Probing the nucleobase-specific binding interaction of hydroxychloroquine sulfate with RNA and subsequent sequestration by a water-soluble molecular basket

Abstract

A thorough understanding of the binding interactions of small molecules with genetic materials of the cell (DNA/RNA) has a persistent importance in pharmaceutical industries for the development of new drugs for treating various life-threatening ailments. Hydroxychloroquine sulfate (HCQS), an antimalarial drug, was potentially used for clinical trials with the hope of treating patients suffering from SARS-CoV-2 during the COVID-19 pandemic. Herein, we have extensively delineated the binding interactions of HCQS with RNA under physiological conditions using multi-spectroscopic and calorimetric approaches. Our results demonstrated that HCQS binds to RNA through the groove-binding mode in uridine- and cytidine-rich regions. The mode of binding was meticulously characterized by fluorescence quenching studies and circular dichroism spectroscopy, well complemented by other experiments. Our results obtained from isothermal titration calorimetry reveal the phenomenon of the release of bound water molecules when HCQS binds at the groove position of RNA, the process being entropically driven. Furthermore, we have employed the concept of host–guest chemistry for the sequestration of RNA-bound HCQS using a water-soluble, non-toxic, 4-sulfocalix[4]arene as a basket-type macrocyclic host. This investigation may be conducive to the development of safe RNA-based therapeutics like RNA-based vaccines that comprise small molecule–RNA interactions.