Investigating natural plant products as potential inhibitors to disrupt NS1 β-roll domain polymerisation in DENV2: a detailed computational chemistry approach

References

• Fan J, Liu Y, Yuan Z. Critical role of dengue virus NS1 protein in viral replication. Virol Sin. 2014;29(3):162–169. doi:10.1007/s12250-014-3459-1
   PubMedGoogle Scholar
• Thiemmeca S, Tamdet C, Punyadee N, et al. Secreted NS1 protects dengue virus from mannose-binding lectin–mediated neutralization. J Immunol. 2016;197(10):4053–4065. doi:10.4049/jimmunol.1600323
   PubMed Web of Science ®Google Scholar
• Yung CF, Lee KS, Thein TL, et al. Dengue serotype-specific differences in clinical manifestation, laboratory parameters and risk of severe disease in adults, Singapore. Am J Trop Med Hyg. 2015;92(5):999–1005. doi:10.4269/ajtmh.14-0628
   PubMed Web of Science ®Google Scholar
• Rosales Ramirez R, Ludert JE. The dengue virus nonstructural protein 1 (NS1) is secreted from mosquito cells in association with the intracellular cholesterol transporter chaperone caveolin complex. J Virol. 2019;93(4):e01985–18. doi:10.1128/JVI.01985-18
   PubMed Web of Science ®Google Scholar
• Gutsche I, Coulibaly F, Voss JE, et al. Secreted dengue virus nonstructural protein NS1 is an atypical barrel-shaped high-density lipoprotein. Proc Nat Acad Sci USA. 2011;108(19):8003–8008. doi:10.1073/pnas.1017338108
   PubMed Web of Science ®Google Scholar
• Pryor MJ, Wright PJ. The effects of site-directed mutagenesis on the dimerization and secretion of the NS1 protein specified by dengue virus. Virology. 1993;194(2):769–780. doi:10.1006/viro.1993.1318
   PubMed Web of Science ®Google Scholar
• Eyre NS, Johnson SM, Eltahla AA, et al. Genome-wide mutagenesis of dengue virus reveals plasticity of the NS1 protein and enables generation of infectious tagged reporter viruses. J Virol. 2017;91(23):e01455–17. doi:10.1128/JVI.01455-17
   PubMed Web of Science ®Google Scholar
• Scaturro P, Cortese M, Chatel-Chaix L, et al. Dengue virus non-structural protein 1 modulates infectious particle production via interaction with the structural proteins. PLoS Pathogens. 2015;11(11):e1005277. doi:10.1371/journal.ppat.1005277
   PubMed Web of Science ®Google Scholar
• Srikiatkhachorn A, Mathew A, Rothman AL. Immune-mediated cytokine storm and its role in severe dengue. Semin Immunopathol. 2017;39(5):563–574. doi:10.1007/s00281-017-0625-1
   PubMed Web of Science ®Google Scholar
• Chen HR, Chao CH, Liu CC, et al. Macrophage migration inhibitory factor is critical for dengue NS1-induced endothelial glycocalyx degradation and hyperpermeability. PLoS Pathogens. 2018;14(4):e1007033. doi:10.1371/journal.ppat.1007033
   PubMed Web of Science ®Google Scholar
• Jasso-Miranda C, Herrera-Camacho I, Flores-Mendoza LK, et al. Antiviral and immunomodulatory effects of polyphenols on macrophages infected with dengue virus serotypes 2 and 3 enhanced or not with antibodies. Infect Drug Resist. 2019;12:1833–1852. doi:10.2147/IDR.S210890
   PubMed Web of Science ®Google Scholar
• Botanical leads for drug discovery. Singapore: Springer; 2020. doi:10.1007/978-981-15-5917-4
   Google Scholar
• Razak MRMA, Mohmad Misnan N, Md Jelas NH, et al. The effect of freeze-dried Carica papaya leaf juice treatment on NS1 and viremia levels in dengue fever mice model. BMC Complemen Altern Med. 2018;18(1):320. doi:10.1186/s12906-018-2390-7
   PubMedGoogle Scholar
• Mhatre S, Srivastava T, Naik S, et al. Antiviral activity of green tea and black tea polyphenols in prophylaxis and treatment of COVID-19: a review. Phytomedi: Int J Phytother Phytopharmacol. 2021;85:153286. doi:10.1016/j.phymed.2020.153286
   PubMed Web of Science ®Google Scholar
• Rathore AP, Paradkar PN, Watanabe S, et al. Celgosivir treatment misfolds dengue virus NS1 protein, induces cellular pro-survival genes and protects against lethal challenge mouse model. Antiviral Res. 2011;92(3):453–460. doi:10.1016/j.antiviral.2011.10.002
   PubMed Web of Science ®Google Scholar
• Modhiran N, Gandhi NS, Wimmer N, et al. Dual targeting of dengue virus virions and NS1 protein with the heparan sulfate mimic PG545. Antiviral Res. 2019;168:121–127. doi:10.1016/j.antiviral.2019.05.004
