydney 2560, Australia;
| | - Muhammad Alqudah
- Faculty of Health and Medicine, University of Newcastle, Callaghan 2308, Australia;
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26
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Soltani-Zangbar MS, Aghebati-Maleki L, Hajivalili M, Haji-Fatahaliha M, Motavalli R, Mahmoodpoor A, Kafil HS, Farhang S, Pourakbari R, Jadidi-Niaragh F, Roshangar L, Heris JA, Kamrani A, Siahmansouri H, Hosseini M, Miahipour A, Shareghi-Oskoue O, Parhizkar F, Yousefi M. Application of newly developed SARS-CoV2 serology test along with real-time PCR for early detection in health care workers and on-time plasma donation. GENE REPORTS 2021; 23:101140. [PMID: 33869895 PMCID: PMC8041740 DOI: 10.1016/j.genrep.2021.101140] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 04/06/2021] [Indexed: 01/02/2023]
Abstract
Background As the daily number of coronavirus infection disease 19 (COVID19) patients increases, the necessity of early diagnosis becomes more obvious. In this respect, we aimed to develop a serological test for specifically detecting anti-SARS-CoV2 antibodies. Methods We collected serum and saliva samples from 609 individuals who work at TBZMED affiliated hospitals in Tabriz, Iran, from April to June of 2020. Real-time PCR technique was used to detect SARS-CoV-2 genome using specific primers. An enzyme linked immunosorbent assay (ELISA) test was designed based on virus nucleocapsid (N), spike (S) and its receptor binding domain (RBD) protein, and the collected sera were subjected to IgM and/or IgG analysis. Result Real-time PCR results showed that 66 people were infected with the SARS-CoV-2. Our designed ELISA kit showed 93.75% and 98% of sensitivity and specificity, respectively. In this study, 5.74% of participants had specific IgG against RBD, whereas the percentage for IgM positive individuals was 5.58%. Approximately the same results were observed for S protein. The number of positive participants for NP increased further, and the results of this antigen showed 7.38% for IgG and 7.06% for IgM. Conclusion The ELISA test beside real-time PCR could provide a reliable serologic profile for the status of the disease progress and early detection of individuals. More importantly, it possesses the potential to identify the best candidates for plasma donation according to the antibody titers.
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Affiliation(s)
- Mohammad Sadegh Soltani-Zangbar
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.,Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Leili Aghebati-Maleki
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mahsa Hajivalili
- Department of Immunology, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Roza Motavalli
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ata Mahmoodpoor
- Department of Anesthesiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sara Farhang
- Research Center of Psychiatry and Behavioral Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ramin Pourakbari
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Farhad Jadidi-Niaragh
- Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.,Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Leila Roshangar
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Javad Ahmadian Heris
- Department of Allergy and Clinical Immunology, Pediatric Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Amin Kamrani
- Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Homayoon Siahmansouri
- Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Maryam Hosseini
- Department of Immunology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Abolfazl Miahipour
- Department of Medical Parasitology and Mycology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Oldouz Shareghi-Oskoue
- Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Forough Parhizkar
- Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Yousefi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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27
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Abedini E, Khodadadi E, Zeinalzadeh E, Moaddab SR, Asgharzadeh M, Mehramouz B, Dao S, Samadi Kafil H. A Comprehensive Study on the Antimicrobial Properties of Resveratrol as an Alternative Therapy. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2021; 2021:8866311. [PMID: 33815561 PMCID: PMC7987421 DOI: 10.1155/2021/8866311] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 02/16/2021] [Accepted: 03/10/2021] [Indexed: 12/15/2022]
Abstract
Resveratrol is a polyphenolic antioxidant whose possible health benefits include anticarcinogenic, antiaging, and antimicrobial properties that have gained significant attention. The compound is well accepted by individuals and has been commonly used as a nutraceutical in recent decades. Its widespread usage makes it essential to study as a single agent as well as in combination with traditional prescription antibiotics as regards to antimicrobial properties. Resveratrol demonstrates the action of antimicrobials against a remarkable bacterial diversity, viruses, and fungus. This report explains resveratrol as an all-natural antimicrobial representative. It may modify the bacterial virulence qualities resulting in decreased toxic substance production, biofilm inhibition, motility reduction, and quorum sensing disturbance. Moreover, in conjunction with standard antibiotics, resveratrol improves aminoglycoside efficacy versus Staphylococcus aureus, while it antagonizes the deadly function of fluoroquinolones against S. aureus and also Escherichia coli. The present study aimed to thoroughly review and study the antimicrobial potency of resveratrol, expected to help researchers pave the way for solving antimicrobial resistance.
