A more detailed picture of the interactions between virtual screening-derived hits and the DNA G-quadruplex: NMR, molecular modelling and ITC studies

publication · 6 years ago
by Luciana Marinelli, Ettore Novellino, Sandro Cosconati, Roberta Trotta, Stefano De Tito, Ilaria Lauri, Valeria La Pietra, Luigi Martino, Maria R. Conte, Luciano Mayol, Antonio Randazzo (Università degli Studi di Napoli Federico II, King’s College London)
The growing amount of literature about G-quadruplex DNA clearly demonstrates that such a structure is no longer viewed as just a biophysical strangeness but it is instead being considered as an important target for the treatment of various human disorders such as cancers or venous thrombosis. In this scenario, with the aim of finding brand new molecular scaffolds able to interact with the groove of the DNA quadruplex [d(TGGGGT)]4, we recently performed a successful structure-based virtual screening (VS) campaign. As a result, six molecules were found to be somehow groove binders. Herein, we report the results of novel NMR titration experiments of these VS-derived ligands with modified quadruplexes, namely [d(TGGBrGGT)]4 and [d(TGGGGBrT)]4. The novel NMR spectroscopy experiments combined with molecular modelling studies, allow for a more detailed picture of the interaction between each binder and the quadruplex DNA. Noteworthy, isothermal titration calorimetry (ITC) measurements on the above-mentioned compounds revealed that 2, 4, and 6 besides their relatively small dimensions bind the DNA quadruplex [d(TGGGGT)]4 with higher affinity than distamycin A, to the best of our knowledge, the most potent groove binder identified thus far.
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