Phytochemicals of Different Medicinal Herbs as Potential Inhibitors Against Dengue Serotype 2 Virus: A Computational Approach

doi:10.1007/s12033-024-01282-8

. 2024 Sep 12.

doi: 10.1007/s12033-024-01282-8. Online ahead of print.

Phytochemicals of Different Medicinal Herbs as Potential Inhibitors Against Dengue Serotype 2 Virus: A Computational Approach

Diya Roy^#¹, M Manumol^#¹, Kalichamy Alagarasu², Deepti Parashar², Sarah Cherian³

Affiliations

¹ Bioinformatics Group, ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune, Maharashtra, 411001, India.
² Dengue & Chikungunya Group, ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune, Maharashtra, 411001, India.
³ Bioinformatics Group, ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune, Maharashtra, 411001, India. sarahcherian100@gmail.com.

^# Contributed equally.

PMID: 39264526
DOI: 10.1007/s12033-024-01282-8

Phytochemicals of Different Medicinal Herbs as Potential Inhibitors Against Dengue Serotype 2 Virus: A Computational Approach

Diya Roy et al. Mol Biotechnol. 2024.

. 2024 Sep 12.

doi: 10.1007/s12033-024-01282-8. Online ahead of print.

Authors

Diya Roy^#¹, M Manumol^#¹, Kalichamy Alagarasu², Deepti Parashar², Sarah Cherian³

Affiliations

¹ Bioinformatics Group, ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune, Maharashtra, 411001, India.
² Dengue & Chikungunya Group, ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune, Maharashtra, 411001, India.
³ Bioinformatics Group, ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune, Maharashtra, 411001, India. sarahcherian100@gmail.com.

^# Contributed equally.

PMID: 39264526
DOI: 10.1007/s12033-024-01282-8

Abstract

Dengue is one of the major mosquito-borne infectious diseases of the present century, reported to affect about 100-400 million people globally. The lack of effective therapeutic options has inspired several in vitro and in silico studies for the search of antivirals. Our previous study revealed the anti-dengue activity of different plant extracts from Plumeria alba, Bacopa monnieri, Vitex negundo, and Ancistrocladus heyneanus. Therefore, the current in silico study was designed to identify the phytochemicals present in the aforementioned plants, which are possibly responsible for the anti-dengue activity. Different plant databases as well as relevant literature were explored to find out the major compounds present in the above-stated plants followed by screening of the retrieved phytochemicals for the assessment of their binding affinity against different dengue viral proteins via molecular docking. The best poses of protein-ligand complexes obtained after molecular docking were selected for the calculation of binding free energy via MM-GBSA method. Based on the highest docking score and binding energy, six complexes were considered for further analysis. To analyze the stability of the complex, 100 ns molecular dynamics (MD) simulations were carried out using Desmond module in the Schrodinger suite. The MD simulation analysis showed that four compounds viz. liriodendrin, bacopaside VII, isoorientin, and cynaroside exhibited stability with viral _targets including the RdRp, NS3 helicase, and E protein indicating their potential as novel anti-dengue antivirals.

Keywords: Antivirals; Dengue virus; MD simulations: molecular dynamics Simulations; Molecular docking; Phytochemicals.

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References

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1. Natali, E. N., Babrak, L. M., & Miho, E. (2021). Prospective artificial intelligence to dissect the dengue immune response and discover therapeutics. Frontiers in Immunology, 12, 574411. https://doi.org/10.3389/fimmu.2021.574411 - DOI - PubMed - PMC
1. Amemiya, T., Gromiha, M. M., Horimoto, K., & Fukui, K. (2019). Drug repositioning for dengue haemorrhagic fever by integrating multiple omics analyses. Science and Reports, 9(1), 523. https://doi.org/10.1038/s41598-018-36636-1 - DOI
1. Bandyopadhyay, S., Lum, L. C., & Kroeger, A. (2006). Classifying dengue: A review of the difficulties in using the WHO case classification for dengue haemorrhagic fever. Tropical Medicine & International Health, 11(8), 1238–1255. https://doi.org/10.1111/j.1365-3156.2006.01678.x - DOI
1. Robinson, M., Sweeney, T. E., Barouch-Bentov, R., Sahoo, M. K., Kalesinskas, L., Vallania, F., Sanz, A. M., Ortiz-Lasso, E., Albornoz, L. L., Rosso, F., & Montoya, J. G. (2019). A 20-gene set predictive of progression to severe dengue. Cell Reports, 26(5), 1104–1111. https://doi.org/10.1016/j.celrep.2019.01.033 - DOI - PubMed

