肽
生物信息学
抗菌肽
抗菌剂
冠状病毒
配体(生物化学)
化学
病毒学
穗蛋白
生物
2019年冠状病毒病(COVID-19)
计算生物学
严重急性呼吸综合征冠状病毒2型(SARS-CoV-2)
严重急性呼吸综合征冠状病毒
受体
肽序列
生物化学
微生物学
医学
基因
传染病(医学专业)
疾病
病理
作者
Ritu Bansal,Sanika Mohagaonkar,Anamitra Sen,Uzma Khanam,Brijesh Rathi
标识
DOI:10.1007/s40203-021-00103-z
摘要
This study is an attempt to find a suitable therapy using antimicrobial peptides (AMPs) by identifying peptide-protein interaction of AMPs and nucleocapsid protein of SARS and SARS-CoV- 2. The AMPs were shortlisted from the APD3 database (Antimicrobial peptide database) based on various physicochemical parameters. The binding efficacy of AMPs was measured using the lowest energy score of the docked complexes with 10 selected AMPs. For SARS-CoV, AP00180 showed the best pose with a binding affinity value of - 6.4 kcal/mol. Prominent hydrogen bonding interactions were observed between Lys85 (nucleocapsid receptor) and Arg13 (antimicrobial peptide ligand) having the least intermolecular distance of 1.759 Å. For SARS-CoV-2, AP00549 was docked with a binding affinity value of - 3.4 kcal/mol and Arg119 and Glu14 of receptor nucleocapsid protein and ligand AMP having the least intermolecular distance of 2.104 The dynamic simulation was performed at 50 ns to check the stability of the final docked complexes, one with each protein. The two best AMPs were AP00180 (Human Defensin-5) for SARS and AP00549 (Plectasin) for SARS-CoV-2. From positive results of dynamic simulation and previously known knowledge that some AMPs interact with the nucleocapsid of coronaviruses, these AMPs might be used as a potential therapeutic agent for the treatment regime of SARS-CoV-2 and SARS infection.The online version contains supplementary material available at 10.1007/s40203-021-00103-z.
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