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Electrospray ionization mass spectrometry probing of binding affinity of berbamine, a flexible cyclic alkaloid from traditional Chinese medicine, with G‐quadruplex DNA
Author(s) -
Tan Wei,
Zhou Jiang,
Yuan Gu
Publication year - 2013
Publication title -
rapid communications in mass spectrometry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.528
H-Index - 136
eISSN - 1097-0231
pISSN - 0951-4198
DOI - 10.1002/rcm.6763
Subject(s) - chemistry , electrospray ionization , g quadruplex , mass spectrometry , stereochemistry , chromatography , dna , biochemistry
RATIONALE Classic G‐quadruplex binders typically have a large aromatic core and interact with G‐quadruplexes through π–π stacking with the quartets. There are rather few reports on natural flexible cyclic molecule from traditional Chinese medicine which has high binding affinity with G‐quadruplex. METHODS Electrospray ionization mass spectrometry (ESI‐MS) experiments were performed to evaluate the binding affinities of a natural alkaloid, berbamine, with seven G‐quadruplexes. Furthermore, we utilized autodock4 analysis to uncover the binding mode of berbamine with the G‐quadruplex. RESULTS ESI‐MS experiments showed that berbamine has the best binding affinity toward the (GGA) 8 G‐quadruplex compared with the other six G‐quadruplexes. Autodock4 analysis indicated that berbamine interacted with the (GGA) 8 G‐quadruplex through hydrogen bonding and van der Waals forces with a binding site at the lateral groove formed by DG8‐DA9‐DA15‐DG16. CONCLUSIONS In this study, we discovered a novel G‐quadruplex binder, berbamine, which has high binding affinity toward the (GGA) 8 G‐quadruplex. This study provided important clues regarding the probing of small molecule from traditional Chinese medicine which can target the G‐quadruplex with high affinity. Copyright © 2013 John Wiley & Sons, Ltd.