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Rizka Nurcahyaningtyas H, Irene A, Tri Wibowo J, Yunovilsa Putra M, Yanuar A. Identification of potential Indonesian marine invertebrate bioactive compounds as TMPRSS2 and SARS-CoV-2 Omicron spike protein inhibitors through computational screening. ARAB J CHEM 2023; 16:104984. [PMID: 37234226 PMCID: PMC10186851 DOI: 10.1016/j.arabjc.2023.104984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 05/08/2023] [Indexed: 05/27/2023] Open
Abstract
The coronavirus pandemic led to the announcement of a worldwide health emergency. The SARS-CoV-2 Omicron variant, which swiftly spread worldwide, has fueled existing challenges. Appropriate medication is necessary to avoid severe SARS-CoV-2 disease. The human TMPRSS2 and SARS-CoV-2 Omicron spike protein, which are required for viral entry into the host phase, were identified as the target proteins through computational screening. Structure-based virtual screening; molecular docking; absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis; and molecular dynamics simulation were the methods applied for TMPRSS2 and spike protein inhibitors. Bioactive marine invertebrates from Indonesia were employed as test ligands. Camostat and nafamostat (co-crystal) were utilized as reference ligands against TMPRSS2, whereas mefloquine was used as a reference ligand against spike protein. Following a molecular docking and dynamics simulation, we found that acanthomanzamine C has remarkable effectiveness against TMPRSS2 and spike protein. Compared to camostat (-8.25 kcal/mol), nafamostat (-6.52 kcal/mol), and mefloquine (-6.34 kcal/mol), acanthomanzamine C binds to TMPRSS2 and spike protein with binding energies of -9.75 kcal/mol and -9.19 kcal/mol, respectively. Furthermore, slight variances in the MD simulation demonstrated consistent binding to TMPRSS2 and spike protein after the initial 50 ns. These results are highly valuable in the search for a treatment for SARS-CoV-2 infection.
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Affiliation(s)
| | - Alfrina Irene
- Faculty of Pharmacy Universitas Indonesia, Depok 16424, West Java, Indonesia
| | - Joko Tri Wibowo
- Research Center for Vaccine and Drug, National Research and Innovation Agency of Indonesia (BRIN), Cibinong, Indonesia
| | - Masteria Yunovilsa Putra
- Research Center for Vaccine and Drug, National Research and Innovation Agency of Indonesia (BRIN), Cibinong, Indonesia
- National Metabolomics Collaborative Research Center, Faculty of Pharmacy, Universitas Indonesia, Depok, 16424, West Java, Indonesia
| | - Arry Yanuar
- Faculty of Pharmacy Universitas Indonesia, Depok 16424, West Java, Indonesia
- National Metabolomics Collaborative Research Center, Faculty of Pharmacy, Universitas Indonesia, Depok, 16424, West Java, Indonesia
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Shams AHM, Helaly AA, Algeblawi AM, Awad-Allah EFA. Efficacy of Seed-Biopriming with Trichoderma spp. and Foliar Spraying of ZnO-Nanoparticles Induce Cherry Tomato Growth and Resistance to Fusarium Wilt Disease. PLANTS (BASEL, SWITZERLAND) 2023; 12:3117. [PMID: 37687362 PMCID: PMC10489679 DOI: 10.3390/plants12173117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 08/19/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023]
Abstract
Several microbes that cause plant diseases drastically lower the production of agriculture and jeopardize the safety of the world's food supply. As a result, sustainable agriculture requires disease management tactics based on modern, eco-friendly techniques as alternatives to various agrochemicals. The current study aimed to assess the antifungal activity of ZnO-nanoparticles against Fusarium solani in-vitro, and the ability of two antagonistic Trichoderma isolates, Trichoderma viride and Trichoderma harzianum, to produce antifungal secondary metabolites and identify them using gas chromatography-mass spectrometry, and to evaluate the combined effects of foliar spray of ZnO-nanoparticles and bioprimed seeds of cherry tomato (Solanum lycopersicum L.) with two antagonistic Trichoderma isolates against Fusarium wilt disease caused by Fusarium solani in greenhouse conditions. The results revealed that, in-vitro, the highest concentration of ZnO nanoparticles (3000 ppm) resulted in the greatest decrease in Fusarium solani mycelial growth (90.91% inhibition). The scanning electron microscopy demonstrated the evident distortion in Fusarium solani growing mycelia treated with ZnO-nanoparticles, which might be the source of growth suppression. Additionally, twenty-eight bioactive chemical compounds were isolated and identified from Trichoderma spp. ethyl acetate crude extracts using gas chromatography-mass spectrometry. In a greenhouse experiment, the combination of bioprimed cherry tomato plants with Trichoderma harzianum and foliar spraying of ZnO-nanoparticles at 3000 ppm was the most effective interaction treatment for reducing disease severity index (23.4%) and improving the vegetative growth parameters, micronutrient contents (Mn, Zn, and Fe in leaves), and chlorophyll content (SPAD unit), as well as stimulating phenylalanine ammonia-lyase activity of cherry tomato leaves at 75 days after sowing. In conclusion, the antifungal potential of seed-biopriming with antagonistic Trichoderma isolates and the foliar spraying of ZnO-nanoparticles can boost cherry tomato growth and confer resistance to Fusarium wilt caused by Fusarium solani.
