931
Views
25
CrossRef citations to date
0
Altmetric
Research Articles

Pharmacophore modeling, molecular docking and molecular dynamics simulation for screening and identifying anti-dengue phytocompounds

, , ORCID Icon, , , ORCID Icon & show all
Pages 1726-1740 | Received 02 Apr 2019, Accepted 29 Apr 2019, Published online: 14 May 2019

References

  • Adikari, T. N., Gomes, L., Wickramasinghe, N., Salimi, M., Wijesiriwardana, N., Kamaladasa, A., … Malavige, G. N. (2016). Dengue NS1 antigen contributes to disease severity by inducing interleukin (IL)-10 by monocytes. Clinical & Experimental Immunology, 184(1), 90–100. doi:10.1111/cei.12747
  • Alayli, F., & Scholle, F. (2016). Dengue virus NS1 enhances viral replication and pro-inflammatory cytokine production in human dendritic cells. Virology, 496, 227–236. doi:10.1016/j.virol.2016.06.008
  • Anusuya, S., & Gromiha, M. M. (2019). Structural basis of flavonoids as dengue polymerase inhibitors: Insights from QSAR and docking studies. Journal of Biomolecular Structure and Dynamics, 37(1), 104–115. doi:10.1080/07391102.2017.1419146
  • Banks, J. L., Beard, H. S., Cao, Y., Cho, A. E., Damm, W., Farid, R., … Levy, R. M. (2005). Integrated modeling program, applied chemical theory (IMPACT). Journal of Computational Chemistry, 26(16), 1752–1780. doi:10.1002/jcc.20292
  • Bardiot, D., Koukni, M., Smets, W., Carlens, G., McNaughton, M., Kaptein, S., … Marchand, A. (2018). Discovery of indole derivatives as novel and potent dengue virus inhibitors. Journal of Medicinal Chemistry, 61(18), 8390–8401. doi:10.1021/acs.jmedchem.8b00913
  • Behnam, M. A. M., Nitsche, C., Boldescu, V., & Klein, C. D. (2016). The medicinal chemistry of dengue virus. Journal of Medicinal Chemistry, 59(12), 5622–5649. doi:10.1021/acs.jmedchem.5b01653
  • Chen, J., Sun, J., Liu, X., Liu, F., Liu, R., & Wang, J. (2019). Structure-based prediction of West Nile virus-human protein–protein interactions. Journal of Biomolecular Structure and Dynamics, 37(9), 2310–2321. doi:10.1080/07391102.2018.1479659
  • Chu, J. J. H., Lee, R. C. H., Ang, M. J. Y., Wang, W.-L., Lim, H. A., Wee, J. L. K., … Brian Chia, C. S. (2015). Antiviral activities of 15 dengue NS2B-NS3 protease inhibitors using a human cell-based viral quantification assay. Antiviral Research, 118, 68–74. doi:10.1016/j.antiviral.2015.03.010
  • Coulerie, P., Nour, M., Maciuk, A., Eydoux, C., Guillemot, J.-C., Lebouvier, N., … Figadere, B. (2013). Structure-activity relationship study of biflavonoids on the Dengue virus polymerase DENV-NS5 RdRp. Planta Medica, 79(14), 1313–1318. doi:10.1055/s-0033-1350672
  • Dias, D. A., Urban, S., & Roessner, U. (2012). A historical overview of natural products in drug discovery. Metabolites, 2(2), 303–336. doi:10.3390/metabo2020303
  • Dixon, S. L., Smondyrev, A. M., Knoll, E. H., Rao, S. N., Shaw, D. E., & Friesner, R. A. (2006). PHASE: A new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results. Journal of Computer-Aided Molecular Design, 20(10-11), 647–671. doi:10.1007/s10822-006-9087-6
  • El Sahili, A., & Lescar, J. (2017). Dengue virus non-structural protein 5. Viruses, 9(4), pii:E91. https://doi.org/10.3390/v9040091