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[1] Wilder-Smith, A., Ooi, E. E., Horstick, O., & Wills, B. (2019). Dengue. The Lancet, 393(10169), 350–363. https://doi.org/10.1016/S0140-6736(18)32560-1 - DOI

[2] Wilder-Smith, A., Ooi, E. E., Horstick, O., & Wills, B. (2019). Dengue. The Lancet, 393(10169), 350–363. https://doi.org/10.1016/S0140-6736(18)32560-1 - DOI

[3] Natali, E. N., Babrak, L. M., & Miho, E. (2021). Prospective artificial intelligence to dissect the dengue immune response and discover therapeutics. Frontiers in Immunology, 12, 574411. https://doi.org/10.3389/fimmu.2021.574411 - DOI - PubMed - PMC

[4] Natali, E. N., Babrak, L. M., & Miho, E. (2021). Prospective artificial intelligence to dissect the dengue immune response and discover therapeutics. Frontiers in Immunology, 12, 574411. https://doi.org/10.3389/fimmu.2021.574411 - DOI - PubMed - PMC

[5] Amemiya, T., Gromiha, M. M., Horimoto, K., & Fukui, K. (2019). Drug repositioning for dengue haemorrhagic fever by integrating multiple omics analyses. Science and Reports, 9(1), 523. https://doi.org/10.1038/s41598-018-36636-1 - DOI

[6] Amemiya, T., Gromiha, M. M., Horimoto, K., & Fukui, K. (2019). Drug repositioning for dengue haemorrhagic fever by integrating multiple omics analyses. Science and Reports, 9(1), 523. https://doi.org/10.1038/s41598-018-36636-1 - DOI

[7] Bandyopadhyay, S., Lum, L. C., & Kroeger, A. (2006). Classifying dengue: A review of the difficulties in using the WHO case classification for dengue haemorrhagic fever. Tropical Medicine & International Health, 11(8), 1238–1255. https://doi.org/10.1111/j.1365-3156.2006.01678.x - DOI

[8] Bandyopadhyay, S., Lum, L. C., & Kroeger, A. (2006). Classifying dengue: A review of the difficulties in using the WHO case classification for dengue haemorrhagic fever. Tropical Medicine & International Health, 11(8), 1238–1255. https://doi.org/10.1111/j.1365-3156.2006.01678.x - DOI

[9] Robinson, M., Sweeney, T. E., Barouch-Bentov, R., Sahoo, M. K., Kalesinskas, L., Vallania, F., Sanz, A. M., Ortiz-Lasso, E., Albornoz, L. L., Rosso, F., & Montoya, J. G. (2019). A 20-gene set predictive of progression to severe dengue. Cell Reports, 26(5), 1104–1111. https://doi.org/10.1016/j.celrep.2019.01.033 - DOI - PubMed

[10] Robinson, M., Sweeney, T. E., Barouch-Bentov, R., Sahoo, M. K., Kalesinskas, L., Vallania, F., Sanz, A. M., Ortiz-Lasso, E., Albornoz, L. L., Rosso, F., & Montoya, J. G. (2019). A 20-gene set predictive of progression to severe dengue. Cell Reports, 26(5), 1104–1111. https://doi.org/10.1016/j.celrep.2019.01.033 - DOI - PubMed

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Phytochemicals of Different Medicinal Herbs as Potential Inhibitors Against Dengue Serotype 2 Virus: A Computational Approach

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Phytochemicals of Different Medicinal Herbs as Potential Inhibitors Against Dengue Serotype 2 Virus: A Computational Approach

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