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Affiliation(s)
- Amany H. M. Shams
- Plant Pathology Department, Faculty of Agriculture, Alexandria University, Alexandria 21545, Egypt;
| | - Amira A. Helaly
- Vegetable Crops Department, Faculty of Agriculture, Alexandria University, Alexandria 21545, Egypt;
| | - Abeer M. Algeblawi
- Plant Protection Department, Faculty of Agriculture, University of Tripoli, Tripoli 13479, Libya;
| | - Eman F. A. Awad-Allah
- Soil and Water Sciences Department, Faculty of Agriculture, Alexandria University, Alexandria 21545, Egypt
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Tassakka ACMAR, Iskandar IW, Alam JF, Permana AD, Massi MN, Jompa J, Liao LM. Docking Studies and Molecular Dynamics Simulations of Potential Inhibitors from the Brown Seaweed Sargassum polycystum (Phaeophyceae) against PLpro of SARS-CoV-2. BIOTECH 2023; 12:46. [PMID: 37366794 DOI: 10.3390/biotech12020046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/28/2023] Open
Abstract
The COVID-19 disease is a major problem affecting human health all over the world. Consequently, researchers have been trying to find solutions to treat this pandemic-scale disease. Even if there are vaccines and approved drugs that could decrease the spread of this pandemic, multidisciplinary approaches are still needed to identify new small molecules as alternatives to combat COVID-19, especially those from nature. In this study, we employed computational approaches by screening 17 natural compounds from the tropical brown seaweed Sargassum polycystum known to have anti-viral properties that benefit human health. This study assessed some seaweed natural products that are bound to the PLpro of SARS-CoV-2. By employing pharmacophore and molecular docking, these natural compounds from S. polycystum showed remarkable scores for protein targets with competitive scores compared to X-ray crystallography ligands and well-known antiviral compounds. This study provides insightful information for advanced study and further in vitro examination and clinical investigation for drug development prospects of abundant yet underexploited tropical seaweeds.
