Solution Structure of Ternary Complex of Berberine Bound to a dGMP–Fill-In Vacancy G‑Quadruplex Formed in the PDGFR‑β Promoter

• Published in: Journal of the American Chemical Society 2021-10, Vol.143 (40), p.16549-16555
• Main Authors: Wang, Kai-Bo, Dickerhoff, Jonathan, Yang, Danzhou
• Format: Article
• Language: English
• Subjects: Berberine - chemistry; Berberine - metabolism; G-Quadruplexes; Humans; Models, Molecular; Molecular Structure; Promoter Regions, Genetic; Receptor, Platelet-Derived Growth Factor beta - chemistry; Receptor, Platelet-Derived Growth Factor beta - genetics; Receptor, Platelet-Derived Growth Factor beta - metabolism; Solutions
• ISSN: 0002-7863; 1520-5126; 1520-5126
• DOI: 10.1021/jacs.1c06200

The G-quadruplexes (G4s) formed in the PDGFR-β gene promoter are transcriptional modulators and amenable to small-molecule targeting. Berberine (BER), a clinically important natural isoquinoline alkaloid, has gained increasing attention due to its potential as anticancer drug. We previously showed that the PDGFR-β gene promoter forms a unique vacancy G4 (vG4) that can be filled in and stabilized by guanine metabolites, such as dGMP. Herein, we report the high-resolution NMR structure of a ternary complex of berberine bound to the dGMP-fill-in PDGFR-β vG4 in potassium solution. This is the first small-molecule complex structure of a fill-in vG4. This ternary complex has a 2:1:1 binding stoichiometry with a berberine molecule bound at each the 5′- and 3′-end of the 5′-dGMP-fill-in PDGFR-β vG4. Each berberine recruits the adjacent adenine residue from the 5′- or 3′-flanking sequence to form a “quasi-triad plane” that covers the external G-tetrad of the fill-in vG4, respectively. Significantly, berberine covers and stabilizes the fill-in dGMP. The binding of berberine involves both π-stacking and electrostatic interactions, and the fill-in dGMP is covered and well-protected by berberine. The NMR structure can guide rational design of berberine analogues that target the PDGFR-β vG4 or dGMP-fill-in vG4. Moreover, our structure provides a molecular basis for designing small-molecule guanine conjugates to target vG4s.