In silico studies of the inhibition mechanism of dengue with papain

References

• Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1–2, 19–25. 10.1016/j.softx.2015.06.001
   Google Scholar
• Ahmad, N., Fazal, H., Ayaz, M., Abbasi, B. H., Mohammad, I., & Fazal, L. (2011). Dengue fever treatment with Carica papaya leaves extracts. Asian Pacific Journal of Tropical Biomedicine, 1(4), 330–333. 10.1016/S2221-1691(11)60055-5
   PubMedGoogle Scholar
• Alhoot, M. A., Rathinam, A. K., Wang, S. M., Manikam, R., & Sekaran, S. D. (2013). Inhibition of dengue virus entry into target cells using synthetic antiviral peptides. International Journal of Medical Sciences, 10(6), 719–729. 10.7150/ijms.5037
   PubMed Web of Science ®Google Scholar
• Amir-Hassan, A., Lee, V. S., Baharuddin, A., Othman, S., Xu, Y., Huang, M., Yusof, R., Rahman, N. A., & Othman, R. (2017). Conformational and energy evaluations of novel peptides binding to dengue virus envelope protein. Journal of Molecular Graphics and Modelling, 74, 273–287. 10.1016/j.jmgm.2017.03.010
   PubMed Web of Science ®Google Scholar
• 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. 10.1080/07391102.2017.1419146
   PubMed Web of Science ®Google Scholar
• Beckel-Mitchener, A. C., Miera, A., Keller, R., & Perrone-Bizzozero, N. (2002). Poly(A) Tail Length-dependent Stabilization of GAP-43 mRNA by the RNA-binding Protein HuD. Journal of Biological Chemistry 277(31), 27996–8002. doi:10.1074/jbc.M201982200
   Google Scholar
• Bergamaschi, G., Fassi, E. M. A., Romanato, A., D'Annessa, I., Odinolfi, M. T., Brambilla, D., Damin, F., Chiari, M., Gori, A., Colombo, G., & Cretich, M. (2019). Computational analysis of dengue virus envelope protein (E) reveals an epitope with flavivirus immunodiagnostic potential in peptide microarrays. International Journal of Molecular Sciences, 20(8), 1921. 10.3390/ijms20081921
   Web of Science ®Google Scholar
• Bernardes, C. E. S., Canongia Lopes, J. N., & Da Piedade, M. E. M. (2013). All-atom force field for molecular dynamics simulations on organotransition metal solids and liquids. The Journal of Physical Chemistry A, 117(43), 11107–11113. 10.1021/jp407739h
   PubMed Web of Science ®Google Scholar
• Best, S. M. (2017). The many faces of the flavivirus NS5 protein in antagonism of type I interferon signaling. Journal of Virology, 91(3), e01970–16. 10.1128/JVI.01970-16
   PubMed Web of Science ®Google Scholar
• Beveridge, A. J. (1996). A theoretical study of the active sites of papain and S195C rat trypsin: Implications for the low reactivity of mutant serine proteinases. Protein Science, 5(7), 1355–1365. 10.1002/pro.5560050714
   PubMed Web of Science ®Google Scholar
• Boopathi, S., & Kolandaivel, P. (2016). Fe2 + binding on amyloid β-peptide promotes aggregation. Proteins: Structure, Function, and Bioinformatics, 84(9), 1257–1274. 10.1002/prot.25075
   PubMed Web of Science ®Google Scholar
• Borhani, D. W., & Shaw, D. E. (2012). The future of molecular dynamics simulations in drug discovery. Journal of Computer-Aided Molecular Design, 26(1), 15–26. 10.1007/s10822-011-9517-y
   PubMed Web of Science ®Google Scholar
• Bornot, A., Etchebest, C., & De Brevern, A. G. (2011). Predicting protein flexibility through the prediction of local structures. Proteins: Structure, Function, and Bioinformatics, 79(3), 839–852. 10.1002/prot.22922
   PubMed Web of Science ®Google Scholar
• Bryantsev, V. S., Diallo, M. S., van Duin, A. C. T., & Goddard, W. A. (2009). Evaluation of B3LYP, X3LYP, and M06-class density functionals for predicting the binding energies of neutral, protonated, and deprotonated water clusters. Journal of Chemical Theory and Computation, 5(4), 1016–1026. 10.1021/ct800549f
   PubMed Web of Science ®Google Scholar
• Caflisch, A. (2018). Protein structure-based drug design: From docking to molecular dynamics Pawe ł Sled z and Amedeo Caflisch. Current Opinion in Structural Biology, (48), 93–102. 10.1016/j.sbi.2017.10.010
