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Research Articles

Affinity enhancement of nanobody binding to EGFR: in silico site-directed mutagenesis and molecular dynamics simulation approaches

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Pages 1710-1728 | Received 05 Apr 2016, Accepted 17 May 2016, Published online: 03 Oct 2016

References

  • Bai, Q., Shen, Y., Jin, N., Liu, H., & Yao, X. (2014). Molecular modeling study on the dynamical structural features of human smoothened receptor and binding mechanism of antagonist LY2940680 by metadynamics simulation and free energy calculation. Biochimica et Biophysica Acta (BBA) – General Subjects, 1840, 2128–2138. doi:10.1016/j.bbagen.2014.03.010
  • Camacho, C. J., & Zhang, C. (2005). FastContact: Rapid estimate of contact and binding free energies. Bioinformatics, 21, 2534–2536. doi:10.1093/bioinformatics/bti322
  • Chakravarty, R., Goel, S., & Cai, W. (2014). Nanobody: The “magic bullet” for molecular imaging? Theranostics, 4, 386–398. doi:10.7150/thno.8006
  • De Meyer, T., Muyldermans, S., & Depicker, A. (2014). Nanobody-based products as research and diagnostic tools. Trends in Biotechnology, 32, 263–270. doi:10.1016/j.tibtech.2014.03.001
  • Ding, L., Tian, C., Feng, S., Fida, G., Zhang, C., Ma, Y., … Gu, Y. (2015). Small sized EGFR1 and HER2 specific bifunctional antibody for targeted cancer therapy. Theranostics, 5, 378–398. doi:10.7150/thno.10084
  • Downward, J., Yarden, Y., Mayes, E., Scrace, G., Totty, N., Stockwell, P., … Waterfield, M. (1984). Close similarity of epidermal growth factor receptor and v-erb-B oncogene protein sequences. Nature, 307, 521–527. doi:10.1038/307521a0
  • Gainkam, L. O. T., Huang, L., Caveliers, V., Keyaerts, M., Hernot, S., Vaneycken, I., … Lahoutte, T. (2008). Comparison of the biodistribution and tumor targeting of two 99mTc-labeled anti-EGFR nanobodies in mice, using pinhole SPECT/micro-CT. Journal of Nuclear Medicine, 49, 788–795. doi:10.2967/jnumed.107.048538
  • Garrett, T. P., McKern, N. M., Lou, M., Elleman, T. C., Adams, T. E., Lovrecz, G. O., … Hoyne, P. A. (2002). Crystal structure of a truncated epidermal growth factor receptor extracellular domain bound to transforming growth factor α. Cell, 110, 763–773.10.1016/S0092-8674(02)00940-6
  • Ghaffari, M. A., Zeinali, M., Barzegari Asadabadi, E., Jamalan, M., & Jahandideh, S. (2014). Affinity enhancement of HER2-binding Z (HER2: 342) affibody via rational design approach: A molecular dynamics study. Journal of Biomolecular Structure and Dynamics, 32, 1919–1928. doi:10.1080/07391102.2013.842499
  • Gschwind, A., Fischer, O. M., & Ullrich, A. (2004). The discovery of receptor tyrosine kinases: Targets for cancer therapy. Nature Reviews Cancer, 4, 361–370. doi:10.1038/nrc1360
  • Hamers-Casterman, C., Atarhouch, T., Muyldermans, S., Robinson, G., Hamers, C., Songa, E. B., … Hamers, R. (1993). Naturally occurring antibodies devoid of light chains. Nature, ( 363), 446–448.10.1038/363446a0
  • Jura, N., Endres, N. F., Engel, K., Deindl, S., Das, R., Lamers, M. H., … Kuriyan, J. (2009). Mechanism for activation of the EGF receptor catalytic domain by the juxtamembrane segment. Cell, 137, 1293–1307. doi:10.1016/j.cell.2009.04.025
  • Keränen, H., Åqvist, J., & Gutiérrez-de-Terán, H. (2015). Free energy calculations of A 2A adenosine receptor mutation effects on agonist binding. Chemical Communications, 51, 3522–3525. doi:10.1039/c4cc09517 k
  • Kubala, M. H., Kovtun, O., Alexandrov, K., & Collins, B. M. (2010). Structural and thermodynamic analysis of the GFP: GFP-nanobody complex. Protein Science, 19, 2389–2401. doi:10.1002/pro.519
  • Kumar, S., Rosenberg, J. M., Bouzida, D., Swendsen, R. H., & Kollman, P. A. (1995). Multidimensional free-energy calculations using the weighted histogram analysis method. Journal of Computational Chemistry, 16, 1339–1350. doi:10.1002/jcc.540161104
