Host-Guest Systems for the SAMPL9 Blinded Prediction Challenge: Phenothiazine as a Privileged Scaffold for Binding to Cyclodextrins

14 December 2023, Version 3
This content is a preprint and has not undergone peer review at the time of posting.


Model systems are widely used in biology and chemistry to gain insight into more complex systems. In the field of computational chemistry, researchers use host-guest systems, relatively simple exemplars of noncovalent binding, to train and test the computational methods used in drug discovery. Indeed, host-guest systems have been developed to support the community-wide blinded SAMPL prediction challenges for over a decade. While seeking new host-guest systems for the recent SAMPL9 binding prediction challenge, which is the focus of the present PCCP Themed Collection, we identified phenothiazine as a privileged scaffold for guests of β cyclodextrin (βCD) and its derivatives. Building on this observation, we used calorimetry and NMR spectroscopy to characterize the noncovalent association of native βCD and three methylated derivatives of βCD with five phenothiazine drugs. The strongest association observed, that of thioridazine and one of the methyl derivatives, exceeds the well-known high affinity of rimantidine with βCD. Intriguingly, however, methylation of βCD at the 3 position abolished detectible binding for all of the drugs studied. The dataset has a clear pattern of entropy-enthalpy compensation. The NMR data show that all of the drugs position at least one aromatic proton at the secondary face of the CD, and most also show evidence of deep penetration of the binding site. The results of this study were used in the SAMPL9 blinded binding affinity-prediction challenge, which are detailed in accompanying papers of the present Themed Collection. These data also open the phenothiazines and, potentially, chemically similar drugs, such as the tricyclic antidepressants, as relatively potent binders of βCD, setting the stage for future SAMPL challenge datasets and for possible applications as drug reversal agents.


free energy

Supplementary materials

Details of the Experimental Data
1. SAMPL9-Andrade-Chen-Gilson-ITC-complexes.xlsx: Results of analysis of ITC data for triplicate runs for each host-guest system, Host and guest SMILES strings, and binding thermodynamic summary. 2. compressed file with numerical data from the ITC runs. 3. SAMPL9-Andrade-Chen-Gilson-Enthalpograms.pptx: Images of combined enthalpogram for each cyclodextrin-phenothiazine pair. 4. SAMPL9-Andrade-Chen-Gilson-2DNMR-BCD.pptx: 2D NMR spectra of β-cyclodextrin and phenothiazine complexes 5. SAMPL9-Andrade-Chen-Gilson-2DNMR-H6MBCD.pptx: 2D NMR Heptakis-(2,6-di-methyl)-β-cyclodextrin and phenothiazine complexes 6. SAMPL9-Andrade-Chen-Gilson-2DNMR-H26DMBCD.pptx: 2D NMR Heptakis-(2,6-di-methyl)-β-cyclodextrin and phenothiazine complexes
1D 1H NMR spectra of the host-guest complexes


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