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Zhou J, Zhang R, Yan H, Liu X, Shang C, Chen Y. Evaluation of natural products from virtual screenings as SARS-CoV-2 main protease inhibitors using combinational experiments. Nat Prod Res 2024:1-4. [PMID: 38189351 DOI: 10.1080/14786419.2023.2301466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/26/2023] [Indexed: 01/09/2024]
Abstract
Recently, andrographolide, kaempferol, maslinic acid, rutin, and schaftoside have been identified as potent SARS-CoV-2 main protease (Mpro) inhibitors via molecular docking studies. However, no comprehensive in vitro testing of these compounds against Mpro has been conducted. In this study, we rigorously evaluated the in vitro inhibition of Mpro by these compounds using combinational experiments, including fluorescence resonance energy transfer (FRET), fluorescence polarization (FP), and dimerization-dependent red fluorescent protein (ddRFP) assays. Our data revealed that these compounds are not Mpro inhibitors based on the results from a set of in vitro assays. These results suggest that an efficient combination of a molecular docking approach and an experimental assay is essential for the discovery of Mpro inhibitors in the future.
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Affiliation(s)
- Jiahao Zhou
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, P. R. China
| | - Rui Zhang
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, P. R. China
| | - Haohao Yan
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, P. R. China
| | - Xiaoping Liu
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, P. R. China
| | - Chao Shang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, P. R. China
| | - Yunyu Chen
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, P. R. China
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2
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Abd-Alla HI, Souguir D, Radwan MO. Genus Sophora: a comprehensive review on secondary chemical metabolites and their biological aspects from past achievements to future perspectives. Arch Pharm Res 2021; 44:903-986. [PMID: 34907492 PMCID: PMC8671057 DOI: 10.1007/s12272-021-01354-2] [Citation(s) in RCA: 15] [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: 07/16/2020] [Accepted: 10/29/2021] [Indexed: 12/13/2022]
Abstract
Sophora is deemed as one of the most remarkable genera of Fabaceae, and the third largest family of flowering plants. The genus Sophora comprises approximately 52 species, 19 varieties, and 7 forms that are widely distributed in Asia and mildly in Africa. Sophora species are recognized to be substantial sources of broad spectrum biopertinent secondary metabolites namely flavonoids, isoflavonoids, chalcones, chromones, pterocarpans, coumarins, benzofuran derivatives, sterols, saponins (mainly triterpene glycosides), oligostilbenes, and mainly alkaloids. Meanwhile, extracts and isolated compounds from Sophora have been identified to possess several health-promising effects including anti-inflammatory, anti-arthritic, antiplatelets, antipyretic, anticancer, antiviral, antimicrobial, antioxidant, anti-osteoporosis, anti-ulcerative colitis, antidiabetic, anti-obesity, antidiarrheal, and insecticidal activities. Herein, the present review aims to provide comprehensive details about the phytochemicals and biological effects of Sophora species. The review spotlighted on the promising phytonutrients extracted from Sophora and their plethora of bioactivities. The review also clarifies the remaining gaps and thus qualifies and supplies a platform for further investigations of these compounds.
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Affiliation(s)
- Howaida I Abd-Alla
- Chemistry of Natural Compounds Department, National Research Centre, El-Bohouth Street, Giza-Dokki, 12622, Egypt.
| | - Dalila Souguir
- Institut National de Recherches en Génie Rural, Eaux et Forêts (INRGREF), Université de Carthage, 10 Rue Hédi Karray, Manzeh IV, 2080, Ariana, Tunisia
| | - Mohamed O Radwan
- Chemistry of Natural Compounds Department, National Research Centre, El-Bohouth Street, Giza-Dokki, 12622, Egypt.
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan.
