Department of Basic Sciences, School of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran.
Nuclear Agriculture Research School, Nuclear Science and Technology Research Institute (NSTRI), Karaj, Iran.
Comput Biol Med. 2022 Jul;146:105575. doi: 10.1016/j.compbiomed.2022.105575. Epub 2022 Apr 30.
SARS-CoV-2, the causal agent of COVID-19, is primarily a pulmonary virus that can directly or indirectly infect several organs. Despite many studies carried out during the current COVID-19 pandemic, some pathological features of SARS-CoV-2 have remained unclear. It has been recently attempted to address the current knowledge gaps on the viral pathogenicity and pathological mechanisms via cellular-level tropism of SARS-CoV-2 using human proteomics, visualization of virus-host protein-protein interactions (PPIs), and enrichment analysis of experimental results. The synergistic use of models and methods that rely on graph theory has enabled the visualization and analysis of the molecular context of virus/host PPIs. We review current knowledge on the SARS-COV-2/host interactome cascade involved in the viral pathogenicity through the graph theory concept and highlight the hub proteins in the intra-viral network that create a subnet with a small number of host central proteins, leading to cell disintegration and infectivity. Then we discuss the putative principle of the "gene-for-gene and "network for network" concepts as platforms for future directions toward designing efficient anti-viral therapies.
严重急性呼吸综合征冠状病毒 2(SARS-CoV-2)是引发 COVID-19 的病原体,主要是一种肺部病毒,可直接或间接感染多个器官。尽管在当前的 COVID-19 大流行期间进行了许多研究,但 SARS-CoV-2 的一些病理学特征仍不清楚。最近,人们试图通过使用人类蛋白质组学来研究 SARS-CoV-2 的细胞水平趋向性、病毒-宿主蛋白-蛋白相互作用(PPI)的可视化以及对实验结果的富集分析,来解决当前关于病毒致病性和病理机制的知识空白。协同使用基于图论的模型和方法,使病毒/宿主 PPI 的分子上下文的可视化和分析成为可能。我们通过图论概念回顾了 SARS-CoV-2/宿主相互作用组级联反应在病毒致病性中的现有知识,并强调了病毒网络内的枢纽蛋白,这些蛋白形成了一个具有少数宿主中央蛋白的子网,导致细胞解体和感染性。然后,我们讨论了“基因对基因”和“网络对网络”概念的假设原理,作为设计高效抗病毒治疗方法的未来方向的平台。