   PubMed Web of Science ®Google Scholar
• Carter, P., Andersen, C. A. F., & Rost, B. (2003). DSSPcont: Continuous secondary structure assignments for proteins. Nucleic Acids Research, 31(13), 3293–3295. 10.1093/nar/gkg626
   PubMed Web of Science ®Google Scholar
• Chepkorir, E., Lutomiah, J., Mutisya, J., Mulwa, F., Orindi, B., Ng’ang’a, Z., & Sang, R. (2014). The vector competence of Ae. aegypti mosquito populations from Kilifi and Nairobi for dengue-2 virus and the effect of temperature. International Journal of Infectious Diseases, 21, 3–4. 10.1016/j.ijid.2014.03.413
   Web of Science ®Google Scholar
• Chohan, T. A., Qian, H. Y., Pan, Y. L., & Chen, J. Z. (2016). Molecular simulation studies on the binding selectivity of 2-anilino-4-(thiazol-5-yl)-pyrimidines in complexes with CDK2 and CDK7. Molecular Biosystems, 12(1), 145–161. 10.1039/C5MB00630A
   PubMedGoogle Scholar
• Da Silva, R. R., Santos, J. M., Ramalho, T. C., & Figueroa-Villar, J. D. (2006). Concerning the FERMO concept and Pearson’s Hard and Soft acid-base principle. Journal of the Brazilian Chemical Society, 17(2), 223–226. 10.1590/S0103-50532006000200002
   Web of Science ®Google Scholar
• Deepa, P., Kolandaivel, P., & Senthilkumar, K. (2011). Structural properties and the effect of 2,6-diaminoanthraquinone on G-tetrad, non-G-tetrads, and mixed tetrads-A density functional theory study. International Journal of Quantum Chemistry, 111(12), 3239–3250. 10.1002/qua.22720
   Web of Science ®Google Scholar
• Degrève, L., Fuzo, C. A., & Caliri, A. (2012). Extensive structural change of the envelope protein of dengue virus induced by a tuned ionic strength: Conformational and energetic analyses. Journal of Computer-Aided Molecular Design, 26(12), 1311–1325. 10.1007/s10822-012-9616-4
   PubMed Web of Science ®Google Scholar
• Drenth, J., Kalk, K. H., & Swen, M. (1976). Binding of chloromethyl ketone substrate analogs to crystalline papain. Biochemistry, 15(17), 3731–3738. 10.1021/bi00662a014
   PubMed Web of Science ®Google Scholar
• Durrant, J. D., & Mccammon, J. A. (2011). Molecular dynamics simulations and drug discovery. BMC Biology, 9(1), 1–9. 10.1186/1741-7007-9-71
   PubMed Web of Science ®Google Scholar
• Eerde, V., Gottschamel, J., Bock, R., Eraker, K., Hansen, A., Mweemba, H., & Clarke, J. L. (2019). Production of tetravalent dengue virus envelope protein domain III based antigens in lettuce chloroplasts and immunologic analysis for future oral vaccine development. Plant Biotechnology Journal, 17(7), 1408–1417. 10.1111/pbi.13065
   PubMed Web of Science ®Google Scholar
• Fogarty, R. M., Rowe, R., Matthews, R. P., Clough, M. T., Ashworth, C. R., Brandt, A., Corbett, P. J., Palgrave, R. G., Smith, E. F., Bourne, R. A., Chamberlain, T. W., Thompson, P. B. J., Hunt, P. A., & Lovelock, K. R. J. (2018). Atomic charges of sulfur in ionic liquids: Experiments and calculations. Faraday Discussions, 206, 183–201. 10.1039/C7FD00155J
   Web of Science ®Google Scholar
• Fraser, J. E., Rawlinson, S. M., Heaton, S. M., & Jans, D. A. (2016). Dynamic nucleolar targeting of dengue virus polymerase NS5 in response to extracellular pH. Journal of Virology, 90(12), 5797–5807. 10.1128/JVI.02727-15
   PubMed Web of Science ®Google Scholar
• Ganesan, A., Coote, M. L., & Barakat, K. (2017). Molecular dynamics-driven drug discovery: Leaping forward with confidence. Drug Discovery Today., 22(2), 249–269. 10.1016/j.drudis.2016.11.001
   PubMed Web of Science ®Google Scholar
• Gao, Z., & Ding, Y. (2017). DFT study of CO2and H2O co-adsorption on carbon models of coal surface. Journal of Molecular Modeling, 23(6), 187. 10.1007/s00894-017-3356-2
   PubMed Web of Science ®Google Scholar
• Ghosh, I., & Talukdar, P. (2019). Molecular docking and pharmacokinetics study for selected leaf phytochemicals from Carica papaya Linn. against dengue virus protein, NS2B / NS3 protease. World Scientific News, 124(2), 264–278.
