395
Views
7
CrossRef citations to date
0
Altmetric
Research Articles

Elucidation the binding mechanism of Nelumbo nucifera-derived isoquinoline alkaloids as Rho-kinase 1 inhibitors by molecular docking and dynamic simulation

, , , , &
Pages 379-394 | Received 27 Nov 2019, Accepted 23 Dec 2019, Published online: 25 Jan 2020

References

  • Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., & Haak, J. R. (1984). Molecular-dynamics with coupling to an external bath. Journal of Chemical Physics, 81(8), 3684–3690. doi:10.1063/1.448118
  • Bussi, G., Donadio, D., & Parrinello, M. (2007). Canonical sampling through velocity rescaling. Journal of Chemical Physics, 126, 1–7. doi:10.1063/1.2408420
  • Chinese Pharmacopoeia Commission. (2015). Chinese pharmacopoeia (Vol. 1, pp. 273–276). Beijing, China: Chinese Medical Science and Technology Press.
  • Colligris, B., Crooke, A., Huete, F., & Pintor, J. (2012). Potential role of Rho-associated protein kinase inhibitors for glaucoma treatment. Recent Patents on Endocrine, Metabolic & Immune Drug Discovery, 6(2), 89–98. doi:10.2174/187221412800604554
  • Coutsias, E. A., Seok, C., & Dill, K. A. (2004). Using quaternions to calculate RMSD. Journal of Computational Chemistry, 25(15), 1849–1857. doi:10.1002/jcc.20110
  • Dan, G., Yarui, L., Yifei, C., Dan, Z., Xin, W., Guifang, L., … Shuixiang, H. (2019). DANCR promotes HCC progression and regulates EMT by sponging miR-27a-3p via ROCK1/LIMK1/COFILIN1 pathway. Cell Proliferation, 52, 1–14. doi:10.1111/cpr.12628
  • Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N-Log (N) method for Ewald sums in large systems. Journal of Chemical Physics, 98(12), 10089–10092. doi:10.1063/1.464397
  • Duke, J. A., Bogenschutz-Godwin, M. J., duCellier, J., & Duke, P.-A. K. (2002). Handbook of mediinal herbs (2nd ed.). Boca Raton, FL: CRC Press Inc.
  • Fang, X., Yin, Y., Chen, Y. T., Yao, L., Wang, B., Cameron, M. D., … Feng, Y. (2010). Tetrahydroisoquinoline derivatives as highly selective and potent Rho kinase inhibitors. Journal of Medicinal Chemistry, 53(15), 5727–5737. doi:10.1021/jm100579r
  • Fanta, C. H. (2009). Asthma. The New England Journal of Medicine, 360, 1012–1014.
  • Feng, Y., Cameron, M. D., Frackowiak, B., Griffin, E., Lin, L., Ruiz, C., … LoGrasso, P. (2007). Structure-activity relationships, and drug metabolism and pharmacokinetic properties for indazole piperazine and indazole piperidine inhibitors of ROCK II. Bioorganic & Medicinal Chemistry Letters, 17(8), 2355–2360. doi:10.1016/j.bmcl.2006.12.043
  • Fukata, Y., Kaibuchi, K., Amano, M., & Kaibuchi, K. (2001). Rho-Rho-kinase pathway in smooth muscle contraction and cytoskeletal reorganization of non-muscle cells. Trends in Pharmacological Sciences, 22(1), 32–39. doi:10.1016/S0165-6147(00)01596-0
  • Goodsell, D. S., Morris, G. M., & Olson, A. J. (1996). Automated docking of flexible ligands: Applications of AutoDock. Journal of Molecular Recognition, 9(1), 1–5. doi:10.1002/(sici)1099-1352(199601)9:1 < 1::aid-jmr241 > 3.0.co;2-6
  • He, J. T., & Yu, S. (2012). The modern clinical use of Lianzixin. Journal of Changchun University of Traditional Chinese Medicine, 28, 5444–5546.
  • He, W.-Q., Peng, Y.-J., Zhang, W.-C., Lv, N., Tang, J., Chen, C., … Zhu, M.-S. (2008). Myosin light chain kinase is central to smooth muscle contraction and required for gastrointestinal motility in mice. Gastroenterology, 135(2), 610–620. doi:10.1053/j.gastro.2008.05.032
  • Heinze, C., Seniuk, A., Sokolov, M. V., Huebner, A. K., Klementowicz, A. E., Szijártó, I. A., … Hübner, C. A. (2014). Disruption of vascular Ca2+-activated chloride currents lowers blood pressure. Journal of Clinical Investigation, 124(2), 675–686. doi:10.1172/JCI70025
