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Pavlidou E, Poulios E, Papadopoulou SK, Fasoulas A, Dakanalis A, Giaginis C. Clinical Evidence on the Potential Beneficial Effects of Diet and Dietary Supplements against COVID-19 Infection Risk and Symptoms' Severity. Med Sci (Basel) 2024; 12:11. [PMID: 38390861 PMCID: PMC10885051 DOI: 10.3390/medsci12010011] [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: 01/14/2024] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND Diet and dietary supplements aim to add trace elements, vitamins, and minerals to the body to improve human health and boost the immune system. In the previous few years, the new SARS-CoV-2 coronavirus strain has been threatening the health of individuals and public health more broadly, with rates of intensive care unit cases on the rise, while long-term COVID-19 complications are persisting until today. In the peculiar circumstances of the COVID-19 pandemic, in combination with disease prevention techniques, the strengthening of the immune system is considered particularly important to enable it to effectively respond to and eliminate the SARS-CoV-2 viral pathogen in the event of infection. The purpose of the current literature review is to thoroughly summarize and critically analyze the current clinical data concerning the potential beneficial effects of diet and dietary supplements against COVID-19 infection risk and symptoms' severity. The micronutrients/supplements examined in this study in relation to COVID-19 infection are vitamins A, B, C, and D, zinc, selenium, magnesium, iron, omega-3 fatty acids, glutamine, resveratrol, beta-glucans, and probiotics. The potential effects of dietary patterns such as the Mediterranean diet against SARS-CoV-2 infection risk and symptoms' severity were also analyzed. Our literature review suggests that micro- and macronutrient supplementation and a healthy diet and lifestyle may provide support to immune system function, with beneficial effects both before and during SARS-CoV-2 infection. However, additional studies are recommended to draw safe conclusions and formulate dietary recommendations concerning dietary supplements and their possible effects on preventing and co-treating COVID-19 disease.
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Affiliation(s)
- Eleni Pavlidou
- Department of Food Science and Nutrition, School of Environment, University of the Aegean, 81400 Lemnos, Greece; (E.P.); (E.P.); (A.F.)
| | - Efthymios Poulios
- Department of Food Science and Nutrition, School of Environment, University of the Aegean, 81400 Lemnos, Greece; (E.P.); (E.P.); (A.F.)
| | - Sousana K. Papadopoulou
- Department of Nutritional Sciences and Dietetics, School of Health Sciences, International Hellenic University, 57400 Thessaloniki, Greece
| | - Aristeidis Fasoulas
- Department of Food Science and Nutrition, School of Environment, University of the Aegean, 81400 Lemnos, Greece; (E.P.); (E.P.); (A.F.)
| | - Antonios Dakanalis
- Department of Mental Health, Fondazione IRCCS San Gerardo dei Tintori, Via G.B. Pergolesi 33, 20900 Monza, MB, Italy;
- Department of Medicine and Surgery, University of Milan Bicocca, Via Cadore 38, 20900 Monza, MB, Italy
| | - Constantinos Giaginis
- Department of Food Science and Nutrition, School of Environment, University of the Aegean, 81400 Lemnos, Greece; (E.P.); (E.P.); (A.F.)
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Comunale BA, Larson RJ, Jackson-Ward E, Singh A, Koback FL, Engineer LD. The Functional Implications of Broad Spectrum Bioactive Compounds Targeting RNA-Dependent RNA Polymerase (RdRp) in the Context of the COVID-19 Pandemic. Viruses 2023; 15:2316. [PMID: 38140557 PMCID: PMC10747147 DOI: 10.3390/v15122316] [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: 10/31/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND As long as COVID-19 endures, viral surface proteins will keep changing and new viral strains will emerge, rendering prior vaccines and treatments decreasingly effective. To provide durable targets for preventive and therapeutic agents, there is increasing interest in slowly mutating viral proteins, including non-surface proteins like RdRp. METHODS A scoping review of studies was conducted describing RdRp in the context of COVID-19 through MEDLINE/PubMed and EMBASE. An iterative approach was used with input from content experts and three independent reviewers, focused on studies related to either RdRp activity inhibition or RdRp mechanisms against SARS-CoV-2. RESULTS Of the 205 records screened, 43 studies were included in the review. Twenty-five evaluated RdRp activity inhibition, and eighteen described RdRp mechanisms of existing drugs or compounds against SARS-CoV-2. In silico experiments suggested that RdRp inhibitors developed for other RNA viruses may be effective in disrupting SARS-CoV-2 replication, indicating a possible reduction of disease progression from current and future variants. In vitro, in vivo, and human clinical trial studies were largely consistent with these findings. CONCLUSIONS Future risk mitigation and treatment strategies against forthcoming SARS-CoV-2 variants should consider targeting RdRp proteins instead of surface proteins.
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Affiliation(s)
- Brittany A. Comunale
- Department of Health Policy and Management, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Robin J. Larson
- Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
- Department of Palliative Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756, USA
| | - Erin Jackson-Ward
- Department of Health Policy and Management, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
- Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Aditi Singh
- Department of Biological Sciences, University of California San Diego, La Jolla, CA 92161, USA
| | | | - Lilly D. Engineer
- Department of Health Policy and Management, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
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Wiśniewski OW, Czyżniewski B, Żukiewicz-Sobczak W, Gibas-Dorna M. Nutritional Behavior in European Countries during COVID-19 Pandemic-A Review. Nutrients 2023; 15:3451. [PMID: 37571387 PMCID: PMC10420667 DOI: 10.3390/nu15153451] [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: 06/18/2023] [Revised: 07/23/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023] Open
Abstract
COVID-19 is highly linked with hyperinflammation and dysfunction of the immune cells. Studies have shown that adequate nutrition, a modifiable factor affecting immunity and limiting systemic inflammation, may play an adjunct role in combating the negative consequences of SARS-CoV-2 infection. Due to the global lockdown conditions, the COVID-19 pandemic has contributed, among others, to restrictions on fresh food availability and changes in lifestyle and eating behaviors. The aim of this paper was to review the data regarding eating habits in European countries within the general population of adults and some specific subpopulations, including obese, diabetic, and psychiatric patients, during the COVID-19 pandemic. The PubMed database and the official websites of medical organizations and associations were searched for the phrases "COVID" and "eating habits". Papers regarding the pediatric population, non-European countries, presenting aggregated data from different countries worldwide, and reviews were excluded. During the COVID-19 pandemic, unhealthy lifestyles and eating behaviors were commonly reported. These included increased snacking, intake of caloric foods, such as sweets, pastries, and beverages, and a decline in physical activity. Data suggest that poor eating habits that create a positive energy balance have persisted over time as an additional post-COVID negative consequence.
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Affiliation(s)
- Oskar Wojciech Wiśniewski
- Department of Cardiology-Intensive Therapy and Internal Medicine, Poznan University of Medical Sciences, 49 Przybyszewskiego Street, 60-355 Poznan, Poland
- Department of Nutrition and Food, Faculty of Health Sciences, Calisia University, 62-800 Kalisz, Poland;
| | - Bartłomiej Czyżniewski
- Faculty of Medicine, Collegium Medicum, University of Zielona Gora, 28 Zyty Street, 65-046 Zielona Gora, Poland;
| | - Wioletta Żukiewicz-Sobczak
- Department of Nutrition and Food, Faculty of Health Sciences, Calisia University, 62-800 Kalisz, Poland;
| | - Magdalena Gibas-Dorna
- Collegium Medicum, Institute of Health Sciences, University of Zielona Gora, 28 Zyty Street, 65-046 Zielona Gora, Poland
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Gunathilaka MDTL. Utilization of Marine Seaweeds as a Promising Defense Against COVID-19: a Mini-review. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023:10.1007/s10126-023-10214-7. [PMID: 37243809 DOI: 10.1007/s10126-023-10214-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/04/2023] [Indexed: 05/29/2023]
Abstract
COVID-19 is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which mainly affects the respiratory system. It has been declared as a "pandemic" in March 2020 by the World Health Organization due to the high spreading rate. SARS-CoV-2 binds with the angiotensin-converting enzyme 2 (ACE2) receptors on the cell surface which leads to the downregulation of ACE2 and upregulation of angiotensin-converting enzyme (ACE) receptors. The elevated level of cytokines and ACE receptors leads to the severity of SARS-CoV-2 infection. Due to the limited availability of vaccines and recurrent attacks of COVID-19 mainly in low-income countries, it is important to search for natural remedies to prevent or treat COVID-19 infection. Marine seaweeds are a rich source of bioactive compounds such as phlorotannins; fucoidan; carotenoids; omega-3 and omega-6 fatty acids; vitamins B12, D, and C; and minerals including zinc and selenium that exhibit antioxidant, antiviral, and anti-inflammatory activities. Furthermore, bioactive compounds present in marine seaweeds have the ability to inhibit ACEs by inducing ACE2 which exhibits anti-inflammatory effects in COVID-19. Correspondingly, soluble dietary fibers present in seaweeds are served as prebiotics by generating short-chain fatty acids through fermentation. Hence, seaweeds can be utilized to reduce the gastrointestinal infections associated with SARS-CoV-2 infection.
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Affiliation(s)
- M D T L Gunathilaka
- Department of Biomedical Science, Faculty of Health Science, NSBM Green University, Mahenwatta, Pitipana, Homagama, Sri Lanka.
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Shen J, Fan J, Zhao Y, Jiang D, Niu Z, Zhang Z, Cao G. Innate and adaptive immunity to SARS-CoV-2 and predisposing factors. Front Immunol 2023; 14:1159326. [PMID: 37228604 PMCID: PMC10203583 DOI: 10.3389/fimmu.2023.1159326] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 04/27/2023] [Indexed: 05/27/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus (SARS-CoV-2), has affected all countries worldwide. Although some symptoms are relatively mild, others are still associated with severe and even fatal clinical outcomes. Innate and adaptive immunity are important for the control of SARS-CoV-2 infections, whereas a comprehensive characterization of the innate and adaptive immune response to COVID-19 is still lacking and the mechanisms underlying immune pathogenesis and host predisposing factors are still a matter of scientific debate. Here, the specific functions and kinetics of innate and adaptive immunity involved in SARS-CoV-2 recognition and resultant pathogenesis are discussed, as well as their immune memory for vaccinations, viral-mediated immune evasion, and the current and future immunotherapeutic agents. We also highlight host factors that contribute to infection, which may deepen the understanding of viral pathogenesis and help identify targeted therapies that attenuate severe disease and infection.
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Affiliation(s)
- Jiaying Shen
- Tongji University School of Medicine, Tongji University, Shanghai, China
| | - Junyan Fan
- Department of Epidemiology, Shanghai Key Laboratory of Medical Bioprotection, Key Laboratory of Biological Defense, Ministry of Education, Second Military Medical University, Shanghai, China
| | - Yue Zhao
- Department of Epidemiology, Shanghai Key Laboratory of Medical Bioprotection, Key Laboratory of Biological Defense, Ministry of Education, Second Military Medical University, Shanghai, China
| | - Doming Jiang
- Tongji University School of Medicine, Tongji University, Shanghai, China
| | - Zheyun Niu
- Tongji University School of Medicine, Tongji University, Shanghai, China
| | - Zihan Zhang
- Tongji University School of Medicine, Tongji University, Shanghai, China
| | - Guangwen Cao
- Tongji University School of Medicine, Tongji University, Shanghai, China
- Department of Epidemiology, Shanghai Key Laboratory of Medical Bioprotection, Key Laboratory of Biological Defense, Ministry of Education, Second Military Medical University, Shanghai, China
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Goel N, Ghosh M, Jain D, Sinha R, Khare SK. Inhibition and eradication of Pseudomonas aeruginosa biofilms by secondary metabolites of Nocardiopsis lucentensis EMB25. RSC Med Chem 2023; 14:745-756. [PMID: 37122537 PMCID: PMC10131674 DOI: 10.1039/d2md00439a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/02/2023] [Indexed: 03/09/2023] Open
Abstract
Millions of people worldwide have been impacted by biofilm-associated disorders, which are impregnable owing to frequent changes in surface antigens and gene expression. Globally, about 11% of nosocomial infections, including cystic fibrosis, chronic wound infections, and post-surgical infections, are caused by Pseudomonas aeruginosa, the most prevalent Gram-negative bacterial species. Moreover, biofilms are highly resistant to the host's immune system, and exhibit increased tolerance to stress factors such as starvation, dehydration, and antimicrobials. Here, we have isolated a rare halophilic actinobacteria, Nocardiopsis lucentensis EMB25, and utilized the secondary metabolites for inhibition and eradication of P. aeruginosa biofilm. For the first time, N. lucentensis EMB25 bacteria was explored to study the anti-effect of secondary metabolites on pre-established biofilm. The secondary metabolites targeted the quorum sensing pathway and were found to bind to LasR and RhlR, as confirmed via molecular docking. Also, the reduction in virulence factors, rhamnolipids and pyocyanin further supported the study as these two are regulated by LasR and RhlR. In addition, the downregulation of various QS system genes lasA, lasB, rhlA, rhlB, and pqsA confirmed that the secondary metabolites act on two main regulators of the quorum sensing pathway, LasR, and RhlR. The findings of this study support the bioprospecting of previously unknown and extreme-condition actinobacteria as a rich source of novel bioactives against infections caused by bacterial biofilms.
