Deciphering ACE2-RBD binding affinity through peptide scanning: A molecular dynamics simulation approach

Tang，Jiahu1,2; Hu，Ruibin1,3; Liu，Yiyi1; Liu，Jingchao4; Wang，Guanghui1; Lv，Jiahui1; Cheng，Li1; He，Tingzhen1; Liu，Ying1; Shao，Pan Lin2; Zhang，Bo1

2024-05-01

10.1016/j.compbiomed.2024.108325

Computers in Biology and Medicine   影响因子和分区

0010-4825

1879-0534

Rapid discovery of target information for protein-protein interactions (PPIs) is significant in drug design, diagnostics, vaccine development, antibody therapy, etc. Peptide microarray is an ideal tool for revealing epitope information of PPIs. In this work, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) spike receptor-binding domain (RBD) and the host cell receptor angiotensin-converting enzyme 2 (ACE2) were introduced as a model to study the epitope information of RBD-specific binding to ACE2 via a combination of theoretical calculations and experimental validation. Through dock and molecular dynamics simulations, it was found that among the 22 peptide fragments that consist of RBD, #14 (YNYLYRLFRKSNLKP) has the highest binding strength. Subsequently, the experiments of peptide microarray constructed based on plasmonic materials chip also confirmed the theoretical calculation data. Compared to other methods, such as phage display technology and surface plasmon resonance (SPR), this method is rapid and cost-effective, providing insights into the investigation of pathogen invasion processes and the timely development of peptide drugs and other fields.

Molecular dynamics simulation Peptides Plasmonic materials Protein-protein interactions SARS-CoV-2

EI

英语

第一 ; 通讯

COMPUTER SCIENCE

2-s2.0-85188516966

Scopus

1.Guangdong Provincial Key Laboratory of Advanced Biomaterials,Department of Biomedical Engineering,Southern University of Science and Technology,Shenzhen,518055,China
2.Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease,School of Pharmaceutical Sciences & the Fifth Affiliated Hospital,Guangzhou Medical University,Guangzhou,511436,China
3.Xianghu Laboratory,Hangzhou,311231,China
4.Institute of Forestry and Pomology,Tianjin Academy of Agricultural Sciences,Tianjin,300384,China

Tang，Jiahu,Hu，Ruibin,Liu，Yiyi,et al. Deciphering ACE2-RBD binding affinity through peptide scanning: A molecular dynamics simulation approach[J]. Computers in Biology and Medicine,2024,173.

Tang，Jiahu.,Hu，Ruibin.,Liu，Yiyi.,Liu，Jingchao.,Wang，Guanghui.,...&Zhang，Bo.(2024).Deciphering ACE2-RBD binding affinity through peptide scanning: A molecular dynamics simulation approach.Computers in Biology and Medicine,173.

Tang，Jiahu,et al."Deciphering ACE2-RBD binding affinity through peptide scanning: A molecular dynamics simulation approach".Computers in Biology and Medicine 173(2024).