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Sales AH, Fu I, Durandin A, Ciervo S, Lupoli TJ, Shafirovich V, Broyde S, Geacintov NE. Variable Inhibition of DNA Unwinding Rates Catalyzed by the SARS-CoV-2 Helicase Nsp13 by Structurally Distinct Single DNA Lesions. Int J Mol Sci 2024; 25:7930. [PMID: 39063172 PMCID: PMC11276626 DOI: 10.3390/ijms25147930] [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: 05/23/2024] [Revised: 07/09/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
The SARS-CoV-2 helicase, non-structural protein 13 (Nsp13), plays an essential role in viral replication, translocating in the 5' → 3' direction as it unwinds double-stranded RNA/DNA. We investigated the impact of structurally distinct DNA lesions on DNA unwinding catalyzed by Nsp13. The selected lesions include two benzo[a]pyrene (B[a]P)-derived dG adducts, the UV-induced cyclobutane pyrimidine dimer (CPD), and the pyrimidine (6-4) pyrimidone (6-4PP) photolesion. The experimentally observed unwinding rate constants (kobs) and processivities (P) were examined. Relative to undamaged DNA, the kobs values were diminished by factors of up to ~15 for B[a]P adducts but only by factors of ~2-5 for photolesions. A minor-groove-oriented B[a]P adduct showed the smallest impact on P, which decreased by ~11% compared to unmodified DNA, while an intercalated one reduced P by ~67%. However, the photolesions showed a greater impact on the processivities; notably, the CPD, with the highest kobs value, exhibited the lowest P, which was reduced by ~90%. Our findings thus show that DNA unwinding efficiencies are lesion-dependent and most strongly inhibited by the CPD, leading to the conclusion that processivity is a better measure of DNA lesions' inhibitory effects than unwinding rate constants.
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Affiliation(s)
- Ana H. Sales
- Chemistry Department, New York University, 31 Washington Place, New York, NY 10003, USA; (A.H.S.); (A.D.); (S.C.); (T.J.L.); (V.S.)
| | - Iwen Fu
- Biology Department, New York University, 24 Waverly Place, New York, NY 10003, USA; (I.F.); (S.B.)
| | - Alexander Durandin
- Chemistry Department, New York University, 31 Washington Place, New York, NY 10003, USA; (A.H.S.); (A.D.); (S.C.); (T.J.L.); (V.S.)
| | - Sam Ciervo
- Chemistry Department, New York University, 31 Washington Place, New York, NY 10003, USA; (A.H.S.); (A.D.); (S.C.); (T.J.L.); (V.S.)
| | - Tania J. Lupoli
- Chemistry Department, New York University, 31 Washington Place, New York, NY 10003, USA; (A.H.S.); (A.D.); (S.C.); (T.J.L.); (V.S.)
| | - Vladimir Shafirovich
- Chemistry Department, New York University, 31 Washington Place, New York, NY 10003, USA; (A.H.S.); (A.D.); (S.C.); (T.J.L.); (V.S.)
| | - Suse Broyde
- Biology Department, New York University, 24 Waverly Place, New York, NY 10003, USA; (I.F.); (S.B.)
| | - Nicholas E. Geacintov
- Chemistry Department, New York University, 31 Washington Place, New York, NY 10003, USA; (A.H.S.); (A.D.); (S.C.); (T.J.L.); (V.S.)
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Zhou Y, Shen W, Gao Y, Peng J, Li Q, Wei X, Liu S, Lam FS, Mayol-Llinàs J, Zhao G, Li G, Li Y, Sun H, Cao Y, Li X. Protein-templated ligand discovery via the selection of DNA-encoded dynamic libraries. Nat Chem 2024; 16:543-555. [PMID: 38326646 DOI: 10.1038/s41557-024-01442-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 01/04/2024] [Indexed: 02/09/2024]
Abstract
DNA-encoded chemical libraries (DELs) have become a powerful technology platform in drug discovery. Dual-pharmacophore DELs display two sets of small molecules at the termini of DNA duplexes, thereby enabling the identification of synergistic binders against biological targets, and have been successfully applied in fragment-based ligand discovery and affinity maturation of known ligands. However, dual-pharmacophore DELs identify separate binders that require subsequent linking to obtain the full ligands, which is often challenging. Here we report a protein-templated DEL selection approach that can identify full ligand/inhibitor structures from DNA-encoded dynamic libraries (DEDLs) without the need for subsequent fragment linking. Our approach is based on dynamic DNA hybridization and target-templated in situ ligand synthesis, and it incorporates and encodes the linker structures in the library, along with the building blocks, to be sampled by the target protein. To demonstrate the performance of this method, 4.35-million- and 3.00-million-member DEDLs with different library architectures were prepared, and hit selection was achieved against four therapeutically relevant target proteins.
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Grants
- AoE/P-705/16, 17301118, 17111319, 17303220, 17300321, 17318322, C7005-20G, C7016-22G, and 2122-7S04 Research Grants Council, University Grants Committee (RGC, UGC)
- 21877093, 22222702, and 91953119 National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)
- Health@InnoHK Innovation and Technology Commission (ITF)
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Affiliation(s)
- Yu Zhou
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission, Hong Kong SAR, China
| | - Wenyin Shen
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Ying Gao
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Jianzhao Peng
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Qingrong Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Xueying Wei
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Shihao Liu
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Fong Sang Lam
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Joan Mayol-Llinàs
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission, Hong Kong SAR, China
| | - Guixian Zhao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences; Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Gang Li
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences; Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Hongzhe Sun
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China.
| | - Yan Cao
- School of Pharmacy, Naval Medical University, Shanghai, China.
| | - Xiaoyu Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China.
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission, Hong Kong SAR, China.
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3
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Corona A, Madia VN, De Santis R, Manelfi C, Emmolo R, Ialongo D, Patacchini E, Messore A, Amatore D, Faggioni G, Artico M, Iaconis D, Talarico C, Di Santo R, Lista F, Costi R, Tramontano E. Diketo acid inhibitors of nsp13 of SARS-CoV-2 block viral replication. Antiviral Res 2023; 217:105697. [PMID: 37562607 DOI: 10.1016/j.antiviral.2023.105697] [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: 03/28/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/12/2023]
Abstract
For RNA viruses, RNA helicases have long been recognized to play critical roles during virus replication cycles, facilitating proper folding and replication of viral RNAs, therefore representing an ideal target for drug discovery. SARS-CoV-2 helicase, the non-structural protein 13 (nsp13) is a highly conserved protein among all known coronaviruses, and, at the moment, is one of the most explored viral targets to identify new possible antiviral agents. In the present study, we present six diketo acids (DKAs) as nsp13 inhibitors able to block both SARS-CoV-2 nsp13 enzymatic functions. Among them four compounds were able to inhibit viral replication in the low micromolar range, being active also on other human coronaviruses such as HCoV229E and MERS CoV. The experimental investigation of the binding mode revealed ATP-non-competitive kinetics of inhibition, not affected by substrate-displacement effect, suggesting an allosteric binding mode that was further supported by molecular modelling calculations predicting the binding into an allosteric conserved site located in the RecA2 domain.
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Affiliation(s)
- Angela Corona
- Dipartimento di Scienze della vita e dell'ambiente. Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, SS-554, Monserrato, Cagliari, Italy
| | - Valentina Noemi Madia
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci-Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185, Rome, Italy
| | - Riccardo De Santis
- Defense Institute for Biomedical Sciences, Via Santo Stefano Rotondo 4, 00184, Rome, Italy
| | - Candida Manelfi
- EXSCALATE - Dompé Farmaceutici SpA, via Tommaso De Amicis 95, 80131, Napoli, Italy
| | - Roberta Emmolo
- Dipartimento di Scienze della vita e dell'ambiente. Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, SS-554, Monserrato, Cagliari, Italy
| | - Davide Ialongo
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci-Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185, Rome, Italy
| | - Elisa Patacchini
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci-Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185, Rome, Italy
| | - Antonella Messore
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci-Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185, Rome, Italy
| | - Donatella Amatore
- Defense Institute for Biomedical Sciences, Via Santo Stefano Rotondo 4, 00184, Rome, Italy
| | - Giovanni Faggioni
- Defense Institute for Biomedical Sciences, Via Santo Stefano Rotondo 4, 00184, Rome, Italy
| | - Marco Artico
- Department of Sensory Organs, "Sapienza" Università di Roma, V.le Regina Elena 324, I-00161, Rome, Italy
| | - Daniela Iaconis
- EXSCALATE - Dompé Farmaceutici SpA, via Tommaso De Amicis 95, 80131, Napoli, Italy
| | - Carmine Talarico
- EXSCALATE - Dompé Farmaceutici SpA, via Tommaso De Amicis 95, 80131, Napoli, Italy
| | - Roberto Di Santo
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci-Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185, Rome, Italy
| | - Florigio Lista
- Defense Institute for Biomedical Sciences, Via Santo Stefano Rotondo 4, 00184, Rome, Italy
| | - Roberta Costi
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci-Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185, Rome, Italy.
| | - Enzo Tramontano
- Dipartimento di Scienze della vita e dell'ambiente. Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, SS-554, Monserrato, Cagliari, Italy.
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Mehyar N. Coronaviruses SARS-CoV, MERS-CoV, and SARS-CoV-2 helicase inhibitors: A systematic review of in vitro studies. J Virus Erad 2023:100327. [PMID: 37363132 PMCID: PMC10214743 DOI: 10.1016/j.jve.2023.100327] [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: 01/18/2023] [Revised: 05/11/2023] [Accepted: 05/22/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction The recent outbreak of SARS-CoV-2 significantly increased the need to find inhibitors that target the essential enzymes for virus replication in the host cells. This systematic review was conducted to identify potential inhibitors of SARS-CoV, MERS-CoV, and SARS-CoV-2 helicases that have been tested by in vitro methods. The inhibition mechanisms of these compounds were discussed in this review, in addition to their cytotoxic and viral infection protection properties. Methods The databases PUBMED/MEDLINE, EMBASE, SCOPUS, and Web of Science were searched using different combinations of the keywords "helicase", "nsp13", "inhibitors", "coronaviridae", "coronaviruses", "virus replication", "replication", and "antagonists and inhibitors". Results By the end of this search, a total of 6854 articles had been identified. Thirty-one articles were included in this review. These studies reported the inhibitory effects of 309 compounds on SARS-CoV, MERS-CoV, and SARS-CoV-2 helicase activities measured by in vitro methods. Helicase inhibitors were categorized according to the type of coronavirus and the type of tested enzymatic activity, nature, approval, inhibition level, cytotoxicity, and viral infection protection effects. These inhibitors are classified according to the site of their interaction with the coronavirus helicases into four types: zinc-binding site inhibitors, nucleic acid binding site inhibitors, nucleotide-binding site inhibitors, and inhibitors with no clear interaction site. Conclusion Evidence from in vitro studies suggests that helicase inhibitors have a high potential as antiviral agents. Several helicase inhibitors tested in vitro showed good antiviral activities while maintaining moderate cytotoxicity. These inhibitors should be clinically investigated to determine their efficiency in treating different coronavirus infections, particularly COVID-19.
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Affiliation(s)
- Nimer Mehyar
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Abdulaziz Medical City, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
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Srividya K, Mir SS, Thiyagarajan S, Nazir A. Dietary factors and SARS-CoV-2 contagion: in silico studies on modulation of viral and host proteins by spice actives. J Biomol Struct Dyn 2022; 40:10771-10782. [PMID: 34256681 DOI: 10.1080/07391102.2021.1948448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The SARS-CoV-2 contagion has had a huge impact on world population. It has been observed that despite massive spread of the contagion in India particularly during the second wave, the overall case fatality rates remain low. This prompted us to look into dietary factors that can possibly modulate the viral impact and/or host response. In silico studies were carried out on forty-two commonly used spices and their 637 known active compounds with an aim of identifying such compounds that may have propensity to reduce viral impact or boost host immune response. We chose to study SARS-Cov-2 helicase on account of its functional importance in maintaining viral load within the host, and the human tank binding protein (TBK1) for its important role in host immunity. We carried out in silico virtual screening, docking studies with 637 phytochemical against these two proteins, using in silico methods. Upon assessing the strength of the ligand-target interactions and post simulation binding energy profile, our study identifies procyanidin-B4 from bay leaf, fenugreekine from fenugreek seed and gallotannin from pomegranate seed as active interactors that docked to viral helicase. Similarly, we identified eruboside B from garlic, gallotannin from pomegranate seed, as strong interacting partners to human TBK1. Our studies thus present dietary spice constituents as potential protagonists for further experimentation to understand how spices in the diet might help the hosts in countering the viral assault and mount a robust protective response against COVID and other infections.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kottapalli Srividya
- Division of Neuroscience and Ageing Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Snober S Mir
- Department of Bioengineering, Integral University, Lucknow, India
| | | | - Aamir Nazir
- Division of Neuroscience and Ageing Biology, CSIR-Central Drug Research Institute, Lucknow, India
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6
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Chen YM, Wei JL, Qin RS, Hou JP, Zang GC, Zhang GY, Chen TT. Folic acid: a potential inhibitor against SARS-CoV-2 nucleocapsid protein. PHARMACEUTICAL BIOLOGY 2022; 60:862-878. [PMID: 35594385 PMCID: PMC9132477 DOI: 10.1080/13880209.2022.2063341] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 02/03/2022] [Accepted: 04/01/2022] [Indexed: 06/01/2023]
Abstract
CONTEXT Coronavirus disease 2019 is a global pandemic. Studies suggest that folic acid has antiviral effects. Molecular docking shown that folic acid can act on SARS-CoV-2 Nucleocapsid Phosphoprotein (SARS-CoV-2 N). OBJECTIVE To identify novel molecular therapeutic targets for SARS-CoV-2. MATERIALS AND METHODS Traditional Chinese medicine targets and virus-related genes were identified with network pharmacology and big data analysis. Folic acid was singled out by molecular docking, and its potential target SARS-CoV-2 N was identified. Inhibition of SARS-CoV-2 N of folic acid was verified at the cellular level. RESULTS In total, 8355 drug targets were potentially involved in the inhibition of SARS-CoV-2. 113 hub genes were screened by further association analysis between targets and virus-related genes. The hub genes related compounds were analysed and folic acid was screened as a potential new drug. Moreover, molecular docking showed folic acid could target on SARS-CoV-2 N which inhibits host RNA interference (RNAi). Therefore, this study was based on RNAi to verify whether folic acid antagonises SARS-CoV-2 N. Cell-based experiments shown that RNAi decreased mCherry expression by 81.7% (p < 0.001). This effect was decreased by 8.0% in the presence of SARS-CoV-2 N, indicating that SARS-CoV-2 N inhibits RNAi. With increasing of folic acid concentration, mCherry expression decreased, indicating that folic acid antagonises the regulatory effect of SARS-CoV-2 N on host RNAi. DISCUSSION AND CONCLUSIONS Folic acid may be an antagonist of SARS-CoV-2 N, but its effect on viruses unclear. In future, the mechanisms of action of folic acid against SARS-CoV-2 N should be studied.