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Affiliation(s)
- Nikky Goel
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi Hauz Khas New Delhi-110016 India
| | - Moumita Ghosh
- Transcription Regulation Lab, Regional Centre for Biotechnology, NCR Biotech Science Cluster 3 Milestone, Faridabad-Gurgaon Expressway Faridabad 121001 India
| | - Deepti Jain
- Transcription Regulation Lab, Regional Centre for Biotechnology, NCR Biotech Science Cluster 3 Milestone, Faridabad-Gurgaon Expressway Faridabad 121001 India
| | - Rajeshwari Sinha
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi Hauz Khas New Delhi-110016 India
| | - Sunil Kumar Khare
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi Hauz Khas New Delhi-110016 India
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Kumar R, Singh U, Tiwari A, Tiwari P, Sahu JK, Sharma S. Vitamin B12: Strategies for enhanced production, fortified functional food products and health benefits. Process Biochem 2023. [DOI: 10.1016/j.procbio.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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8
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Yang JY, Ma YX, Liu Y, Peng XJ, Chen XZ. A Comprehensive Review of Natural Flavonoids with Anti-SARS-CoV-2 Activity. Molecules 2023; 28:molecules28062735. [PMID: 36985705 PMCID: PMC10054335 DOI: 10.3390/molecules28062735] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/11/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has majorly impacted public health and economies worldwide. Although several effective vaccines and drugs are now used to prevent and treat COVID-19, natural products, especially flavonoids, showed great therapeutic potential early in the pandemic and thus attracted particular attention. Quercetin, baicalein, baicalin, EGCG (epigallocatechin gallate), and luteolin are among the most studied flavonoids in this field. Flavonoids can directly or indirectly exert antiviral activities, such as the inhibition of virus invasion and the replication and inhibition of viral proteases. In addition, flavonoids can modulate the levels of interferon and proinflammatory factors. We have reviewed the previously reported relevant literature researching the pharmacological anti-SARS-CoV-2 activity of flavonoids where structures, classifications, synthetic pathways, and pharmacological effects are summarized. There is no doubt that flavonoids have great potential in the treatment of COVID-19. However, most of the current research is still in the theoretical stage. More studies are recommended to evaluate the efficacy and safety of flavonoids against SARS-CoV-2.
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Affiliation(s)
- Jun-Yu Yang
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000, China
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, China
| | - Yi-Xuan Ma
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000, China
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, China
| | - Yan Liu
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000, China
| | - Xiang-Jun Peng
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000, China
- Jiangxi Province Key Laboratory of Biomaterials and Biofabrication for Tissue Engineering, Gannan Medical University, Ganzhou 341000, China
| | - Xiang-Zhao Chen
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000, China
- Jiangxi Province Key Laboratory of Biomaterials and Biofabrication for Tissue Engineering, Gannan Medical University, Ganzhou 341000, China
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Shrivastava AK, Sahu PK, Cecchi T, Shrestha L, Shah SK, Gupta A, Palikhey A, Joshi B, Gupta PP, Upadhyaya J, Paudel M, Koirala N. An emerging natural antioxidant therapy for COVID‐19 infection patients: Current and future directions. FOOD FRONTIERS 2023. [DOI: 10.1002/fft2.207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Amit Kumar Shrivastava
- Department of Pharmacology Universal College of Medical Sciences Bhairahawa Rupandehi Nepal
| | - Prafulla Kumar Sahu
- School of Pharmacy Centurion University of Technology and Management Bhubaneswar Odisha India
| | | | - Laxmi Shrestha
- Department of Pharmacology Universal College of Medical Sciences Bhairahawa Rupandehi Nepal
| | - Sanjay Kumar Shah
- Department of Reproductive MedicineJoint Inter‐national Research Laboratory of Reproduction and DevelopmentChongquing Medical University ChongqingPeople's Republic of China
| | - Anamika Gupta
- Sharjah Institute for Medical Sciences University of Sharjah Sharjah United Arab Emirates
| | - Anjan Palikhey
- Department of Pharmacology Universal College of Medical Sciences Bhairahawa Rupandehi Nepal
| | - Bishal Joshi
- Department of Physiology, Universal College of Medical Sciences Bhairahawa Rupandehi Nepal
| | - Pramodkumar P. Gupta
- School of Biotechnology and Bioinformatics D. Y. Patil Deemed to be University, CBD Belapur Navi Mumbai India
| | - Jitendra Upadhyaya
- Institute of Agriculture and Animal Science Tribhuvan University Chitwan Nepal
| | - Mahendra Paudel
- Department of Agri‐Botany and Ecology Institute of Agriculture and Animal Science Tribhuvan University Mahendranagar Nepal
| | - Niranjan Koirala
- Natural Products Research FacilityGandaki Province Academy of Science and Technology Pokhara, Gandaki Province Nepal
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Yang Z, Cai X, Ye Q, Zhao Y, Li X, Zhang S, Zhang L. High-Throughput Screening for the Potential Inhibitors of SARS-CoV-2 with Essential Dynamic Behavior. Curr Drug Targets 2023; 24:532-545. [PMID: 36876836 DOI: 10.2174/1389450124666230306141725] [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: 06/18/2022] [Revised: 11/09/2022] [Accepted: 01/11/2023] [Indexed: 03/07/2023]
Abstract
Global health security has been challenged by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic. Due to the lengthy process of generating vaccinations, it is vital to reposition currently available drugs in order to relieve anti-epidemic tensions and accelerate the development of therapies for Coronavirus Disease 2019 (COVID-19), the public threat caused by SARS-CoV-2. High throughput screening techniques have established their roles in the evaluation of already available medications and the search for novel potential agents with desirable chemical space and more cost-effectiveness. Here, we present the architectural aspects of highthroughput screening for SARS-CoV-2 inhibitors, especially three generations of virtual screening methodologies with structural dynamics: ligand-based screening, receptor-based screening, and machine learning (ML)-based scoring functions (SFs). By outlining the benefits and drawbacks, we hope that researchers will be motivated to adopt these methods in the development of novel anti- SARS-CoV-2 agents.
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Affiliation(s)
- Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Xinhui Cai
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Qiushi Ye
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Yizhen Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Xuhua Li
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Shengli Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
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Dey SK, Saini M, Dhembla C, Bhatt S, Rajesh AS, Anand V, Das HK, Kundu S. Suramin, penciclovir, and anidulafungin exhibit potential in the treatment of COVID-19 via binding to nsp12 of SARS-CoV-2. J Biomol Struct Dyn 2022; 40:14067-14083. [PMID: 34784490 DOI: 10.1080/07391102.2021.2000498] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
COVID-19, for which no confirmed therapeutic agents are available, has claimed over 48,14,000 lives globally. A feasible and quicker method to resolve this problem may be 'drug repositioning'. We investigated selected FDA and WHO-EML approved drugs based on their previously promising potential as antivirals, antibacterials or antifungals. These drugs were docked onto the nsp12 protein, which reigns the RNA-dependent RNA polymerase activity of SARS-CoV-2, a key therapeutic target for coronaviruses. Docked complexes were reevaluated using MM-GBSA analysis and the top three inhibitor-protein complexes were subjected to 100 ns long molecular dynamics simulation followed by another round of MM-GBSA analysis. The RMSF plots, binding energies and the mode of physicochemical interaction of the active site of the protein with the drugs were evaluated. Suramin, Penciclovir, and Anidulafungin were found to bind to nsp12 with similar binding energies as that of Remdesivir, which has been used as a therapy for COVID-19. In addition, recent experimental evidences indicate that these drugs exhibit antiviral efficacy against SARS-CoV-2. Such evidence, along with the significant and varied physical interactions of these drugs with the key viral enzyme outlined in this investigation, indicates that they might have a prospective therapeutic potential in the treatment of COVID-19 as monotherapy or combination therapy with Remdesivir.
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Affiliation(s)
- Sanjay Kumar Dey
- Center for Advanced Biotechnology and Medicine, Rutgers University, New Brunswick, New Jersey, USA.,Department of Biochemistry, University of Delhi South Campus, New Delhi, India.,Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Manisha Saini
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Chetna Dhembla
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Shruti Bhatt
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - A Sai Rajesh
- Department of Biosciences and Biotechnology, Fakir Mohan University, Odisha, India
| | - Varnita Anand
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | | | - Suman Kundu
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
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Verma DK, Kapoor S, Das S, Thakur KG. Potential Inhibitors of SARS-CoV-2 Main Protease (M pro) Identified from the Library of FDA-Approved Drugs Using Molecular Docking Studies. Biomedicines 2022; 11:85. [PMID: 36672593 PMCID: PMC9856154 DOI: 10.3390/biomedicines11010085] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/22/2022] [Accepted: 11/24/2022] [Indexed: 12/31/2022] Open
Abstract
The Corona Virus Infectious Disease-2019 (COVID-19) outbreak originated at Wuhan, China, in December 2019. It has already spread rapidly and caused more than 6.5 million deaths worldwide. Its causal agent is a beta-coronavirus named SARS-CoV-2. Many efforts have already been made to develop new vaccines and drugs against these viruses, but over time, it has changed its molecular nature and evolved into more lethal variants, such as Delta and Omicron. These will lead us to target its more-conserved proteins. The sequences' BLAST and crystal structure of the main protease Mpro suggest a high sequence and structural conservation. Mpro is responsible for the proteolytic maturation of the polyprotein essential for the viral replication and transcription, which makes it an important drug target. Discovery of new drug molecules may take years before getting to the clinics. So, considering urgency, we performed molecular docking studies using FDA-approved drugs to identify molecules that could potentially bind to the substrate-binding site and inhibit SARS-CoV-2's main protease (Mpro). We used the Glide module in the Schrödinger software suite to perform molecular docking studies, followed by MM-GBSA-based energy calculations to score the hit molecules. Molecular docking and manual analysis suggest that several drugs may bind and potentially inhibit Mpro. We also performed molecular simulations studies for selected compounds to evaluate protein-drug interactions. Considering bioavailability, lesser toxicity, and route of administration, some of the top-ranked drugs, including lumefantrine (antimalarial), dipyridamole (coronary vasodilator), dihydroergotamine (used for treating migraine), hexoprenaline (anti asthmatic), riboflavin (vitamin B2), and pantethine (vitamin B5) may be taken forward for further in vitro and in vivo experiments to investigate their therapeutic potential.
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Affiliation(s)
| | | | | | - Krishan Gopal Thakur
- Structural Biology Laboratory, CSIR-Institute of Microbial Technology, Chandigarh 160036, India
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13
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Budipramana K, Sangande F. Molecular docking-based virtual screening: Challenges in hits identification for Anti-SARS-Cov-2 activity. PHARMACIA 2022. [DOI: 10.3897/pharmacia.69.e89812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) requires finding new drugs or repurposing drugs for clinical use. Molecular docking belongs to structure-based drug design providing a fast method for identifying the hit compounds with antiviral activity against SARS-Cov-2. However, the weakness of the docking method is compounded by the limited crystallographic information and comparison drugs due to the novelty of this virus can present challenges in identifying hits of anti-SARS-Cov-2. In the current review, we highlighted several aspects, especially those related to the target structure, docking validation, and virtual hit selection, that need to be considered to obtain reliable docking results. Here, we discussed several cases pertaining to the issue highlighted and approaches that could be used to solve them.
