Download MendeleyBerberine Molecular Recognition of the Parallel MYC G-Quadruplex in Solution.
Dickerhoff, J., Brundridge, N., McLuckey, S.A., Yang, D.(2021) J Med Chem 64: 16205-16212
- PubMed: 34677968
- DOI: https://doi.org/10.1021/acs.jmedchem.1c01508
- Primary Citation of Related Structures:
7N7D, 7N7E - PubMed Abstract:
The medicinal natural product berberine is one of the most actively studied and pursued G-quadruplex (G4)-ligands. The major G-quadruplex formed in the promoter region of the MYC oncogene (MycG4) is an attractive drug target and a prominent example and model structure for parallel G-quadruplexes. G4-targeted berberine derivatives have been actively developed; however, the analogue design was based on a previous crystal structure in which berberine binds as a dimer to a parallel G-quadruplex. Herein, we show that in solution, the binding mode and stoichiometry of berberine are substantially different from the crystal structure: berberine binds as a monomer to MycG4 using a base-recruitment mechanism with a reversed orientation in that the positively charged convex side is actually positioned above the tetrad center. Our structure provides a physiologically relevant basis for the future structure-based rational design of G4-targeted berberine derivatives, and this study demonstrates that it is crucial to validate the ligand-DNA interactions.
Organizational Affiliation:
Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 W Stadium Avenue, West Lafayette, Indiana 47904, United States.
