Binding of Telomestatin, TMPyP4, BSU6037, and BRACO19 to a Telomeric G-Quadruplex-Duplex Hybrid Probed by All-Atom Molecular Dynamics Simulations with Explicit Solvent

Abstract

A promising anticancer therapeutic strategy is the stabilization of telomeric G-quadruplexes using G-quadruplex-binding small molecules. Although many G-quadruplex-specific ligands have been developed, their low potency and selectivity to G-quadruplexes over duplex remains unsolved. Recently, a crystal structure of a telomeric 3' quadruplex-duplex hybrid was reported and the quadruplex-duplex interface was suggested to a good target to address the issues. However, there are no high-resolution complex structures reported for G-quadruplex ligands except for a docked BSU6037. In this study, molecular dynamic (MD) binding simulations with a free ligand were used to study binding poses and dynamics of four representative ligands: telomestatin, TMPyP4, BSU6037, and BRACO19. The MD data showed that BSU6037 was able to fully intercalate into the interface whereas TMPyP4 and BRACO19 could only maintain partial intercalation into the interface and telomestatin only binds at the quadruplex and duplex ends. Both linear ligands, BSU6037 and BRACO19, were able to interact with the interface, yet they were not selective over duplex DNA. The DNA geometry, binding modes, and binding pathways were systematically characterized, and the binding energy was calculated and compared for each system. The interaction of the ligands to the interface was by the means of an induced-fit binding mechanism rather than a lock-key mechanism, consisting of the DNA unfolding at the interface to allow entrance of the drug and then the refolding and repacking of the DNA and the ligand to further stabilize the G-quadruplex. On the basis of the findings in this study, modifications were suggested to optimize the interface binding for TMPyp4 and telomestatin.

Figure 1

Structures of the telomeric DNA quadruplex–duplex hybrid (A), telomestatin (B), TMPyP4 (C), BSU6037 (D), and BRACO19 (E).

Figure 2

Representative trajectory of the DNA-only simulation and the order parameter plot illustrating the breaking and reforming of hydrogen bonds (at the quadruplex (1), interface (2), and duplex (3)), RMSD (Å) with reference to the final structure (4), K⁺ to K⁺ distance (5), and the MM-GBSA binding energy (ΔE in kcal/mol) (6). 5′ and 3′ of the DNA chain are indicated by a red and blue ball, respectively. K⁺ ions are indicated by a yellow ball.

Figure 3

Root-mean-square fluctuation (RMSF) plot of the five systems (DNA-only, top binding of telomestatin, interface intercalation mode of BSU6037, and the interface interacting mode of TMPyP4 and BRACO19). The x axis refers to the residue number of the DNA quadruplex hybrid structure (Figure 1a); the residue 1 of the second chain was missed in the crystal structure.

Figure 4

Major binding modes between ligands and human telomeric quadruplex–duplex (PDB ID: 5DWW). 5′ and 3′ of the DNA chain are indicated by a red and blue ball, respectively. K⁺ ions are indicated by yellow balls. Overall population abundance (MM-GBSA binding energy) of each binding mode is annotated.

Figure 5

Representative trajectory of the top stacking mode of telomestatin (run 9) and the order parameter plot, illustrating the breaking and reforming of hydrogen bonds (at the quadruplex (1), interface (2), and duplex (3)), drug-base dihedral angle (4), ligand (black)/DNA (red) RMSD (Å) with reference to the final structure (5), ligand center-to-DNA center distance (black) and K⁺-to-K⁺ distance (red) (6), and the MM-GBSA binding energy (ΔE in kcal/mol) (7). 5′ and 3′ of the DNA chain are indicated by a red and blue ball, respectively. K⁺ ions are indicated by yellow balls.

Figure 6

Representative trajectory of the interface interacting mode of TMPyP4 (run 5) and the order parameter plot, illustrating the breaking and reforming of hydrogen bonds (at the quadruplex (1), interface (2), and duplex (3)), drug-base dihedral angle (4), ligand (black)/DNA (red) RMSD (Å) with reference to the final structure (5), ligand center-to-DNA center distance (black) and K⁺-to-K⁺ distance (red) (6), and the MM-GBSA binding energy (ΔE in kcal/mol) (7). 5′ and 3′ of the DNA chain are indicated by a red and blue ball, respectively. K⁺ ions are indicated by yellow balls.

Figure 7

BSU6037, run 19, trajectory snapshots and the order parameter plot, illustrating the breaking and reforming of hydrogen bonds (at the quadruplex (1), interface (2), and duplex (3)), drug-base dihedral angle (4), ligand (black)/DNA (red) RMSD (Å) with reference to the final structure (5), ligand center-to-DNA center distance (black) and K⁺-to-K⁺ distance (red) (6), and the MM-GBSA binding energy (ΔE in kcal/mol) (7). 5′ and 3′ of the DNA chain are indicated by a red and blue ball, respectively. K⁺ ions are indicated by yellow balls.

Figure 8

BRACO19, run 06, trajectory snapshots and the order parameter plot, illustrating the breaking and reforming of hydrogen bonds (at the quadruplex (1), interface (2), and duplex (3)), drug-base dihedral angle (4), ligand (black)/DNA (red) RMSD (Å) with reference to the final structure (5), ligand center-to-DNA center distance (black) and K⁺-to-K⁺ distance (red) (6), and the MM-GBSA binding energy (ΔE in kcal/mol) (7). 5′ and 3′ of the DNA chain are indicated by a red and blue ball, respectively. K⁺ ions are indicated by yellow balls.

Figure 9

Suggested modifications for telomestatin and TMPyP4.

Figure 10

Comparison of the G-quadruplex end binding mode from the ligand binding simulations and from the crystallography studies. 5′ and 3′ are represented by red and blue balls, respectively. Potassium cations are represented as yellow balls.