Binding of anticancer drug daunomycin to a TGGGGT G-quadruplex DNA probed by all-atom molecular dynamics simulations: additional pure groove binding mode and implications on designing more selective G-quadruplex ligands

Abstract

DNA G-quadruplex structures are emerging cancer-specific targets for chemotherapeutics. Ligands that bind to and stabilize DNA G-quadruplexes have the potential to be anti-cancer drugs. Lack of binding selectivity to DNA G-quadruplex over DNA duplex remains a major challenge when attempting to develop G-quadruplex ligands into successful anti-cancer drugs. Thorough understanding of the binding nature of existing non-selective ligands that bind to both DNA quadruplex and DNA duplex will help to address this challenge. Daunomycin and doxorubicin, two commonly used anticancer drugs, are examples of non-selective DNA ligands. In this study, we extended our early all-atom binding simulation studies between doxorubicin and a DNA duplex (d(CGATCG)) to probe the binding between daunomycin and a parallel DNA quadruplex (d(TGGGGT)) and DNA duplex. In addition to the end stacking mode, which mimics the mode in the crystal structure, a pure groove binding mode was observed in our free binding simulations. The dynamic and energetic properties of these two binding modes are thoroughly examined, and a detailed comparison is made between DNA quadruplex binding modes and DNA duplex binding modes. Implications on the design of more selective DNA quadruplex ligands are also discussed. Graphical abstract Top stacking and groov binding modes from the MD simulations.

Molecular Recognition of Parallel G-quadruplex [d-(TTGGGGT)]4 Containing Tetrahymena Telomeric DNA Sequence by Anticancer Drug Daunomycin: NMR-Based Structure and Thermal Stability

“…In addition, the observed CD spectra did not exhibit any bisignate peaks ( Figure 2 e), which is an independent proof of the non-existence of stacked layers of daunomycin or the presence of daunomycin dimer in parallel or antiparallel orientation in our solution studies. This is in accordance with the findings by rMD simulations of daunomycin-[d-(TGGGGT)] 4 [ 25 ] complexes, in which only a monomer is found to bind to DNA.…”

“…The observed intermolecular short distance NOE contacts between daunomycin and DNA as well as the rMD structure provided direct confirmation of end-stacking and external groove-binding at G6-T7 and T1-T2 sites, respectively. This is at variance with the X-ray crystallographic structure, which showed layers of daunomycin stacked between two quadruplexes [ 23 ], but in accord with the MD simulations in explicit solvent for daunomycin-[d-(TGGGGT)] 4 [ 25 ]. The end-stacking mode was also inferred from the collision-induced fragmentation patterns in the daunomycin-[d-(TGGGGT)] 4 complex [ 30 ] and NMR studies on the doxorubicin-[d-(TTAGGGT)] 4 complex [ 26 ].…”

“…It has been suggested [ 26 ] that crystal-packing forces may be responsible for the observed difference in the structure of the complex. The present NMR experiments and molecular dynamics simulations [ 25 ] have been performed in explicit water solvent, which may offer structural flexibility to the DNA.…”

“…Long telomeric sequences usually exist in several conformations involving different folded forms with different topologies as well as intermolecular aggregates in equilibrium, making ligand–intramolecular G-quadruplex interactions difficult to interpret by structural techniques. Therefore, intermolecular G-quadruplex [d-(TTGGGGT)] 4 and similar sequences are a viable option for structural studies as a model system [ 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 ]. Although the simplified model does not contain loops, it contains a similar G-tetrad surface and grooves to biologically relevant G-quadruplexes such as that in antiparallel and hybrid G-quadruplexes; so, despite their limitations, the studies on model systems are found to be informative.…”

“…The first X-ray crystallographic structure of daunomycin-[d-(TGGGGT)] 4 complex [ 23 ] showed two layers of daunomycin containing three molecules each, which were sandwiched between two G-quadruplexes with daunosamine sugar moiety inserted in grooves, while another daunomycin-d-(GGGG)] 4 complex indicated the absence of any such interaction [ 24 ]. Molecular Dynamics (MD) simulations of the daunomycin-d-(TGGGGT) 4 [ 25 ] complex, on the contrary, showed that daunomycin binds in a monomeric state through stacking interactions with the last G-quartet as well as at grooves, both with practically the same binding affinity. Nuclear magnetic resonance (NMR) studies on the interaction of daunomycin analogues, nemorubicin and doxorubicin, with G-quadruplex sequences containing three guanine repeats, e.g., [d-(TTAGGGT)] 4 , showed [ 26 ] that binding takes place at A3pG4 and terminal G-tetrad.…”