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Discovering new potential inhibitors to SARS-CoV-2 RNA dependent RNA polymerase (RdRp) using high throughput virtual screening and molecular dynamics simulations. Sci Rep 2022; 12:19986. [PMID: 36411383 PMCID: PMC9676757 DOI: 10.1038/s41598-022-24695-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 03/14/2022] [Indexed: 11/23/2022] Open
Abstract
RNA dependent RNA polymerase (RdRp), is an essential in the RNA replication within the life cycle of the severely acute respiratory coronavirus-2 (SARS-CoV-2), causing the deadly respiratory induced sickness COVID-19. Remdesivir is a prodrug that has seen some success in inhibiting this enzyme, however there is still the pressing need for effective alternatives. In this study, we present the discovery of four non-nucleoside small molecules that bind favorably to SARS-CoV-2 RdRp over the active form of the popular drug remdesivir (RTP) and adenosine triphosphate (ATP) by utilizing high-throughput virtual screening (HTVS) against the vast ZINC compound database coupled with extensive molecular dynamics (MD) simulations. After post-trajectory analysis, we found that the simulations of complexes containing both ATP and RTP remained stable for the duration of their trajectories. Additionally, it was revealed that the phosphate tail of RTP was stabilized by both the positive amino acid pocket and magnesium ions near the entry channel of RdRp which includes residues K551, R553, R555 and K621. It was also found that residues D623, D760, and N691 further stabilized the ribose portion of RTP with U10 on the template RNA strand forming hydrogen pairs with the adenosine motif. Using these models of RdRp, we employed them to screen the ZINC database of ~ 17 million molecules. Using docking and drug properties scoring, we narrowed down our selection to fourteen candidates. These were subjected to 200 ns simulations each underwent free energy calculations. We identified four hit compounds from the ZINC database that have similar binding poses to RTP while possessing lower overall binding free energies, with ZINC097971592 having a binding free energy two times lower than RTP.
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Tanimoto S, Itoh SG, Okumura H. State-of-the-Art Molecular Dynamics Simulation Studies of RNA-Dependent RNA Polymerase of SARS-CoV-2. Int J Mol Sci 2022; 23:ijms231810358. [PMID: 36142270 PMCID: PMC9499461 DOI: 10.3390/ijms231810358] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/26/2022] [Accepted: 08/31/2022] [Indexed: 01/18/2023] Open
Abstract
Molecular dynamics (MD) simulations are powerful theoretical methods that can reveal biomolecular properties, such as structure, fluctuations, and ligand binding, at the level of atomic detail. In this review article, recent MD simulation studies on these biomolecular properties of the RNA-dependent RNA polymerase (RdRp), which is a multidomain protein, of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are presented. Although the tertiary structures of RdRps in SARS-CoV-2 and SARS-CoV are almost identical, the RNA synthesis activity of RdRp of SARS-CoV is higher than SARS-CoV-2. Recent MD simulations observed a difference in the dynamic properties of the two RdRps, which may cause activity differences. RdRp is also a drug target for Coronavirus disease 2019 (COVID-19). Nucleotide analogs, such as remdesivir and favipiravir, are considered to be taken up by RdRp and inhibit RNA replication. Recent MD simulations revealed the recognition mechanism of RdRp for these drug molecules and adenosine triphosphate (ATP). The ligand-recognition ability of RdRp decreases in the order of remdesivir, favipiravir, and ATP. As a typical recognition process, it was found that several lysine residues of RdRp transfer these ligand molecules to the binding site such as a “bucket brigade.” This finding will contribute to understanding the mechanism of the efficient ligand recognition by RdRp. In addition, various simulation studies on the complexes of SARS-CoV-2 RdRp with several nucleotide analogs are reviewed, and the molecular mechanisms by which these compounds inhibit the function of RdRp are discussed. The simulation studies presented in this review will provide useful insights into how nucleotide analogs are recognized by RdRp and inhibit the RNA replication.
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Affiliation(s)
- Shoichi Tanimoto
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8787, Aichi, Japan
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki 444-8787, Aichi, Japan
| | - Satoru G. Itoh
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8787, Aichi, Japan
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki 444-8787, Aichi, Japan
- Department of Structural Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki 444-8787, Aichi, Japan
| | - Hisashi Okumura
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8787, Aichi, Japan
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki 444-8787, Aichi, Japan
- Department of Structural Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki 444-8787, Aichi, Japan
- Correspondence:
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Low ZY, Zabidi NZ, Yip AJW, Puniyamurti A, Chow VTK, Lal SK. SARS-CoV-2 Non-Structural Proteins and Their Roles in Host Immune Evasion. Viruses 2022; 14:v14091991. [PMID: 36146796 PMCID: PMC9506350 DOI: 10.3390/v14091991] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/02/2022] [Accepted: 09/03/2022] [Indexed: 12/02/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) has caused an unprecedented global crisis and continues to threaten public health. The etiological agent of this devastating pandemic outbreak is the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). COVID-19 is characterized by delayed immune responses, followed by exaggerated inflammatory responses. It is well-established that the interferon (IFN) and JAK/STAT signaling pathways constitute the first line of defense against viral and bacterial infections. To achieve viral replication, numerous viruses are able to antagonize or hijack these signaling pathways to attain productive infection, including SARS-CoV-2. Multiple studies document the roles of several non-structural proteins (NSPs) of SARS-CoV-2 that facilitate the establishment of viral replication in host cells via immune escape. In this review, we summarize and highlight the functions and characteristics of SARS-CoV-2 NSPs that confer host immune evasion. The molecular mechanisms mediating immune evasion and the related potential therapeutic strategies for controlling the COVID-19 pandemic are also discussed.
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Affiliation(s)
- Zheng Yao Low
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Subang Jaya 47500, Malaysia
| | - Nur Zawanah Zabidi
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Subang Jaya 47500, Malaysia
| | - Ashley Jia Wen Yip
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Subang Jaya 47500, Malaysia
| | - Ashwini Puniyamurti
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Subang Jaya 47500, Malaysia
| | - Vincent T. K. Chow
- Infectious Diseases Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Kent Ridge, Singapore 117545, Singapore
- Correspondence: (V.T.K.C.); (S.K.L.)
| | - Sunil K. Lal
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Subang Jaya 47500, Malaysia
- Tropical Medicine & Biology Platform, Monash University, Subang Jaya 47500, Malaysia
- Correspondence: (V.T.K.C.); (S.K.L.)
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Zhao T, Wang B, Shen J, Wei Y, Zhu Y, Tian X, Wen G, Xu B, Fu C, Xie Z, Xi Y, Li Z, Peng J, Wu Y, Tang X, Wan C, Pan L, Zhu W, Li Z, Qin D. Third dose of anti-SARS-CoV-2 inactivated vaccine for patients with RA: Focusing on immunogenicity and effects of RA drugs. Front Med (Lausanne) 2022; 9:978272. [PMID: 36117981 PMCID: PMC9470915 DOI: 10.3389/fmed.2022.978272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 08/15/2022] [Indexed: 11/23/2022] Open
Abstract
Objectives To evaluate the immunogenicity of the third dose of inactivated SARS-CoV-2 vaccine in rheumatoid arthritis (RA) patients and explore the effect of RA drugs on vaccine immunogenicity. Methods We recruited RA patients (n = 222) and healthy controls (HC, n = 177) who had been injected with a third dose of inactivated SARS-CoV-2 vaccine, and their neutralizing antibody (NAb) titer levels were assessed. Results RA patients and HC were age- and gender-matched, and the mean interval between 3rd vaccination and sampling was comparable. The NAb titers were significantly lower in RA patients after the third immunization compared with HC. The positive rate of NAb in HC group was 90.4%, while that in RA patients was 80.18%, and the difference was significant. Furthermore, comparison of NAb titers between RA treatment subgroups and HC showed that the patients in the conventional synthetic (cs) disease-modifying anti-rheumatic drugs (DMARDs) group exhibited no significant change in NAb titers, while in those receiving the treatment of biological DMARDs (bDMARDs), Janus Kinase (JAK) inhibitors, and prednisone, the NAb titers were significantly lower. Spearman correlation analysis revealed that NAb responses to SARS-CoV-2 in HC did differ significantly according to the interval between 3rd vaccination and sampling, but this finding was not observed in RA patients. In addition, NAb titers were not significantly correlated with RA-related laboratory indicators, including RF-IgA, RF-IgG, RF-IgM, anti-CCP antibody; C-RP; ESR; NEUT% and LYMPH%. Conclusion Serum antibody responses to the third dose of vaccine in RA patients were weaker than HC. Our study will help to evaluate the efficacy and safety of booster vaccination in RA patients and provide further guidance for adjusting vaccination strategies.
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Affiliation(s)
- Ting Zhao
- School of Basic Medical Sciences, Yunnan University of Chinese Medicine, Kunming, China
- The First School of Clinical Medicine, Yunnan University of Chinese Medicine, Kunming, China
| | - Bo Wang
- The Department of Educational Administration, Yunnan University of Chinese Medicine, Kunming, China
| | - Jiayan Shen
- School of Basic Medical Sciences, Yunnan University of Chinese Medicine, Kunming, China
- The First School of Clinical Medicine, Yunnan University of Chinese Medicine, Kunming, China
| | - Yuanyuan Wei
- School of Basic Medical Sciences, Yunnan University of Chinese Medicine, Kunming, China
| | - Youyang Zhu
- The Third Affiliated Hospital, Yunnan University of Chinese Medicine, Kunming, China
| | - Xiaofang Tian
- The First School of Clinical Medicine, Yunnan University of Chinese Medicine, Kunming, China
| | - Guangfen Wen
- The First School of Clinical Medicine, Yunnan University of Chinese Medicine, Kunming, China
| | - Bonan Xu
- School of Basic Medical Sciences, Yunnan University of Chinese Medicine, Kunming, China
| | - Chenyang Fu
- School of Basic Medical Sciences, Yunnan University of Chinese Medicine, Kunming, China
| | - Zhaohu Xie
- School of Basic Medical Sciences, Yunnan University of Chinese Medicine, Kunming, China
| | - Yujiang Xi
- The First School of Clinical Medicine, Yunnan University of Chinese Medicine, Kunming, China
| | - Zhenmin Li
- School of Basic Medical Sciences, Yunnan University of Chinese Medicine, Kunming, China
| | - Jiangyun Peng
- The First School of Clinical Medicine, Yunnan University of Chinese Medicine, Kunming, China
| | - Yang Wu
- The First School of Clinical Medicine, Yunnan University of Chinese Medicine, Kunming, China
| | - Xiaohu Tang
- The First School of Clinical Medicine, Yunnan University of Chinese Medicine, Kunming, China
| | - Chunping Wan
- The First School of Clinical Medicine, Yunnan University of Chinese Medicine, Kunming, China
| | - Lei Pan
- The Second School of Clinical Medicine, Yunnan University of Chinese Medicine, Kunming, China
| | - Wenxin Zhu
- Department of Rehabilitation, The People's Hospital of Yunxian, Yunxian, China
- Wenxin Zhu
| | - Zhaofu Li
- School of Basic Medical Sciences, Yunnan University of Chinese Medicine, Kunming, China
- Zhaofu Li
| | - Dongdong Qin
- School of Basic Medical Sciences, Yunnan University of Chinese Medicine, Kunming, China
- *Correspondence: Dongdong Qin
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Kell DB, Pretorius E. The potential role of ischaemia-reperfusion injury in chronic, relapsing diseases such as rheumatoid arthritis, Long COVID, and ME/CFS: evidence, mechanisms, and therapeutic implications. Biochem J 2022; 479:1653-1708. [PMID: 36043493 PMCID: PMC9484810 DOI: 10.1042/bcj20220154] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 02/07/2023]
Abstract
Ischaemia-reperfusion (I-R) injury, initiated via bursts of reactive oxygen species produced during the reoxygenation phase following hypoxia, is well known in a variety of acute circumstances. We argue here that I-R injury also underpins elements of the pathology of a variety of chronic, inflammatory diseases, including rheumatoid arthritis, ME/CFS and, our chief focus and most proximally, Long COVID. Ischaemia may be initiated via fibrin amyloid microclot blockage of capillaries, for instance as exercise is started; reperfusion is a necessary corollary when it finishes. We rehearse the mechanistic evidence for these occurrences here, in terms of their manifestation as oxidative stress, hyperinflammation, mast cell activation, the production of marker metabolites and related activities. Such microclot-based phenomena can explain both the breathlessness/fatigue and the post-exertional malaise that may be observed in these conditions, as well as many other observables. The recognition of these processes implies, mechanistically, that therapeutic benefit is potentially to be had from antioxidants, from anti-inflammatories, from iron chelators, and via suitable, safe fibrinolytics, and/or anti-clotting agents. We review the considerable existing evidence that is consistent with this, and with the biochemical mechanisms involved.
