In silico evaluation of COVID-19 main protease interactions with honeybee natural products for discovery of high potential antiviral compounds

2021 ◽  
pp. 1-7
Author(s):  
Armin Zarei ◽  
Ali Ramazani ◽  
Saeed Pourmand ◽  
Ahmad Sattari ◽  
Aram Rezaei ◽  
...  
Keyword(s):  
Natural Products ◽  
In Silico ◽  
High Potential ◽  
Antiviral Compounds ◽  
Main Protease

scholarly journals An Overview of Coronaviruses: In-Silico Approach to Decipher Anti-SARS-CoV-2 Natural Products

2020 ◽  
Author(s):  
Patil Shivprasad Suresh ◽  
Shiv Shankar Gupta ◽  
Anmol Sharma ◽  
Upendra Sharma
Keyword(s):  
Natural Products ◽  
In Silico ◽  
Natural Source ◽  
Effective Drug ◽  
Drug Molecule ◽  
Current Crisis ◽  
Docking Score ◽  
Lead Compounds ◽  
Main Protease ◽  
Molecule Docking

In current study, we have focused on the outline of different coronaviruses including COVID-19, along with potential therapeutic targets of SARC-CoV-2. Moreover, experimentally evident anti-coronavirus natural molecules were subjected for <i>in silico</i> screening against M<sup>pro</sup> and RdRp of COVID-19, in order to predict effective cure agent for same.Docking analysis have revealed hit molecules namely tetra-<i>O</i>-galloyl-<i>β</i>-D-glucose (<b>2</b>) and juglanin (<b>25</b>) against main protease, in reference of N3 molecule (docking score = -5.95 Kcal/mol), while glycyrrhizin (<b>1</b>) and tetra-<i>O</i>-galloyl-β-D-glucose (<b>2</b>) are good against RdRp in reference of Remdesivir (docking score = -4.23 Kcal/mol). <i>In-silico</i> parameter revealed three lead compounds i.e. glycyrrhizin (<b>1</b>), tetra-<i>O</i>-galloyl-β-D-glucose (<b>2</b>) and juglanin (<b>25</b>) which can be seen as hopeful molecule for COVID-19 treatment in upcoming time. Overall review lesson is to develop a specific and effective drug molecule against the current crisis i.e. COVID-19 derived from natural source.<p></p> <br>

scholarly journals An Overview of Coronaviruses: In-Silico Approach to Decipher Anti-SARS-CoV-2 Natural Products

2020 ◽  
Author(s):  
Patil Shivprasad Suresh ◽  
Shiv Shankar Gupta ◽  
Anmol Sharma ◽  
Upendra Sharma
Keyword(s):  
Natural Products ◽  
In Silico ◽  
Natural Source ◽  
Effective Drug ◽  
Drug Molecule ◽  
Current Crisis ◽  
Docking Score ◽  
Lead Compounds ◽  
Main Protease ◽  
Molecule Docking

In current study, we have focused on the outline of different coronaviruses including COVID-19, along with potential therapeutic targets of SARC-CoV-2. Moreover, experimentally evident anti-coronavirus natural molecules were subjected for <i>in silico</i> screening against M<sup>pro</sup> and RdRp of COVID-19, in order to predict effective cure agent for same.Docking analysis have revealed hit molecules namely tetra-<i>O</i>-galloyl-<i>β</i>-D-glucose (<b>2</b>) and juglanin (<b>25</b>) against main protease, in reference of N3 molecule (docking score = -5.95 Kcal/mol), while glycyrrhizin (<b>1</b>) and tetra-<i>O</i>-galloyl-β-D-glucose (<b>2</b>) are good against RdRp in reference of Remdesivir (docking score = -4.23 Kcal/mol). <i>In-silico</i> parameter revealed three lead compounds i.e. glycyrrhizin (<b>1</b>), tetra-<i>O</i>-galloyl-β-D-glucose (<b>2</b>) and juglanin (<b>25</b>) which can be seen as hopeful molecule for COVID-19 treatment in upcoming time. Overall review lesson is to develop a specific and effective drug molecule against the current crisis i.e. COVID-19 derived from natural source.<p></p> <br>

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

2020 ◽  
Vol 10 (5) ◽  
pp. 297-306 ◽  
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

In Silico Molecular Docking and Molecular Dynamic Simulation of Potential Inhibitors of 3C-like Main Proteinase (3CLpro) from Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) Using Selected African Medicinal Plants