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Affiliation(s)
- Ehsan Abedini
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ehsaneh Khodadadi
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Elham Zeinalzadeh
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Seyyed Reza Moaddab
- Pharmaceutical Nanotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Asgharzadeh
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Bahareh Mehramouz
- Connective Tissue Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sounkalo Dao
- Faculté de Médecine, de Pharmacie et d'Odonto-Stomatologie (FMPOS), University of Bamako, Bamako, Mali
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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28
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Berezin V, Bogoyavlenskiy A, Alexyuk M, Alexyuk P. Plant Metabolites as Antiviral Preparations Against Coronaviruses. J Med Food 2021; 24:1028-1038. [PMID: 33689397 DOI: 10.1089/jmf.2020.0190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In 2019-2020, the Coronavirus (CoV) disease 2019 pandemic created a serious challenge for health care systems in several countries worldwide. A cure has not been developed yet and currently used treatment protocols are aimed at relieving clinical symptoms of the disease. This article presents a retrospective review of biologically active compounds of plant origin that can inhibit the reproduction of CoVs, which makes them potential candidates for creating medicinal antiviral preparations against severe acute respiratory syndrome CoV-2 infections. A literature review of articles from highly rated journals was performed using public databases. The search was carried out using keywords related to CoVs, targets for therapy, and plant as antiviral agents. Although inhibition of viral replication is often considered the common mechanism of antiviral activity exerted by most natural products, several plant-derived compounds show specific activity for particular target viruses. In this context, certain classes of plant preparations can serve as a basis for designing modern antiviral agents. In addition, a large number of plant compounds that are potentially active against CoVs are the main components of certain common dietary supplements that can be used to improve the resistance of a population against certain respiratory infections. In this review, we have attempted to characterize the main groups of biologically active plant compounds that have the potential to disrupt the key stages of CoV replication. It has been shown that the use of certain herbal preparations can change the course of infection.
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Affiliation(s)
- Vladimir Berezin
- Research and Production Center fоr Microbiology and Virology, Almaty, Kazakhstan
| | | | - Madina Alexyuk
- Research and Production Center fоr Microbiology and Virology, Almaty, Kazakhstan
| | - Pavel Alexyuk
- Research and Production Center fоr Microbiology and Virology, Almaty, Kazakhstan
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29
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Mohammed MEA. SARS-CoV-2 proteins: Are they useful as targets for COVID-19 drugs and vaccines? Curr Mol Med 2021; 22:50-66. [PMID: 33622224 DOI: 10.2174/1566524021666210223143243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 01/28/2021] [Accepted: 02/02/2021] [Indexed: 11/22/2022]
Abstract
The proteins of coronavirus are classified to nonstructural, structural, and accessory. There are 16 nonstructural viral proteins beside their precursors (1a and 1ab polyproteins). The nonstructural proteins are named as nsp1 to nsp16 and they act as enzymes, coenzymes, and binding proteins to facilitate the replication, transcription, and translation of the virus. The structural proteins are bound to the RNA in the nucleocapsid (N- protein) or to the lipid bilayer membrane of the viral envelope. The lipid bilayer proteins include the membrane protein (M), envelope protein (E), and spike protein (S). Beside their role as structural proteins, they are essential for the host cells binding and invasion. The SARS-CoV-2 contains six accessory proteins which participates in the viral replication, assembly and virus- host interactions. The SARS-CoV-2 accessory proteins are orf3a, orf6, orf7a, orf7b, orf8, and orf10. The functions of the SARS-CoV-2 are not well known, while the functions of their corresponding proteins in SARS-CoV are either well known or poorly studied. Recently, the Oxford University and Pfizer and BioNTech made SARS-CoV-2 vaccines through targeting the spike protein gene. The US Food and Drug Administration (FDA) and the health authorities of the United Kingdom approved and started vaccination using the Pfizer and BioNTech mRNA vaccine. Also, The FDA of USA approved the treatment of COVID-19 using two monoclonal antibodies produced by Regeneron pharmaceuticals to target the spike protein. The SARS-CoV-2 proteins can be used for the diagnosis, as drug targets and in vaccination trials for COVID-19. For future COVID-19 research, more efforts should be done to elaborate the functions and structure of the SARS-CoV-2 proteins so as to use them as targets for COVID-19 drug and vaccines. Special attention should be drawn to extensive research on the SARS-CoV-2 nsp3, orf8, and orf10.