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Affiliation(s)
- Yu-meng Chen
- Laboratory of Tissue and Cell Biology, Lab Teaching & Management Center, Chongqing Medical University, Chongqing, PR China
| | - Jin-lai Wei
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, PR China
| | - Rui-si Qin
- Laboratory of Tissue and Cell Biology, Lab Teaching & Management Center, Chongqing Medical University, Chongqing, PR China
| | - Jin-ping Hou
- General Surgery of Neonatal Surgery, Liangjiang District, Children's Hospital of Chongqing Medical University, Chongqing, PR China
| | - Guang-chao Zang
- Laboratory of Tissue and Cell Biology, Lab Teaching & Management Center, Chongqing Medical University, Chongqing, PR China
| | - Guang-yuan Zhang
- Laboratory of Tissue and Cell Biology, Lab Teaching & Management Center, Chongqing Medical University, Chongqing, PR China
- Pathogen Biology and Immunology Laboratory, Lab Teaching & Management Center, Chongqing Medical University, Chongqing, PR China
| | - Ting-ting Chen
- Laboratory of Tissue and Cell Biology, Lab Teaching & Management Center, Chongqing Medical University, Chongqing, PR China
- Pathogen Biology and Immunology Laboratory, Lab Teaching & Management Center, Chongqing Medical University, Chongqing, PR China
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Yazdi AK, Pakarian P, Perveen S, Hajian T, Santhakumar V, Bolotokova A, Li F, Vedadi M. Kinetic Characterization of SARS-CoV-2 nsp13 ATPase Activity and Discovery of Small-Molecule Inhibitors. ACS Infect Dis 2022; 8:1533-1542. [PMID: 35822715 PMCID: PMC9305828 DOI: 10.1021/acsinfecdis.2c00165] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Indexed: 11/29/2022]
Abstract
SARS-CoV-2 non-structural protein 13 (nsp13) is a highly conserved helicase and RNA 5'-triphosphatase. It uses the energy derived from the hydrolysis of nucleoside triphosphates for directional movement along the nucleic acids and promotes the unwinding of double-stranded nucleic acids. Nsp13 is essential for replication and propagation of all human and non-human coronaviruses. Combined with its defined nucleotide binding site and druggability, nsp13 is one of the most promising candidates for the development of pan-coronavirus therapeutics. Here, we report the development and optimization of bioluminescence assays for kinetic characterization of nsp13 ATPase activity in the presence and absence of single-stranded DNA. Screening of a library of 5000 small molecules in the presence of single-stranded DNA resulted in the discovery of six nsp13 small-molecule inhibitors with IC50 values ranging from 6 ± 0.5 to 50 ± 6 μM. In addition to providing validated methods for high-throughput screening of nsp13 in drug discovery campaigns, the reproducible screening hits we present here could potentially be chemistry starting points toward the development of more potent and selective nsp13 inhibitors, enabling the discovery of antiviral therapeutics.
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Affiliation(s)
| | - Paknoosh Pakarian
- Structural Genomics Consortium,
University of Toronto, Toronto, Ontario M5G 1L7,
Canada
| | - Sumera Perveen
- Structural Genomics Consortium,
University of Toronto, Toronto, Ontario M5G 1L7,
Canada
| | - Taraneh Hajian
- Structural Genomics Consortium,
University of Toronto, Toronto, Ontario M5G 1L7,
Canada
| | | | - Albina Bolotokova
- Structural Genomics Consortium,
University of Toronto, Toronto, Ontario M5G 1L7,
Canada
| | - Fengling Li
- Structural Genomics Consortium,
University of Toronto, Toronto, Ontario M5G 1L7,
Canada
| | - Masoud Vedadi
- Structural Genomics Consortium,
University of Toronto, Toronto, Ontario M5G 1L7,
Canada
- Department of Pharmacology and Toxicology,
University of Toronto, Toronto, Ontario M5S 1A8,
Canada
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8
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León-Gutiérrez G, Elste JE, Cabello-Gutiérrez C, Millán-Pacheco C, Martínez-Gómez MH, Mejía-Alvarez R, Tiwari V, Mejía A. A potent virucidal activity of functionalized TiO 2 nanoparticles adsorbed with flavonoids against SARS-CoV-2. Appl Microbiol Biotechnol 2022; 106:5987-6002. [PMID: 35951081 PMCID: PMC9366830 DOI: 10.1007/s00253-022-12112-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/22/2022] [Accepted: 07/27/2022] [Indexed: 12/24/2022]
Abstract
Abstract The coronavirus SARS-CoV-2 has caused a pandemic with > 550 millions of cases and > 6 millions of deaths worldwide. Medical management of COVID-19 relies on supportive care as no specific targeted therapies are available yet. Given its devastating effects on the economy and mental health, it is imperative to develop novel antivirals. An ideal candidate will be an agent that blocks the early events of viral attachment and cell entry, thereby preventing viral infection and spread. This work reports functionalized titanium dioxide (TiO2)-based nanoparticles adsorbed with flavonoids that block SARS-CoV-2 entry and fusion. Using molecular docking analysis, two flavonoids were chosen for their specific binding to critical regions of the SARS-CoV-2 spike glycoprotein that interacts with the host cell angiotensin-converting enzyme-2 (ACE-2) receptor. These flavonoids were adsorbed onto TiO2 functionalized nanoparticles (FTNP). This new nanoparticulate compound was assayed in vitro against two different coronaviruses; HCoV 229E and SARS-CoV-2, in both cases a clear antiviral effect was observed. Furthermore, using a reporter-based cell culture model, a potent antiviral activity is demonstrated. The adsorption of flavonoids to functionalized TiO2 nanoparticles induces a ~ threefold increase of that activity. These studies also indicate that FTNP interferes with the SARS-CoV-2 spike, impairing the cell fusion mechanism. Key points/Highlights • Unique TiO2nanoparticles displaying flavonoid showed potent anti-SARS-CoV-2 activity. • The nanoparticles precisely targeting SARS-CoV-2 were quantitatively verified by cell infectivity in vitro. • Flavonoids on nanoparticles impair the interactions between the spike glycoprotein and ACE-2 receptor. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1007/s00253-022-12112-9.
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Affiliation(s)
- Gabriela León-Gutiérrez
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, Ciudad de Mexico, Mexico
| | - James Edward Elste
- Department of Microbiology and Immunology, Midwestern University, Downers Grove, IL, USA
| | - Carlos Cabello-Gutiérrez
- Departamento de Virología e Investigación en Micología, Instituto Nacional de Enfermedades Respiratorias, Ciudad de Mexico, Mexico
| | - Cesar Millán-Pacheco
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Mario H Martínez-Gómez
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, Ciudad de Mexico, Mexico
| | - Rafael Mejía-Alvarez
- Department of Physiology, College of Graduate Studies, Midwestern University, Downers Grove, IL, USA
| | - Vaibhav Tiwari
- Department of Microbiology and Immunology, Midwestern University, Downers Grove, IL, USA
| | - Armando Mejía
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, Ciudad de Mexico, Mexico.
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9
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Zulkipli M, Mahbub N, Fatima A, Wan-Lin SL, Khoo TJ, Mahboob T, Rajagopal M, Samudi C, Kathirvalu G, Abdullah NH, Pinho AR, Oliveira SMR, Pereira MDL, Rahmatullah M, Hasan A, Paul AK, Butler MS, Nawaz M, Wilairatana P, Nissapatorn V, Wiart C. Isolation and Characterization of Werneria Chromene and Dihydroxyacidissimol from Burkillanthus malaccensis (Ridl.) Swingle. PLANTS (BASEL, SWITZERLAND) 2022; 11:1388. [PMID: 35684161 PMCID: PMC9182682 DOI: 10.3390/plants11111388] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
The secondary metabolites of endemic plants from the Rutaceae family, such as Burkillanthusmalaccensis (Ridl.) Swingle from the rainforest of Malaysia, has not been studied. Burkillanthusmalaccensis (Ridl.) Swingle may produce antibacterial and antibiotic-potentiating secondary metabolites. Hexane, chloroform, and methanol extracts of leaves, bark, wood, pericarps, and endocarps were tested against bacteria by broth microdilution assay and their antibiotic-potentiating activities. Chromatographic separations of hexane extracts of seeds were conducted to investigate effective phytochemicals and their antibacterial activities. Molecular docking studies of werneria chromene and dihydroxyacidissiminol against SARS-CoV-2 virus infection were conducted using AutoDock Vina. The methanol extract of bark inhibited the growth of Staphylococcusaureus, Escherichiacoli, and Pseudomonasaeruginosa with the minimum inhibitory concentration of 250, 500, and 250 µg/mL, respectively. The chloroform extract of endocarps potentiated the activity of imipenem against imipenem-resistant Acinetobacterbaumannii. The hexane extract of seeds increased the sensitivity of P. aeruginosa against ciprofloxacin and levofloxacin. The hexane extract of seeds and chloroform extract of endocarps were chromatographed, yielding werneria chromene and dihydroxyacidissiminol. Werneria chromene was bacteriostatic for P.aeruginosa and P.putida, with MIC/MBC values of 1000 > 1000 µg/mL. Dihydroxyacidissiminol showed the predicted binding energies of −8.1, −7.6, −7.0, and −7.5 kcal/mol with cathepsin L, nsp13 helicase, SARS-CoV-2 main protease, and SARS-CoV-2 spike protein receptor-binding domain S-RBD. Burkillanthusmalaccensis (Ridl.) Swingle can be a potential source of natural products with antibiotic-potentiating activity and that are anti-SARS-CoV-2.
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Affiliation(s)
- Masyitah Zulkipli
- School of Pharmacy, University of Nottingham Malaysia Campus, Semenyih 43500, Malaysia; (M.Z.); (N.M.); (S.L.W.-L.); (T.-J.K.)
| | - Nuzum Mahbub
- School of Pharmacy, University of Nottingham Malaysia Campus, Semenyih 43500, Malaysia; (M.Z.); (N.M.); (S.L.W.-L.); (T.-J.K.)
| | - Ayesha Fatima
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Istanbul 34093, Turkey;
| | - Stefanie Lim Wan-Lin
- School of Pharmacy, University of Nottingham Malaysia Campus, Semenyih 43500, Malaysia; (M.Z.); (N.M.); (S.L.W.-L.); (T.-J.K.)
| | - Teng-Jin Khoo
- School of Pharmacy, University of Nottingham Malaysia Campus, Semenyih 43500, Malaysia; (M.Z.); (N.M.); (S.L.W.-L.); (T.-J.K.)
| | - Tooba Mahboob
- Department of Medical Microbiology, University of Malaya, Kuala Lumpur 50603, Malaysia; (T.M.); (C.S.); (G.K.)
| | - Mogana Rajagopal
- Faculty of Pharmaceutical Sciences, UCSI University, Kuala Lumpur 56000, Malaysia;
| | - Chandramathi Samudi
- Department of Medical Microbiology, University of Malaya, Kuala Lumpur 50603, Malaysia; (T.M.); (C.S.); (G.K.)
| | - Gheetanjali Kathirvalu
- Department of Medical Microbiology, University of Malaya, Kuala Lumpur 50603, Malaysia; (T.M.); (C.S.); (G.K.)
| | - Nor Hayati Abdullah
- Natural Product Division, Forest Research Institute Malaysia (FRIM), Kepong 52109, Malaysia;
| | - Ana Rita Pinho
- Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal; (A.R.P.); (M.d.L.P.)
- Neuroscience and Signaling Laboratory, Institute of Biomedicine-IBIMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Sonia M. R. Oliveira
- CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal;
- Hunter Medical Research Institute (HMRI), New Lambton Heights, NSW 2305, Australia
| | - Maria de Lourdes Pereira
- Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal; (A.R.P.); (M.d.L.P.)
- CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Mohammed Rahmatullah
- Department of Biotechnology & Genetic Engineering, University of Development Alternative, Lalmatia, Dhaka 1207, Bangladesh; (M.R.); (A.H.)
| | - Anamul Hasan
- Department of Biotechnology & Genetic Engineering, University of Development Alternative, Lalmatia, Dhaka 1207, Bangladesh; (M.R.); (A.H.)
| | - Alok K. Paul
- School of Pharmacy and Pharmacology, University of Tasmania, Hobart, TAS 7001, Australia;
| | - Mark S. Butler
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia;
| | - Muhammad Nawaz
- Department of Nano-Medicine, Institute for Research and Medical Consultations (IRM), Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia;
| | - Polrat Wilairatana
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Veeranoot Nissapatorn
- School of Allied Health Sciences, World Union for Herbal Drug Discovery (WUHeDD), Research Excellence Center for Innovation and Health Products (RECIHP), Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Christophe Wiart
- Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Malaysia
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10
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Lee J, Kwon KH. Development of customized inner beauty products and customized cosmetics apps according to the use of NRF2 through DTC genetic testing after the COVID‐19 pandemic. J Cosmet Dermatol 2022; 21:2288-2297. [PMID: 35466548 PMCID: PMC9115250 DOI: 10.1111/jocd.14467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 04/02/2022] [Accepted: 09/08/2021] [Indexed: 10/26/2022]
Affiliation(s)
- Jinkyung Lee
- Division of Beauty Arts Care Department of Practical Arts Graduate School of Culture and Arts Dongguk University Seoul Republic of Korea
- Daily Beauty Unit Amorepacific Co. Seoul Republic of Korea
| | - Ki Han Kwon
- College of General Education Kookmin University Seoul Republic of Korea
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11
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Khazaneha M, Tajedini O, Esmaeili O, Abdi M, Khasseh AA, Sadatmoosavi A. Thematic evolution of coronavirus disease: a longitudinal co-word analysis. LIBRARY HI TECH 2022. [DOI: 10.1108/lht-10-2021-0370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PurposeUsing science mapping analysis approach and co-word analysis, the present study explores and visualizes research fields and thematic evolution of the coronavirus. Based on this method, one can get a picture of the real content of the themes in the mentioned thematic area and identify the main minor and emerging themes.Design/methodology/approachThis study was conducted based on co-word science mapping analysis under a longitudinal study (from 1988 to 2020). The collection of documents in this study was further divided into three subperiods: 1988–1998, 1999–2009 and 2010–2020. In order to perform science mapping analysis based on co-word bibliographic networks, SciMAT was utilized as a bibliometric tool. Moreover, WoS, PubMed and Scopus bibliographic databases were used to download all records.FindingsIn this study, strategic diagrams were demonstrated for the coronavirus research for a chronological period to assess the most relevant themes. Each diagram depended on the sum of documents linked to each research topic. In the first period (1988–1998), the most centralizations were on virology and evaluation of coronavirus structure and its structural and nonstructural proteins. In the second period (1999–2009), with due attention to high population density in eastern Asia and the increasing number of people affected with the new generation of coronavirus (named severe acute respiratory syndrome virus or SARS virus), publications have been concentrated on “antiviral activity.” In the third period (2010–2020), there was a tendency to investigate clinical syndromes, and most of the publications and citations were about hot topics like “severe acute respiratory syndrome,” “coronavirus” and “respiratory tract disease.” Scientometric analysis of the field of coronavirus can be regarded as a roadmap for future research and policymaking in this important area.Originality/valueThe originality of this research can be considered in two ways. First, the strategic diagrams of coronavirus are drawn in four thematic areas including motor cluster, basic and transversal cluster, highly developed cluster and emerging and declining cluster. Second, COVID-19 is mentioned as a hot topic of research.
