Combining Electrospray Mass Spectrometry (ESI-MS) and Computational Techniques in the Assessment of G-Quadruplex Ligands: A Hybrid Approach to Optimize Hit Discovery

Abstract

Guanine-rich sequences forming G-quadruplexes (GQs) are present in several genomes, ranging from viral to human. Given their peculiar localization, the induction of GQ formation or GQ stabilization with small molecules represents a strategy for interfering with crucial biological functions. Investigating the recognition event at the molecular level, with the aim of fully understanding the triggered pharmacological effects, is challenging. Native electrospray ionization mass spectrometry (ESI-MS) is being optimized to study these noncovalent assemblies. Quantitative parameters retrieved from ESI-MS studies, such as binding affinity, the equilibrium binding constant, and sequence selectivity, will be overviewed. Computational experiments supporting the ESI-MS investigation and boosting its efficiency in the search for GQ ligands will also be discussed with practical examples. The combination of ESI-MS and in silico techniques in a hybrid high-throughput-screening workflow represents a valuable tool for the medicinal chemist, providing data on the quantitative and structural aspects of ligand–GQ interactions.

An Updated Overview on the Role of Small Molecules and Natural Compounds in the “Young Science” of Rejuvenation

“…Mammalian somatic cells in tissue cultures divide symmetrically, and they die after a limited number of divisions (50)(51)(52)(53)(54)(55)(56)(57)(58)(59)(60); this is usually referred to as the "Hayflick limit". This is connected to the progressive shortening of telomeres and DNA sequences at the ends of chromosomes, which occurs as a result of successive divisions.…”

“…G4-forming sequences are not randomly distributed throughout the genome, as they are mainly located in telomeres and oncogenes [49]. They represent attractive targets for developing novel antiproliferative and anti-infective agents of natural and synthetic origin [50][51][52]. In general, the stabilization of the G4 structures using small molecules can regulate transcription and translation, either via upregulation or downregulation, depending on the target gene [53].…”

Binding of Quercetin Derivatives toward G-Tetrads as Studied by the Survival Yield Method

“…Recently, there is growing interest to design molecules that are able to interact with G-quadruplexes, which may be of importance toward cancer therapy , and antiviral therapy or to design G-quadruplex probes . It gives motivation to develop computational and physicochemical methods for searching for effective G-quadruplex ligands. − The ligands can be both synthetic or of natural origin. , Among the latter ligands, quercetin has attracted notable attention . Quercetin binding to G-quadruplexes has been studied by spectroscopic methods (e.g., NMR, circular dichroism), calorimetric titration, molecular docking, and density functional theory. − On the other hand, quercetin conjugates binding to G-quadruplexes has not been widely studied.…”

“… 16 It gives motivation to develop computational and physicochemical methods for searching for effective G-quadruplex ligands. 17 − 19 The ligands can be both synthetic or of natural origin. 20 , 21 Among the latter ligands, quercetin has attracted notable attention.…”