References
- Ahmad, N., Farman, A., Badshah, S. L., Ur Rahman, A., Ur Rashid, H., & Khan, K. (2017). Molecular modeling, simulation and docking study of ebola virus glycoprotein. Journal of Molecular Graphics and Modelling, 72, 266–271. https://doi.org/10.1016/j.jmgm.2016.12.010
- Ahmad, N., Rehman, A. U., Badshah, S. L., Ullah, A., Mohammad, A., & Khan, K. (2020). Molecular dynamics simulation of zika virus NS5 RNA dependent RNA polymerase with selected novel non-nucleoside inhibitors. Journal of Molecular Structure, 1203, 127428. https://doi.org/10.1016/j.molstruc.2019.127428
- Akey, D. L., Brown, W. C., Dutta, S., Konwerski, J., Jose, J., Jurkiw, T. J., DelProposto, J., Ogata, C. M., Skiniotis, G., Kuhn, R. J., & Smith, J. L. (2014). Flavivirus NS1 structures reveal surfaces for associations with membranes and the immune system. Science, 343(6173), 881–885. https://doi.org/10.1126/science.1247749
- Avirutnan, P., Fuchs, A., Hauhart, R. E., Somnuke, P., Youn, S., Diamond, M. S., & Atkinson, J. P. (2010). Antagonism of the complement component C4 by flavivirus nonstructural protein NS1. The Journal of Experimental Medicine, 207(4), 793–806. https://doi.org/10.1084/jem.20092545
- Badshah, S. L., Ahmad, N., Ur Rehman, A., Khan, K., Ullah, A., Alsayari, A., Muhsinah, A. B., & N. Mabkhot, Y. (2019). Molecular docking and simulation of Zika virus NS3 helicase. BMC Chemistry, 13(1), 67. https://doi.org/10.1186/s13065-019-0582-y
- Badshah, S. L., Khan, A. N., & Mabkhot, Y. N. (2016). Molecular dynamics simulation of cholera toxin A-1 polypeptide. Open Chemistry, 14(1), 188–196. https://doi.org/10.1515/chem-2016-0021
- Badshah, S. L., Mabkhot, Y. N., Ahmad, N., Syed, S., & Naeem, A. (2018). Zika virus, microcephaly and its possible global spread. In A. J. Rodriguez-Morales (Ed.), Current topics in Zika. Intech Open. https://doi.org/10.5772/intechopen.72507
- Badshah, S. L., Naeem, A., & Mabkhot, Y. (2017). The new high resolution crystal structure of NS2B-NS3 protease of Zika virus. Viruses, 9(1), 7. https://doi.org/10.3390/v9010007
- Badshah, S. L., Ullah, A., Badshah, S. H., & Ahmad, I. (2020). Spread of Novel coronavirus by returning pilgrims from Iran to Pakistan. Journal of Travel Medicine, 27(2), taaa044. https://doi.org/10.1093/jtm/taaa044
- Baronti, C., Piorkowski, G., Charrel, R. N., Boubis, L., Leparc-Goffart, I., & de Lamballerie, X. (2014). Complete coding sequence of Zika virus from a French Polynesia outbreak in 2013. Genome Announcements, 2(3), e00500–14. https://doi.org/10.1128/genomeA.00500-14
- Brown, W. C., Akey, D. L., Konwerski, J. R., Tarrasch, J. T., Skiniotis, G., Kuhn, R. J., & Smith, J. L. (2016). Extended surface for membrane association in Zika virus NS1 structure. Nature Structural and Molecular Biology, 23, 865–867. https://doi.org/10.1038/nsmb.3268
- Certara. (2012). SYBYL-X Suite, version 2.1.1.
