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Research Articles

Identification of novel insect β-N-acetylhexosaminidase OfHex1 inhibitors based on virtual screening, biological evaluation, and molecular dynamics simulation

, , , , , & ORCID Icon show all
Pages 1735-1743 | Received 06 Jan 2020, Accepted 26 Feb 2020, Published online: 30 Mar 2020

References

  • Cantarel, B. L., Coutinho, P. M., Rancurel, C., Bernard, T., Lombard, V., & Henrissat, B. (2009). The carbohydrate-active enzymes database (Cazy): An expert resource for glycogenomics. Nucleic Acids Research, 37(Database), D233–238. doi:10.1093/nar/gkn663
  • Case, D. A., Babin, V., Berryman, J. T., Betz, R. M., Cai, Q., Cerutti, D. S., Cheatham, T. E., Darden, T. A., Duke, R. E., Gohlke, H., Goetz, A. W., Gusarov, S., Homeyer, N., Janowski, P., Kaus, J., Kolossváry, I., Kovalenko, A., Lee, T. S., LeGrand, S., … Kollman, P. A. (2014). AMBER 14, University of California.
  • Darden, T., York, D., & Pedersen, L. (1993). Particle mesh ewald: An n·log(n) method for ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089–10092. doi:10.1063/1.464397
  • Duan, Y., Liu, T., Zhou, Y., Dou, T., & Yang, Q. (2018). Glycoside hydrolase family 18 and 20 enzymes are novel targets of the traditional medicine berberine. Journal of Biological Chemistry, 293(40), 15429–15438. doi:10.1074/jbc.RA118.004351
  • Duan, Y., Wu, C., Chowdhury, S., Lee, M. C., Xiong, G., Zhang, W., Yang, R., Cieplak, P., Luo, R., Lee, T., Caldwell, J., Wang, J., & Kollman, P. (2003). A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. Journal of Computational Chemistry, 24(16), 1999–2012. doi:10.1002/jcc.10349
  • Hao, G., Dong, Q., & Yang, G. (2011). A comparative study on the constitutive properties of marketed pesticides. Molecular Informatics, 30(6–7), 614–622. doi:10.1002/minf.201100020
  • Henrissat, B., & Davies, G. (1997). Structural and sequence-based classification of glycoside hydrolases. Current Opinion in Structural Biology, 7(5), 637–644. doi:10.1016/S0959-440X(97)80072-3
  • Irwin, J. J., Sterling, T., Mysinger, M. M., Bolstad, E. S., & Coleman, R. G. (2012). Zinc: A free tool to discover chemistry for biology. Journal of Chemical Information and Modeling, 52(7), 1757–1768. doi:10.1021/ci3001277
  • Kong, H., Chen, W., Liu, T., Lu, H., Yang, Q., Dong, Y., Liang, X., Jin, S., & Zhang, J. (2016). Synthesis of nam-thiazoline derivatives as novel o-glcnacase inhibitors. Carbohydrate Research, 429, 54–61. doi:10.1016/j.carres.2016.04.008
  • Kumari, M., & Subbarao, N. (2019). Virtual screening to identify novel potential inhibitors for glutamine synthetase of mycobacterium tuberculosis. Journal of Biomolecular Structure and Dynamics, 1–19. doi:10.1080/07391102.2019.1695670
  • 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. doi:10.1002/jcc.20933
  • Liu, T., Guo, P., Zhou, Y., Wang, J., Chen, L., Yang, H., Qian, X., & Yang, Q. (2014). A crystal structure-guided rational design switching non-carbohydrate inhibitors’ specificity between two β-Glcnacase homologs. Scientific Reports, 4(1), 6188. doi:10.1038/srep06188
  • Liu, T., Xia, M., Wang, J., Zhang, H., Shen, X., Zhou, H., & Yang, Q. (2015). Exploring NAG-thiazoline and its derivatives as inhibitors of chitinolytic β-Acetylglucosaminidases. FEBS Letters, 589(1), 110–116. doi:10.1016/j.febslet.2014.11.032
  • Liu, T., Zhang, H., Liu, F., Chen, L., Shen, X., & Yang, Q. (2011). Active-pocket size differentiating insectile from bacterial chitinolytic β-N-acetyl-D-Hexosaminidases. Biochemical Journal, 438(3), 467–474. doi:10.1042/BJ20110390
  • Liu, T., Zhang, H.-T., Liu, F.-Y., Wu, Q.-Y., Shen, X., & Yang, Q. (2011). Structural determinants of an insect β-N-acetyl-D-Hexosaminidase specialized as a chitinolytic enzyme. Journal of Biological Chemistry, 286(6), 4049–4058. doi:10.1074/jbc.M110.184796
  • Macauley, M. S., Whitworth, G. E., Debowski, A. W., Chin, D., & Vocadlo, D. J. (2005). O-glcnacase uses substrate-assisted catalysis: Kinetic analysis and development of highly selective mechanism-inspired inhibitors. Journal of Biological Chemistry, 280(27), 25313–25322. doi:10.1074/jbc.M413819200
  • Mahuran, D. J. (1999). Biochemical consequences of mutations causing the GM2 gangliosidoses. Biochimica ET Biophysica Acta (BBA) - Molecular Basis of Disease, 1455(2–3), 105–138. doi:10.1016/S0925-4439(99)00074-5
  • Merzendorfer, H., & Zimoch, L. (2003). Chitin metabolism in insects: Structure, function and regulation of chitin synthases and chitinases. Journal of Experimental Biology, 206(24), 4393–4412. doi:10.1242/jeb.00709
  • Molecular Operating Environment (MOE). (2016). Molecular operating environment. Chemical Computing Group Inc.
