An in-silico receptor-pharmacophore based multistep molecular docking and simulation study to evaluate the inhibitory potentials against NS1 of DENV-2

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. https://doi.org/10.1016/j.softx.2015.06.001
   Google Scholar
• Akey, D. L., Brown, W. C., Jose, J., Kuhn, R. J., & Smith, J. L. (2015). Structure-guided insights on the role of NS1 in flavivirus infection. BioEssays, 37(5), 489–494. https://doi.org/10.1002/bies.201400182
   PubMed Web of Science ®Google Scholar
• Alam, S., & Khan, F. (2019). 3D-QSAR, Docking, ADME/Tox studies on flavone analogs reveal anticancer activity through Tankyrase inhibition. Scientific Reports, 9(1), 5414. https://doi.org/10.1038/s41598-019-41984-7
   PubMedGoogle Scholar
• Alcalá, A. C., Palomares, L. A., & Ludert, J. E. (2018). Secretion of nonstructural protein 1 of dengue virus from infected mosquito cells: Facts and speculations. Journal of Virology, 92, e00275-18. https://doi.org/10.1128/JVI.00275-18
   PubMed Web of Science ®Google Scholar
• Ali, S. A., Hassan, M. I., Islam, A., & Ahmad, F. (2014). A review of methods available to estimate solvent-accessible surface areas of soluble proteins in the folded and unfolded states. Current Protein & Peptide Science, 15(5), 456–476. https://doi.org/10.2174/1389203715666140327114232
   PubMed Web of Science ®Google Scholar
• Armen, R., Alonso, D. O., & Daggett, V. (2003). The role of alpha-, 3(10)-, and pi-helix in helix–>coil transitions. Protein Science, 12(6), 1145–1157. https://doi.org/10.1110/ps.0240103
   PubMed Web of Science ®Google Scholar
• Asthagiri, D., Neal, B. L., & Lenhoff, A. M. (1999). Calculation of short-range interactions between proteins. Biophysical Chemistry, 78(3), 219–231. https://doi.org/10.1016/S0301-4622(99)00028-9
   PubMed Web of Science ®Google Scholar
• Avirutnan, P., Hauhart, R. E., Somnuke, P., Blom, A. M., Diamond, M. S., & Atkinson, J. P. (2011). Binding of flavivirus nonstructural protein NS1 to C4b binding protein modulates complement activation. Journal of Immunology, 187(1), 424–433. https://doi.org/10.4049/jimmunol.1100750
   PubMed Web of Science ®Google Scholar
• Shekhawat, P. B., & Pokharkar, V. B. (2017). Understanding peroral absorption: Regulatory aspects and contemporary approaches to tackling solubility and permeability hurdles. Acta Pharmaceutica Sinica. B, 7, 260–280. https://doi.org/10.1016/j.apsb.2016.09.005
   PubMed Web of Science ®Google Scholar
• Baba, Y., Isomura, T., & Kashima, H. (2018). Wisdom of crowds for synthetic accessibility evaluation. Journal of Molecular Graphics & Modelling, 80, 217–223. https://doi.org/10.1016/j.jmgm.2018.01.011
   PubMed Web of Science ®Google Scholar
• Bachmann, K. A., & Lewis, J. D. (2005). Predicting inhibitory drug-drug interactions and evaluating drug interaction reports using inhibition constants. The Annals of Pharmacotherapy, 39(6), 1064–1072. https://doi.org/10.1345/aph.1e508
   PubMed Web of Science ®Google Scholar
• Banerjee, P., Eckert, A. O., Schrey, A. K., & Preissner, R. (2018). ProTox-II: A webserver for the prediction of toxicity of chemicals. Nucleic Acids Research, 46(W1), W257–W263. https://doi.org/10.1093/nar/gky318
   PubMed Web of Science ®Google Scholar
• Barbour, L., Hanna, M., & Xiao, W. (2006). Mutagenesis. Methods in Molecular Biology, 313, 121–127. https://doi.org/10.1385/1-59259-958-3:121
   PubMedGoogle Scholar
