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Research Articles

Targeting the microRNA binding domain of argonaute 2: rational inhibitor design and study of mutation effects on protein-ligand interaction

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Pages 4710-4717 | Received 28 Feb 2019, Accepted 23 Oct 2019, Published online: 03 Dec 2019

References

  • Ameyar-Zazoua, M., Rachez, C., Souidi, M., Robin, P., Fritsch, L., Young, R., … Harel-Bellan, A. (2012). Argonaute proteins couple chromatin silencing to alternative splicing. Nature Structural & Molecular Biology, 19(10), 998. doi:10.1038/nsmb.2373
  • Balasubramanian, C., Ojha, R. P., Maiti, S., & Desideri, A. (2010). Sampling the structure of the noncanonical lin-4: Lin-14 microRNA: MRNA complex by molecular dynamics simulations. The Journal of Physical Chemistry B, 114(49), 16443–16449. doi:10.1021/jp104193r
  • Baraas, R. C., Hagen, L. A., Dees, E. W., & Neitz, M. (2012). Substitution of isoleucine for threonine at position 190 of S-opsin causes S-cone-function abnormalities. Vision Research, 73, 1–9. doi:10.1016/j.visres.2012.09.007
  • Bartel, D. P. (2009). MicroRNAs: Target recognition and regulatory functions. Cell, 136(2), 215–233. doi:10.1016/j.cell.2009.01.002
  • Benhamed, M., Herbig, U., Ye, T., Dejean, A., & Bischof, O. (2012). Senescence is an endogenous trigger for microRNA-directed transcriptional gene silencing in human cells. Nature cell Biology, 14(3), 266. doi:10.1038/ncb2443
  • Bhandare, V., & Ramaswamy, A. (2016). Structural dynamics of human argonaute2 and its interaction with siRNAs designed to target mutant tdp43. Advances in Bioinformatics, 2016, 1. doi:10.1155/2016/8792814
  • Blencke, S., Ullrich, A., & Daub, H. (2003). Mutation of threonine 766 in the epidermal growth factor receptor reveals a hotspot for resistance formation against selective tyrosine kinase inhibitors. Journal of Biological Chemistry, 278(17), 15435–15440. doi:10.1074/jbc.M211158200
  • Boland, A., Tritschler, F., Heimstädt, S., Izaurralde, E., & Weichenrieder, O. (2010). Crystal structure and ligand binding of the MID domain of a eukaryotic Argonaute protein. EMBO Reports, 11(7), 522. doi:10.1038/embor.2010.81
  • Brás, A., Rodrigues, A. S., Gomes, B., & Rueff, J. (2018). Down syndrome and microRNAs. Biomedical Reports, 8(1), 11–16. doi:10.3892/br.2017.1019
  • Cheloufi, S., Dos Santos, C. O., Chong, M. M., & Hannon, G. J. (2010). A dicer-independent miRNA biogenesis pathway that requires Ago catalysis. Nature, 465(7298), 584. doi:10.1038/nature09092
  • Chendrimada, T. P., Gregory, R. I., Kumaraswamy, E., Norman, J., Cooch, N., Nishikura, K., & Shiekhattar, R. (2005). TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature, 436(7051), 740. doi:10.1038/nature03868
  • 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
  • Denli, A. M., Tops, B. B., Plasterk, R. H., Ketting, R. F., & Hannon, G. J. (2004). Processing of primary microRNAs by the Microprocessor complex. Nature, 432(7014), 231. doi:10.1038/nature03049
  • Elkayam, E., Kuhn, C.-D., Tocilj, A., Haase, A. D., Greene, E. M., Hannon, G. J., & Joshua-Tor, L. (2012). The structure of human argonaute-2 in complex with miR-20a. Cell, 150(1), 100–110. doi:10.1016/j.cell.2012.05.017
  • Faehnle, C. R., & Joshua‐Tor, L. (2010). Argonaute MID domain takes centre stage. EMBO Reports, 11(8), 564–565. doi:10.1038/embor.2010.110
  • Fareh, M., Yeom, K.-H., Haagsma, A. C., Chauhan, S., Heo, I., & Joo, C. (2016). TRBP ensures efficient Dicer processing of precursor microRNA in RNA-crowded environments. Nature Communications, 7(1), 13694. doi:10.1038/ncomms13694
  • Fazi, F., Rosa, A., Fatica, A., Gelmetti, V., De Marchis, M. L., Nervi, C., & Bozzoni, I. (2005). A minicircuitry comprised of microRNA-223 and transcription factors NFI-A and C/EBPα regulates human granulopoiesis. Cell, 123(5), 819–831. doi:10.1016/j.cell.2005.09.023
  • Friedman, R. C., Farh, K. K.-H., Burge, C. B., & Bartel, D. P. (2008). Most mammalian mRNAs are conserved targets of microRNAs. Genome Research, 19(1), 92–105. doi:10.1101/gr.082701.108[Mismatch] http://www.otavachemicals.com.
