Skip to main content
SpringerLink
Log in

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

  • Original Article
  • Published:
Journal of Inclusion Phenomena and Macrocyclic Chemistry Aims and scope Submit manuscript

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  1. Rasheed, A.: Cyclodextrins as drug carrier molecule: a review. Sci. Pharm. 76, 567–598 (2008). https://doi.org/10.3797/scipharm.0808-05

    Article  CAS  Google Scholar 

  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

    Article  CAS  PubMed  Google Scholar 

  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

    Article  CAS  PubMed  Google Scholar 

  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

    Article  Google Scholar 

  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

    Article  CAS  PubMed  Google Scholar 

  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

    Article  CAS  PubMed  Google Scholar 

  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

    Article  PubMed  Google Scholar 

  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

    Article  CAS  PubMed  Google Scholar 

  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

    Article  CAS  Google Scholar 

  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

    Article  CAS  Google Scholar 

  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

    Article  CAS  Google Scholar 

  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

    Article  CAS  Google Scholar 

  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)

    Article  CAS  PubMed  Google Scholar 

  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

    Article  CAS  PubMed  Google Scholar 

  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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Holtje, H.-D., Folkers, G.: Molecular Modeling: Basic Principles and Applications, pp. 9–64. Wiley-VCH, Weinheim (1996)

    Book  Google Scholar 

  19. Hestenes, M.R., Stiefel, E.: Methods of conjugate gradients for solving linear systems. J. Res. Natl. Bur. Stand. 49, 409–436 (1952)

    Article  Google Scholar 

  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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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

    Article  PubMed  Google Scholar 

Download references

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).

Author information

Authors and Affiliations

  1. Central of Analysis of Drugs, Medicines and Food, Federal University of San Francisco Valley, Petrolina, PE, 56304-205, Brazil

    Marcelo Montenegro Rabello & Larissa Araújo Rolim

  2. Department of Pharmaceutical Sciences, Federal University of Pernambuco, Recife, PE, 50740-521, Brazil

    Pedro José Rolim Neto & Marcelo Zaldini Hernandes

Authors
  1. Marcelo Montenegro Rabello
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Larissa Araújo Rolim
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Pedro José Rolim Neto
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Marcelo Zaldini Hernandes
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Marcelo Montenegro Rabello.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Montenegro Rabello, M., Rolim, L.A., Rolim Neto, P.J. et al. CycloMolder software: building theoretical cyclodextrin derivatives models and evaluating their host:guest interactions. J Incl Phenom Macrocycl Chem 93, 301–308 (2019). https://doi.org/10.1007/s10847-019-00880-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10847-019-00880-3

Keywords

Search

Navigation