Assessment of GO-Based Protein Interaction Affinities in the Large-Scale Human–Coronavirus Family Interactome
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 Internation...
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| Format: | Article |
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MDPI AG
2023-02-01
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| Series: | Vaccines |
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| Online Access: | https://www.mdpi.com/2076-393X/11/3/549 |
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| author | Soumyendu Sekhar Bandyopadhyay Anup Kumar Halder Sovan Saha Piyali Chatterjee Mita Nasipuri Subhadip Basu |
| author_facet | Soumyendu Sekhar Bandyopadhyay Anup Kumar Halder Sovan Saha Piyali Chatterjee Mita Nasipuri Subhadip Basu |
| author_sort | Soumyendu Sekhar Bandyopadhyay |
| collection | DOAJ |
| description | 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, <i>viz.</i>, SARS-CoV-2, SARS, MERS, <i>Bat coronavirus</i> HKU3, <i>Bat coronavirus</i> Rp3/2004, <i>Bat coronavirus</i> HKU5, <i>Murine coronavirus</i>, <i>Bovine coronavirus</i>, Rat coronavirus, <i>Bat coronavirus</i> HKU4, <i>Bat coronavirus</i> 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 <i>state-of-the-art</i> experimental networks. The study has also been extended further toward the drug-repurposing study by analyzing the FDA-listed COVID drugs. |
| first_indexed | 2024-03-11T05:48:49Z |
| format | Article |
| id | doaj.art-f6ed6eb51ee64b4dbf6771b9988862ff |
| institution | Directory Open Access Journal |
| issn | 2076-393X |
| language | English |
| last_indexed | 2024-03-11T05:48:49Z |
| publishDate | 2023-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Vaccines |
| spelling | doaj.art-f6ed6eb51ee64b4dbf6771b9988862ff2023-11-17T14:17:37ZengMDPI AGVaccines2076-393X2023-02-0111354910.3390/vaccines11030549Assessment of GO-Based Protein Interaction Affinities in the Large-Scale Human–Coronavirus Family InteractomeSoumyendu Sekhar Bandyopadhyay0Anup Kumar Halder1Sovan Saha2Piyali Chatterjee3Mita Nasipuri4Subhadip Basu5Department of Computer Science and Engineering, Jadavpur University, Kolkata 700032, IndiaFaculty of Mathematics and Information Sciences, Warsaw University of Technology, 00-662 Warsaw, PolandDepartment of Computer Science and Engineering (Artificial Intelligence and Machine Learning), Techno Main Salt Lake, Sector V, Kolkata 700091, IndiaDepartment of Computer Science and Engineering, Netaji Subhash Engineering College, Kolkata 700152, IndiaDepartment of Computer Science and Engineering, Jadavpur University, Kolkata 700032, IndiaDepartment of Computer Science and Engineering, Jadavpur University, Kolkata 700032, IndiaSARS-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, <i>viz.</i>, SARS-CoV-2, SARS, MERS, <i>Bat coronavirus</i> HKU3, <i>Bat coronavirus</i> Rp3/2004, <i>Bat coronavirus</i> HKU5, <i>Murine coronavirus</i>, <i>Bovine coronavirus</i>, Rat coronavirus, <i>Bat coronavirus</i> HKU4, <i>Bat coronavirus</i> 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 <i>state-of-the-art</i> experimental networks. The study has also been extended further toward the drug-repurposing study by analyzing the FDA-listed COVID drugs.https://www.mdpi.com/2076-393X/11/3/549COVID-19SARS-CoV-2COVID-19 variantsgo-semantic scoregene ontologyCOVID-19 drugs |
| spellingShingle | Soumyendu Sekhar Bandyopadhyay Anup Kumar Halder Sovan Saha Piyali Chatterjee Mita Nasipuri Subhadip Basu Assessment of GO-Based Protein Interaction Affinities in the Large-Scale Human–Coronavirus Family Interactome Vaccines COVID-19 SARS-CoV-2 COVID-19 variants go-semantic score gene ontology COVID-19 drugs |
| title | Assessment of GO-Based Protein Interaction Affinities in the Large-Scale Human–Coronavirus Family Interactome |
| title_full | Assessment of GO-Based Protein Interaction Affinities in the Large-Scale Human–Coronavirus Family Interactome |
| title_fullStr | Assessment of GO-Based Protein Interaction Affinities in the Large-Scale Human–Coronavirus Family Interactome |
| title_full_unstemmed | Assessment of GO-Based Protein Interaction Affinities in the Large-Scale Human–Coronavirus Family Interactome |
| title_short | Assessment of GO-Based Protein Interaction Affinities in the Large-Scale Human–Coronavirus Family Interactome |
| title_sort | assessment of go based protein interaction affinities in the large scale human coronavirus family interactome |
| topic | COVID-19 SARS-CoV-2 COVID-19 variants go-semantic score gene ontology COVID-19 drugs |
| url | https://www.mdpi.com/2076-393X/11/3/549 |
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