In-silico investigation of RPS6KB1 associated cancer inhibitor: a drug repurposing study

References

• Ahamad, S., Islam, A., Ahmad, F., Dwivedi, N., & Hassan, M. I. (2019). 2/3D-QSAR, molecular docking and MD simulation studies of FtsZ protein targeting benzimidazoles derivatives. Computational Biology and Chemistry, 78, 398–413. https://doi.org/10.1016/j.compbiolchem.2018.12.017
   PubMed Web of Science ®Google Scholar
• Akbarian, F., Tabatabaiefar, M. A., Shaygannejad, V., Shahpouri, M. M., Badihian, N., Sajjadi, R., Dabiri, A., Jalilian, N., & Noori-Daloii, M. R. (2020). Upregulation of MTOR, RPS6KB1, and EIF4EBP1 in the whole blood samples of Iranian patients with multiple sclerosis compared to healthy controls. Metabolic Brain Disease, 35(8), 1309–1316. https://doi.org/10.1007/s11011-020-00590-7
   PubMed Web of Science ®Google Scholar
• Alam, A., Khan, M. S., Mathur, Y., Sulaimani, M. N., Farooqui, N., Ahmad, S. F., Nadeem, A., Yadav, D. K., & Mohammad, T. (2023). Structure-based identification of potential inhibitors of ribosomal protein S6 kinase 1, targeting cancer therapy: A combined docking and molecular dynamics simulations approach. Journal of Biomolecular Structure & Dynamics, 1–12. https://doi.org/10.1080/07391102.2023.2228912
   Google Scholar
• Al-Awsi, G. R. L., Jasim, S. A., Fakri Mustafa, Y., Alhachami, F. R., Ziyadullaev, S., Kandeel, M., Abulkassim, R., Sivaraman, R., M Hameed, N., Mireya Romero Parra, R., Karampoor, S., & Mirzaei, R. (2023). The role of miRNA-128 in the development and progression of gastrointestinal and urogenital cancer. Future Oncology (London, England), 18(38), 4209–4231. https://doi.org/10.2217/fon-2022-0574
   Web of Science ®Google Scholar
• Alshammari, M. M., Soury, R., Alenezi, K. M., Mushtque, M., Rizvi, M. M. A., & Haque, A. (2022). Synthesis, characterization, anticancer and in silico studies of a pyrazole-tethered thiazolidine-2, 4-dione derivative. Journal of Biomolecular Structure & Dynamics, 40(23), 13075–13082. https://doi.org/10.1080/07391102.2021.1981451
   PubMed Web of Science ®Google Scholar
• Alsukaibi, A. K. D., Alenezi, K. M., Haque, A., Ahmad, I., Saeed, M., Verma, M., Ansari, I. A., & Hsieh, M.-F. (2023). Chemical, biological and in silico assessment of date (P. dactylifera L.) fruits grown in Ha’il region. Frontiers in Chemistry, 11, 1138057. https://doi.org/10.3389/fchem.2023.1138057
   PubMed Web of Science ®Google Scholar
• Araujo, R. P., Liotta, L. A., & Petricoin, E. F. (2007). Proteins, drug targets and the mechanisms they control: The simple truth about complex networks. Nature Reviews. Drug Discovery, 6(11), 871–880. https://doi.org/10.1038/nrd2381
   PubMed Web of Science ®Google Scholar
• Arnott, J. A., Kumar, R., & Planey, S. L. (2013). Lipophilicity indices for drug development. J Appl Biopharm Pharmacokinet, 1(1), 31–36.
