Theoretical Analysis on the Transition State of the Anticancer Drug trans-[PtCl2(isopropylamine)2] and Its cis Isomer Binding to DNA Purine Bases

Quantum Chemical Investigations on the Hydrolysis of Gold(III)-Based Anticancer Drugs and Their Interaction with Amino Acid Residues

A comprehensive hydrolysis mechanism of the promising class of Au(III) anticancer drugs [Au(DMDT)Cl₂] (DMDT = N,N-dimethyldithiocarbamate) (R) and [Au(damp)Cl₂] (damp = 2-[(dimethylamino)methyl]phenyl) (R') was done by means of density functional theory (DFT) in combination with the CPCM solvation model to explore the solution behavior and stability under physiological conditions. The activation free energies (ΔG) for the second hydrolysis, R (13.7 kcal/mol) and R' (10.0 kcal/mol) are found to be relatively lower in comparison to the first hydrolysis, and their rate constant values are computed to be 5.62 × 10² and 2.90 × 10⁵ s^-1, respectively. Besides these, the interaction mechanisms of aquated R and R' with the potential protein-binding sites cysteine (Cys) and selenocysteine (Sec) were also investigated in detail. The kinetic study and activation Gibbs free energy profiles reveal that the aquated complexes of R and R' bind more effectively to the Se site of Sec than to the S site of Cys. Intra- and intermolecular hydrogen bonding play a pivotal role in stabilizing the intermediates and transition states involved in the ligand substitution reactions of R and R'. Natural population analysis (NPA) was done to determine the charge distributions on important atoms during the hydrolysis and ligand substitution reactions.

THEORETICAL STUDY ON THE BINDING OF THE ANTICANCER DRUGS Cis/Trans-[PtCl52(NH3){HN = C(CH3)2}] AND Cis/Trans-[PtCl2{HN = C(CH3)2}2] TO PURINE BASES

The monofunctional (the first substitution reactions) and bifunctional (the second substitution reactions) binding of the title antitumor drugs to purine bases were studied computationally by using density functional theory and IEF-PCM solvation models. For the first substitutions with guanine and adenine, our calculations demonstrate that the trans monoaqua and diaqua reactant complexes (RCs) can generate trans- or cis-monoadducts via identical or very similar trigonal-bipyramidal transition-state structures, predicting that the cis-monoadducts generated by trans RCs can subsequently close by coordination to the adjacent purine bases to form 1,2-intrastrand Pt –DNA adducts and eventually distort DNA in the same way as cisplatin. Thus it is likely that the transplatin analogues have the same mechanism of anticancer activity of cisplatin. In general, the monoaqua and diaqua monofunctional substitutions prefer guanine over adenine. The calculated lowest activation free energy in aqueous solution is 15.2 kcal/mol in the monoaqua substitutions (substituted by guanine from trans- [Pt{HN = C(CH3)2}2Cl(H2O)]+ to trans/cis-monoadduct), and 11.4 kcal/mol in the diaqua substitutions (substituted by guanine from cis- [Pt{HN = C(CH3)2}2(H2O)2]2+ to cis-monoadduct). For the second substitutions, all the reactants are started from the diaqua product complexes of the first substitutions substituted by guanine. The data obtained for the complexation energy difference between guanine and adenine RCs suggest that a thermodynamic favors the formation of GG over GA adducts by ∼ 5 - 12 kcal/mol in aqueous solution. Moreover, there is a kinetic preference for the formation of GG over GA adduct for the cis-monoadduct to cis-diadduct paths, while for the trans-monoadduct to trans-diadduct paths there is no certain trend biased toward GG adduct. In addition, the second substitutions of the trans-monoadduct to trans-diadduct paths have lower activation barriers than the corresponding cis-monoadduct to cis-diadduct paths. The lowest activation energy in the bifunctional substitutions from cis-monoadduct to cis-diadduct is 20.5 kcal/mol in the Pt (acetonimine)2GG2+ head-to-head (HH) path, while it is 17.7 kcal/mol from trans-monoadduct to trans-diadduct in the Pt(NH3) (acetonimine)GA2+ head-to-tail (HT) path. For the first and second substitutions, hydrogen-bonds play an important role in stabilizing these species.

Disturbance of DNA conformation by the binding of testosterone-based platinum drugs via groove-face and intercalative interactions: a molecular dynamics simulation study

BACKGROUND

To explore novel platinum-based anticancer agents that are distinct from the structure and interaction mode of the traditional cisplatin by forming the bifunctional intrastrand 1,2 GpG adduct, the monofunctional platinum+DNA adducts with extensive non-covalent interactions had been studied. It was reported that the monofunctional testosterone-based platinum(II) agents present the high anticancer activity. Moreover, it was also found that the testosterone-based platinum agents could cause the DNA helix to undergo significant unwinding and bending over the non-testosterone-based platinum agents. However, the interaction mechanisms of these platinum agents with DNA at the atomic level are not yet clear so far.

RESULTS

In the present work, we used molecular dynamics (MD) simulations and DNA conformational dynamics calculations to study the DNA distortion properties of the testosterone-based platinum+DNA, the improved testosterone-based platinum+DNA and the non-testosterone-based platinum+DNA adducts. The results show that the intercalative interaction of the improved flexible testosterone-based platinum agent with DNA molecule could cause larger DNA conformational distortion than the groove-face interaction of the rigid testosterone-based platinum agent with DNA molecule. Further investigations for the non-testosterone-based platinum agent reveal the occurrence of insignificant change of DNA conformation due to the absence of testosterone ligand in such agent. Based on the DNA dynamics analysis, the DNA base motions relating to DNA groove parameter changes and hydrogen bond destruction of DNA base pairs were also discussed in this work.

CONCLUSIONS

The flexible linker in the improved testosterone-based platinum agent causes an intercalative interaction with DNA in the improved testosterone-based platinum+DNA adduct, which is different from the groove-face interaction caused by a rigid linker in the testosterone-based platinum agent. The present investigations provide useful information of DNA conformation affected by a testosterone-based platinum complex at the atomic level.

Theoretical analysis of trans-[PtCl2(NH3)(thiazole)] and trans-[PtCl2(thiazole)2] binding to biological targets — Factors influence binding kinetics and adduct stability

Full reaction energy profiles for trans-[PtCl2(NH3)(thiazole)] and trans-[PtCl2(thiazole)2] binding to sulfur- and nitrogen-containing biorelevant ligands were constructed by the density functional theory (DFT) method. Calculated results demonstrate that trans-platinum complexes can interact with biological targets, affording cis and trans products via very similar transition states. For different substituents, sulfur-containing ligands constitute kinetically preferred targets for platination, whereas the platination of nitrogen-containing ligands is more favorable thermodynamically. This is consistent with previous experimental studies. Calculated results also suggest that the trans effect, the influence of the ligand, the size of the ligand, and hydrogen bonding play important roles in binding kinetics and stabilizing adducts.