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Villada-Troncoso SM, Arévalo-Romero JA, Hernández Rivera V, Pedraza-Escalona M, Pérez-Tapia SM, Espejo-Mojica AJ, Alméciga-Díaz CJ. Study of Potential Blocking Peptides Targeting the SARS-CoV-2 RBD/hACE2 Interaction. Pharmaceuticals (Basel) 2024; 17:1240. [PMID: 39338402 PMCID: PMC11435355 DOI: 10.3390/ph17091240] [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: 09/02/2024] [Revised: 09/13/2024] [Accepted: 09/18/2024] [Indexed: 09/30/2024] Open
Abstract
BACKGROUND/OBJECTIVES Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, was declared a public health emergency in early 2020. The infection initiates when the receptor-binding domain (RBD) of the viral spike protein binds to human angiotensin-converting enzyme 2 (ACE2). Despite the success of vaccination efforts, the emergence of new variants highlights the ongoing need for treatments targeting these evolving strains. In silico methods previously identified peptides BP2, BP9, and BP11 as being capable of disrupting the RBD-ACE2 interaction, though their efficacy has not been experimentally validated until now. METHODS In this study, these peptides were recombinantly produced in the yeast Komagataella phaffii, and the activity was assessed in vitro using binding assays with multiple RBD variants and the inhibition of the RBD-ACE2 interaction. RESULTS The production yield for BP2, BP9, and BP11 was 14.34, 4.01, and 1.35 mg per culture liter, respectively. Noteworthy, the three BPs interacted with the RBD of SARS-CoV-2 variants of concern, with BP2 showing higher recognition. Finally, the BPs showed an RBD/hACE2 interaction blocking capacity with IC50 values between 1.03 and 5.35 nM, with BP2 showing the lowest values among the evaluated peptides. CONCLUSIONS These results demonstrate that BP2, specifically, is a promising candidate for the development of novel therapeutic interventions targeting SARS-CoV-2 and other coronaviruses that use hACE2 for cellular entry.
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Affiliation(s)
- Sara M. Villada-Troncoso
- Institute for the Study in Inborn Errors of Metabolism—IEIM, Faculty of Science, Pontificia Universidad Javeriana, Bogotá 110231, Colombia; (S.M.V.-T.); (J.A.A.-R.); (A.J.E.-M.)
| | - Jenny Andrea Arévalo-Romero
- Institute for the Study in Inborn Errors of Metabolism—IEIM, Faculty of Science, Pontificia Universidad Javeriana, Bogotá 110231, Colombia; (S.M.V.-T.); (J.A.A.-R.); (A.J.E.-M.)
- Instituto Distrital de Ciencia, Biotecnología e Innovación en Salud—IDCBIS, Bogotá 111611, Colombia
| | - Vanessa Hernández Rivera
- Unidad de Desarrollo e Investigación en Bioterapéuticos (UDIBI), Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico; (V.H.R.); (S.M.P.-T.)
| | - Martha Pedraza-Escalona
- CONAHCyT-Unidad de Desarrollo e Investigación en Bioterapéuticos (UDIBI), Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico;
| | - Sonia M. Pérez-Tapia
- Unidad de Desarrollo e Investigación en Bioterapéuticos (UDIBI), Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico; (V.H.R.); (S.M.P.-T.)
| | - Angela Johana Espejo-Mojica
- Institute for the Study in Inborn Errors of Metabolism—IEIM, Faculty of Science, Pontificia Universidad Javeriana, Bogotá 110231, Colombia; (S.M.V.-T.); (J.A.A.-R.); (A.J.E.-M.)
| | - Carlos Javier Alméciga-Díaz
- Institute for the Study in Inborn Errors of Metabolism—IEIM, Faculty of Science, Pontificia Universidad Javeriana, Bogotá 110231, Colombia; (S.M.V.-T.); (J.A.A.-R.); (A.J.E.-M.)
