scholarly journals Initial study on SARS-CoV-2 main protease inhibition mechanism of some potential drugs using molecular docking simulation

2020 ◽  
Vol 58 (6) ◽  
pp. 665
Author(s):  
Quan Minh PHAM ◽  
Thuy Huong Thi LE ◽  
Toan Quoc TRAN ◽  
Tung Son NGO ◽  
Dan Trong NGUYEN ◽  
...  
Keyword(s):  
Antiviral Treatment ◽  
Docking Simulation ◽  
Data Bank ◽  
Initial Study ◽  
Atomic Level ◽  
Inhibition Mechanism ◽  
Protease Inhibition ◽  
Molecular Docking Simulation ◽  
Main Protease ◽  
Docking Protocol

The infection by the new coronavirus SARS-CoV-2 (called as COVID-19 disease) is a worldwide emergency, however, there is no antiviral treatment or vaccine until now. The crystal structure of SARS-CoV-2 main protease has been made publicity in the Protein Data Bank recently. Many efforts have been conducted by scientists including the use of several commercial medicines, however, understanding at atomic level how these compounds prevent SARS-CoV-2 protease is still lacking. In this context docking protocol was employed to rapidly estimate the binding affinity and binding pose of six drugs on the main protease.

Investigating the Inhibition Effect of Portulaca oleracea against SARS-CoV-2 through Molecular Docking Simulation

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
El-Hoshoudy AN ◽  
◽  
Zaki EG ◽  
Elsaeed SM ◽  
◽  
...  
Keyword(s):  
Molecular Docking ◽  
Docking Simulation ◽  
Data Bank ◽  
Antiviral Effect ◽  
Portulaca Oleracea ◽  
Clinical Implementation ◽  
Viral Protease ◽  
Molecular Docking Simulation ◽  
Inhibition Effect ◽  
Potential Inhibitors

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.

Potential Leads from Liquorice against SARS-CoV-2 Main Protease using Molecular Docking Simulation Studies

2020 ◽  
Vol 23 ◽  
Author(s):  
Saurabh K. Sinha ◽  
Satyendra K. Prasad ◽  
Md Ataul Islam ◽  
Sushil K. Chaudhary ◽  
Shashikant Singh ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Glycyrrhizic Acid ◽  
Docking Simulation ◽  
Simulation Studies ◽  
Autodock Vina ◽  
Molecular Docking Simulation ◽  
Global Pandemic ◽  
Main Protease ◽  
Pandemic Threat ◽  
Inhibitory Potential

Aim and Objective: At present, the world is facing a global pandemic threat of SARS-CoV-2 or COVID-19 and till date, there are no clinically approved vaccines or antiviral drugs available for the treatment of coronavirus infections. Studies conducted in China recommended the use of liquorice (Glycyrrhiza species), an integral medicinal herb of traditional Chinese medicine in the deactivation of COVID-19. Therefore, the present investigation was undertaken to identify the leads from the liquorice plant against COVID-19 using molecular docking simulation studies. Materials and Methods: A set of reported bioactive compounds of liquorice were investigated for COVID-19 main protease (Mpro) inhibitory potential. The study was conducted on Autodock vina software using COVID-19 Mpro as a target protein having PDB ID: 6LU7. Results: Out of the total 20 docked compounds, only six compounds showed the best affinity towards the protein target, which included glycyrrhizic acid, isoliquiritin apioside, glyasperin A, liquiritin, 1-methoxyphaseollidin and hedysarimcoumestan B. From the overall observation, glycyrrhizic acid followed by isoliquiritin apioside demonstrated the best affinity towards Mpro representing the binding energy of -8.6 and -7.9 Kcal/mol respectively. Nevertheless, the other four compounds were also quite comparable with the later one. Conclusion: From the present investigation, we conclude that the compounds having oxane ring and chromenone ring substituted with hydroxyl 3-methylbut-2-enyl group could be the best alternative for the development of new leads from liquorice plant against COVID-19.

scholarly journals CONSTRUCTION AND OPTIMIZATION OF STRUCTURE-BASED VIRTUAL SCREENING PROTOCOLS TO IDENTIFY CYCLOOXYGENASE-1 INHIBITORS USING OPEN BABEL, SPORES AND PLANTS