2020 ◽  
Author(s):  
Sahar Qazi ◽  
Mustafa Alhaji Isa ◽  
Adam Mustapha ◽  
Khalid Raza ◽  
Ibrahim Alkali Allamin ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Severe Acute Respiratory Syndrome ◽  
In Silico ◽  
Md Simulation ◽  
Binding Energies ◽  
Anacardium Occidentale ◽  
Upper Respiratory Tract ◽  
Ligand Complex ◽  
In Silico Docking ◽  
Main Protease

<p>The Severe Acute Respiratory Syndrome 2 (SARS-CoV-2) is an infectious virus that causes mild to severe life-threatening upper respiratory tract infection. The virus emerged in Wuhan, China in 2019, and later spread across the globe. Its genome has been completely sequenced and based on the genomic information, the virus possessed 3C-Like Main Protease (3CLpro), an essential multifunctional enzyme that plays a vital role in the replication and transcription of the virus by cleaving polyprotein at eleven various sites to produce different non-structural proteins. This makes the protein an important target for drug design and discovery. Herein, we analyzed the interaction between the 3CLpro and potential inhibitory compounds identified from the extracts of <i>Zingiber offinale</i> and <i>Anacardium occidentale</i> using in silico docking and Molecular Dynamics (MD) Simulation. The crystal structure of SARS-CoV-2 main protease in complex with 02J (5-Methylisoxazole-3-carboxylic acid) and PEJ (composite ligand) (PDB Code: 6LU7,2.16Å) retrieved from Protein Data Bank (PDB) and subject to structure optimization and energy minimization. A total of twenty-nine compounds were obtained from the extracts of <i>Zingiber offinale </i>and the leaves of <i>Anacardium occidentale. </i>These compounds were screened for physicochemical (Lipinski rule of five, Veber rule, and Egan filter), <i>Pan</i>-Assay Interference Structure (PAINS), and pharmacokinetic properties to determine the Pharmaceutical Active Ingredients (PAIs). Of the 29 compounds, only nineteen (19) possessed drug-likeness properties with efficient oral bioavailability and less toxicity. These compounds subjected to molecular docking analysis to determine their binding energies with the 3CLpro. The result of the analysis indicated that the free binding energies of the compounds ranged between ˗5.08 and -10.24kcal/mol, better than the binding energies of 02j (-4.10kcal/mol) and PJE (-5.07kcal.mol). Six compounds (CID_99615 = -10.24kcal/mol, CID_3981360 = 9.75kcal/mol, CID_9910474 = -9.14kcal/mol, CID_11697907 = -9.10kcal/mol, CID_10503282 = -9.09kcal/mol and CID_620012 = -8.53kcal/mol) with good binding energies further selected and subjected to MD Simulation to determine the stability of the protein-ligand complex. The results of the analysis indicated that all the ligands form stable complexes with the protein, although, CID_9910474 and CID_10503282 had a better stability when compared to other selected phytochemicals (CID_99615, CID_3981360, CID_620012, and CID_11697907). </p>

In Silico Molecular Docking and Molecular Dynamic Simulation of Potential Inhibitors of 3C-like Main Proteinase (3CLpro) from Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) Using Selected African Medicinal Plants

2020 ◽  
Author(s):  
Sahar Qazi ◽  
Mustafa Alhaji Isa ◽  
Adam Mustapha ◽  
Khalid Raza ◽  
Ibrahim Alkali Allamin ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Severe Acute Respiratory Syndrome ◽  
In Silico ◽  
Md Simulation ◽  
Binding Energies ◽  
Anacardium Occidentale ◽  
Upper Respiratory Tract ◽  
Ligand Complex ◽  
In Silico Docking ◽  
Main Protease