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2
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Zhang L, Nishi H, Kinoshita K. Single-cell RNA-seq public data reveal the gene regulatory network landscape of respiratory epithelial and peripheral immune cells in COVID-19 patients. Front Immunol 2023; 14:1194614. [PMID: 37936693 PMCID: PMC10627007 DOI: 10.3389/fimmu.2023.1194614] [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: 03/27/2023] [Accepted: 10/10/2023] [Indexed: 11/09/2023] Open
Abstract
Introduction Infection with SARS-CoV-2 leads to coronavirus disease 2019 (COVID-19), which can result in acute respiratory distress syndrome and multiple organ failure. However, its comprehensive influence on pathological immune responses in the respiratory epithelium and peripheral immune cells is not yet fully understood. Methods In this study, we analyzed multiple public scRNA-seq datasets of nasopharyngeal swabs and peripheral blood to investigate the gene regulatory networks (GRNs) of healthy individuals and COVID-19 patients with mild/moderate and severe disease, respectively. Cell-cell communication networks among cell types were also inferred. Finally, validations were conducted using bulk RNA-seq and proteome data. Results Similar and dissimilar regulons were identified within or between epithelial and immune cells during COVID-19 severity progression. The relative transcription factors (TFs) and their targets were used to construct GRNs among different infection sites and conditions. Between respiratory epithelial and peripheral immune cells, different TFs tended to be used to regulate the activity of a cell between healthy individuals and COVID-19 patients, although they had some TFs in common. For example, XBP1, FOS, STAT1, and STAT2 were activated in both the epithelial and immune cells of virus-infected individuals. In contrast, severe COVID-19 cases exhibited activation of CEBPD in peripheral immune cells, while CEBPB was exclusively activated in respiratory epithelial cells. Moreover, in patients with severe COVID-19, although some inflammatory genes, such as S100A8/A9, were found to be upregulated in both respiratory epithelial and peripheral immune cells, their relative regulators can differ in terms of cell types. The cell-cell communication analysis suggested that epidermal growth factor receptor signaling among epithelia contributes to mild/moderate disease, and chemokine signaling among immune cells contributes to severe disease. Conclusion This study identified cell type- and condition-specific regulons in a wide range of cell types from the initial infection site to the peripheral blood, and clarified the diverse mechanisms of maladaptive responses to SARS-CoV-2 infection.
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Affiliation(s)
- Lin Zhang
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Hafumi Nishi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, Sendai, Japan
- Faculty of Core Research, Ochanomizu University, Tokyo, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
- Department of In Silico Analyses, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai, Japan
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3
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Shukla N, Srivastava N, Gupta R, Srivastava P, Narayan J. COVID Variants, Villain and Victory: A Bioinformatics Perspective. Microorganisms 2023; 11:2039. [PMID: 37630599 PMCID: PMC10459809 DOI: 10.3390/microorganisms11082039] [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: 06/21/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 08/27/2023] Open
Abstract
The SARS-CoV-2 virus, a novel member of the Coronaviridae family, is responsible for the viral infection known as Coronavirus Disease 2019 (COVID-19). In response to the urgent and critical need for rapid detection, diagnosis, analysis, interpretation, and treatment of COVID-19, a wide variety of bioinformatics tools have been developed. Given the virulence of SARS-CoV-2, it is crucial to explore the pathophysiology of the virus. We intend to examine how bioinformatics, in conjunction with next-generation sequencing techniques, can be leveraged to improve current diagnostic tools and streamline vaccine development for emerging SARS-CoV-2 variants. We also emphasize how bioinformatics, in general, can contribute to critical areas of biomedicine, including clinical diagnostics, SARS-CoV-2 genomic surveillance and its evolution, identification of potential drug targets, and development of therapeutic strategies. Currently, state-of-the-art bioinformatics tools have helped overcome technical obstacles with respect to genomic surveillance and have assisted in rapid detection, diagnosis, and delivering precise treatment to individuals on time.
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Affiliation(s)
- Nityendra Shukla
- CSIR Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India; (N.S.); (R.G.)
| | - Neha Srivastava
- Amity Institute of Biotechnology, Amity University, Uttar Pradesh, Lucknow Campus, Lucknow 226010, India; (N.S.); (P.S.)
| | - Rohit Gupta
- CSIR Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India; (N.S.); (R.G.)
| | - Prachi Srivastava
- Amity Institute of Biotechnology, Amity University, Uttar Pradesh, Lucknow Campus, Lucknow 226010, India; (N.S.); (P.S.)
| | - Jitendra Narayan
- CSIR Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India; (N.S.); (R.G.)
