Spiropyran Meets Guanine Quadruplexes: Isomerization Mechanism and DNA Binding Modes of Quinolizidine‐Substituted Spiropyran Probes

The recent delivery of a fluorescent quinolizidine‐substituted spiropyran, which is able to switch in vivo and bind to guanine quadruplexes (G4) at physiological pH values, urged us to elucidate its molecular switching and binding mechanism. Combining multiscale dynamical studies and accurate quantum chemical calculations, we show that, both in water and in the G4 environment, the switching of the spiropyran ring is not promoted by an initial protonation event—as expected by the effect of low pH solutions—but that the deprotonated merocyanine form is an intermediate of the reaction leading to the protonated open species. Additionally, we investigate the binding of both deprotonated and protonated open forms of merocyanine to c‐MYC G4s. Both species bind to G4s albeit with different hydrogen‐bond patterns and provide distinct rotamers around the exocyclic double bond of the merocyanine forms. Altogether, our study sheds light on the pharmacophoric points for the binding of these probes to DNA, and thereby, contributes to future developments of new G4 binders of the remarkable family of quinolizidine‐substituted spiropyrans. Protonate me, if you can: Multiscale calculations show that the opening of the fluorescent quinolizidine‐substituted spiropyran is not proton‐assisted and that the deprotonated merocyanine open form is an intermediate, both in solution and in guanine quadruplexes.