Department of Mathematics and Computer Science, University of the Balearic Islands, Palma de Mallorca, Spain.
Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia, Barcelona, Spain.
PLoS One. 2020 Dec 7;15(12):e0236304. doi: 10.1371/journal.pone.0236304. eCollection 2020.
Beside socio-economic issues, coronavirus pandemic COVID-19, the infectious disease caused by the newly discovered coronavirus SARS-CoV-2, has caused a deep impact in the scientific community, that has considerably increased its effort to discover the infection strategies of the new virus. Among the extensive and crucial research that has been carried out in the last months, the analysis of the virus-host relationship plays an important role in drug discovery. Virus-host protein-protein interactions are the active agents in virus replication, and the analysis of virus-host protein-protein interaction networks is fundamental to the study of the virus-host relationship.
We have adapted and implemented a recent integer linear programming model for protein-protein interaction network alignment to virus-host networks, and obtained a consensus alignment of the SARS-CoV-1 and SARS-CoV-2 virus-host protein-protein interaction networks. Despite the lack of shared human proteins in these virus-host networks, and the low number of preserved virus-host interactions, the consensus alignment revealed aligned human proteins that share a function related to viral infection, as well as human proteins of high functional similarity that interact with SARS-CoV-1 and SARS-CoV-2 proteins, whose alignment would preserve these virus-host interactions.
除了社会经济问题，由新型冠状病毒 SARS-CoV-2 引起的传染病 COVID-19 大流行，对科学界造成了深远的影响，促使科学界加大力度研究新病毒的感染策略。在过去几个月进行的广泛而重要的研究中，病毒-宿主关系的分析在药物发现中起着重要作用。病毒-宿主蛋白-蛋白相互作用是病毒复制的活性因子，病毒-宿主蛋白-蛋白相互作用网络的分析是研究病毒-宿主关系的基础。
我们对用于蛋白-蛋白互作网络比对的整数线性规划模型进行了调整和实现，并得到了 SARS-CoV-1 和 SARS-CoV-2 病毒-宿主蛋白-蛋白互作网络的一致比对。尽管这些病毒-宿主网络中没有共享的人类蛋白，并且保留的病毒-宿主相互作用数量较少，但一致比对揭示了与病毒感染相关功能的人类蛋白，以及与 SARS-CoV-1 和 SARS-CoV-2 蛋白相互作用的具有高功能相似性的人类蛋白，这些蛋白的比对可以保留这些病毒-宿主相互作用。