  • Hyperchem, H. (2002). Inc. 1115 NW 4th street Gainesville, Florida 32601, USA. Google Scholar.
  • Ma, J.-B., Yuan, Y.-R., Meister, G., Pei, Y., Tuschl, T., & Patel, D. J. (2005). Structural basis for 5′-end-specific recognition of guide RNA by the A. fulgidus Piwi protein. Nature, 434(7033), 666. doi:10.1038/nature03514
  • Makarewicz, T., & Kaźmierkiewicz, R. (2013). Molecular dynamics simulation by GROMACS using GUI plugin for PyMOL. Journal of Chemical Information and Modeling, 53(5), 1229–1234. doi:10.1021/ci400071x
  • Masciarelli, S., Quaranta, R., Iosue, I., Colotti, G., Padula, F., Varchi, G., … Del Rio, A. (2014). A small-molecule targeting the microRNA binding domain of argonaute 2 improves the retinoic acid differentiation response of the acute promyelocytic leukemia cell line NB4. ACS chemical Biology, 9(8), 1674–1679. doi:10.1021/cb500286b
  • Meister, G. (2013). Argonaute proteins: Functional insights and emerging roles. Nature Reviews Genetics, 14(7), 447. doi:10.1038/nrg3462
  • Meister, G., & Tuschl, T. (2004). Mechanisms of gene silencing by double-stranded RNA. Nature, 431(7006), 343. doi:10.1038/nature02873
  • Mishra, P. J. (2012). The miRNA–drug resistance connection: A new era of personalized medicine using noncoding RNA begins. Pharmacogenomics, 13(12), 1321–1324. doi:10.2217/pgs.12.121
  • Piletič, K., & Kunej, T. (2016). MicroRNA epigenetic signatures in human disease. Archives of Toxicology, 90(10), 2405–2419. doi:10.1007/s00204-016-1815-7
  • Ram, G., & Chinen, J. (2011). Infections and immunodeficiency in Down syndrome. Clinical & Experimental Immunology, 164(1), 9–16. doi:10.1111/j.1365-2249.2011.04335.x
  • Rodriguez, A., Vigorito, E., Clare, S., Warren, M. V., Couttet, P., Soond, D. R., … Bradley, A. (2007). Requirement of bic/microRNA-155 for normal immune function. Science, 316(5824), 608–611. doi:10.1126/science.1139253
  • Schmidt, M. F., Korb, O., & Abell, C. (2013). MicroRNA-specific argonaute 2 protein inhibitors. ACS chemical Biology, 8(10), 2122–2126. doi:10.1021/cb400246k
  • Shirafuji, T., Ueyama, T., Yoshino, K-I., Takahashi, H., Adachi, N., Ago, Y., … Saito, N. (2014). The role of Pak-interacting exchange factor-β phosphorylation at serines 340 and 583 by PKCγ in dopamine release. Journal of Neuroscience, 34(28), 9268–9280. doi:10.1523/JNEUROSCI.4278-13.2014
  • Stewart, J. J. P. (2016). Stewart computational chemistry. Colorado Springs, CO. Retrieved from http://OpenMOPAC.net.
  • Tan, G. S., Chiu, C.-H., Garchow, B. G., Metzler, D., Diamond, S. L., & Kiriakidou, M. (2012). Small molecule inhibition of RISC loading. ACS chemical Biology, 7(2), 403–410. doi:10.1021/cb200253h
  • Thai, T.-H., Calado, D. P., Casola, S., Ansel, K. M., Xiao, C., Xue, Y., … Rajewsky, K. (2007). Regulation of the germinal center response by microRNA-155. Science, 316(5824), 604–608. doi:10.1126/science.1141229
  • Trott, O., & Olson, A. J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of computational Chemistry, 31(2), 455–461. doi:10.1002/jcc.21334
  • van Zundert, G. C. P., Rodrigues, J. P. G. L. M., Trellet, M., Schmitz, C., Kastritis, P. L., Karaca, E., … Bonvin, A. M. J. J. (2016). The HADDOCK2. 2 web server: User-friendly integrative modeling of biomolecular complexes. Journal of molecular Biology, 428(4), 720–725. doi:10.1016/j.jmb.2015.09.014
  • 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
  • Wang, Y., Juranek, S., Li, H., Sheng, G., Wardle, G. S., Tuschl, T., & Patel, D. J. (2009). Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes. Nature, 461(7265), 754. doi:10.1038/nature08434
  • Wei, W., Ba, Z., Gao, M., Wu, Y., Ma, Y., Amiard, S., … Qi, Y. (2012). A role for small RNAs in DNA double-strand break repair. Cell, 149(1), 101–112. doi:10.1016/j.cell.2012.03.002
  • Ye, Z., Jin, H., & Qian, Q. (2015). Argonaute 2: A Novel Rising Star in Cancer Research. Journal of Cancer, 6(9), 877–882. doi:10.7150/jca.11735
  • Yeom, K.-H., Lee, Y., Han, J., Suh, M. R., & Kim, V. N. (2006). Characterization of DGCR8/Pasha, the essential cofactor for Drosha in primary miRNA processing. Nucleic acids Research, 34(16), 4622–4629. doi:10.1093/nar/gkl458

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