Molecular Dynamics Studies of Changes in the DNA- Structure as Result of Interactions with Cisplatin

The 3’-monofunctional adduct of cisplatin and d(CTCTGGTCTC)2 duplex DNA in solvent with explicit counter ions and water molecules were subjected to MD- simulation with AMBER force field on a nanosecond time scale. In order to simulate the closure of the bond between the Pt and 5’-guanine-N7 atoms, the forces acting between them were gradually increased during MD. After 500-800 ps the transformation of the mono-adduct (straight DNA with the cisplatin residue linked to one guanine-N7) to the bus-adduct (bent DNA where Pt atom is connected through the N7 atoms of neighboring guanines) was observed. A cavity between palatinate guanines is formed and filled with solvent molecules. The rapid inclination of the center base pairs initiates a slow transition of the whole molecule from the linear to the bent conformation. After about 1000-1300 ps a stable structure was reached, which is very similar to the one described experimentally. The attractive force between the Pt- atom and the N7 of the second guanine plays the main role in the large conformational changes induced by formation of the adduct-adduct. X-N-Pt-N-torsions accelerate the bending but a torsion force constant greater than 0.2 Kcal/mol lead to the breaking of the H-bonds within the base pairs. The present study is the first dynamical simulation that demonstrates in real time scale such a large conformational perturbation of DNA.

💡 Research Summary

This paper presents a detailed molecular dynamics (MD) investigation of the structural changes that occur in a DNA duplex when it reacts with the anticancer drug cisplatin. Using the AMBER 5.0 software suite together with the AMBER 4.1 force field, the authors built a model consisting of a ten‑base‑pair DNA duplex (sequence d(CTCTGGTCTC)₂) and a single cisplatin moiety covalently attached to the N7 atom of the 3′‑terminal guanine (the so‑called 3′‑monoadduct). The system was explicitly solvated with approximately 3500 TIP3P water molecules and neutralized with 16 Na⁺ ions, providing a realistic aqueous environment and allowing long‑range electrostatic interactions to be treated accurately.

A key methodological challenge is that the formation of the second Pt–N7 bond (which converts the monoadduct into the biologically relevant bis‑adduct) cannot be modeled directly with standard harmonic potentials because the initial Pt–N distance (≈3.6 Å) is far longer than a normal Pt–N bond (≈1.7 Å). To overcome this, the authors introduced a stepwise scaling of the Pt–N stretching force constant. Starting from a very weak harmonic restraint, the constant was gradually increased during the simulation, thereby allowing the Pt and the second guanine N7 to approach each other smoothly. At the same time, torsional force constants involving the Pt‑bound atoms (X‑N‑Pt‑N, X‑Pt‑N, etc.) were carefully tuned; values above 0.2 kcal mol⁻¹ were found to destabilize the hydrogen bonds that hold the guanine‑cytosine base pairs together.

The MD runs were performed in the NTP ensemble with a 2 fs timestep, temperature controlled by a Berendsen thermostat, and pressure maintained near 1 atm. All covalent bonds except the forming Pt–N bond were constrained with SHAKE. Coordinates were saved every 200 fs for analysis. The authors monitored global bending (the angle UU defined by Curves), local helical parameters (Rise, Roll, Tilt, Shift, Slide), minor‑groove width, and the Pt–N distance.

During the first 10–50 ps the platinated base pairs equilibrated locally, but the overall duplex remained essentially linear. Between 500 and 800 ps the gradually strengthened Pt–N attraction caused the Pt atom to pull the second guanine toward the platinum center. This induced a rapid increase in the Roll and Tilt angles of the two central base pairs (G5‑G6), creating a cavity that became filled with water molecules. The global bending angle rose from near zero to about 55°–60° by 1000–1300 ps, closely matching experimental values obtained from X‑ray (≈57°) and NMR (≈78°) studies. The minor‑groove width in the G‑G region expanded to ~11 Å, reflecting the opening that facilitates protein recognition (e.g., HMG‑box proteins).

Energy analysis compared the deformation energy (computed from the harmonic force field) with the attractive Pt–N potential derived from density‑functional theory (fitted to a Morse function with bond length 1.7 Å, dissociation energy 86 kcal mol⁻¹, vibrational frequency 1139 cm⁻¹). Throughout the trajectory, the deformation energy remained lower than the Pt–N attraction, confirming that the stepwise scaling provides a physically realistic pathway for bond formation.

When torsional constants were set too high (≥0.2 kcal mol⁻¹), the simulation showed a marked increase in Shear, Stretch, and Stagger (up to 0.5–1 Å), leading to the rupture of the guanine‑cytosine hydrogen bonds and a non‑physiological distortion that never relaxed to the experimental bis‑adduct geometry. This observation underscores the delicate balance between providing enough torque to promote bending and preserving base‑pair integrity.

Two independent simulations were started from experimentally determined structures (one from NMR, one from X‑ray). The NMR‑based run converged faster (≈100–200 ps) because the initial geometry already resembled the solution state, whereas the X‑ray‑based run required an additional 300–400 ps for the duplex to relax from the crystal packing constraints. RMSD maps confirmed that after the initial drift the systems remained in a single conformational basin, indicating that the MD protocol successfully refined the structures toward the equilibrium solution conformation.

In summary, the study demonstrates that (i) the attractive force between the Pt atom and the second guanine N7 is the primary driver of the dramatic DNA bending observed upon cisplatin binding; (ii) a controlled, gradual increase of the Pt–N stretching constant is an effective way to mimic bond formation within a classical force field; (iii) torsional force constants must be limited to avoid breaking essential hydrogen bonds; and (iv) explicit solvent and counter‑ions are essential for reproducing the realistic energetics of the bending process. The authors claim this is the first MD simulation that captures, on a nanosecond timescale, the full transition from a linear monoadduct to a bent bis‑adduct, providing a mechanistic framework that can be extended to other platinum‑DNA interactions and to the rational design of next‑generation metal‑based anticancer agents.