   Google Scholar
• Gonçalves, R. L., de Lima Menezes, G., Sussuchi, L., Moreli, M. L., Mottin, M., Andrade, C. H., Pereira, M., & da Silva, R. A. (2019). Dynamic behavior of Dengue and Zika viruses NS1 protein reveals monomer–monomer interaction mechanisms and insights to rational drug design. Journal of Biomolecular Structure and Dynamics, 1–11. 10.1080/07391102.2019.1677504
   PubMed Web of Science ®Google Scholar
• Grabowski, S. J. (2013). Non-covalent interactions - QTAIM and NBO analysis. Journal of Molecular Modeling, 19(11), 4713–4721. 10.1007/s00894-012-1463-7
   PubMed Web of Science ®Google Scholar
• Grdadolnik, J., Merzel, F., & Avbelj, F. (2017). Origin of hydrophobicity and enhanced water hydrogen bond strength near purely hydrophobic solutes. Proceedings of the National Academy of Sciences, 114(2), 322–327. 10.1073/pnas.1612480114
   PubMed Web of Science ®Google Scholar
• Greener, J. G., & Sternberg, M. J. E. (2018). Structure-based prediction of protein allostery. Current Opinion in Structural Biology, 50, 1–8. 10.1016/j.sbi.2017.10.002
   PubMed Web of Science ®Google Scholar
• Guardia, C. D. L., & Lleonart, R. ( (2014). 2014). Progress in the identification of dengue virus entry / fusion inhibitors. BioMed Research International, 2014, 1–13. 10.1155/2014/825039
   Web of Science ®Google Scholar
• Gubler, D. J. (1998). Dengue and dengue hemorrhagic fever. Clinical Microbiology Reviews, 11(3), 480–496. 10.1128/CMR.11.3.480
   PubMed Web of Science ®Google Scholar
• Harrison, M. J., Burton, N. A., & Hillier, I. H. (1997). Catalytic mechanism of the enzyme papain: Predictions with a hybrid quantum mechanical/molecular mechanical potential. Journal of the American Chemical Society, 119(50), 12285–12291. 10.1021/ja9711472
   Web of Science ®Google Scholar
• Health, P. (2019). An open-label, randomized prospective study to evaluate the efficacy and safety of Carica papaya leaf extract for thrombocytopenia associated with dengue fever in pediatric subjects. Pediatric Health Medicine and Therapeutics, 2019(10), 5–11. 10.2147/PHMT.S176712
   Web of Science ®Google Scholar
• Hunt, P. A., Ashworth, C. R., & Matthews, R. P. (2015). Hydrogen bonding in ionic liquids. Chemical Society Reviews, 44(5), 1257–1288. 10.1039/C4CS00278D
   PubMed Web of Science ®Google Scholar
• Jensen, K. P., & Jorgensen, W. L. (2006). Halide, ammonium, and alkali metal ion parameters for modeling aqueous solutions. Journal of Chemical Theory and Computation, 2(6), 1499–1509. 10.1021/ct600252r
   PubMed Web of Science ®Google Scholar
• Jorgensen, W. L. (2016). Computer-aided discovery of anti-HIV agents. Bioorganic & Medicinal Chemistry, 24(20), 4768–4778. 10.1016/j.bmc.2016.07.039
   PubMed Web of Science ®Google Scholar
• Kahn, K., & Bruice, T. C. (2002). Parameterization of OPLS-AA force field for the conformational analysis of macrocyclic polyketides. Journal of Computational Chemistry, 23(10), 977–996. 10.1002/jcc.10051
   PubMed Web of Science ®Google Scholar
• Kaminski, G. A., Friesner, R. A., Tirado-Rives, J., & Jorgensen, W. L. (2001). Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. The Journal of Physical Chemistry B, 105(28), 6474–6487. 10.1021/jp003919d
   Web of Science ®Google Scholar
• Kaye, S. L., Sansom, M. S. P., & Biggin, P. C. (2006). Molecular dynamics simulations of the ligand-binding domain of an N-methyl-D-aspartate receptor. Journal of Biological Chemistry, 281(18), 12736–12742. 10.1074/jbc.M512728200
   PubMed Web of Science ®Google Scholar
• Khan, R. A., Afroz, S., Minhas, G., Battu, S., & Khan, N. (2019). Cytokine Dengue virus envelope protein domain III induces pro-in fl ammatory signature and triggers activation of in fl ammasome. Cytokine, 123, 154780. 10.1016/j.cyto.2019.154780
   PubMed Web of Science ®Google Scholar
