In silico design of antiviral peptides targeting the spike protein of SARS-CoV-2

•We find that there are highly homology in HR region of SARS-CoV-2 and SARS-CoV.•We firstly used molecular dynamics method in designing antivirus peptide.•Our antivirus peptide can prevent virus membrane fuse with host cell.•Furthermore, we first calculate the binding energy of HR1 and HR2 in SARS-C...

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Published in:Peptides (New York, N.Y. : 1980) N.Y. : 1980), 2020-08, Vol.130, p.170328-170328, Article 170328
Main Authors: Ling, Rongsong, Dai, Yarong, Huang, Boxuan, Huang, Wenjie, Yu, Jianfeng, Lu, Xifeng, Jiang, Yizhou
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Antiviral Agents - therapeutic use
Betacoronavirus - metabolism
Blocking peptide
Computer Simulation
Coronavirus Infections - drug therapy
COVID-19
Drug Design
Humans
Membrane Fusion
Molecular dynamics
Molecular Dynamics Simulation
Pandemics
Peptides - therapeutic use
Pneumonia, Viral - drug therapy
Protein Structure, Secondary
SARS-CoV-2
Sequence Alignment
Spike Glycoprotein, Coronavirus - antagonists & inhibitors
Spike Glycoprotein, Coronavirus - chemistry
Spike Glycoprotein, Coronavirus - metabolism
Spike protein
Viral Envelope Proteins - antagonists & inhibitors
Viral Envelope Proteins - chemistry
Viral Envelope Proteins - metabolism
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Summary:•We find that there are highly homology in HR region of SARS-CoV-2 and SARS-CoV.•We firstly used molecular dynamics method in designing antivirus peptide.•Our antivirus peptide can prevent virus membrane fuse with host cell.•Furthermore, we first calculate the binding energy of HR1 and HR2 in SARS-CoV-2 spike protein. An outbreak caused by 2019 novel coronavirus (2019-nCoV) was first identified in Wuhan City, Hubei Province, China. The new virus was later named SARS-CoV-2. The virus has affected tens of thousands of patients in the world. The infection of SARS-CoV-2 causes severe pneumonia and even death. It is urgently needed to find a therapeutic method to treat patients with SARS-CoV-2 infection. Studies showed that the surface spike (S) protein is essential for the coronavirus binding and entry of host cells. The heptad repeats 1 and 2 (HR1 and HR2) in the S protein play a decisive role in the fusion of the viral membrane with the host cell membrane. We predicted the HR1 and HR2 regions in S protein by sequence alignment. We simulated a computational model of HR1/2 regions and the fusion core. The binding energy of HR1 and HR2 of the fusion core was –33.4 kcal/mol. We then designed antivirus peptides by molecular dynamics simulation of the fusion core. The binding energy of HR2-based antiviral peptide to HR1 was −43.0 kcal/mol, which was stronger than the natural stage of the fusion core, suggesting that the predicted antiviral peptide can competitively bind with HR1 to prevent forming of the fusion core. The antiviral peptides can prevent SARS-CoV-2 membrane fusion and can potentially be used for the prevention and treatment of infections.
ISSN:0196-9781
1873-5169
DOI:10.1016/j.peptides.2020.170328