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Discovering new potential inhibitors to SARS-CoV-2 RNA dependent RNA polymerase (RdRp) using high throughput virtual screening and molecular dynamics simulations. Sci Rep 2022; 12:19986. [PMID: 36411383 PMCID: PMC9676757 DOI: 10.1038/s41598-022-24695-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 03/14/2022] [Indexed: 11/23/2022] Open
Abstract
RNA dependent RNA polymerase (RdRp), is an essential in the RNA replication within the life cycle of the severely acute respiratory coronavirus-2 (SARS-CoV-2), causing the deadly respiratory induced sickness COVID-19. Remdesivir is a prodrug that has seen some success in inhibiting this enzyme, however there is still the pressing need for effective alternatives. In this study, we present the discovery of four non-nucleoside small molecules that bind favorably to SARS-CoV-2 RdRp over the active form of the popular drug remdesivir (RTP) and adenosine triphosphate (ATP) by utilizing high-throughput virtual screening (HTVS) against the vast ZINC compound database coupled with extensive molecular dynamics (MD) simulations. After post-trajectory analysis, we found that the simulations of complexes containing both ATP and RTP remained stable for the duration of their trajectories. Additionally, it was revealed that the phosphate tail of RTP was stabilized by both the positive amino acid pocket and magnesium ions near the entry channel of RdRp which includes residues K551, R553, R555 and K621. It was also found that residues D623, D760, and N691 further stabilized the ribose portion of RTP with U10 on the template RNA strand forming hydrogen pairs with the adenosine motif. Using these models of RdRp, we employed them to screen the ZINC database of ~ 17 million molecules. Using docking and drug properties scoring, we narrowed down our selection to fourteen candidates. These were subjected to 200 ns simulations each underwent free energy calculations. We identified four hit compounds from the ZINC database that have similar binding poses to RTP while possessing lower overall binding free energies, with ZINC097971592 having a binding free energy two times lower than RTP.
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New Sesquiterpene Lactone via Fungal Transformation of Rhizopus oryzae KX685359: Antimicrobial In-Vitro and In-Silico Study. Catal Letters 2022. [DOI: 10.1007/s10562-022-04202-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Mohamed TA, Elshamy AI, Ibrahim MAA, Atia MAM, Ahmed RF, Ali SK, Mahdy KA, Alshammari SO, Al-Abd AM, Moustafa MF, Farrag ARH, Hegazy MEF. Gastroprotection against Rat Ulcers by Nephthea Sterol Derivative. Biomolecules 2021; 11:1247. [PMID: 34439913 PMCID: PMC8393318 DOI: 10.3390/biom11081247] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/16/2021] [Accepted: 08/19/2021] [Indexed: 12/23/2022] Open
Abstract
Different species belonging to the genus Nephthea (Acyonaceae) are a rich resource for bioactive secondary metabolites. The literature reveals that the gastroprotective effects of marine secondary metabolites have not been comprehensively studied in vivo. Hence, the present investigation aimed to examine and determine the anti-ulcer activity of 4α,24-dimethyl-5α-cholest-8β,18-dihydroxy,22E-en-3β-ol (ST-1) isolated from samples of a Nephthea species. This in vivo study was supported by in silico molecular docking and protein-protein interaction techniques. Oral administration of ST-1 reduced rat stomach ulcers with a concurrent increase in gastric mucosa. Molecular docking calculations against the H+/K+-ATPase transporter showed a higher binding affinity of ST-1, with a docking score value of -9.9 kcal/mol and a pKi value of 59.7 nM, compared to ranitidine (a commercial proton pump inhibitor, which gave values of -6.2 kcal/mol and 27.9 µM, respectively). The combined PEA-reactome analysis results revealed promising evidence of ST-1 potency as an anti-ulcer compound through significant modulation of the gene set controlling the PI3K signaling pathway, which subsequently plays a crucial role in signaling regarding epithelialization and tissue regeneration, tissue repairing and tissue remodeling. These results indicate a probable protective role for ST-1 against ethanol-induced gastric ulcers.
