Unveiling ancestral relations, host–pathogen interactions and comparative viral miRNA insights of dengue virus serotypes

Rahman, A. H. M. Mahbubur; Susmi, Tasmina Ferdous; Yasmin, Farzana; Bhattacharjee, Arittra; Hossain, Mohammad Uzzal; Das, Keshob Chandra; Keya, Chaman Ara; Salimullah, Md.

doi:10.1007/s13721-021-00297-4

Cited by 3 publications

(3 citation statements)

References 47 publications

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“…DENV is a member of the Flaviviridae family, which also comprises the four serotypes DENV1, DENV2, DENV3, and DENV4 [ 2 ]. In DENV-endemic regions, all four serotypes often coexist.…”

Section: Introductionmentioning

confidence: 99%

Phenolic compounds of Theobroma cacao L. show potential against dengue RdRp protease enzyme inhibition by In-silico docking, DFT study, MD simulation and MMGBSA calculation

Huq,

Roney,

Dubey

et al. 2024

PLoS ONE

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Background Currently, there is no antiviral medication for dengue, a potentially fatal tropical infectious illness spread by two mosquito species, Aedes aegypti and Aedes albopictus. The RdRp protease of dengue virus is a potential therapeutic target. This study focused on the in silico drug discovery of RdRp protease inhibitors. Methods To assess the potential inhibitory activity of 29 phenolic acids from Theobroma cacao L. against DENV3-NS5 RdRp, a range of computational methods were employed. These included docking, drug-likeness analysis, ADMET prediction, density functional theory (DFT) calculations, and molecular dynamics (MD) simulations. The aim of these studies was to confirm the stability of the ligand-protein complex and the binding pose identified during the docking experiment. Results Twenty-one compounds were found to have possible inhibitory activities against DENV according to the docking data, and they had a binding affinity of ≥-37.417 kcal/mol for DENV3- enzyme as compared to the reference compound panduratin A. Additionally, the drug-likeness investigation produced four hit compounds that were subjected to ADMET screening to obtain the lead compound, catechin. Based on ELUMO, EHOMO, and band energy gap, the DFT calculations showed strong electronegetivity, favouravle global softness and chemical reactivity with considerable intra-molecular charge transfer between electron-donor to electron-acceptor groups for catechin. The MD simulation result also demonstrated favourable RMSD, RMSF, SASA and H-bonds in at the binding pocket of DENV3-NS5 RdRp for catechin as compared to panduratin A. Conclusion According to the present findings, catechin showed high binding affinity and sufficient drug-like properties with the appropriate ADMET profiles. Moreover, DFT and MD studies further supported the drug-like action of catechin as a potential therapeutic candidate. Therefore, further in vitro and in vivo research on cocoa and its phytochemical catechin should be taken into consideration to develop as a potential DENV inhibitor.

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“…DENV is a member of the Flaviviridae family, which also comprises the four serotypes DENV1, DENV2, DENV3, and DENV4 [ 2 ]. In DENV-endemic regions, all four serotypes often coexist.…”

Section: Introductionmentioning

confidence: 99%

Phenolic compounds of Theobroma cacao L. show potential against dengue RdRp protease enzyme inhibition by In-silico docking, DFT study, MD simulation and MMGBSA calculation

Huq,

Roney,

Dubey

et al. 2024

PLoS ONE

View full text Add to dashboard Cite

show abstract

“…It is endemic in more than 100 countries, predominantly in American, Asian and Australian regions, and accounts for ~70% disease burden in Asia 4 . DENV‐2 is the most infectious serotype as it is chiefly responsible for majority of outbreaks 5 . As per global epidemiological report of 1990‐2015, DENV‐2 has shown highest mortality rate 6 .…”

Section: Introductionmentioning

confidence: 99%

Computational design of immunogenic peptide constructs comprising multiple human leukocyte antigen restricted dengue virus envelope epitopes

