Structural Unfolding of G-Quadruplexes: From Small Molecules to Antisense Strategies

Abstract

G-quadruplexes (G4s) are non-canonical nucleic acid secondary structures that have gathered significant interest in medicinal chemistry over the past two decades due to their unique structural features and potential roles in a variety of biological processes and disorders. Traditionally, research efforts have focused on stabilizing G4s, while in recent years, the attention has progressively shifted to G4 destabilization, unveiling new therapeutic perspectives. This review provides an in-depth overview of recent advances in the development of small molecules, starting with the controversial role of TMPyP4. Moreover, we described effective metal complexes in addition to G4-disrupting small molecules as well as good G4 stabilizing ligands that can destabilize G4s in response to external stimuli. Finally, we presented antisense strategies as a promising approach for destabilizing G4s, with a particular focus on 2'-OMe antisense oligonucleotide, peptide nucleic acid, and locked nucleic acid. Overall, this review emphasizes the importance of understanding G4 dynamics as well as ongoing efforts to develop selective G4-unfolding strategies that can modulate their biological function and therapeutic potential.

Keywords: G-clamp; G-quadruplex; antisense strategy; disrupting small molecules; locked nucleic acid; new therapeutic strategies.

Figure 1

Schematic representation of G-quadruplex structures. (A) Square-planar G-quartet; (B) backbone of the intramolecular G4 structures, common to every G4s, with loops and flanking regions differentiating structural elements; and (C) parallel-, antiparallel-, and hybrid-type topologies of G4 structures.

Figure 2

Chemical structures of TMPyP4; its positional isomers TMPyP2 and TMPyP3; its metal-complexes ZnTMPyP4, CuTMPyP4, or PtTMPyP4; and H₂TCPPSpm4 derivative.

Figure 3

Chemical structures of the Ru(II) complexes RuPDC3, RuS, and RuSe, and of NMM-Cisplatin combination, Eu 15-MC-5, and Tb 15-MC-5.

Figure 4

Chemical structures of the main small molecules capable of unfolding G-quadruplex structures. For the two rotamers ThT and TO the rotation is evidenced by blue arrows.

Figure 5

Chemical structures of the ligands that alter their affinity and unfolding capacity in response to G4’s changing experimental circumstances.

Figure 6

Chemical modifications of various ASOs, 2′-OMe, MOE, PMO, LNA, and PNA.

Figure 7

Schematic representation of the oligonucleotide-based strategy to disrupt G-quadruplex structures. The best-performing strategy lies in hybridizing the central loop and the two adjacent G-tracts on both sides. Blue lines represent G-tracts; red lines represent the central loop in the G4 structure. The complementary bases in the Anti-G4 ASO were represented with the same colors.

Figure 8

Schematic representation of invasion of TBA quadruplex by complementary 7-mer PNA (P1), and the effect of ionic strength on thermal denaturation pathway of TBA-P1 hetero duplex.

Figure 9

Schematic representation of PNA₂-DNA heteroduplex and heteroquadruplex formed by Myc19 DNA quadruplex and complementary or homologous 7-mer PNA.

Figure 10

Schematic representation of the mechanism htelo-fl unfolding with complementary 13-mer PNA.

Figure 11

Schematic representation of the comparison of the cations’ effects (NH₄⁺ versus K⁺) on the unfolding of cKit87up quadruplex in the presence of P2–P4 PNAs.

Figure 12

Schematic representation of the effect of the number of LNA modifications (LNA5 10 modifications, LNA2 5 modification, and control DNA) on the unfolding of a G-quadruplex structure formed by a 22-mer purine-rich sequence of NHE III of the c-MYC. The percentage values represent the amount of duplex formation, consistently with G4-unfolding.

Figure 13

Schematic representation of the unfolding of cKIT1 G4 by KIT_LNA3 by targeting the central guanine of each G-tract. The red tract is related to loop bases.