scholarly journals COVID-2019-associated overexpressed Prevotella proteins mediated host–pathogen interactions and their role in coronavirus outbreak

2020 ◽  
Vol 36 (13) ◽  
pp. 4065-4069 ◽  
Author(s):  
Abdul Arif Khan ◽  
Zakir Khan
Keyword(s):  
Interaction Analysis ◽  
Clinical Severity ◽  
Whole Genome Sequence ◽  
Supplementary Information ◽  
Protein Protein Interaction ◽  
Host Pathogen ◽  
Pathogen Protein ◽  
Rapid Transmission ◽  
Global Threat ◽  
Overrepresentation Analysis

Abstract Motivation The outbreak of COVID-2019 initiated at Wuhan, China has become a global threat by rapid transmission and severe fatalities. Recent studies have uncovered whole genome sequence of SARS-CoV-2 (causing COVID-2019). In addition, lung metagenomic studies on infected patients revealed overrepresented Prevotella spp. producing certain proteins in abundance. We performed host–pathogen protein–protein interaction analysis between SARS-CoV-2 and overrepresented Prevotella proteins with human proteome. We also performed functional overrepresentation analysis of interacting proteins to understand their role in COVID-2019 severity. Results It was found that overexpressed Prevotella proteins can promote viral infection. As per the results, Prevotella proteins, but not viral proteins, are involved in multiple interactions with NF-kB, which is involved in increasing clinical severity of COVID-2019. Prevotella may have role in COVID-2019 outbreak and should be given importance for understanding disease mechanisms and improving treatment outcomes. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Comparative host–pathogen protein–protein interaction analysis of recent coronavirus outbreaks and important host targets identification

2020 ◽  
Author(s):  
Abdul Arif Khan ◽  
Zakir Khan
Keyword(s):  
Protein Interactions ◽  
Interaction Analysis ◽  
Safety Evaluation ◽  
Drug Repurposing ◽  
Economic Cost ◽  
Medical Practitioners ◽  
Therapeutic Modalities ◽  
Host Pathogen ◽  
Pathogen Protein ◽  
Human Proteins

Abstract Last two decades have witnessed several global infectious outbreaks. Among these, coronavirus is identified as a prime culprit ranging from its involvement in severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS) to COVID-19. These infections involved in huge healthcare and economic cost incurred globally. Every time, coronavirus improved its infection ability and surprised the medical practitioners and researchers. Currently, COVID-19 is also causing numerous infections and stalled global activities. Global efforts are underway to identify potential viral targets for management of these outbreaks, but significant progress in prevention of these outbreaks is not yet achieved. We explored host–pathogen protein–protein interactions of MERS, SARS and COVID-19, and identified host targets common among all recent coronavirus outbreaks. Further, we tried to understand their potential for management of coronavirus. The common proteins involved in coronavirus host–pathogen interactions indicate their indispensable role in the pathogenesis and therefore targeting these proteins can give strategies to prevent current and future coronavirus outbreaks. Viral variability necessitates development of new therapeutic modalities for every outbreak, in contrast targeting necessary human proteins required by all coronaviruses can provide us a clue to prevent current and future coronavirus outbreaks. We found that targeting FURIN and TMPRSS2 can provide good results due to their common involvement in current and previous outbreaks. We also listed some known molecules against these two targets for their potential drug repurposing evaluation. Although, several recent studies undergoing with targeting these proteins for management of coronavirus, but safety evaluation and risk assessment must be given prime importance while targeting human proteins.

scholarly journals Comprehensive host-pathogen protein-protein interaction network analysis

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Babak Khorsand ◽  
Abdorreza Savadi ◽  
Mahmoud Naghibzadeh
Keyword(s):  
Protein Interaction ◽  
Protein Interaction Network ◽  
Interaction Network ◽  
Essential Proteins ◽  
Protein Protein Interaction ◽  
Host Pathogen ◽  
Pathogen Protein ◽  
Human Proteins ◽  
Protein Protein Interaction Network ◽  
Virus Proteins

Abstract Background Infectious diseases are a cruel assassin with millions of victims around the world each year. Understanding infectious mechanism of viruses is indispensable for their inhibition. One of the best ways of unveiling this mechanism is to investigate the host-pathogen protein-protein interaction network. In this paper we try to disclose many properties of this network. We focus on human as host and integrate experimentally 32,859 interaction between human proteins and virus proteins from several databases. We investigate different properties of human proteins targeted by virus proteins and find that most of them have a considerable high centrality scores in human intra protein-protein interaction network. Investigating human proteins network properties which are targeted by different virus proteins can help us to design multipurpose drugs. Results As host-pathogen protein-protein interaction network is a bipartite network and centrality measures for this type of networks are scarce, we proposed seven new centrality measures for analyzing bipartite networks. Applying them to different virus strains reveals unrandomness of attack strategies of virus proteins which could help us in drug design hence elevating the quality of life. They could also be used in detecting host essential proteins. Essential proteins are those whose functions are critical for survival of its host. One of the proposed centralities named diversity of predators, outperforms the other existing centralities in terms of detecting essential proteins and could be used as an optimal essential proteins’ marker. Conclusions Different centralities were applied to analyze human protein-protein interaction network and to detect characteristics of human proteins targeted by virus proteins. Moreover, seven new centralities were proposed to analyze host-pathogen protein-protein interaction network and to detect pathogens’ favorite host protein victims. Comparing different centralities in detecting essential proteins reveals that diversity of predator (one of the proposed centralities) is the best essential protein marker.

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