• Bickerton, G. R., Paolini, G. V., Besnard, J., Muresan, S., & Hopkins, A. L. (2012). Quantifying the chemical beauty of drugs. Nature Chemistry, 4(2), 90–98. https://doi.org/10.1038/nchem.1243
   PubMed Web of Science ®Google Scholar
• Bjelkmar, P., Larsson, P., Cuendet, M. A., Hess, B., & Lindahl, E. (2010). Implementation of the CHARMM Force Field in GROMACS: Analysis of protein stability effects from correction maps, virtual interaction sites, and water models. Journal of Chemical Theory and Computation, 6(2), 459–466. https://doi.org/10.1021/ct900549r
   PubMed Web of Science ®Google Scholar
• Borges, M. C., Castro, L. A., & Fonseca, B. A. (2013). Chloroquine use improves dengue-related symptoms. Memorias Do Instituto Oswaldo Cruz, 108(5), 596–599. https://doi.org/10.1590/0074-0276108052013010
   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, 79(3), 839–852. https://doi.org/10.1002/prot.22922
   PubMed Web of Science ®Google Scholar
• Cheng, P. N., Pham, J. D., & Nowick, J. S. (2013). The supramolecular chemistry of β-sheets. Journal of the American Chemical Society, 135(15), 5477–5492. https://doi.org/10.1021/ja3088407
   PubMed Web of Science ®Google Scholar
• Cheng, T., Zhao, Y., Li, X., Lin, F., Xu, Y., Zhang, X., Li, Y., Wang, R., & Lai, L. (2007). Computation of octanol-water partition coefficients by guiding an additive model with knowledge. Journal of Chemical Information and Modeling, 47(6), 2140–2148. https://doi.org/10.1021/ci700257y
   PubMed Web of Science ®Google Scholar
• Chen, C., Huang, Y., Ji, X., & Xiao, Y. (2013). Efficiently finding the minimum free energy path from steepest descent path. The Journal of Chemical Physics, 138(16), 164122. https://doi.org/10.1063/1.4799236
   PubMed Web of Science ®Google Scholar
• Chen, H. R., Lai, Y. C., & Yeh, T. M. (2018). Dengue virus non-structural protein 1: A pathogenic factor, therapeutic target, and vaccine candidate. Journal of Biomedical Science, 25(1), 58. https://doi.org/10.1186/s12929-018-0462-0
   PubMedGoogle Scholar
• Chen, D., Oezguen, N., Urvil, P., Ferguson, C., Dann, S. M., & Savidge, T. C. (2016). Regulation of protein-ligand binding affinity by hydrogen bond pairing. Science Advances, 2(3), e1501240. https://doi.org/10.1126/sciadv.1501240
   PubMed Web of Science ®Google Scholar
• Dahlbäck, B., Smith, C. A., & Müller-Eberhard, H. J. (1983). Visualization of human C4b-binding protein and its complexes with vitamin K-dependent protein S and complement protein C4b. Proceedings of the National Academy of Sciences of the United States of America, 80(11), 3461–3465. https://doi.org/10.1073/pnas.80.11.3461
   PubMed Web of Science ®Google Scholar
• Dahlin, J. L., Nissink, J. W., Strasser, J. M., Francis, S., Higgins, L., Zhou, H., Zhang, Z., & Walters, M. A. (2015). PAINS in the assay: Chemical mechanisms of assay interference and promiscuous enzymatic inhibition observed during a sulfhydryl-scavenging HTS. Journal of Medicinal Chemistry, 58(5), 2091–2113. https://doi.org/10.1021/jm5019093
   PubMed Web of Science ®Google Scholar
• Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7, 42717. https://doi.org/10.1038/srep42717
   PubMed Web of Science ®Google Scholar
• Daina, A., & Zoete, V. (2016). A BOILED-egg to predict gastrointestinal absorption and brain penetration of small molecules. ChemMedChem, 11(11), 1117–1121. https://doi.org/10.1002/cmdc.201600182
   PubMed Web of Science ®Google Scholar
• David, S., & Hamilton, J. P. (2010). Drug-induced liver injury. US Gastroenterology & Hepatology Review, 6, 73–80.