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Affiliation(s)
- Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, U.K
- The Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Kemitorvet 200, 2800 Kgs Lyngby, Denmark
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch, Private Bag X1 Matieland 7602, South Africa
| | - Etheresia Pretorius
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, U.K
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch, Private Bag X1 Matieland 7602, South Africa
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Jimenez-Guardeño JM, Ortega-Prieto AM, Menendez Moreno B, Maguire TJA, Richardson A, Diaz-Hernandez JI, Diez Perez J, Zuckerman M, Mercadal Playa A, Cordero Deline C, Malim MH, Martinez-Nunez RT. Drug repurposing based on a quantum-inspired method versus classical fingerprinting uncovers potential antivirals against SARS-CoV-2. PLoS Comput Biol 2022; 18:e1010330. [PMID: 35849631 PMCID: PMC9333455 DOI: 10.1371/journal.pcbi.1010330] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 07/28/2022] [Accepted: 06/27/2022] [Indexed: 01/18/2023] Open
Abstract
The COVID-19 pandemic has accelerated the need to identify new antiviral therapeutics at pace, including through drug repurposing. We employed a Quadratic Unbounded Binary Optimization (QUBO) model, to search for compounds similar to Remdesivir, the first antiviral against SARS-CoV-2 approved for human use, using a quantum-inspired device. We modelled Remdesivir and compounds present in the DrugBank database as graphs, established the optimal parameters in our algorithm and resolved the Maximum Weighted Independent Set problem within the conflict graph generated. We also employed a traditional Tanimoto fingerprint model. The two methods yielded different lists of lead compounds, with some overlap. While GS-6620 was the top compound predicted by both models, the QUBO model predicted BMS-986094 as second best. The Tanimoto model predicted different forms of cobalamin, also known as vitamin B12. We then determined the half maximal inhibitory concentration (IC50) values in cell culture models of SARS-CoV-2 infection and assessed cytotoxicity. We also demonstrated efficacy against several variants including SARS-CoV-2 Strain England 2 (England 02/2020/407073), B.1.1.7 (Alpha), B.1.351 (Beta) and B.1.617.2 (Delta). Lastly, we employed an in vitro polymerization assay to demonstrate that these compounds directly inhibit the RNA-dependent RNA polymerase (RdRP) of SARS-CoV-2. Together, our data reveal that our QUBO model performs accurate comparisons (BMS-986094) that differed from those predicted by Tanimoto (different forms of vitamin B12); all compounds inhibited replication of SARS-CoV-2 via direct action on RdRP, with both models being useful. While Tanimoto may be employed when performing relatively small comparisons, QUBO is also accurate and may be well suited for very complex problems where computational resources may limit the number and/or complexity of possible combinations to evaluate. Our quantum-inspired screening method can therefore be employed in future searches for novel pharmacologic inhibitors, thus providing an approach for accelerating drug deployment.
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Affiliation(s)
- Jose M. Jimenez-Guardeño
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Ana Maria Ortega-Prieto
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | | | - Thomas J. A. Maguire
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Adam Richardson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | | | - Javier Diez Perez
- Fujitsu Technology Solutions S.A., Pozuelo de Alarcón, Madrid, Spain
| | - Mark Zuckerman
- South London Virology Centre, King’s College Hospital, London, United Kingdom
| | | | | | - Michael H. Malim
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Rocio Teresa Martinez-Nunez
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
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20
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Vere G, Alam MR, Farrar S, Kealy R, Kessler BM, O’Brien DP, Pinto-Fernández A. Targeting the Ubiquitylation and ISGylation Machinery for the Treatment of COVID-19. Biomolecules 2022; 12:biom12020300. [PMID: 35204803 PMCID: PMC8869442 DOI: 10.3390/biom12020300] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 12/15/2022] Open
Abstract
Ubiquitylation and ISGylation are protein post-translational modifications (PTMs) and two of the main events involved in the activation of pattern recognition receptor (PRRs) signals allowing the host defense response to viruses. As with similar viruses, SARS-CoV-2, the virus causing COVID-19, hijacks these pathways by removing ubiquitin and/or ISG15 from proteins using a protease called PLpro, but also by interacting with enzymes involved in ubiquitin/ISG15 machinery. These enable viral replication and avoidance of the host immune system. In this review, we highlight potential points of therapeutic intervention in ubiquitin/ISG15 pathways involved in key host-pathogen interactions, such as PLpro, USP18, TRIM25, CYLD, A20, and others that could be targeted for the treatment of COVID-19, and which may prove effective in combatting current and future vaccine-resistant variants of the disease.
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Affiliation(s)
- George Vere
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Md Rashadul Alam
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
| | - Sam Farrar
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
| | - Rachel Kealy
- Environmental Futures & Big Data Impact Lab, University of Exeter, Stocker Rd., Exeter EX4 4PY, UK;
| | - Benedikt M. Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Darragh P. O’Brien
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
- Correspondence: (D.P.O.); (A.P.-F.)
| | - Adán Pinto-Fernández
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
- Correspondence: (D.P.O.); (A.P.-F.)
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21
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Batista KS, Cintra VM, Lucena PAF, Manhães-de-Castro R, Toscano AE, Costa LP, Queiroz MEBS, de Andrade SM, Guzman-Quevedo O, Aquino JDS. The role of vitamin B12 in viral infections: a comprehensive review of its relationship with the muscle-gut-brain axis and implications for SARS-CoV-2 infection. Nutr Rev 2022; 80:561-578. [PMID: 34791425 PMCID: PMC8689946 DOI: 10.1093/nutrit/nuab092] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
This comprehensive review establishes the role of vitamin B12 as adjunct therapy for viral infections in the treatment and persistent symptoms of COVID-19, focusing on symptoms related to the muscle-gut-brain axis. Vitamin B12 can help balance immune responses to better fight viral infections. Furthermore, data from randomized clinical trials and meta-analysis indicate that vitamin B12 in the forms of methylcobalamin and cyanocobalamin may increase serum vitamin B12 levels, and resulted in decreased serum methylmalonic acid and homocysteine concentrations, and decreased pain intensity, memory loss, and impaired concentration. Among studies, there is much variation in vitamin B12 doses, chemical forms, supplementation time, and administration routes. Larger randomized clinical trials of vitamin B12 supplementation and analysis of markers such as total vitamin B12, holotranscobalamin, total homocysteine and methylmalonic acid, total folic acid, and, if possible, polymorphisms and methylation of genes need to be conducted with people with and without COVID-19 or who have had COVID-19 to facilitate the proper vitamin B12 form to be administered in individual treatment.
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Affiliation(s)
- Kamila S Batista
- K.S. Batista and J.d.S. Aquino are with the Experimental Nutrition Laboratory, Department of Nutrition and Post Graduate Program in Nutrition Sciences, Federal University of Paraíba, Paraíba, Brazil. V.M. Cintra and P.A.F Lucena are with the Department of Medicine, Faculty of Medical Sciences of Paraíba, and the Department of Nutrition, Integrated Colleges of Patos, Paraíba, Brazil. V.M. Cintra is with the the Multiprofessional Residence in Child Health of Secretariat of Health of the State of Paraíba, Brazil. P.A.F Lucena is with Coordination of Neurology Services, Hospital Metropolitano Dom José Maria Pires, Santa Rita, Paraíba and Emergency, Trauma Hospital Senador Humberto Lucena, João Pessoa, Paraíba, Brazil. R. Manhães-de-Castro is with the Studies in Nutrition and Phenotypic Plasticity Unit, Department of Nutrition, Federal University of Pernambuco, Recife, Pernambuco, Brazil. R. Manhães-de-Castro and A.E. Toscano are with the Post Graduate Program in Nutrition, Health Sciences Center, Federal University of Pernambuco, Recife, Pernambuco, Brazil. A.E. Toscano is with the Department of Nursing, CAV, Federal University of Pernambuco, Pernambuco, Brazil. A.E. Toscano and O. Guzman-Quevedo are with the Post Graduate Program in Neuropsychiatry and Behavioral Sciences, Federal University of Pernambuco, Recife, Pernambuco, Brazil. L.P. Costa, M.E.B.S. Queirozj, and S.M. de Andrade are with the Ageing and Neuroscience Laboratory, Health Sciences Center, Federal University of Paraíba, Paraíba, Brazil. O. Guzman-Quevedo is with the Higher Technological Institute of Tacámbaro, Tacámbaro, Michoacán, Mexico. O. Guzman-Quevedo is with the Center for Biomedical Research of Michoacán, Mexican Institute of Social Security, Morelia, Michoacán, Mexico
| | - Vanessa M Cintra
- K.S. Batista and J.d.S. Aquino are with the Experimental Nutrition Laboratory, Department of Nutrition and Post Graduate Program in Nutrition Sciences, Federal University of Paraíba, Paraíba, Brazil. V.M. Cintra and P.A.F Lucena are with the Department of Medicine, Faculty of Medical Sciences of Paraíba, and the Department of Nutrition, Integrated Colleges of Patos, Paraíba, Brazil. V.M. Cintra is with the the Multiprofessional Residence in Child Health of Secretariat of Health of the State of Paraíba, Brazil. P.A.F Lucena is with Coordination of Neurology Services, Hospital Metropolitano Dom José Maria Pires, Santa Rita, Paraíba and Emergency, Trauma Hospital Senador Humberto Lucena, João Pessoa, Paraíba, Brazil. R. Manhães-de-Castro is with the Studies in Nutrition and Phenotypic Plasticity Unit, Department of Nutrition, Federal University of Pernambuco, Recife, Pernambuco, Brazil. R. Manhães-de-Castro and A.E. Toscano are with the Post Graduate Program in Nutrition, Health Sciences Center, Federal University of Pernambuco, Recife, Pernambuco, Brazil. A.E. Toscano is with the Department of Nursing, CAV, Federal University of Pernambuco, Pernambuco, Brazil. A.E. Toscano and O. Guzman-Quevedo are with the Post Graduate Program in Neuropsychiatry and Behavioral Sciences, Federal University of Pernambuco, Recife, Pernambuco, Brazil. L.P. Costa, M.E.B.S. Queirozj, and S.M. de Andrade are with the Ageing and Neuroscience Laboratory, Health Sciences Center, Federal University of Paraíba, Paraíba, Brazil. O. Guzman-Quevedo is with the Higher Technological Institute of Tacámbaro, Tacámbaro, Michoacán, Mexico. O. Guzman-Quevedo is with the Center for Biomedical Research of Michoacán, Mexican Institute of Social Security, Morelia, Michoacán, Mexico
| | - Paulo A F Lucena
