Bagheri-Far Mostafa, Assadizadeh Mohammad, Azimzadeh-Irani Maryam, Yaghoubi-Avini Mohammad, Hosseini Seyed Massoud
Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran.
Mol Biol Res Commun. 2025;14(1):73-91. doi: 10.22099/mbrc.2024.50245.2001.
The recent pernicious COVID-19 pandemic is caused by SARS-CoV-2. While most therapeutic strategies have focused on the viral spike protein, Open Reading Frame 8 (ORF8) plays a critical role in causing the severity of the disease. Nonetheless, there still needs to be more information on the ORF8 binding epitopes and their appropriate safe inhibitors. Herein, the protein binding sites were detected through comprehensive structural analyses. The validation of the binding sites was investigated through protein conservation analysis and blind docking. The potential natural product (NP) inhibitors were selected based on a structure-function approach. The solo and combined inhibition functions of these NPs were examined through molecular docking studies. Two binding epitopes were identified, one between the ORF8 monomers (DGBM) and the other on the surface (Gal1-Like). E92 was predicted to be pivotal for DGBM, and R101 for Gal1-like, which was then confirmed through molecular dockings. The inhibitory effects of selected phytochemical (Artemisinin), bacterial (Ivermectin), and native-liken (DEG-168) NPs were compared with the Remdesivir. Selected NPs showed solo- and co-functionality against Remdesivir to inhibit functional regions of the ORF8 structure. The DGBM is highly engaged in capturing the NPs. Additionally, the co-functionality study of NPs showed that the Ivermectin-DEG168 combination has the strongest mechanism for inhibiting all the predicted binding sites. Ivermectin can interfere with ORF8-MHC-I interaction through inhibition of A51 and F120. Two new binding sites on this non-infusion protein structure were introduced using a combination of approaches. Additionally, three safe and effective were found to inhibit these binding sites.
近期肆虐的新冠疫情由严重急性呼吸综合征冠状病毒2（SARS-CoV-2）引起。虽然大多数治疗策略都集中在病毒刺突蛋白上，但开放阅读框8（ORF8）在导致疾病严重程度方面起着关键作用。尽管如此，关于ORF8结合表位及其合适的安全抑制剂仍需要更多信息。在此，通过全面的结构分析检测蛋白质结合位点。通过蛋白质保守性分析和盲对接研究对结合位点进行验证。基于结构-功能方法选择潜在的天然产物（NP）抑制剂。通过分子对接研究检查这些NP的单独和联合抑制功能。确定了两个结合表位，一个在ORF8单体之间（DGBM），另一个在表面（Gal1-Like）。预测E92对DGBM至关重要，R101对Gal1-Like至关重要，随后通过分子对接得到证实。将选定的植物化学物质（青蒿素）、细菌（伊维菌素）和天然类似物（DEG-168）NP的抑制作用与瑞德西韦进行比较。选定的NP对瑞德西韦显示出单独和协同功能，以抑制ORF8结构的功能区域。DGBM高度参与捕获NP。此外，NP的协同功能研究表明，伊维菌素-DEG168组合具有抑制所有预测结合位点的最强机制。伊维菌素可通过抑制A51和F120干扰ORF8-MHC-I相互作用。使用多种方法相结合，在这种非输注蛋白结构上引入了两个新的结合位点。此外，还发现了三种安全有效的物质来抑制这些结合位点。