   PubMedGoogle Scholar
• David, C. C., & Jacobs, D. J. (2014). Principal component analysis: A method for determining the essential dynamics of proteins. Methods in Molecular Biology, 1084, 193–226. https://doi.org/10.1007/978-1-62703-658-0_11
   PubMedGoogle Scholar
• Deller, M. C., Kong, L., & Rupp, B. (2016). Protein stability: A crystallographer’s perspective. Acta Crystallographica. Section F, Structural Biology Communications, 72(Pt 2), 72–95. https://doi.org/10.1107/s2053230x15024619
   PubMedGoogle Scholar
• Du, X., Li, Y., Xia, Y. L., Ai, S. M., Liang, J., Sang, P., Ji, X. L., & Liu, S. Q. (2016). Insights into protein-ligand interactions: Mechanisms, models, and methods. International Journal of Molecular Sciences, 17, 144. https://doi.org/10.3390/ijms17020144
   PubMed Web of Science ®Google Scholar
• Eberhardt, J., Santos-Martins, D., Tillack, A. F., & Forli, S. (2021). AutoDock Vina 1.2.0: New docking methods, expanded force field, and python bindings. Journal of Chemical Information and Modeling, 61(8), 3891–3898. https://doi.org/10.1021/acs.jcim.1c00203
   PubMed Web of Science ®Google Scholar
• Ertl, P., & Schuffenhauer, A. (2009). Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions. Journal of Cheminformatics, 1(1), 8. https://doi.org/10.1186/1758-2946-1-8
   PubMed Web of Science ®Google Scholar
• Fan, J., Liu, Y., & Yuan, Z. (2014). Critical role of dengue virus NS1 protein in viral replication. Virologica Sinica, 29(3), 162–169. https://doi.org/10.1007/s12250-014-3459-1
   PubMedGoogle Scholar
• Farmer, J., Kanwal, F., Nikulsin, N., Tsilimigras, M. C. B., & Jacobs, D. J. (2017). Statistical measures to quantify similarity between molecular dynamics simulation trajectories. Entropy, 19, 646. https://doi.org/10.3390/e19120646
   PubMed Web of Science ®Google Scholar
• Flamand, M., Megret, F., Mathieu, M., Lepault, J., Rey, F. A., & Deubel, V. (1999). Dengue virus type 1 nonstructural glycoprotein NS1 is secreted from mammalian cells as a soluble hexamer in a glycosylation-dependent fashion. Journal of Virology, 73(7), 6104–6110. https://doi.org/10.1128/JVI.73.7.6104-6110.1999
   PubMed Web of Science ®Google Scholar
• Gao, Y., Mei, Y., & Zhang, J. Z. H. (1988). Treatment of hydrogen bonds in protein simulations. Molecular Simulation, 1, 173–185. https://doi.org/10.5772/61049
   Google Scholar
• Goebel, J., Chmielewski, J., & Hrycyna, C. A. (2021). The roles of the human ATP-binding cassette transporters P-glycoprotein and ABCG2 in multidrug resistance in cancer and at endogenous sites: Future opportunities for structure-based drug design of inhibitors. Cancer Drug Resistance, 4(4), 784–804. https://doi.org/10.20517/cdr.2021.19
   PubMedGoogle Scholar
• Guan, W., Ozakin, A., Gray, A., Borreguero, J., Pandit, S., Jagielska, A., Wroblewska, L., & Skolnick, J. (2011). Learning protein folding energy functions. In Proceedings. IEEE International Conference on Data Mining (pp. 1062–1067). https://doi.org/10.1109/icdm.2011.88
   Google Scholar
• Guan, L., Yang, H., Cai, Y., Sun, L., Di, P., Li, W., Liu, G., & Tang, Y. (2019). ADMET-score – A comprehensive scoring function for evaluation of chemical drug-likeness. MedChemComm, 10(1), 148–157. https://doi.org/10.1039/c8md00472b
   PubMed Web of Science ®Google Scholar
• Guo, Z., Li, B., Cheng, L. T., Zhou, S., McCammon, J. A., & Che, J. (2015). Identification of protein-ligand binding sites by the level-set variational implicit-solvent approach. Journal of Chemical Theory and Computation, 11(2), 753–765. https://doi.org/10.1021/ct500867u
