ArticleJournal of biomedical informatics2021
A scheme for inferring viral-host associations based on codon usage patterns identifies the most affected signaling pathways during COVID-19.
Article in Journal of biomedical informatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers, 1 of them a synthesis that pooled it.
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Who cites it
12 citing papers in PubMed, 1 synthesis or guideline pooled it, 15 citations in OpenAlex.
- A Comprehensive Review of Artificial Intelligence in Prevention and Treatment of COVID-19 Pandemic.Frontiers in genetics · 2022Pooled it
- Viral Mechanisms and Drug Influences on Janus Kinase/Signal Transducers and Activators of Transcription (JAK/STAT) Pathway in Human Coronaviruses Infection: A Systematic Review.Health science reports · 2026Review
- HIF-1α Pathway in COVID-19: A Scoping Review of Its Modulation and Related Treatments.International journal of molecular sciences · 2025Article
- Molecular docking, pharmacological profiling, and MD simulations of glycolytic inhibitors targeting novel SARS CoV-2 main protease and spike protein.In silico pharmacology · 2025Article
- Comprehensive analysis of the codon usage patterns in the polyprotein coding sequences of the honeybee viruses.Frontiers in veterinary science · 2025Article
- Review
- Novel informatics approaches to COVID-19 Research: From methods to applications.Journal of biomedical informatics · 2022Article
- Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic.Virology · 2022Article
- Review
- Human genes with relative synonymous codon usage analogous to that of polyomaviruses are involved in the mechanism of polyomavirus nephropathy.Frontiers in cellular and infection microbiology · 2022Article
- Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants.ACS omega · 2021Article
- Analyzing host-viral interactome of SARS-CoV-2 for identifying vulnerable host proteins during COVID-19 pathogenesis.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2021Article
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Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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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