- Chan, J. F. W., Choi, G. K. Y., Yip, C. C. Y., Cheng, V. C. C., & Yuen, K. Y. (2016). Zika fever and congenital Zika syndrome: An unexpected emerging arboviral disease. Journal of Infection, 72(5), 507–524. https://doi.org/10.1016/j.jinf.2016.02.011
- Chang, C., Ortiz, K., Ansari, A., & Gershwin, M. E. (2016). The Zika outbreak of the 21st century. Journal of Autoimmunity, 68, 1–13. https://doi.org/10.1016/j.jaut.2016.02.006
- DeLano, W. L. (2014). The PyMOL molecular graphics system, Version 1.8. Schrödinger LLC. http://www.pymol.org
- Dussart, P., Labeau, B., Lagathu, G., Louis, P., Nunes, M. R. T., Rodrigues, S. G., Storck-Herrmann, C., Cesaire, R., Morvan, J., Flamand, M., & Baril, L. (2006). Evaluation of an enzyme immunoassay for detection of dengue virus NS1 antigen in human serum. Clinical and Vaccine Immunology, 13(11), 1185–1189. https://doi.org/10.1128/CVI.00229-06
- Edeling, M. a., Diamond, M. S., & Fremont, D. H. (2014). Structural basis of Flavivirus NS1 assembly and antibody recognition. Proceedings of the National Academy of Sciences of Sciences, 111(11), 4285–4290. https://doi.org/10.1073/pnas.1322036111
- Gonzalez-Freire, M., De Cabo, R., Bernier, M., Sollott, S. J., Fabbri, E., Navas, P., & Ferrucci, L. (2015). Reconsidering the role of mitochondria in aging. The Journals of Gerontology Series A: Biological Sciences and Medical Sciences, 70(11), 1334–1342. https://doi.org/10.1093/gerona/glv070
- Grienke, U., Richter, M., Walther, E., Hoffmann, A., Kirchmair, J., Makarov, V., Nietzsche, S., Schmidtke, M., & Rollinger, J. M. (2016). Discovery of prenylated flavonoids with dual activity against influenza virus and Streptococcus pneumoniae. Scientific Reports, 6(1), 27156. https://doi.org/10.1038/srep27156
- Havsteen, B. H. (2002). The biochemistry and medical significance of the flavonoids. Pharmacology & Therapeutics, 96(2–3), 67–202. https://doi.org/10.1016/S0163-7258(02)00298-X
- Hou, T., Wang, J., Li, Y., & Wang, W. (2011). Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. Journal of Chemical Information and Modeling, 51(1), 69–82. https://doi.org/10.1021/ci100275a
- Ioos, S., Mallet, H. P., Leparc Goffart, I., Gauthier, V., Cardoso, T., & Herida, M. (2014). Current Zika virus epidemiology and recent epidemics. Medecine et Maladies Infectieuses, 44(7), 302–307. https://doi.org/10.1016/j.medmal.2014.04.008
- Khan, H., Amin, H., Ullah, A., Saba, S., Rafique, J., Khan, K., Ahmad, N., & Badshah, S. L. (2016). Antioxidant and antiplasmodial activities of bergenin and 11-O-galloylbergenin isolated from Mallotus philippensis. Oxidative Medicine and Cellular Longevity, 2016, 1–6. https://doi.org/10.1155/2016/1051925
- Khan, K., Rasool, S., Khan, K., Badshah, S. L., Ahmad, N., Jan, M. T., Hizbullah, S. M., Khan, I., Ullah, A., & Muhammad, A. (2019). Computational evaluation and anti-inflammatory and analgesic activities of nebrodenside a isolated from Dodonaea viscosa. Natural Product Communications, 14(5), 1934578X1984815. https://doi.org/10.1177/1934578X19848157
- King, A. M. Q., Adams, M. J., Carsten, E. B., & Lefkowitz, E. J. (2012). Virus taxonomy: Classification and nomenclature of viruses. Ninth Report of the International Committee on Taxonomy of Viruses. Elsevier Inc.
- Kuno, G., Chang, G., Tsuchiya, K., Karabatsos, N., & Cropp, C. (1998). Phylogeny of the genus Flavivirus. Journal of Virology, 72(1), 73–83. https://doi.org/10.1128/JVI.72.1.73-83.1998
- Kwon, H.-J., Kim, H.-H., Ryu, Y. B., Kim, J. H., Jeong, H. J., Lee, S.-W., Chang, J. S., Cho, K.-O., Rho, M.-C., Park, S.-J., & Lee, W. S. (2010). In vitro anti-rotavirus activity of polyphenol compounds isolated from the roots of Glycyrrhiza uralensis. Bioorganic & Medicinal Chemistry, 18(21), 7668–7674. https://doi.org/10.1016/j.bmc.2010.07.073
- Labute, P. (2008). The generalized born/volume integral implicit solvent model: Estimation of the free energy of hydration using London dispersion instead of atomic surface area. Journal of Computational Chemistry, 29(10), 1693–1698. https://doi.org/10.1002/jcc.20933
- Lani, R., Hassandarvish, P., Shu, M.-H., Phoon, W. H., Chu, J. J. H., Higgs, S., Vanlandingham, D., Abu Bakar, S., & Zandi, K. (2016). Antiviral activity of selected flavonoids against Chikungunya virus. Antiviral Research, 133, 50–61. https://doi.org/10.1016/j.antiviral.2016.07.009
- Li, B. Q., Fu, T., Dongyan, Y., Mikovits, J. A., Ruscetti, F. W., & Wang, J. M. (2000). Flavonoid baicalin inhibits HIV-1 infection at the level of viral entry. Biochemical and Biophysical Research Communications, 276(2), 534–538. https://doi.org/10.1006/bbrc.2000.3485
- Lyu, S.-Y., Rhim, J.-Y., & Park, W.-B. (2005). Antiherpetic activities of flavonoids against herpes simplex virus type 1 (HSV-1) and type 2 (HSV-2) in vitro. Archives of Pharmacal Research, 28(11), 1293–1301. https://doi.org/10.1024/0301-1526.34.4.281a https://doi.org/10.1007/BF02978215
- Martinez, A. M., & Kak, A. C. (2001). PCA versus LDA. IEEE Transactions on Pattern Analysis and Machine Intelligence, 23(2), 228–233. https://doi.org/10.1109/34.908974
- Matias, A. A., Serra, A. T., Silva, A. C., Perdigão, R., Ferreira, T. B., Marcelino, I., Silva, S., Coelho, A. V., Alves, P. M., & Duarte, C. M. M. (2010). Portuguese winemaking residues as a potential source of natural anti-adenoviral agents. International Journal of Food Sciences and Nutrition, 61(4), 357–368. https://doi.org/10.3109/09637480903430990
- Miller, B. R. I., Mcgee, T. D., Swails, J. M., Homeyer, N., Gohlke, H., & Roitberg, A. E. (2012). MMPBSA. py: An efficient program for end-state free energy calculations. Journal of Chemical Theory and Computation, 8(9), 3314–3321. https://doi.org/10.1021/ct300418h
- Molecular Operating Environment (MOE). (2009). Scientific computing & instrumentation, Vol. 2009, 10 Rev ed. Reed Business.