<p>The Severe Acute Respiratory Syndrome 2 (SARS-CoV-2) is an infectious virus that causes mild to severe life-threatening upper respiratory tract infection. The virus emerged in Wuhan, China in 2019, and later spread across the globe. Its genome has been completely sequenced and based on the genomic information, the virus possessed 3C-Like Main Protease (3CLpro), an essential multifunctional enzyme that plays a vital role in the replication and transcription of the virus by cleaving polyprotein at eleven various sites to produce different non-structural proteins. This makes the protein an important target for drug design and discovery. Herein, we analyzed the interaction between the 3CLpro and potential inhibitory compounds identified from the extracts of <i>Zingiber offinale</i> and <i>Anacardium occidentale</i> using in silico docking and Molecular Dynamics (MD) Simulation. The crystal structure of SARS-CoV-2 main protease in complex with 02J (5-Methylisoxazole-3-carboxylic acid) and PEJ (composite ligand) (PDB Code: 6LU7,2.16Å) retrieved from Protein Data Bank (PDB) and subject to structure optimization and energy minimization. A total of twenty-nine compounds were obtained from the extracts of <i>Zingiber offinale </i>and the leaves of <i>Anacardium occidentale. </i>These compounds were screened for physicochemical (Lipinski rule of five, Veber rule, and Egan filter), <i>Pan</i>-Assay Interference Structure (PAINS), and pharmacokinetic properties to determine the Pharmaceutical Active Ingredients (PAIs). Of the 29 compounds, only nineteen (19) possessed drug-likeness properties with efficient oral bioavailability and less toxicity. These compounds subjected to molecular docking analysis to determine their binding energies with the 3CLpro. The result of the analysis indicated that the free binding energies of the compounds ranged between ˗5.08 and -10.24kcal/mol, better than the binding energies of 02j (-4.10kcal/mol) and PJE (-5.07kcal.mol). Six compounds (CID_99615 = -10.24kcal/mol, CID_3981360 = 9.75kcal/mol, CID_9910474 = -9.14kcal/mol, CID_11697907 = -9.10kcal/mol, CID_10503282 = -9.09kcal/mol and CID_620012 = -8.53kcal/mol) with good binding energies further selected and subjected to MD Simulation to determine the stability of the protein-ligand complex. The results of the analysis indicated that all the ligands form stable complexes with the protein, although, CID_9910474 and CID_10503282 had a better stability when compared to other selected phytochemicals (CID_99615, CID_3981360, CID_620012, and CID_11697907). </p>

In-silico Analyses of Natural Products on Leishmania Enzyme Targets

2015 ◽  
Vol 15 (3) ◽  
pp. 253-269 ◽  
Author(s):  
L. Scotti ◽  
H. Ishiki ◽  
F.J.B. Mendonca ◽  
M.S. Silva ◽  
M.T. Scotti
Keyword(s):  
Natural Products ◽  
In Silico ◽  
In Silico Analyses

Virtual Screening, Molecular docking and in-silico ADME-Tox analysis for identification of potential main protease (Mpro) enzyme inhibitors

2020 ◽  
Vol 18 ◽  
Author(s):  
Debadash Panigrahi ◽  
Ganesh Prasad Mishra
Keyword(s):  
Molecular Docking ◽  
Virtual Screening ◽  
In Silico ◽  
Data Bank ◽  
Future Research ◽  
Reference Compound ◽  
Unexpected Death ◽  
Main Protease ◽  
In Silico Admet

Objective:: Recent pandemic caused by SARS-CoV-2 described in Wuhan China in December-2019 spread widely almost all the countries of the world. Corona virus (COVID-19) is causing the unexpected death of many peoples and severe economic loss in several countries. Virtual screening based on molecular docking, drug-likeness prediction, and in silico ADMET study has become an effective tool for the identification of small molecules as novel antiviral drugs to treat diseases. Methods:: In the current study, virtual screening was performed through molecular docking for identifying potent inhibitors against Mpro enzyme from the ZINC library for the possible treatment of COVID-19 pandemic. Interestingly, some compounds are identified as possible anti-covid-19 agents for future research. 350 compounds were screened based on their similarity score with reference compound X77 from ZINC data bank and were subjected to docking with crystal structure available of Mpro enzyme. These compounds were then filtered by their in silico ADME-Tox and drug-likeness prediction values. Result:: Out of these 350 screened compounds, 10 compounds were selected based on their docking score and best docked pose in comparison to the reference compound X77. In silico ADME-Tox and drug likeliness predictions of the top compounds were performed and found to be excellent results. All the 10 screened compounds showed significant binding pose with the target enzyme main protease (Mpro) enzyme and satisfactory pharmacokinetic and toxicological properties. Conclusion:: Based on results we can suggest that the identified compounds may be considered for therapeutic development against the COVID-19 virus and can be further evaluated for in vitro activity, preclinical, clinical studies and formulated in a suitable dosage form to maximize their bioavailability.

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