   Google Scholar
• Bahrami-B, F., Ataie-Kachoie, P., Pourgholami, M. H., & Morris, D. L. (2014). p70 Ribosomal protein S6 kinase (Rps6kb1): An update. Journal of Clinical Pathology, 67(12), 1019–1025. https://doi.org/10.1136/jclinpath-2014-202560
   PubMed Web of Science ®Google Scholar
• Berendsen, H. J., van der Spoel, D., & van Drunen, R. (1995). GROMACS: A message-passing parallel molecular dynamics implementation. Computer Physics Communications, 91(1-3), 43–56. https://doi.org/10.1016/0010-4655(95)00042-E
   Web of Science ®Google Scholar
• Briggs, K., Wang, L., Nagashima, K., Zengel, J., Tripp, R. A., & He, B. (2020). Regulation of mumps virus replication and transcription by kinase RPS6KB1. Journal of Virology, 94(12). https://doi.org/10.1128/jvi.00387-00320
   Web of Science ®Google Scholar
• Cai, C., Chen, Q.-B., Han, Z.-D., Zhang, Y.-Q., He, H.-C., Chen, J.-H., Chen, Y.-R., Yang, S.-B., Wu, Y.-D., Zeng, Y.-R., Qin, G.-Q., Liang, Y.-X., Dai, Q.-S., Jiang, F.-N., Wu, S-L., Zeng, G.-H., Zhong, W.-D., & Wu, C.-L. (2015). miR-195 inhibits tumor progression by targeting RPS6KB1 in human prostate cancer. Clinical Cancer Research: An Official Journal of the American Association for Cancer Research, 21(21), 4922–4934. https://doi.org/10.1158/1078-0432.CCR-15-0217
   PubMed Web of Science ®Google Scholar
• Cao, S., Shen, W.-B., Reece, E. A., & Yang, P. (2020). Deficiency of the oxidative stress–responsive kinase p70S6K1 restores autophagy and ameliorates neural tube defects in diabetic embryopathy. American Journal of Obstetrics and Gynecology, 223(5), 753.e1–753.714. https://doi.org/10.1016/j.ajog.2020.05.015
   PubMed Web of Science ®Google Scholar
• Catalán, V., Gómez-Ambrosi, J., Rodríguez, A., Ramírez, B., Andrada, P., Rotellar, F., Valentí, V., Moncada, R., Martí, P., Silva, C., Salvador, J., & Frühbeck, G. (2015). Expression of S6K1 in human visceral adipose tissue is upregulated in obesity and related to insulin resistance and inflammation. Acta Diabetologica, 52(2), 257–266. https://doi.org/10.1007/s00592-014-0632-9
   PubMed Web of Science ®Google Scholar
• Chen, B., Yang, L., Zhang, R., Gan, Y., Zhang, W., Liu, D., Chen, H., & Tang, H. (2017). Hyperphosphorylation of RPS6KB1, rather than overexpression, predicts worse prognosis in non-small cell lung cancer patients. PLoS One, 12(8), e0182891. https://doi.org/10.1371/journal.pone.0182891
   PubMed Web of Science ®Google Scholar
• Ciobanu, L. G., Sachdev, P. S., Trollor, J. N., Reppermund, S., Thalamuthu, A., Mather, K. A., Cohen-Woods, S., Stacey, D., Toben, C., Schubert, K. O., & Baune, B. T. (2018). Co-expression network analysis of peripheral blood transcriptome identifies dysregulated protein processing in endoplasmic reticulum and immune response in recurrent MDD in older adults. Journal of Psychiatric Research, 107, 19–27. https://doi.org/10.1016/j.jpsychires.2018.09.017
   PubMed Web of Science ®Google Scholar
• Cui, B., Lin, H., Yu, J., Yu, J., & Hu, Z. (2019). Autophagy and the immune response. Autophagy: Biology and Diseases: Basic Science, 1206, 595–634.
   Google Scholar
• DeLano, W. L. (2002). Pymol: An open-source molecular graphics tool. CCP4 Newsl Protein Crystallogr, 40(1), 82–92.