- K.S. Batista and J.d.S. Aquino are with the Experimental Nutrition Laboratory, Department of Nutrition and Post Graduate Program in Nutrition Sciences, Federal University of Paraíba, Paraíba, Brazil. V.M. Cintra and P.A.F Lucena are with the Department of Medicine, Faculty of Medical Sciences of Paraíba, and the Department of Nutrition, Integrated Colleges of Patos, Paraíba, Brazil. V.M. Cintra is with the the Multiprofessional Residence in Child Health of Secretariat of Health of the State of Paraíba, Brazil. P.A.F Lucena is with Coordination of Neurology Services, Hospital Metropolitano Dom José Maria Pires, Santa Rita, Paraíba and Emergency, Trauma Hospital Senador Humberto Lucena, João Pessoa, Paraíba, Brazil. R. Manhães-de-Castro is with the Studies in Nutrition and Phenotypic Plasticity Unit, Department of Nutrition, Federal University of Pernambuco, Recife, Pernambuco, Brazil. R. Manhães-de-Castro and A.E. Toscano are with the Post Graduate Program in Nutrition, Health Sciences Center, Federal University of Pernambuco, Recife, Pernambuco, Brazil. A.E. Toscano is with the Department of Nursing, CAV, Federal University of Pernambuco, Pernambuco, Brazil. A.E. Toscano and O. Guzman-Quevedo are with the Post Graduate Program in Neuropsychiatry and Behavioral Sciences, Federal University of Pernambuco, Recife, Pernambuco, Brazil. L.P. Costa, M.E.B.S. Queirozj, and S.M. de Andrade are with the Ageing and Neuroscience Laboratory, Health Sciences Center, Federal University of Paraíba, Paraíba, Brazil. O. Guzman-Quevedo is with the Higher Technological Institute of Tacámbaro, Tacámbaro, Michoacán, Mexico. O. Guzman-Quevedo is with the Center for Biomedical Research of Michoacán, Mexican Institute of Social Security, Morelia, Michoacán, Mexico
| | - Raul Manhães-de-Castro
- K.S. Batista and J.d.S. Aquino are with the Experimental Nutrition Laboratory, Department of Nutrition and Post Graduate Program in Nutrition Sciences, Federal University of Paraíba, Paraíba, Brazil. V.M. Cintra and P.A.F Lucena are with the Department of Medicine, Faculty of Medical Sciences of Paraíba, and the Department of Nutrition, Integrated Colleges of Patos, Paraíba, Brazil. V.M. Cintra is with the the Multiprofessional Residence in Child Health of Secretariat of Health of the State of Paraíba, Brazil. P.A.F Lucena is with Coordination of Neurology Services, Hospital Metropolitano Dom José Maria Pires, Santa Rita, Paraíba and Emergency, Trauma Hospital Senador Humberto Lucena, João Pessoa, Paraíba, Brazil. R. Manhães-de-Castro is with the Studies in Nutrition and Phenotypic Plasticity Unit, Department of Nutrition, Federal University of Pernambuco, Recife, Pernambuco, Brazil. R. Manhães-de-Castro and A.E. Toscano are with the Post Graduate Program in Nutrition, Health Sciences Center, Federal University of Pernambuco, Recife, Pernambuco, Brazil. A.E. Toscano is with the Department of Nursing, CAV, Federal University of Pernambuco, Pernambuco, Brazil. A.E. Toscano and O. Guzman-Quevedo are with the Post Graduate Program in Neuropsychiatry and Behavioral Sciences, Federal University of Pernambuco, Recife, Pernambuco, Brazil. L.P. Costa, M.E.B.S. Queirozj, and S.M. de Andrade are with the Ageing and Neuroscience Laboratory, Health Sciences Center, Federal University of Paraíba, Paraíba, Brazil. O. Guzman-Quevedo is with the Higher Technological Institute of Tacámbaro, Tacámbaro, Michoacán, Mexico. O. Guzman-Quevedo is with the Center for Biomedical Research of Michoacán, Mexican Institute of Social Security, Morelia, Michoacán, Mexico
| | - Ana E Toscano
- K.S. Batista and J.d.S. Aquino are with the Experimental Nutrition Laboratory, Department of Nutrition and Post Graduate Program in Nutrition Sciences, Federal University of Paraíba, Paraíba, Brazil. V.M. Cintra and P.A.F Lucena are with the Department of Medicine, Faculty of Medical Sciences of Paraíba, and the Department of Nutrition, Integrated Colleges of Patos, Paraíba, Brazil. V.M. Cintra is with the the Multiprofessional Residence in Child Health of Secretariat of Health of the State of Paraíba, Brazil. P.A.F Lucena is with Coordination of Neurology Services, Hospital Metropolitano Dom José Maria Pires, Santa Rita, Paraíba and Emergency, Trauma Hospital Senador Humberto Lucena, João Pessoa, Paraíba, Brazil. R. Manhães-de-Castro is with the Studies in Nutrition and Phenotypic Plasticity Unit, Department of Nutrition, Federal University of Pernambuco, Recife, Pernambuco, Brazil. R. Manhães-de-Castro and A.E. Toscano are with the Post Graduate Program in Nutrition, Health Sciences Center, Federal University of Pernambuco, Recife, Pernambuco, Brazil. A.E. Toscano is with the Department of Nursing, CAV, Federal University of Pernambuco, Pernambuco, Brazil. A.E. Toscano and O. Guzman-Quevedo are with the Post Graduate Program in Neuropsychiatry and Behavioral Sciences, Federal University of Pernambuco, Recife, Pernambuco, Brazil. L.P. Costa, M.E.B.S. Queirozj, and S.M. de Andrade are with the Ageing and Neuroscience Laboratory, Health Sciences Center, Federal University of Paraíba, Paraíba, Brazil. O. Guzman-Quevedo is with the Higher Technological Institute of Tacámbaro, Tacámbaro, Michoacán, Mexico. O. Guzman-Quevedo is with the Center for Biomedical Research of Michoacán, Mexican Institute of Social Security, Morelia, Michoacán, Mexico
| | - Larissa P Costa
- K.S. Batista and J.d.S. Aquino are with the Experimental Nutrition Laboratory, Department of Nutrition and Post Graduate Program in Nutrition Sciences, Federal University of Paraíba, Paraíba, Brazil. V.M. Cintra and P.A.F Lucena are with the Department of Medicine, Faculty of Medical Sciences of Paraíba, and the Department of Nutrition, Integrated Colleges of Patos, Paraíba, Brazil. V.M. Cintra is with the the Multiprofessional Residence in Child Health of Secretariat of Health of the State of Paraíba, Brazil. P.A.F Lucena is with Coordination of Neurology Services, Hospital Metropolitano Dom José Maria Pires, Santa Rita, Paraíba and Emergency, Trauma Hospital Senador Humberto Lucena, João Pessoa, Paraíba, Brazil. R. Manhães-de-Castro is with the Studies in Nutrition and Phenotypic Plasticity Unit, Department of Nutrition, Federal University of Pernambuco, Recife, Pernambuco, Brazil. R. Manhães-de-Castro and A.E. Toscano are with the Post Graduate Program in Nutrition, Health Sciences Center, Federal University of Pernambuco, Recife, Pernambuco, Brazil. A.E. Toscano is with the Department of Nursing, CAV, Federal University of Pernambuco, Pernambuco, Brazil. A.E. Toscano and O. Guzman-Quevedo are with the Post Graduate Program in Neuropsychiatry and Behavioral Sciences, Federal University of Pernambuco, Recife, Pernambuco, Brazil. L.P. Costa, M.E.B.S. Queirozj, and S.M. de Andrade are with the Ageing and Neuroscience Laboratory, Health Sciences Center, Federal University of Paraíba, Paraíba, Brazil. O. Guzman-Quevedo is with the Higher Technological Institute of Tacámbaro, Tacámbaro, Michoacán, Mexico. O. Guzman-Quevedo is with the Center for Biomedical Research of Michoacán, Mexican Institute of Social Security, Morelia, Michoacán, Mexico
| | - Maria E B S Queiroz
- K.S. Batista and J.d.S. Aquino are with the Experimental Nutrition Laboratory, Department of Nutrition and Post Graduate Program in Nutrition Sciences, Federal University of Paraíba, Paraíba, Brazil. V.M. Cintra and P.A.F Lucena are with the Department of Medicine, Faculty of Medical Sciences of Paraíba, and the Department of Nutrition, Integrated Colleges of Patos, Paraíba, Brazil. V.M. Cintra is with the the Multiprofessional Residence in Child Health of Secretariat of Health of the State of Paraíba, Brazil. P.A.F Lucena is with Coordination of Neurology Services, Hospital Metropolitano Dom José Maria Pires, Santa Rita, Paraíba and Emergency, Trauma Hospital Senador Humberto Lucena, João Pessoa, Paraíba, Brazil. R. Manhães-de-Castro is with the Studies in Nutrition and Phenotypic Plasticity Unit, Department of Nutrition, Federal University of Pernambuco, Recife, Pernambuco, Brazil. R. Manhães-de-Castro and A.E. Toscano are with the Post Graduate Program in Nutrition, Health Sciences Center, Federal University of Pernambuco, Recife, Pernambuco, Brazil. A.E. Toscano is with the Department of Nursing, CAV, Federal University of Pernambuco, Pernambuco, Brazil. A.E. Toscano and O. Guzman-Quevedo are with the Post Graduate Program in Neuropsychiatry and Behavioral Sciences, Federal University of Pernambuco, Recife, Pernambuco, Brazil. L.P. Costa, M.E.B.S. Queirozj, and S.M. de Andrade are with the Ageing and Neuroscience Laboratory, Health Sciences Center, Federal University of Paraíba, Paraíba, Brazil. O. Guzman-Quevedo is with the Higher Technological Institute of Tacámbaro, Tacámbaro, Michoacán, Mexico. O. Guzman-Quevedo is with the Center for Biomedical Research of Michoacán, Mexican Institute of Social Security, Morelia, Michoacán, Mexico
| | - Suellen M de Andrade
- K.S. Batista and J.d.S. Aquino are with the Experimental Nutrition Laboratory, Department of Nutrition and Post Graduate Program in Nutrition Sciences, Federal University of Paraíba, Paraíba, Brazil. V.M. Cintra and P.A.F Lucena are with the Department of Medicine, Faculty of Medical Sciences of Paraíba, and the Department of Nutrition, Integrated Colleges of Patos, Paraíba, Brazil. V.M. Cintra is with the the Multiprofessional Residence in Child Health of Secretariat of Health of the State of Paraíba, Brazil. P.A.F Lucena is with Coordination of Neurology Services, Hospital Metropolitano Dom José Maria Pires, Santa Rita, Paraíba and Emergency, Trauma Hospital Senador Humberto Lucena, João Pessoa, Paraíba, Brazil. R. Manhães-de-Castro is with the Studies in Nutrition and Phenotypic Plasticity Unit, Department of Nutrition, Federal University of Pernambuco, Recife, Pernambuco, Brazil. R. Manhães-de-Castro and A.E. Toscano are with the Post Graduate Program in Nutrition, Health Sciences Center, Federal University of Pernambuco, Recife, Pernambuco, Brazil. A.E. Toscano is with the Department of Nursing, CAV, Federal University of Pernambuco, Pernambuco, Brazil. A.E. Toscano and O. Guzman-Quevedo are with the Post Graduate Program in Neuropsychiatry and Behavioral Sciences, Federal University of Pernambuco, Recife, Pernambuco, Brazil. L.P. Costa, M.E.B.S. Queirozj, and S.M. de Andrade are with the Ageing and Neuroscience Laboratory, Health Sciences Center, Federal University of Paraíba, Paraíba, Brazil. O. Guzman-Quevedo is with the Higher Technological Institute of Tacámbaro, Tacámbaro, Michoacán, Mexico. O. Guzman-Quevedo is with the Center for Biomedical Research of Michoacán, Mexican Institute of Social Security, Morelia, Michoacán, Mexico
| | - Omar Guzman-Quevedo
- K.S. Batista and J.d.S. Aquino are with the Experimental Nutrition Laboratory, Department of Nutrition and Post Graduate Program in Nutrition Sciences, Federal University of Paraíba, Paraíba, Brazil. V.M. Cintra and P.A.F Lucena are with the Department of Medicine, Faculty of Medical Sciences of Paraíba, and the Department of Nutrition, Integrated Colleges of Patos, Paraíba, Brazil. V.M. Cintra is with the the Multiprofessional Residence in Child Health of Secretariat of Health of the State of Paraíba, Brazil. P.A.F Lucena is with Coordination of Neurology Services, Hospital Metropolitano Dom José Maria Pires, Santa Rita, Paraíba and Emergency, Trauma Hospital Senador Humberto Lucena, João Pessoa, Paraíba, Brazil. R. Manhães-de-Castro is with the Studies in Nutrition and Phenotypic Plasticity Unit, Department of Nutrition, Federal University of Pernambuco, Recife, Pernambuco, Brazil. R. Manhães-de-Castro and A.E. Toscano are with the Post Graduate Program in Nutrition, Health Sciences Center, Federal University of Pernambuco, Recife, Pernambuco, Brazil. A.E. Toscano is with the Department of Nursing, CAV, Federal University of Pernambuco, Pernambuco, Brazil. A.E. Toscano and O. Guzman-Quevedo are with the Post Graduate Program in Neuropsychiatry and Behavioral Sciences, Federal University of Pernambuco, Recife, Pernambuco, Brazil. L.P. Costa, M.E.B.S. Queirozj, and S.M. de Andrade are with the Ageing and Neuroscience Laboratory, Health Sciences Center, Federal University of Paraíba, Paraíba, Brazil. O. Guzman-Quevedo is with the Higher Technological Institute of Tacámbaro, Tacámbaro, Michoacán, Mexico. O. Guzman-Quevedo is with the Center for Biomedical Research of Michoacán, Mexican Institute of Social Security, Morelia, Michoacán, Mexico
