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Research Articles

Design single-stranded DNA aptamer of cluster of differentiation 47 protein by stochastic tunnelling-basin hopping-discrete molecular dynamics method

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Pages 3969-3982 | Received 27 Jan 2023, Accepted 18 May 2023, Published online: 01 Jun 2023

References

  • Bavi, R., Hang, Z., Banerjee, P., Aquib, M., Jadhao, M., Rane, N., Bavi, S., Bhosale, R., Kodam, K., Jeon, B.-H., & Gu, Y. (2020). Doxorubicin-conjugated innovative 16-mer DNA aptamer-based Annexin A1 targeted anti-cancer drug delivery. Molecular Therapy. Nucleic Acids, 21, 1074–1086. https://doi.org/10.1016/j.omtn.2020.07.038
  • Bell, D. R., Weber, J. K., Yin, W., Huynh, T., Duan, W., & Zhou, R. (2020). In silico design and validation of high-affinity RNA aptamers targeting epithelial cellular adhesion molecule dimers. Proceedings of the National Academy of Sciences of the United States of America, 117(15), 8486–8493. https://doi.org/10.1073/pnas.1913242117
  • Best, R. B., Mittal, J., Feig, M., & MacKerell, A. D. (2012). Inclusion of many-body effects in the additive CHARMM protein CMAP potential results in enhanced cooperativity of α-helix and β-hairpin formation. Biophysical Journal, 103(5), 1045–1051. https://doi.org/10.1016/j.bpj.2012.07.042
  • Billerhart, M., Schönhofer, M., Schueffl, H., Polzer, W., Pichler, J., Decker, S., Taschauer, A., Maier, J., Anton, M., Eckmann, S., Blaschek, M., Heffeter, P., Sami, H., & Ogris, M. (2021). CD47-targeted cancer immunogene therapy: Secreted SIRPα-Fc fusion protein eradicates tumors by macrophage and NK cell activation. Molecular Therapy Oncolytics, 23, 192–204. https://doi.org/10.1016/j.omto.2021.09.005
  • Catalán, R., Orozco-Morales, M., Hernández-Pedro, N. Y., Guijosa, A., Colín-González, A. L., Ávila-Moreno, F., & Arrieta, O. (2020). CD47-SIRPα axis as a biomarker and therapeutic target in cancer: Current perspectives and future challenges in nonsmall cell lung cancer. Journal of Immunology Research, 2020, 9435030. https://doi.org/10.1155/2020/9435030
  • Chen, K., Fu, T., Sun, W., Huang, Q., Zhang, P., Zhao, Z., Zhang, X., & Tan, W. (2019). DNA-supramolecule conjugates in theranostics. Theranostics, 9(11), 3262–3279. https://doi.org/10.7150/thno.31885
  • Chumakov Stepan Petrovich, K. Y. E. R., Lezhnin, Y. N., & Frolova, E. I. (2016). Aptamers specific to extracellular glycosylated domain of the human CD47 receptor. Russia patent.
  • Cui, X., Song, M., Liu, Y., Yuan, Y., Huang, Q., Cao, Y., & Lu, F. (2020). Identifying conformational changes of aptamer binding to theophylline: A combined biolayer interferometry, surface-enhanced Raman spectroscopy, and molecular dynamics study. Talanta, 217, 121073. https://doi.org/10.1016/j.talanta.2020.121073
  • Feng, R., Zhao, H., Xu, J., & Shen, C. (2020). CD47: The next checkpoint target for cancer immunotherapy. Critical Reviews in Oncology/Hematology, 152, 103014. https://doi.org/10.1016/j.critrevonc.2020.103014
  • Hatherley, D., Graham, S. C., Turner, J., Harlos, K., Stuart, D. I., & Barclay, A. N. (2008). Paired receptor specificity explained by structures of signal regulatory proteins alone and complexed with CD47. Molecular Cell, 31(2), 266–277. https://doi.org/10.1016/j.molcel.2008.05.026
  • Hayashi, T., Oshima, H., Mashima, T., Nagata, T., Katahira, M., & Kinoshita, M. (2014). Binding of an RNA aptamer and a partial peptide of a prion protein: Crucial importance of water entropy in molecular recognition. Nucleic Acids Research, 42(11), 6861–6875. https://doi.org/10.1093/nar/gku382
