Probing the Binding Pathway of BRACO19 to a Parallel-Stranded Human Telomeric G‑Quadruplex Using Molecular Dynamics Binding Simulation with AMBER DNA OL15 and Ligand GAFF2 Force Fields

Human
telomeric DNA G-quadruplex has been identified as a good
therapeutic target in cancer treatment. G-quadruplex-specific ligands
that stabilize the G-quadruplex have great potential to be developed
as anticancer agents. Two crystal structures (an apo form of parallel
stranded human telomeric G-quadruplex and its holo form in complex
with BRACO19, a potent G-quadruplex ligand) have been solved, yet
the binding mechanism and pathway remain elusive. In this study, we
simulated the binding of a free BRACO19 molecule to the apo form of
the G-quadruplex using the latest AMBER DNA (OL15) and ligand (GAFF2)
force fields. Three binding modes have been identified: top stacking,
bottom intercalation, and groove binding. Bottom intercalation (51%
of the population) resembles the bottom binding pose in the complex
crystal structure very well. The groove binding mode is less stable
than the bottom binding mode and is likely to be an intermediate state
leading to the bottom binding mode. A flip–insertion mechanism
was observed in the bottom intercalation mode, during which flipping
of the bases outward makes space for ligand insertion, after which
the bases flip back to increase the stability of the complex. In addition
to reproducing the base-flipping behavior for some loop residues upon
ligand binding, the direct alignment type of the ATAT-tetrad was observed
in our simulations for the first time. These successes provide initial
support for using this combination of the OL15 and GAFF2 force fields
to study quadruplex–ligand interactions.