Investigation on penetration of saffron components through lipid bilayer bound to spike protein of SARS-CoV-2 using steered molecular dynamics simulation
A coronavirus identified as COVID-19 is the reason for an infection outbreak which is started in December 2019. NO completely effective drugs and treatments are not recognized for this virus. Recently, saffron and its compounds were used to treat different viral diseases. Saffron extract and its maj...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2020-12-01
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| Series: | Heliyon |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S240584402032524X |
| _version_ | 1818662136687099904 |
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| author | Azadeh Kordzadeh Ahmad Ramazani Saadatabadi Amin Hadi |
| author_facet | Azadeh Kordzadeh Ahmad Ramazani Saadatabadi Amin Hadi |
| author_sort | Azadeh Kordzadeh |
| collection | DOAJ |
| description | A coronavirus identified as COVID-19 is the reason for an infection outbreak which is started in December 2019. NO completely effective drugs and treatments are not recognized for this virus. Recently, saffron and its compounds were used to treat different viral diseases. Saffron extract and its major ingredients have shown antiviral effects. In this study, the steered molecular dynamics simulation was used for investigating the effect of four main components of saffron that include: crocin, crocetin, safranal, and picrocrocin as candidate for drug molecules, on COVID-19. The binding energies between drug molecules and spike protein and the main protease of the virus were evaluated. The obtained results based on Lennard-Jones and electrostatic potentials demonstrated that crocetin has a high affinity towards spike protein and also the main protease of the virus. Also, the quantum mechanics calculations elucidated that the crocetin could overcome energy barrier of lipid bilayer with strong dipole moment and polarizability. The pharmacokinetic and ADMET properties proved that crocetin could be a suitable drug candidate. So, crocetin could be a promising drug for treatment of COVID-19. |
| first_indexed | 2024-12-17T04:56:09Z |
| format | Article |
| id | doaj.art-34f709127e854b3c8c299a5a2b1850a1 |
| institution | Directory Open Access Journal |
| issn | 2405-8440 |
| language | English |
| last_indexed | 2024-12-17T04:56:09Z |
| publishDate | 2020-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Heliyon |
| spelling | doaj.art-34f709127e854b3c8c299a5a2b1850a12022-12-21T22:02:41ZengElsevierHeliyon2405-84402020-12-01612e05681Investigation on penetration of saffron components through lipid bilayer bound to spike protein of SARS-CoV-2 using steered molecular dynamics simulationAzadeh Kordzadeh0Ahmad Ramazani Saadatabadi1Amin Hadi2Chemial and Petroleum Egineering Department, Sharif University of Technology, Tehran, IranChemial and Petroleum Egineering Department, Sharif University of Technology, Tehran, Iran; Corresponding author.Cellular and Molecular Research Center, School of Medicine, Yasuj University of Medical Sciences, Yasuj, Iran; Corresponding author.A coronavirus identified as COVID-19 is the reason for an infection outbreak which is started in December 2019. NO completely effective drugs and treatments are not recognized for this virus. Recently, saffron and its compounds were used to treat different viral diseases. Saffron extract and its major ingredients have shown antiviral effects. In this study, the steered molecular dynamics simulation was used for investigating the effect of four main components of saffron that include: crocin, crocetin, safranal, and picrocrocin as candidate for drug molecules, on COVID-19. The binding energies between drug molecules and spike protein and the main protease of the virus were evaluated. The obtained results based on Lennard-Jones and electrostatic potentials demonstrated that crocetin has a high affinity towards spike protein and also the main protease of the virus. Also, the quantum mechanics calculations elucidated that the crocetin could overcome energy barrier of lipid bilayer with strong dipole moment and polarizability. The pharmacokinetic and ADMET properties proved that crocetin could be a suitable drug candidate. So, crocetin could be a promising drug for treatment of COVID-19.http://www.sciencedirect.com/science/article/pii/S240584402032524XSARS-CoV-2Molecular dynamics simulationCrocinCrocetinSafranalPicrocrocin |
| spellingShingle | Azadeh Kordzadeh Ahmad Ramazani Saadatabadi Amin Hadi Investigation on penetration of saffron components through lipid bilayer bound to spike protein of SARS-CoV-2 using steered molecular dynamics simulation Heliyon SARS-CoV-2 Molecular dynamics simulation Crocin Crocetin Safranal Picrocrocin |
| title | Investigation on penetration of saffron components through lipid bilayer bound to spike protein of SARS-CoV-2 using steered molecular dynamics simulation |
| title_full | Investigation on penetration of saffron components through lipid bilayer bound to spike protein of SARS-CoV-2 using steered molecular dynamics simulation |
| title_fullStr | Investigation on penetration of saffron components through lipid bilayer bound to spike protein of SARS-CoV-2 using steered molecular dynamics simulation |
| title_full_unstemmed | Investigation on penetration of saffron components through lipid bilayer bound to spike protein of SARS-CoV-2 using steered molecular dynamics simulation |
| title_short | Investigation on penetration of saffron components through lipid bilayer bound to spike protein of SARS-CoV-2 using steered molecular dynamics simulation |
| title_sort | investigation on penetration of saffron components through lipid bilayer bound to spike protein of sars cov 2 using steered molecular dynamics simulation |
| topic | SARS-CoV-2 Molecular dynamics simulation Crocin Crocetin Safranal Picrocrocin |
| url | http://www.sciencedirect.com/science/article/pii/S240584402032524X |
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