| | - Jailane de S Aquino
- K.S. Batista and J.d.S. Aquino are with the Experimental Nutrition Laboratory, Department of Nutrition and Post Graduate Program in Nutrition Sciences, Federal University of Paraíba, Paraíba, Brazil. V.M. Cintra and P.A.F Lucena are with the Department of Medicine, Faculty of Medical Sciences of Paraíba, and the Department of Nutrition, Integrated Colleges of Patos, Paraíba, Brazil. V.M. Cintra is with the the Multiprofessional Residence in Child Health of Secretariat of Health of the State of Paraíba, Brazil. P.A.F Lucena is with Coordination of Neurology Services, Hospital Metropolitano Dom José Maria Pires, Santa Rita, Paraíba and Emergency, Trauma Hospital Senador Humberto Lucena, João Pessoa, Paraíba, Brazil. R. Manhães-de-Castro is with the Studies in Nutrition and Phenotypic Plasticity Unit, Department of Nutrition, Federal University of Pernambuco, Recife, Pernambuco, Brazil. R. Manhães-de-Castro and A.E. Toscano are with the Post Graduate Program in Nutrition, Health Sciences Center, Federal University of Pernambuco, Recife, Pernambuco, Brazil. A.E. Toscano is with the Department of Nursing, CAV, Federal University of Pernambuco, Pernambuco, Brazil. A.E. Toscano and O. Guzman-Quevedo are with the Post Graduate Program in Neuropsychiatry and Behavioral Sciences, Federal University of Pernambuco, Recife, Pernambuco, Brazil. L.P. Costa, M.E.B.S. Queirozj, and S.M. de Andrade are with the Ageing and Neuroscience Laboratory, Health Sciences Center, Federal University of Paraíba, Paraíba, Brazil. O. Guzman-Quevedo is with the Higher Technological Institute of Tacámbaro, Tacámbaro, Michoacán, Mexico. O. Guzman-Quevedo is with the Center for Biomedical Research of Michoacán, Mexican Institute of Social Security, Morelia, Michoacán, Mexico
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22
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Yan W, Zheng Y, Zeng X, He B, Cheng W. Structural biology of SARS-CoV-2: open the door for novel therapies. Signal Transduct Target Ther 2022; 7:26. [PMID: 35087058 PMCID: PMC8793099 DOI: 10.1038/s41392-022-00884-5] [Citation(s) in RCA: 130] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 02/08/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is the causative agent of the pandemic disease COVID-19, which is so far without efficacious treatment. The discovery of therapy reagents for treating COVID-19 are urgently needed, and the structures of the potential drug-target proteins in the viral life cycle are particularly important. SARS-CoV-2, a member of the Orthocoronavirinae subfamily containing the largest RNA genome, encodes 29 proteins including nonstructural, structural and accessory proteins which are involved in viral adsorption, entry and uncoating, nucleic acid replication and transcription, assembly and release, etc. These proteins individually act as a partner of the replication machinery or involved in forming the complexes with host cellular factors to participate in the essential physiological activities. This review summarizes the representative structures and typically potential therapy agents that target SARS-CoV-2 or some critical proteins for viral pathogenesis, providing insights into the mechanisms underlying viral infection, prevention of infection, and treatment. Indeed, these studies open the door for COVID therapies, leading to ways to prevent and treat COVID-19, especially, treatment of the disease caused by the viral variants are imperative.
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Affiliation(s)
- Weizhu Yan
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Yanhui Zheng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Xiaotao Zeng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Bin He
- Department of Emergency Medicine, West China Hospital of Sichuan University, 610041, Chengdu, China.
- The First People's Hospital of Longquanyi District Chengdu, 610100, Chengdu, China.
| | - Wei Cheng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China.
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23
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Effect of a Nutritional Support System to Increase Survival and Reduce Mortality in Patients with COVID-19 in Stage III and Comorbidities: A Blinded Randomized Controlled Clinical Trial. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19031172. [PMID: 35162195 PMCID: PMC8835093 DOI: 10.3390/ijerph19031172] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/20/2021] [Accepted: 12/31/2021] [Indexed: 02/08/2023]
Abstract
The COVID-19 evolution depends on immunological capacity. The global hospital mortality rate is 15–20%, but in México it is 46%. There are several therapeutic protocols, however, integral nutrition is not considered. In this study, a Nutritional Support System (NSS) was employed to increase survival and reduce mortality in patients with stage III COVID-19. A randomized, blinded, controlled clinical trial was performed. Eighty patients (aged 30 to 75 years, both sexes) were assigned to (1) “Control Group” (CG) hospital diet and medical treatment or (2) “Intervention Group” (IG) hospital diet, medical treatment, and the NSS (vitamins, minerals, fiber, omega-3, amino acids, B-complex, and probiotics). IG significantly increased survival and reduced mortality compared to CG (p = 0.027). IG decreased progression to Mechanical Ventilation Assistance (MVA) by 10%, reduced the intubation period by 15 days, and increased survival in intubated patients by 38% compared to CG. IG showed improvement compared to CG in decrease in supplemental oxygen (p = 0.014), the qSOFA test (p = 0.040), constipation (p = 0.014), the PHQ-9 test (p = 0.003), and in the follow-up, saturation with oxygen (p = 0.030). The NSS increases survival and decreases mortality in patients with stage III COVID-19.
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24
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The Effect of Vitamin B12 Levels on Prognosis in COVID-19 Patients. JOURNAL OF CONTEMPORARY MEDICINE 2022. [DOI: 10.16899/jcm.1035078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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25
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Barber MS, Barrett R, Bradley RD, Walker E. A naturopathic treatment approach for mild and moderate COVID-19: A retrospective chart review. Complement Ther Med 2021; 63:102788. [PMID: 34748955 PMCID: PMC8570825 DOI: 10.1016/j.ctim.2021.102788] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/08/2021] [Accepted: 11/03/2021] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVES The coronavirus disease 2019 (COVID-19) pandemic has led to significant morbidity and mortality. Although COVID-19 vaccination is available, therapeutic options are still needed. The goal of the present manuscript is to report on a treatment strategy used in a naturopathic medical practice for mild and moderate COVID-19. DESIGN A retrospective chart review was conducted of 30 consecutive patients diagnosed with mild and moderate COVID-19 who were provided multi-nutrient, herbal, and probiotic treatment in a rural, out-patient, naturopathic primary care setting. MAIN OUTCOMES MEASURES The primary outcome was treatment safety; secondary outcomes included changes in symptoms, progression to severe COVID-19, incidence of long COVID, and recovery time. RESULTS No side effects or adverse events were reported from treatment and all patients experienced resolution of symptoms presumed to be associated with COVID-19 infection. One patient who had been ill for 28 days prior to presentation was hospitalized. Five patients had an illness duration of more than one month. Time to treatment was correlated with duration of illness post-treatment (r = 0.63, p < 0.001) and more symptoms at presentation was correlated with a longer duration of illness (r = 0.52, p < 0.01). CONCLUSIONS In this retrospective chart review, a multi-nutrient, herbal, and probiotic therapeutic approach for mild and moderate COVID-19 appeared to be well-tolerated. Delay in seeking treatment after symptom onset, as well as more symptoms at presentation, were correlated with a longer duration of illness. This treatment strategy may have clinical benefit, warranting prospective clinical trials with confirmed COVID-19 cases.
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Affiliation(s)
- Melissa S Barber
- National University of Natural Medicine, Helfgott Research Institute, 2220 SW 1st Ave, Portland, OR, United States.
| | - Richard Barrett
- National University of Natural Medicine, Helfgott Research Institute, 2220 SW 1st Ave, Portland, OR, United States.
| | - Ryan D Bradley
- National University of Natural Medicine, Helfgott Research Institute, 2220 SW 1st Ave, Portland, OR, United States.
| | - Erin Walker
- Canby Clinic, 452 NW 1st Ave, Canby, OR, United States.
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26
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Jimenez-Guardeño JM, Ortega-Prieto AM, Moreno BM, Maguire TJ, Richardson A, Diaz-Hernandez JI, Diez Perez J, Zuckerman M, Playa AM, Deline CC, Malim MH, Martinez-Nunez RT. Drug repurposing based on a Quantum-Inspired method versus classical fingerprinting uncovers potential antivirals against SARS-CoV-2 including vitamin B12. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.06.25.449609. [PMID: 34401881 PMCID: PMC8366797 DOI: 10.1101/2021.06.25.449609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The COVID-19 pandemic has accelerated the need to identify new therapeutics at pace, including through drug repurposing. We employed a Quadratic Unbounded Binary Optimization (QUBO) model, to search for compounds similar to Remdesivir (RDV), the only antiviral against SARS-CoV-2 currently approved for human use, using a quantum-inspired device. We modelled RDV and compounds present in the DrugBank database as graphs, established the optimal parameters in our algorithm and resolved the Maximum Weighted Independent Set problem within the conflict graph generated. We also employed a traditional Tanimoto fingerprint model. The two methods yielded different lists of compounds, with some overlap. While GS-6620 was the top compound predicted by both models, the QUBO model predicted BMS-986094 as second best. The Tanimoto model predicted different forms of cobalamin, also known as vitamin B12. We then determined the half maximal inhibitory concentration (IC 50 ) values in cell culture models of SARS-CoV-2 infection and assessed cytotoxicity. Lastly, we demonstrated efficacy against several variants including SARS-CoV-2 Strain England 2 (England 02/2020/407073), B.1.1.7 (Alpha), B.1.351 (Beta) and B.1.617.2 (Delta). Our data reveal that BMS-986094 and different forms of vitamin B12 are effective at inhibiting replication of all these variants of SARS-CoV-2. While BMS-986094 can cause secondary effects in humans as established by phase II trials, these findings suggest that vitamin B12 deserves consideration as a SARS-CoV-2 antiviral, particularly given its extended use and lack of toxicity in humans, and its availability and affordability. Our screening method can be employed in future searches for novel pharmacologic inhibitors, thus providing an approach for accelerating drug deployment.