  • Henkelman, G., & Jónsson, H. (2000). Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points. The Journal of Chemical Physics, 113(22), 9978–9985. https://doi.org/10.1063/1.1323224
  • Henkelman, G., Uberuaga, B. P., & Jónsson, H. (2000). A climbing image nudged elastic band method for finding saddle points and minimum energy paths. The Journal of Chemical Physics, 113(22), 9901–9904. https://doi.org/10.1063/1.1329672
  • Herges, T., Schug, A., & Wenzel, W. 2004/01/01 (2004). Exploration of the free-energy surface of a three-helix peptide with stochastic optimization methods. International Journal of Quantum Chemistry, 99(5), 854–863. https://doi.org/10.1002/qua.20052
  • https://www.rcsb.org/.
  • Hu, Y., Zhao, T., Zou, L., Wang, X., & Zhang, Y. (2019). Molecular dynamics simulations of membrane properties affected by plasma ROS based on the GROMOS force field. Biophysical Chemistry, 253, 106214. https://doi.org/10.1016/j.bpc.2019.106214
  • Huang, B., Bai, Z., Ye, X., Zhou, C., Xie, X., Zhong, Y., Lin, K., & Ma, L. (2021). Structural analysis and binding sites of inhibitors targeting the CD47/SIRPα interaction in anticancer therapy. Computational and Structural Biotechnology Journal, 19, 5494–5503. https://doi.org/10.1016/j.csbj.2021.09.036
  • Kaur, S., Cicalese, K. V., Bannerjee, R., & Roberts, D. D. (2020). Preclinical and clinical development of therapeutic antibodies targeting functions of CD47 in the tumor microenvironment. Antibody Therapeutics, 3(3), 179–192. https://doi.org/10.1093/abt/tbaa017
  • Lehn, J.-M. (1988). Supramolecular chemistry—Scope and perspectives molecules, supermolecules, and molecular devices (Nobel lecture). Angewandte Chemie International Edition in English, 27(1), 89–112. https://doi.org/10.1002/anie.198800891
  • Lian, S., Xie, X., Lu, Y., & Jia, L. (2019). Checkpoint CD47 function on tumor metastasis and immune therapy. OncoTargets and Therapy, 12, 9105–9114. https://doi.org/10.2147/OTT.S220196
  • Macdonald, J., Henri, J., Goodman, L., Xiang, D., Duan, W., & Shigdar, S. (2017). Development of a bifunctional aptamer targeting the transferrin receptor and epithelial cell adhesion molecule (EpCAM) for the treatment of brain cancer metastases. ACS Chemical Neuroscience, 8(4), 777–784. https://doi.org/10.1021/acschemneuro.6b00369
  • Mohan, M., Pandya, V., & Anindya, R. (2018). Escherichia coli AlkB and single-stranded DNA binding protein SSB interaction explored by molecular dynamics simulation. Journal of Molecular Graphics & Modelling, 84, 29–35. https://doi.org/10.1016/j.jmgm.2018.05.007
  • Monticelli, L., Kandasamy, S. K., Periole, X., Larson, R. G., Tieleman, D. P., & Marrink, S.-J. (2008). The MARTINI coarse-grained force field: Extension to proteins. Journal of Chemical Theory and Computation, 4(5), 819–834. https://doi.org/10.1021/ct700324x
  • Nayeem, S. M., Sohail, E. M., Sudhir, G. P., & Reddy, M. S. (2021). Computational and theoretical exploration for clinical suitability of Remdesivir drug to SARS-CoV-2. European Journal of Pharmacology, 890, 173642. https://doi.org/10.1016/j.ejphar.2020.173642
  • Pang, Y.-P. (2015). At least 10% shorter C–H bonds in cryogenic protein crystal structures than in current AMBER forcefields. Biochemical and Biophysical Research Communications, 458(2), 352–355. https://doi.org/10.1016/j.bbrc.2015.01.115
  • Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF chimera—A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084