   Google Scholar
• El-Tanani, M., Nsairat, H., Aljabali, A. A., Serrano-Aroca, Á., Mishra, V., Mishra, Y., Naikoo, G. A., Alshaer, W., & Tambuwala, M. M. (2023). Role of mammalian target of rapamycin (mTOR) signalling in oncogenesis. Life Sciences, 323, 121662. https://doi.org/10.1016/j.lfs.2023.121662
   PubMed Web of Science ®Google Scholar
• Farhood, B., Raei, B., Malekzadeh, R., Shirvani, M., Najafi, M., & Mortezazadeh, T. (2019). A review of incidence and mortality of colorectal, lung, liver, thyroid, and bladder cancers in Iran and compared to other countries. Contemporary Oncology (Poznan, Poland), 23(1), 7–15. https://doi.org/10.5114/wo.2019.84112
   PubMed Web of Science ®Google Scholar
• Fenton, T. R., & Gout, I. T. (2011). Functions and regulation of the 70 kDa ribosomal S6 kinases. The International Journal of Biochemistry & Cell Biology, 43(1), 47–59. https://doi.org/10.1016/j.biocel.2010.09.018
   PubMed Web of Science ®Google Scholar
• Harvey, M., & De Fabritiis, G. (2009). An implementation of the smooth particle mesh Ewald method on GPU hardware. Journal of Chemical Theory and Computation, 5(9), 2371–2377. https://doi.org/10.1021/ct900275y
   PubMed Web of Science ®Google Scholar
• Hess, B., Bekker, H., Berendsen, H. J., & Fraaije, J. G. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. https://doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.3.CO;2-L
   Web of Science ®Google Scholar
• Kwintkiewicz, J., Spaczynski, R. Z., Foyouzi, N., Pehlivan, T., & Duleba, A. J. (2006). Insulin and oxidative stress modulate proliferation of rat ovarian theca-interstitial cells through diverse signal transduction pathways. Biology of Reproduction, 74(6), 1034–1040. https://doi.org/10.1095/biolreprod.105.049908
   PubMed Web of Science ®Google Scholar
• Laskowski, R. A. (2001). PDBsum: Summaries and analyses of PDB structures. Nucleic Acids Research, 29(1), 221–222. https://doi.org/10.1093/nar/29.1.221
   PubMed Web of Science ®Google Scholar
• Laskowski, R., MacArthur, M., & Thornton, J. (2006). PROCHECK: Validation of protein-structure coordinates.
   Google Scholar
• Li, Z., Rong, Y. L., & Zhang, Y. S. (2023). MiR‐33‐5p alleviates spinal cord injury in rats and protects PC12 cells from lipopolysaccharide‐induced apoptosis. The Kaohsiung Journal of Medical Sciences, 39(1), 52–60. https://doi.org/10.1002/kjm2.12610
   PubMed Web of Science ®Google Scholar
• Neufeld, T. P. (2012). Autophagy and cell growth–the yin and yang of nutrient responses. Journal of Cell Science, 125(Pt 10), 2359–2368. https://doi.org/10.1242/jcs.103333
   PubMed Web of Science ®Google Scholar
• Niwa, H., Mikuni, J., Sasaki, S., Tomabechi, Y., Honda, K., Ikeda, M., Ohsawa, N., Wakiyama, M., Handa, N., Shirouzu, M., Honma, T., Tanaka, A., & Yokoyama, S. (2014). Crystal structures of the S6K1 kinase domain in complexes with inhibitors. Journal of Structural and Functional Genomics, 15(3), 153–164. https://doi.org/10.1007/s10969-014-9188-8
   PubMedGoogle Scholar
• Rajappa, S., Singh, M., Uehara, R., Schachterle, S. E., & Setia, S. (2023). Cancer incidence and mortality trends in Asia based on regions and human development index levels: An analyses from GLOBOCAN 2020. Current Medical Research and Opinion, 39(8), 1127–1137. https://doi.org/10.1080/03007995.2023.2231761
   PubMedGoogle Scholar
• Ramaiah, M. J., Lavanya, A., Honarpisheh, M., Zarea, M., Bhadra, U., & Bhadra, M. P. (2014). miR-15/16 complex targets p70S6 kinase1 and controls cell proliferation in MDA-MB-231 breast cancer cells. Gene, 552(2), 255–264. https://doi.org/10.1016/j.gene.2014.09.052