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Gholizadeh P, Sanogo M, Oumarou A, Mohamed MN, Cissoko Y, Saliou Sow M, Pagliano P, Akouda P, Soufiane S, Iknane AA, Oury M, Diallo S, Köse Ş, Dao S, Samadi Kafil H. Fighting COVID-19 in the West Africa after experiencing the Ebola epidemic. Health Promot Perspect 2021; 11:5-11. [PMID: 33758750 PMCID: PMC7967127 DOI: 10.34172/hpp.2021.02] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 12/22/2020] [Indexed: 12/24/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) dissemination occurred from December 2019 and quickly spread to all countries. Infected patients with COVID-19 have had a wide range of symptoms, ranging from mild to severe illness. The most mortality was observed in patients with underlying disease and over 45 years. World statistics have shown that the COVID-19 outbreak is most expanded in Middle Eastern, West Asian, European, North, and South American countries, and is least expanded in African countries. Therefore, the aim of the paper was the evaluation of six African countries including Mali, Mauritania, Niger, Guinea, Togo, and Djibouti to find why this disease is least expanded in African countries. Study was conducted by Questioner for countries health organizers to define their different aspect exposure and fight with COVID-19 including epidemiology, clinical aspects of the disease, case definitions, diagnosis laboratory confirmation, and referral of cases by the portal of entry, case management, and disease prevention in these countries. According to this opinion review, due to the low international flights and low domestic travel, the spread, and prevalence of COVID-19 was low and the return of the immigrants of these countries has caused the spread of COVID-19 among these countries. Experience, preparation, and impact of previous infections epidemic such as the Ebola virus epidemic would have beneficial, which have promoted certain reflexes among people that cause low dissemination in these countries.
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Affiliation(s)
- Pourya Gholizadeh
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran.,Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Moussa Sanogo
- Faculté de Médecine, de Pharmacie et d'Odonto-Stomatologie (FMPOS), University of Bamako, Bamako, Mali
| | - Amadou Oumarou
- Faculte des sciences la santé de l universite Dan Dicko DanKoulodo de Maradi, Niger
| | - Maad Nasser Mohamed
- Service des maladies infectieuses et tropicales de l'hôpital général peltier, Djibouti
| | - Yacouba Cissoko
- Faculty of Medicine and Dentistry, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Mamadou Saliou Sow
- Service des Maladies Infectieuses, Hôpital National Donka, CHU Conakry, Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Guinea
| | | | | | | | - Akory Ag Iknane
- Faculté de Médecine, de Pharmacie et d'Odonto-Stomatologie (FMPOS), University of Bamako, Bamako, Mali.,Institut National de Santé Publique, Bamako, Mali
| | - Mamadou Oury
- Service des Maladies Infectieuses, Hôpital National Donka, CHU Conakry, Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Guinea
| | - Safiatou Diallo
- Service des Maladies Infectieuses, Hôpital National Donka, CHU Conakry, Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Guinea
| | - Şükran Köse
- Department of Infectious Diseases and Clinical Microbiology, University of Health Sciences, Tepecik Training and Research Hospital, İzmir, Turkey
| | - Sounkalo Dao
- Faculté de Médecine, de Pharmacie et d'Odonto-Stomatologie (FMPOS), University of Bamako, Bamako, Mali
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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Balmeh N, Mahmoudi S, Fard NA. Manipulated bio antimicrobial peptides from probiotic bacteria as proposed drugs for COVID-19 disease. INFORMATICS IN MEDICINE UNLOCKED 2021; 23:100515. [PMID: 33521241 PMCID: PMC7832255 DOI: 10.1016/j.imu.2021.100515] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 01/06/2021] [Accepted: 01/06/2021] [Indexed: 02/07/2023] Open
Abstract
Coronavirus disease 19 (COVID-19) is the latest pandemic resulted from the coronavirus family. Due to the high prevalence of this disease, its high mortality rate, and the lack of effective treatment, the need for affordable and accessible drugs is one of the main challenges in this regard. It has been proved that RdRp, 3CL, Spike, and Nucleocapsid are the most important viral proteins playing vital roles in the processes of proliferation and infection. Therefore, we started studying a wide range of bio-peptides and then conducted molecular docking analyses to investigate their binding affinity for the inhibition of these proteins. After obtaining the best bio-peptides with the highest affinity scores, they were examined for further study and then manipulated to eliminate their side effects. Additionally, the molecular dynamic simulation was performed to validate the structure and interaction stability. The results of this study reveal that glycocin F from Lactococcus lactis and lactococcine G from Lactobacillus plantarum had the high affinities to bind to the viral proteins, and the manipulation of their sequence also led to the side effects' elimination. In addition, in some cases, their affinities to attach the SARS-CoV-2 proteins have increased. It seems that these two drugs which were discovered and designed, are optimal for treating the COVID-19 infection. However, experimental and pre-clinical studies are necessary to assay their therapeutic effects.