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12
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Corona A, Wycisk K, Talarico C, Manelfi C, Milia J, Cannalire R, Esposito F, Gribbon P, Zaliani A, Iaconis D, Beccari AR, Summa V, Nowotny M, Tramontano E. Natural Compounds Inhibit SARS-CoV-2 nsp13 Unwinding and ATPase Enzyme Activities. ACS Pharmacol Transl Sci 2022; 5:226-239. [PMID: 35434533 PMCID: PMC9003574 DOI: 10.1021/acsptsci.1c00253] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Indexed: 12/27/2022]
Abstract
![]()
SARS-CoV-2 infection
is still spreading worldwide, and new antiviral
therapies are an urgent need to complement the approved vaccine preparations.
SARS-CoV-2 nps13 helicase is a validated drug target participating
in the viral replication complex and possessing two associated activities:
RNA unwinding and 5′-triphosphatase. In the search of SARS-CoV-2
direct antiviral agents, we established biochemical assays for both
SARS-CoV-2 nps13-associated enzyme activities and screened both in silico and in vitro a small in-house
library of natural compounds. Myricetin, quercetin, kaempferol, and
flavanone were found to inhibit the SARS-CoV-2 nps13 unwinding activity
at nanomolar concentrations, while licoflavone C was shown to block
both SARS-CoV-2 nps13 activities at micromolar concentrations. Mode
of action studies showed that all compounds are nsp13 noncompetitive
inhibitors versus ATP, while computational studies suggested that
they can bind both nucleotide and 5′-RNA nsp13 binding sites,
with licoflavone C showing a unique pattern of interaction with nsp13
amino acid residues. Overall, we report for the first time natural
flavonoids as selective inhibitors of SARS-CoV-2 nps13 helicase with
low micromolar activity.
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Affiliation(s)
- Angela Corona
- Dipartimento di Scienze della vita e dell'ambiente, Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, SS-554, 09042 Monserrato, Cagliari, Italy
| | - Krzysztof Wycisk
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Ks. Trojdena 4, Warsaw 02-109, Poland
| | - Carmine Talarico
- Dompé Farmaceutici SpA, via Campo di Pile, 67100 L'Aquila, Italy
| | - Candida Manelfi
- Dompé Farmaceutici SpA, via Campo di Pile, 67100 L'Aquila, Italy
| | - Jessica Milia
- Dipartimento di Scienze della vita e dell'ambiente, Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, SS-554, 09042 Monserrato, Cagliari, Italy
| | - Rolando Cannalire
- Department of Pharmacy, University of Napoli "Federico II", via D. Montesano 49, Napoli 80131, Italy
| | - Francesca Esposito
- Dipartimento di Scienze della vita e dell'ambiente, Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, SS-554, 09042 Monserrato, Cagliari, Italy
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany.,Fraunhofer Cluster of Excellence for Immune Mediated Diseases (CIMD), Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany.,Fraunhofer Cluster of Excellence for Immune Mediated Diseases (CIMD), Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Daniela Iaconis
- Dompé Farmaceutici SpA, via Campo di Pile, 67100 L'Aquila, Italy
| | - Andrea R Beccari
- Dompé Farmaceutici SpA, via Campo di Pile, 67100 L'Aquila, Italy
| | - Vincenzo Summa
- Department of Pharmacy, University of Napoli "Federico II", via D. Montesano 49, Napoli 80131, Italy
| | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Ks. Trojdena 4, Warsaw 02-109, Poland
| | - Enzo Tramontano
- Dipartimento di Scienze della vita e dell'ambiente, Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, SS-554, 09042 Monserrato, Cagliari, Italy
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13
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Agraharam G, Girigoswami A, Girigoswami K. Myricetin: a Multifunctional Flavonol in Biomedicine. CURRENT PHARMACOLOGY REPORTS 2022; 8:48-61. [PMID: 35036292 PMCID: PMC8743163 DOI: 10.1007/s40495-021-00269-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 11/17/2021] [Indexed: 12/13/2022]
Abstract
PURPOSE OF REVEIW The root cause of many diseases like CVD, cancer, and aging is free radicals which exert their effect by interfering with different metabolic pathways. The sources of free radicals can be exogenous, like UV rays from sunlight, and endogenous due to different metabolic by-products.In our body, there are defense mechanisms present, such as antioxidant enzymes and antioxidant molecules to combat these free radicals, but if there is an overload of these free radicals in our body, the defense system may not be sufficient to neutralize these free radicals. In such situations, we are exposed to a chronic low dose of oxidants creating oxidative stress, which is responsible for eliciting different diseases. RECENT FINDINGS Pubmed and Google Scholar are the search engines used to sort out relevant papers on myricetin and its role in combating many diseases. Myricetin is present in many fruits and vegetables and is a known antioxidant. It can elevate the antioxidant enzyme levels; reduces the lipid peroxidation; and is known to protect against cancer. In the case of myocardial dysfunction, myricetin has been shown to suppress the inflammatory cytokines and reduced the mortality rate. Myricetin has also been found to reduce platelet aggregation and control the viral infections by interfering in the DNA replication pathways. SUMMARY In this paper, we have briefly reviewed about the different type and site of free radicals and the role of myricetin in addressing the ROS and different diseases.
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Affiliation(s)
- Gopikrishna Agraharam
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, 603103 Tamilnadu India
| | - Agnishwar Girigoswami
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, 603103 Tamilnadu India
| | - Koyeli Girigoswami
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, 603103 Tamilnadu India
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14
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A Complexed Crystal Structure of a Single-Stranded DNA-Binding Protein with Quercetin and the Structural Basis of Flavonol Inhibition Specificity. Int J Mol Sci 2022; 23:ijms23020588. [PMID: 35054774 PMCID: PMC8775380 DOI: 10.3390/ijms23020588] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/29/2021] [Accepted: 01/04/2022] [Indexed: 02/04/2023] Open
Abstract
Single-stranded DNA (ssDNA)-binding protein (SSB) plays a crucial role in DNA replication, repair, and recombination as well as replication fork restarts. SSB is essential for cell survival and, thus, is an attractive target for potential antipathogen chemotherapy. Whether naturally occurring products can inhibit SSB remains unknown. In this study, the effect of the flavonols myricetin, quercetin, kaempferol, and galangin on the inhibition of Pseudomonas aeruginosa SSB (PaSSB) was investigated. Furthermore, SSB was identified as a novel quercetin-binding protein. Through an electrophoretic mobility shift analysis, myricetin could inhibit the ssDNA binding activity of PaSSB with an IC50 of 2.8 ± 0.4 μM. The effect of quercetin, kaempferol, and galangin was insignificant. To elucidate the flavonol inhibition specificity, the crystal structure of PaSSB complexed with the non-inhibitor quercetin was solved using the molecular replacement method at a resolution of 2.3 Å (PDB entry 7VUM) and compared with a structure with the inhibitor myricetin (PDB entry 5YUN). Although myricetin and quercetin bound PaSSB at a similar site, their binding poses were different. Compared with myricetin, the aromatic ring of quercetin shifted by a distance of 4.9 Å and an angle of 31° for hydrogen bonding to the side chain of Asn108 in PaSSB. In addition, myricetin occupied and interacted with the ssDNA binding sites Lys7 and Glu80 in PaSSB whereas quercetin did not. This result might explain why myricetin could, but quercetin could not, strongly inhibit PaSSB. This molecular evidence reveals the flavonol inhibition specificity and also extends the interactomes of the natural anticancer products myricetin and quercetin to include the OB-fold protein SSB.
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15
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Hao S, Ning K, Küz ÇA, McFarlin S, Cheng F, Qiu J. Eight years' advances on Bourbon virus, a tick-born Thogotovirus of the Orthomyxovirus family. ZOONOSES (BURLINGTON, MASS.) 2022; 2:18. [PMID: 35727718 PMCID: PMC9206863 DOI: 10.15212/zoonoses-2022-0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Bourbon virus (BRBV) was first isolated from a blood sample collected from a male patient living in Bourbon county, Kansas, during the spring of 2014. The patient later died due to complications associated with multiorgan failure. Currently, several BRBV infection-caused deaths have been reported in the United States, and misdiagnosed cases are often undercounted. BRBV is a member of the genus Thogotovirus of the Orthomyxoviridae family, and is transmitted through the Lone Star tick, Amblyomma Americanum, in North America. Currently, there are no specific antivirals or vaccinations available to treat or prevent BRBV infection. Several small molecular compounds have been identified to effectively inhibit BRBV infection of in vitro cell cultures at a single- or sub-micromolar level. Favipiravir, an RNA-dependent RNA polymerase inhibitor, prevented the death of Type I interferon receptor knockout mice infected with BRBV infection.
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Affiliation(s)
| | | | | | | | | | - Jianming Qiu
- Corresponding author: Jianming Qiu, Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Mail Stop 3029, 3901 Rainbow Blvd. Kansas City, KS 66160, Phone: (913) 588-4329, Fax: (913) 588-7295,
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16
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In silico screening, SAR and kinetic studies of naturally occurring flavonoids against SARS CoV-2 main protease. ARAB J CHEM 2022; 15:103473. [PMID: 34909065 PMCID: PMC8502681 DOI: 10.1016/j.arabjc.2021.103473] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 10/03/2021] [Indexed: 12/20/2022] Open
Abstract
The Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) pandemic has become a global challenge based on its replication within the host cells that relies on non-structural proteins, protease (Mpro). Flavonoids, an important class of naturally occurring compounds with medicinal importance, are frequently available within fruits and vegetables. Herein, we report the in silico studies on naturally occurring flavonoids consisting of molecular docking studies and evaluation of theoretical kinetics. In this study, we prepared a library of nine different classes of naturally occurring flavonoids and screened them on Autodock and Autodockvina. The pharmacokinetic properties of most promising compounds have been predicted through ADMET SAR, inhibition constants, ligand efficiency and ligand fit quality have been worked out theoretically. The results revealed that naturally occurring flavonoids could fit well in the receptor's catalytic pocket, interact with essential amino acid residues and could be useful for future drug candidates through in vitro and in vivo studies. Moreover, MD simulation studies were conducted for two most promising flavonoids and the protein-ligand complexes were found quite stable. The selected natural flavonoids are free from any toxic effects and can be consumed as a preventive measure against SARS CoV-2.
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17
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Zhang J, Li Q, Cruz Cosme RS, Gerzanich V, Tang Q, Simard JM, Zhao RY. Genome-wide characterization of SARS-CoV-2 cytopathogenic proteins in the search of antiviral targets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.11.23.469747. [PMID: 34845452 PMCID: PMC8629195 DOI: 10.1101/2021.11.23.469747] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Therapeutic inhibition of critical viral functions is important for curtailing coronavirus disease-2019 (COVID-19). We sought to identify antiviral targets through genome-wide characterization of SARS-CoV-2 proteins that are crucial for viral pathogenesis and that cause harmful cytopathic effects. All twenty-nine viral proteins were tested in a fission yeast cell-based system using inducible gene expression. Twelve proteins including eight non-structural proteins (NSP1, NSP3, NSP4, NSP5, NSP6, NSP13, NSP14 and NSP15) and four accessory proteins (ORF3a, ORF6, ORF7a and ORF7b) were identified that altered cellular proliferation and integrity, and induced cell death. Cell death correlated with the activation of cellular oxidative stress. Of the twelve proteins, ORF3a was chosen for further study in mammalian cells. In human pulmonary and kidney epithelial cells, ORF3a induced cellular oxidative stress associated with apoptosis and necrosis, and caused activation of pro-inflammatory response with production of the cytokines TNF-α, IL-6, and IFN-β1, possibly through the activation of NF-κB. To further characterize the mechanism, we tested a natural ORF3a Beta variant, Q57H, and a mutant with deletion of the highly conserved residue, ΔG188. Compared to wild type ORF3a, the ΔG188 variant yielded more robust activation of cellular oxidative stress, cell death, and innate immune response. Since cellular oxidative stress and inflammation contribute to cell death and tissue damage linked to the severity of COVID-19, our findings suggest that ORF3a is a promising, novel therapeutic target against COVID-19.
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Affiliation(s)
- Jiantao Zhang
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Qi Li
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Ruth S. Cruz Cosme
- Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Volodymyr Gerzanich
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Qiyi Tang
- Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD 21201
| | - J. Marc Simard
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Richard Y. Zhao
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201
- Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD 21201
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18
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Nanotechnology Applications of Flavonoids for Viral Diseases. Pharmaceutics 2021; 13:pharmaceutics13111895. [PMID: 34834309 PMCID: PMC8625292 DOI: 10.3390/pharmaceutics13111895] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/14/2021] [Accepted: 11/01/2021] [Indexed: 12/14/2022] Open
Abstract
Recent years have witnessed the emergence of several viral diseases, including various zoonotic diseases such as the current pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Other viruses, which possess pandemic-causing potential include avian flu, Ebola, dengue, Zika, and Nipah virus, as well as the re-emergence of SARS (Severe Acute Respiratory Syndrome) and MERS (Middle East Respiratory Syndrome) coronaviruses. Notably, effective drugs or vaccines against these viruses are still to be discovered. All the newly approved vaccines against the SARS-CoV-2-induced disease COVID-19 possess real-time possibility of becoming obsolete because of the development of ‘variants of concern’. Flavonoids are being increasingly recognized as prophylactic and therapeutic agents against emerging and old viral diseases. Around 10,000 natural flavonoid compounds have been identified, being phytochemicals, all plant-based. Flavonoids have been reported to have lesser side effects than conventional anti-viral agents and are effective against more viral diseases than currently used anti-virals. Despite their abundance in plants, which are a part of human diet, flavonoids have the problem of low bioavailability. Various attempts are in progress to increase the bioavailability of flavonoids, one of the promising fields being nanotechnology. This review is a narrative of some anti-viral dietary flavonoids, their bioavailability, and various means with an emphasis on the nanotechnology system(s) being experimented with to deliver anti-viral flavonoids, whose systems show potential in the efficient delivery of flavonoids, resulting in increased bioavailability.