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Affiliation(s)
- Jose M. Jimenez-Guardeño
- Dept Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London (UK)
| | - Ana Maria Ortega-Prieto
- Dept Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London (UK)
| | - Borja Menendez Moreno
- Fujitsu Technology Solutions S.A., Camino del Cerro de los Gamos, 1, 28224, Pozuelo de Alarcón, Madrid (Spain)
| | - Thomas J.A. Maguire
- Dept Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London (UK)
| | - Adam Richardson
- Dept Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London (UK)
| | - Juan Ignacio Diaz-Hernandez
- Fujitsu Technology Solutions S.A., Camino del Cerro de los Gamos, 1, 28224, Pozuelo de Alarcón, Madrid (Spain)
| | - Javier Diez Perez
- Fujitsu Technology Solutions S.A., Camino del Cerro de los Gamos, 1, 28224, Pozuelo de Alarcón, Madrid (Spain)
| | - Mark Zuckerman
- South London Virology Centre, King’s College Hospital, London (UK)
| | - Albert Mercadal Playa
- Fujitsu Technology Solutions S.A., Camino del Cerro de los Gamos, 1, 28224, Pozuelo de Alarcón, Madrid (Spain)
| | - Carlos Cordero Deline
- Fujitsu Technology Solutions S.A., Camino del Cerro de los Gamos, 1, 28224, Pozuelo de Alarcón, Madrid (Spain)
| | - Michael H. Malim
- Dept Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London (UK)
| | - Rocio T Martinez-Nunez
- Dept Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London (UK)
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27
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Bhatia S, Narayanan N, Nagpal S, Nair DT. Antiviral therapeutics directed against RNA dependent RNA polymerases from positive-sense viruses. Mol Aspects Med 2021; 81:101005. [PMID: 34311994 DOI: 10.1016/j.mam.2021.101005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 07/14/2021] [Accepted: 07/16/2021] [Indexed: 01/18/2023]
Abstract
Viruses with positive-sense single stranded RNA (+ssRNA) genomes are responsible for different diseases and represent a global health problem. In addition to developing new vaccines that protect against severe illness on infection, it is imperative to identify new antiviral molecules to treat infected patients. The genome of these RNA viruses generally codes for an enzyme with RNA dependent RNA polymerase (RdRP) activity. This molecule is centrally involved in the duplication of the RNA genome. Inhibition of this enzyme by small molecules will prevent duplication of the RNA genome and thus reduce the viral titer. An overview of the different therapeutic strategies used to inhibit RdRPs from +ssRNA viruses is provided, along with an analysis of these enzymes to highlight new binding sites for inhibitors.
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Affiliation(s)
- Sonam Bhatia
- Regional Centre for Biotechnology, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, India
| | - Naveen Narayanan
- Regional Centre for Biotechnology, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, India
| | - Shilpi Nagpal
- Regional Centre for Biotechnology, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, India; National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - Deepak T Nair
- Regional Centre for Biotechnology, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, India.
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Abstract
The coronavirus disease 2019 (COVID-19) pandemic in Japan is not as disastrous as it is in other Western countries, possibly because of certain lifestyle factors. One such factor might be the seaweed-rich diet commonly consumed in Japan. COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which binds to angiotensin-converting enzyme 2 (ACE2) on the cell surface and downregulates ACE2, likely elevating the ratio of angiotensin-converting enzyme (ACE) to ACE2. The overreaction of the immune system, combined with the cytokine storm and ACE dominance, is purported to cause the condition of COVID-19 patients to deteriorate rapidly. Dietary seaweeds contain numerous components, including ACE inhibitory peptides, soluble dietary fibers (eg, fucoidan, porphyran), omega-3 fatty acids, fucoxanthin, fucosterol, vitamins D3 and B12, and phlorotannins. These components exert antioxidant, anti-inflammatory, and antiviral effects directly as well as indirectly through prebiotic effects. It is possible that ACE inhibitory components could minimize the ACE dominance caused by SARS-CoV-2 infection. Thus, dietary seaweeds might confer protection against COVID-19 through multiple mechanisms. Overconsumption of seaweeds should be avoided, however, as seaweeds contain high levels of iodine.
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Affiliation(s)
- Kenichi Tamama
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; the Clinical Laboratories, University of Pittsburgh Medical Center Presbyterian Hospital, Pittsburgh, Pennsylvania, USA; the McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA; and the Clinical Laboratory, UMPC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Mahluji S, Jalili M, Ostadrahimi A, Hallajzadeh J, Ebrahimzadeh-Attari V, Saghafi-Asl M. Nutritional management of diabetes mellitus during the pandemic of COVID-19: a comprehensive narrative review. J Diabetes Metab Disord 2021; 20:963-972. [PMID: 33842400 PMCID: PMC8021300 DOI: 10.1007/s40200-021-00784-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 03/20/2021] [Indexed: 01/08/2023]
Abstract
Objectives According to the recent epidemiological studies, patients with diabetes mellitus (DM) may be at higher risk of hospitalization due to COVID-19. Regarding the important role of nutrition on the immunity, the present review article aimed to outline nutritional support of DM during the outbreak of COVID-19 with a mechanistic insight. Methods Searches were performed in PubMed/MEDLINE, ScienceDirect, Scopus, and Google Scholar databases from 2000 until December 2020 using the following keywords. All relevant clinical and experimental studies published in English were included. Results Evidences revealed that hyperglycemia is a significant predictor of some viral infections including COVID-19 which can exacerbate the complications of DM. According to the literature review, adequate intake of dietary protein, fiber, essential fatty acids and some micronutrients especially vitamins D, C, B12, folate, zinc and selenium has beneficial effects on the prevention and treatment of COVID-19 in diabetic patients through modulation of innate and adaptive immune responses or direct effects on virus enzymes or the rate of cell entrance. Conclusions It is well understood that malnutrition may increase susceptibility to viral infections and disease progression. Therefore, considering nutritional status of diabetic patients and reasonable supplementation of the above mentioned nutrients can ameliorate the symptoms of COVID-19 in DM. However, further well-designed clinical trials are needed to determine their therapeutic dose.
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Affiliation(s)
- Sepideh Mahluji
- Nutrition Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mahsa Jalili
- Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Alireza Ostadrahimi
- Nutrition Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Clinical Nutrition, Faculty of Nutrition & Food Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jamal Hallajzadeh
- Department of Biochemistry, Maragheh University of Medical Sciences, Maragheh, Iran
| | | | - Maryam Saghafi-Asl
- Nutrition Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Clinical Nutrition, Faculty of Nutrition & Food Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
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Lordan R, Rando HM, Greene CS. Dietary Supplements and Nutraceuticals under Investigation for COVID-19 Prevention and Treatment. mSystems 2021; 6:e00122-21. [PMID: 33947804 PMCID: PMC8269209 DOI: 10.1128/msystems.00122-21] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) has caused global disruption and a significant loss of life. Existing treatments that can be repurposed as prophylactic and therapeutic agents may reduce the pandemic's devastation. Emerging evidence of potential applications in other therapeutic contexts has led to the investigation of dietary supplements and nutraceuticals for COVID-19. Such products include vitamin C, vitamin D, omega 3 polyunsaturated fatty acids, probiotics, and zinc, all of which are currently under clinical investigation. In this review, we critically appraise the evidence surrounding dietary supplements and nutraceuticals for the prophylaxis and treatment of COVID-19. Overall, further study is required before evidence-based recommendations can be formulated, but nutritional status plays a significant role in patient outcomes, and these products may help alleviate deficiencies. For example, evidence indicates that vitamin D deficiency may be associated with a greater incidence of infection and severity of COVID-19, suggesting that vitamin D supplementation may hold prophylactic or therapeutic value. A growing number of scientific organizations are now considering recommending vitamin D supplementation to those at high risk of COVID-19. Because research in vitamin D and other nutraceuticals and supplements is preliminary, here we evaluate the extent to which these nutraceutical and dietary supplements hold potential in the COVID-19 crisis.IMPORTANCE Sales of dietary supplements and nutraceuticals have increased during the pandemic due to their perceived "immune-boosting" effects. However, little is known about the efficacy of these dietary supplements and nutraceuticals against the novel coronavirus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) or the disease that it causes, CoV disease 2019 (COVID-19). This review provides a critical overview of the potential prophylactic and therapeutic value of various dietary supplements and nutraceuticals from the evidence available to date. These include vitamin C, vitamin D, and zinc, which are often perceived by the public as treating respiratory infections or supporting immune health. Consumers need to be aware of misinformation and false promises surrounding some supplements, which may be subject to limited regulation by authorities. However, considerably more research is required to determine whether dietary supplements and nutraceuticals exhibit prophylactic and therapeutic value against SARS-CoV-2 infection and COVID-19. This review provides perspective on which nutraceuticals and supplements are involved in biological processes that are relevant to recovery from or prevention of COVID-19.
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Affiliation(s)
- Ronan Lordan
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Halie M Rando
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
- Center for Health AI, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Casey S Greene
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
- Center for Health AI, University of Colorado School of Medicine, Aurora, Colorado, USA
- Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Philadelphia, Pennsylvania, USA
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Chen Z, Cui Q, Cooper L, Zhang P, Lee H, Chen Z, Wang Y, Liu X, Rong L, Du R. Ginkgolic acid and anacardic acid are specific covalent inhibitors of SARS-CoV-2 cysteine proteases. Cell Biosci 2021; 11:45. [PMID: 33640032 PMCID: PMC7914117 DOI: 10.1186/s13578-021-00564-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 02/21/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND In the urgent campaign to develop therapeutics against SARS-CoV-2, natural products have been an important source of new lead compounds. RESULTS We herein identified two natural products, ginkgolic acid and anacardic acid, as inhibitors using a high-throughput screen targeting the SARS-CoV-2 papain-like protease (PLpro). Moreover, our study demonstrated that the two hit compounds are dual inhibitors targeting the SARS-CoV-2 3-chymotrypsin-like protease (3CLpro) in addition to PLpro. A mechanism of action study using enzyme kinetics further characterized the two compounds as irreversible inhibitors against both 3CLpro and PLpro. Significantly, both identified compounds inhibit SARS-CoV-2 replication in vitro at nontoxic concentrations. CONCLUSIONS Our finding provides two novel natural products as promising SARS-CoV-2 antivirals.
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Affiliation(s)
- Zinuo Chen
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Qinghua Cui
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
- Qingdao Academy of Chinese Medicinal Sciences, Shandong University of Traditional Chinese Medicine, Qingdao, 266122, China
| | - Laura Cooper
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Pin Zhang
- Chicago BioSolutions Inc, 2242 W Harrison Street, Chicago, Illinois, 60612, United States
| | - Hyun Lee
- Department of Pharmaceutical Sciences, Center for Biomolecular Sciences, College of Pharmacy, Biophysics Core at Research Resources Center, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Zhaoyu Chen
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Yanyan Wang
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Xiaoyun Liu
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Lijun Rong
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA.
| | - Ruikun Du
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China.
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China.
- Qingdao Academy of Chinese Medicinal Sciences, Shandong University of Traditional Chinese Medicine, Qingdao, 266122, China.
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32
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McCaddon A, Regland B. COVID-19: A methyl-group assault? Med Hypotheses 2021; 149:110543. [PMID: 33657459 PMCID: PMC7890339 DOI: 10.1016/j.mehy.2021.110543] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 01/28/2021] [Accepted: 02/14/2021] [Indexed: 12/22/2022]
Abstract
The socio-economic implications of COVID-19 are devastating. Considerable morbidity is attributed to ‘long-COVID’ – an increasingly recognized complication of infection. Its diverse symptoms are reminiscent of vitamin B12 deficiency, a condition in which methylation status is compromised. We suggest why SARS-CoV-2 infection likely leads to increased methyl-group requirements and other disturbances of one-carbon metabolism. We propose these might explain the varied symptoms of long-COVID. Our suggested mechanism might also apply to similar conditions such as myalgic encephalomyelitis/chronic fatigue syndrome. The hypothesis is evaluable by detailed determination of vitamin B12 and folate status, including serum formate as well as homocysteine and methylmalonic acid, and correlation with viral and host RNA methylation and symptomatology. If confirmed, methyl-group support should prove beneficial in such individuals.
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Affiliation(s)
- Andrew McCaddon
- Gardden Road Surgery, Rhosllanerchrugog Wrexham, LL14 2EN, UK.
| | - Björn Regland
- Institute of Neuroscience and Physiology, Gothenburg University, Gothenburg, Sweden.