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Affiliation(s)
| | | | - Jamaluddin Fitrah Alam
- Faculty of Marine Science and Fisheries, Universitas Hasanuddin, Makassar 90245, Indonesia
| | - Andi Dian Permana
- Faculty of Pharmacy, Universitas Hasanuddin, Makassar 90245, Indonesia
| | | | - Jamaluddin Jompa
- Faculty of Marine Science and Fisheries, Universitas Hasanuddin, Makassar 90245, Indonesia
| | - Lawrence Manzano Liao
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8528, Japan
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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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Campos MF, Mendonça SC, Peñaloza EMC, de Oliveira BAC, Rosa AS, Leitão GG, Tucci AR, Ferreira VNS, Oliveira TKF, Miranda MD, Allonso D, Leitão SG. Anti-SARS-CoV-2 Activity of Ampelozizyphus amazonicus (Saracura-Mirá): Focus on the Modulation of the Spike-ACE2 Interaction by Chemically Characterized Bark Extracts by LC-DAD-APCI-MS/MS. Molecules 2023; 28:molecules28073159. [PMID: 37049921 PMCID: PMC10095690 DOI: 10.3390/molecules28073159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/22/2023] [Accepted: 03/29/2023] [Indexed: 04/05/2023] Open
Abstract
Traditional medicine shows several treatment protocols for COVID-19 based on natural products, revealing its potential as a possible source of anti-SARS-CoV-2 agents. Ampelozizyphus amazonicus is popularly used in the Brazilian Amazon as a fortifier and tonic, and recently, it has been reported to relieve COVID-19 symptoms. This work aimed to investigate the antiviral potential of A. amazonicus, focusing on the inhibition of spike and ACE2 receptor interaction, a key step in successful infection. Although saponins are the major compounds of this plant and often reported as its active principles, a polyphenol-rich extract was the best inhibitor of the spike and ACE2 interaction. Chemical characterization of A. amazonicus bark extracts by LC-DAD-APCI-MS/MS before and after clean-up steps for polyphenol removal showed that the latter play an essential role in maintaining this activity. The effects of the extracts on viral replication were also assessed, and all samples (aqueous and ethanol extracts) demonstrated in vitro activity, inhibiting viral titers in the supernatant of Calu-3 cells after 24 hpi. By acting both in the SARS-CoV-2 cell entry process and its replication, A. amazonicus bark extracts stand out as a multitarget agent, highlighting the species as a promising candidate in the development of anti-SARS-CoV-2 drugs.
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Affiliation(s)
- Mariana Freire Campos
- Programa de Pós-Graduação em Biotecnologia Vegetal e Bioprocessos, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21.941-902, RJ, Brazil
- Departamento de Produtos Naturais e Alimentos, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Ilha do Fundão, Centro de Ciências da Saúde, Rio de Janeiro 21.941-902, RJ, Brazil
| | - Simony Carvalho Mendonça
- Departamento de Produtos Naturais e Alimentos, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Ilha do Fundão, Centro de Ciências da Saúde, Rio de Janeiro 21.941-902, RJ, Brazil
| | - Evelyn Maribel Condori Peñaloza
- Departamento de Produtos Naturais e Alimentos, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Ilha do Fundão, Centro de Ciências da Saúde, Rio de Janeiro 21.941-902, RJ, Brazil
| | - Beatriz A. C. de Oliveira
- Departamento de Produtos Naturais e Alimentos, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Ilha do Fundão, Centro de Ciências da Saúde, Rio de Janeiro 21.941-902, RJ, Brazil
| | - Alice S. Rosa
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21.941-902, RJ, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, IOC-Fiocruz, Rio de Janeiro 21.941-902, RJ, Brazil
| | - Gilda Guimarães Leitão
- Instituto de Pesquisas de Produtos Naturais, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21.941-902, RJ, Brazil
| | - Amanda R. Tucci
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21.941-902, RJ, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, IOC-Fiocruz, Rio de Janeiro 21.941-902, RJ, Brazil
| | - Vivian Neuza S. Ferreira
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21.941-902, RJ, Brazil
| | - Thamara Kelcya F. Oliveira
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21.941-902, RJ, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, IOC-Fiocruz, Rio de Janeiro 21.941-902, RJ, Brazil
| | - Milene Dias Miranda
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21.941-902, RJ, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, IOC-Fiocruz, Rio de Janeiro 21.941-902, RJ, Brazil
| | - Diego Allonso
- Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21.941-902, RJ, Brazil
| | - Suzana Guimarães Leitão
- Departamento de Produtos Naturais e Alimentos, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Ilha do Fundão, Centro de Ciências da Saúde, Rio de Janeiro 21.941-902, RJ, Brazil
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Schultz JV, Tonel MZ, Martins MO, Fagan SB. Graphene oxide and flavonoids as potential inhibitors of the spike protein of SARS-CoV-2 variants and interaction between ligands: a parallel study of molecular docking and DFT. Struct Chem 2023; 34:1-11. [PMID: 36721714 PMCID: PMC9880933 DOI: 10.1007/s11224-023-02135-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 01/19/2023] [Indexed: 01/28/2023]
Abstract
Nanocarriers allow the connection between biomolecules and other structures to enhance the treatment efficacy, through the biomolecule's properties to an existing drug, or to allow a better and specific delivery. Apigenin and orientin are biomolecules with excellent therapeutic properties that are proposed in the fight against COVID-19. Besides that, graphene oxide is a nanomaterial that exhibits antiviral activity and is used as a nanocarrier of several drugs. We evaluated in this work, through molecular docking, the binding affinity between these structures to the receptor-binding domain of spike protein of two coronavirus variants, Delta and Omicron. The results indicate that all the structures exhibit affinity with the two protein targets, with binding affinity values of -11.88 to -6.65 kcal/mol for the Delta variant and values of -9.58 to -13.20 kcal/mol for the Omicron variant, which is a successful value as found in the literature as a potential inhibitor of SARS-CoV-2 infection. Also, through first-principles calculations based on Density Functional Theory, the interaction of graphene oxide with the biomolecules apigenin and orientin occurred. The results exhibit weak binding energy, which indicates that physical adsorption occurs, with better results when the biomolecule is set in parallel to the nanomaterial due to attractive π-π staking. These results are conducive to the development of a nanocarrier.