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19
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Liu Q, Wan J, Wang G. A survey on computational methods in discovering protein inhibitors of SARS-CoV-2. Brief Bioinform 2021; 23:6384382. [PMID: 34623382 PMCID: PMC8524468 DOI: 10.1093/bib/bbab416] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/25/2021] [Accepted: 09/12/2021] [Indexed: 12/13/2022] Open
Abstract
The outbreak of acute respiratory disease in 2019, namely Coronavirus Disease-2019 (COVID-19), has become an unprecedented healthcare crisis. To mitigate the pandemic, there are a lot of collective and multidisciplinary efforts in facilitating the rapid discovery of protein inhibitors or drugs against COVID-19. Although many computational methods to predict protein inhibitors have been developed [
1–
5], few systematic reviews on these methods have been published. Here, we provide a comprehensive overview of the existing methods to discover potential inhibitors of COVID-19 virus, so-called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). First, we briefly categorize and describe computational approaches by the basic algorithms involved in. Then we review the related biological datasets used in such predictions. Furthermore, we emphatically discuss current knowledge on SARS-CoV-2 inhibitors with the latest findings and development of computational methods in uncovering protein inhibitors against COVID-19.
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Affiliation(s)
- Qiaoming Liu
- Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang 150001, China
| | - Jun Wan
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Guohua Wang
- Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang 150001, China.,Information and Computer Engineering College, Northeast Forestry University, Harbin, Heilongjiang 150001, China
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Xing M, Cao Y, Ren C, Liu Y, Li J, Grierson D, Martin C, Sun C, Chen K, Xu C, Li X. Elucidation of myricetin biosynthesis in Morella rubra of the Myricaceae. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:411-425. [PMID: 34331782 DOI: 10.1111/tpj.15449] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/17/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
Flavonols are health-promoting bioactive compounds important for plant defense and human nutrition. Quercetin (Q) and kaempferol (K) biosynthesis have been studied extensively while little is known about myricetin (M) biosynthesis. The roles of flavonol synthases (FLSs) and flavonoid 3',5'-hydroxylase (F3'5'H) in M biosynthesis in Morella rubra, a member of the Myricaceae rich in M-based flavonols, were investigated. The level of MrFLS transcripts alone did not correlate well with the accumulation of M-based flavonols. However, combined transcript data for MrFLS1 and MrF3'5'H showed a good correlation with the accumulation of M-based flavonols in different tissues of M. rubra. Recombinant MrFLS1 and MrFLS2 proteins showed strong activity with dihydroquercetin (DHQ), dihydrokaempferol (DHK), and dihydromyricetin (DHM) as substrates, while recombinant MrF3'5'H protein preferred converting K to M, amongst a range of substrates. Tobacco (Nicotiana tabacum) overexpressing 35S::MrFLSs produced elevated levels of K-based and Q-based flavonols without affecting M-based flavonol levels, while tobacco overexpressing 35S::MrF3'5'H accumulated significantly higher levels of M-based flavonols. We conclude that M accumulation in M. rubra is affected by gene expression and enzyme specificity of FLS and F3'5'H as well as substrate availability. In the metabolic grid of flavonol biosynthesis, the strong activity of MrF3'5'H with K as substrate additionally promotes metabolic flux towards M in M. rubra.
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Affiliation(s)
- Mengyun Xing
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Yunlin Cao
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Chuanhong Ren
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Yilong Liu
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Jiajia Li
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Donald Grierson
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Cathie Martin
- Department of Metabolic Biology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Chongde Sun
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Kunsong Chen
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Changjie Xu
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Xian Li
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
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Dejani NN, Elshabrawy HA, Bezerra Filho CDSM, de Sousa DP. Anticoronavirus and Immunomodulatory Phenolic Compounds: Opportunities and Pharmacotherapeutic Perspectives. Biomolecules 2021; 11:biom11081254. [PMID: 34439920 PMCID: PMC8394099 DOI: 10.3390/biom11081254] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 08/14/2021] [Accepted: 08/15/2021] [Indexed: 02/06/2023] Open
Abstract
In 2019, COVID-19 emerged as a severe respiratory disease that is caused by the novel coronavirus, Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). The disease has been associated with high mortality rate, especially in patients with comorbidities such as diabetes, cardiovascular and kidney diseases. This could be attributed to dysregulated immune responses and severe systemic inflammation in COVID-19 patients. The use of effective antiviral drugs against SARS-CoV-2 and modulation of the immune responses could be a potential therapeutic strategy for COVID-19. Studies have shown that natural phenolic compounds have several pharmacological properties, including anticoronavirus and immunomodulatory activities. Therefore, this review discusses the dual action of these natural products from the perspective of applicability at COVID-19.
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Affiliation(s)
- Naiara Naiana Dejani
- Department of Physiology and Pathology, Federal University of Paraíba, João Pessoa 58051-900, Brazil;
| | - Hatem A. Elshabrawy
- Department of Molecular and Cellular Biology, College of Osteopathic Medicine, Sam Houston State University, Conroe, TX 77304, USA;
| | - Carlos da Silva Maia Bezerra Filho
- Department of Pharmaceutical Sciences, Federal University of Paraíba, João Pessoa 58051-900, Brazil;
- Postgraduate Program in Bioactive Natural and Synthetic Products, Federal University of Paraíba, João Pessoa 58051-900, Brazil
| | - Damião Pergentino de Sousa
- Department of Pharmaceutical Sciences, Federal University of Paraíba, João Pessoa 58051-900, Brazil;
- Postgraduate Program in Bioactive Natural and Synthetic Products, Federal University of Paraíba, João Pessoa 58051-900, Brazil
- Correspondence: ; Tel.: +55-83-3216-7347
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22
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Joshi RS, Jagdale SS, Bansode SB, Shankar SS, Tellis MB, Pandya VK, Chugh A, Giri AP, Kulkarni MJ. Discovery of potential multi-target-directed ligands by targeting host-specific SARS-CoV-2 structurally conserved main protease. J Biomol Struct Dyn 2021; 39:3099-3114. [PMID: 32329408 PMCID: PMC7212545 DOI: 10.1080/07391102.2020.1760137] [Citation(s) in RCA: 161] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 04/20/2020] [Indexed: 12/24/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has resulted in the current COVID-19 pandemic. Worldwide this disease has infected over 2.5 million individuals with a mortality rate ranging from 5 to 10%. There are several efforts going on in the drug discovery to control the SARS-CoV-2 viral infection. The main protease (MPro) plays a critical role in viral replication and maturation, thus can serve as the primary drug target. To understand the structural evolution of MPro, we have performed phylogenetic and Sequence Similarity Network analysis, that depicted divergence of Coronaviridae MPro in five clusters specific to viral hosts. This clustering was corroborated with the comparison of MPro structures. Furthermore, it has been observed that backbone and binding site conformations are conserved despite variation in some of the residues. These attributes can be exploited to repurpose available viral protease inhibitors against SARS-CoV-2 MPro. In agreement with this, we performed screening of ∼7100 molecules including active ingredients present in the Ayurvedic anti-tussive medicines, anti-viral phytochemicals and synthetic anti-virals against SARS-CoV-2 MPro as the primary target. We identified several natural molecules like δ-viniferin, myricitrin, taiwanhomoflavone A, lactucopicrin 15-oxalate, nympholide A, afzelin, biorobin, hesperidin and phyllaemblicin B that strongly binds to SARS-CoV-2 MPro. Intrestingly, these molecules also showed strong binding with other potential targets of SARS-CoV-2 infection like viral receptor human angiotensin-converting enzyme 2 (hACE-2) and RNA dependent RNA polymerase (RdRp). We anticipate that our approach for identification of multi-target-directed ligand will provide new avenues for drug discovery against SARS-CoV-2 infection.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rakesh S. Joshi
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Shounak S. Jagdale
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, India
| | - Sneha B. Bansode
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, India
| | - S. Shiva Shankar
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Meenakshi B. Tellis
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, India
- Department of Botany, Savitribai Phule Pune University, Pune, India
| | | | | | - Ashok P. Giri
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Mahesh J. Kulkarni
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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23
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Shiryaev VA, Klimochkin YN. Main Chemotypes of SARS-CoV-2 Reproduction Inhibitors. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2021. [PMCID: PMC8188765 DOI: 10.1134/s107042802105002x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The COVID-19 pandemic has forced scientists all over the world to focus their effort on searching for targeted drugs for coronavirus chemotherapy. The present review is an attempt to systematize low-molecular-weight compounds, including well-known pharmaceuticals and natural substances that have exhibited high anti-coronavirus activity, not in terms of action on their targets, but in terms of their structural type.
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Affiliation(s)
- V. A. Shiryaev
- Samara State Technical University, 443100 Samara, Russia
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24
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Spratt AN, Gallazzi F, Quinn TP, Lorson CL, Sönnerborg A, Singh K. Coronavirus helicases: attractive and unique targets of antiviral drug-development and therapeutic patents. Expert Opin Ther Pat 2021; 31:339-350. [PMID: 33593200 PMCID: PMC8074651 DOI: 10.1080/13543776.2021.1884224] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Introduction: Coronaviruses encode a helicase that is essential for viral replication and represents an excellent antiviral target. However, only a few coronavirus helicase inhibitors have been patented. These patents include drug-like compound SSYA10-001, aryl diketo acids (ADK), and dihydroxychromones. Additionally, adamantane-derived bananins, natural flavonoids, one acrylamide derivative [(E)-3-(furan-2-yl)-N-(4-sulfamoylphenyl)acrylamide], a purine derivative (7-ethyl-8-mercapto-3-methyl-3,7-dihydro-1 H-purine-2,6-dione), and a few bismuth complexes. The IC50 of patented inhibitors ranges between 0.82 μM and 8.95 μM, depending upon the assays used. Considering the urgency of clinical interventions against Coronavirus Disease-19 (COVID-19), it is important to consider developing antiviral portfolios consisting of small molecules. Areas covered: This review examines coronavirus helicases as antiviral targets, and the potential of previously patented and experimental compounds to inhibit the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) helicase. Expert opinion: Small molecule coronavirus helicase inhibitors represent attractive pharmacological modalities for the treatment of coronaviruses such as SARS-CoV and SARS-CoV-2. Rightfully so, the current emphasis is focused upon the development of vaccines. However, vaccines may not work for everyone and broad-based adoption of vaccinations is an increasingly challenging societal endeavor. Therefore, it is important to develop additional pharmacological antivirals against the highly conserved coronavirus helicases to broadly protect against this and subsequent coronavirus epidemics.
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Affiliation(s)
- Austin N Spratt
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Fabio Gallazzi
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.,Department of Chemistry, University of Missouri, Columbia, MO, USA
| | - Thomas P Quinn
- cDepartment of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Christian L Lorson
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.,dDepartment of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA
| | - Anders Sönnerborg
- eDivision of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Huddinge, Stockholm, Sweden.,fDepartment of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
| | - Kamal Singh
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.,Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA.,Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Huddinge, Stockholm, Sweden.,gSanctum Therapeutics Corporation, Sunnyvale, CA, USA
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25
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Wu YH, Yeh IJ, Phan NN, Yen MC, Hung JH, Chiao CC, Chen CF, Sun Z, Hsu HP, Wang CY, Lai MD. Gene signatures and potential therapeutic targets of Middle East respiratory syndrome coronavirus (MERS-CoV)-infected human lung adenocarcinoma epithelial cells. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2021; 54:845-857. [PMID: 34176764 PMCID: PMC7997684 DOI: 10.1016/j.jmii.2021.03.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 12/03/2020] [Accepted: 03/07/2021] [Indexed: 12/23/2022]
Abstract
Background Pathogenic coronaviruses include Middle East respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus (SARS-CoV), and SARS-CoV-2. These viruses have induced outbreaks worldwide, and there are currently no effective medications against them. Therefore, there is an urgent need to develop potential drugs against coronaviruses. Methods High-throughput technology is widely used to explore differences in messenger (m)RNA and micro (mi)RNA expression profiles, especially to investigate protein–protein interactions and search for new therapeutic compounds. We integrated miRNA and mRNA expression profiles in MERS-CoV-infected cells and compared them to mock-infected controls from public databases. Results Through the bioinformatics analysis, there were 251 upregulated genes and eight highly differentiated miRNAs that overlapped in the two datasets. External validation verified that these genes had high expression in MERS-CoV-infected cells, including RC3H1, NF-κB, CD69, TNFAIP3, LEAP-2, DUSP10, CREB5, CXCL2, etc. We revealed that immune, olfactory or sensory system-related, and signal-transduction networks were discovered from upregulated mRNAs in MERS-CoV-infected cells. In total, 115 genes were predicted to be related to miRNAs, with the intersection of upregulated mRNAs and miRNA-targeting prediction genes such as TCF4, NR3C1, and POU2F2. Through the Connectivity Map (CMap) platform, we suggested potential compounds to use against MERS-CoV infection, including diethylcarbamazine, harpagoside, bumetanide, enalapril, and valproic acid. Conclusions The present study illustrates the crucial roles of miRNA-mRNA interacting networks in MERS-CoV-infected cells. The genes we identified are potential targets for treating MERS-CoV infection; however, these could possibly be extended to other coronavirus infections.
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Affiliation(s)
- Yen-Hung Wu
- Department of Emergency Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - I-Jeng Yeh
- Department of Emergency Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Nam Nhut Phan
- NTT Institute of Hi-Technology, Nguyen Tat Thanh University, Ho Chi Minh City, Viet Nam
| | - Meng-Chi Yen
- Department of Emergency Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Jui-Hsiang Hung
- Department of Biotechnology, Chia Nan University of Pharmacy and Science, Tainan 71710, Taiwan
| | - Chung-Chieh Chiao
- School of Chinese Medicine for Post-Baccalaureate, I-Shou University, Kaohsiung 82445, Taiwan
| | - Chien-Fu Chen
- School of Chinese Medicine for Post-Baccalaureate, I-Shou University, Kaohsiung 82445, Taiwan
| | - Zhengda Sun
- Kaiser Permanente, Northern California Regional Laboratories, The Permanente Medical Group, 1725 Eastshore Hwy, Berkeley, CA 94710, USA
| | - Hui-Ping Hsu
- Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan; Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN37232, USA.
| | - Chih-Yang Wang
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan.
| | - Ming-Derg Lai
- Department of Biochemistry and Molecular Biology, National Cheng Kung University, Tainan 70101, Taiwan; Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan.