• Komáromi, A. F., & Komáromi, I. (2016). Modeling the archetype cysteine protease reaction using dispersion corrected density functional methods in ONIOM-type hybrid QM/MM calculations; the proteolytic reaction of papain. Physical Chemistry Chemical Physics, 18(48), 32847–32861. 10.1039/C6CP06869C
   PubMed Web of Science ®Google Scholar
• Kroschewski, H., Sagripanti, J., Davidson, A. D., & Davidson, A. D. (2009). Communication Identification of amino acids in the dengue virus type 2 envelope glycoprotein critical to virus infectivity. Journal of General Virology, 90(10), 2457–2461. 10.1099/vir.0.011486-0
   PubMed Web of Science ®Google Scholar
• Leal, E. S., Adler, N. S., Fernández, G. A., Gebhard, L. G., Battini, L., Aucar, M. G., Videla, M., Monge, M. E., Hernández de los Ríos, A., Acosta Dávila, J. A., Morell, M. L., Cordo, S. M., García, C. C., Gamarnik, A. V., Cavasotto, C. N., & Bollini, M. (2019). De novo design approaches targeting an envelope protein pocket to identify small molecules against dengue virus. European Journal of Medicinal Chemistry, 182, 111628. 10.1016/j.ejmech.2019.111628
   PubMed Web of Science ®Google Scholar
• Liao, K. H., Chen, K. B., Lee, W. Y., Sun, M. F., Lee, C. C., & Chen, C. Y. C. (2014). Ligand-based and structure-based investigation for Alzheimer’s disease from traditional Chinese medicine. Evidence-Based Complementary and Alternative Medicine, 2014, 1–16. 10.1155/2014/364819
   Web of Science ®Google Scholar
• Lim, W. Z., Cheng, P. G., Abdulrahman, A. Y., & Teoh, T. C. (2019). The identification of active compounds in Ganoderma lucidum var. antler extract inhibiting dengue virus serine protease and its computational studies. Journal of Biomolecular Structure and Dynamics, 1–16. 10.1080/07391102.2019.1678523
   Web of Science ®Google Scholar
• Lonkala, S., & Reddy, A. R. N. (2019). Antibacterial Activity of Carica papaya Leaves and Allium sativum Cloves Alone and in Combination against Multiple Strains. Pharmacognosy Journal, 11(3), 600–602. 10.5530/pj.2019.11.95
   Google Scholar
• Lourenço, J., Tennant, W., Faria, N. R., Walker, A., Gupta, S., & Recker, M. (2018). Challenges in dengue research: A computational perspective. Evolutionary Applications, 11(4), 516–533. 10.1111/eva.12554
   PubMed Web of Science ®Google Scholar
• 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. 10.1093/infdis/jiw423
   PubMed Web of Science ®Google Scholar
• Madjos, G. G. (2019). Comparative cytotoxic properties of two varieties of Carica papaya leaf extracts from Mindanao, Philippines using Brine Shrimp Lethality Assay Comparative Cytotoxic Properties of Two Varieties of Carica papaya leaf extracts from Mindanao, Philippines using Brine Shrimp Lethality Assay. Bulletin of Environment, Pharmacology and Life Sciences, 8(2), 113–118.
   Google Scholar
• Manjula, S., & Kumaradhas, P. (2019). Evaluating the suitability of RNA intervention mechanism exerted by some flavonoid molecules against dengue virus MTase RNA capping site: A molecular docking, molecular dynamics simulation, and binding free energy study. Journal of Biomolecular Structure and Dynamics, 1–11. 10.1080/07391102.2019.1666744
   PubMed Web of Science ®Google Scholar
• Marques, S. M., Bednar, D., & Damborsky, J. (2019, January). Computational study of protein-ligand unbinding for enzyme engineering. Frontiers in Chemistry, 6, 1–15. 10.3389/fchem.2018.00650
   Web of Science ®Google Scholar
• Martı, G., & Fabritiis, G. D. (2018). Simulations meet machine learning in structural biology. Current Opinion in Structural Biology, 49, 1339–1144. 10.1016/j.sbi.2018.02.004
   Web of Science ®Google Scholar
• Mathammal, R., Jayamani, N., & Geetha, N. (2013). Molecular structure, NMR, HOMO, LUMO, and vibrational analysis of O-anisic acid and anisic acid based on DFT calculations. Journal of Spectroscopy, 2013, 1–18. 10.1155/2013/171735
   Web of Science ®Google Scholar