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Affiliation(s)
- Júlia Vaz Schultz
- PPGNANO - Postgraduate Program in Nanoscience, Universidade Franciscana-UFN, Rua dos Andradas, 1614, ZIP 97010-032, Santa Maria, RS Brazil
| | - Mariana Zancan Tonel
- PPGNANO - Postgraduate Program in Nanoscience, Universidade Franciscana-UFN, Rua dos Andradas, 1614, ZIP 97010-032, Santa Maria, RS Brazil
| | - Mirkos Ortiz Martins
- PPGNANO - Postgraduate Program in Nanoscience, Universidade Franciscana-UFN, Rua dos Andradas, 1614, ZIP 97010-032, Santa Maria, RS Brazil
| | - Solange Binotto Fagan
- PPGNANO - Postgraduate Program in Nanoscience, Universidade Franciscana-UFN, Rua dos Andradas, 1614, ZIP 97010-032, Santa Maria, RS Brazil
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Feng L, Fu S, Zhang P, Zhang Y, Zhao Y, Yao Y, Luo L, Ping P. Potential use of the S-protein-Angiotensin converting enzyme 2 binding pathway in the treatment of coronavirus disease 2019. Front Public Health 2022; 10:1050034. [PMID: 36518573 PMCID: PMC9742547 DOI: 10.3389/fpubh.2022.1050034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/15/2022] [Indexed: 11/29/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogen that causes coronavirus disease 2019 (COVID-19), infects humans through a strong interaction between the viral spike protein (S-protein) and angiotensin converting enzyme 2 (ACE2) receptors on the cell surface. The infection of host lung cells by SARS-CoV-2 leads to clinical symptoms in patients. However, ACE2 expression is not restricted to the lungs; altered receptors have been found in the nasal and oral mucosa, vessel, brain, pancreas, gastrointestinal tract, kidney, and heart. The future of COVID-19 is uncertain, however, new viral variants are likely to emerge. The SARS-CoV-2 Omicron variant has a total of 50 gene mutations compared with the original virus; 15 of which occur in the receptor binding domain (RBD). The RBD of the viral S-protein binds to the human ACE2 receptor for viral entry. Mutations of the ACE2-RBD interface enhance tight binding by increasing hydrogen bond interactions and expanding the accessible surface area. Extracorporeal membrane oxygenation, hyperbaric oxygen, and aggressive dialysis for the treatment of COVID-19 have shown various degrees of clinical success. The use of decoy receptors based on the ACE2 receptor as a broadly potent neutralizer of SARS-CoV-2 variants has potential as a therapeutic mechanism. Drugs such as 3E8 could block binding of the S1-subunit to ACE2 and restrict the infection of ACE2-expressing cells by a variety of coronaviruses. Here, we discuss the development of ACE2-targeted strategies for the treatment and prevention of COVID-19.