   PubMed Web of Science ®Google Scholar
• Gutsche, I., Coulibaly, F., Voss, J. E., Salmon, J., d’Alayer, J., Ermonval, M., Larquet, E., Charneau, P., Krey, T., Mégret, F., Guittet, E., Rey, F. A., & Flamand, M. (2011). Secreted dengue virus nonstructural protein NS1 is an atypical barrel-shaped high-density lipoprotein. Proceedings of the National Academy of Sciences of the United States of America, 108(19), 8003–8008. https://doi.org/10.1073/pnas.1017338108
   PubMed Web of Science ®Google Scholar
• Heinig, M., & Frishman, D. (2004). STRIDE: A web server for secondary structure assignment from known atomic coordinates of proteins. Nucleic Acids Research, 32(Web Server issue), W500–W502. https://doi.org/10.1093/nar/gkh429
   PubMedGoogle Scholar
• Khrustalev, V. V., Khrustaleva, T. A., & Barkovsky, E. V. (2013). Random coil structures in bacterial proteins. Relationships of their amino acid compositions to flanking structures and corresponding genic base compositions. Biochimie, 95(9), 1745–1754. https://doi.org/10.1016/j.biochi.2013.05.014
   PubMed Web of Science ®Google Scholar
• Klose, D. P., Wallace, B. A., & Janes, R. W. (2010). 2Struc: The secondary structure server. Bioinformatics, 26(20), 2624–2625. https://doi.org/10.1093/bioinformatics/btq480
   PubMed Web of Science ®Google Scholar
• Koes, D. R., & Camacho, C. J. (2012). ZINCPharmer: Pharmacophore search of the ZINC database. Nucleic Acids Research, 40(Web Server issue), W409–W414. https://doi.org/10.1093/nar/gks378
   PubMed Web of Science ®Google Scholar
• Kony, D. B., Hünenberger, P. H., & van Gunsteren, W. F. (2007). Molecular dynamics simulations of the native and partially folded states of ubiquitin: Influence of methanol cosolvent, pH, and temperature on the protein structure and dynamics. Protein Science, 16(6), 1101–1118. https://doi.org/10.1110/ps.062323407
   PubMed Web of Science ®Google Scholar
• Kufareva, I., & Abagyan, R. (2012). Methods of protein structure comparison. Methods in Molecular Biology, 857, 231–257. https://doi.org/10.1007/978-1-61779-588-6_10
   PubMedGoogle Scholar
• Leung, E., Blom, A. M., Clemenza, L., & Isenman, D. E. (2006). The complement regulator C4b-binding protein (C4BP) interacts with both the C4c and C4dg subfragments of the parent C4b ligand: Evidence for synergy in C4BP subsite binding. Biochemistry, 45(27), 8378–8392. https://doi.org/10.1021/bi0603827
   PubMed Web of Science ®Google Scholar
• Limongelli, V., Marinelli, L., Cosconati, S., La Motta, C., Sartini, S., Mugnaini, L., Da Settimo, F., Novellino, E., & Parrinello, M. (2012). Sampling protein motion and solvent effect during ligand binding. Proceedings of the National Academy of Sciences of the United States of America, 109(5), 1467–1472. https://doi.org/10.1073/pnas.1112181108
   PubMed Web of Science ®Google Scholar
• Lin, J. H., & Yamazaki, M. (2003). Role of P-glycoprotein in pharmacokinetics: Clinical implications. Clinical Pharmacokinetics, 42(1), 59–98. https://doi.org/10.2165/00003088-200342010-00003
   PubMed Web of Science ®Google Scholar
• Liu, Y. J., Tran, T., Postma, G., Buydens, L. M. C., & Jansen, J. (2018). Estimating the number of components and detecting outliers using angle distribution of loading subspaces (ADLS) in PCA analysis. Analytica Chimica Acta, 1020, 17–29. https://doi.org/10.1016/j.aca.2018.03.044
   PubMed Web of Science ®Google Scholar
• Lobanov, M. I., Bogatyreva, N. S., & Galzitskaia, O. V. (2008). Radius of gyration is indicator of compactness of protein structure. Molekuliarnaia Biologiia, 42(4), 701–706.