2012 ◽  
Vol 12 (2) ◽  
pp. 141-145
Author(s):  
Enade Perdana Istyastono
Keyword(s):  
Virtual Screening ◽  
Docking Simulation ◽  
Data Bank ◽  
Mean Square ◽  
Computational Statistics ◽  
Molecular Docking Simulation ◽  
Cyclooxygenase 1 ◽  
Reference Protein ◽  
Reference Ligand ◽  
Cox 1

Structure-Based Virtual Screening (SBVS) protocols to identify cyclooxygenase-1 (COX-1) inhibitors have been constructed and optimized based on their Root Mean Square Deviation (RMSD) values of the docked pose and the crystal structure pose of the reference ligand. Employing a COX-1 structure obtained from the Protein Data Bank (pdb) with code 2OYE as the reference protein and PLANTS1.2 as the molecular docking simulation program, the SBVS protocols were mainly built. The preparation steps involved SPORES and Open Babel, while the results analysis involved PyMOL to calculate the RMSD and R computational statistics software to perform the statistics calculations. The results show that these construction and optimization processes could provide an SBVS protocol to identify COX-1 inhibitors that is accurately able to redock the reference ligand with the RMSD value of 0.633 Å.

scholarly journals Biological activity, molecular docking, and ADME predictions of amphibine analogues of Ziziphus spina-christi towards SARS-CoV-2 Mpro

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Taufik Muhammad Fakih ◽  
Dwi Syah Fitra Ramadhan ◽  
Fitrianti Darusman
Keyword(s):  
Biological Activity ◽  
Molecular Docking ◽  
Binding Energy ◽  
Docking Simulation ◽  
Oral Drug ◽  
Molecular Docking Simulation ◽  
Main Protease ◽  
Promising Target ◽  
Quantum Espresso ◽  
Native Ligand

The main protease of the SARS-CoV-2 virus, SARS-CoV-2 Mpro, can be discovered as a promising target to treat the COVID-19 pandemic. The peptide-based inhibitors may present better options than small molecules for inhibits SARS-CoV-2 Mpro. Ziziphus spina-christi species reported have a peptide-based of alkaloids group, i.e. Amphibine that the analogues can be identified the potential as an inhibitor of SARS-CoV-2 Mpro. The compound structure was drawn and optimized using semi-empirical AM-1 method using Quantum ESPRESSO v.6.6, then the biological activity using PASS Prediction server and molecular docking simulation using MGLTools 1.5.6 with AutoDock 4.2 were performed. Afterward, the ADME profiles were predicted using the SWISS-ADME server. PASS server was predicting Amphibine B-F and H showed potency both as antiviral and as a protease inhibitor. The molecular docking simulation of Amphibine analogues showed lower binding energy than the native ligand. The binding energy of the native ligand was −7.69 Kcal/mol compared to the lowest binding energy of Amphibine analogues was −10.10 Kcal/mol (Amphibine-F). The ADME prediction showed, as an oral drug Amphibine-F has the best bioavailability, Amphibine-B, C, and D have good bioavailability, and Amphibine-E and H have poor bioavailability. Concluded, Amphibine B-F and H of Amphibine analogues showed potency as COVID-19 treatment targeting SARS-CoV-2 Mpro.

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.

Enzyme activity enhancement of chondroitinase ABC I from Proteus vulgaris by site-directed mutagenesis

RSC Advances ◽  
2015 ◽  
Vol 5 (93) ◽  
pp. 76040-76047 ◽  
Author(s):  
Zhenya Chen ◽  
Ye Li ◽  
Yue Feng ◽  
Liang Chen ◽  
Qipeng Yuan
Keyword(s):  
Active Site ◽  
Simulation Analysis ◽  
Docking Simulation ◽  
Site Directed Mutagenesis ◽  
Directed Mutagenesis ◽  
Wild Type ◽  
Proteus Vulgaris ◽  
Molecular Docking Simulation ◽  
Activity Enhancement ◽  
First Time

Arg660 was found as a new active site and Asn795Ala and Trp818Ala mutants showed higher activities than the wild type based on molecular docking simulation analysis for the first time.

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