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Affiliation(s)
- Negar Balmeh
- Department of Cell and Molecular Biology, School of Biology, Nour Danesh Institution of Higher Education, Meymeh, Iran
| | - Samira Mahmoudi
- Department of Microbial Biotechnology, School of Biological Sciences, Islamic Azad University Tehran North Branch, Tehran, Iran
| | - Najaf Allahyari Fard
- Department of Systems Biotechnology, National Institute of Genetic Engineering & Biotechnology (NIGEB), Tehran, Iran
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Soumia M, Hanane Z, Benaissa M, Younes FZ, Chakib A, Mohammed B, Mohamed B. Towards potential inhibitors of COVID-19 main protease Mpro by virtual screening and molecular docking study. JOURNAL OF TAIBAH UNIVERSITY FOR SCIENCE 2020. [DOI: 10.1080/16583655.2020.1850002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Moujane Soumia
- Biochemistry of natural substances, Faculty of Science and Techniques, Moulay Ismail University, Errachdia, Morocco
| | - Zaki Hanane
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University, Meknes, Morocco
- EST Khenifra, Sultan Moulay Sliman University, Khenifra, Morocco
| | - Moualij Benaissa
- Biochemistry of natural substances, Faculty of Science and Techniques, Moulay Ismail University, Errachdia, Morocco
| | - Filali Zegzouti Younes
- LABASE Laboratory, Faculty of Science of Meknes, Moulay Ismail University, Meknes, Morocco
- Health & Environment Skills Cluster, Moulay Ismail University, Meknes, Morocco
| | - Alem Chakib
- Biochemistry of natural substances, Faculty of Science and Techniques, Moulay Ismail University, Errachdia, Morocco
| | - Bouachrine Mohammed
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University, Meknes, Morocco
- EST Khenifra, Sultan Moulay Sliman University, Khenifra, Morocco
| | - Benlyas Mohamed
- Biochemistry of natural substances, Faculty of Science and Techniques, Moulay Ismail University, Errachdia, Morocco
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Bhardwaj VK, Singh R, Das P, Purohit R. Evaluation of acridinedione analogs as potential SARS-CoV-2 main protease inhibitors and their comparison with repurposed anti-viral drugs. Comput Biol Med 2020; 128:104117. [PMID: 33217661 PMCID: PMC7659809 DOI: 10.1016/j.compbiomed.2020.104117] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/01/2020] [Accepted: 11/07/2020] [Indexed: 12/11/2022]
Abstract
Background The main protease (Mpro) of SARS-CoV-2 is involved in the processing of vital polypeptides required for viral genome replication and transcription and is one of the best-characterized targets to inhibit the progression of SARS-CoV-2 in infected individuals. Methods We screened a set of novel classes of acridinediones molecules to efficiently bind and inhibit the activity of the SARS-CoV-2 by targeting the Mpro. The repurposed FDA-approved antivirals were taken as standard molecules for this study. Long term (1.1 μs) MD simulations were performed to analyze the conformational space of the binding pocket of Mpro bound to the selected molecules. Results The molecules DSPD-2 and DSPD-6 showed more favorable MM-PBSA interaction energies and were seated more deeply inside the binding pocket of Mpro than the topmost antiviral drug (Saquinavir). Moreover, DSPD-5 also exhibited comparable binding energy to Saquinavir. The analysis of per residue contribution energy and SASA studies indicated that the molecules showed efficient binding by targeting the S1 subsite of the Mpro binding pocket. Conclusion The DSPD-2, DSPD-6, and DSPD-5 could be developed as potential inhibitors of SARS-CoV-2. Moreover, we suggest that targeting molecules to bind effectively to the S1 subsite could potentially increase the binding of molecules to the SARS-CoV-2 Mpro. A robust computational strategy applied to identify the potential lead for COVID-19. Repurposed FDA approved antiviral drugs were compared with a set of acridinedione analogs against Mpro of SARS-CoV-2. The acridinedione analogs have acceptable ADMET values and low toxicity profile. In-house synthesized acridinedione analogs showed good amount of interaction with Mpro of SARS-CoV-2.