- Muhammad, A., Anis, I., Khan, A., Marasini, B. P., Choudhary, M. I., & Shah, M. R. (2012). Biologically active C-alkylated flavonoids from Dodonaea viscosa. Archives of Pharmacal Research, 35(3), 431–436. https://doi.org/10.1007/s12272-012-0305-6
- Muhammad, A., Khan, B., Iqbal, Z., Khan, A. Z., Khan, I., Khan, K., Alamzeb, M., Ahmad, N., Khan, K., Lal Badshah, S., Ullah, A., Muhammad, S., Jan, M. T., Nadeem, S., & Kabir, N. (2019). Viscosine as a potent and safe antipyretic agent evaluated by yeast-induced pyrexia model and molecular docking studies. ACS Omega, 4(10), 14188–14192. https://doi.org/10.1021/acsomega.9b01041
- Muhammad, A., Tel-Cayan, G., Öztürk, M., Nadeem, S., Duru, M. E., Anis, I., Ng, S. W., & Shah, M. R. (2015). Biologically active flavonoids from Dodonaea viscosa and their structure-activity relationships. Industrial Crops and Products, 78, 66–72. https://doi.org/10.1016/j.indcrop.2015.10.011
- Muller, D. A., & Young, P. R. (2013). The flavivirus NS1 protein: Molecular and structural biology, immunology, role in pathogenesis and application as a diagnostic biomarker. Antiviral Research, 98(2), 192–208. https://doi.org/10.1016/j.antiviral.2013.03.008
- Qamar, M., Mumtaz, A., Naseem, R., Ali, A., Fatima, T., Jabbar, T., Ahmad, Z., & Ashfaq, U. A. (2014). Molecular docking based screening of plant flavonoids as dengue NS1 inhibitors. Bioinformation, 10(7), 460–465. https://doi.org/10.6026/97320630010460
- Ruhle, V. (2007). Berendsen and nose-hoover thermostats thesis. https://www2.mpip-mainz.mpg.de/∼andrienk/journal_club/thermostats.pdf
- Sajitha Lulu, S., Thabitha, A., Vino, S., Mohana Priya, A., & Rout, M. (2016). Naringenin and quercetin: Potential anti-HCV agents for NS2 protease targets. Natural Product Research, 30(4), 464–468. https://doi.org/10.1080/14786419.2015.1020490
- Salomon-Ferrer, R., Case, D. A., & Walker, R. C. (2013). An overview of the amber biomolecular simulation package. Wiley Interdisciplinary Reviews: Computational Molecular Science, 3(2), 198–210. https://doi.org/10.1002/wcms.1121
- Song, H., Qi, J., Haywood, J., Shi, Y., & Gao, G. F. (2016). Zika virus NS1 structure reveals diversity of electrostatic surfaces among flaviviruses. Nature Structural & Molecular Biology, 23(5), 456–458. https://doi.org/10.1038/nsmb.3213
- Su, X., & D’Souza, D. H. (2013). Naturally occurring flavonoids against human norovirus surrogates. Food and Environmental Virology, 5(2), 97–102. https://doi.org/10.1007/s12560-013-9106-4
- Suthar, M. S., Diamond, M. S., & Gale, M. (2013). West Nile virus infection and immunity. Nature Reviews Microbiology, 11(2), 115–128. https://doi.org/10.1038/nrmicro2950
- Wang, C., Greene, D., Xiao, L., Qi, R., & Luo, R. (2018). Recent developments and applications of the MMPBSA method. Frontiers in Molecular Biosciences, 4, 87. https://doi.org/10.3389/fmolb.2017.00087
- Zandi, K., Teoh, B., Sam, S., Wong, P., & Mustafa, M. R. (2011). In vitro antiviral activity of fisetin, rutin and naringenin against dengue virus type-2. Journal of Medicinal Plants Research, 5(23), 5534–5539. https://doi.org/10.5897/JMPR11.1046
- Zhang, T., Wu, Z., Du, J., Hu, Y., Liu, L., Yang, F., & Jin, Q. (2012). Anti-Japanese-encephalitis-viral effects of kaempferol and daidzin and their RNA-binding characteristics. PLoS One, 7(1), e30259. https://doi.org/10.1371/journal.pone.0030259