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Zhang J, Li Q, Cruz Cosme RS, Gerzanich V, Tang Q, Simard JM, Zhao RY. Genome-Wide Characterization of SARS-CoV-2 Cytopathogenic Proteins in the Search of Antiviral Targets. mBio 2021; 13:e0016922. [PMID: 35164548 PMCID: PMC8844912 DOI: 10.1128/mbio.00169-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 12/11/2022] Open
Abstract
Therapeutic inhibition of critical viral functions is important for curtailing coronavirus disease 2019 (COVID-19). We sought to identify antiviral targets through the genome-wide characterization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins that are crucial for viral pathogenesis and that cause harmful cytopathogenic effects. All 29 viral proteins were tested in a fission yeast cell-based system using inducible gene expression. Twelve proteins, including eight nonstructural proteins (NSP1, NSP3, NSP4, NSP5, NSP6, NSP13, NSP14, and NSP15) and four accessory proteins (ORF3a, ORF6, ORF7a, and ORF7b), were identified that altered cellular proliferation and integrity and induced cell death. Cell death correlated with the activation of cellular oxidative stress. Of the 12 proteins, ORF3a was chosen for further study in mammalian cells because it plays an important role in viral pathogenesis and its activities are linked to lung tissue damage and a cytokine storm. In human pulmonary and kidney epithelial cells, ORF3a induced cellular oxidative stress associated with apoptosis and necrosis and caused activation of proinflammatory response with production of the cytokines tumor necrosis factor alpha (TNF-α), interleukin-6 (IL-6), and IFN-β1, possibly through the activation of nuclear factor kappa B (NF-κB). To further characterize the mechanism, we tested a natural ORF3a Beta variant, Q57H, and a mutant with deletion of the highly conserved residue, ΔG188. Compared with wild-type ORF3a, the ΔG188 variant yielded more robust activation of cellular oxidative stress, cell death, and innate immune response. Since cellular oxidative stress and inflammation contribute to cell death and tissue damage linked to the severity of COVID-19, our findings suggest that ORF3a is a promising, novel therapeutic target against COVID-19. IMPORTANCE The ongoing COVID-19 pandemic caused by SARS-CoV-2 has claimed over 5.5 million lives with more than 300 million people infected worldwide. While vaccines are effective, the emergence of new viral variants could jeopardize vaccine protection. Treatment of COVID-19 by antiviral drugs provides an alternative to battle against the disease. The goal of this study was to identify viral therapeutic targets that can be used in antiviral drug discovery. Utilizing a genome-wide functional analysis in a fission yeast cell-based system, we identified 12 viral candidates, including ORF3a, which cause cellular oxidative stress, inflammation, apoptosis, and necrosis that contribute to cytopathogenicity and COVID-19. Our findings indicate that antiviral agents targeting ORF3a could have a great impact on COVID-19.
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Affiliation(s)
- Jiantao Zhang
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Research & Development Service, VA Maryland Health Care System, Baltimore, Maryland, USA
| | - Qi Li
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Ruth S. Cruz Cosme
- Surgical Care Clinical Center, VA Maryland Health Care System, Baltimore, Maryland, USA
| | - Volodymyr Gerzanich
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Research & Development Service, VA Maryland Health Care System, Baltimore, Maryland, USA
| | - Qiyi Tang
- Department of Microbiology, Howard University College of Medicine, Washington, DC, USA
| | - J. Marc Simard
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Surgical Care Clinical Center, VA Maryland Health Care System, Baltimore, Maryland, USA
| | - Richard Y. Zhao
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Institute of Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Research & Development Service, VA Maryland Health Care System, Baltimore, Maryland, USA
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27
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Mapping major SARS-CoV-2 drug targets and assessment of druggability using computational fragment screening: Identification of an allosteric small-molecule binding site on the Nsp13 helicase. PLoS One 2021; 16:e0246181. [PMID: 33596235 PMCID: PMC7888625 DOI: 10.1371/journal.pone.0246181] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/14/2021] [Indexed: 01/18/2023] Open
Abstract
The 2019 emergence of, SARS-CoV-2 has tragically taken an immense toll on human life and far reaching impacts on society. There is a need to identify effective antivirals with diverse mechanisms of action in order to accelerate preclinical development. This study focused on five of the most established drug target proteins for direct acting small molecule antivirals: Nsp5 Main Protease, Nsp12 RNA-dependent RNA polymerase, Nsp13 Helicase, Nsp16 2'-O methyltransferase and the S2 subunit of the Spike protein. A workflow of solvent mapping and free energy calculations was used to identify and characterize favorable small-molecule binding sites for an aromatic pharmacophore (benzene). After identifying the most favorable sites, calculated ligand efficiencies were compared utilizing computational fragment screening. The most favorable sites overall were located on Nsp12 and Nsp16, whereas the most favorable sites for Nsp13 and S2 Spike had comparatively lower ligand efficiencies relative to Nsp12 and Nsp16. Utilizing fragment screening on numerous possible sites on Nsp13 helicase, we identified a favorable allosteric site on the N-terminal zinc binding domain (ZBD) that may be amenable to virtual or biophysical fragment screening efforts. Recent structural studies of the Nsp12:Nsp13 replication-transcription complex experimentally corroborates ligand binding at this site, which is revealed to be a functional Nsp8:Nsp13 protein-protein interaction site in the complex. Detailed structural analysis of Nsp13 ZBD conformations show the role of induced-fit flexibility in this ligand binding site and identify which conformational states are associated with efficient ligand binding. We hope that this map of over 200 possible small-molecule binding sites for these drug targets may be of use for ongoing discovery, design, and drug repurposing efforts. This information may be used to prioritize screening efforts or aid in the process of deciphering how a screening hit may bind to a specific target protein.
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28
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Goris T, Pérez‐Valero Á, Martínez I, Yi D, Fernández‐Calleja L, San León D, Bornscheuer UT, Magadán‐Corpas P, Lombó F, Nogales J. Repositioning microbial biotechnology against COVID-19: the case of microbial production of flavonoids. Microb Biotechnol 2021; 14:94-110. [PMID: 33047877 PMCID: PMC7675739 DOI: 10.1111/1751-7915.13675] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 12/19/2022] Open
Abstract
Coronavirus-related disease 2019 (COVID-19) became a pandemic in February 2020, and worldwide researchers try to tackle the disease with approved drugs of all kinds, or to develop novel compounds inhibiting viral spreading. Flavonoids, already investigated as antivirals in general, also might bear activities specific for the viral agent causing COVID-19, SARS-CoV-2. Microbial biotechnology and especially synthetic biology may help to produce flavonoids, which are exclusive plant secondary metabolites, at a larger scale or indeed to find novel pharmaceutically active flavonoids. Here, we review the state of the art in (i) antiviral activity of flavonoids specific for coronaviruses and (ii) results derived from computational studies, mostly docking studies mainly inhibiting specific coronaviral proteins such as the 3CL (main) protease, the spike protein or the RNA-dependent RNA polymerase. In the end, we strive towards a synthetic biology pipeline making the fast and tailored production of valuable antiviral flavonoids possible by applying the last concepts of division of labour through co-cultivation/microbial community approaches to the DBTL (Design, Build, Test, Learn) principle.
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Affiliation(s)
- Tobias Goris
- Department of Molecular Toxicology, Research Group Intestinal MicrobiologyGerman Institute of Human Nutrition Potsdam‐RehbrueckeArthur‐Scheunert‐Allee 114‐116NuthetalBrandenburg14558Germany
| | - Álvaro Pérez‐Valero
- Research Unit “Biotechnology in Nutraceuticals and Bioactive Compounds‐BIONUC”Departamento de Biología Funcional, Área de MicrobiologíaUniversidad de OviedoOviedoSpain
- Instituto Universitario de Oncología del Principado de AsturiasOviedoSpain
- Instituto de Investigación Sanitaria del Principado de AsturiasOviedoSpain
| | - Igor Martínez
- Department of Systems BiologyCentro Nacional de BiotecnologíaCSICMadridSpain
| | - Dong Yi
- Department of Biotechnology & Enzyme CatalysisInstitute of BiochemistryUniversity GreifswaldFelix‐Hausdorff‐Str. 4GreifswaldD‐17487Germany
| | - Luis Fernández‐Calleja
- Research Unit “Biotechnology in Nutraceuticals and Bioactive Compounds‐BIONUC”Departamento de Biología Funcional, Área de MicrobiologíaUniversidad de OviedoOviedoSpain
- Instituto Universitario de Oncología del Principado de AsturiasOviedoSpain
- Instituto de Investigación Sanitaria del Principado de AsturiasOviedoSpain
| | - David San León
- Department of Systems BiologyCentro Nacional de BiotecnologíaCSICMadridSpain
| | - Uwe T. Bornscheuer
- Department of Biotechnology & Enzyme CatalysisInstitute of BiochemistryUniversity GreifswaldFelix‐Hausdorff‐Str. 4GreifswaldD‐17487Germany
| | - Patricia Magadán‐Corpas
- Research Unit “Biotechnology in Nutraceuticals and Bioactive Compounds‐BIONUC”Departamento de Biología Funcional, Área de MicrobiologíaUniversidad de OviedoOviedoSpain
- Instituto Universitario de Oncología del Principado de AsturiasOviedoSpain
- Instituto de Investigación Sanitaria del Principado de AsturiasOviedoSpain
| | - Felipe Lombó
- Research Unit “Biotechnology in Nutraceuticals and Bioactive Compounds‐BIONUC”Departamento de Biología Funcional, Área de MicrobiologíaUniversidad de OviedoOviedoSpain
- Instituto Universitario de Oncología del Principado de AsturiasOviedoSpain
- Instituto de Investigación Sanitaria del Principado de AsturiasOviedoSpain
| | - Juan Nogales
- Department of Systems BiologyCentro Nacional de BiotecnologíaCSICMadridSpain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy‐Spanish National Research Council (SusPlast‐CSIC)MadridSpain
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29
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Solnier J, Fladerer JP. Flavonoids: A complementary approach to conventional therapy of COVID-19? PHYTOCHEMISTRY REVIEWS : PROCEEDINGS OF THE PHYTOCHEMICAL SOCIETY OF EUROPE 2021; 20:773-795. [PMID: 32982616 PMCID: PMC7500502 DOI: 10.1007/s11101-020-09720-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 08/29/2020] [Indexed: 05/02/2023]
Abstract
COVID-19, the highly contagious novel disease caused by SARS-CoV-2, has become a major international concern as it has spread quickly all over the globe. However, scientific knowledge and therapeutic treatment options for this new coronavirus remain limited. Although previous outbreaks of human coronaviruses (CoVs) such as SARS and MERS stimulated research, there are, to date, no antiviral therapeutics available that specifically target these kinds of viruses. Natural compounds with a great diversity of chemical structures may provide an alternative approach for the discovery of new antivirals. In fact, numerous flavonoids were found to have antiviral effects against SARS-and MERS-CoV by mainly inhibiting the enzymes 3-chymotrypsin-like protease (3CLpro) and papain-like protease (PLpro). In this review, we specifically focused on the search for flavonoids, polyphenolic compounds, which are proven to be effective against human CoVs. We therefore summarized and analyzed the latest progress in research to identify flavonoids for antiviral therapy and proposed strategies for future work on medicinal plants against coronaviruses such as SARS-CoV-2. We discovered quercetin, herbacetin, and isobavachalcone as the most promising flavonoids with anti-CoV potential.
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Affiliation(s)
- Julia Solnier
- Institute of Pharmaceutical Sciences, Department of Pharmacognosy, University of Graz, Universitätsplatz 4, 8010 Graz, Austria
| | - Johannes-Paul Fladerer
- Institute of Pharmaceutical Sciences, Department of Pharmacognosy, University of Graz, Universitätsplatz 4, 8010 Graz, Austria
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30
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Monticolo F, Palomba E, De Santis R, Assentato L, Triscino V, Langella MC, Lanzotti V, Chiusano ML. anti-HCoV: A web resource to collect natural compounds against human coronaviruses. Trends Food Sci Technol 2020; 106:1-11. [PMID: 32982062 PMCID: PMC7505852 DOI: 10.1016/j.tifs.2020.09.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 07/29/2020] [Accepted: 09/14/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND A novel coronavirus, the SARS-CoV2, was revealed to be the cause of COVID19, the pandemic disease that already provoked more than 555.324 deaths in the world (July 10, 2020). No vaccine treatment has been defined against SARS-CoV2 or other human coronaviruses (HCoVs), including those causing epidemic infections, neither appropriate strategies for prevention and care are yet officially suggested. SCOPE AND APPROACH We reviewed scientific literature on natural compounds that were defined as potentially effective against human coronaviruses. Our desk research identified non-chemically modified natural compounds that were shown (in vitro) and/or predicted (in silico) to act against one or more phases of human coronaviruses cell cycle.We selected all available information, merged and annotated the data to define a comprehensive list of natural compounds, describing their chemical classification, the source, the action, the specific target in the viral infection. Our aim was to collect possible compounds for prevention and care against human coronaviruses. KEY FINDINGS AND CONCLUSIONS The definition of appropriate interventions against viral diseases need a comprehensive view on the infection dynamics and on necessary treatments. Viral targeting compounds to be exploited in food sciences could be of relevant interest to this aim.We collected 174 natural compounds showing effects against human infecting coronaviruses, providing a curated annotation on actions and targets.The data are available in anti-HCoV, a web accessible resource to be exploited for testing and in vivo trials. The website is here launched to favour a community based cooperative effort to call for contribution and expand the collection. To be ready to fight.