• Minai, R., Matsuo, Y., Onuki, H., & Hirota, H. (2008). Method for comparing the structures of protein ligand-binding sites and application for predicting protein-drug interactions. Proteins: Structure, Function, and Bioinformatics, 72(1), 367–381. 10.1002/prot.21933
   PubMed Web of Science ®Google Scholar
• Modis, Y., Ogata, S., Clements, D., & Harrison, S. C. (2005). Variable surface epitopes in the crystal structure of dengue virus type 3 envelope glycoprotein †. Journal of Virology, 79(2), 1223–1231. 10.1128/JVI.79.2.1223-1231.2005
   PubMed Web of Science ®Google Scholar
• Mohd Abd Razak, M. R., Norahmad, N. A., Md Jelas, N. H., Jusoh, B., Muhammad, A., Mohmad Misnan, N., Zainol, M., Thayan, R., & Syed Mohamed, A. F. (2019). Preliminary study on the expression of endothelial cell biology related genes in the liver of dengue virus infected mice treated with Carica papaya leaf juice. BMC Research Notes, 12(1), 206. 10.1186/s13104-019-4242-z
   PubMed Web of Science ®Google Scholar
• Mondotte, J. A., Lozach, P., Amara, A., & Gamarnik, A. V. (2007). Essential role of dengue virus envelope protein N glycosylation at asparagine-67 during viral propagation. Journal of Virology, 81(13), 7136–7148. 10.1128/JVI.00116-07
   PubMed Web of Science ®Google Scholar
• Mortier, J., Rakers, C., Bermudez, M., Murgueitio, M. S., Riniker, S., & Wolber, G. (2015). The impact of molecular dynamics on drug design: Applications for the characterization of ligand – macromolecule complexes. Drug Discovery Today., 20(6), 686–702. 10.1016/j.drudis.2015.01.003
   PubMed Web of Science ®Google Scholar
• Musyoka, T. M., Kanzi, A. M., Lobb, K. A., & Tastan Bishop, Ö. (2016). Structure based docking and molecular dynamic studies of plasmodial cysteine proteases against a South African natural compound and its analogs. Scientific Reports, 6(1), 23690. 10.1038/srep23690
   PubMed Web of Science ®Google Scholar
• Mutter, S. T., Deeth, R. J., Turner, M., & Platts, J. A. (2018). Benchmarking of copper(II) LFMM parameters for studying amyloid-β peptides. Journal of Biomolecular Structure and Dynamics, 36(5), 1145–1153. 10.1080/07391102.2017.1313780
   PubMed Web of Science ®Google Scholar
• Nakhate, Y. D., Talekar, K. S., Giri, S. V., & Vasekar, R. D. (2019). Pharmacological and chemical composition of Carica papaya: On overview. World Journal of Pharmaceutical Research, 8(5), 811–821. 10.20959/wjpr20195-14650
   Google Scholar
• Nguyen, N. M., Duong, B. T., Azam, M., Phuong, T. T., Park, H., Thuy, P. T. B., & Yeo, S.-J. (2019). Diagnostic performance of dengue virus envelope domain III in acute dengue infection. International Journal of Molecular Sciences, 20(14), 3464. 10.3390/ijms20143464
   Web of Science ®Google Scholar
• Nguyen, T. T., Viet, M. H., & Li, M. S. (2014). Effects of water models on binding affinity: Evidence from all-atom simulation of binding of tamiflu to A/H5N1 neuraminidase. The Scientific World Journal, 2014, 1–14. 10.1155/2014/536084
   Web of Science ®Google Scholar
• Norahmad, N. A., Mohd Abd Razak, M. R., Mohmad Misnan, N., Md Jelas, N. H., Sastu, U. R., Muhammad, A., Ho, T. C. D., Jusoh, B., Zolkifli, N. A., Thayan, R., Mat Ripen, A., Zainol, M., & Syed Mohamed, A. F. (2019). Effect of freeze-dried Carica papaya leaf juice on inflammatory cytokines production during dengue virus infection in AG129 mice. BMC Complementary and Alternative Medicine, 19(1), 1–13. 10.1186/s12906-019-2438-3
   PubMed Web of Science ®Google Scholar
• Nouchi, I., & Toyama, S. (1988). Nouchi88 effects of ozone and peroxyacetyl nitrate on polar lipids and fatty acids in leaves of morning glory and kidney bean. Plant Physiology, 87(3), 638–646. 10.1104/pp.87.3.638
   PubMed Web of Science ®Google Scholar
• Ohyashiki, T., Taka, M., & Mohri, T. (1985). The effects of ionic strength on the protein conformation and the fluidity of porcine intestinal brush border membranes. Fluorometric studies using N-[7-dimethylamino-4-methylcoumarinyl]maleimide and pyrene. Journal of Biological Chemistry, 260(11), 6857–6861.