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Affiliation(s)
- Tarik A. Mohamed
- National Research Centre, Chemistry of Medicinal Plants Department, 33 El−Bohouth St., Dokki, Giza 12622, Egypt; (T.A.M.); (S.K.A.); (M.-E.F.H.)
| | - Abdelsamed I. Elshamy
- National Research Centre, Chemistry of Natural Compounds Department, Dokki, Giza 12622, Egypt; (A.I.E.); (R.F.A.)
| | - Mahmoud A. A. Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt;
| | - Mohamed A. M. Atia
- Molecular Genetics and Genome Mapping Laboratory, Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza 12619, Egypt;
| | - Rania F. Ahmed
- National Research Centre, Chemistry of Natural Compounds Department, Dokki, Giza 12622, Egypt; (A.I.E.); (R.F.A.)
| | - Sherin K. Ali
- National Research Centre, Chemistry of Medicinal Plants Department, 33 El−Bohouth St., Dokki, Giza 12622, Egypt; (T.A.M.); (S.K.A.); (M.-E.F.H.)
| | - Karam A. Mahdy
- National Research Centre, Medical Biochemistry Department, 33 El Bohouth St., Dokki, Giza 12622, Egypt;
| | - Shifaa O. Alshammari
- Department of Biology, College of Science, University of Hafr Al Batin, Hafar Al Batin 39524, Saudi Arabia;
| | - Ahmed M. Al-Abd
- Department of Pharmaceutical Sciences, College of Pharmacy & Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman 4184, United Arab Emirates
- Pharmacology Department, Medical Division, National Research Centre, Cairo 12622, Egypt
| | - Mahmoud F. Moustafa
- Department of Biology, College of Science, King Khalid University, Abha 9004, Saudi Arabia;
- Department of Botany & Microbiology, Faculty of Science, South Valley University, Qena 83523, Egypt
| | - Abdel Razik H. Farrag
- National Research Centre, Pathology Department, 33 El Bohouth St., Dokki, Giza 12622, Egypt;
| | - Mohamed-Elamir F. Hegazy
- National Research Centre, Chemistry of Medicinal Plants Department, 33 El−Bohouth St., Dokki, Giza 12622, Egypt; (T.A.M.); (S.K.A.); (M.-E.F.H.)
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Yosri N, Abd El-Wahed AA, Ghonaim R, Khattab OM, Sabry A, Ibrahim MAA, Moustafa MF, Guo Z, Zou X, Algethami AFM, Masry SHD, AlAjmi MF, Afifi HS, Khalifa SAM, El-Seedi HR. Anti-Viral and Immunomodulatory Properties of Propolis: Chemical Diversity, Pharmacological Properties, Preclinical and Clinical Applications, and In Silico Potential against SARS-CoV-2. Foods 2021; 10:1776. [PMID: 34441553 PMCID: PMC8391193 DOI: 10.3390/foods10081776] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/25/2021] [Accepted: 07/28/2021] [Indexed: 12/24/2022] Open
Abstract
Propolis, a resin produced by honeybees, has long been used as a dietary supplement and folk remedy, and more recent preclinical investigations have demonstrated a large spectrum of potential therapeutic bioactivities, including antioxidant, antibacterial, anti-inflammatory, neuroprotective, immunomodulatory, anticancer, and antiviral properties. As an antiviral agent, propolis and various constituents have shown promising preclinical efficacy against adenoviruses, influenza viruses, respiratory tract viruses, herpes simplex virus type 1 (HSV-1) and type 2 (HSV-2), human immunodeficiency virus (HIV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Over 300 chemical components have been identified in propolis, including terpenes, flavonoids, and phenolic acids, with the specific constituent profile varying widely according to geographic origin and regional flora. Propolis and its constituents have demonstrated potential efficacy against SARS-CoV-2 by modulating multiple pathogenic and antiviral pathways. Molecular docking studies have demonstrated high binding affinities of propolis derivatives to multiple SARS-CoV-2 proteins, including 3C-like protease (3CLpro), papain-like protease (PLpro), RNA-dependent RNA polymerase (RdRp), the receptor-binding domain (RBD) of the spike protein (S-protein), and helicase (NSP13), as well as to the viral target angiotensin-converting enzyme 2 (ACE2). Among these compounds, retusapurpurin A has shown high affinity to 3CLpro (ΔG = -9.4 kcal/mol), RdRp (-7.5), RBD (-7.2), NSP13 (-9.4), and ACE2 (-10.4) and potent inhibition of viral entry by forming hydrogen bonds with amino acid residues within viral and human target proteins. In addition, propolis-derived baccharin demonstrated even higher binding affinity towards PLpro (-8.2 kcal/mol). Measures of drug-likeness parameters, including metabolism, distribution, absorption, excretion, and toxicity (ADMET) characteristics, also support the potential of propolis as an effective agent to combat COVID-19.
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Affiliation(s)
- Nermeen Yosri
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China; (N.Y.); (Z.G.); (X.Z.)
