Computational modeling of human-nCoV protein-protein interaction network

Saha, Sovan; Bandyopadhyay, Soumyendu Sekhar; Chatterjee, Piyali; Nasipuri, Mita; Basu, Subhadip

doi:10.1016/j.ymeth.2021.12.003

Cited by 6 publications

(5 citation statements)

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“…It has around 60% of FDA-approved medications and 10% of investigational drugs. It has been determined through adequate analysis that some spreader nodes in COVID19-human PPIN are the protein targets of possible COVID-19 FDA-listed medicines [ 116 ]: hydroxychloroquine [ 117 ], azithromycin [ 117 ], lopinavir [ 118 ], remdesivir [ 119 , 120 ], etc. Not only the list of drugs for COVID-19, but we have obtained a list of FDA-approved drugs from level 1 vulnerable host proteins for the entire coronavirus family by using Drug Consensus Score algorithm (DCS).…”

Section: Resultsmentioning

confidence: 99%

“…Copper has an enormous effect in defeating COVID-19, which helps it to dominate with a high DCS score. The study proposed in [ 120 ] aims to investigate the effects of a highly specialized drug, “Hinokitiol Copper Chelate”, on enormous quantities of 2019-nCoV Spike Glycoprotein with a single receptor binding domain. This investigation offers a superior version of Hinokitiol Copper Chelate for in vitro testing against 2019-nCoV Main Protease.…”

Section: Discussionmentioning

confidence: 99%

“…Because SARS-CoV-2 proteins could not be directly mapped into matching UniProt accession ids, direct comparison and validation concerning Gordon et al were impossible. However, using the COVID-19 UniProtKB reference database, an attempt has been made to map the UniProt ids of Gordon et al SARS-CoV-2 proteins [ 120 ].…”

Section: Discussionmentioning

confidence: 99%

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Assessment of GO-Based Protein Interaction Affinities in the Large-Scale Human–Coronavirus Family Interactome

Bandyopadhyay

Saha

Chatterjee³

et al. 2023

Vaccines

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SARS-CoV-2 is a novel coronavirus that replicates itself via interacting with the host proteins. As a result, identifying virus and host protein-protein interactions could help researchers better understand the virus disease transmission behavior and identify possible COVID-19 drugs. The International Committee on Virus Taxonomy has determined that nCoV is genetically 89% compared to the SARS-CoV epidemic in 2003. This paper focuses on assessing the host–pathogen protein interaction affinity of the coronavirus family, having 44 different variants. In light of these considerations, a GO-semantic scoring function is provided based on Gene Ontology (GO) graphs for determining the binding affinity of any two proteins at the organism level. Based on the availability of the GO annotation of the proteins, 11 viral variants, viz., SARS-CoV-2, SARS, MERS, Bat coronavirus HKU3, Bat coronavirus Rp3/2004, Bat coronavirus HKU5, Murine coronavirus, Bovine coronavirus, Rat coronavirus, Bat coronavirus HKU4, Bat coronavirus 133/2005, are considered from 44 viral variants. The fuzzy scoring function of the entire host–pathogen network has been processed with ~180 million potential interactions generated from 19,281 host proteins and around 242 viral proteins. ~4.5 million potential level one host–pathogen interactions are computed based on the estimated interaction affinity threshold. The resulting host–pathogen interactome is also validated with state-of-the-art experimental networks. The study has also been extended further toward the drug-repurposing study by analyzing the FDA-listed COVID drugs.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Assessment of GO-Based Protein Interaction Affinities in the Large-Scale Human–Coronavirus Family Interactome

Bandyopadhyay

Saha

Chatterjee³

et al. 2023

Vaccines

Self Cite

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show abstract

“…In the second category, host-pathogen interaction networks of COVID-19 have been exploited in two works by Barman et al [4] and Saha et al [5] since these networks are always considered one of the significant resources for identifying potential drug targets. In the work of Barman et al [4] , a combination of essential network centrality measures and functional properties of the human proteins have been utilized to identify the critical human targets of SARS-CoV-2 from the host-pathogen interaction networks.…”

mentioning

confidence: 99%

“…, PRKACA, RHOA, CDK5RAP2, and CEP250, have emerged as the best therapeutic targets, of which another group also found PRKACA and CEP250 as potential candidates for drug targets in COVID-19. In the work of Saha et al [5] , the COVID-19-Human Interaction network is generated by a fuzzy affinity function. In addition, spreader nodes and edges through which infection of COVID-19 gets mediated from one protein to another are also highlighted in the developed interaction network by applying the spreadability index.…”

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confidence: 99%