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4
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Yeh YC, Doan LH, Huang ZY, Chu LW, Shi TH, Lee YR, Wu CT, Lin CH, Chiang ST, Liu HK, Chuang TH, Ping YH, Liu HS, Huang CYF. Honeysuckle ( Lonicera japonica) and Huangqi ( Astragalus membranaceus) Suppress SARS-CoV-2 Entry and COVID-19 Related Cytokine Storm in Vitro. Front Pharmacol 2022; 12:765553. [PMID: 35401158 PMCID: PMC8990830 DOI: 10.3389/fphar.2021.765553] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/15/2021] [Indexed: 12/14/2022] Open
Abstract
COVID-19 is threatening human health worldwide but no effective treatment currently exists for this disease. Current therapeutic strategies focus on the inhibition of viral replication or using anti-inflammatory/immunomodulatory compounds to improve host immunity, but not both. Traditional Chinese medicine (TCM) compounds could be promising candidates due to their safety and minimal toxicity. In this study, we have developed a novel in silico bioinformatics workflow that integrates multiple databases to predict the use of honeysuckle (Lonicera japonica) and Huangqi (Astragalus membranaceus) as potential anti-SARS-CoV-2 agents. Using extracts from honeysuckle and Huangqi, these two herbs upregulated a group of microRNAs including let-7a, miR-148b, and miR-146a, which are critical to reduce the pathogenesis of SARS-CoV-2. Moreover, these herbs suppressed pro-inflammatory cytokines including IL-6 or TNF-α, which were both identified in the cytokine storm of acute respiratory distress syndrome, a major cause of COVID-19 death. Furthermore, both herbs partially inhibited the fusion of SARS-CoV-2 spike protein-transfected BHK-21 cells with the human lung cancer cell line Calu-3 that was expressing ACE2 receptors. These herbs inhibited SARS-CoV-2 Mpro activity, thereby alleviating viral entry as well as replication. In conclusion, our findings demonstrate that honeysuckle and Huangqi have the potential to be used as an inhibitor of SARS-CoV-2 virus entry that warrants further in vivo analysis and functional assessment of miRNAs to confirm their clinical importance. This fast-screening platform can also be applied to other drug discovery studies for other infectious diseases.
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Affiliation(s)
- Yuan-Chieh Yeh
- Department of Traditional Chinese Medicine, Chang Gung Memorial Hospital, Keelung, Taiwan.,Program in Molecular Medicine, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Ly Hien Doan
- Institute of Biopharmaceutical Sciences, College of Pharmaceutical Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Zi-Yi Huang
- Program in Molecular Medicine, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan.,ASUS Intelligent Cloud Services, Taipei, Taiwan
| | - Li-Wei Chu
- Department and Institute of Pharmacology, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Tzu-Hau Shi
- Department of Life Sciences and Institute of Genome Sciences, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Ying-Ray Lee
- Department of Medical Research, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi, Taiwan.,Department of Microbiology and Immunology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Cheng-Tao Wu
- Division of Big Data, Phalanx Biotech Group, Hsinchu, Taiwan
| | - Chao-Hsiung Lin
- Institute of Biopharmaceutical Sciences, College of Pharmaceutical Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Department of Life Sciences and Institute of Genome Sciences, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Aging and Health Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Shu-Tuan Chiang
- Chuang Song Zong Pharmaceutical Co., Ltd. Ligang Plant, Pingtung, Taiwan
| | - Hui-Kang Liu
- National Research Institute of Chinese Medicine (NRICM), Ministry of Health and Welfare, Taipei, Taiwan.,Ph. D. Program in the Clinical Drug Development of Herbal Medicine, Taipei Medical University, Taipei, Taiwan
| | - Tsung-Hsien Chuang
- Immunology Research Center, National Health Research Institutes, Miaoli, Taiwan.,Program in Environmental and Occupational Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yueh-Hsin Ping
- Department and Institute of Pharmacology, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Institute of Biophotonics, College of Biomedical Science and Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Hsiao-Sheng Liu