   PubMed Web of Science ®Google Scholar
• Balasubramanian A, Pilankatta R, Teramoto T, et al. Inhibition of dengue virus by curcuminoids. Antiviral Res. 2019;162:71–78. doi:10.1016/j.antiviral.2018.12.002
   PubMed Web of Science ®Google Scholar
• Asmilia N, Fahrimal Y, Abrar M, et al. Chemical compounds of Malacca leaf (Phyllanthus emblica) after triple extraction with N-hexane, ethyl acetate, and ethanol. Sci World J. 2020;2020:2739056. doi:10.1155/2020/2739056
   Google Scholar
• Alzohairy MA. Therapeutics role of Azadirachta indica (Neem) and their active constituents in diseases prevention and treatment. Evid-Based Complemen Altern Med: eCAM. 2016;2016:7382506. doi:10.1155/2016/7382506
   PubMed Web of Science ®Google Scholar
• Zeng X, Zhang P, Wang Y, et al. CMAUP: a database of collective molecular activities of useful plants. Nucleic Acids Research. 2019;47(D1):D1118–D1127. doi:10.1093/nar/gky965
   PubMed Web of Science ®Google Scholar
• Nandi K, Saha D. Rule of five: the five men army to cross the blood brain barrier for therapeutically potent functional magnetic resonance imaging: a new diversion in medical diagnosis view project SPeicherung und REcherche Struktur chemischer information: the innovative unscramble scientific literature in chemical world as SPRESI view project. [Online]. Available from: https://www.researchgate.net/publication/351945081.
   Google Scholar
• Trott O, Olson AJ. Autodock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem. 2010;31(2):455–461. doi:10.1002/jcc.21334
   PubMed Web of Science ®Google Scholar
• Brown N. Bioisosteres and scaffold hopping in medicinal chemistry. Molr Inf. 2014;33(6–7):458–462. doi:10.1002/minf.201400037
   PubMed Web of Science ®Google Scholar
• Yang H, Sun L, Wang Z, et al. ADMETopt: a web server for ADMET optimization in drug design via scaffold hopping. J Chem Inf Model. 2018;58(10):2051–2056. doi:10.1021/acs.jcim.8b00532
   PubMed Web of Science ®Google Scholar
• Langdon SR, Ertl P, Brown N. Bioisosteric replacement and scaffold hopping in lead generation and optimization. Mol Inf. 2010;29(5):366–385. doi:10.1002/minf.201000019
   PubMed Web of Science ®Google Scholar
• Shan J, Ji C. Molopt: a web server for drug design using bioisosteric transformation. Curr Comput-Aided Drug Des. 2020;16(4):460–466. doi:10.2174/1573409915666190704093400
   PubMed Web of Science ®Google Scholar
• Daina A, Michielin O, Zoete V. SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep. 2017;7:42717. doi:10.1038/srep42717
   PubMed Web of Science ®Google Scholar
• Banerjee P, Eckert AO, Schrey AK, et al. ProTox-II: a webserver for the prediction of toxicity of chemicals. Nucleic Acids Res. 2018;46(W1):W257–W263. doi:10.1093/nar/gky318
   PubMed Web of Science ®Google Scholar
• Jiménez J, Škalič M, Martínez-Rosell G, et al. KDEEP: protein-ligand absolute binding affinity prediction via 3D-convolutional neural networks. J Chem Inf Model. 2018;58(2):287–296. doi:10.1021/acs.jcim.7b00650
   PubMed Web of Science ®Google Scholar
• Abraham MJ, Murtola T, Schulz R, et al. Gromacs: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX. 2015;1–2:19–25. doi:10.1016/j.softx.2015.06.001
   Google Scholar
• Durham E, Dorr B, Woetzel N, et al. Solvent accessible surface area approximations for rapid and accurate protein structure prediction. J Mol Model. 2009;15(9):1093–1108. doi:10.1007/s00894-009-0454-9
   PubMed Web of Science ®Google Scholar
• Lobanov MY, Bogatyreva NS, Galzitskaya OV. Radius of gyration as an indicator of protein structure compactness. Mol Biol. 2008;42(4):623–628. doi:10.1134/S0026893308040195
   Web of Science ®Google Scholar
• Barbosa DA, Piccoli FP. Comparing the force due to the Lennard-Jones potential and the Coulomb force in the SPH method. J Ocean Eng Sci. 2018;3(4):310–315. doi:10.1016/j.joes.2018.10.007
   Web of Science ®Google Scholar
• Bekker H, Berendsen HJC, Dijkstra EJ, et al. Gromacs: a parallel computer for molecular dynamics simulations. In: RA de Groot, J Nadrchal, editor. Physics computing 92. Singapore: World Scientific; 1993. p. 252–256.
