Unravelling the drugability of MSI2 RNA recognition motif (RRM) protein and the prediction of their effective antileukemia inhibitors from traditional herb concoctions

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/https://doi.org/10.1016/j.softx.2015.06.001
   Google Scholar
• Byers, R. J., Currie, T., Tholouli, E., Rodig, S. J., & Kutok, J. L. (2011). MSI2 protein expression predicts unfavorable outcome in acute myeloid leukemia. Blood, 118(10), 2857–2867. https://doi.org/https://doi.org/10.1182/blood-2011-04-346767
   PubMed Web of Science ®Google Scholar
• Case, D. A., Ben-Shalom, I. Y., Brozell, S. R., Cerutti, D. S., T. E., Cheatham, I., Cruzeiro, V. W. D., … Kollman, P. A. (2018). Amber 18. University of California.
   Google Scholar
• CLC-bio (2013). Molegro virtual docker. CLC bio company.
   Google Scholar
• de Vries, S. J., van Dijk, A. D. J., Krzeminski, M., van Dijk, M., Thureau, A., Hsu, V., Wassenaar, T., & Bonvin, A. M. J. J. (2007). HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets. Proteins, 69(4), 726–733. https://doi.org/https://doi.org/10.1002/prot.21723
   PubMed Web of Science ®Google Scholar
• Dominguez, C., Boelens, R., & Bonvin, A. M. J. J. (2003). HADDOCK: A protein-protein docking approach based on biochemical or biophysical information. Journal of the American Chemical Society, 125(7), 1731–1737. https://doi.org/https://doi.org/10.1021/ja026939x
   PubMed Web of Science ®Google Scholar
• Dupradeau, F.-Y., Pigache, A., Zaffran, T., Savineau, C., Lelong, R., Grivel, N., Lelong, D., Rosanski, W., & Cieplak, P. (2010). The R.E.D. tools: Advances in RESP and ESP charge derivation and force field library building. Physical Chemistry Chemical Physics : Pccp, 12(28), 7821–7839. https://doi.org/https://doi.org/10.1039/c0cp00111b
   PubMed Web of Science ®Google Scholar
• Friesner, R. A., Murphy, R. B., Repasky, M. P., Frye, L. L., Greenwood, J. R., Halgren, T. A., Sanschagrin, P. C., & Mainz, D. T. (2006). Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. Journal of Medicinal Chemistry, 49(21), 6177–6196. https://doi.org/https://doi.org/10.1021/jm051256o
   PubMed Web of Science ®Google Scholar
• Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., … Fox, D. J. (2016). Gaussian 16, Revision B.01.,. Gaussian, Inc.
   Google Scholar
• Halgren, T. A., Murphy, R. B., Friesner, R. A., Beard, H. S., Frye, L. L., Pollard, W. T., & Banks, J. L. (2004). Glide: A New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening. Journal of Medicinal Chemistry, 47(7), 1750–1759. https://doi.org/https://doi.org/10.1021/jm030644s
   PubMed Web of Science ®Google Scholar
• Huang, J., Rauscher, S., Nawrocki, G., Ran, T., Feig, M., de Groot, B. L., Grubmüller, H., & MacKerell, A. D. (2017). CHARMM36m: An improved force field for folded and intrinsically disordered proteins. Nature Methods, 14(1), 71–73. https://doi.org/https://doi.org/10.1038/nmeth.4067
   PubMed Web of Science ®Google Scholar
• Kharas, M. G., Lengner, C. J., Al-Shahrour, F., Bullinger, L., Ball, B., Zaidi, S., Morgan, K., Tam, W., Paktinat, M., Okabe, R., Gozo, M., Einhorn, W., Lane, S. W., Scholl, C., Fröhling, S., Fleming, M., Ebert, B. L., Gilliland, D. G., Jaenisch, R., & Daley, G. Q. (2010). Musashi-2 regulates normal hematopoiesis and promotes aggressive myeloid leukemia. Nature Medicine, 16(8), 903–908. https://doi.org/https://doi.org/10.1038/nm.2187
   PubMed Web of Science ®Google Scholar
• Kudinov, A. E., Karanicolas, J., Golemis, E. A., & Boumber, Y. (2017). Musashi RNA-binding proteins as cancer drivers and novel therapeutic targets. Clinical Cancer Research : An Official Journal of the American Association for Cancer Research, 23(9), 2143–2153. https://doi.org/https://doi.org/10.1158/1078-0432.CCR-16-2728
   PubMed Web of Science ®Google Scholar
• Liu, F. F., Huang, B., Dong, X. Y., & Sun, Y. (2013). Molecular Basis for the Dissociation Dynamics of Protein A-Immunoglobulin G1 Complex. PLoS One, 8(6), e66935. https://doi.org/https://doi.org/10.1371/journal.pone.0066935
   PubMed Web of Science ®Google Scholar
