The CycloMolder software consists of two modules: CycloGen and CycloDock. The first module builds theoretical models 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.
As an example a sulfobutyl ether β-CD (SBE-β-CD) model was calculated to evaluate the binding energy of the complex formed with β-Lapachone (β-Lap) molecule. This model consist of 40 configurations with 25 conformers for each configuration. For each SBE unit added during the construction of the structures, the following probability rates of the substitutional positions were considered: 70% for OH (6), 20% for OH (2) and 10% for OH (3), for substitutional positions.
Evaluating the binding energy from all 1000 docking calculations, it was possible to observe the binding energy distribution among the configurations. This approach also makes it possible to identify different orientations regarding the position of the guest molecule (β-Lap) included in the host molecule (SBE-β-CD).
Montenegro Rabello, M., Rolim, L. A., Rolim Neto, P. J., & Hernandes, M. Z. (2019). CycloMolder software: building theoretical cyclodextrin derivatives models and evaluating their host:guest interactions. Journal of Inclusion Phenomena and Macrocyclic Chemistry. doi:10.1007/s10847-019-00880-3 . https://doi.org/10.1007/s10847-019-00880-3