   PubMed Web of Science ®Google Scholar
• Ourique, G. S., Vianna, J. F., Neto, J. X. L., Oliveira, J. I. N., Mauriz, P. W., Vasconcelos, M. S., Caetano, E. W. S., Freire, V. N., Albuquerque, E. L., & Fulco, U. L. (2016). A quantum chemistry investigation of a potential inhibitory drug against the dengue virus. RSC Advances, 6(61), 56562–56570. 10.1039/C6RA10121F
   Web of Science ®Google Scholar
• Pace, C. N., Fu, H., Lee Fryar, K., Landua, J., Trevino, S. R., Schell, D., Thurlkill, R. L., Imura, S., Scholtz, J. M., Gajiwala, K., Sevcik, J., Urbanikova, L., Myers, J. K., Takano, K., Hebert, E. J., Shirley, B. A., & Grimsley, G. R. (2014). Contribution of hydrogen bonds to protein stability. Protein Science, 23(5), 652–661. 10.1002/pro.2449
   PubMed Web of Science ®Google Scholar
• Patel, B., Longo, P., Miley, M. J., Montoya, M., Harris, E., & de Silva, A. M. (2017). Dissecting the human serum antibody response to secondary dengue virus infections. PLOS Neglected Tropical Diseases, 11(5), e0005554–15. 10.1371/journal.pntd.0005554
   PubMed Web of Science ®Google Scholar
• Paton, R. S., & Goodman, J. M. (2009). Hydrogen bonding and π-stacking: How reliable are force fields? A critical evaluation of force field descriptions of nonbonded interactions. Journal of Chemical Information and Modeling, 49(4), 944–955. 10.1021/ci900009f
   PubMed Web of Science ®Google Scholar
• Patra, M., Hyvönen, M. T., Falck, E., Sabouri-Ghomi, M., Vattulainen, I., & Karttunen, M. (2007). Long-range interactions and parallel scalability in molecular simulations. Computer Physics Communications, 176(1), 14–22. 10.1016/j.cpc.2006.07.017
   Web of Science ®Google Scholar
• Perera, S. D., Jayawardena, U. A., & Jayasinghe, C. D. (2018). Potential use of Euphorbia hirta for dengue: A systematic review of scientific evidence. Journal of Tropical Medicine, 2018, 1–9686. 10.1155/2018/2048530
   Web of Science ®Google Scholar
• Plumley, J. A., & Dannenberg, J. J. (2011). A comparison of the behavior of functional/basis set combinations for hydrogen-bonding in the water dimer with emphasis on basis set superposition error. Journal of Computational Chemistry, 32(8), 1519–1527. 10.1002/jcc.21729
   PubMed Web of Science ®Google Scholar
• Qing, X., Sun, N., Yeh, J., Yue, C., & Cai, J. (2014). Dengue fever and bone marrow myelofibrosis. Experimental and Molecular Pathology, 97(2), 208–210. 10.1016/j.yexmp.2014.07.004
   PubMed Web of Science ®Google Scholar
• Radhika, R., Shankar, R., Vijayakumar, S., & Kolandaivel, P. (2018). Role of 6-Mercaptopurine in the potential therapeutic targets DNA base pairs and G-quadruplex DNA: Insights from quantum chemical and molecular dynamics simulations. Journal of Biomolecular Structure and Dynamics, 36(6), 1369–1401. 10.1080/07391102.2017.1323013
   PubMed Web of Science ®Google Scholar
• Ramachandran, N. (1967). Conformation of polypeptides and proteins. Advances in Protein Chemistry, 23, 283–438. 10.1016/s0065-3233(08)60402-7
   Google Scholar
• Rathore, A. S., Sarker, A., Devi, R., & Id, G. (2019). Designing antibody against highly conserved region of dengue envelope protein by in silico screening of scFv mutant library. PLoS One, 14(1), e0209576. 10.1371/journal.pone.0209576
   PubMed Web of Science ®Google Scholar
• Raut, R., Beesetti, H., Tyagi, P., Khanna, I., Jain, S. K., Jeankumar, V. U., Yogeeswari, P., Sriram, D., & Swaminathan, S. (2015). A small molecule inhibitor of dengue virus type 2 protease inhibits the replication of all four dengue virus serotypes in cell culture. Virology Journal, 12(1), 16–17. 10.1186/s12985-015-0248-x
   PubMed Web of Science ®Google Scholar
• Rey, A. (2003). Dengue virus envelope glycoprotein structure: New insight into its interactions during viral entry. Proceedings of the National Academy of Sciences of the United States of America., 100(12), 6899–6901. 10.1073/pnas.1332695100
   PubMed Web of Science ®Google Scholar
• Robertson, M. J., Tirado-Rives, J., & Jorgensen, W. L. (2015). Improved peptide and protein torsional energetics with the OPLS-AA force field. Journal of Chemical Theory and Computation, 11(7), 3499–3509. 10.1021/acs.jctc.5b00356