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Affiliation(s)
- Long Feng
- Department of Anesthesia, Hainan Hospital of Chinese People's Liberation Army General Hospital, Sanya, China
| | - Shihui Fu
- Department of Geriatric Cardiology, Chinese People's Liberation Army General Hospital, Beijing, China
- Department of Cardiology, Hainan Hospital of Chinese People's Liberation Army General Hospital, Sanya, China
| | - Pei Zhang
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Yujie Zhang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yali Zhao
- Central Laboratory, Hainan Hospital of Chinese People's Liberation Army General Hospital, Sanya, China
| | - Yao Yao
- Center for Healthy Aging and Development Studies, National School of Development, Peking University, Beijing, China
| | - Leiming Luo
- Department of Geriatric Cardiology, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Ping Ping
- General Station for Drug and Instrument Supervision and Control, Joint Logistic Support Force of Chinese People's Liberation Army, Beijing, China
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Xu J, Yang W, Pan Y, Xu H, He L, Zheng B, Xie Y, Wu X. Lucidenic acid A inhibits the binding of hACE2 receptor with spike protein to prevent SARS-CoV-2 invasion. Food Chem Toxicol 2022; 169:113438. [PMID: 36179993 PMCID: PMC9526994 DOI: 10.1016/j.fct.2022.113438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 09/07/2022] [Accepted: 09/15/2022] [Indexed: 11/20/2022]
Abstract
High infection caused by mutations of SARS-CoV-2 calls for new prevention strategy. Ganoderma lucidum known as a superior immunoenhancer exhibits various antiviral effects, whether it can resist SARS-CoV-2 remains unclear. Herein, virtual screening combined with in vitro hACE2 inhibition assays were used to investigate its anti SARS-CoV-2 effect. Potential 54 active components, 80 core targets and 20 crucial pathways were identified by the component-target-pathway network. The binding characters of these components to hACE2 and its complexes with spike protein including omicron variant was analyzed by molecular docking. Lucidenic acid A was selected as the top molecule with high affinity to all receptors by forming hydrogen bonds. Molecular dynamics simulation showed it had good binding stability with the receptor proteins. Finally, in vitro FRET test demonstrated it inhibited the hACE2 activity with IC50 2 μmol/mL. Therefore, lucidenic acid A can prevent the virus invasion by blocking hACE2 binding with SARS-CoV-2.
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Affiliation(s)
- Juan Xu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, PR China; Zhejiang Provincial Key Laboratory of Characteristic Traditional Chinese Medicine Resources Protection and Innovative Utilization, Zhejiang A&F University, Lin'an, 311300, PR China
| | - WenTao Yang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, PR China; Zhejiang Provincial Key Laboratory of Characteristic Traditional Chinese Medicine Resources Protection and Innovative Utilization, Zhejiang A&F University, Lin'an, 311300, PR China
| | - YiFeng Pan
- Hangzhou Xihu District Center for Disease Control and Prevention, Hangzhou, 310030, PR China
| | - HaiShun Xu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, PR China
| | - Liang He
- Zhejiang Provincial Academy of Forestry, Hangzhou, 310000, Zhejiang, China
| | - BingSong Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, PR China
| | - YingQiu Xie
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - XueQian Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, PR China; Zhejiang Provincial Key Laboratory of Characteristic Traditional Chinese Medicine Resources Protection and Innovative Utilization, Zhejiang A&F University, Lin'an, 311300, PR China; National Innovation Alliance of Lingzhi and Sanyeqing Industry, Lin'an, 311300, China.
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Kalasariya HS, Patel NB, Gacem A, Alsufyani T, Reece LM, Yadav VK, Awwad NS, Ibrahium HA, Ahn Y, Yadav KK, Jeon BH. Marine Alga Ulva fasciata-Derived Molecules for the Potential Treatment of SARS-CoV-2: An In Silico Approach. Mar Drugs 2022; 20:md20090586. [PMID: 36135775 PMCID: PMC9506351 DOI: 10.3390/md20090586] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 12/13/2022] Open
Abstract
SARS-CoV-2 is the causative agent of the COVID-19 pandemic. This in silico study aimed to elucidate therapeutic efficacies against SARS-CoV-2 of phyco-compounds from the seaweed, Ulva fasciata. Twelve phyco-compounds were isolated and toxicity was analyzed by VEGA QSAR. Five compounds were found to be nonmutagenic, noncarcinogenic and nontoxic. Moreover, antiviral activity was evaluated by PASS. Binding affinities of five of these therapeutic compounds were predicted to possess probable biological activity. Fifteen SARS-CoV-2 target proteins were analyzed by the AutoDock Vina program for molecular docking binding energy analysis and the 6Y84 protein was determined to possess optimal binding affinities. The Desmond program from Schrödinger’s suite was used to study high performance molecular dynamic simulation properties for 3,7,11,15-Tetramethyl-2-hexadecen-1-ol—6Y84 for better drug evaluation. The ligand with 6Y84 had stronger binding affinities (−5.9 kcal/mol) over two standard drugs, Chloroquine (−5.6 kcal/mol) and Interferon α-2b (−3.8 kcal/mol). Swiss ADME calculated physicochemical/lipophilicity/water solubility/pharmacokinetic properties for 3,7,11,15-Tetramethyl-2-hexadecen-1-ol, showing that this therapeutic agent may be effective against SARS-CoV-2.