- Department of Chemistry, Faculty of Science, Menoufia University, Shebin El-Kom 32512, Egypt; (R.G.); (O.M.K.); (A.S.)
| | - Aida A. Abd El-Wahed
- Department of Bee Research, Plant Protection Research Institute, Agricultural Research Centre, Giza 12627, Egypt;
| | - Reem Ghonaim
- Department of Chemistry, Faculty of Science, Menoufia University, Shebin El-Kom 32512, Egypt; (R.G.); (O.M.K.); (A.S.)
| | - Omar M. Khattab
- Department of Chemistry, Faculty of Science, Menoufia University, Shebin El-Kom 32512, Egypt; (R.G.); (O.M.K.); (A.S.)
| | - Aya Sabry
- Department of Chemistry, Faculty of Science, Menoufia University, Shebin El-Kom 32512, Egypt; (R.G.); (O.M.K.); (A.S.)
| | - Mahmoud A. A. Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt;
| | - Mahmoud F. Moustafa
- Department of Biology, College of Science, King Khalid University, Abha 9004, Saudi Arabia;
- Department of Botany & Microbiology, Faculty of Science, South Valley University, Qena 83523, Egypt
| | - Zhiming Guo
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China; (N.Y.); (Z.G.); (X.Z.)
| | - Xiaobo Zou
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China; (N.Y.); (Z.G.); (X.Z.)
| | | | - Saad H. D. Masry
- Department of Plant Protection and Biomolecular Diagnosis, Arid Lands Cultivation Research Institute (ALCRI), City of Scientific Research and Technological Applications, New Borg El-Arab City, Alexandria 21934, Egypt;
- Abu Dhabi Agriculture and Food Safety Authority (ADAFSA), Al Ain 52150, United Arab Emirates
| | - Mohamed F. AlAjmi
- Pharmacognosy Group, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Hanan S. Afifi
- Food Research Section, R&D Division, Abu Dhabi Agriculture and Food Safety Authority (ADAFSA), Abu Dhabi P.O. Box 52150, United Arab Emirates;
| | - Shaden A. M. Khalifa
- Department of Molecular Biosciences, Stockholm University, The Wenner-Gren Institute, SE-106 91 Stockholm, Sweden
| | - Hesham R. El-Seedi
- Department of Chemistry, Faculty of Science, Menoufia University, Shebin El-Kom 32512, Egypt; (R.G.); (O.M.K.); (A.S.)
- International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China
- Division of Pharmacognosy, Department of Pharmaceutical Biosciences, Uppsala University, Biomedical Centre, P.O. Box 591, SE 751 24 Uppsala, Sweden
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Elshamy AI, Mohamed TA, Ibrahim MAA, Atia MAM, Yoneyama T, Umeyama A, Hegazy MEF. Two novel oxetane containing lignans and a new megastigmane from Paronychia arabica and in silico analysis of them as prospective SARS-CoV-2 inhibitors. RSC Adv 2021; 11:20151-20163. [PMID: 35479905 PMCID: PMC9033657 DOI: 10.1039/d1ra02486h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 05/15/2021] [Indexed: 12/22/2022] Open
Abstract
The chemical characterization of the extract of the aerial parts of Paronychia arabica afforded two oxetane containing lignans, paronychiarabicine A (1) and B (2), and one new megastigmane, paronychiarabicastigmane A (3), alongside a known lignan (4), eight known phenolic compounds (5–12), one known elemene sesquiterpene (13) and one steroid glycoside (14). The chemical structures of the isolated compounds were constructed based upon the HRMS, 1D, and 2D-NMR results. The absolute configurations were established via NOESY experiments as well as experimental and TDDFT-calculated electronic circular dichroism (ECD). Utilizing molecular docking, the binding scores and modes of compounds 1–3 towards the SARS-CoV-2 main protease (Mpro), papain-like protease (PLpro), and RNA-dependent RNA polymerase (RdRp) were revealed. Compound 3 exhibited a promising docking score (−9.8 kcal mol−1) against SARS-CoV-2 Mpro by forming seven hydrogen bonds inside the active site with the key amino acids. The reactome pathway enrichment analysis revealed a correlation between the inhibition of GSK3 and GSK3B genes (identified as the main targets of megastigmane treatment) and significant inhibition of SARS-CoV-1 viral replication in infected Vero E6 cells. Our results manifest a novel understanding of genes, proteins and corresponding pathways against SARS-CoV-2 infection and could facilitate the identification and characterization of novel therapeutic targets as treatments of SARS-CoV-2 infection. The hydromethanolic extract of Paronychia arabica aerial parts afforded two oxetane containing lignans, paronychiarabicine A (1) and B (2), and one new megastigmane, paronychiarabicastigmane A (3), alongside a known secondary metabolites (4–14).![]()
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Affiliation(s)
- Abdelsamed I Elshamy
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University Yamashiro-cho Tokushima 770-8514 Japan.,Chemistry of Natural Compounds Department, National Research Centre Dokki Giza 12622 Egypt
| | - Tarik A Mohamed
- Chemistry of Medicinal Plants Department, National Research Centre 33 El-Bohouth St., Dokki Giza 12622 Egypt +20-233370931 +20-233371635