   PubMed Web of Science ®Google Scholar
• Roderick, E. H., & Haider, M. K. (2010, February). Hydrogen bonds in proteins: Role and strength. Encyclopedia of Life Sciences. Chichester: John Wiley & Sons, Ltd. doi:10.1002/9780470015902.a0003011.pub2
   Google Scholar
• Ruggerone, P., Vargiu, A. V., Collu, F., Fischer, N., & Kandt, C. (2013). Molecular dynamics computer simulations of multidrug Rnd efflux pumps. Computational and Structural Biotechnology Journal, 5(6), e201302008. 10.5936/csbj.201302008
   PubMedGoogle Scholar
• Rullmann, J. A. C., Bellido, M. N., & van Duijnen, P. T. (1989). The active site of papain. All-atom study of interactions with protein matrix and solvent. Journal of Molecular Biology, 206(1), 101–118. 10.1016/0022-2836(89)90527-5
   PubMed Web of Science ®Google Scholar
• Sabarinathan, R., Aishwarya, K., Sarani, R., Vaishnavi, M. K., & Sekar, K. (2011). Water-mediated ionic interactions in protein structures. Journal of Biosciences, 36(2), 253–263. 10.1007/s12038-011-9067-4
   PubMed Web of Science ®Google Scholar
• Sabetian, S., Nezafat, N., Dorosti, H., Zarei, M., & Ghasemi, Y. (2019). Exploring dengue proteome to design an effective epitope-based vaccine against dengue virus. Journal of Biomolecular Structure and Dynamics, 37(10), 2546–2563. 10.1080/07391102.2018.1491890
   PubMed Web of Science ®Google Scholar
• Saotome, T., Doret, M., Kulkarni, M., Yang, Y., Barthe, P., Kuroda, Y., & Roumestand, C. (2019). Folding of the Ig-like domain of the dengue virus envelope protein analyzed by high-hydrostatic-pressure NMR at a residue-level resolution. Biomolecules, 9(8), 309. 10.3390/biom9080309
   Web of Science ®Google Scholar
• Saravanan, K. M., & Selvaraj, S. (2017). Dihedral angle preferences of amino acid residues forming various non-local interactions in proteins. Journal of Biological Physics, 43(2), 265–278. 10.1007/s10867-017-9451-x
   PubMed Web of Science ®Google Scholar
• Selvaraman, N., Selvam, S. K., & Muthusamy, K. (2016). The binding mode prediction and similar ligand potency in the active site of vitamin D receptor with QM/MM interaction, MESP, and MD simulation. Chemical Biology & Drug Design, 88(2), 272–280. 10.1111/cbdd.12754
   PubMed Web of Science ®Google Scholar
• Shah, M., Wadood, A., Rahman, Z., & Husnain, T. (2013). Interaction and inhibition of dengue envelope glycoprotein with mammalian receptor DC-sign, an in-silico approach. PLoS One, 8(3), e59211–10. 10.1371/journal.pone.0059211
   PubMed Web of Science ®Google Scholar
• Sharma, A., & Pan, A. (2012). Identification of potential drug targets in Yersinia pestis using metabolic pathway analysis: MurE ligase as a case study. European Journal of Medicinal Chemistry, 57, 185–195. 10.1016/j.ejmech.2012.09.018
   PubMed Web of Science ®Google Scholar
• Shokhen, M., Khazanov, N., & Albeck, A. (2009). Challenging a paradigm: Theoretical calculations of the protonation state of the Cys25-His159 catalytic diad in free papain. Proteins: Structure, Function, and Bioinformatics, 77(4), 916–926. 10.1002/prot.22516
   PubMed Web of Science ®Google Scholar
• Simanjuntak, K., Simanjuntak, J. E., & Prasasty, V. D. (2017). Structure-based drug design of quercetin and its derivatives against HMGB1. Biomedical and Pharmacology Journal, 10(4), 1973–1982. 10.13005/bpj/1318
   Google Scholar
• Simonelli, L., Pedotti, M., Beltramello, M., Livoti, E., Calzolai, L., Sallusto, F., Lanzavecchia, A., & Varani, L. (2013). Rational engineering of a human anti-dengue antibody through experimentally validated computational docking. PLoS One, 8(2), e55561. 10.1371/journal.pone.0055561
   PubMed Web of Science ®Google Scholar
• Singh, W., Karabencheva-Christova, T. G., Sparagano, O., Black, G. W., Petrov, P. Y., & Christov, C. Z. (2016). Dimerization and ligand binding in tyrosylprotein sulfotransferase-2 are influenced by molecular motions. RSC Advances, 6(22), 18542–18548. 10.1039/C6RA01899H
   Web of Science ®Google Scholar
• Svejgaard, E. (1986). Humoral antibody responses in the immunopathogenesis of dermatophytosis. Acta Dermato-Venereologica. Supplementum, 121, 85–91.
