In Silico Screening of Natural Products as Potential Inhibitors of SARS-CoV-2 Using Molecular Docking Simulation

Recently a new virus strain designated as SARS coronavirus result in a fatal pandemic known as COVID-19. Bioinformatics and drug screening are directed for the assessment of potential inhibitors before their clinical implementation for the treatment of this fatal pneumonia. One of the expected natural potent inhibitors is Portulaca oleracea which has been assigned as an effective drug to different human ailments throughout the whole world. P. oleracea is widely spread in most areas of Egypt. In the current study, hydrophilic polysaccharides were purified from Portulaca oleracea extracts. Molecular docking simulation is implemented to investigate the antiviral effect of the purified polysaccharides to inhibit COVID-19. The viral protease was downloaded from a Protein Data Bank (PDB# 6y84) then docked with the potent inhibitors. The docking results indicate that the purified polysaccharides can bind tightly to the SARS-CoV-2 viral protease, which indicates that P. oleracea is a potential inhibitor for COVID-19.

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Discovery of Natural Product Compounds as Dengue Virus NS5 Methyltransferase Inhibitor Candidate through in Silico Method

Key Engineering Materials ◽

10.4028/www.scientific.net/kem.840.270 ◽

2020 ◽

Vol 840 ◽

pp. 270-276

Author(s):

Anjas Randy Bagastama ◽

Ahmad Husein Alkaff ◽

Usman Sumo Friend Tambunan

Keyword(s):

Molecular Docking ◽

Dengue Virus ◽

Natural Product ◽

In Silico ◽

Antiviral Agents ◽

Docking Simulation ◽

Simulation Method ◽

Molecular Docking Simulation ◽

Drug Candidates ◽

Natural Product Compounds

Dengue is a global health problem which predominantly affected the tropical and subtropical region of Asia, Africa, and America. However, there are no available antiviral agents to treat dengue virus (DENV) infection. This study was conducted to utilize natural product compounds as an inhibitor of NS5 Methyltransferase, a viral protein which plays an essential role in the synthesis of DENV RNA. The natural product compounds were collected from the Universal Natural Product Database (UNPD), totaling 229,000 compounds. The in silico screening of the natural product compounds was performed by molecular docking simulation method, which simulates the interaction of the compounds on the active site of the NS5 methyltransferase. From the molecular docking simulation, about 51 compounds showed better affinity and interaction compared to the standard compound, S-Adenosyl-L-Homocysteine (SAH). Then, a series of pharmacological tests were performed to find the best drug candidates by employing DataWarrior and SwissADME software. Finally, three natural product compounds, namely UNPD98966, UNPD183023, and UNDP104952, were regarded as the best inhibitor against NS5 methyltransferase based on its molecular affinity and interaction. These compounds also showed potential as drug candidates due to their desirable pharmacological properties.

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Molecular Docking Simulation based Virtual Screening for The Design of Potential Inhibitors of Heme Oxygenase of Corney Bacterium Diphtheria

International Journal of Recent Technology and Engineering - 2 ◽

10.35940/ijrte.a3411.078219 ◽

2019 ◽

Vol 8 (2) ◽

pp. 1086-1091

Keyword(s):

Molecular Docking ◽

Virtual Screening ◽

Docking Simulation ◽

Upper Respiratory Tract ◽

Molecular Docking Simulation ◽

Simulation Based ◽

Cardiac Muscles ◽

Oxidase Enzyme ◽

Corynebacterium Diphtheria ◽

Potential Inhibitors

Diphtheria is an infectious human disorder affecting upper respiratory tract which is characterized by fever, sore throat, and malaise. It is caused by Corynebacterium diphtheria and other pathogenic strains of Corynebacterium. The pathogen invades in the nasopharynx and infects the host by releasing an exotoxin leading to the severe concerns in thekidneys, nervous system and cardiac muscles. Sometimes diphtheria infections may be fatal because of the circulatory failure caused by myocarditis.Hemeoxygenase is the rate limiting enzyme in heme degradation and catalyzes the NADPHcytochrome P450 reductase-dependent cleavage of heme to biliverdin with the release of iron and carbon monoxide. In the present paper we have performed molecular docking simulation based in-silico virtual screening of an NCI diversity set-II containing 1593 diverse ligands to identify potential inhibitor of the Heme oxidase enzyme of Corneybacterium diphtheria. The lead molecules are shortlisted on the basis of their binding energy and these molecules are supposed to be further evaluated experimentally for development of a newer therapy for the treatment of diphtheria.

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Synthesis and in-silico molecular docking simulation of 3-chloro-4-substituted-1-(2-(1H-benzimidazol-2-yl)phenyl))-azetidin-2-ones as novel analgesic anti-inflammatory agent

Arabian Journal of Chemistry ◽

10.1016/j.arabjc.2012.04.038 ◽

2016 ◽

Vol 9 ◽

pp. S1779-S1785 ◽

Cited By ~ 5

Author(s):

Santosh S. Chhajed ◽

Chandrashekhar D. Upasani

Keyword(s):

Molecular Docking ◽

In Silico ◽

Docking Simulation ◽

Molecular Docking Simulation ◽

Inflammatory Agent ◽

Anti Inflammatory ◽

In Silico Molecular Docking ◽

Substituted 1

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Recognition of Natural Products as Potential Inhibitors of COVID-19 Main Protease (Mpro): In-Silico Evidences

Natural Products and Bioprospecting ◽

10.1007/s13659-020-00253-1 ◽

2020 ◽

Vol 10 (5) ◽

pp. 297-306 ◽

Cited By ~ 9

Author(s):

Rohan R. Narkhede ◽

Ashwini V. Pise ◽

Rameshwar S. Cheke ◽

Sachin D. Shinde

Keyword(s):

Natural Products ◽

Molecular Docking ◽

Antiviral Activity ◽

Drug Development ◽

In Silico ◽

Herbal Remedies ◽

Active Compounds ◽

Main Protease ◽

Future Drug ◽

Potential Inhibitors

Abstract SARS-CoV-2 (2019-nCoV) emerged in 2019 and proliferated rapidly across the globe. Scientists are attempting to investigate antivirals specific to COVID-19 treatment. The 2019-nCoV and SARS-CoV utilize the same receptor of the host which is COVID-19 of the main protease (Mpro).COVID-19 caused by SARS-CoV-2 is burdensome to overcome by presently acquired antiviral candidates. So the objective and purpose of this work was to investigate the plants with reported potential antiviral activity. With the aid of in silico techniques such as molecular docking and druggability studies, we have proposed several natural active compounds including glycyrrhizin, bicylogermecrene, tryptanthrine, β-sitosterol, indirubin, indican, indigo, hesperetin, crysophanic acid, rhein, berberine and β-caryophyllene which can be encountered as potential herbal candidate exhibiting anti-viral activity against SARS-CoV-2. Promising docking outcomes have been executed which evidenced the worthy of these selected herbal remedies for future drug development to combat coronavirus disease. Graphic Abstract

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