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3
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Al-Sanea MM, Abelyan N, Abdelgawad MA, Musa A, Ghoneim MM, Al-Warhi T, Aljaeed N, Alotaibi OJ, Alnusaire TS, Abdelwahab SF, Helmy A, Abdelmohsen UR, Youssif KA. Strawberry and Ginger Silver Nanoparticles as Potential Inhibitors for SARS-CoV-2 Assisted by In Silico Modeling and Metabolic Profiling. Antibiotics (Basel) 2021; 10:824. [PMID: 34356745 PMCID: PMC8300822 DOI: 10.3390/antibiotics10070824] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 06/27/2021] [Accepted: 06/29/2021] [Indexed: 02/05/2023] Open
Abstract
SARS-CoV-2 (COVID-19), a novel coronavirus causing life-threatening pneumonia, caused a pandemic starting in 2019 and caused unprecedented economic and health crises all over the globe. This requires the rapid discovery of anti-SARS-CoV-2 drug candidates to overcome this life-threatening pandemic. Strawberry (Fragaria ananassa Duch.) and ginger (Zingiber officinale) methanolic extracts were used for silver nanoparticle (AgNPs) synthesis to explore their SARS-CoV-2 inhibitory potential. Moreover, an in silico study was performed to explore the possible chemical compounds that might be responsible for the anti-SARS-CoV-2 potential. The characterization of the green synthesized AgNPs was carried out with transmission electron microscope (TEM), Fourier-transform infrared, spectroscopy ultraviolet-visible spectroscopy, zeta potential, and a dynamic light-scattering technique. The metabolic profiling of strawberry and ginger methanolic extract was assessed using liquid chromatography coupled with high-resolution mass spectrometry. The antiviral potential against SARS-CoV-2 was evaluated using an MTT assay. Moreover, in silico modeling and the molecular dynamic study were conducted via AutoDock Vina to demonstrate the potential of the dereplicated compounds to bind to some of the SARS-CoV-2 proteins. The TEM analysis of strawberry and ginger AgNPs showed spherical nanoparticles with mean sizes of 5.89 nm and 5.77 nm for strawberry and ginger, respectively. The UV-Visible spectrophotometric analysis showed an absorption peak at λmax of 400 nm for strawberry AgNPs and 405 nm for ginger AgNPs. The Zeta potential values of the AgNPs of the methanolic extract of strawberry was -39.4 mV, while for AgNPs of ginger methanolic extract it was -42.6 mV, which indicates a high stability of the biosynthesized nanoparticles. The strawberry methanolic extract and the green synthesized AgNPs of ginger showed the highest antiviral activity against SARS-CoV-2. Dereplication of the secondary metabolites from the crude methanolic extracts of strawberry and ginger resulted in the annotation of different classes of compounds including phenolic, flavonoids, fatty acids, sesquiterpenes, triterpenes, sterols, and others. The docking study was able to predict the different patterns of interaction between the different compounds of strawberry and ginger with seven SARS-CoV-2 protein targets including five viral proteins (Mpro, ADP ribose phosphatase, NSP14, NSP16, PLpro) and two humans (AAK1, Cathepsin L). The molecular docking and dynamics simulation study showed that neohesperidin demonstrated the potential to bind to both human AAK1 protein and SARS-CoV-2 NSP16 protein, which makes this compound of special interest as a potential dual inhibitor. Overall, the present study provides promise for Anti-SARS-CoV-2 green synthesized AgNPs, which could be developed in the future into a new anti-SARS-CoV-2 drug.