   PubMedGoogle Scholar
• Tautermann, C. S., Seeliger, D., & Kriegl, J. M. (2015). What can we learn from molecular dynamics simulations for GPCR drug design? Computational and Structural Biotechnology Journal, 13, 111–121. 10.1016/j.csbj.2014.12.002
   PubMed Web of Science ®Google Scholar
• Tjaden, N. B., Thomas, S. M., Fischer, D., & Beierkuhnlein, C. (2013). Extrinsic incubation period of dengue: Knowledge, backlog, and applications of temperature dependence. PLoS Neglected Tropical Diseases, 7(6), e2207–5. 10.1371/journal.pntd.0002207
   PubMed Web of Science ®Google Scholar
• Tseng, Y.-T., Chang, F.-S., Chao, D.-Y., & Lian, I.-B. (2016). Re-model the relation of vector indices, meteorological factors and dengue fever. Journal of Tropical Diseases, 4(2), 4–11. 10.4172/2329-891X.1000200
   Google Scholar
• Vaccaro, L., Koronakis, V., & Sansom, M. S. P. (2006). Flexibility in a drug transport accessory protein: Molecular dynamics simulations of MexA. Biophysical Journal, 91(2), 558–564. 10.1529/biophysj.105.080010
   PubMed Web of Science ®Google Scholar
• Vernet, T., Tessier, D. C., Chatellier, J., Plouffe, C., Lee, T. S., Thomas, D. Y., Storer, A. C., & Menard, R. (1995). Structural and functional roles of asparagine 175 in the cysteine protease papain. Journal of Biological Chemistry, 270(28), 16645–16652. 10.1074/jbc.270.28.16645
   PubMed Web of Science ®Google Scholar
• Vora, J., Patel, S., Athar, M., Sinha, S., Chhabria, M. T., Jha, P. C., & Shrivastava, N. (2019). Pharmacophore modeling, molecular docking and molecular dynamics simulation for screening and identifying anti-dengue phytocompounds. Journal of Biomolecular Structure and Dynamics, 1–15. 10.1080/07391102.2019.1615002
   Web of Science ®Google Scholar
• Wong, L. P., & AbuBakar, S. (2013). Health beliefs and practices related to dengue fever: A focus group study. PLoS Neglected Tropical Diseases, 7(7), e2310. 10.1371/journal.pntd.0002310
   PubMed Web of Science ®Google Scholar
• Xie, L., Li, J., Xie, L., & Bourne, P. E. (2009). Drug discovery using chemical systems biology: Identification of the protein-ligand binding network to explain the side effects of CETP inhibitors. PLoS Computational Biology, 5(5), e1000387. 10.1371/journal.pcbi.1000387
   PubMed Web of Science ®Google Scholar
• Xu, X., & Truhlar, D. G. (2011). Accuracy of effective core potentials and basis sets for density functional calculations, including relativistic effects, as illustrated by calculations on arsenic compounds. Journal of Chemical Theory and Computation, 7(9), 2766–2779. 10.1021/ct200234r
   PubMed Web of Science ®Google Scholar
• Ye, Y. H., Carrasco, A. M., Dong, Y., Sgrò, C. M., & McGraw, E. A. (2016). The effect of temperature on Wolbachia-mediated dengue virus blocking in Aedes aegypti. The American Journal of Tropical Medicine and Hygiene, 94(4), 812–819. 10.4269/ajtmh.15-0801
   PubMed Web of Science ®Google Scholar
• Zacharias, J., & Knapp, E. W. (2014). Protein secondary structure classification revisited: Processing DSSP information with PSSC. Journal of Chemical Information and Modeling, 54(7), 2166–2179. 10.1021/ci5000856
   PubMed Web of Science ®Google Scholar
• Zajc, T., Suban, D., Rajković, J., & Dolenc, I. (2011). Baculoviral expression and characterization of human recombinant PGCP in the form of an active mature dimer and an inactive precursor protein. Protein Expression and Purification, 75(2), 119–126. 10.1016/j.pep.2010.10.005
   PubMed Web of Science ®Google Scholar
• Zhang, Z., Benabbas, A., Ye, X., Yu, A., & Champion, P. M. (2015). Measurements of heme relaxation and ligand recombination in strong magnetic fields. Journal of Physical Chemistry B., 6(9), 790–795. 10.1016/j.pmrj.2014.02.014.Lumbar
   Google Scholar
• Zhang, X., Jia, R., Shen, H., Wang, M., Yin, Z., & Cheng, A. (2017). Structures and functions of the envelope glycoprotein in flavivirus infections. Viruses, 9(11), 338–314. 10.3390/v9110338
   PubMed Web of Science ®Google Scholar
• Zhao, Y., & Truhlar, D. G. (2008). The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: Two new functionals and systematic testing of four M06-class functionals and 12 other function. Theoretical Chemistry Accounts, 120(1–3), 215–241. 10.1007/s00214-007-0310-x
   Web of Science ®Google Scholar