   PubMed Web of Science ®Google Scholar
• Mackenzie, J. M., Jones, M. K., & Young, P. R. (1996). Immunolocalization of the dengue virus nonstructural glycoprotein NS1 suggests a role in viral RNA replication. Virology, 220(1), 232–240. https://doi.org/10.1006/viro.1996.0307
   PubMed Web of Science ®Google Scholar
• Maisuradze, G. G., Liwo, A., & Scheraga, H. A. (2009). Principal component analysis for protein folding dynamics. Journal of Molecular Biology, 385(1), 312–329. https://doi.org/10.1016/j.jmb.2008.10.018
   PubMed Web of Science ®Google Scholar
• Marcelino, A. M., & Gierasch, L. M. (2008). Roles of beta-turns in protein folding: From peptide models to protein engineering. Biopolymers, 89(5), 380–391. https://doi.org/10.1002/bip.20960
   PubMed Web of Science ®Google Scholar
• Martin, Y. C. (2005). A bioavailability score. Journal of Medicinal Chemistry, 48(9), 3164–3170. https://doi.org/10.1021/jm0492002
   PubMed Web of Science ®Google Scholar
• McArthur, M. A., Sztein, M. B., & Edelman, R. (2013). Dengue vaccines: Recent developments, ongoing challenges and current candidates. Expert Review of Vaccines, 12(8), 933–953. https://doi.org/10.1586/14760584.2013.815412
   PubMed Web of Science ®Google Scholar
• Meyer, E. E., Rosenberg, K. J., & Israelachvili, J. (2006). Recent progress in understanding hydrophobic interactions. Proceedings of the National Academy of Sciences of the United States of America, 103(43), 15739–15746. https://doi.org/10.1073/pnas.0606422103
   PubMed Web of Science ®Google Scholar
• Murugesan, A., & Manoharan, M. (2020). Dengue virus. In Emerging and reemerging viral pathogens (pp. 281–359). https://doi.org/10.1016/B978-0-12-819400-3.00016-8
   Google Scholar
• Mustafa, M. S., Rasotgi, V., Jain, S., & Gupta, V. (2015). Discovery of fifth serotype of dengue virus (DENV-5): A new public health dilemma in dengue control. Medical Journal, Armed Forces India, 71(1), 67–70. https://doi.org/10.1016/j.mjafi.2014.09.011
   PubMedGoogle Scholar
• Mutheneni, S. R., Morse, A. P., Caminade, C., & Upadhyayula, S. M. (2017). Dengue burden in India: Recent trends and importance of climatic parameters. Emerging Microbes & Infections, 6(8), e70. https://doi.org/10.1038/emi.2017.57
   PubMedGoogle Scholar
• Ogata, K., Hatakeyama, M., & Nakamura, S. (2018). Effect of atomic charges on octanol-water partition coefficient using alchemical free energy calculation. Molecules, 23, 425. https://doi.org/10.3390/molecules23020425
   PubMed Web of Science ®Google Scholar
• Ogu, C. C., & Maxa, J. L. (2000). Drug interactions due to cytochrome P450. Proceedings (Baylor University. Medical Center), 13(4), 421–423. https://doi.org/10.1080/08998280.2000.11927719
   PubMedGoogle Scholar
• Ortiz, C. L. D., Completo, G. C., Nacario, R. C., & Nellas, R. B. (2019). Potential inhibitors of galactofuranosyltransferase 2 (GlfT2): Molecular docking, 3D-QSAR, and in silico ADMETox studies. Scientific Reports, 9(1), 17096. https://doi.org/10.1038/s41598-019-52764-8
   PubMedGoogle Scholar
• Pantsar, T., & Poso, A. (2018). Binding affinity via docking: Fact and fiction. Molecules, 23, 1899. https://doi.org/10.3390/molecules23081899
   PubMed Web of Science ®Google Scholar
• Pardridge, W. M. (2012). Drug transport across the blood-brain barrier. Journal of Cerebral Blood Flow and Metabolism, 32(11), 1959–1972. https://doi.org/10.1038/jcbfm.2012.126
   PubMed Web of Science ®Google Scholar
• Patil, R., Das, S., Stanley, A., Yadav, L., Sudhakar, A., & Varma, A. K. (2010). Optimized hydrophobic interactions and hydrogen bonding at the target-ligand interface leads the pathways of drug-designing. PLOS One, 5(8), e12029. https://doi.org/10.1371/journal.pone.0012029
   PubMed Web of Science ®Google Scholar
• Perera, R., & Kuhn, R. J. (2008). Structural proteomics of dengue virus. Current Opinion in Microbiology, 11(4), 369–377. https://doi.org/10.1016/j.mib.2008.06.004
   PubMed Web of Science ®Google Scholar
• Peterson, R. W., Nicholson, E. M., Thapar, R., Klevit, R. E., & Scholtz, J. M. (1999). Increased helix and protein stability through the introduction of a new tertiary hydrogen bond. Journal of Molecular Biology, 286(5), 1609–1619. https://doi.org/10.1006/jmbi.1999.2574
   PubMed Web of Science ®Google Scholar