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Center for Cancer Research, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,M.Sc. Program in Tropical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chi-Ying F Huang
- Program in Molecular Medicine, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Institute of Biopharmaceutical Sciences, College of Pharmaceutical Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Institute of Clinical Medicine, College of Medicine, National Yang Ming Chiao Tung, Taipei, Taiwan.,Department of Biotechnology and Laboratory Science in Medicine, School of Biomedical Science and Engineering, National Yang Ming Chiao Tung, Taipei, Taiwan.,Department of Biochemistry, School of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
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5
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Vivek-Ananth RP, Krishnaswamy S, Samal A. Potential phytochemical inhibitors of SARS-CoV-2 helicase Nsp13: a molecular docking and dynamic simulation study. Mol Divers 2022; 26:429-442. [PMID: 34117992 PMCID: PMC8196922 DOI: 10.1007/s11030-021-10251-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/08/2021] [Indexed: 02/07/2023]
Abstract
The SARS-CoV-2 helicase Nsp13 is a promising target for developing anti-COVID drugs. In the present study, we have identified potential natural product inhibitors of SARS-CoV-2 Nsp13 targeting the ATP-binding site using molecular docking and molecular dynamics (MD) simulations. MD simulation of the prepared crystal structure of SARS-CoV-2 Nsp13 was performed to generate an ensemble of structures of helicase Nsp13 capturing the conformational diversity of the ATP-binding site. A natural product library of more than 14,000 phytochemicals from Indian medicinal plants was used to perform virtual screening against the ensemble of Nsp13 structures. Subsequently, a two-stage filter, first based on protein-ligand docking binding energy value and second based on protein residues in the ligand-binding site and non-covalent interactions between the protein residues and the ligand in the best-docked pose, was used to identify 368 phytochemicals as potential inhibitors of SARS-CoV-2 helicase Nsp13. MD simulations of the top inhibitors complexed with protein were performed to confirm stable binding, and to compute MM-PBSA based binding energy. From among the 368 potential phytochemical inhibitors, the top identified potential inhibitors of SARS-CoV-2 helicase Nsp13 namely, Picrasidine M, (+)-Epiexcelsin, Isorhoeadine, Euphorbetin and Picrasidine N, can be taken up initially for experimental studies.
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Affiliation(s)
- R P Vivek-Ananth
- The Institute of Mathematical Sciences (IMSc), Chennai, 600113, India
- Homi Bhabha National Institute (HBNI), Mumbai, 400094, India
| | | | - Areejit Samal
- The Institute of Mathematical Sciences (IMSc), Chennai, 600113, India.
- Homi Bhabha National Institute (HBNI), Mumbai, 400094, India.
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6
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Lopes AA, Souza GRS, de Castro França S, Lourenço MV. Biosynthetic studies through feeding experiments in Eclipta prostrata (L.) L. hairy roots. PLANT CELL, TISSUE AND ORGAN CULTURE 2022; 151:215-219. [PMID: 35875188 PMCID: PMC9288585 DOI: 10.1007/s11240-022-02342-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/15/2022] [Indexed: 05/13/2023]
Abstract
UNLABELLED Eclipta prostrata (L.) L. is a medicinal plant of the Asteraceae family, and several extracts and isolated compounds of E. prostrata (L.) L. showed a wide range of biological activities such as antimicrobial, anticancer, hepatoprotective, neuroprotective, hair growth promoting activities, and more recently against covid-19. Eclipta prostrata (L.) L. hairy roots produce wedelolactone (WL), demethylwedelolactone (DWL) and 3,5-di-O-caffeoylquinic acid (3,5-diCQA), and there is no data in literature regarding biosynthetic pathways are involved. To verify the biosynthetic route, feeding experiments were carried out using sodium [2-13C]acetate, [3-13C]dl-phenylalanine, and 13C-labeled compounds (WL, DWL and 3,5-diCQA) were detected by ultra-high-performance liquid chromatography-quadrupole time of flight mass spectrometry (HPLC-QTOF-MS). Analysis showed that the metabolic pathways operative of coumestans (WL and DWL) are derived from acetate and shikimate pathways, while that the phenylpropanoid (3,5-diCQA) biosynthesis is exclusively from shikimate pathway. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11240-022-02342-0.