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Affiliation(s)
- Mohammad M. Al-Sanea
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka 72341, Saudi Arabia;
| | - Narek Abelyan
- Institute of Biomedicine and Pharmacy, Russian-Armenian University, Yerevan 0051, Armenia;
- Foundation for Armenian Science and Technology, Yerevan 0033, Armenia
| | - Mohamed A. Abdelgawad
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka 72341, Saudi Arabia;
| | - Arafa Musa
- Department of Pharmacognosy, College of Pharmacy, Jouf University, Sakaka 72341, Saudi Arabia;
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Cairo 11371, Egypt
| | - Mohammed M. Ghoneim
- Department of Pharmacy, College of Pharmacy, Al Maarefa University, Ad Diriyah 13713, Saudi Arabia;
| | - Tarfah Al-Warhi
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh 11564, Saudi Arabia; (T.A.-W.); (N.A.); (O.J.A.)
| | - Nada Aljaeed
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh 11564, Saudi Arabia; (T.A.-W.); (N.A.); (O.J.A.)
| | - Ohoud J. Alotaibi
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh 11564, Saudi Arabia; (T.A.-W.); (N.A.); (O.J.A.)
| | - Taghreed S. Alnusaire
- Biology Department, College of Science, Jouf University, Sakaka 72388, Saudi Arabia;
- Olive Research Center, Jouf University, Sakaka 72341, Saudi Arabia
| | - Sayed F. Abdelwahab
- Department of Pharmaceutics and Industrial Pharmacy, Taif College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Aya Helmy
- Department of Pharmacognosy, Faculty of Pharmacy, Modern University for Technology and Information, Cairo 11865, Egypt; (A.H.); (K.A.Y.)
| | - Usama Ramadan Abdelmohsen
- Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, Minia 61111, Egypt
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia 61519, Egypt
| | - Khayrya A. Youssif
- Department of Pharmacognosy, Faculty of Pharmacy, Modern University for Technology and Information, Cairo 11865, Egypt; (A.H.); (K.A.Y.)
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Shady NH, Hayallah AM, Mohamed MFA, Ghoneim MM, Chilingaryan G, Al-Sanea MM, Fouad MA, Kamel MS, Abdelmohsen UR. Targeting 3CLpro and SARS-CoV-2 RdRp by Amphimedon sp. Metabolites: A Computational Study. Molecules 2021; 26:3775. [PMID: 34205768 PMCID: PMC8235472 DOI: 10.3390/molecules26123775] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/13/2021] [Accepted: 06/16/2021] [Indexed: 01/10/2023] Open
Abstract
Since December 2019, novel coronavirus disease 2019 (COVID-19) pandemic has caused tremendous economic loss and serious health problems worldwide. In this study, we investigated 14 natural compounds isolated from Amphimedon sp. via a molecular docking study, to examine their ability to act as anti-COVID-19 agents. Moreover, the pharmacokinetic properties of the most promising compounds were studied. The docking study showed that virtually screened compounds were effective against the new coronavirus via dual inhibition of SARS-CoV-2 RdRp and the 3CL main protease. In particular, nakinadine B (1), 20-hepacosenoic acid (11) and amphimedoside C (12) were the most promising compounds, as they demonstrated good interactions with the pockets of both enzymes. Based on the analysis of the molecular docking results, compounds 1 and 12 were selected for molecular dynamics simulation studies. Our results showed Amphimedon sp. to be a rich source for anti-COVID-19 metabolites.
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Affiliation(s)
- Nourhan Hisham Shady
- Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, Universities Zone, New Minia City 61111, Egypt; (N.H.S.); (M.S.K.)
| | - Alaa M. Hayallah
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt;
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Sphinx University, New Assiut 71515, Egypt
| | - Mamdouh F. A. Mohamed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Sohag University, Sohag 82524, Egypt;
| | - Mohammed M. Ghoneim
- Department of Pharmacy Practice, College of Pharmacy, AlMaarefa University, Ad Diriyah 13713, Saudi Arabia;
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Cairo 11371, Egypt
| | - Garri Chilingaryan
- Institute of Molecular Biology of NAS RA, Yerevan 0014, Armenia;
- Institute of Biomedicine and Pharmacy, Russian-Armenian University, Yerevan 0051, Armenia
| | - Mohammad M. Al-Sanea
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Aljouf 72341, Saudi Arabia;
| | - Mostafa A. Fouad
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia 61519, Egypt;
| | - Mohamed Salah Kamel
- Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, Universities Zone, New Minia City 61111, Egypt; (N.H.S.); (M.S.K.)