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33
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Ali SG, Ansari MA, Alzohairy MA, Almatroudi A, Alomary MN, Alghamdi S, Rehman S, Khan HM. Natural Products and Nutrients against Different Viral Diseases: Prospects in Prevention and Treatment of SARS-CoV-2. MEDICINA (KAUNAS, LITHUANIA) 2021; 57:169. [PMID: 33673004 PMCID: PMC7917779 DOI: 10.3390/medicina57020169] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/04/2021] [Accepted: 02/07/2021] [Indexed: 02/06/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused a global pandemic and is posing a serious challenge to mankind. As per the current scenario, there is an urgent need for antiviral that could act as a protective and therapeutic against SARS-CoV-2. Previous studies have shown that SARS-CoV-2 is much similar to the SARS-CoV bat that occurred in 2002-03. Since it is a zoonotic virus, the exact source is still unknown, but it is believed bats may be the primary reservoir of SARS-CoV-2 through which it has been transferred to humans. In this review, we have tried to summarize some of the approaches that could be effective against SARS-CoV-2. Firstly, plants or plant-based products have been effective against different viral diseases, and secondly, plants or plant-based natural products have the minimum adverse effect. We have also highlighted a few vitamins and minerals that could be beneficial against SARS-CoV-2.
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Affiliation(s)
- Syed Ghazanfar Ali
- Viral Research Diagnostic Laboratory, Department of Microbiology, Jawaharlal Nehru Medical College A.M.U., Aligarh U.P.202002, India;
| | - Mohammad Azam Ansari
- Department of Epidemic Disease Research, Institutes for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (M.A.A.); (S.R.)
| | - Mohammad A. Alzohairy
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Qassim 51431, Saudi Arabia; (M.A.A.); (A.A.)
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Qassim 51431, Saudi Arabia; (M.A.A.); (A.A.)
| | - Mohammad N. Alomary
- National Centre for Biotechnology, King Abdulaziz City for Science and Technology (KACST), P.O. Box 6086, Riyadh 11442, Saudi Arabia
| | - Saad Alghamdi
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah21955, Saudi Arabia;
| | - Suriya Rehman
- Department of Epidemic Disease Research, Institutes for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (M.A.A.); (S.R.)
| | - Haris M. Khan
- Viral Research Diagnostic Laboratory, Department of Microbiology, Jawaharlal Nehru Medical College A.M.U., Aligarh U.P.202002, India;
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Zhang Y, Tang LV. Overview of Targets and Potential Drugs of SARS-CoV-2 According to the Viral Replication. J Proteome Res 2021; 20:49-59. [PMID: 33347311 PMCID: PMC7770889 DOI: 10.1021/acs.jproteome.0c00526] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Indexed: 01/18/2023]
Abstract
Since the novel coronavirus pandemic, people around the world have been touched in varying degrees, and this pandemic has raised a major global health concern. As there is no effective drug or vaccine, it is urgent to find therapeutic drugs that can serve to deal with the current epidemic situation in all countries and regions. We searched drugs and response measures for SARS-CoV-2 in the PubMed database, and then updated the potential targets and therapeutic drugs from the perspective of the viral replication cycle. The drug research studies of the viral replication cycle are predominantly focused on the process of the virus entering cells, proteases, and RdRp. The inhibitors of the virus entry to cells and RdRp, such as Arbidol, remdesivir, favipiravir, EIDD-2081, and ribavirin, are in clinical trials, while most of the protease inhibitors are mainly calculated by molecular docking technology, which needs in vivo and in vitro experiments to prove the effect for SARS-CoV-2. This review summarizes the drugs targeting the viral replication process and provides a basis and directions for future drug development and reuse on the protein level of COVID-19.
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Affiliation(s)
- Yi Zhang
- Institute
of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Liang V. Tang
- Institute
of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
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35
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Amini Pouya M, Afshani SM, Maghsoudi AS, Hassani S, Mirnia K. Classification of the present pharmaceutical agents based on the possible effective mechanism on the COVID-19 infection. Daru 2020; 28:745-764. [PMID: 32734518 PMCID: PMC7391927 DOI: 10.1007/s40199-020-00359-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 07/14/2020] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVES There are several types of research on the COVID-19 disease which have been conducting. It seems that prevailing over the pandemic would be achieved only by mastering over the virus pathophysiology. We tried to categorize the massive amount of available information for useful interpretation. EVIDENCE ACQUISITION We searched databases with different keywords and search strategies that focus on virulence and pathophysiology of COVID-19. The present review has aimed to gather and categorize all implemented drugs based on the susceptible virulence mechanisms, and the pathophysiological events in the host cells, discussing and suggesting treatments. RESULTS As a result, the COVID-19 lifecycle were categorized as following steps: "Host Cell Attachment" which is mainly conducted with ACE2 receptors and TMPRSS2 from the host cell and Spike (S) protein, "Endocytosis Pathway" which is performed mainly by clathrin-mediated endocytosis, and "Viral Replication" which contains translation and replication of RNA viral genome. The virus pathogenicity is continued by "Inflammatory Reactions" which mainly caused moderate to severe COVID-19 disease. Besides, the possible effective therapeutics' mechanism and the pharmaceutical agents that had at least one experience as a preclinical or clinical study on COVID-19 were clearly defined. CONCLUSION The treatment protocol would be occasional based on the stage of the infection and the patient situation. The cocktail of medicines, which could affect almost all mentioned stages of COVID-19 disease, might be vital for patients with severe phenomena. The classification of the possible mechanism of medicines based on COVID-19 pathogenicity.
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Affiliation(s)
- Maryam Amini Pouya
- Department of Pharmaceutics, School of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyyedeh Maryam Afshani
- Department of Pharmacoeconomics, School of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Armin Salek Maghsoudi
- Department of Toxicology and Pharmacology, School of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Shokoufeh Hassani
- Department of Toxicology and Pharmacology, School of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran.
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), the Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran.
| | - Kayvan Mirnia
- Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.
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Junaid K, Ejaz H, Abdalla AE, Abosalif KOA, Ullah MI, Yasmeen H, Younas S, Hamam SSM, Rehman A. Effective Immune Functions of Micronutrients against SARS-CoV-2. Nutrients 2020; 12:E2992. [PMID: 33003648 PMCID: PMC7599934 DOI: 10.3390/nu12102992] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 09/26/2020] [Accepted: 09/28/2020] [Indexed: 12/15/2022] Open
Abstract
The third coronavirus outbreak in the last two decades has caused significant damage to the world's economy and community health. The highly contagious COVID-19 infection has affected millions of people to date and has led to hundreds of thousands of deaths worldwide. Aside from the highly infectious nature of SARS-CoV-2, the lack of a treatment or vaccine has been the main reason for its spread. Thus, it has become necessary to find alternative methods for controlling SARS-CoV-2. For the present review, we conducted an online search for different available nutrition-based therapies for previously known coronavirus infections and RNA-based virus infections as well as general antiviral therapies. These treatments have promise for combating COVID-19, as various nutrients and minerals play direct and indirect roles in the control and prevention of this newly emerged viral infection. The patients' nutritional status with COVID-19 must be analyzed before administering any treatment, and nutritional supplements should be given to the affected individuals along with routine treatment. We suggest a potential interventional role of nutrients to strengthen the immune system against the emerging infection caused by COVID-19.
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Affiliation(s)
- Kashaf Junaid
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 72388, Al Jouf, Saudi Arabia; (H.E.); (A.E.A.); (K.O.A.A.); (M.I.U.)
| | - Hasan Ejaz
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 72388, Al Jouf, Saudi Arabia; (H.E.); (A.E.A.); (K.O.A.A.); (M.I.U.)
| | - Abualgasim Elgaili Abdalla
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 72388, Al Jouf, Saudi Arabia; (H.E.); (A.E.A.); (K.O.A.A.); (M.I.U.)
- Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, Omdurman Islamic University, Omdurman 14415, Sudan
| | - Khalid O. A. Abosalif
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 72388, Al Jouf, Saudi Arabia; (H.E.); (A.E.A.); (K.O.A.A.); (M.I.U.)
- Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, Omdurman Islamic University, Omdurman 14415, Sudan
| | - Muhammad Ikram Ullah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 72388, Al Jouf, Saudi Arabia; (H.E.); (A.E.A.); (K.O.A.A.); (M.I.U.)
| | - Humaira Yasmeen
- Department of Microbiology and Molecular Genetics, The Women University Multan, Multan 60000, Pakistan;
| | - Sonia Younas
- Department of Pathology, Tehsil Headquarter Hospital Kamoke, District Gujranwala, Kamoke 50661, Pakistan;
| | - Sanaa S. M. Hamam
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Menoufia University, Shebin El-koom 32511, Egypt;
- Department of Microbiology, King Abdulaziz Specialist Hospital, Sakaka 72341, Saudi Arabia
| | - Abdul Rehman
- Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore 54590, Pakistan;
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Narayanan N, Nair DT. Vitamin B12 may inhibit RNA-dependent-RNA polymerase activity of nsp12 from the SARS-CoV-2 virus. IUBMB Life 2020; 72:2112-2120. [PMID: 32812340 PMCID: PMC7461454 DOI: 10.1002/iub.2359] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 01/18/2023]
Abstract
SARS‐CoV‐2 is the causative agent for the ongoing COVID19 pandemic, and this virus belongs to the Coronaviridae family. Like other members of this family, the virus possesses a positive‐sense single‐stranded RNA genome. The genome encodes for the nsp12 protein, which houses the RNA‐dependent‐RNA polymerase (RdRP) activity responsible for the replication of the viral genome. A homology model of nsp12 was prepared using the structure of the SARS nsp12 (6NUR) as a model. The model was used to carry out in silico screening to identify molecules among natural products, or Food and Drug Administration‐approved drugs that can potentially inhibit the activity of nsp12. This exercise showed that vitamin B12 (methylcobalamin) may bind to the active site of the nsp12 protein. A model of the nsp12 in complex with substrate RNA and incoming NTP showed that vitamin B12 binding site overlaps with that of the incoming nucleotide. A comparison of the calculated energies of binding for RNA plus NTP and methylcobalamin suggested that the vitamin may bind to the active site of nsp12 with significant affinity. It is, therefore, possible that methylcobalamin binding may prevent association with RNA and NTP and thus inhibit the RdRP activity of nsp12. Overall, our computational studies suggest that methylcobalamin form of vitamin B12 may serve as an effective inhibitor of the nsp12 protein.
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Affiliation(s)
- Naveen Narayanan
- Laboratory of Genomic Integrity and Evolution, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, India.,Manipal Academy of Higher Education, Manipal, India
| | - Deepak T Nair
- Laboratory of Genomic Integrity and Evolution, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, India
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38
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Sharma A, Tiwari V, Sowdhamini R. Computational search for potential COVID-19 drugs from FDAapproved drugs and small molecules of natural origin identifies several anti-virals and plant products. J Biosci 2020; 45:100. [PMID: 32713863 PMCID: PMC7366452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/23/2020] [Indexed: 08/23/2024]
Abstract
The world is currently facing the COVID-19 pandemic, for which mild symptoms include fever and dry cough. In severe cases, it could lead to pneumonia and ultimately death in some instances. Moreover, the causative pathogen is highly contagious and there are no drugs or vaccines for it yet. The pathogen, SARS-CoV-2, is one of the human coronaviruses which was identified to infect humans first in December 2019. SARS-CoV-2 shares evolutionary relationship to other highly pathogenic viruses such as Severe Acute Respiratory Syndrome (SARS) and Middle East respiratory syndrome (MERS). We have exploited this similarity to model a target non-structural protein, NSP1, since it is implicated in the regulation of host gene expression by the virus and hijacking of host machinery. We next interrogated the capacity to repurpose around 2300 FDA-approved drugs and more than 3,00,000 small molecules of natural origin towards drug identification through virtual screening and molecular dynamics. Interestingly, we observed simple molecules like lactose, previously known anti-virals and few secondary metabolites of plants as promising hits. These herbal plants are already practiced in Ayurveda over centuries to treat respiratory problems and inflammation. Disclaimer: we would not like to recommend uptake of these small molecules for suspect COVID patients until it is approved by competent national or international authorities.
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Affiliation(s)
- Abhishek Sharma
- National Centre for Biological Sciences, GKVK Campus, Bengaluru, 560 065 India
| | - Vikas Tiwari
- National Centre for Biological Sciences, GKVK Campus, Bengaluru, 560 065 India
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