  • Lemkul, J. A., & Bevan, D. R. (2010). Assessing the stability of Alzheimer’s amyloid protofibrils using molecular dynamics. The Journal of Physical Chemistry B, 114, 1652–1660. doi:10.1021/jp9110794
  • Lin, M.-H., Chang, C. A., & Fischer, W. B. (2015). Estimating binding free energy of a putative growth factors EGF–VEGF complex – A computational bioanalytical study. Journal of Biomolecular Structure and Dynamics, 34, 1717–1724. doi: 10.1080/07391102.2015.1090342
  • Lippow, S. M., Wittrup, K. D., & Tidor, B. (2007). Computational design of antibody-affinity improvement beyond in vivo maturation. Nature Biotechnology, 25, 1171–1176. doi:10.1038/nbt1336
  • Marzinek, J. K., Bond, P. J., Lian, G., Zhao, Y., Han, L., Noro, M. G., … Mantalaris, A. (2014). Free energy predictions of ligand binding to an α-helix using steered molecular dynamics and umbrella sampling simulations. Journal of Chemical Information and Modeling, 54, 2093–2104. doi:10.1021/ci500164q
  • Niu, X., Wang, X., Wang, H., Gao, X., Wang, Y., & Wang, S. (2013). Insights into the specific binding site of adenosine to the Stx2, the protein toxin from Escherichia coli O157: H7 using molecular dynamics simulations and free energy calculations. Molecular Simulation, 39, 199–205. doi:10.1080/08927022.2012.713483
  • Ogiso, H., Ishitani, R., Nureki, O., Fukai, S., Yamanaka, M., Kim, J.-H., … Shirouzu, M. (2002). Crystal structure of the complex of human epidermal growth factor and receptor extracellular domains. Cell, 110, 775–787.10.1016/S0092-8674(02)00963-7
  • Oliveira, S., Schiffelers, R. M., van der Veeken, J., van der Meel, R., Vongpromek, R., … van Bergen En Henegouwen, P. M., … Roovers, R. C. (2010). Downregulation of EGFR by a novel multivalent nanobody-liposome platform. Journal of Controlled Release, 145, 165–175. doi:10.1016/j.jconrel.2010.03.020
  • Pardon, E., Laeremans, T., Triest, S., Rasmussen, S. G., Wohlkönig, A., Ruf, A., … Steyaert, J. (2014). A general protocol for the generation of nanobodies for structural biology. Nature Protocols, 9, 674–693. doi:10.1038/nprot.2014.039
  • Patey, G., & Valleau, J. (1973). The free energy of spheres with dipoles: Monte Carlo with multistage sampling. Chemical Physics Letters, 21, 297–300. doi:10.1016/0009-2614(73)80139-3
  • Planesas, J. M., Pérez-Nueno, V. I., Borrell, J. I., & Teixidó, J. (2015). Studying the binding interactions of allosteric agonists and antagonists of the CXCR4 receptor. Journal of Molecular Graphics and Modelling, 60(1), 1–14. doi:10.1016/j.jmgm.2015.05.004
  • Priya, P., Maity, A., Majumdar, S., & Ghosh Dastidar, S. G. (2015). Interactions between Bcl-xl and its inhibitors: Insights into ligand design from molecular dynamics simulation. Journal of Molecular Graphics and Modelling, 59(1), 1–13. doi:10.1016/j.jmgm.2015.02.005
  • Rahbarizadeh, F., Rasaee, M. J., Forouzandeh, M., & Allameh, A.-A. (2006). Over expression of anti-MUC1 single-domain antibody fragments in the yeast pichia pastoris. Molecular Immunology, 43, 426–435.10.1016/j.molimm.2005.03.003
  • Rahbarizadeh, F., Rasaee, M., Forouzandeh Moghadam, M., Allameh, A., & Sadroddiny, E. (2004). Production of novel recombinant single-domain antibodies against tandem repeat region of MUC1 mucin. Hybridoma and Hybridomics, 23, 151–159.10.1089/1536859041224334
  • Roovers, R. C., Vosjan, M. J., Laeremans, T., el Khoulati, R., de Bruin, R. C., Ferguson, K. M., … van Bergen en Henegouwen, P. M. (2011). A biparatopic anti-EGFR nanobody efficiently inhibits solid tumour growth. International Journal of Cancer, 129, 2013–2024. doi:10.1002/ijc.26145