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia 61519, Egypt;
| | - Usama Ramadan Abdelmohsen
- Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, Universities Zone, New Minia City 61111, Egypt; (N.H.S.); (M.S.K.)
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia 61519, Egypt;
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Orfali R, Rateb ME, Hassan HM, Alonazi M, Gomaa MR, Mahrous N, GabAllah M, Kandeil A, Perveen S, Abdelmohsen UR, Sayed AM. Sinapic Acid Suppresses SARS CoV-2 Replication by Targeting Its Envelope Protein. Antibiotics (Basel) 2021; 10:420. [PMID: 33920366 PMCID: PMC8069661 DOI: 10.3390/antibiotics10040420] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/07/2021] [Accepted: 04/09/2021] [Indexed: 12/17/2022] Open
Abstract
SARS CoV-2 is still considered a global health issue, and its threat keeps growing with the emergence of newly evolved strains. Despite the success in developing some vaccines as a protective measure, finding cost-effective treatments is urgent. Accordingly, we screened a number of phenolic natural compounds for their in vitro anti-SARS CoV-2 activity. We found sinapic acid (SA) selectively inhibited the viral replication in vitro with an half-maximal inhibitory concentration (IC50) value of 2.69 µg/mL with significantly low cytotoxicity (CC50 = 189.3 µg/mL). Subsequently, we virtually screened all currently available molecular targets using a multistep in silico protocol to find out the most probable molecular target that mediates this compound's antiviral activity. As a result, the viral envelope protein (E-protein) was suggested as the most possible hit for SA. Further in-depth molecular dynamic simulation-based investigation revealed the essential structural features of SA antiviral activity and its binding mode with E-protein. The structural and experimental results presented in this study strongly recommend SA as a promising structural motif for anti-SARS CoV-2 agent development.
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Affiliation(s)
- Raha Orfali
- Department of Pharmacognosy, College of Pharmacy, King Saud University, P.O. Box 22452, Riyadh 11495, Saudi Arabia; (R.O.); (S.P.)
| | - Mostafa E. Rateb
- School of Computing, Engineering & Physical Sciences, University of the West of Scotland, Paisley PA1 2BE, UK;
| | - Hossam M. Hassan
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, Beni-Suef 62513, Egypt;
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62513, Egypt
| | - Mona Alonazi
- Department of Biochemistry, Faculty of Science, King Saud University. P.O. Box 12372, Riyadh 11495, Saudi Arabia;
| | - Mokhtar R. Gomaa
- Center of Scientific Excellence for Influenza Virus, Environmental Research Division, National Research Centre, Giza 12622, Egypt; (M.R.G.); (N.M.); (M.G.); (A.K.)
| | - Noura Mahrous
- Center of Scientific Excellence for Influenza Virus, Environmental Research Division, National Research Centre, Giza 12622, Egypt; (M.R.G.); (N.M.); (M.G.); (A.K.)
| | - Mohamed GabAllah
- Center of Scientific Excellence for Influenza Virus, Environmental Research Division, National Research Centre, Giza 12622, Egypt; (M.R.G.); (N.M.); (M.G.); (A.K.)
| | - Ahmed Kandeil
- Center of Scientific Excellence for Influenza Virus, Environmental Research Division, National Research Centre, Giza 12622, Egypt; (M.R.G.); (N.M.); (M.G.); (A.K.)
| | - Shagufta Perveen
- Department of Pharmacognosy, College of Pharmacy, King Saud University, P.O. Box 22452, Riyadh 11495, Saudi Arabia; (R.O.); (S.P.)
| | - Usama Ramadan Abdelmohsen
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia 61519, Egypt
- Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, 7 Universities Zone, New Minia 61111, Egypt
| | - Ahmed M. Sayed
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, Beni-Suef 62513, Egypt;
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