• Phadnis-Moghe, A. S., & Kaminski, N. E. (2017). Immunotoxicity testing using human primary leukocytes: An adjunct approach for the evaluation of human risk. Current Opinion in Toxicology, 3, 25–29. https://doi.org/10.1016/j.cotox.2017.04.005
   PubMedGoogle Scholar
• Płaszczyca, A., Scaturro, P., Neufeldt, C. J., Cortese, M., Cerikan, B., Ferla, S., Brancale, A., Pichlmair, A., & Bartenschlager, R. (2019). A novel interaction between dengue virus nonstructural protein 1 and the NS4A-2K-4B precursor is required for viral RNA replication but not for formation of the membranous replication organelle. PLOS Pathogens, 15(5), e1007736. https://doi.org/10.1371/journal.ppat.1007736
   PubMed Web of Science ®Google Scholar
• Potts, R. O., & Guy, R. H. (1992). Predicting skin permeability. Pharmaceutical Research, 9(5), 663–669. https://doi.org/10.1023/a:1015810312465
   PubMed Web of Science ®Google Scholar
• Pryor, M. J., & Wright, P. J. (1993). The effects of site-directed mutagenesis on the dimerization and secretion of the NS1 protein specified by dengue virus. Virology, 194(2), 769–780. https://doi.org/10.1006/viro.1993.1318
   PubMed Web of Science ®Google Scholar
• Raj, J., Chandra, M., Dogra, T. D., Pahuja, M., & Raina, A. (2013). Determination of median lethal dose of combination of endosulfan and cypermethrin in Wistar rat. Toxicology International, 20(1), 1–5. https://doi.org/10.4103/0971-6580.111531
   PubMedGoogle Scholar
• Rastogi, M., Sharma, N., & Singh, S. K. (2016). Flavivirus NS1: A multifaceted enigmatic viral protein. Virology Journal, 13(1), 131. https://doi.org/10.1186/s12985-016-0590-7
   PubMed Web of Science ®Google Scholar
• Rawal, N., Rajagopalan, R., & Salvi, V. P. (2009). Stringent regulation of complement lectin pathway C3/C5 convertase by C4b-binding protein (C4BP). Molecular Immunology, 46(15), 2902–2910. https://doi.org/10.1016/j.molimm.2009.07.006
   PubMed Web of Science ®Google Scholar
• Rohl, C. A., & Doig, A. J. (1996). Models for the 3(10)-helix/coil, pi-helix/coil, and alpha-helix/3(10)-helix/coil transitions in isolated peptides. Protein Science, 5(8), 1687–1696. https://doi.org/10.1002/pro.5560050822
   PubMed Web of Science ®Google Scholar
• Savjani, K. T., Gajjar, A. K., & Savjani, J. K. (2012). Drug solubility: Importance and enhancement techniques. ISRN Pharmaceutics, 2012, 195727. https://doi.org/10.5402/2012/195727
   PubMedGoogle Scholar
• Schüttelkopf, A. W., & van Aalten, D. M. (2004). PRODRG: A tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallographica Section D Biological Crystallography, 60(8), 1355–1363. https://doi.org/10.1107/S0907444904011679
   PubMedGoogle Scholar
• Senapathi, T., Bray, S., Barnett, C. B., Grüning, B., & Naidoo, K. J. (2019). Biomolecular reaction and interaction dynamics global environment (BRIDGE). Bioinformatics, 35(18), 3508–3509. https://doi.org/10.1093/bioinformatics/btz107
   PubMed Web of Science ®Google Scholar
• Sittel, F., Jain, A., & Stock, G. (2014). Principal component analysis of molecular dynamics: On the use of Cartesian vs. internal coordinates. The Journal of Chemical Physics, 141(1), 014111. https://doi.org/10.1063/1.4885338
   PubMed Web of Science ®Google Scholar
• Sluga, J., Venko, K., Drgan, V., & Novic, M. (2020). QSPR models for prediction of aqueous solubility: Exploring the potency of Randic-type indices. Croatica Chemica Acta, 93(4), 311–319. https://doi.org/10.5562/cca3776
   Web of Science ®Google Scholar
• Somnuke, P., Hauhart, R. E., Atkinson, J. P., Diamond, M. S., & Avirutnan, P. (2011). N-linked glycosylation of dengue virus NS1 protein modulates secretion, cell-surface expression, hexamer stability, and interactions with human complement. Virology, 413(2), 253–264. https://doi.org/10.1016/j.virol.2011.02.022
   PubMed Web of Science ®Google Scholar
• Spoel, D. V. D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. C. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718. https://doi.org/10.1002/jcc.20291
   PubMed Web of Science ®Google Scholar
• Srikiatkhachorn, A. (2009). Plasma leakage in dengue haemorrhagic fever. Thrombosis and Haemostasis, 102(6), 1042–1049. https://doi.org/10.1160/TH09-03-0208
   PubMed Web of Science ®Google Scholar
• Taylor, W., & Jaffe, R. L. (2018). The physics of energy (p. 874). Cambridge University Press.
