Tags

Type your tag names separated by a space and hit enter

In silico design of antiviral peptides targeting the spike protein of SARS-CoV-2.
Peptides. 2020 08; 130:170328.P

Abstract

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.

Authors+Show Affiliations

Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China.Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China.Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China.Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China.Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China.Department of Physiology, Health Science Center, Shenzhen University, Guangdong 518055, China. Electronic address: x.lu@szu.edu.cn.Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China. Electronic address: jiangyz@szu.edu.cn.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

32380200

Citation

Ling, Rongsong, et al. "In Silico Design of Antiviral Peptides Targeting the Spike Protein of SARS-CoV-2." Peptides, vol. 130, 2020, p. 170328.
Ling R, Dai Y, Huang B, et al. In silico design of antiviral peptides targeting the spike protein of SARS-CoV-2. Peptides. 2020;130:170328.
Ling, R., Dai, Y., Huang, B., Huang, W., Yu, J., Lu, X., & Jiang, Y. (2020). In silico design of antiviral peptides targeting the spike protein of SARS-CoV-2. Peptides, 130, 170328. https://doi.org/10.1016/j.peptides.2020.170328
Ling R, et al. In Silico Design of Antiviral Peptides Targeting the Spike Protein of SARS-CoV-2. Peptides. 2020;130:170328. PubMed PMID: 32380200.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - In silico design of antiviral peptides targeting the spike protein of SARS-CoV-2. AU - Ling,Rongsong, AU - Dai,Yarong, AU - Huang,Boxuan, AU - Huang,Wenjie, AU - Yu,Jianfeng, AU - Lu,Xifeng, AU - Jiang,Yizhou, Y1 - 2020/05/05/ PY - 2020/03/19/received PY - 2020/04/16/revised PY - 2020/04/30/accepted PY - 2020/5/8/pubmed PY - 2020/7/21/medline PY - 2020/5/8/entrez KW - Blocking peptide KW - Molecular dynamics KW - SARS-CoV-2 KW - Spike protein SP - 170328 EP - 170328 JF - Peptides JO - Peptides VL - 130 N2 - 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. SN - 1873-5169 UR - https://www.unboundmedicine.com/medline/citation/32380200/In_silico_design_of_antiviral_peptides_targeting_the_spike_protein_of_SARS_CoV_2_ DB - PRIME DP - Unbound Medicine ER -