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Affiliation(s)
- Francesco Monticolo
- Department of Agricultural Sciences, Università degli studi di Napoli Federico II, Reggia di Portici - Via Università, 100 - 80055, Portici (NA), Italy
| | - Emanuela Palomba
- Department of Research Infrastructures for marine biological resources (RIMAR), Stazione Zoologica "Anton Dohrn", Villa Comunale 80121 - Napoli, Italy
| | - Rosa De Santis
- Department of Agricultural Sciences, Università degli studi di Napoli Federico II, Reggia di Portici - Via Università, 100 - 80055, Portici (NA), Italy
| | - Lorenzo Assentato
- Department of Agricultural Sciences, Università degli studi di Napoli Federico II, Reggia di Portici - Via Università, 100 - 80055, Portici (NA), Italy
| | - Viviana Triscino
- Department of Agricultural Sciences, Università degli studi di Napoli Federico II, Reggia di Portici - Via Università, 100 - 80055, Portici (NA), Italy
| | - Maria Chiara Langella
- Department of Agricultural Sciences, Università degli studi di Napoli Federico II, Reggia di Portici - Via Università, 100 - 80055, Portici (NA), Italy
| | - Virginia Lanzotti
- Department of Agricultural Sciences, Università degli studi di Napoli Federico II, Reggia di Portici - Via Università, 100 - 80055, Portici (NA), Italy
| | - Maria Luisa Chiusano
- Department of Agricultural Sciences, Università degli studi di Napoli Federico II, Reggia di Portici - Via Università, 100 - 80055, Portici (NA), Italy.,Department of Research Infrastructures for marine biological resources (RIMAR), Stazione Zoologica "Anton Dohrn", Villa Comunale 80121 - Napoli, Italy
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31
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Choudhry N, Zhao X, Xu D, Zanin M, Chen W, Yang Z, Chen J. Chinese Therapeutic Strategy for Fighting COVID-19 and Potential Small-Molecule Inhibitors against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). J Med Chem 2020; 63:13205-13227. [PMID: 32845145 PMCID: PMC7489051 DOI: 10.1021/acs.jmedchem.0c00626] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Indexed: 02/06/2023]
Abstract
The coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to more than 20 million people infected worldwide with an average mortality rate of 3.6%. This virus poses major challenges to public health, as it not only is highly contagious but also can be transmitted by asymptomatic infected individuals. COVID-19 is clinically difficult to manage due to a lack of specific antiviral drugs or vaccines. In this article, Chinese therapy strategies for treating COVID-19 patients, including current applications of traditional Chinese medicine (TCM), are comprehensively reviewed. Furthermore, 72 small molecules from natural products and TCM with reported antiviral activity against human coronaviruses (CoVs) are identified from published literature, and their potential applications in combating SARS-CoV-2 are discussed. Among these, the clinical efficacies of some accessible drugs such as remdesivir (RDV) and favipiravir (FPV) for COVID-19 are emphatically summarized. We hope this review provides a foundation for managing the worsening pandemic and developing antivirals against SARS-CoV-2.
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Affiliation(s)
- Namrta Choudhry
- Guangdong Provincial Key Laboratory of
Veterinary Pharmaceutics Development and Safety Evaluation, Guangdong
Laboratory for Lingnan Modern Agriculture, College of Veterinary
Medicine, South China Agricultural
University, Guangzhou 510642,
China
| | - Xin Zhao
- Guangdong Institute of
Analysis (China National Analytical Center,
Guangzhou), Guangzhou 510070,
China
| | - Dan Xu
- Guangdong Provincial Key Laboratory of
Veterinary Pharmaceutics Development and Safety Evaluation, Guangdong
Laboratory for Lingnan Modern Agriculture, College of Veterinary
Medicine, South China Agricultural
University, Guangzhou 510642,
China
| | - Mark Zanin
- State Key Laboratory of Respiratory
Disease, National Clinical Research Center for Respiratory Disease,
Guangzhou Institute of Respiratory Health, First
Affiliated Hospital of Guangzhou Medical
University, Guangzhou 510120,
China
- School of Public Health,
The University of Hong Kong, 7
Sassoon Road, Pokfulam, Hong Kong, SAR, China
| | - Weisan Chen
- Department of Biochemistry and
Genetics, La Trobe Institute for Molecular Science, La
Trobe University, Melbourne, Victoria 3086,
Australia
| | - Zifeng Yang
- State Key Laboratory of Respiratory
Disease, National Clinical Research Center for Respiratory Disease,
Guangzhou Institute of Respiratory Health, First
Affiliated Hospital of Guangzhou Medical
University, Guangzhou 510120,
China
| | - Jianxin Chen
- Guangdong Provincial Key Laboratory of
Veterinary Pharmaceutics Development and Safety Evaluation, Guangdong
Laboratory for Lingnan Modern Agriculture, College of Veterinary
Medicine, South China Agricultural
University, Guangzhou 510642,
China
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Silva LR, da Silva Santos-Júnior PF, de Andrade Brandão J, Anderson L, Bassi ÊJ, Xavier de Araújo-Júnior J, Cardoso SH, da Silva-Júnior EF. Druggable targets from coronaviruses for designing new antiviral drugs. Bioorg Med Chem 2020; 28:115745. [PMID: 33007557 PMCID: PMC7836322 DOI: 10.1016/j.bmc.2020.115745] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/26/2020] [Accepted: 08/29/2020] [Indexed: 01/18/2023]
Abstract
Severe respiratory infections were highlighted in the SARS-CoV outbreak in 2002, as well as MERS-CoV, in 2012. Recently, the novel CoV (COVID-19) has led to severe respiratory damage to humans and deaths in Asia, Europe, and Americas, which allowed the WHO to declare the pandemic state. Notwithstanding all impacts caused by Coronaviruses, it is evident that the development of new antiviral agents is an unmet need. In this review, we provide a complete compilation of all potential antiviral agents targeting macromolecular structures from these Coronaviruses (Coronaviridae), providing a medicinal chemistry viewpoint that could be useful for designing new therapeutic agents.
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Affiliation(s)
- Leandro Rocha Silva
- Chemistry and Biotechnology Institute, Federal University of Alagoas, Campus A.C. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil; Laboratory of Organic and Medicinal Synthesis, Federal University of Alagoas, Campus Arapiraca, Manoel Severino Barbosa Avenue, Arapiraca 57309-005, Brazil
| | | | - Júlia de Andrade Brandão
- IMUNOREG - Immunoregulation Research Group, Laboratory of Research in Virology and Immunology, Institute of Biological Sciences and Health, Federal University of Alagoas, Campus AC. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil
| | - Letícia Anderson
- IMUNOREG - Immunoregulation Research Group, Laboratory of Research in Virology and Immunology, Institute of Biological Sciences and Health, Federal University of Alagoas, Campus AC. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil; CESMAC University Center, Cônego Machado Street, Maceió 57051-160, Brazil
| | - Ênio José Bassi
- IMUNOREG - Immunoregulation Research Group, Laboratory of Research in Virology and Immunology, Institute of Biological Sciences and Health, Federal University of Alagoas, Campus AC. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil
| | - João Xavier de Araújo-Júnior
- Chemistry and Biotechnology Institute, Federal University of Alagoas, Campus A.C. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil; Laboratory of Medicinal Chemistry, Pharmaceutical Sciences Institute, Federal University of Alagoas, Campus A.C. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil
| | - Sílvia Helena Cardoso
- Laboratory of Organic and Medicinal Synthesis, Federal University of Alagoas, Campus Arapiraca, Manoel Severino Barbosa Avenue, Arapiraca 57309-005, Brazil
| | - Edeildo Ferreira da Silva-Júnior
- Chemistry and Biotechnology Institute, Federal University of Alagoas, Campus A.C. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil; Laboratory of Medicinal Chemistry, Pharmaceutical Sciences Institute, Federal University of Alagoas, Campus A.C. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil.
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Nadeau R, Shahryari Fard S, Scheer A, Hashimoto-Roth E, Nygard D, Abramchuk I, Chung YE, Bennett SAL, Lavallée-Adam M. Computational Identification of Human Biological Processes and Protein Sequence Motifs Putatively Targeted by SARS-CoV-2 Proteins Using Protein-Protein Interaction Networks. J Proteome Res 2020; 19:4553-4566. [PMID: 33103435 PMCID: PMC7640966 DOI: 10.1021/acs.jproteome.0c00422] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Indexed: 12/13/2022]
Abstract
While the COVID-19 pandemic is causing important loss of life, knowledge of the effects of the causative SARS-CoV-2 virus on human cells is currently limited. Investigating protein-protein interactions (PPIs) between viral and host proteins can provide a better understanding of the mechanisms exploited by the virus and enable the identification of potential drug targets. We therefore performed an in-depth computational analysis of the interactome of SARS-CoV-2 and human proteins in infected HEK 293 cells published by Gordon et al. (Nature2020, 583, 459-468) to reveal processes that are potentially affected by the virus and putative protein binding sites. Specifically, we performed a set of network-based functional and sequence motif enrichment analyses on SARS-CoV-2-interacting human proteins and on PPI networks generated by supplementing viral-host PPIs with known interactions. Using a novel implementation of our GoNet algorithm, we identified 329 Gene Ontology terms for which the SARS-CoV-2-interacting human proteins are significantly clustered in PPI networks. Furthermore, we present a novel protein sequence motif discovery approach, LESMoN-Pro, that identified 9 amino acid motifs for which the associated proteins are clustered in PPI networks. Together, these results provide insights into the processes and sequence motifs that are putatively implicated in SARS-CoV-2 infection and could lead to potential therapeutic targets.
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Affiliation(s)
- Rachel Nadeau
- Department of Biochemistry,
Microbiology and Immunology, University
of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Soroush Shahryari Fard
- Department of Biochemistry,
Microbiology and Immunology, University
of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Amit Scheer
- Department of Biochemistry,
Microbiology and Immunology, University
of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Emily Hashimoto-Roth
- Department of Biochemistry,
Microbiology and Immunology, University
of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Dallas Nygard
- Department of Biochemistry,
Microbiology and Immunology, University
of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Iryna Abramchuk
- Department of Biochemistry,
Microbiology and Immunology, University
of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Yun-En Chung
- Department of Biochemistry,
Microbiology and Immunology, University
of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Steffany A. L. Bennett
- Department of Biochemistry,
Microbiology and Immunology, University
of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- uOttawa Brain and Mind Research Institute, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- uOttawa Brain and Mind Research Institute, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Department of Chemistry and Biomolecular Sciences, Centre
for Catalysis and Research Innovation, University
of Ottawa, 150 Louis-Pasteur Pvt, Ottawa, Ontario K1N 6N5, Canada
| | - Mathieu Lavallée-Adam
- Department of Biochemistry,
Microbiology and Immunology, University
of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
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Metallodrug ranitidine bismuth citrate suppresses SARS-CoV-2 replication and relieves virus-associated pneumonia in Syrian hamsters. Nat Microbiol 2020; 5:1439-1448. [PMID: 33028965 DOI: 10.1038/s41564-020-00802-x] [Citation(s) in RCA: 123] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/21/2020] [Indexed: 12/15/2022]
Abstract
SARS-CoV-2 is causing a pandemic of COVID-19, with high infectivity and significant mortality1. Currently, therapeutic options for COVID-19 are limited. Historically, metal compounds have found use as antimicrobial agents, but their antiviral activities have rarely been explored. Here, we test a set of metallodrugs and related compounds, and identify ranitidine bismuth citrate, a commonly used drug for the treatment of Helicobacter pylori infection, as a potent anti-SARS-CoV-2 agent, both in vitro and in vivo. Ranitidine bismuth citrate exhibited low cytotoxicity and protected SARS-CoV-2-infected cells with a high selectivity index of 975. Importantly, ranitidine bismuth citrate suppressed SARS-CoV-2 replication, leading to decreased viral loads in both upper and lower respiratory tracts, and relieved virus-associated pneumonia in a golden Syrian hamster model. In vitro studies showed that ranitidine bismuth citrate and its related compounds exhibited inhibition towards both the ATPase (IC50 = 0.69 µM) and DNA-unwinding (IC50 = 0.70 µM) activities of the SARS-CoV-2 helicase via an irreversible displacement of zinc(II) ions from the enzyme by bismuth(III) ions. Our findings highlight viral helicase as a druggable target and the clinical potential of bismuth(III) drugs or other metallodrugs for the treatment of SARS-CoV-2 infection.
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35
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Coronaviruses and Nature's Pharmacy for the Relief of Coronavirus Disease 2019. ACTA ACUST UNITED AC 2020; 30:603-621. [PMID: 33041391 PMCID: PMC7537782 DOI: 10.1007/s43450-020-00104-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/14/2020] [Indexed: 12/16/2022]
Abstract
Current challenges to the treatment of coronavirus disease 2019 should open new prospects in the search for novel drugs from medicinal plants and other natural products. This paper provides details of natural agents that inhibit human coronavirus entry into cells, general replication, and specific chymotrypsin-like protease (3CLpro)-mediated replication. Medicinal plants, fungi, and marine organisms as remedies for human coronaviruses in China, Lebanon, Malaysia, Singapore, and South Africa are described. Common species include Alnus japonica (Thunb.) Steud., Artemisia annua L., Artemisia apiacea Hance, Astragalus membranaceus (Fisch.) Bunge, Cinnamomum cassia (L.) J.Presl, edible brown algae Ecklonia cava Kjellman, Euphorbia neriifolia L., Glycyrrhiza glabra L., Lonicera japonica Thunb., Pelargonium sidoides DC., Polygonum cuspidatum Siebold & Zucc., Sanguisorba officinalis L., Scutellaria baicalensis Georgi, Toona sinensis (Juss.) M.Roem., and Torreya nucifera (L.) Siebold & Zucc. At least fifty natural compounds, including alkaloids, flavonoids, glycosides, anthraquinones, lignins, and tannins, which inhibit various strains of human coronaviruses, are presented. Given the scarcity of efficacious and safe vaccines or drugs for coronavirus disease 2019, natural products are low-hanging fruits that should be harnessed as the new global frontier against severe acute respiratory syndrome coronavirus 2.
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36
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Senger MR, Evangelista TCS, Dantas RF, Santana MVDS, Gonçalves LCS, de Souza Neto LR, Ferreira SB, Silva-Junior FP. COVID-19: molecular targets, drug repurposing and new avenues for drug discovery. Mem Inst Oswaldo Cruz 2020; 115:e200254. [PMID: 33027420 PMCID: PMC7534958 DOI: 10.1590/0074-02760200254] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 09/01/2020] [Indexed: 01/18/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly contagious infection that may break the healthcare system of several countries. Here, we aimed at presenting a critical view of ongoing drug repurposing efforts for COVID-19 as well as discussing opportunities for development of new treatments based on current knowledge of the mechanism of infection and potential targets within. Finally, we also discuss patent protection issues, cost effectiveness and scalability of synthetic routes for some of the most studied repurposing candidates since these are key aspects to meet global demand for COVID-19 treatment.