   Google Scholar
• Tong, L., Zheng, J., Wang, X., Wang, X., Huang, H., Yang, H., Tu, T., Wang, Y., Bai, Y., Yao, B., Luo, H., & Qin, X. (2021). Improvement of thermostability and catalytic efficiency of glucoamylase from Talaromyces leycettanus JCM12802 via site-directed mutagenesis to enhance industrial saccharification applications. Biotechnology for Biofuels, 14(1), 202. https://doi.org/10.1186/s13068-021-02052-3
   PubMed Web of Science ®Google Scholar
• Torres-Flores, J. M., Reyes-Sandoval, A., & Salazar, M. I. (2022). Dengue vaccines: An update. BioDrugs, 36(3), 325–336. https://doi.org/10.1007/s40259-022-00531-z
   PubMed Web of Science ®Google Scholar
• Van Gunsteren, W. F., & Berendsen, H. J. (1988). A leap-frog algorithm for stochastic dynamics. Molecular Simulation, 1(3), 173–185. https://doi.org/10.1080/08927028808080941
   Web of Science ®Google Scholar
• Vangone, A., & Bonvin, A. M. J. J. (2017). PRODIGY: A contact-based predictor of binding affinity in protein-protein complexes. Bio-protocol, 7(3), e2124. https://doi.org/10.21769/BioProtoc.2124
   PubMedGoogle Scholar
• Wang, Y., Xing, J., Xu, Y., Zhou, N., Peng, J., Xiong, Z., Liu, X., Luo, X., Luo, C., Chen, K., Zheng, M., & Jiang, H. (2015). In silico ADME/T modelling for rational drug design. Quarterly Reviews of Biophysics, 48(4), 488–515. https://doi.org/10.1017/S0033583515000190
   PubMed Web of Science ®Google Scholar
• Williams, G. M. &Weisburger, J. H. (1985). Carcinogenicity testing of drugs. Progress in drug research. Fortschritte der Arzneimittelforschung. Progres des recherches pharmaceutiques, 29, 155–213. https://doi.org/10.1007/978-3-0348-9315-2_6
   Google Scholar
• Williams, M. A. Ladbury, J. E., Böhm H-J., Schneider, G. (2003). Hydrogen Bonds in Protein-Ligand Complexes, Methods and Principles in Medicinal Chemistry. Journal of Medicinal Chemistry, 52, 4073–4086.
   Google Scholar
• Xu, Y., Wang, S., Hu, Q., Gao, S., Ma, X., Zhang, W., Shen, Y., Chen, F., Lai, L., & Pei, J. (2018). CavityPlus: A web server for protein cavity detection with pharmacophore modelling, allosteric site identification and covalent ligand binding ability prediction. Nucleic Acids Research, 46(W1), W374–W379. https://doi.org/10.1093/nar/gky380
   PubMed Web of Science ®Google Scholar
• Yap, S. S. L., Nguyen-Khuong, T., Rudd, P. M., & Alonso, S. (2017). Dengue virus glycosylation: What do we know? Frontiers in Microbiology, 8, 1415. https://doi.org/10.3389/fmicb.2017.01415
   PubMed Web of Science ®Google Scholar
• Zhang, D., & Lazim, R. (2017). Application of conventional molecular dynamics simulation in evaluating the stability of apomyoglobin in urea solution. Scientific Reports, 7, 44651. https://doi.org/10.1038/srep44651
   PubMed Web of Science ®Google Scholar