Volume 14 - Journal of Control, Vol. 14, No. 5, Special Issue on COVID-19
JoC 2021, 14 - Journal of Control, Vol. 14, No. 5, Special Issue on COVID-19: 39-47 |
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Abidi M, Soheilifard R, Hasanzadeh Ghasemi R. The effect of temperature on the binding affinity of Remdesivir and RdRp enzyme of SARS-COV-2 virus using steered molecular dynamics simulation. JoC 2021; 14 (S1) :39-47
URL: http://joc.kntu.ac.ir/article-1-815-en.html
URL: http://joc.kntu.ac.ir/article-1-815-en.html
1- Hakim Sabzevari University
Abstract: (5042 Views)
The fatal SARS-COV-2 virus appeared in China at the end of 2019 for the first time. This virus has similar sequence with SARS-COV in 2002, but its infection is very high rate. On the other hand, SARS-COV-2 is a RNA virus and requires RNA-dependent RNA polymerase (RdRp) to transcribe its viral genome. Due to the availability of the active site of this enzyme, an effective treatment is targeting it to inhibit SARS-COV-2 reproduction. Remdesivir is an inhibitor for Hepatitis C and Ebola that is approved by Food and Drug Administration. Also, it has shown good results in inhibition of main protease and RdRp enzyme of SARS-COV-2. In this paper, the inhibitory of Remdesivir in various temperatures has been observed using steered molecular dynamics simulation. For this reason, the binding affinity of Remdesivir and RdRp were evaluated by molecular docking at four different temperatures (from 17 to 47 °C). According to the results, the rupture force and pulling work to separate the Remdesivir from RdRp decrease with increasing temperature. It is also shown that at higher temperatures, Gibbs free energy is reduced due to its relation with pulling work.
Keywords: SARS-COV-2, RNA-dependent RNA polymerase, Molecular Docking, Steered Molecular Dynamics Simulation, Remdesivir
Type of Article: Research paper |
Subject:
COVID-19
Received: 2020/12/29 | Accepted: 2021/02/13 | Published: 2021/02/28
Received: 2020/12/29 | Accepted: 2021/02/13 | Published: 2021/02/28
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