  • Fahimi, H., Mohammadipour, M., Haddad Kashani, H., Parvini, F., & Sadeghizadeh, M. (2018). Dengue viruses and promising envelope protein domain III-based vaccines. Applied Microbiology and Biotechnology, 102(7), 2977–2996. doi:10.1007/s00253-018-8822-y
  • Fan, J., Liu, Y., & Yuan, Z. (2014). Critical role of dengue virus NS1 protein in viral replication. Virologica Sinica, 29(3), 162–169. doi:10.1007/s12250-014-3459-1
  • Friesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., … Shenkin, P. S. (2004). Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. Journal of Medicinal Chemistry, 47(7), 1739–1749. doi:10.1021/jm0306430
  • Gadaleta, D., Mangiatordi, G. F., Catto, M., Carotti, A., & Nicolotti, O. (2016). Applicability domain for QSAR models: Where theory meets reality. International Journal of Quantitative Structure-Property Relationships, 1(1), 45–63. doi:10.4018/IJQSPR.2016010102
  • Hasan, S., Jamdar, S. F., Alalowi, M., & Al Ageel Al Beaiji, S. M. (2016). Dengue virus: A global human threat: Review of literature. Journal of International Society of Preventive and Community Dentistry, 6(1), 1–6. doi:10.4103/2231-0762.175416
  • Julander, J. G., Perry, S. T., & Shresta, S. (2011). Important advances in the field of anti-dengue virus research. Antiviral Chemistry and Chemotherapy, 21(3), 105–116. doi:10.3851/IMP1690
  • Kato, D., Era, S., Watanabe, I., Arihara, M., Sugiura, N., Kimata, K., … Suzuki, T. (2010). Antiviral activity of chondroitin sulphate E targeting dengue virus envelope protein. Antiviral Research, 88(2), 236–243. doi:10.1016/j.antiviral.2010.09.002
  • Kaur, M., Kumari, A., Bahia, M. S., & Silakari, O. (2013). Designing of new multi-targeted inhibitors of spleen tyrosine kinase (Syk) and zeta-associated protein of 70kDa (ZAP-70) using hierarchical virtual screening protocol. Journal of Molecular Graphics & Modelling, 39, 165–175. doi:10.1016/j.jmgm.2012.11.011
  • Khan, M. F., Verma, G., Akhtar, W., Shaquiquzzaman, M., Akhter, M., Rizvi, M. A., & Alam, M. M. (2016). Pharmacophore modeling, 3D-QSAR, docking study and ADME prediction of acyl 1,3,4-thiadiazole amides and sulfonamides as antitubulin agents. Arabian Journal of Chemistry. https://doi.org/10.1016/j.arabjc.2016.11.004
  • Klema, V. J., Ye, M., Hindupur, A., Teramoto, T., Gottipati, K., Padmanabhan, R., & Choi, K. H. (2016). Dengue virus nonstructural protein 5 (NS5) assembles into a dimer with a unique methyltransferase and polymerase interface. PLOS Pathogens, 12(2), 1–21. https://doi.org/10.1371/journal.ppat.1005451
  • Lim, S. P., Wen, D., Yap, T. L., Yan, C. K., Lescar, J., & Vasudevan, S. G. (2008). A scintillation proximity assay for dengue virus NS5 2’-O-methyltransferase-kinetic and inhibition analyses. Antiviral Research, 80(3), 360–369. doi:10.1016/j.antiviral.2008.08.005
  • Lin, K., Ali, A., Rusere, L., Soumana, D. I., Kurt Yilmaz, N., & Schiffer, C. A. (2017). Dengue virus NS2B/NS3 protease inhibitors exploiting the prime side. Journal of Virology, 91(10), e00045–17. https://doi.org/10.1128/JVI.00045-17.
  • Low, J. G. H., Ooi, E. E., & Vasudevan, S. G. (2017). Current status of dengue therapeutics research and development. The Journal of Infectious Diseases, 215(suppl_2), S96–S102. doi:10.1093/infdis/jiw423
  • Natarajan, S. (2010). NS3 protease from flavivirus as a target for designing antiviral inhibitors against dengue virus. Genetics and Molecular Biology, 33(2), 214–219. doi:10.1590/S1415-47572010000200002
