3D-QSAR for binding constants of β-cyclodextrin host-guest complexes by utilising spectrophores as molecular descriptors.

The increasing use of cyclodextrins (CDs) as host-molecules for host-guest complexes and their remediation application in environmental science requires to establish easily accessible models of "quantitative structure-activity relationships" (QSARs) to predict the binding constants. A new open-source molecular descriptor, so called spectrophores, was utilised to build 3D-QSAR models which have R2 of 0.95 and RMSE of 0.20.

[1]  Erhan Zor,et al.  Discriminative sensing of DOPA enantiomers by cyclodextrin anchored graphene nanohybrids. , 2017, Analytica chimica acta.

[2]  Jahan B. Ghasemi,et al.  QSPR approaches to elucidate the stability constants between β-cyclodextrin and some organic compounds: Docking based 3D conformer , 2016 .

[3]  William R. Dichtel,et al.  Rapid removal of organic micropollutants from water by a porous β-cyclodextrin polymer , 2015, Nature.

[4]  Rafaela Gladysz,et al.  Spectrophores as one-dimensional descriptors calculated from three-dimensional atomic properties: applications ranging from scaffold hopping to multi-target virtual screening , 2018, Journal of Cheminformatics.

[5]  Chris Morley,et al.  Open Babel: An open chemical toolbox , 2011, J. Cheminformatics.

[6]  Jie Xu,et al.  Quantitative structure–property relationship study of β-cyclodextrin complexation free energies of organic compounds , 2015 .

[7]  M. Wszelaka-Rylik,et al.  Isothermal titration calorimetry (ITC) study of natural cyclodextrins inclusion complexes with tropane alkaloids , 2015, Journal of Thermal Analysis and Calorimetry.

[8]  T. Mano,et al.  Development of machine learning models of β-cyclodextrin and sulfobutylether-β-cyclodextrin complexation free energies. , 2011, International journal of pharmaceutics.

[9]  T. Halgren.  Merck molecular force field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions , 1996 .

[10]  Â. Denadai,et al.  Structural and thermodynamic investigation of pentoxifylline-cyclodextrin inclusion complex , 2017 .

[11]  Thomas A. Halgren,et al.  Merck molecular force field. IV. conformational energies and geometries for MMFF94 , 1996 .

[12]  V. Solov'ev,et al.  3D molecular fragment descriptors for structure–property modeling: predicting the free energies for the complexation between antipodal guests and β-cyclodextrins , 2017, Journal of Inclusion Phenomena and Macrocyclic Chemistry.

[13]  Gaël Varoquaux,et al.  Scikit-learn: Machine Learning in Python , 2011, J. Mach. Learn. Res..

[14]  Y. Inoue,et al.  Complexation Thermodynamics of Cyclodextrins. , 1998, Chemical reviews.

[15]  Thomas A. Halgren,et al.  Merck molecular force field. III. Molecular geometries and vibrational frequencies for MMFF94 , 1996, J. Comput. Chem..

[16]  Evan Bolton,et al.  PubChem 2019 update: improved access to chemical data , 2018, Nucleic Acids Res..

[17]  Andrew G. Leach,et al.  Binding affinities of host-guest, protein-ligand, and protein-transition-state complexes. , 2003, Angewandte Chemie.

[18]  L. Wilson,et al.  Nano-Sized Cyclodextrin-Based Molecularly Imprinted Polymer Adsorbents for Perfluorinated Compounds—A Mini-Review , 2015, Nanomaterials.

[19]  Jinhua Chen,et al.  Recent advances for cyclodextrin-based materials in electrochemical sensing , 2016 .

[20]  Takahiro Suzuki,et al.  A Nonlinear Group Contribution Method for Predicting the Free Energies of Inclusion Complexation of Organic Molecules with - and -Cyclodextrins , 2001, J. Chem. Inf. Comput. Sci..

[21]  M. Melle‐Franco,et al.  Microencapsulation of herbicide MCPA with native β-cyclodextrin and its methyl and hydroxypropyl derivatives: An experimental and theoretical investigation , 2014 .

[22]  Ruibin Guo,et al.  Advances in the use of functional composites of β-cyclodextrin in electrochemical sensors , 2018, Microchimica Acta.

[23]  Kanak Roy,et al.  Study to explore the mechanism to form inclusion complexes of β-cyclodextrin with vitamin molecules , 2016, Scientific Reports.

[24]  Feifei Yang,et al.  Development of QSAR model for predicting the inclusion constants of organic chemicals with α-cyclodextrin , 2018, Environmental Science and Pollution Research.

[25]  T. Halgren.  Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94 , 1996, J. Comput. Chem..

[26]  P. Corvini,et al.  A cyclodextrin-based polymer for sensing diclofenac in water. , 2015, Journal of hazardous materials.

[27]  S. Endo,et al.  3D-QSAR predictions for α-cyclodextrin binding constants using quantum mechanically based descriptors. , 2017, Chemosphere.

[28]  Alexander Tropsha,et al.  Best Practices for QSAR Model Development, Validation, and Exploitation , 2010, Molecular informatics.

[29]  Chris Morley,et al.  Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit , 2008, Chemistry Central journal.

[30]  Jahan B. Ghasemi,et al.  Computer‐aided drug design to explore cyclodextrin therapeutics and biomedical applications , 2017, Chemical biology & drug design.

[31]  Jahan B. Ghasemi,et al.  3D-QSAR and docking studies of the stability constants of different guest molecules with beta-cyclodextrin , 2014, Journal of Inclusion Phenomena and Macrocyclic Chemistry.

[32]  Yong Chen,et al.  Molecular binding thermodynamics of spherical guests by β-cyclodextrins bearing aromatic substituents , 2014 .