• Minuesa, G., Albanese, S. K., Xie, W., Kazansky, Y., Worroll, D., Chow, A., Schurer, A., Park, S.-M., Rotsides, C. Z., Taggart, J., Rizzi, A., Naden, L. N., Chou, T., Gourkanti, S., Cappel, D., Passarelli, M. C., Fairchild, L., Adura, C., Glickman, J. F., … Kharas, M. G. (2019). Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia. Nature Communications, 10(1), 15. https://doi.org/https://doi.org/10.1038/s41467-019-10523-3
   PubMedGoogle Scholar
• Minuesa, G., Antczak, C., Shum, D., Radu, C., Bhinder, B., Li, Y., Djaballah, H., & Kharas, M. G. (2014). A 1536-Well Fluorescence Polarization Assay to Screen for Modulators of the MUSASHI Family of RNA-Binding Proteins. Combinatorial Chemistry & High Throughput Screening, 17(7), 596–609. https://doi.org/https://doi.org/10.2174/1386207317666140609122714
   PubMed Web of Science ®Google Scholar
• Nosé, S., & Klein, M. L. (1983). Constant pressure molecular dynamics for molecular systems. Molecular Physics, 50(5), 1055–1076. https://doi.org/https://doi.org/10.1080/00268978300102851
   Web of Science ®Google Scholar
• Park, S.-M., Gönen, M., Vu, L., Minuesa, G., Tivnan, P., Barlowe, T. S., Taggart, J., Lu, Y., Deering, R. P., Hacohen, N., Figueroa, M. E., Paietta, E., Fernandez, H. F., Tallman, M. S., Melnick, A., Levine, R., Leslie, C., Lengner, C. J., & Kharas, M. G. (2015). Musashi2 sustains the mixed-lineage leukemia-driven stem cell regulatory program. The Journal of Clinical Investigation, 125(3), 1286–1298. https://doi.org/https://doi.org/10.1172/JCI78440
   PubMed Web of Science ®Google Scholar
• Permyakov, S. E., Denesyuk, A. I., Denessiouk, K. A., Permyakova, M. E., Kazakov, A. S., Ismailov, R. G., Rastrygina, V. A., Sokolov, A. S., & Permyakov, E. A. (2019). Monomeric state of S100P protein: Experimental and molecular dynamics study. Cell Calcium, 80(March), 152–159. https://doi.org/https://doi.org/10.1016/j.ceca.2019.04.008
   PubMedGoogle Scholar
• Rungsung, I., Rajagopalan, M., & Ramaswamy, A. (2018). Molecular dynamics study of TMPA mediated dissociation of Nur77-LKB1 complex. Computational Biology and Chemistry, 76(February), 67–78. https://doi.org/https://doi.org/10.1016/j.compbiolchem.2018.06.002
   PubMedGoogle Scholar
• Ruth Zearfoss, N., Deveau, L. M., Clingman, C. C., Schmidt, E., Johnson, E. S., Massi, F., & Ryder, S. P. (2014). A conserved three-nucleotide core motif defines musashi RNA binding specificity. The Journal of Biological Chemistry, 289(51), 35530–35541. https://doi.org/https://doi.org/10.1074/jbc.M114.597112
   PubMed Web of Science ®Google Scholar
• Taggart, J., Ho, T.-C., Amin, E., Xu, H., Barlowe, T. S., Perez, A. R., Durham, B. H., Tivnan, P., Okabe, R., Chow, A., Vu, L., Park, S. M., Prieto, C., Famulare, C., Patel, M., Lengner, C. J., Verma, A., Roboz, G., Guzman, M., … Kharas, M. G. (2016). MSI2 is required for maintaining activated myelodysplastic syndrome stem cells. Nature Communications, 7, 10739–10738. https://doi.org/https://doi.org/10.1038/ncomms10739
   PubMed Web of Science ®Google Scholar
• Thol, F., Winschel, C., Sonntag, A.-K., Damm, F., Wagner, K., Chaturvedi, A., Göhring, G., Schlegelberger, B., Lübbert, M., Fiedler, W., Kirchner, H., Krauter, J., Ganser, A., & Heuser, M. (2013). Prognostic significance of expression levels of stem cell regulators MSI2 and NUMB in acute myeloid leukemia. Annals of Hematology, 92(3), 315–323. https://doi.org/https://doi.org/10.1007/s00277-012-1637-5
   PubMed Web of Science ®Google Scholar
• 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. https://doi.org/https://doi.org/10.1002/jcc.21334
   PubMed Web of Science ®Google Scholar
• 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 & Modelling, 25(2), 247–260. https://doi.org/https://doi.org/10.1016/j.jmgm.2005.12.005
   PubMed Web of Science ®Google Scholar
• Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2004). Development and testing of a general Amber force field. Journal of Computational Chemistry, 25(9), 1157–1174. https://doi.org/https://doi.org/10.1002/jcc.20035
   PubMed Web of Science ®Google Scholar
• Zhang, L., Borthakur, S., & Buck, M. (2016). Dissociation of a Dynamic Protein Complex Studied by All-Atom Molecular Simulations. Biophysical Journal, 110(4), 877–886. https://doi.org/https://doi.org/10.1016/j.bpj.2015.12.036
   PubMed Web of Science ®Google Scholar