  • Patel, S. K., Athar, M., Jha, P. C., Khedkar, V. M., & Jasrai, Y. (2018). Assessing the antimalarial potentials of phytochemicals: Virtual screening, molecular dynamics and in-vitro investigations. Letters in Drug Design & Discovery. https://doi.org/10.2174/1570180815666180604085626
  • Patel, S., Modi, P., & Chhabria, M. (2018). Rational approach to identify newer caspase-1 inhibitors using pharmacophore based virtual screening, docking and molecular dynamic simulation studies. Journal of Molecular Graphics & Modelling, 81, 106–115. doi:10.1016/j.jmgm.2018.02.017
  • Rathore, A. P. S., Paradkar, P. N., Watanabe, S., Tan, K. H., Sung, C., Connolly, J. E., … Vasudevan, S. G. (2011). Celgosivir treatment misfolds dengue virus NS1 protein, induces cellular pro-survival genes and protects against lethal challenge mouse model. Antiviral Research, 92(3), 453–460. doi:10.1016/j.antiviral.2011.10.002
  • Roy, K., Das, R. N., Ambure, P., & Aher, R. B. (2016). Be aware of error measures. Further studies on validation of predictive QSAR models. Chemometrics and Intelligent Laboratory Systems, 152(Supplement C), 18–33. doi:10.1016/j.chemolab.2016.01.008
  • Sabetian, S., Nezafat, N., Dorosti, H., Zarei, M., & Ghasemi, Y. (2018). Exploring dengue proteome to design an effective epitope-based vaccine against dengue virus. Journal of Biomolecular Structure and Dynamics, 1–18. doi:10.1080/07391102.2018.1491890
  • Sastry, G. M., Dixon, S. L., & Sherman, W. (2011). Rapid shape-based ligand alignment and virtual screening method based on atom/feature-pair similarities and volume overlap scoring. Journal of Chemical Information and Modeling, 51(10), 2455–2466. doi:10.1021/ci2002704
  • Tian, Y., Zhou, Y., Takagi, T., Kameoka, M., & Kawashita, N. (2018). Dengue virus and its inhibitors: A brief review. Chemical &Amp; Pharmaceutical Bulletin, 66(3), 191–206. doi:10.1248/cpb.c17-00794
  • Tripathy, S., Azam, M. A., Jupudi, S., & Sahu, S. K. (2018). Pharmacophore generation, atom-based 3D-QSAR, molecular docking and molecular dynamics simulation studies on benzamide analogues as FtsZ inhibitors. Journal of Biomolecular Structure & Dynamics, 36(12), 3218–3230. doi:10.1080/07391102.2017.1384401
  • Vora, J., Patel, S., Sinha, S., Sharma, S., Srivastava, A., Chhabria, M., & Shrivastava, N. (2018a). Molecular docking, QSAR and ADMET based mining of natural compounds against prime targets of HIV. Journal of Biomolecular Structure and Dynamics, 0(0), 1–16. https://doi.org/10.1080/07391102.2017.1420489
  • Vora, J., Patel, S., Sinha, S., Sharma, S., Srivastava, A., Chhabria, M., & Shrivastava, N. (2018). Structure based virtual screening, 3D-QSAR, Molecular dynamics and ADMET studies for selection of natural inhibitors against structural and non-structural targets of Chikungunya. Journal of Biomolecular Structure and Dynamics, 1–31. doi:10.1080/07391102.2018.1509732
  • World Health Organization (2009). Dengue: guidelines for diagnosis, treatment, prevention and control (New ed. 20). Geneva: World Health Organization. Retrieved from http://whqlibdoc.who.int/publications/2009/9789241547871_eng.pdf

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.