Comprehensive characterization of human–virus protein-protein interactions reveals disease comorbidities and potential antiviral drugs

Li, Si; Zhou, Weiwei; Li, Donghao; Pan, Tao; Guo, Jing; Zou, Haozhe; Tian, Zhanyu; Li, Kongning; Xu, Juan; Li, Xia; Li, Yongsheng

doi:10.1016/j.csbj.2022.03.002

Cited by 11 publications

(8 citation statements)

References 57 publications

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“…The results showed that virus-related RBPs were closer to the network center and played more important functions. These results were consistent with one of our recent studies [ 21 ], suggesting that SARS-CoV-2 was likely to perturb the network center thus to disturb the biological pathway in a more efficient way.…”

Section: Discussionsupporting

confidence: 93%

“…The PPIs among human and virus mediate viral infection and host immune response [ 21 , 43 ]. The function importance of proteins can be represented by their locations in human PPI or regulatory networks [ [44] , [45] , [46] ].…”

Section: Resultsmentioning

confidence: 99%

“…We obtained the protein-protein interactions among human proteins or between SARS-CoV-2 proteins and human proteins from one of our recent studies [ 21 ]. There were 2,724,723 interactions among 19,779 human proteins, and 389 interactions between SARS-CoV-2 proteins and human proteins, which involved in 28 SARS-CoV-2 proteins and 384 human proteins ( Table S2 ).…”

Section: Methodsmentioning

confidence: 99%

“…Finally, the index

was calculated, where

<0 suggests a network-based overlap between the viral-related RBPs

and proteins associated with complex disease

[ 21 , 27 ].

was calculated as follows:

…”

Section: Methodsmentioning

confidence: 99%

“…We prioritized the candidate drugs or small molecules based on the network-based method [ 21 , 26 ]. Based on the protein

encoded by the host gene and interacted with SARS-CoV-2, and the drug targets

, the network proximity between them of each candidate drug was calculated as follows:

where

is the shortest distance between protein

(viral interacting proteins) and

(drug target proteins) in the human protein interaction networks.…”

Section: Methodsmentioning

confidence: 99%

See 4 more Smart Citations

Multi-omics characterization of RNA binding proteins reveals disease comorbidities and potential drugs in COVID-19

Pan

Gao

Han

et al. 2023

Computers in Biology and Medicine

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Section: Discussionsupporting

confidence: 93%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

“…Finally, the index

was calculated, where

<0 suggests a network-based overlap between the viral-related RBPs

and proteins associated with complex disease

[ 21 , 27 ].

was calculated as follows:

…”

Section: Methodsmentioning

confidence: 99%

“…We prioritized the candidate drugs or small molecules based on the network-based method [ 21 , 26 ]. Based on the protein

encoded by the host gene and interacted with SARS-CoV-2, and the drug targets

, the network proximity between them of each candidate drug was calculated as follows:

where

is the shortest distance between protein

(viral interacting proteins) and

(drug target proteins) in the human protein interaction networks.…”

Section: Methodsmentioning

confidence: 99%

See 3 more Smart Citations

Multi-omics characterization of RNA binding proteins reveals disease comorbidities and potential drugs in COVID-19

Pan

Gao

Han

et al. 2023

Computers in Biology and Medicine

Self Cite

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Human‐virus protein‐protein interactions maps assist in revealing the pathogenesis of viral infection

Chen,

Liu,

Liu

et al. 2024

Reviews in Medical Virology

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Many significant viral infections have been recorded in human history, which have caused enormous negative impacts worldwide. Human‐virus protein‐protein interactions (PPIs) mediate viral infection and immune processes in the host. The identification, quantification, localization, and construction of human‐virus PPIs maps are critical prerequisites for understanding the biophysical basis of the viral invasion process and characterising the framework for all protein functions. With the technological revolution and the introduction of artificial intelligence, the human‐virus PPIs maps have been expanded rapidly in the past decade and shed light on solving complicated biomedical problems. However, there is still a lack of prospective insight into the field. In this work, we comprehensively review and compare the effectiveness, potential, and limitations of diverse approaches for constructing large‐scale PPIs maps in human‐virus, including experimental methods based on biophysics and biochemistry, databases of human‐virus PPIs, computational methods based on artificial intelligence, and tools for visualising PPIs maps. The work aims to provide a toolbox for researchers, hoping to better assist in deciphering the relationship between humans and viruses.

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Prediction of human protein interactome of dengue virus non-structural protein 5 (NS5) and its downstream immunological implications

et al. 2023

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Comprehensive characterization of human–virus protein-protein interactions reveals disease comorbidities and potential antiviral drugs

Cited by 11 publications

References 57 publications

Multi-omics characterization of RNA binding proteins reveals disease comorbidities and potential drugs in COVID-19

Multi-omics characterization of RNA binding proteins reveals disease comorbidities and potential drugs in COVID-19

Human‐virus protein‐protein interactions maps assist in revealing the pathogenesis of viral infection

Prediction of human protein interactome of dengue virus non-structural protein 5 (NS5) and its downstream immunological implications

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