Kaushal

Jain

Baranwal

2022

J of Molecular Recognition

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Dengue virus (DENV) is endemic in 100 countries with the ability to impact nearly 50% of world population. DENV envelope (E) protein is responsible for viral attachment to host cells and has been target of various countermeasure development efforts. The current study focuses on a consensus computational approach to identify cross-reactive, immunogenic DENV-2 E peptides displaying promiscuity with a wide array of human leukocyte antigen (HLA) molecules. Four conserved peptides (FP-1, FP-2, FP-3 and FP-4) containing multiple CD8 + and CD4 + T cell epitopes were identified by employment of various immunoinformatics tools. FP-1, FP-2, FP-3 and FP-4 were estimated to bind with 227, 1787, 1008 and 834 HLA alleles, respectively. Root mean square deviation (RMSD) values obtained by molecular docking (CABS-Dock) with 20 HLA alleles (10 each of HLA classes I and II) resulted into comparable RMSD values of identified epitopes with native peptides, which represents the natural presentation of epitopes to HLA molecules. These peptides were also found to be part of previous experimentally validated immunogenic peptides. Further, a dengue immunogenic peptide construct was generated by linking the four peptides, an adjuvant and a 6Â histidine tag. The construct showed strong binding and stability with Tolllike receptor. Collectively, these results provide strong evidence in the support of the immunogenic potential of the dengue immunogenic peptide construct.

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“…Secondly, it can induce the target gene (mRNA) to degrade or repress its translation by forming incomplete base complementation with the 3’UTR of the target gene [ 23 ]. Some studies suggest that the Japanese encephalitis virus, dengue virus, porcine epidemic strains virus (PEDV), and other viruses could induce a significant variation of miRNA in the host, and miRNA not only regulates virus replication and pathogenicity but also adjusts the immune response of the host [ 24 , 25 , 26 ]. CircRNA, a closed-loop RNA molecule, is the product of gene cutting, but it participates in gene transcription and protein translation and plays an important role in the occurrence and development of tumors, neurodegenerative diseases, cardiovascular diseases, diabetes, nephropathy, arthritis, viruses, and other diseases.…”

Section: Introductionmentioning

confidence: 99%

Separation, Purification, Structure Analysis, In Vitro Antioxidant Activity and circRNA-miRNA-mRNA Regulatory Network on PRV-Infected RAW264.7 Cells of a Polysaccharide Derived from Arthrospira platensis

et al. 2021

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To investigate the structure of Arthrospira platensis polysaccharide (PAP) (intracellular polysaccharide) and the antioxidant activity of the first component of PAP (PAP-1) on pseudorabies virus (PRV) -infected RAW264.7 cells. The PAP was separated and purified by the Cellulose DE-52 chromatography column and Sephacryl S-200 high-resolution gel column to obtain PAP-1. The antioxidant activity and regulation of PAP-1 on PRV-infected RAW264.7 cells of circRNA-miRNA-mRNA network were investigated by chemical kit, Q-PCR, and ce-RNA seq. The results indicated that the molecular weight (Mw) of PAP-1, which was mainly composed of glucose and eight other monosaccharides, was 1.48 × 106 Da. The main glycosidic bond structure of PAP-1 was →4)-α-D-Glcp-(1→. PAP-1 may be increased the antioxidant capacity by regulating the circRNA-miRNA-mRNA network in PRV-infected RAW264.7 cells. This study provided a scientific foundation for further exploring the antioxidant activity of PAP-1 based on its structure.

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Unveiling ancestral relations, host–pathogen interactions and comparative viral miRNA insights of dengue virus serotypes

Cited by 3 publications

References 47 publications

Phenolic compounds of Theobroma cacao L. show potential against dengue RdRp protease enzyme inhibition by In-silico docking, DFT study, MD simulation and MMGBSA calculation

Phenolic compounds of Theobroma cacao L. show potential against dengue RdRp protease enzyme inhibition by In-silico docking, DFT study, MD simulation and MMGBSA calculation

Computational design of immunogenic peptide constructs comprising multiple human leukocyte antigen restricted dengue virus envelope epitopes

Separation, Purification, Structure Analysis, In Vitro Antioxidant Activity and circRNA-miRNA-mRNA Regulatory Network on PRV-Infected RAW264.7 Cells of a Polysaccharide Derived from Arthrospira platensis

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