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Affiliation(s)
- Vijay Kumar Bhardwaj
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India; Academy of Scientific & Innovative Research (AcSIR), CSIR-IHBT Campus, Palampur, HP, 176061, India
| | - Rahul Singh
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India
| | - Pralay Das
- Academy of Scientific & Innovative Research (AcSIR), CSIR-IHBT Campus, Palampur, HP, 176061, India; Natural Product Chemistry and Process Development, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, India
| | - Rituraj Purohit
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India; Academy of Scientific & Innovative Research (AcSIR), CSIR-IHBT Campus, Palampur, HP, 176061, India.
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Toor HG, Banerjee DI, Lipsa Rath S, Darji SA. Computational drug re-purposing targeting the spike glycoprotein of SARS-CoV-2 as an effective strategy to neutralize COVID-19. Eur J Pharmacol 2020; 890:173720. [PMID: 33160938 PMCID: PMC7644434 DOI: 10.1016/j.ejphar.2020.173720] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 10/30/2020] [Accepted: 10/30/2020] [Indexed: 01/12/2023]
Abstract
COVID-19 has intensified into a global pandemic with over a million deaths worldwide. Experimental research analyses have been implemented and executed with the sole rationale to counteract SARS-CoV-2, which has initiated potent therapeutic strategy development in coherence with computational biology validation focusing on the characterized viral drug targets signified by proteomic and genomic data. Spike glycoprotein is one of such potential drug target that promotes viral attachment to the host cellular membrane by binding to its receptor ACE-2 via its Receptor-Binding Domain (RBD). Multiple Sequence alignment and relative phylogenetic analysis revealed significant sequential disparities of SARS-CoV-2 as compared to previously encountered SARS-CoV and MERS-CoV strains. We implemented a drug re-purposing approach wherein the inhibitory efficacy of a cluster of thirty known drug candidates comprising of antivirals, antibiotics and phytochemicals (selection contingent on their present developmental status in underway clinical trials) was elucidated by subjecting them to molecular docking analyses against the spike protein RBD model (developed using homology modelling and validated using SAVES server 5.0) and the composite trimeric structures of spike glycoprotein of SARS-CoV-2. Our results indicated that Camostat, Favipiravir, Tenofovir, Raltegravir and Stavudine showed significant interactions with spike RBD of SARS-CoV-2. Proficient bioavailability coupled with no predicted in silico toxicity rendered them as prospective alternatives for designing and development of novel combinatorial therapy formulations for improving existing treatment regimes to combat COVID-19.
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Affiliation(s)
- Himanshu G Toor
- P.G. Department of Genetics, Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences (ARIBAS), Charutar Vidya Mandal University, P.O. Box No. 61, New Vallabh Vidyanagar, Vitthal Udyognagar, 388121, Anand, Gujarat, India; Sardar Patel University, Gujarat, India.
| | - Devjani I Banerjee
- Dr. Vikram Sarabhai Institute of Cell and Molecular Biology, Faculty of Science, The Maharaja Sayajirao University of Baroda, Pratapganj, Vadodara, 390002, Gujarat, India.
| | - Soumya Lipsa Rath
- National Institute of Technology, Warangal, Telangana, 506004, India.
| | - Siddhi A Darji
- Dr. Vikram Sarabhai Institute of Cell and Molecular Biology, Faculty of Science, The Maharaja Sayajirao University of Baroda, Pratapganj, Vadodara, 390002, Gujarat, India.