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Affiliation(s)
- Adriana A. Lopes
- Biotechnology Unit, Universidade de Ribeirão Preto (UNAERP), Ribeirão Preto, SP Brazil
| | - Giuliana R. S. Souza
- Biotechnology Unit, Universidade de Ribeirão Preto (UNAERP), Ribeirão Preto, SP Brazil
| | | | - Miriam V. Lourenço
- Biotechnology Unit, Universidade de Ribeirão Preto (UNAERP), Ribeirão Preto, SP Brazil
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7
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Maciel G, Lopes AA, Cantrell CL, de Castro França S, Bertoni BW, Lourenço MV. Jasmonates promote enhanced production of bioactive caffeoylquinic acid derivative in Eclipta prostrata (L.) L. hairy roots. PLANT CELL, TISSUE AND ORGAN CULTURE 2022; 149:363-369. [PMID: 34840370 PMCID: PMC8606271 DOI: 10.1007/s11240-021-02201-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/16/2021] [Indexed: 05/02/2023]
Abstract
UNLABELLED Eclipta prostrata (L.) L. is widely used in traditional medicine for treatment of hepatitis, poisoning from snake bites and viral infections. Pharmacological studies confirmed its antioxidant, anti-inflammatory and anticancer activities. The efficacy of E. prostrata (L.) L. extracts has been correlated to phenylpropanoids such as flavonoids, coumestans and caffeoylquinic acid derivatives. In this work, the production of wedelolactone, demethylwedelolactone and 3,5-di-O-caffeoylquinic acid (3,5-diCQA) in hairy root cultures of E. prostrata (L.) L. C19 clone was increased after addition of eliciting agents jasmonic acid (JA) or methyl jasmonate (MeJA) at multiple concentrations. Cultures elicited with 100 μM of JA saw a 5.2 fold increase in wedelolactone (from 0.72 to 3.72 mg/g d.w.), a 1.6 fold increase in demethylwedelolactone (from 5.54 to 9.04 mg/g d.w.) and a 2.47 fold increase in 3,5-diCQA (from 18.08 to 44.71 mg/g d.w.). Obtained data validate the potential of E. prostrata (L.) L. hairy root cultures as a production system of wedelolactone, demethylwedelolactone and especially 3,5-diCQA, which has recently been reported to possess activity against coronavirus disease (Covid-19) by in silico computational studies. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11240-021-02201-4.
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Affiliation(s)
- Geveraldo Maciel
- Biotechnology Unit, Universidade de Ribeirão Preto (UNAERP), Ribeirão Preto, SP 14096-900 Brazil
| | - Adriana Aparecida Lopes
- Biotechnology Unit, Universidade de Ribeirão Preto (UNAERP), Ribeirão Preto, SP 14096-900 Brazil
| | - Charles L. Cantrell
- Natural Products Utilization Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), University, Oxford, MS 38655 USA
| | - Suzelei de Castro França
- Biotechnology Unit, Universidade de Ribeirão Preto (UNAERP), Ribeirão Preto, SP 14096-900 Brazil
| | - Bianca Waleria Bertoni
- Biotechnology Unit, Universidade de Ribeirão Preto (UNAERP), Ribeirão Preto, SP 14096-900 Brazil
| | - Miriam Verginia Lourenço
- Biotechnology Unit, Universidade de Ribeirão Preto (UNAERP), Ribeirão Preto, SP 14096-900 Brazil
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Islam F, Bibi S, Meem AFK, Islam MM, Rahaman MS, Bepary S, Rahman MM, Rahman MM, Elzaki A, Kajoak S, Osman H, ElSamani M, Khandaker MU, Idris AM, Emran TB. Natural Bioactive Molecules: An Alternative Approach to the Treatment and Control of COVID-19. Int J Mol Sci 2021; 22:12638. [PMID: 34884440 PMCID: PMC8658031 DOI: 10.3390/ijms222312638] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/11/2021] [Accepted: 11/19/2021] [Indexed: 02/07/2023] Open
Abstract
Several coronaviruses (CoVs) have been associated with serious health hazards in recent decades, resulting in the deaths of thousands around the globe. The recent coronavirus pandemic has emphasized the importance of discovering novel and effective antiviral medicines as quickly as possible to prevent more loss of human lives. Positive-sense RNA viruses with group spikes protruding from their surfaces and an abnormally large RNA genome enclose CoVs. CoVs have already been related to a range of respiratory infectious diseases possibly fatal to humans, such as MERS, SARS, and the current COVID-19 outbreak. As a result, effective prevention, treatment, and medications against human coronavirus (HCoV) is urgently needed. In recent years, many natural substances have been discovered with a variety of biological significance, including antiviral properties. Throughout this work, we reviewed a wide range of natural substances that interrupt the life cycles for MERS and SARS, as well as their potential application in the treatment of COVID-19.