  • Plimpton, S. (1995). Fast parallel algorithms for short-range molecular dynamics. Journal of Computational Physics, 117(1), 1–19. https://doi.org/10.1006/jcph.1995.1039
  • Poma, A. B., Cieplak, M., & Theodorakis, P. E. (2017). Combining the MARTINI and structure-based coarse-grained approaches for the molecular dynamics studies of conformational transitions in proteins. Journal of Chemical Theory and Computation, 13(3), 1366–1374. https://doi.org/10.1021/acs.jctc.6b00986
  • Schürch, C. M., Forster, S., Brühl, F., Yang, S. H., Felley-Bosco, E., & Hewer, E. (2017). The "don’t eat me" signal CD47 is a novel diagnostic biomarker and potential therapeutic target for diffuse malignant mesothelioma. Oncoimmunology, 7(1), e1373235. https://doi.org/10.1080/2162402X.2017.1373235
  • Song, Y., Zhu, Z., An, Y., Zhang, W., Zhang, H., Liu, D., Yu, C., Duan, W., & Yang, C. J. (2013). Selection of DNA aptamers against epithelial cell adhesion molecule for cancer cell imaging and circulating tumor cell capture. Analytical Chemistry, 85(8), 4141–4149. https://doi.org/10.1021/ac400366b
  • Stukowski, A. (2010). Visualization and analysis of atomistic simulation data with OVITO–the Open Visualization Tool. Modelling and Simulation in Materials Science and Engineering, 18(1), 015012. https://doi.org/10.1088/0965-0393/18/1/015012
  • Su, C.-H., Chen, H.-L., Ju, S.-P., You, T.-D., Lin, Y.-S., & Tseng, T.-F. (2021). Exploring the most stable aptamer/target molecule complex by the stochastic tunnelling-basin hopping-discrete molecular dynamics method. Scientific Reports, 11(1), 11406. https://doi.org/10.1038/s41598-021-90907-y
  • Uusitalo, J. J., Ingólfsson, H. I., Akhshi, P., Tieleman, D. P., & Marrink, S. J. (2015). Martini coarse-grained force field: Extension to DNA. Journal of Chemical Theory and Computation, 11(8), 3932–3945. https://doi.org/10.1021/acs.jctc.5b00286
  • Varty, K., O’Brien, C., & Ignaszak, A. (2021). Breast cancer aptamers: current sensing targets, available aptamers, and their evaluation for clinical use in diagnostics. Cancers, 13(16), 3984. https://doi.org/10.3390/cancers13163984
  • Vonderheide, R. H. (2015). CD47 blockade as another immune checkpoint therapy for cancer. Nature Medicine, 21(10), 1122–1123. https://doi.org/10.1038/nm.3965
  • Yang, H.-W., Ju, S.-P., Cheng, C.-H., Chen, Y.-T., Lin, Y.-S., & Pang, S.-T. (2018). Aptasensor designed via the stochastic tunnelling-basin hopping method for biosensing of vascular endothelial growth factor. Biosensors & Bioelectronics, 119, 25–33. https://doi.org/10.1016/j.bios.2018.07.073
  • Yang, H. W., Ju, S. P., & Lin, Y. S. (2019). Predicting the most stable aptamer/target molecule complex configuration using a stochastic-tunnelling basin-hopping discrete molecular dynamics method: A novel global minimum search method for a biomolecule complex. Computational and Structural Biotechnology Journal, 17, 812–820. https://doi.org/10.1016/j.csbj.2019.06.021
  • Zeng, D., Sun, Q., Chen, A., Fan, J., Yang, X., Xu, L., Du, P., Qiu, W., Zhang, W., Wang, S., & Sun, Z. (2016). A fully human anti-CD47 blocking antibody with therapeutic potential for cancer. Oncotarget, 7(50), 83040–83050. https://doi.org/10.18632/oncotarget.13349
  • Zhang, W., Huang, Q., Xiao, W., Zhao, Y., Pi, J., Xu, H., Zhao, H., Xu, J., Evans, C. E., & Jin, H. (2020). Advances in anti-tumor treatments targeting the CD47/SIRPα axis. Frontiers in Immunology, 11, 18. [Online]. https://doi.org/10.3389/fimmu.2020.00018

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