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Affiliation(s)
- Haresh S. Kalasariya
- Centre for Natural Products Discovery, School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK
| | - Nikunj B. Patel
- Microbiology Department, Sankalchand Patel University, Visnagar 384315, India
| | - Amel Gacem
- Department of Physics, Faculty of Sciences, University 20 Août 1955, Skikda 21000, Algeria
| | - Taghreed Alsufyani
- Department of Chemistry, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Lisa M. Reece
- Reece Life Science Consulting Agency, 819 N Amburn Rd, Texas City, TX 77591, USA
| | - Virendra Kumar Yadav
- Department of Biosciences, School of Liberal Arts & Sciences, Mody University of Science and Technology, Lakshmangarh, Sikar 332311, India
| | - Nasser S. Awwad
- Department of Chemistry, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Hala A. Ibrahium
- Biology Department, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
- Department of Semi Pilot Plant, Nuclear Materials Authority, El Maadi, P.O. Box 530, Cairo 11381, Egypt
| | - Yongtae Ahn
- Department of Earth Resources & Environmental Engineering, Hanyang University, 222-Wangsimni-ro, Seongdong-gu, Seoul 04763, Korea
| | - Krishna Kumar Yadav
- Faculty of Science and Technology, Madhyanchal Professional University, Ratibad, Bhopal 462044, India
- Correspondence: (K.K.Y.); (B.-H.J.)
| | - Byong-Hun Jeon
- Department of Earth Resources & Environmental Engineering, Hanyang University, 222-Wangsimni-ro, Seongdong-gu, Seoul 04763, Korea
- Correspondence: (K.K.Y.); (B.-H.J.)
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Are Nutraceuticals Effective in COVID-19 and Post-COVID Prevention and Treatment? Foods 2022; 11:foods11182884. [PMID: 36141012 PMCID: PMC9498392 DOI: 10.3390/foods11182884] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/09/2022] [Accepted: 09/15/2022] [Indexed: 11/17/2022] Open
Abstract
The beginning of the end or the end of the beginning? After two years mastered by coronavirus disease 19 (COVID-19) pandemic, we are now witnessing a turnaround. The reduction of severe cases and deaths from COVID-19 led to increasing importance of a new disease called post-COVID syndrome. The term post-COVID is used to indicate permanency of symptoms in patients who have recovered from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Immune, antiviral, antimicrobial therapies, as well as ozone therapy have been used to treat COVID-19 disease. Vaccines have then become available and administered worldwide to prevent the insurgence of the disease. However, the pandemic is not over yet at all given the emergence of new omicron variants. New therapeutic strategies are urgently needed. In this view, great interest was found in nutraceutical products, including vitamins (C, D, and E), minerals (zinc), melatonin, probiotics, flavonoids (quercetin), and curcumin. This review summarizes the role of nutraceuticals in the prevention and/or treatment of COVID-19 disease and post-COVID syndrome.