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Affiliation(s)
- Mario Roberto Senger
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório
de Bioquímica Experimental e Computacional de Fármacos, Rio de Janeiro, RJ,
Brasil
| | - Tereza Cristina Santos Evangelista
- Universidade Federal do Rio de Janeiro, Instituto de Química,
Laboratório de Síntese Orgânica e Prospecção Biológica, Rio de Janeiro, RJ,
Brasil
| | - Rafael Ferreira Dantas
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório
de Bioquímica Experimental e Computacional de Fármacos, Rio de Janeiro, RJ,
Brasil
| | - Marcos Vinicius da Silva Santana
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório
de Bioquímica Experimental e Computacional de Fármacos, Rio de Janeiro, RJ,
Brasil
| | - Luiz Carlos Saramago Gonçalves
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório
de Bioquímica Experimental e Computacional de Fármacos, Rio de Janeiro, RJ,
Brasil
| | - Lauro Ribeiro de Souza Neto
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório
de Bioquímica Experimental e Computacional de Fármacos, Rio de Janeiro, RJ,
Brasil
| | - Sabrina Baptista Ferreira
- Universidade Federal do Rio de Janeiro, Instituto de Química,
Laboratório de Síntese Orgânica e Prospecção Biológica, Rio de Janeiro, RJ,
Brasil
| | - Floriano Paes Silva-Junior
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório
de Bioquímica Experimental e Computacional de Fármacos, Rio de Janeiro, RJ,
Brasil
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Hao S, Ning K, Wang X, Wang J, Cheng F, Ganaie SS, Tavis JE, Qiu J. Establishment of a Replicon Reporter of the Emerging Tick-Borne Bourbon Virus and Use It for Evaluation of Antivirals. Front Microbiol 2020; 11:572631. [PMID: 33013808 PMCID: PMC7506111 DOI: 10.3389/fmicb.2020.572631] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/21/2020] [Indexed: 01/01/2023] Open
Abstract
Bourbon virus (BRBV) was first isolated from a patient hospitalized at the University of Kansas Hospital in 2014. Since then, several deaths have been reported to be caused by BRBV infection in the Midwest and Southern United States. BRBV is a tick-borne virus that is widely carried by lone star ticks. It belongs to genus Thogotovirus of the Orthomyxoviridae family. Currently, there are no treatments or vaccines available for BRBV or thogotovirus infection caused diseases. In this study, we reconstituted a replicon reporter system, composed of plasmids expressing the RNA-dependent RNA polymerase (RdRP) complex (PA, PB1, and PB2), nucleocapsid (NP) protein, and a reporter gene flanked by the 3′ and 5′ untranslated region (UTR) of the envelope glycoprotein (GP) genome segment. By using the luciferase reporter, we screened a few small molecule compounds of anti-endonuclease that inhibited the nicking activity by parvovirus B19 (B19V) NS1, as well as FDA-approved drugs targeting the RdRP of influenza virus. Our results demonstrated that myricetin, an anti-B19V NS1 nicking inhibitor, efficiently inhibited the RdRP activity of BRBV and virus replication. The IC50 and EC50 of myricetin are 2.22 and 4.6 μM, respectively, in cells. Myricetin had minimal cytotoxicity in cells, and therefore the therapeutic index of the compound is high. In conclusion, the BRBV replicon system is a useful tool to study viral RNA replication and to develop antivirals, and myricetin may hold promise in treatment of BRBV infected patients.
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Affiliation(s)
- Siyuan Hao
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, United States
| | - Kang Ning
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, United States
| | - Xiaomei Wang
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, United States
| | - Jianke Wang
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, United States
| | - Fang Cheng
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, United States
| | - Safder S Ganaie
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, United States
| | - John E Tavis
- Department of Molecular Microbiology and Immunology, Saint Louis University St. Louis, MO, United States
| | - Jianming Qiu
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, United States
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Russo M, Moccia S, Spagnuolo C, Tedesco I, Russo GL. Roles of flavonoids against coronavirus infection. Chem Biol Interact 2020; 328:109211. [PMID: 32735799 PMCID: PMC7385538 DOI: 10.1016/j.cbi.2020.109211] [Citation(s) in RCA: 189] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/13/2020] [Accepted: 07/23/2020] [Indexed: 01/18/2023]
Abstract
In terms of public health, the 21st century has been characterized by coronavirus pandemics: in 2002-03 the virus SARS-CoV caused SARS; in 2012 MERS-CoV emerged and in 2019 a new human betacoronavirus strain, called SARS-CoV-2, caused the unprecedented COVID-19 outbreak. During the course of the current epidemic, medical challenges to save lives and scientific research aimed to reveal the genetic evolution and the biochemistry of the vital cycle of the new pathogen could lead to new preventive and therapeutic strategies against SARS-CoV-2. Up to now, there is no cure for COVID-19 and waiting for an efficacious vaccine, the development of "savage" protocols, based on "old" anti-inflammatory and anti-viral drugs represents a valid and alternative therapeutic approach. As an alternative or additional therapeutic/preventive option, different in silico and in vitro studies demonstrated that small natural molecules, belonging to polyphenol family, can interfere with various stages of coronavirus entry and replication cycle. Here, we reviewed the capacity of well-known (e.g. quercetin, baicalin, luteolin, hesperetin, gallocatechin gallate, epigallocatechin gallate) and uncommon (e.g. scutellarein, amentoflavone, papyriflavonol A) flavonoids, secondary metabolites widely present in plant tissues with antioxidant and anti-microbial functions, to inhibit key proteins involved in coronavirus infective cycle, such as PLpro, 3CLpro, NTPase/helicase. Due to their pleiotropic activities and lack of systemic toxicity, flavonoids and their derivative may represent target compounds to be tested in future clinical trials to enrich the drug arsenal against coronavirus infections.
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Affiliation(s)
| | | | | | | | - Gian Luigi Russo
- National Research Council, Institute of Food Sciences, 83100, Avellino, Italy.
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Di Matteo G, Spano M, Grosso M, Salvo A, Ingallina C, Russo M, Ritieni A, Mannina L. Food and COVID-19: Preventive/Co-therapeutic Strategies Explored by Current Clinical Trials and in Silico Studies. Foods 2020; 9:E1036. [PMID: 32752217 PMCID: PMC7466271 DOI: 10.3390/foods9081036] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/26/2020] [Accepted: 07/29/2020] [Indexed: 12/13/2022] Open
Abstract
Foods, food ingredients, and their balanced consumption are recognized to have an important role in achieving or maintaining a state of wellbeing by acting as carriers of functional components and bioactive molecules. However, the potential contribution of foods to consumers' health has so far only been partially exploited. The rapidly evolving scenario of the coronavirus disease 2019 (COVID-19) pandemic is stimulating profound reflection on the relationships between food and the etiological agent, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, the status of knowledge regarding food as a possible defense/co-therapeutic strategy against the SARS-CoV-2 coronavirus is considered through the discussion of two main current lines of research. One line of research relates to the role of micronutrients, food components, and diets in the strengthening of the immune system through clinical trials; formulations could be developed as immune system enhancers or as co-adjuvants in therapies. The other line of research relates to investigation of the chemical interactions that specific food compounds can have with host or virus targets so as to interfere with the viral infective cycle of SARS-CoV-2. This line requires, as a first step, an in silico evaluation to discover lead compounds, which may be further developed through drug-design studies, in vitro and in vivo tests, and, finally, clinical trials to obtain therapeutic molecules. All of these promising strategies promote the role of food in preventive/co-therapeutic strategies to tackle the COVID-19 pandemic.
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Affiliation(s)
- Giacomo Di Matteo
- Laboratory of Food Chemistry, Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, 00185 Rome, Italy; (G.D.M.); (M.S.); (A.S.); (C.I.); (L.M.)
| | - Mattia Spano
- Laboratory of Food Chemistry, Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, 00185 Rome, Italy; (G.D.M.); (M.S.); (A.S.); (C.I.); (L.M.)
| | - Michela Grosso
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, CEINGE-Biotecnologie Avanzate, 80131 Naples, Italy;
| | - Andrea Salvo
- Laboratory of Food Chemistry, Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, 00185 Rome, Italy; (G.D.M.); (M.S.); (A.S.); (C.I.); (L.M.)
| | - Cinzia Ingallina
- Laboratory of Food Chemistry, Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, 00185 Rome, Italy; (G.D.M.); (M.S.); (A.S.); (C.I.); (L.M.)
| | - Mariateresa Russo
- Department of Agriculture, Food Chemistry Safety and Sensoromic Laboratory (FoCuSS Lab), University of Reggio Calabria, 89124 Reggio Calabria, Italy;
| | - Alberto Ritieni
- Department of Pharmacy, School of Medicine, University of Naples Federico II, 80131 Naples, Italy
- UNESCO Chair of Health Education and Sustainable Development, University of Naples, 80131 Naples, Italy
| | - Luisa Mannina
- Laboratory of Food Chemistry, Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, 00185 Rome, Italy; (G.D.M.); (M.S.); (A.S.); (C.I.); (L.M.)
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Chledzik S, Strawa J, Matuszek K, Nazaruk J. Pharmacological Effects of Scutellarin, An Active Component of Genus Scutellaria and Erigeron: A Systematic Review. THE AMERICAN JOURNAL OF CHINESE MEDICINE 2018; 46:319-337. [PMID: 29433387 DOI: 10.1142/s0192415x18500167] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Flavonoid compound scutellarin (Scu) is quite frequently met in the plant kingdom, particularly in the genus Scutellaria (Lamiaceae) and Erigeron (Asteraceae). The extract of the herb of Erigeron breviscapus, containing this component in high amount, has been used for many years in traditional Chinese medicine. In recent years, studies have made great progress on the usefulness of Scu for treating various diseases by testing its mechanism of action. They support the traditional use of Scu rich plant in heart and cerebral ischemia. Scu can potentially be applied in Alzheimer's disease, Helicobacter pylori infection, vascular complications of diabetes and as an inhibitor of certain carcinomas. Various methods were designed to improve its isolation from plant material, solubility, absorption and bioavailability. On the basis of recent studies, it is suggested that Scu could be a promising candidate for new natural drug and deserves particular attention in further research and development.
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Affiliation(s)
- Sebastian Chledzik
- 1 Department of Pharmacognosy, Medical University of Bialystok, Bialystok, Poland
| | - Jakub Strawa
- 1 Department of Pharmacognosy, Medical University of Bialystok, Bialystok, Poland
| | - Katarzyna Matuszek
- 1 Department of Pharmacognosy, Medical University of Bialystok, Bialystok, Poland
| | - Jolanta Nazaruk
- 1 Department of Pharmacognosy, Medical University of Bialystok, Bialystok, Poland
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Flavonoids: promising natural compounds against viral infections. Arch Virol 2017; 162:2539-2551. [PMID: 28547385 PMCID: PMC7087220 DOI: 10.1007/s00705-017-3417-y] [Citation(s) in RCA: 256] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 04/05/2017] [Indexed: 01/12/2023]
Abstract
Flavonoids are widely distributed as secondary metabolites produced by plants and play important roles in plant physiology, having a variety of potential biological benefits such as antioxidant, anti-inflammatory, anticancer, antibacterial, antifungal and antiviral activity. Different flavonoids have been investigated for their potential antiviral activities and several of them exhibited significant antiviral properties in in vitro and even in vivo studies. This review summarizes the evidence for antiviral activity of different flavonoids, highlighting, where investigated, the cellular and molecular mechanisms of action on viruses. We also present future perspectives on therapeutic applications of flavonoids against viral infections.
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Wang Q, Wong G, Lu G, Yan J, Gao GF. MERS-CoV spike protein: Targets for vaccines and therapeutics. Antiviral Res 2016; 133:165-77. [PMID: 27468951 PMCID: PMC7113765 DOI: 10.1016/j.antiviral.2016.07.015] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 07/07/2016] [Accepted: 07/22/2016] [Indexed: 02/05/2023]
Abstract
The disease outbreak caused by Middle East respiratory syndrome coronavirus (MERS-CoV) is still ongoing in the Middle East. Over 1700 people have been infected since it was first reported in September 2012. Despite great efforts, licensed vaccines or therapeutics against MERS-CoV remain unavailable. The MERS-CoV spike (S) protein is an important viral antigen known to mediate host-receptor binding and virus entry, as well as induce robust humoral and cell-mediated responses in humans during infection. In this review, we highlight the importance of the S protein in the MERS-CoV life cycle, summarize recent advances in the development of vaccines and therapeutics based on the S protein, and discuss strategies that can be explored to develop new medical countermeasures against MERS-CoV. A licensed vaccine or therapeutic against MERS-CoV remains unavailable to date. The S protein plays a pivotal role for virus entry and thus is an ideal target for vaccine and antiviral development. DNA vaccines expressing the S protein merit further development for potential human application. nAbs and peptides targeting the S protein needs to be evaluated in NHPs before clinical trials.
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MESH Headings
- Animals
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/immunology
- Antiviral Agents/pharmacology
- Antiviral Agents/therapeutic use
- Coronavirus Infections/prevention & control
- Coronavirus Infections/therapy
- Drug Discovery
- Humans
- Middle East Respiratory Syndrome Coronavirus/immunology
- Middle East Respiratory Syndrome Coronavirus/physiology
- Receptors, Virus/chemistry
- Receptors, Virus/metabolism
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
- Structure-Activity Relationship
- Vaccines, DNA/immunology
- Vaccines, Subunit/immunology
- Vaccines, Virus-Like Particle/immunology
- Viral Vaccines/immunology
- Virus Internalization
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Affiliation(s)
- Qihui Wang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen 518112, China.
| | - Gary Wong
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen 518112, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences, Beijing 100101, China
| | - Guangwen Lu
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, China
| | - Jinghua Yan
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen 518112, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - George F Gao
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen 518112, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China.
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Myricetin: A Dietary Molecule with Diverse Biological Activities. Nutrients 2016; 8:90. [PMID: 26891321 PMCID: PMC4772053 DOI: 10.3390/nu8020090] [Citation(s) in RCA: 364] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 12/16/2015] [Accepted: 12/23/2015] [Indexed: 01/09/2023] Open
Abstract
Myricetin is a common plant-derived flavonoid and is well recognised for its nutraceuticals value. It is one of the key ingredients of various foods and beverages. The compound exhibits a wide range of activities that include strong anti-oxidant, anticancer, antidiabetic and anti-inflammatory activities. It displays several activities that are related to the central nervous system and numerous studies have suggested that the compound may be beneficial to protect against diseases such as Parkinson's and Alzheimer's. The use of myricetin as a preserving agent to extend the shelf life of foods containing oils and fats is attributed to the compound's ability to protect lipids against oxidation. A detailed search of existing literature revealed that there is currently no comprehensive review available on this important molecule. Hence, the present work includes the history, synthesis, pharmaceutical applications and toxicity studies of myricetin. This report also highlights structure-activity relationships and mechanisms of action for various biological activities.
