G-quadruplex DNA: a novel target for drug design

Abstract

G-quadruplex (G4) DNA is a type of quadruple helix structure formed by a continuous guanine-rich DNA sequence. Emerging evidence in recent years authenticated that G4 DNA structures exist both in cell-free and cellular systems, and function in different diseases, especially in various cancers, aging, neurological diseases, and have been considered novel promising targets for drug design. In this review, we summarize the detection method and the structure of G4, highlighting some non-canonical G4 DNA structures, such as G4 with a bulge, a vacancy, or a hairpin. Subsequently, the functions of G4 DNA in physiological processes are discussed, especially their regulation of DNA replication, transcription of disease-related genes (c-MYC, BCL-2, KRAS, c-KIT et al.), telomere maintenance, and epigenetic regulation. Typical G4 ligands that target promoters and telomeres for drug design are also reviewed, including ellipticine derivatives, quinoxaline analogs, telomestatin analogs, berberine derivatives, and CX-5461, which is currently in advanced phase I/II clinical trials for patients with hematologic cancer and BRCA1/2-deficient tumors. Furthermore, since the long-term stable existence of G4 DNA structures could result in genomic instability, we summarized the G4 unfolding mechanisms emerged recently by multiple G4-specific DNA helicases, such as Pif1, RecQ family helicases, FANCJ, and DHX36. This review aims to present a general overview of the field of G-quadruplex DNA that has progressed in recent years and provides potential strategies for drug design and disease treatment.

Keywords: Aging; Cancer; DNA replication; Epigenetic; G-quadruplex; G4 ligand; Helicase; Telomere.

Fig. 1

Structures and topologies of G-quadruplex DNA. A The chemical structure of the G-quartet. The G-quartet is formed by four guanines and is stabilized via Hoogsteen hydrogen bonding in the presence of a central cation. B, C Representative topologies of intermolecular G-quadruplex structures. D–F Schematic representation of canonical intramolecular G-quadruplex structures. According to the orientation of the G4 sequences, these can be divided into parallel, antiparallel, and hybrid G4 structures. G–I Schematic representation of non-canonical intramolecular G-quadruplex structures

Fig. 2

The biological function of G-quadruplex DNA in DNA replication, transcription, and telomere maintenance. A G4 can initiate DNA replication via the recruitment of replication initiation factors, such as the origin recognition complex, treslin-MTBP complex, and Rif1. B G4 can stall DNA polymerase during the DNA replication process, causing DNA replication disorder and genome instability. The replication of G4 can be resolved through the participation of G4-specific helicases such as Pif1, FANCJ, BLM and WRN, and TLS polymerases such as Rev1, Pol κ, Pol η, and Primpol. C G4 on the template strand can directly impede RNA polymerase during the transcription process. D G4 sequences on the non-template strand can form hybrid G4 with the newly synthesized RNA, inducing transcription termination. E The formation of G4 upstream of the TSS will usually inhibit transcription. G4 can also recruit certain transcription factors, which may either facilitate or restrain transcription. F A string of G-quadruplexes in the telomeric 3′-overhang involves telomere metabolism and telomere integrity maintenance. The G-quadruplex can protect telomeres from nuclease and interfere with telomerase activity

Fig. 3

G-quadruplexes can affect epigenetic modifications. A G4 can become epigenetic modification sites when the levels of oxidative stress increase. The presence of 8-oxoguanine (8OG) on the G-tetrad decreases the stability of the promoter G4, leading to an increase in gene expression. Meanwhile, 8OG could stimulate the binding of PARP-1 to the promoter G4 and promote the recruitment of MAZ and hnRNPA1 to the promoter, thereby stimulating transcription. B The formation of G4 at CpG islands can directly inhibit the activity of DNA methyltransferase after G4-preferred methyltransferase binding to the G4 structure. A typical example of this involves the DNA (cytosine-5)-methyltransferase DNMT1, DNMT3A, and DNMT3B. C G4 can affect histone epigenetics through the recruitment of proteins with histone-modifying activity, such as NME2 or TRF2, which can selectively bind to G4 and recruit the REST-LSD1 complex to remove the methylation of histone H3 Lys4 (H3K4) and inhibit gene expression. D In the promoter of ZEB1, nucleolin could bind to the G4 motif, remodel the local genomic region, facilitate the binding of SP1, and recruit P300 acetyltransferase, leading to enriched acetyl-histone H3 at the promoter, inducing gene transcription and oncogenic progression. E G4 can cause epigenetic reprogramming after the replication fork stalls at the G4 site in the presence of G4 ligands or the deficiency of G4-specific helicases. G4 structures may also impair histone recycling and lead to the localized loss of repressive chromatin, causing epigenetic reprogramming