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CycloMolder software: building theoretical cyclodextrin derivatives models and evaluating their host:guest interactions

  • Marcelo Montenegro RabelloEmail author
  • Larissa Araújo Rolim
  • Pedro José Rolim Neto
  • Marcelo Zaldini Hernandes
Original Article
  • 14 Downloads

Abstract

This paper presents a software to build theoretical models of cyclodextrin derivatives and evaluate their host:guest interactions, using a graphical user interface in an intuitive way. This goal was outlined to facilitate the studies of molecular modeling, particularly from experimental groups with demands in this research field. The software (CycloMolder) consists of two modules: CycloGen and CycloDock. The first module builds theoretical models with more than one chemical structure to represent a cyclodextrin derivative. These structures are divided into configurations and conformations. The configurations can be homologous structures, with different molar substitution ratio, or just positional isomers. Conformers are generated from the built configurations. The second module performs the docking calculations between the host (cyclodextrins and/or their derivatives) and guest molecules, using the AutoDock Vina program, and displays the final results of the modeled inclusion complexes, including graphs showing the distribution energy and intermolecular interactions present in the host:guest complex.

Keywords

Cyclomolder Cyclodextrin Inclusion complex Molecular modeling Molecular docking 

Notes

Funding

This study was funded by the Foundation to Support Science and Technology in the State of Pernambuco, Brazil (Grant Number APQ-0278-4.03/16); and National Council for Scientific and Technological Development, Brazil (Grant Number 300070/2018-7).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