  • Hess, B. (2008). P-LINCS: A parallel linear constraint solver for molecular simulation. Journal of Chemical Theory and Computation, 4(1), 116–122. doi:10.1021/ct700200b
  • Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. CO; 2-H doi:10.1002/(SICI)1096-987X(199709)18:12 < 1463::AID-JCC4 > 3.0
  • Horn, H. W., Swope, W. C., Pitera, J. W., Madura, J. D., Dick, T. J., Hura, G. L., & Head-Gordon, T. (2004). Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew. Journal of Chemical Physics, 120(20), 9665–9678. doi:10.1063/1.1683075
  • Jorgensen, W. L. (1991). Rusting of the lock and key model for protein-ligand binding. Science, 254(5034), 954–955. doi:10.1126/science.1719636
  • Kabsch, W. (1976). A solution for the best rotation to relate two sets of vectors. Acta Crystallographica Section A, 32(5), 922–923. doi:10.1107/S0567739476001873
  • Khalil, R. A. (2010). Chapter 7: Regulation of vascular smooth muscle function. In Rho kinase in vascular smooth muscle. San Rafael, CA: Morgan & Claypool Life Sciences. doi:10.4199/C00012ED1V01Y201005ISP007
  • Khare, C. P. (2004). Indian herbal remedies: Rational western therapy ayurvedic and other traditional usage. New York, NY: Springer Science and Business Media.
  • Kumar, R., Schmidt, J. R., & Skinner, J. L. (2007). Hydrogen bonding definitions and dynamics in liquid water. Journal of Chemical Physics, 126(20), 204107. doi:10.1063/1.2742385
  • Kumari, R., Kumar, R., Open Source Drug Discovery Consortium, & Lynn, A. (2014). g_mmpbsa–a GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. doi:10.1021/ci500020m
  • Li, P., Yang, G. M., Zhang, Y. L., Gu, Z. Y., Li, M., & Pan, Y. (2016). Isolation and identification of the lipopholic alkaloids of embryo loti. Journal of Food Science and Biotechnology, 35, 19–27.
  • Lindorff-Larsen, K., Piana, S., Palmo, K., Maragakis, P., Klepeis, J. L., Dror, R. O., & Shaw, D. E. (2010). Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins: Structure, Function, and Bioinformatics, 78, 1950–1958. doi:10.1002/prot.22711
  • Madlung, A. (1999). Digital chemical intelligence. Science, 285(5435), 1866–1867. doi:10.1126/science.285.5435.1866
  • Mali, R. S., Ramdas, B., Ma, P., Shi, J., Munugalavadla, V., Sims, E., … Kapur, R. (2011). Rho kinase regulates the survival and transformation of cells bearing oncogenic forms of KIT, FLT3, and BCR-ABL. Cancer Cell, 20(3), 357–369. doi:10.1016/j.ccr.2011.07.016
  • Mak, G., & Hanania, N. A. (2012). New bronchodilators. Current Opinion in Pharmacology, 12(3), 238–245. doi:10.1016/j.coph.2012.02.019
  • Mammoto, A., Huang, S., Moore, K., Oh, P., & Ingber, D. E. (2004). Role of RhoA, mDia, and ROCK in cell shape-dependent control of the Skp2-p27kip1 pathway and the G1/S transition. Journal of Biological Chemistry, 279(25), 26323–26330. doi:10.1074/jbc.M402725200
  • Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock 4 and AutoDockTool 4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. doi:10.1002/jcc.21256
  • Nagumo, H., Sasaki, Y., Ono, Y., Okamoto, H., Seto, M., & Takuwa, Y. (2000). Rho kinase inhibitor HA-1077 prevents Rho-mediated myosin phosphatase inhibition in smooth muscle cells. The American Journal of Physiology-Cell Physiology, 278, 57–65. doi:10.1152/ajpcell.2000.278.1.C57
  • Nose, S., & Klein, M. L. (1983). Constant pressure molecular-dynamics for molecular-systems. Molecular Physics, 50, 1055–1076. doi:10.1080/00268978300102851
  • Ohga, I. (1926a). A double maximum in the rate of water absorption by Indian lotus seeds. American Journal of Botany, 13(10), 766–772. doi:10.1002/j.1537-2197.1926.tb05910.x