  • Oikawa, A., Itoh, E., Ishihara, A., & Iwamura, H. (2003). Purification and characterization of β-N-acetylhexosaminidase from maize seedlings. Journal of Plant Physiology, 160(9), 991–999. doi:10.1078/0176-1617-01089
  • Onufriev, A., Bashford, D., & Case, D. A. (2004). Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins: Structure, Function, and Bioinformatics, 55(2), 383–394. doi:10.1002/prot.20033
  • Ropon-Palacios, G., Chenet-Zuta, M. E., Olivos-Ramirez, G. E., Otazu, K., Acurio-Saavedra, J., & Camps, I. (2019). Potential novel inhibitors against emerging zoonotic pathogen nipah virus: A virtual screening and molecular dynamics approach. Journal of Biomolecular Structure and Dynamics, 1–10. doi:10.1080/07391102.2019.1655480
  • Ryckaert, J. P., Ciccotti, G., & Berendsen, H. J. C. (1977). Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. Journal of Computational Physics, 23(3), 327–341. doi:10.1016/0021-9991(77)90098-5
  • Shen, S., Chen, W., Dong, L., Yang, Q., Lu, H., & Zhang, J. (2018). Design and synthesis of naphthalimide group-bearing thioglycosides as novel β-N-acetylhexosaminidases inhibitors. Journal of Enzyme Inhibition and Medicinal Chemistry, 33(1), 445–452. doi:10.1080/14756366.2017.1419217
  • Shen, S., Dong, L., Chen, W., Wu, R., Lu, H., Yang, Q., & Zhang, J. (2019). Synthesis, optimization, and evaluation of glycosylated naphthalimide derivatives as efficient and selective insect β-N-acetylhexosaminidase ofhex1 inhibitors. Journal of Agricultural and Food Chemistry, 67(22), 6387–6396. doi:10.1021/acs.jafc.9b02281
  • Sterling, T., & Irwin, J. J. (2015). Zinc 15 - ligand discovery for everyone. Journal of Chemical Information and Modeling, 55(11), 2324–2337. doi:10.1021/acs.jcim.5b00559
  • Strasser, R., Bondili, J. S., Schoberer, J., Svoboda, B., Liebminger, E., Glössl, J., Altmann, F., Steinkellner, H., & Mach, L. (2007). Enzymatic properties and subcellular localization of arabidopsis β-N-acetylhexosaminidases. Plant Physiology, 145(1), 5–16. doi:10.1104/pp.107.101162
  • Tang, S., Sun, L., & Wang, F. (2020). Identification of highly active natural thyroid hormone receptor agonists by pharmacophore-based virtual screening. Journal of Biomolecular Structure and Dynamics, 1–10. doi:10.1080/07391102.2020.1719890
  • Terwisscha, V. S. A. C., Kalk, K. H., Beintema, J. J., & Dijkstra, B. W. (1994). Crystal structures of hevamine, a plant defence protein with chitinase and lysozyme activity, and its complex with an inhibitor. Structure, 2(12), 1181–1189.
  • Tews, I., Perrakis, A., Oppenheim, A., Dauter, Z., Wilson, K. S., & Vorgias, C. E. (1996). Bacterial chitobiase structure provides insight into catalytic mechanism and the basis of tay-sachs disease. Nature Structural Biology, 3(7), 638–648. doi:10.1038/nsb0796-638
  • Thirumal Kumar, D., Jain, N., Udhaya Kumar, S., George Priya Doss, C., & Zayed, H. (2020). Identification of potential inhibitors against pathogenic missense mutations of pmm2 using a structure-based virtual screening approach. Journal of Biomolecular Structure and Dynamics, 1–17. doi:10.1080/07391102.2019.1708797
  • Vanajothi, R., Hemamalini, V., Jeyakanthan, J., & Premkumar, K. (2019). Ligand-based pharmacophore mapping and virtual screening for identification of potential discoidin domain receptor 1 inhibitors. Journal of Biomolecular Structure and Dynamics, 1–9. doi:10.1080/07391102.2019.1640132
  • Vocadlo, D. J., & Withers, S. G. (2005). Detailed comparative analysis of the catalytic mechanisms of β-n-acetylglucosaminidases from families 3 and 20 of glycoside hydrolases. Biochemistry, 44(38), 12809–12818. doi:10.1021/bi051121k
  • Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2005). Development and testing of a general amber force field. Journal of Computational Chemistry, 26(1), 114–114. doi:10.1002/jcc.20145
  • Weiser, J., Shenkin, P. S., & Still, W. C. (1999). Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO). Journal of Computational Chemistry, 20(2), 217–230. doi:10.1002/(SICI)1096-987X(19990130)20:2<217::AID-JCC4>3.0.CO;2-A
  • Yang, Q., Liu, T., Liu, F., Qu, M., & Qian, X. (2008). A novel β-N-acetyl-D-hexosaminidase from the insect Ostrinia furnacalis (Guenee). FEBS Journal, 275(22), 5690–5702. doi:10.1111/j.1742-4658.2008.06695.x10.1111/j.1742-4658.2008.06695.x
  • Zhu, Y., Gao, Y., Sun, X., Wang, C., Rui, X., Si, D., Zhu, J., Li, W., & Liu, J. (2019). Discovery of novel serine/threonine protein phosphatase 1 inhibitors from traditional Chinese medicine through virtual screening and biological assays. Journal of Biomolecular Structure and Dynamics, 1–18. doi:10.1080/07391102.2019.1702588

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