References

  1. 1.
    Rasheed, A.: Cyclodextrins as drug carrier molecule: a review. Sci. Pharm. 76, 567–598 (2008).  https://doi.org/10.3797/scipharm.0808-05 CrossRefGoogle Scholar
  2. 2.
    Saenger, W., Jacob, J., Gessler, K., Steiner, T., Hoffmann, D., Sanbe, H., Koizumi, K., Smith, S.M., Takaha, T.: Structures of the common cyclodextrins and their larger analoguesbeyond the doughnut. Chem. Rev. 98, 1787–1802 (1998).  https://doi.org/10.1021/cr9700181 CrossRefGoogle Scholar
  3. 3.
    Loftsson, T., Duchêne, D.: Cyclodextrins and their pharmaceutical applications. Int J Pharm. 329, 1–11 (2007).  https://doi.org/10.1016/j.ijpharm.2006.10.044 CrossRefGoogle Scholar
  4. 4.
    Wenz, G.: Cyclodextrins as building blocks for supramolecular structures and functional units. Angew. Chemie. Int. Ed. 33, 803–822 (1994).  https://doi.org/10.1002/anie.199408031 CrossRefGoogle Scholar
  5. 5.
    Seyedi, S.M., Sadeghian, H., Jabbari, A., Assadieskandar, A., Momeni, H.: Synthesis of new series of alpha-cyclodextrin esters as dopamine carrier molecule. Bioorg. Med. Chem. 19, 4307–4311 (2011).  https://doi.org/10.1016/j.bmc.2011.05.048 CrossRefGoogle Scholar
  6. 6.
    Miletic, T., Kyriakos, K., Graovac, A., Ibric, S.: Spray-dried voriconazole-cyclodextrin complexes: Solubility, dissolution rate and chemical stability. Carbohydr. Polym. 98, 122–131 (2013).  https://doi.org/10.1016/j.carbpol.2013.05.084 CrossRefGoogle Scholar
  7. 7.
    Bikádi, Z., Kurdi, R., Balogh, S., Szemán, J., Hazai, E.: Aggregation of cyclodextrins as an important factor to determine their complexation behavior. Chem. Biodivers. 3, 1266–1278 (2006).  https://doi.org/10.1002/cbdv.200690129 CrossRefGoogle Scholar
  8. 8.
    Illapakurthy, A.C., Sabnis, Y.A., Avery, B.A., Avery, M.A., Wyandt, C.M.: Interaction of artemisinin and its related compounds with hydroxypropyl-beta-cyclodextrin in solution state: experimental and molecular-modeling studies. J. Pharm. Sci. 92, 649–655 (2003).  https://doi.org/10.1002/jps.10319 CrossRefGoogle Scholar
  9. 9.
    Bandyopadhyay, M.L., Klein, G.S.: Molecular dynamics studies of the hexagonal mesophase of sodium dodecylsulphate in aqueous solution. Mol. Phys. 95, 377–384 (1998).  https://doi.org/10.1080/002689798167304 CrossRefGoogle Scholar
  10. 10.
    Aicart, E., Junquera, E.: Complex formation between purine derivatives and cyclodextrins: a fluorescence spectroscopy study. J. Incl. Phenom. 47, 161–165 (2003).  https://doi.org/10.1023/B:JIPH.0000011786.89533.0e CrossRefGoogle Scholar
  11. 11.
    Sapino, S., Trotta, M., Ermondi, G., Caron, G., Cavalli, R., Carlotti, M.E.: On the complexation of Trolox with methyl-β-cyclodextrin: characterization, molecular modelling and photostabilizing properties. J. Incl. Phenom. Macrocycl. Chem. 62, 179–186 (2008).  https://doi.org/10.1007/s10847-008-9454-0 CrossRefGoogle Scholar
  12. 12.
    Mura, P., Bettinetti, G., Melani, F., Manderioli, A.: Interaction between naproxen and chemically modified β-cyclodextrins in the liquid and solid state. Eur J Pharm Sci. 3, 347–355 (1995).  https://doi.org/10.1016/0928-0987(95)00025-X CrossRefGoogle Scholar
  13. 13.
    Liu, X.I.N., Lin, H., Thenmozhiyal, J.C., Chan, S.U.I.Y., Ho, P.C.: Inclusion of acitretin into cyclodextrins: phase solubility, photostability, and physicochemical characterization. J. Pharm. Sci. 92, 2449–2457 (2003)CrossRefGoogle Scholar
  14. 14.
    Treib, J., Baron, J.F., Grauer, M.T., Strauss, R.G.: An international view of hydroxyethyl starches. Intensive Care Med. 25, 258–268 (1999).  https://doi.org/10.1007/s001340050833 CrossRefGoogle Scholar
  15. 15.
    Hanwell, M.D., Curtis, D.E., Lonie, D.C., Vandermeersch, T., Zurek, E., Hutchison, G.R.: Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. J. Cheminform. 4, 17 (2012).  https://doi.org/10.1186/1758-2946-4-17 CrossRefGoogle Scholar
  16. 16.
    O’Boyle, N.M., Banck, M., James, C.A., Morley, C., Vandermeersch, T., Hutchison, G.R.: Open Babel: An open chemical toolbox. J. Cheminform. 3, 33 (2011).  https://doi.org/10.1186/1758-2946-3-33 CrossRefGoogle Scholar
  17. 17.
    Trott, O., Olson, A.J.: AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem. 31, 455–461 (2010).  https://doi.org/10.1002/jcc.21334 Google Scholar
  18. 18.
    Holtje, H.-D., Folkers, G.: Molecular Modeling: Basic Principles and Applications, pp. 9–64. Wiley-VCH, Weinheim (1996)CrossRefGoogle Scholar
  19. 19.
    Hestenes, M.R., Stiefel, E.: Methods of conjugate gradients for solving linear systems. J. Res. Natl. Bur. Stand. 49, 409–436 (1952)CrossRefGoogle Scholar
  20. 20.
    O’Boyle, N.M., Vandermeersch, T., Flynn, C.J., Maguire, A.R., Hutchison, G.R.: Confab—systematic generation of diverse low-energy conformers. J. Cheminform. 3, 8 (2011).  https://doi.org/10.1186/1758-2946-3-8 CrossRefGoogle Scholar
  21. 21.
    Durrant, J.D., McCammon, J.A.: BINANA: a novel algorithm for ligand-binding characterization. J. Mol. Graph. Model. 29, 888–893 (2011).  https://doi.org/10.1016/j.jmgm.2011.01.004 CrossRefGoogle Scholar
  22. 22.
    Xavier-Junior, F.H., Rabello, M.M., Hernandes, M.Z., Dias, M.E.S., Andrada, O.H.M.S., Bezerra, B.P., Ayala, A.P., Santos-Magalhães, N.S.: (2017) Supramolecular interactions between β-lapachone with cyclodextrins studied using isothermal titration calorimetry and molecular modeling. J. Mol. Recognit.  https://doi.org/10.1002/jmr.2646 Google Scholar

Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Central of Analysis of Drugs, Medicines and FoodFederal University of San Francisco ValleyPetrolinaBrazil
  2. 2.Department of Pharmaceutical SciencesFederal University of PernambucoRecifeBrazil

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