Computational investigation of Arbutus serratifolia Salisb molecules as new potential SARS-CoV-2 inhibitors
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Nadjah Belattar
,
Ratiba Mekkiou
Abstract
The outbreak of the current pandemic and the evolution of virus resistance against standard drugs led to the emergency of new and potent antiviral agents. Owing to its crucial role in viral replication, the protease enzyme is taken into survey to be a promising target for antiviral drug therapy using computational methods. In order to bring this important class of natural products in the limelight of research for prospective application as chemotherapeutic agents, the anti-SARS-CoV-2 activity of some bioactive molecules obtained from Arbutus serratifolia Salisb which is an Algerian medicinal plant, was investigated using in-silico methods. The molecular docking was performed by AutoDock Vina and UCSF Chimera, as well as ADMET and drug-likeness properties of these molecules were calculated using preADMET web-based application and the Swiss ADME server respectively. The phytochemicals (from Pr(1) to Pr(12)) were tested for their pharmacokinetic properties and docked into the main protease binding site on (PDB ID: 6Y84) in order to find a promising antiviral ligand. All tested molecules induced binding affinities into the binding pocket of (PDB ID: 6Y84) with energy scores ranging from moderate to better (from −6.4 to −8.00 kcal/mol). It is worthy to note that both Pr(2): (1S,5R,6S,8S,9S)-6,8-Dihydroxy-8-methyl-1,5,6,7,8,9-hexahydrocyclopenta [c] pyran-1-yl-β-D-glucopyranoside and Pr(7): ((1S,5S,6S,9S)-1-(β-D-Glucopyranosyloxy)-14-oxo-1,5,6,9-tetrahydro-1H-2,15-dioxacyclopenta [cd] inden-8-yl) methyl acetate, were found to be the best inhibitors with binding affinities (−7.7 kcal/mol and −8.0 kcal/mol), respectively, by virtue of the fact that all these tested molecules exhibited good binding affinities compared with those of Ritonavir and Nirmatrelvir (−1.73 and −1.93 kcal/mol), respectively, which are used as standard antiviral drugs to prevent viral growth. The amino acids: His-163; Glu-166; Arg-188; Thr-190 and Gln-192 represent the key residues of the interaction of SARS-CoV-2 main protease with Pr(7). Furthermore, the results of pharmacodynamic and pharmacokinetic investigations revealed that Pr(6), Pr(8) and Pr(9) uphold the drug-likeness criteria and more particularly, these substances can be absorbed by the human intestine. In addition, all these molecules were shown to be neither hepatotoxic nor significantly noxious to human organism. These natural products are therefore promising inhibitor candidates of viral main protease. However, further in-vitro, in-vivo and even clinical assays are required to probe their functional mechanisms and then to assess their antiviral potency against COVID-19.
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Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.
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Research funding: None declared.
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Conflict of interest statement: The authors declare no conflicts of interest regarding this article.
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- Barley thermoplastic starch nanocomposite films reinforced with nanocellulose
- Integration of chemo- and bio-catalysis to intensify bioprocesses
- Fabrication of starch-based packaging materials
- Potato thermoplastic starch nanocomposite films reinforced with nanocellulose
- Review on sago thermoplastic starch composite films reinforced with nanocellulose
- Wheat thermoplastic starch composite films reinforced with nanocellulose
- Synergistic effect in bimetallic gold catalysts: recent trends and prospects
- Simultaneous removal of methylene blue, copper Cu(II), and cadmium Cd(II) from synthetic wastewater using fennel-based adsorbents
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Articles in the same Issue
- Frontmatter
- Reviews
- Modern analytical approach in biopolymer characterization
- Development of nanocellulose fiber reinforced starch biopolymer composites: a review
- Recent developments in sago starch thermoplastic bio-composites
- Mechanical degradation of sugar palm crystalline nanocellulose reinforced thermoplastic sugar palm starch (TPS)/poly (lactic acid) (PLA) blend bionanocomposites in aqueous environments
- Computational design of the novel building blocks for the metal-organic frameworks based on the organic ligand protected Cu4 cluster
- Highly functional nanocellulose-reinforced thermoplastic starch-based nanocomposites
- Spectral peak areas do not vary according to spectral averaging scheme used in functional MRS experiments at 3 T with interleaved visual stimulation
- Triterpenoids of antibacterial extracts from the leaves of Bersama abyssinica Fresen (Francoaceae)
- Immediate effects of atrazine application on soil organic carbon and selected macronutrients and amelioration by sawdust biochar pretreatment
- Process configuration of combined ozonolysis and anaerobic digestion for wastewater treatment
- Concentration levels and risk assessment of organochlorine and organophosphate pesticide residue in selected cereals and legumes sold in Anambra State, south-eastern Nigeria
- XRD and cytotoxicity assay of submitted nanomaterial industrial samples in the Philippines
- Comparative study of the photocatalytic degradation of tetracycline under visible light irradiation using Bi24O31Br11-anchored carbonaceous and silicates catalyst support
- Xanthoangelol, geranilated chalcone compound, isolation from pudau leaves (Artocarpus kemando Miq.) as antibacterial and anticancer
- Barley thermoplastic starch nanocomposite films reinforced with nanocellulose
- Integration of chemo- and bio-catalysis to intensify bioprocesses
- Fabrication of starch-based packaging materials
- Potato thermoplastic starch nanocomposite films reinforced with nanocellulose
- Review on sago thermoplastic starch composite films reinforced with nanocellulose
- Wheat thermoplastic starch composite films reinforced with nanocellulose
- Synergistic effect in bimetallic gold catalysts: recent trends and prospects
- Simultaneous removal of methylene blue, copper Cu(II), and cadmium Cd(II) from synthetic wastewater using fennel-based adsorbents
- The investigation of the physical properties of an electrical porcelain insulator manufactured from locally sourced materials
- Concentration evaluation and risk assessment of pesticide residues in selected vegetables sold in major markets of Port Harcourt South-South Nigeria
- Detection of iodine in aqueous extract of plants through modified Mohr’s method
- Exploration of bioactive compounds from Mangifera indica (Mango) as probable inhibitors of thymidylate synthase and nuclear factor kappa-B (NF-Κb) in colorectal cancer management
- A new sphingoid derivative from Acacia hockii De Wild (Fabaceae) with antimicrobial and insecticidal properties
- Protection of wood against bio-attack and research of new effective and environmental friendly fungicides
- Computational investigation of Arbutus serratifolia Salisb molecules as new potential SARS-CoV-2 inhibitors
- Exploring the solvation of water molecules around radioactive elements in nuclear waste water treatment
