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A scheme for inferring viral-host associations based on codon usage patterns identifies the most affected signaling pathways during COVID-19.
Das, Jayanta Kumar; Chakraborty, Subhadip; Roy, Swarup.
  • Das JK; Department of Pediatrics, Johns Hopkins University, School of Medicine, MD, USA.
  • Chakraborty S; Department of Botany, Nabadwip Vidyasagar College, Nabadwip, India.
  • Roy S; Network Reconstruction & Analysis (NetRA) Lab, Department of Computer Applications, Sikkim University, Gangtok, India. Electronic address: sroy01@cus.ac.in.
J Biomed Inform ; 118: 103801, 2021 06.
Article in English | MEDLINE | ID: covidwho-1219153
ABSTRACT
Understanding the molecular mechanism of COVID-19 pathogenesis helps in the rapid therapeutic target identification. Usually, viral protein targets host proteins in an organized fashion. The expression of any viral gene depends mostly on the host translational machinery. Recent studies report the great significance of codon usage biases in establishing host-viral protein-protein interactions (PPI). Exploring the codon usage patterns between a pair of co-evolved host and viral proteins may present novel insight into the host-viral protein interactomes during disease pathogenesis. Leveraging the similarity in codon usage patterns, we propose a computational scheme to recreate the host-viral protein-protein interaction network. We use host proteins from seventeen (17) essential signaling pathways for our current work towards understanding the possible targeting mechanism of SARS-CoV-2 proteins. We infer both negatively and positively interacting edges in the network. Further, extensive analysis is performed to understand the host PPI network topologically and the attacking behavior of the viral proteins. Our study reveals that viral proteins mostly utilize codons, rare in the targeted host proteins (negatively correlated interaction). Among them, non-structural proteins, NSP3 and structural protein, Spike (S), are the most influential proteins in interacting with multiple host proteins. While ranking the most affected pathways, MAPK pathways observe to be the worst affected during the SARS-CoV-2 infection. Several proteins participating in multiple pathways are highly central in host PPI and mostly targeted by multiple viral proteins. We observe many potential targets (host proteins) from the affected pathways associated with the various drug molecules, including Arsenic trioxide, Dexamethasone, Hydroxychloroquine, Ritonavir, and Interferon beta, which are either under clinical trial or in use during COVID-19.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Signal Transduction / Host-Pathogen Interactions / Protein Interaction Maps / Codon Usage / COVID-19 Type of study: Diagnostic study / Prognostic study / Randomized controlled trials Limits: Humans Language: English Journal: J Biomed Inform Journal subject: Medical Informatics Year: 2021 Document Type: Article Affiliation country: J.jbi.2021.103801

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Signal Transduction / Host-Pathogen Interactions / Protein Interaction Maps / Codon Usage / COVID-19 Type of study: Diagnostic study / Prognostic study / Randomized controlled trials Limits: Humans Language: English Journal: J Biomed Inform Journal subject: Medical Informatics Year: 2021 Document Type: Article Affiliation country: J.jbi.2021.103801