Hanafiah Alfizah, Abd Aziz Siti Nur Arifah, Md Nesran Zarith Nameyrra, Wezen Xavier Chee, Ahmad Mohd Fadzli
Dept. of Medical Microbiology & Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, 56000, Cheras, Kuala Lumpur, Malaysia.
GUT Research Group, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
Heliyon. 2024 Mar 17;10(6):e28128. doi: 10.1016/j.heliyon.2024.e28128. eCollection 2024 Mar 30.
The impact of resistance on patient's treatment failure is a major concern. Therefore, the development of novel or alternative therapies for is urgently needed. The purpose of this study was to investigate the molecular interactions of various antimicrobial peptides (AMPs) to proteins. We performed the peptide-protein molecular docking using HADDOCK 2.4 webserver. Fourteen AMPs were tested for their binding efficacy against four proteins. Simulation of the peptide-protein complex was performed using molecular dynamic software package AMBER20. From molecular docking analysis, five peptides (LL-37, Tilapia piscidin 4, napin, snakin-1 and EcAMP1) showed strong binding interactions against proteins. The strongest binding affinity was observed in the interactions between Snakin-1 and PBP2, TP4 and type I HopQ and EcAMP1 and type I HopQ with -11.1, -13.6 and -13.8 kcal/mol, respectively. The dynamic simulation was performed for two complexes (snakin1-PBP2 and EcAMP1-HopQ). Results of the dynamics simulation showed that EcAMP1 had stable interaction and binding to type I HopQ protein without significant structural changes. In conclusion, both results of docking and simulation showed that EcAMP1 might be useful as a potential therapeutic agent for treatment. This molecular approach provides deep understanding of the interaction insights between AMPs and proteins. It paves the way for the development of novel anti- using antimicrobial peptides.
耐药性对患者治疗失败的影响是一个主要关注点。因此，迫切需要开发针对[疾病名称未给出]的新型或替代疗法。本研究的目的是研究各种抗菌肽（AMPs）与[疾病相关蛋白未给出]蛋白的分子相互作用。我们使用HADDOCK 2.4网络服务器进行了肽 - 蛋白分子对接。测试了14种抗菌肽对4种[疾病相关蛋白未给出]蛋白的结合效力。使用分子动力学软件包AMBER20对肽 - 蛋白复合物进行了模拟。从分子对接分析来看，5种肽（LL - 37、罗非鱼抗菌肽4、napin、蛇形抗菌肽 - 1和EcAMP1）对[疾病相关蛋白未给出]蛋白表现出强烈的结合相互作用。在蛇形抗菌肽 - 1与PBP2、TP4与I型HopQ以及EcAMP1与I型HopQ之间的相互作用中观察到最强的结合亲和力，分别为 - 11.1、 - 13.6和 - 13.8千卡/摩尔。对两种复合物（蛇形抗菌肽1 - PBP2和EcAMP1 - HopQ）进行了动力学模拟。动力学模拟结果表明，EcAMP1与I型HopQ蛋白具有稳定的相互作用和结合，且结构无明显变化。总之，对接和模拟结果均表明，EcAMP1可能作为治疗[疾病名称未给出]的潜在治疗剂。这种分子方法为深入了解抗菌肽与[疾病相关蛋白未给出]蛋白之间的相互作用提供了见解。它为开发使用抗菌肽的新型抗[疾病名称未给出]药物铺平了道路。