  • Ohga, I. (1926b). The germination of century old and recently harvested India lotus fruits, with special reference to the effect of oxygen supply. American Journal of Botany, 13, 289–294. doi:10.2307/2435478
  • Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. (2004). UCSF Chimera- a visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. doi:10.1002/jcc.20084
  • Qian, J. Q. (2002). Cardiovascular pharmacological effects of bisbenzylisoquinoline alkaloid derivatives. Acta Pharmacol Sin, 23(12), 1086–1092.
  • Satoh, S., Utsunomiya, T., Tsurui, K., Kobayashi, T., Ikegaki, I., Sasaki, Y., & Asano, T. (2001). Pharmacological profile of hydroxy fasudil as a selective rho kinase inhibitor on ischemic brain damage. Life Sciences, 69(12), 1441–1453. doi:10.1016/S0024-3205(01)01229-2
  • SATCM EB. (1999). Zhong hua ben cao (Vol. 3, pp. 399–411). Shanghai, China: Shanghai Science and Technology Press.
  • Schirok, H., Kast, R., Figueroa-Pérez, S., Bennabi, S., Gnoth, M. J., Feurer, A., … Stasch, J.-P. (2008). Design and synthesis of potent and selective azaindole-based rho kinase (ROCK) inhibitors. ChemMedChem, 3(12), 1893–1904. doi:10.1002/cmdc.200800211
  • Schüttelkopf, A. W., & Van Aalten, D. M. F. (2004). PRODRG: A tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallographica Section D Biological Crystallography, D60, 1355–1363. doi:10.1107/S0907444904011679
  • Shamma, M., Foy, J. E., Govindachari, T. R., & Viswanathan, N. (1976). The position of the phenolic function in tiliacorine and related alkaloids. The Journal of Organic Chemistry, 41(7), 1293–1294. doi:10.1021/jo00869a059
  • Sharma, B. R., Gautam, L. N., Adhikari, D., & Karki, R. (2017). A comprehensive review on chemical profiling of Nelumbo nucifera: Potential for drug development. Phytotherapy Research, 31(1), 3–26. doi:10.1002/ptr.5732
  • Takata, M., Tanaka, H., Kimura, M., Nagahara, Y., Tanaka, K., Kawasaki, K., & Hara, H. (2015). Fasudil, a rho kinase inhibitor, limits motor neuron loss in experimental models of amyotrophic lateral sclerosis. British Journal of Pharmacology, 170, 341–351. doi:10.1111/bph.12277
  • Takami, A., Iwakubo, M., Okada, Y., Kawata, T., Odai, H., Takahashi, N., … Iijima, H. (2004). Design and synthesis of Rho kinase inhibitors (I). Bioorganic & Medicinal Chemistry, 12(9), 2115–2137. doi:10.1111/bph.12277
  • Uehata, M., Ishizaki, T., Satoh, H., Ono, T., Kawahara, T., Morishita, T., … Narumiya, S. (1997). Calcium sensitization of smooth muscle mediated by a Rho-associated protein kinase in hypertension. Nature, 389(6654), 990–994. doi:10.1038/40187
  • Wallace, A. C., Laskowski, R. A., & Thornton, J. M. (1995). LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Engineering, Design and Selection, 8(2), 127–134. doi:10.1093/protein/8.2.127
  • Wang, J., Wang, W., Kollman, P. A., & Case, D. A. (2006). Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics and Modelling, 25(2), 247–260. doi:10.1016/j.jmgm.2005.12.005
  • Wei, B. Q., Weaver, L. H., Ferrari, A. M., Matthews, B. W., & Shoichet, B. K. (2004). Testing a flexible-receptor docking algorithm in a model binding site. Journal of Molecular Biology, 337(5), 1161–1182. doi:10.1016/j.jmgm.2005.12.005
  • Wu, Z. Y., Raven, H. P., & Hong, D. Y. (2001). Flora of China (Vol. 6). Beijing, China and St. Louis, MO: Science Press (China) and Missouri Botanical Garden. doi:10.3100/1043-4534-13.2.301
  • Yang, G. M., Sun, J., Pan, Y., Zhang, J. L., Xiao, M., & Zhu, M. S. (2018). Isolation and identification of a tribenzylisoquinoline alkaloid from Nelumbo nucifera Gaertn, a novel potential smooth muscle relaxant. Fitoterapia, 124, 58–65. doi:10.1016/j.fitote.2017.10.020
  • 张,X.,状语从句:潘,Y.(2002)。药用植物莲子生物碱的研究进展。 [中国南京中医药大学学报(自然科学版), 18,382–384。

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.