SARS-CoV-2-human protein-protein interaction network

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the novel coronavirus which caused the coronavirus disease 2019 pandemic and infected more than 12 million victims and resulted in over 560,000 deaths in 213 countries around the world. Having no symptoms in the first week of infection increases the rate of spreading the virus. The increasing rate of the number of infected individuals and its high mortality necessitates an immediate development of proper diagnostic methods and effective treatments. SARS-CoV-2, similar to other viruses, needs to interact with the host proteins to reach the host cells and replicate its genome. Consequently, virus-host protein-protein interaction (PPI) identification could be useful in predicting the behavior of the virus and the design of antiviral drugs. Identification of virus-host PPIs using experimental approaches are very time consuming and expensive. Computational approaches could be acceptable alternatives for many preliminary investigations. In this study, we developed a new method to predict SARS-CoV-2-human PPIs. Our model is a three-layer network in which the first layer contains the most similar Alphainfluenzavirus proteins to SARS-CoV-2 proteins. The second layer contains protein-protein interactions between Alphainfluenzavirus proteins and human proteins. The last layer reveals protein-protein interactions between SARS-CoV-2 proteins and human proteins by using the clustering coefficient network property on the first two layers. To further analyze the results of our prediction network, we investigated human proteins targeted by SARS-CoV-2 proteins and reported the most central human proteins in human PPI network. Moreover, differentially expressed genes of previous researches were investigated and PPIs of SARS-CoV-2-human network, the human proteins of which were related to upregulated genes, were reported.

SARS CoV-2 nucleoprotein enhances the infectivity of lentiviral spike particles

“…This point is particularly crucial in light of the manifold roles adopted by various genes of the SARS CoV-2, as has been highlighted in recent interactome studies 12,13 . Indeed, the specific effects of these genes continue to be investigated and represent a wide diversity of specialized functions.…”

A SARS-CoV-2 –human metalloproteome interaction map

“…Consequently, virus-host protein-protein interaction (PPI) identification can help us to understand the virus invasion mechanism better and to design proper therapeutic strategies. Experimental and computational studies have revealed PPIs between human targets and SARS-CoV-2 [ 7 , 8 ] and other viruses [ [9] , [10] , [11] ] involved in important host biological processes. Specifically, SARS-CoV-2 interacts with i) innate immune pathways (the interferon and the NF-κB pathway and E3 ubiquitin ligases that regulate antiviral innate immune signaling: TRIM59 and MIB1), ii) bromodomain proteins (BRD2 and BRD4 members of the extra-terminal (BET) domain family of epigenetic readers that bind to acetylated histones to regulate gene transcription), and iii) hijacks ubiquitination pathways for replication and pathogenesis (interacts with members of a cullin-2 RING E3 ligase complex) [ 7 ].…”

Perspectives About Modulating Host Immune System in Targeting SARS-CoV-2 in India

“…India has also been largely affected by instances of COVID-19. SARS-CoV-2 viral protein interacts with various host proteins to mediate viral entry and replication in the human host ( Khorsand et al, 2020 ). Targeting virus and host protein-protein interactions or downstream signaling cascades using novel or repositioned drugs, serves as one of the strategies for COVID-19 therapy.…”