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Affiliation(s)
- Fahadul Islam
- Department of Pharmacy, Daffodil International University, Dhaka 1207, Bangladesh; (F.I.); (A.F.K.M.); (M.M.I.); (M.S.R.); (S.B.); (M.M.R.); (M.M.R.)
| | - Shabana Bibi
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, China;
- International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming 650091, China
| | - Atkia Farzana Khan Meem
- Department of Pharmacy, Daffodil International University, Dhaka 1207, Bangladesh; (F.I.); (A.F.K.M.); (M.M.I.); (M.S.R.); (S.B.); (M.M.R.); (M.M.R.)
| | - Md. Mohaimenul Islam
- Department of Pharmacy, Daffodil International University, Dhaka 1207, Bangladesh; (F.I.); (A.F.K.M.); (M.M.I.); (M.S.R.); (S.B.); (M.M.R.); (M.M.R.)
| | - Md. Saidur Rahaman
- Department of Pharmacy, Daffodil International University, Dhaka 1207, Bangladesh; (F.I.); (A.F.K.M.); (M.M.I.); (M.S.R.); (S.B.); (M.M.R.); (M.M.R.)
| | - Sristy Bepary
- Department of Pharmacy, Daffodil International University, Dhaka 1207, Bangladesh; (F.I.); (A.F.K.M.); (M.M.I.); (M.S.R.); (S.B.); (M.M.R.); (M.M.R.)
| | - Md. Mizanur Rahman
- Department of Pharmacy, Daffodil International University, Dhaka 1207, Bangladesh; (F.I.); (A.F.K.M.); (M.M.I.); (M.S.R.); (S.B.); (M.M.R.); (M.M.R.)
| | - Md. Mominur Rahman
- Department of Pharmacy, Daffodil International University, Dhaka 1207, Bangladesh; (F.I.); (A.F.K.M.); (M.M.I.); (M.S.R.); (S.B.); (M.M.R.); (M.M.R.)
| | - Amin Elzaki
- Department of Radiological Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.E.); (S.K.); (H.O.); (M.E.)
| | - Samih Kajoak
- Department of Radiological Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.E.); (S.K.); (H.O.); (M.E.)
| | - Hamid Osman
- Department of Radiological Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.E.); (S.K.); (H.O.); (M.E.)
| | - Mohamed ElSamani
- Department of Radiological Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.E.); (S.K.); (H.O.); (M.E.)
| | - Mayeen Uddin Khandaker
- Centre for Applied Physics and Radiation Technologies, School of Engineering and Technology, Sunway University, Bandar Sunway 47500, Selangor, Malaysia;
| | - Abubakr M. Idris
- Department of Chemistry, College of Science, King Khalid University, Abha 62529, Saudi Arabia;
- Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha 62529, Saudi Arabia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
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9
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Santos-Beneit F, Raškevičius V, Skeberdis VA, Bordel S. A metabolic modeling approach reveals promising therapeutic targets and antiviral drugs to combat COVID-19. Sci Rep 2021; 11:11982. [PMID: 34099831 PMCID: PMC8184994 DOI: 10.1038/s41598-021-91526-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 05/26/2021] [Indexed: 02/07/2023] Open
Abstract
In this study we have developed a method based on Flux Balance Analysis to identify human metabolic enzymes which can be targeted for therapeutic intervention against COVID-19. A literature search was carried out in order to identify suitable inhibitors of these enzymes, which were confirmed by docking calculations. In total, 10 targets and 12 bioactive molecules have been predicted. Among the most promising molecules we identified Triacsin C, which inhibits ACSL3, and which has been shown to be very effective against different viruses, including positive-sense single-stranded RNA viruses. Similarly, we also identified the drug Celgosivir, which has been successfully tested in cells infected with different types of viruses such as Dengue, Zika, Hepatitis C and Influenza. Finally, other drugs targeting enzymes of lipid metabolism, carbohydrate metabolism or protein palmitoylation (such as Propylthiouracil, 2-Bromopalmitate, Lipofermata, Tunicamycin, Benzyl Isothiocyanate, Tipifarnib and Lonafarnib) are also proposed.
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Affiliation(s)
| | - Vytautas Raškevičius
- Cell Culture Laboratory, Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Vytenis A Skeberdis
- Cell Culture Laboratory, Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Sergio Bordel
- Institute of Sustainable Processes, Universidad de Valladolid, Valladolid, Spain.
- Cell Culture Laboratory, Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania.
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