   Google Scholar
• Guan W, Ozakin A, Gray A, et al. (2011). Learning protein folding energy functions. Proceedings. IEEE International Conference on Data Mining; 2011. p. 1062–1067. doi:10.1109/ICDM.2011.88
   Google Scholar
• Kaihatsu K, Yamabe M, Ebara Y. Antiviral mechanism of action of epigallocatechin-3-O-gallate and its fatty acid esters. Molecules (Basel, Switzerland). 2018;23(10):MDPI AG. doi:10.3390/molecules23102475
   Web of Science ®Google Scholar
• Fatriansyah JF, Rizqillah RK, Yandi MY, et al. Molecular docking and dynamics studies on propolis sulabiroin-A as a potential inhibitor of SARS-CoV-2. J King Saud Univ. Sci. 2022;34(1):101707. doi:10.1016/j.jksus.2021.101707
   PubMed Web of Science ®Google Scholar
• Varma AK, Patil R, Das S, et al. Optimized hydrophobic interactions and hydrogen bonding at the target-ligand interface leads the pathways of drug-designing. PLoS ONE. 2010;5(8):e12029. doi:10.1371/journal.pone.0012029
   PubMed Web of Science ®Google Scholar
• Ferenczy GG, Kellermayer M. Contribution of hydrophobic interactions to protein mechanical stability. Comput Struct Biotechnol J. 2022;20:1946–1956. doi:10.1016/j.csbj.2022.04.025
   PubMed Web of Science ®Google Scholar
• Wang Z, Xu J. Predicting protein contact map using evolutionary and physical constraints by integer programming. Bioinformatics. 2013;29(13):i266–i273. doi:10.1093/bioinformatics/btt211
   PubMed Web of Science ®Google Scholar
• Kumar SU, Sankar S, Kumar DT, et al. Molecular dynamics, residue network analysis, and cross-correlation matrix to characterize the deleterious missense mutations in GALE causing galactosemia III. Cell Biochem Biophys. 2021;79(2):201–219. doi:10.1007/s12013-020-00960-z
   PubMed Web of Science ®Google Scholar
• Subair TI, Soremekun OS, Olotu FA, et al. Prospecting the therapeutic edge of a novel compound (B12) over berberine in the selective targeting of retinoid X receptor in colon cancer. J Mol Model. 2021;27(8):231. doi:10.1007/s00894-021-04848-4
   PubMed Web of Science ®Google Scholar
• King E, Aitchison E, Li H, et al. Recent developments in free energy calculations for drug discovery. Front Mol Biosci. 2021;8:712085. doi:10.3389/fmolb.2021.712085
   PubMed Web of Science ®Google Scholar
• Ertl P, Schuffenhauer A. Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions. J Cheminf. 2009;1(1):8. doi:10.1186/1758-2946-1-8
   PubMed Web of Science ®Google Scholar
• Gupta S, Parihar D, Shah M, et al. Computational screening of promising beta-secretase 1 inhibitors through multi-step molecular docking and molecular dynamics simulations - pharmacoinformatics approach. J Mol Struct. 2020;1205:127660. doi:10.1016/j.molstruc.2019.127660
   Web of Science ®Google Scholar
• Kim R, Skolnick J. Assessment of programs for ligand binding affinity prediction. J Comput Chem. 2008;29(8):1316–1331. doi:10.1002/jcc.20893
   PubMed Web of Science ®Google Scholar
• Nascimento F, Diaz AP, Sanches M, et al. Concomitant deep brain stimulation and vagus nerve stimulation for treatment-resistant depression: a case report. Revista Brasileira de Psiquiatria (Sao Paulo, Brazil: 1999). 2021;43(6):679–680. doi:10.1590/1516-4446-2021-0039
   PubMedGoogle Scholar
• Parks C, Gaieb Z, Amaro RE. An analysis of proteochemometric and conformal prediction machine learning protein-ligand binding affinity models. Front Mol Biosci. 2020;7:93. doi:10.3389/fmolb.2020.00093
   PubMed Web of Science ®Google Scholar
• Bhattarai BR, Adhikari B, Basnet S, et al. In silico elucidation of potent inhibitors from natural products for nonstructural proteins of dengue virus. J Chem. 2022;5398239:12. doi:10.1155/2022/5398239
   Google Scholar
• Akash S, Arefin F, Aovi FI. In silico investigation of potential therapeutic medication for the inhibition of dengue virus (DENV NS2B/NS3 and NS1) by modification of polycyclic quaternary alkaloid (sanguinarine derivatives) with different computational approaches. Biointerf Res Appl Chem. 2023;13:5. doi:10.33263/BRIAC135.403
   Google Scholar
• Qaddir I, Majeed A, Hussain W, et al. An in silico investigation of phytochemicals as potential inhibitors against non-structural protein 1 from dengue virus 4. Braz J Pharm Sci. 2020;56:e17420. doi:10.1590/s2175-97902020000117420
   Web of Science ®Google Scholar
• Roy A, Paul I, Paul T, et al. An in-silico receptor-pharmacophore based multistep molecular docking and simulation study to evaluate the inhibitory potentials against NS1 of DENV-2. J Biomol Struct Dynam. 2023: 1–29. doi:10.1080/07391102.2023.2239925
   Web of Science ®Google Scholar