Summary of - Pharmacogenomics deliberations of 2-deoxy-D-glucose in the treatment of COVID-19 disease: an in silico approach

Document Type

Article

Abstract

Background: COVID-19 outbreak led to the discovery of 2-deoxy-D-glucose (2-DG) for COVID-19 treatment. 2-DG accumulates in infected cells to prevent energy production and viral replication. In silico analysis suggested efficient binding of 2-DG with SARS-CoV-2 viral main protease 3CLpro and NSP15 endoribonuclease. There is a need to integrate the information from 2DG interacting genes by in silico analysis.

Aim of the study: To investigate the influence of functional or regulatory SNPs on the potency and pernicious effect of 2-DG

Materials and methods

  • Identification of interacting genes of 2-DG and pathway analysis of interacting genes
  • Retrieval and characterization of SNPs
  • Protein modelling to interpret the effect of deleterious SNPs on protein structure
  • Prediction of functional microRNA target SNPs
  • SNP analysis at transcription factor binding sites and enhancer SNP analysis

Results

  • 48 interacting genes for 2-DG were identified and pathway enrichment network showed 13 Kappa score groups.
  • 9,66,482 SNPs obtained using Ensembl genome browser and 1,04,034 SNPs generated from retrieved variants.
  • SIFT analysis predicted 248 SNPs (40.25%) as “deleterious”, while PolyPhen-2 predicted 149 (24.18%) as “probably damaging”.
  • Out of three deleterious SNPs, A2M (rs778604418) showed more stability with a predicted ΔΔG value of 3.35 kcal/mol and A2M (rs201769751), PARP1 (rs193238922) affects the protein stability with predicted ΔΔG value of − 5.07 kcal/mol and − 0.51 kcal/mol, respectively
  • 12 functional microRNA targeting SNPs were predicted

Conclusion

The study provides insights into the relationship between genetic variations and drug effects of 2-DG, which may assist in assigning the right individuals to benefit from the treatment.

Citation to the base paper: Prabhu, N. B., Vinay, C. M., Satyamoorthy, K., & Rai, P. S. (2022). Pharmacogenomics deliberations of 2-deoxy-d-glucose in the treatment of COVID-19 disease: an in silico approach. 3 Biotech, 12(11), 287.

Publication Date

2022

Publication Date

2022

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