  • Ruan, Z., & Kannan, N. (2015). 57 Activation mechanism of R776H mutation in epidermal growth factor receptor (EGFR). Journal of Biomolecular Structure and Dynamics, 33(Suppl 1), 38–39. doi:10.1080/07391102.2015.1032673
  • Rungnim, C., Rungrotmongkol, T., Kungwan, N., & Hannongbua, S. (2016). Protein–protein interactions between SWCNT/chitosan/EGF and EGF receptor: A model of drug delivery system. Journal of Biomolecular Structure and Dynamics, 1–11. doi: 10.1080/07391102.2015.1095114
  • Schmitz, K. R., Bagchi, A., Roovers, R. C., van Bergen En Henegouwen, P. M., & Ferguson, K. M. (2013). Structural evaluation of EGFR inhibition mechanisms for nanobodies/VHH domains. Structure, 21, 1214–1224. doi:10.1016/j.str.2013.05.008
  • Stamos, J., Sliwkowski, M. X., & Eigenbrot, C. (2002). Structure of the epidermal growth factor receptor kinase domain alone and in complex with a 4-anilinoquinazoline inhibitor. Journal of Biological Chemistry, 277, 46265–46272. doi:10.1074/jbc.m207135200
  • Torrie, G. M., & Valleau, J. P. (1977). Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling. Journal of Computational Physics, 23, 187–199. doi:10.1016/0021-9991(77)90121-8
  • Ullrich, A., & Schlessinger, J. (1990). Signal transduction by receptors with tyrosine kinase activity. Cell, 61, 203–212.10.1016/0092-8674(90)90801-K
  • Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26, 1701–1718. doi:10.1002/jcc.20291
  • van Dongen, G. A., & Vosjan, M. J. (2010). Immuno-positron emission tomography: Shedding light on clinical antibody therapy. Cancer biotherapy & radiopharmaceuticals, 25, 375–385. doi:10.1089/cbr.2010.0812
  • Virnau, P., & Müller, M. (2004). Calculation of free energy through successive umbrella sampling. The Journal of Chemical Physics, 120, 10925–10930. doi:10.1063/1.1739216
  • Vosjan, M. J., Perk, L. R., Roovers, R. C., Visser, G. W., Stigter-van Walsum, M., van Bergen En Henegouwen, P. M., … van Dongen, G. A. (2011). Facile labelling of an anti-epidermal growth factor receptor nanobody with 68 Ga via a novel bifunctional desferal chelate for immuno-PET. European Journal of Nuclear Medicine and Molecular Imaging, 38, 753–763. doi:10.1007/s00259-010-1700-1
  • Wang, Y.-T., & Chuang, L.-Y. (2015). Insight into the modified Ibalizumab–human CD4 receptor interactions: Using a computational binding free energy approach. Journal of Computer-Aided Molecular Design, 29, 69–78. doi:10.1007/s10822-014-9805-4
  • Webb, B., & Sali, A. (2014). Comparative protein structure modeling using modeller. Current protocols in bioinformatics, 1, 5–6. doi:10.1002/0471250953.bi0506s47
  • Wu, X., Wan, S., Wang, G., Jin, H., Li, Z., Tian, Y., … Zhang, J. (2015). Molecular dynamics simulation and free energy calculation studies of kinase inhibitors binding to active and inactive conformations of VEGFR-2. Journal of Molecular Graphics and Modelling, 56, 103–112. doi:10.1016/j.jmgm.2014.12.006
  • Yang, M., Yang, L., Gao, Y., & Hu, H. (2014). Combine umbrella sampling with integrated tempering method for efficient and accurate calculation of free energy changes of complex energy surface. The Journal of Chemical Physics, 141, 044108. doi:10.1063/1.4887340
  • Zhao, Z.-B., Liu, Y., & Yao, Y. (2014). Computational determination of binding structures and free energies of glucose 6-phosphate dehydrogenase with novel steroid inhibitors. Journal of Molecular Graphics and Modelling, 51, 168–172. doi:10.1016/j.jmgm.2014.05.009
  • Zhao, F.-L., Yang, G.-H., Xiang, S., Gao, D.-D., & Zeng, C. (2016). Insilico analysis of the effect of mutation on epidermal growth factor receptor in non-small-cell-lung-carcinoma: From mutational analysis to drug designing. Journal of Biomolecular Structure and Dynamics, 1–26. doi: 10.1080/07391102.2016.1146165

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