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Huang YH, Huang CC, Chen CC, Yang KJ, Huang CY. Inhibition of Staphylococcus aureus PriA Helicase by Flavonol Kaempferol. Protein J 2016; 34:169-72. [PMID: 25894858 PMCID: PMC7088215 DOI: 10.1007/s10930-015-9609-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Staphylococcus aureus is an important etiological agent responsible for healthcare-associated infections. In this study, the effect of flavonoids on the inhibition of S. aureus PriA (SaPriA), an essential helicase for DNA replication restart, which is critical for bacterial survival, was investigated. Using vanadate-sensitive colorimetric assay, the concentration of phosphate, from ATP hydrolysis by SaPriA, was decreased to 37 and 69 %, respectively, in the presence of 35 μM kaempferol and myricetin. The effect of quercetin, galangin, dihydromyricetin, and myricitrin was insignificant. From titration curve, IC50 of kaempferol for SaPriA was determined to be 22 ± 2 μM. Using fluorescence quenching, we identified that kaempferol can bind to SaPriA with Kd of 9.1 ± 3.2 μM. To our knowledge, these preliminary results constituted the first study regarding that naturally occurring product such as flavonols kaempferol and myricetin can be potent inhibitors targeting PriA.
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Affiliation(s)
- Yen-Hua Huang
- School of Biomedical Sciences, Chung Shan Medical University, No. 110, Sec. 1, Chien-Kuo N. Rd., Taichung City, Taiwan
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Recent insights into the development of therapeutics against coronavirus diseases by targeting N protein. Drug Discov Today 2015; 21:562-72. [PMID: 26691874 PMCID: PMC7108309 DOI: 10.1016/j.drudis.2015.11.015] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/11/2015] [Accepted: 11/30/2015] [Indexed: 12/18/2022]
Abstract
Coronavirus nucleocapsid proteins are appealing drug targets against coronavirus-induced diseases. A variety of compounds targeting the coronavirus nucleocapsid protein have been developed. Many of these compounds show potential antiviral activity.
The advent of severe acute respiratory syndrome (SARS) in the 21st century and the recent outbreak of Middle-East respiratory syndrome (MERS) highlight the importance of coronaviruses (CoVs) as human pathogens, emphasizing the need for development of novel antiviral strategies to combat acute respiratory infections caused by CoVs. Recent studies suggest that nucleocapsid (N) proteins from coronaviruses and other viruses can be useful antiviral drug targets against viral infections. This review aims to provide readers with a concise survey of the structural features of coronavirus N proteins and how these features provide insights into structure-based development of therapeutics against coronaviruses. We will also present our latest results on MERS-CoV N protein and its potential as an antiviral drug target.
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Wu CH, Chen PJ, Yeh SH. Nucleocapsid phosphorylation and RNA helicase DDX1 recruitment enables coronavirus transition from discontinuous to continuous transcription. Cell Host Microbe 2015; 16:462-72. [PMID: 25299332 PMCID: PMC7104987 DOI: 10.1016/j.chom.2014.09.009] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Revised: 07/11/2014] [Accepted: 08/22/2014] [Indexed: 11/27/2022]
Abstract
Coronaviruses contain a positive-sense single-stranded genomic (g) RNA, which encodes nonstructural proteins. Several subgenomic mRNAs (sgmRNAs) encoding structural proteins are generated by template switching from the body transcription regulatory sequence (TRS) to the leader TRS. The process preferentially generates shorter sgmRNA. Appropriate readthrough of body TRSs is required to produce longer sgmRNAs and full-length gRNA. We find that phosphorylation of the viral nucleocapsid (N) by host glycogen synthase kinase-3 (GSK-3) is required for template switching. GSK-3 inhibition selectively reduces the generation of gRNA and longer sgmRNAs, but not shorter sgmRNAs. N phosphorylation allows recruitment of the RNA helicase DDX1 to the phosphorylated-N-containing complex, which facilitates template readthrough and enables longer sgmRNA synthesis. DDX1 knockdown or loss of helicase activity markedly reduces the levels of longer sgmRNAs. Thus, coronaviruses employ a unique strategy for the transition from discontinuous to continuous transcription to ensure balanced sgmRNAs and full-length gRNA synthesis.
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Affiliation(s)
- Chia-Hsin Wu
- Department of Microbiology, National Taiwan University College of Medicine, No. 1, Jen-Ai Road, Section 1, Taipei 10051, Taiwan
| | - Pei-Jer Chen
- Department of Microbiology, National Taiwan University College of Medicine, No. 1, Jen-Ai Road, Section 1, Taipei 10051, Taiwan; Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, No. 1, Jen-Ai Road, Section 1, Taipei 10051, Taiwan; National Taiwan University Research Center for Medical Excellence, No. 2, Syu-Jhou Road, Taipei 10055, Taiwan
| | - Shiou-Hwei Yeh
- Department of Microbiology, National Taiwan University College of Medicine, No. 1, Jen-Ai Road, Section 1, Taipei 10051, Taiwan; National Taiwan University Research Center for Medical Excellence, No. 2, Syu-Jhou Road, Taipei 10055, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, No. 1, Changde Street, Taipei 10048, Taiwan.
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Huang CY. Inhibition of a Putative Dihydropyrimidinase from Pseudomonas aeruginosa PAO1 by Flavonoids and Substrates of Cyclic Amidohydrolases. PLoS One 2015; 10:e0127634. [PMID: 25993634 PMCID: PMC4437985 DOI: 10.1371/journal.pone.0127634] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 04/16/2015] [Indexed: 02/04/2023] Open
Abstract
Dihydropyrimidinase is a member of the cyclic amidohydrolase family, which also includes allantoinase, dihydroorotase, hydantoinase, and imidase. These metalloenzymes possess very similar active sites and may use a similar mechanism for catalysis. However, whether the substrates and inhibitors of other cyclic amidohydrolases can inhibit dihydropyrimidinase remains unclear. This study investigated the inhibition of dihydropyrimidinase by flavonoids and substrates of other cyclic amidohydrolases. Allantoin, dihydroorotate, 5-hydantoin acetic acid, acetohydroxamate, orotic acid, and 3-amino-1,2,4-triazole could slightly inhibit dihydropyrimidinase, and the IC50 values of these compounds were within the millimolar range. The inhibition of dihydropyrimidinase by flavonoids, such as myricetin, quercetin, kaempferol, galangin, dihydromyricetin, and myricitrin, was also investigated. Some of these compounds are known as inhibitors of allantoinase and dihydroorotase. Although the inhibitory effects of these flavonoids on dihydropyrimidinase were substrate-dependent, dihydromyricetin significantly inhibited dihydropyrimidinase with IC50 values of 48 and 40 μM for the substrates dihydrouracil and 5-propyl-hydantoin, respectively. The results from the Lineweaver−Burk plot indicated that dihydromyricetin was a competitive inhibitor. Results from fluorescence quenching analysis indicated that dihydromyricetin could form a stable complex with dihydropyrimidinase with the Kd value of 22.6 μM. A structural study using PatchDock showed that dihydromyricetin was docked in the active site pocket of dihydropyrimidinase, which was consistent with the findings from kinetic and fluorescence studies. This study was the first to demonstrate that naturally occurring product dihydromyricetin inhibited dihydropyrimidinase, even more than the substrate analogs (>3 orders of magnitude). These flavonols, particularly myricetin, may serve as drug leads and dirty drugs (for multiple targets) for designing compounds that target several cyclic amidohydrolases.
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Affiliation(s)
- Cheng-Yang Huang
- School of Biomedical Sciences, Chung Shan Medical University, No.110, Sec.1, Chien-Kuo N. Rd., Taichung City, Taiwan
- Department of Medical Research, Chung Shan Medical University Hospital, No.110, Sec.1, Chien-Kuo N. Rd., Taichung City, Taiwan
- * E-mail:
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Yang CH, Tan DH, Hsu WL, Jong TT, Wen CL, Hsu SL, Chang PC. Anti-influenza virus activity of the ethanolic extract from Peperomia sui. JOURNAL OF ETHNOPHARMACOLOGY 2014; 155:320-325. [PMID: 24882727 PMCID: PMC7127046 DOI: 10.1016/j.jep.2014.05.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Revised: 05/13/2014] [Accepted: 05/21/2014] [Indexed: 06/03/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Peperomia sui Lin and Lu (Peperomia sui), a well-known Taiwanese folk medicine, has a broad range of biological effects, especially in treatment of upper respiratory tract diseases. However, no previous study has explored the activity of Peperomia sui against influenza virus infections. This study was carried out to evaluate the anti-influenza virus activity and the potential virucidal effect of the ethanolic extract of Peperomia sui (PSE). METHODS The anti-H6N1 avian influenza viral activity of PSE against the influenza virus A/Chicken/TW/0518/2011 (H6N1) in chicken fibroblast DF-1 cells was evaluated by cell viability assay, hemagglutination assay, neuraminidase activity assay, indirect immunofluorescence assay and quantitative RT-PCR assay. RESULTS PSE significantly increased the viability of cells that were infected by the H6N1 virus. PSE also suppressed the synthesis of viral nucleoprotein (NP), and inhibited the growth of the virus in DF-1 cells. Further, PSE inhibited the neuraminidase activity of H6N1 virus. CONCLUSIONS The findings of this study provide important information for the exploitation and utilization of Peperomia sui in treatment of influenza infection.
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Affiliation(s)
- Chih-Hsueh Yang
- Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taichung 402, Taiwan, Republic of China; Department of Education and Research, Taichung Veterans General Hospital, Taichung 407, Taiwan, Republic of China
| | - Duen-Huey Tan
- Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taichung 402, Taiwan, Republic of China
| | - Wei-Li Hsu
- Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taichung 402, Taiwan, Republic of China
| | - Ting-Ting Jong
- Department of Chemistry, National Chung Hsing University, Taichung 402, Taiwan, Republic of China
| | - Chi-Luan Wen
- Taiwan Seed Improvement and Propagation Station, Council of Agriculture, Taichung 426, Taiwan, Republic of China
| | - Shih-Lan Hsu
- Department of Education and Research, Taichung Veterans General Hospital, Taichung 407, Taiwan, Republic of China.
| | - Poa-Chun Chang
- Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taichung 402, Taiwan, Republic of China.
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Lou Z, Sun Y, Rao Z. Current progress in antiviral strategies. Trends Pharmacol Sci 2014; 35:86-102. [PMID: 24439476 PMCID: PMC7112804 DOI: 10.1016/j.tips.2013.11.006] [Citation(s) in RCA: 164] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 11/23/2013] [Accepted: 11/26/2013] [Indexed: 02/07/2023]
Abstract
Antiviral agents function as either viral targets or host factors. Virus-targeting antivirals (VTAs) function through a direct (DVTAs) or an indirect (InDVTAs) method in the viral life cycle. Host-targeting antivirals (HTAs) include reagents that target the host proteins that are involved in the viral life cycle.
The prevalence of chronic viral infectious diseases, such as human immunodeficiency virus (HIV), hepatitis C virus (HCV), and influenza virus; the emergence and re-emergence of new viral infections, such as picornaviruses and coronaviruses; and, particularly, resistance to currently used antiviral drugs have led to increased demand for new antiviral strategies and reagents. Increased understanding of the molecular mechanisms of viral infection has provided great potential for the discovery of new antiviral agents that target viral proteins or host factors. Virus-targeting antivirals can function directly or indirectly to inhibit the biological functions of viral proteins, mostly enzymatic activities, or to block viral replication machinery. Host-targeting antivirals target the host proteins that are involved in the viral life cycle, regulating the function of the immune system or other cellular processes in host cells. Here we review key targets and considerations for the development of both antiviral strategies.
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Affiliation(s)
- Zhiyong Lou
- Laboratory of Structural Biology and MOE Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, 100084, China.
| | - Yuna Sun
- National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, 100101, China
| | - Zihe Rao
- Laboratory of Structural Biology and MOE Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, 100084, China; National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, 100101, China.
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Peng WF, Huang CY. Allantoinase and dihydroorotase binding and inhibition by flavonols and the substrates of cyclic amidohydrolases. Biochimie 2014; 101:113-22. [PMID: 24418229 DOI: 10.1016/j.biochi.2014.01.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 01/02/2014] [Indexed: 01/10/2023]
Abstract
Allantoinase and dihydroorotase are members of the cyclic amidohydrolases family. Allantoinase and dihydroorotase possess very similar binuclear metal centers in the active site and may use a similar mechanism for catalysis. However, whether the substrate specificities of allantoinase and dihydroorotase overlap and whether the substrates of other cyclic amidohydrolases inhibit allantoinase and dihydroorotase remain unknown. In this study, the binding and inhibition of allantoinase (Salmonella enterica serovar Typhimurium LT2) and dihydroorotase (Klebsiella pneumoniae) by flavonols and the substrates of other cyclic amidohydrolases were investigated. Hydantoin and phthalimide, substrates of hydantoinase and imidase, were not hydrolyzed by allantoinase and dihydroorotase. Hydantoin and dihydroorotate competitively inhibited allantoinase, whereas hydantoin and allantoin bind to dihydroorotase, but do not affect its activity. We further investigated the effects of the flavonols myricetin, quercetin, kaempferol, and galangin, on the inhibition of allantoinase and dihydroorotase. Allantoinase and dihydroorotase were both significantly inhibited by kaempferol, with IC50 values of 35 ± 3 μM and 31 ± 2 μM, respectively. Myricetin strongly inhibited dihydroorotase, with an IC50 of 40 ± 1 μM. The double reciprocal of the Lineweaver-Burk plot indicated that kaempferol was a competitive inhibitor for allantoinase but an uncompetitive inhibitor for dihydroorotase. A structural study using PatchDock showed that kaempferol was docked in the active site pocket of allantoinase but outside the active site pocket of dihydroorotase. These results constituted a first study that naturally occurring product flavonols inhibit the cyclic amidohydrolases, allantoinase, and dihydroorotase, even more than the substrate analogs (>3 orders of magnitude). Thus, flavonols may serve as drug leads for designing compounds that target several cyclic amidohydrolases.
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Affiliation(s)
- Wei-Feng Peng
- School of Biomedical Sciences, Chung Shan Medical University, No. 110, Sec. 1, Chien-Kuo N. Rd., Taichung City, Taiwan; School of Medicine, College of Medicine, Chung Shan Medical University, No. 110, Sec. 1, Chien-Kuo N. Rd., Taichung City, Taiwan
| | - Cheng-Yang Huang
- School of Biomedical Sciences, Chung Shan Medical University, No. 110, Sec. 1, Chien-Kuo N. Rd., Taichung City, Taiwan; Department of Medical Research, Chung Shan Medical University Hospital, No. 110, Sec. 1, Chien-Kuo N. Rd., Taichung City, Taiwan.
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