| | - Mahmoud A A Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University Minia 61519 Egypt
| | - Mohamed A M Atia
- Molecular Genetics and Genome Mapping Laboratory, Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC) Giza 12619 Egypt
| | - Tatsuro Yoneyama
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University Yamashiro-cho Tokushima 770-8514 Japan
| | - Akemi Umeyama
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University Yamashiro-cho Tokushima 770-8514 Japan
| | - Mohamed-Elamir F Hegazy
- Chemistry of Medicinal Plants Department, National Research Centre 33 El-Bohouth St., Dokki Giza 12622 Egypt +20-233370931 +20-233371635.,Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Staudinger Weg 5 55128 Mainz Germany
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Reda EH, Shakour ZTA, El-Halawany AM, El-Kashoury ESA, Shams KA, Mohamed TA, Saleh I, Elshamy AI, Atia MAM, El-Beih AA, Abdel-Azim NS, El-Seedi HR, Hegazy MEF. Comparative Study on the Essential Oils from Five Wild Egyptian Centaurea Species: Effective Extraction Techniques, Antimicrobial Activity and In-Silico Analyses. Antibiotics (Basel) 2021; 10:252. [PMID: 33802470 PMCID: PMC8000757 DOI: 10.3390/antibiotics10030252] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/26/2021] [Accepted: 02/27/2021] [Indexed: 11/17/2022] Open
Abstract
The genus Centaurea is recognized in folk medicine for anti-inflammatory, anti-itch, antitussive, purgative, astringent, and tonic activities. To study the chemical determinant for antimicrobial activity essential oils (EOs), five Centaurea species were analyzed including: C. scoparia, C. calcitrapa, C. glomerata, C. lipii and C. alexandrina. Conventional hydro-distillation (HD) and microwave-assisted extraction (MAE), as new green technologies, were compared for the extraction of essential oils. GC/MS analysis identified 120 EOs including mostly terpenoid except from C. lipii and C. alexandrina in which nonterpenoids were the major constituents. Major terpenoids included spathulenol, caryophyllene oxide and alloaromadendrene oxide-2. To probe antibacterial activity, potential EO inhibitors of a bacterial type II DNA topoisomerase, DNA gyrase B were screened via an in silico molecular docking approach. Spathulenol and alloaromadendrene oxide-2 possessed the best binding affinity in the ATP- binding pocket of Gyrase B enzyme. Principal component analysis and agglomerative hierarchical clustering were used for sample classification and revealed that sesquiterpenes contributed the most for accessions classification. In vitro antimicrobial activity against Staphylococcus aureus, Escherichia coli and Aspergillus niger for all EOs were also evaluated. EOs from C. lipii, C. glomerata and C. calcitrapa exhibited significant MIC against S. aureus with an MIC value of 31.25 µg/mL.
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Affiliation(s)
- Eman H. Reda
- Phytochemistry Laboratory, National Organization for Drug Control and Research, Giza 12622, Egypt; (E.H.R.); (Z.T.A.S.)
| | - Zienab T. Abdel Shakour
- Phytochemistry Laboratory, National Organization for Drug Control and Research, Giza 12622, Egypt; (E.H.R.); (Z.T.A.S.)
| | - Ali M. El-Halawany
- Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt;
| | | | - Khaled A. Shams
- Chemistry of Medicinal Plants Department, National Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt; (K.A.S.); (T.A.M.); (I.S.); (N.S.A.-A.)
| | - Tarik A. Mohamed
- Chemistry of Medicinal Plants Department, National Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt; (K.A.S.); (T.A.M.); (I.S.); (N.S.A.-A.)
| | - Ibrahim Saleh
- Chemistry of Medicinal Plants Department, National Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt; (K.A.S.); (T.A.M.); (I.S.); (N.S.A.-A.)
| | - Abdelsamed I. Elshamy
- Department of Natural Compounds Chemistry, National Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt;
| | - Mohamed A. M. Atia
- Molecular Genetics and Genome Mapping Laboratory, Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza 12619, Egypt;
| | - Ahmed A. El-Beih
- Chemistry of Natural & Microbial Products Department, National Research Centre, Dokki, Giza 12622, Egypt;
| | - Nahla S. Abdel-Azim
- Chemistry of Medicinal Plants Department, National Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt; (K.A.S.); (T.A.M.); (I.S.); (N.S.A.-A.)
| | - Hesham R. El-Seedi
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-10691 Stockholm, Sweden
- International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China
| | - Mohamed-Elamir F. Hegazy
- Chemistry of Medicinal Plants Department, National Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt; (K.A.S.); (T.A.M.); (I.S.); (N.S.A.-A.)
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
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