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Evolutionary progression of collective mutations in Omicron sub-lineages towards efficient RBD-hACE2: Allosteric communications between and within viral and human proteins. Comput Struct Biotechnol J 2022; 20:4562-4578. [PMID: 35989699 PMCID: PMC9384468 DOI: 10.1016/j.csbj.2022.08.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/06/2022] [Accepted: 08/07/2022] [Indexed: 11/23/2022] Open
Abstract
The interaction between the Spike (S) protein of SARS-CoV-2 and the human angiotensin converting enzyme 2 (hACE2) is essential for infection, and is a target for neutralizing antibodies. Consequently, selection of mutations in the S protein is expected to be driven by the impact on the interaction with hACE2 and antibody escape. Here, for the first time, we systematically characterized the collective effects of mutations in each of the Omicron sub-lineages (BA.1, BA.2, BA.3 and BA.4) on both the viral S protein receptor binding domain (RBD) and the hACE2 protein using post molecular dynamics studies and dynamic residue network (DRN) analysis. Our analysis suggested that Omicron sub-lineage mutations result in altered physicochemical properties that change conformational flexibility compared to the reference structure, and may contribute to antibody escape. We also observed changes in the hACE2 substrate binding groove in some sub-lineages. Notably, we identified unique allosteric communication paths in the reference protein complex formed by the DRN metrics betweenness centrality and eigencentrality hubs, originating from the RBD core traversing the receptor binding motif of the S protein and the N-terminal domain of the hACE2 to the active site. We showed allosteric changes in residue network paths in both the RBD and hACE2 proteins due to Omicron sub-lineage mutations. Taken together, these data suggest progressive evolution of the Omicron S protein RBD in sub-lineages towards a more efficient interaction with the hACE2 receptor which may account for the increased transmissibility of Omicron variants.
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Bharathi M, Sivamaruthi BS, Kesika P, Thangaleela S, Chaiyasut C. Phytoncides could potentially inhibit the spike protein of SARS-CoV-2 variants. Phytother Res 2022; 36:4020-4023. [PMID: 35934886 PMCID: PMC9538175 DOI: 10.1002/ptr.7586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Muruganantham Bharathi
- Innovation Center for Holistic Health, Nutraceuticals, and Cosmeceuticals, Faculty of Pharmacy, Chiang Mai University, Chiang Mai, Thailand
| | | | - Periyanaina Kesika
- Innovation Center for Holistic Health, Nutraceuticals, and Cosmeceuticals, Faculty of Pharmacy, Chiang Mai University, Chiang Mai, Thailand.,Office of Research Administration, Chiang Mai University, Chiang Mai, Thailand
| | - Subramanian Thangaleela
- Innovation Center for Holistic Health, Nutraceuticals, and Cosmeceuticals, Faculty of Pharmacy, Chiang Mai University, Chiang Mai, Thailand
| | - Chaiyavat Chaiyasut
- Innovation Center for Holistic Health, Nutraceuticals, and Cosmeceuticals, Faculty of Pharmacy, Chiang Mai University, Chiang Mai, Thailand
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Ngwe Tun MM, Sakura T, Sakurai Y, Kurosaki Y, Inaoka DK, Shioda N, Smith C, Yasuda J, Morita K, Kita K. 5-Aminolevulinic acid antiviral efficacy against SARS-CoV-2 omicron variant in vitro. Trop Med Health 2022; 50:30. [PMID: 35477500 PMCID: PMC9043503 DOI: 10.1186/s41182-022-00422-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 04/08/2022] [Indexed: 11/26/2022] Open
Abstract
The coronavirus disease 2019 (COVID 19) pandemic continues to pose a threat to global health. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant (B.1.1.529) has spread rapidly worldwide and became dominant in many countries. A natural 5-aminolevulinic acid (5-ALA) with sodium ferrous citrate (SFC) has demonstrated antiviral activity in Wuhan, Alpha, Beta, Gamma, and Delta variants of SARS-CoV-2 infections in vitro. In this study, we report antiviral activity of 5-ALA, 5-ALA with SFC led to IC50 of 329 and 765/191, respectively after infection with Omicron variant of SARS-CoV-2 in vitro. Our finding suggests that 5-ALA could be used as antiviral drug candidate to treat Omicron variant infected patients.
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Affiliation(s)
- Mya Myat Ngwe Tun
- Department of Virology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.
| | - Takaya Sakura
- Department of Molecular Infection Dynamics, Shionogi Global Infectious Diseases Division, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Yasuteru Sakurai
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.,National Research Center for the Control and Prevention of Infectious Diseases, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Yohei Kurosaki
- National Research Center for the Control and Prevention of Infectious Diseases, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Daniel Ken Inaoka
- Department of Molecular Infection Dynamics, Shionogi Global Infectious Diseases Division, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Norifumi Shioda
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan.,Graduate of School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Chris Smith
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Jiro Yasuda
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan. .,National Research Center for the Control and Prevention of Infectious Diseases, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.
| | - Kouichi Morita
- Department of Virology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.
| | - Kiyoshi Kita
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan. .,Department of Host-Defense Biochemistry, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.
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