   PubMed Web of Science ®Google Scholar
• Saxton, R. A., & Sabatini, D. M. (2017). mTOR signaling in growth, metabolism, and disease. Cell, 168(6), 960–976. https://doi.org/10.1016/j.cell.2017.02.004
   PubMed Web of Science ®Google Scholar
• So, L., Lee, J., Palafox, M., Mallya, S., Woxland, C. G., Arguello, M., Truitt, M. L., Sonenberg, N., Ruggero, D., & Fruman, D. A. (2016). The 4E-BP–eIF4E axis promotes rapamycin-sensitive growth and proliferation in lymphocytes. Science Signaling, 9(430), ra57. https://doi.org/10.1126/scisignal.aad8463
   PubMed Web of Science ®Google Scholar
• Sterling, T., & Irwin, J. J. (2015). ZINC 15–ligand discovery for everyone. Journal of Chemical Information and Modeling, 55(11), 2324–2337. https://doi.org/10.1021/acs.jcim.5b00559
   PubMed Web of Science ®Google Scholar
• Urbanski, L. M., Leclair, N., & Anczuków, O. (2018). Alternative‐splicing defects in cancer: Splicing regulators and their downstream targets, guiding the way to novel cancer therapeutics. Wiley Interdisciplinary Reviews. RNA, 9(4), e1476. https://doi.org/10.1002/wrna.1476
   PubMed Web of Science ®Google Scholar
• Van Aalten, D. M., Bywater, R., Findlay, J. B., Hendlich, M., Hooft, R. W., & Vriend, G. (1996). PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules. Journal of Computer-Aided Molecular Design, 10(3), 255–262. https://doi.org/10.1007/BF00355047
   PubMed Web of Science ®Google Scholar
• Wang, J., Zhong, C., Wang, F., Qu, F., & Ding, J. (2013). Crystal structures of S6K1 provide insights into the regulation mechanism of S6K1 by the hydrophobic motif. The Biochemical Journal, 454(1), 39–47. https://doi.org/10.1042/BJ20121863
   PubMedGoogle Scholar
• Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F. T., de Beer, T. A. P., Rempfer, C., Bordoli, L., Lepore, R., & Schwede, T. (2018). SWISS-MODEL: Homology modelling of protein structures and complexes. Nucleic Acids Research, 46(W1), W296–W303. https://doi.org/10.1093/nar/gky427
   PubMed Web of Science ®Google Scholar
• Wipperman, M. F., Montrose, D. C., Gotto, A. M., Jr., & Hajjar, D. P. (2019). Mammalian target of rapamycin: A metabolic rheostat for regulating adipose tissue function and cardiovascular health. The American Journal of Pathology, 189(3), 492–501. https://doi.org/10.1016/j.ajpath.2018.11.013
   PubMed Web of Science ®Google Scholar
• Wu, Y., Tepper, H. L., & Voth, G. A. (2006). Flexible simple point-charge water model with improved liquid-state properties. The Journal of Chemical Physics, 124(2), 024503. https://doi.org/10.1063/1.2136877
   PubMed Web of Science ®Google Scholar
• Zhang, H., Zhang, H.-R., Zhang, J., Hu, M.-L., Ren, L., Luo, Q.-Q., & Qi, H.-Z. (2023). Discovery of novel S6K1 inhibitors by an ensemble-based virtual screening method and molecular dynamics simulation. Journal of Molecular Modeling, 29(4), 102. https://doi.org/10.1007/s00894-023-05504-9
   PubMed Web of Science ®Google Scholar
• Zheng, Z., Zhang, L., & Hou, X. (2022). Potential roles and molecular mechanisms of phytochemicals against cancer. Food & Function, 13(18), 9208–9225. https://doi.org/10.1039/d2fo01663j
   PubMed Web of Science ®Google Scholar
• Zheng, Y., Zhang, W., Pendleton, E., Leng, S., Wu, J., Chen, R., & Sun, X. J. (2009). Improved insulin sensitivity by calorie restriction is associated with reduction of ERK and p70S6K activities in the liver of obese Zucker rats. The Journal of Endocrinology, 203(3), 337–347. https://doi.org/10.1677/JOE-09-0181
   PubMed Web of Science ®Google Scholar