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Israa Mohamed Shamkh
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Development of SARS-CoV-2 Inhibitors Using Molecular Docking Study with Different Coronavirus Spike Protein and ACE2 Israa Mohamed Shamkh; Dina Pratiwi
Journal of Molecular Docking Vol 1 No 1 (2021): Journal of Molecular Docking
Publisher : Institute for Research and Community Services Universitas Muhammadiyah Palangkaraya

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (957.657 KB) | DOI: 10.33084/jmd.v1i1.2212

Abstract

The novel coronavirus SARS-CoV-2 is an acute respiratory tract infection that emerged in Wuhan city, China. The spike protein of coronaviruses is the main driving force for host cell recognition and is responsible for binding to the ACE2 receptor on the host cell and mediates the fusion of host and viral membranes. Recognizing compounds that could form a complex with the spike protein (S-protein) potently could inhibit SARS-CoV-2 infections. The software was used to survey 300 plant natural compounds or derivatives for their binding ability with the SARS-CoV-2 S-protein. The docking score for ligands towards each protein was calculated to estimate the binding free energy. Four compounds showed a strong ability to bind with the S-protein (neohesperidin, quercetin 3-O-rutinoside-7-O-glucoside, 14-ketostypodiol diacetate, and hydroxypropyl methylcellulose) and used to predict its docking model and binding regions. The highest predicted ligand/protein affinity was with quercetin 3-O-rutinoside-7-O-glucoside followed by neohesperidin. The four compounds were also tested against other related coronavirus and showed their binding ability to S-protein of the bat, SARS, and MERS coronavirus strains, indicating that they could bind and block the spike activities and subsequently prevent them infection of different coronaviruses. Molecular docking also showed the probability of the four ligands binding to the host cell receptor ACE2. The interaction residues and the binding energy for the complexes were identified. The strong binding ability of the four compounds to the S-protein and the ACE2 protein indicates that they might be used to develop therapeutics specific against SARS-CoV-2 and close related human coronaviruses.
In Silico Study for Similar FDA Approved Drugs as Inhibitors of SARS-CoV-2 Spike and the Host Receptor Proteins Israa Mohamed Shamkh; Dina Pratiwi; Hanaa S. Omar; Nour El-Houda A. Reyad
Journal of Molecular Docking Vol 1 No 2 (2021): Journal of Molecular Docking
Publisher : Institute for Research and Community Services Universitas Muhammadiyah Palangkaraya

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (667.464 KB) | DOI: 10.33084/jmd.v1i2.2213

Abstract

The severe acute respiratory syndrome coronavirus 2, known as COVID-19, has been hideously increased worldwide. The disease began in Wuhan, China, around December 2019, then spread to most countries. Social distancing is the best procedure to prevent infection. Screening the available database containing millions of drug molecules or phytochemicals has become rapid and straightforward because of the computer-aided drug design (CADD) methods. In the present study, 300 phytochemicals and cellulose ether derivatives are screened through a docking study. Docking analysis showed that only four molecules (a-neohesperidin, quercetin 3-O-glucosylrutinoside, 14-ketostypodiol diacetate, and hydroxypropyl methylcellulose) were able to interact with the spike protein. However, two among them (quercetin 3-O-glucosylrutinoside and 14-ketostypodiol diacetate) could interact with the host cell receptor (ACE2) of SARS-CoV-2. The binding affinity of the four compounds is high. Still, according to Lipinski's rule of five, only 14-ketostypodiol diacetate was selected as a drug molecule due to its pharmacokinetic and ADMET properties. Screening for drug analogs to the 14-ketostypodiol diacetate detected five approved drugs. Docking analysis of these drugs with the target proteins showed that the five drugs interact with the host receptor protein, and three interact with viral spike protein. Accordingly, we suggest that molecular docking and drug analogs studies could support rapid drug development. In addition, future perspectives on therapeutic applications of 14-ketostypodiol diacetate are required for using it against SARS-CoV-2 infections.
Corrigendum to "Development of SARS-CoV-2 Inhibitors Using Molecular Docking Study with Different Coronavirus Spike Protein and ACE2” [J Mol Docking. 2021;1(2):1-14] Israa Mohamed Shamkh; Dina Pratiwi; Hanaa S. Omar
Journal of Molecular Docking Vol 1 No 2 (2021): Journal of Molecular Docking
Publisher : Institute for Research and Community Services Universitas Muhammadiyah Palangkaraya

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (118.455 KB) | DOI: 10.33084/jmd.v1i2.3063

Abstract

Authors have found an error in the previous version (Shamkh, IM, & Pratiwi, D. (2021). Development of SARS-CoV-2 Inhibitors Using Molecular Docking Study with Different Coronavirus Spike Protein and ACE2. Journal of Molecular Docking, 1(1), 1-14. https://doi.org/10.33084/jmd.v1i1.2212), of which Dr. Hanaa S. Omar as supervisor of the research, is not listed as one of the authors. In this note, Dr. Hanaa S. Omar was added as one of the authors, with the status of the corresponding author in the study.
Co-Authors Dina Pratiwi Hanaa S. Omar Nour El-Houda A. Reyad