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Babich O, Sukhikh S, Prosekov A, Asyakina L, Ivanova S. Medicinal Plants to Strengthen Immunity during a Pandemic. Pharmaceuticals (Basel) 2020; 13:E313. [PMID: 33076514 PMCID: PMC7602650 DOI: 10.3390/ph13100313] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/11/2020] [Accepted: 10/13/2020] [Indexed: 02/07/2023] Open
Abstract
The development of new effective anti-coronavirus drugs and therapies is important, but it requires significant human, financial and, most importantly, time expenditures. The current pandemic is neither the first nor the last. Humanity has already accumulated considerable survival experience. We cannot do without prevention and epidemiological protection measures. This study reviews medicinal plants that grow in Northeast Asia and whose antioxidant, antiviral, anti-inflammatory and immunomodulatory characteristics are already known, also in the framework of the prevention and treatment of pneumonia of various etiologies. The need for a comprehensive approach to maintaining immunodefences, including functional foods and positive emotions, is emphasized. In the period of pandemics, it is important to research various areas that allow to us accumulate a critical mass of information and cope with the next global disease.
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Affiliation(s)
- Olga Babich
- Institute of Living Systems, Immanuel Kant Baltic Federal University, A. Nevskogo Street 14, 236016 Kaliningrad, Russia; (O.B.); (S.S.)
- Laboratory of Biocatalysis, Kemerovo State University, Krasnaya Street 6, 650043 Kemerovo, Russia;
| | - Stanislav Sukhikh
- Institute of Living Systems, Immanuel Kant Baltic Federal University, A. Nevskogo Street 14, 236016 Kaliningrad, Russia; (O.B.); (S.S.)
- Department of Bionanotechnology, Kemerovo State University, Krasnaya Street 6, 650043 Kemerovo, Russia;
| | - Alexander Prosekov
- Laboratory of Biocatalysis, Kemerovo State University, Krasnaya Street 6, 650043 Kemerovo, Russia;
| | - Lyudmila Asyakina
- Department of Bionanotechnology, Kemerovo State University, Krasnaya Street 6, 650043 Kemerovo, Russia;
| | - Svetlana Ivanova
- Natural Nutraceutical Biotesting Laboratory, Kemerovo State University, Krasnaya Street 6, 650043 Kemerovo, Russia
- Department of General Mathematics and Informatics, Kemerovo State University, Krasnaya Street, 6, 650043 Kemerovo, Russia
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Fathizadeh H, Taghizadeh S, Safari R, Khiabani SS, Babak B, Hamzavi F, Ganbarov K, Esposito S, Zeinalzadeh E, Dao S, Köse Ş, Kafil HS. Study presence of COVID-19 (SARS-CoV-2) in the sweat of patients infected with Covid-19. Microb Pathog 2020; 149:104556. [PMID: 33031898 PMCID: PMC7534876 DOI: 10.1016/j.micpath.2020.104556] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/25/2020] [Accepted: 09/30/2020] [Indexed: 12/11/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease, which started in Wuhan, Chin, has now become a public health challenge in most countries around the world. Proper preventive measures are necessary to prevent the spread of the virus to help control the pandemic. Because, SARS-CoV-2 is new, its transmission route has not been fully understood. In this study, we aimed to investigate the presence of SARS-CoV-2 in the sweat secretion of COVID-19 patients. Sweat specimens of 25 COVID- 19 patients were collected and tested for SARS-CoV-2 RNA by Real-time Polymerase Chain Reaction (RT-PCR) method. After RNA extraction and cDNA amplification, all samples were examined for the presence of ORF-1ab and N genes related to COVID-19. Results annotated by Realtime PCR machines software based on Dynamic algorithm. The results of this study showed the absence of SARS-CoV-2 in the sweat samples taken from the foreheads of infected people. Therefore, it can be concluded that the sweat of patients with COVID- 19 cannot transmit SARS-CoV-2. However they can be easily contaminated with other body liquids.
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Affiliation(s)
- Hadis Fathizadeh
- Department of Microbiology and Immunology, Kashan University of Medical Sciences, Kashan, Iran
| | - Sepehr Taghizadeh
- Imam Reza Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Rohollah Safari
- Imam Reza Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Saeid Shabestari Khiabani
- Imam Reza Hospital, Tabriz University of Medical Sciences, Tabriz, Iran; Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Bayaz Babak
- Imam Reza Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Fatemeh Hamzavi
- Imam Reza Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | | | - Elham Zeinalzadeh
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sounkalo Dao
- Faculté de Médecine, de Pharmacie et d'Odonto-Stomatologie (FMPOS), University of Bamako, Bamako, Mali
| | - Şükran Köse
- Department of Infectious Diseases and Clinical Microbiology, University of Health Sciences, Tepecik Training and Research Hospital, İzmir, Turkey
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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Cuevas-Barragan CE, Buenrostro-Nava MT, Palos-Gómez GM, Ramirez-Padilla EA, Mendoza-Macias BI, Rivas-Caceres RR. Use of Nasoil® via intranasal to control the harmful effects of Covid-19. Microb Pathog 2020; 149:104504. [PMID: 32950636 PMCID: PMC7497547 DOI: 10.1016/j.micpath.2020.104504] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 02/07/2023]
Abstract
In the absence of vaccines and antiviral drugs available to prevent and treat COVID-19, it becomes imperative to find or use all those products with the potential to fight this virus. This article is an attempt to propose ways to prevent, treat and control the COVID-19 virus, using a product based on plant extracts with the potential to reduce the symptoms caused by the SARS-CoV-2 virus. Nasoil® counts as one of its main components, Asclepias curassavica extracts, and in the present study it has been shown that it is an effective adjuvant in the treatment of Covid-19, increasing the respiratory capacity of the patients (SpO2> 90%) and reducing the symptoms from the first application, improving the patients around the fifth to the eighth application. At a preventive level, the individuals in this study who have applied it (400 individuals) only a 3.15% of these presented symptoms, disappearing when increasing the weekly applications. Nasoil® protects from the appearance of symptoms by 96% due to Covid-19. Modifying lung microenvironments reduces Covid-19 symptoms. Promoting new interactions in the elastic protein decreases the elastase activity of neutrophils. The combination of plant extracts in Nasoil® help in respiratory problems. Nasoil® is an co-adjuvant for the control and prevention of the SARS-CoV-2 virus.
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Affiliation(s)
| | | | - Gabriela Monserrat Palos-Gómez
- Especialista en Medicina Familiar, Unidad de Medicina Familiar núm, 19, del Instituto Mexicano del Seguro Social, Colima, Colima, Mexico
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Panossian A, Brendler T. The Role of Adaptogens in Prophylaxis and Treatment of Viral Respiratory Infections. Pharmaceuticals (Basel) 2020; 13:E236. [PMID: 32911682 PMCID: PMC7558817 DOI: 10.3390/ph13090236] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/01/2020] [Accepted: 09/03/2020] [Indexed: 02/07/2023] Open
Abstract
The aim of our review is to demonstrate the potential of herbal preparations, specifically adaptogens for prevention and treatment of respiratory infections, as well as convalescence, specifically through supporting a challenged immune system, increasing resistance to viral infection, inhibiting severe inflammatory progression, and driving effective recovery. The evidence from pre-clinical and clinical studies with Andrographis paniculata, Eleutherococcus senticosus, Glycyrrhiza spp., Panax spp., Rhodiola rosea, Schisandra chinensis, Withania somnifera, their combination products and melatonin suggests that adaptogens can be useful in prophylaxis and treatment of viral infections at all stages of progression of inflammation as well as in aiding recovery of the organism by (i) modulating innate and adaptive immunity, (ii) anti-inflammatory activity, (iii) detoxification and repair of oxidative stress-induced damage in compromised cells, (iv) direct antiviral effects of inhibiting viral docking or replication, and (v) improving quality of life during convalescence.
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Affiliation(s)
- Alexander Panossian
- Phytomed AB, Vaxtorp, 31275 Halland, Sweden
- EuropharmaUSA, Green Bay, WI 54311, USA
| | - Thomas Brendler
- Department of Botany and Plant Biotechnology, University of Johannesburg, Johannesburg 2000, South Africa;
- Traditional Medicinals Inc., Rohnert Park, CA 94928, USA
- Plantaphile, Collingswood, NJ 08108, USA
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KÜÇÜKCANKURTARAN S, ÖZDOĞAN Y. COVID-19 Pandemisinin Yetişkinlerin Beslenme Durumuna Etkisi. DÜZCE ÜNIVERSITESI SAĞLIK BILIMLERI ENSTITÜSÜ DERGISI 2020. [DOI: 10.33631/duzcesbed.754560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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