Interactions of Platinum Based Anticancer Drugs with DNA
Platinum(II) anticancer drugs are currently the most widely used form of chemotherapy in the world with the lead compound, Cisplatin, being used successfully for over three decades. Cisplatin’s cytotoxicity is attributed to the formation of 1,2-GpG intrastrand lesions on binding to DNA producing a distortion of the helical structure that ultimately results in cell death.
Studies within our group have focused on two main categories of platinum(II) antitumour agents these being; Platinum(II) N-Heterocyclic Carbene (NHC) Complexes (direct analogues of Cisplatin), and Polynuclear Platinum Based Anticancer Drugs (second generation analogues). Currently only a handful of platinum(II) NHC complexes have been prepared, mainly for their catalytic activity. We are the first to begin an evaluation of their suitability as potential antitumour agents. The anticancer activity of second generation polynuclear platinum(II) drugs most likely depends on binding to DNA, but the adducts formed are quite different from those formed by Cisplatin. To gain insight into the mechanism of action of compounds from both classes our approach is to use a combination of NMR spectroscopy and molecular modelling to examine the drug-DNA interactions. The results will aid in the selection and design of new agents able to target specific DNA sequences. Rigorous molecular modelling and dynamics simulations in explicit solvent are beyond the capabilities of standard desktop computers. The APAC National Facility allows for the investigation of these more realistic and biologically significant systems within a reasonable time frame.
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Principal Investigator Susan Berners-PriceSchool of Biomedical and Chemical Sciences University of Western Australia |
Project f63 |
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Co-Investigators Scott McPheeDonald Thomas Rasha Ruhayel Joe Moniodis School of Biomedical and Chemical Sciences University of Western Australia |
RFCD Codes 250204 |
Significant Achievements, Anticipated Outcomes and Future Work
Platinum(II) NHC’s
Studies were undertaken on compounds 1 and 2 shown in Figure 1, with parameter sets for use within the AMBER force field developed via a series of both non-relativistic and relativistic scalar ZORA density functional theory calculations. Calculations were performed using ADF on both compounds, on the compounds as complex cations, and bound to the biologically relevant ligands guanosine, and guanosine-5'-monophosphate. The optimised structures and charges generated via ADF were subsequently used as input parameters for molecular dynamics simulations performed using AMBER 8.0 on the 1,2-GpG adducts formed by each complex with a 14 base pair DNA duplex in a solvated and charge balanced environment. Two 10 nanosecond, and several significantly shorter, dynamics simulations were performed on the drug-DNA systems with the outcomes suggesting these compounds warrant further investigation as antitumour agents. Finally 10 nanosecond dynamics simulations were also performed on 1 and 2 bound to guanosine, which aided in the investigation of rotameric species identified by NMR spectroscopy.
Multinuclear Platinum Anti-cancer compounds
Production dynamics simulations have been performed previously to study the interaction of the non-covalently binding platinum anticancer complex 0,0,0/t,t,t with three sequences of DNA. Both semi-empirical and non-relativistic density functional theory calculated charges have been used for the complex in these simulations. In 2005, two production dynamics simulations were performed on 0,0,0/t,t,t with the GG sequence using non-relativistic DFT charges for the complex to complete this set. This work forms part of the PhD thesis of Joe Moniodis (submission mid 2006).
Studies were carried out on 1,1/t,t (Figure 1) bound to a 12 mer 1,4-GG duplex (Figure 2) to form a 3'-3' 1,4-GG interstrand cross-link. The drug-DNA adduct was minimised and solvated, and a molecular dynamics simulation was carried out using AMBER 8.0. A 10 nanosecond simulation was run which confirmed previous molecular biology studies which suggest that the 3'-3' 1,4-GG interstrand cross-link is an unlikely adduct in vivo.
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| Figure 1: (1) (2) | 1,1/t,t |
Figure 2: Binding sites highlighted
Computational Techniques Used
Molecular dynamics simulations were performed on the program Amber. To run 10 ns simulations in water requires significant computer power, which we did not have access to anywhere else. The density functional theory calculations were performed on the Amsterdam Density Functional (ADF) program. These calculations were performed on APAC because we do not have access to ADF on our computers.
Publications, Awards and External Funding
External Funding and Awards
Australian Research Council, Discovery Project DP0208117, Berners-Price and Farrell 1/1/2002-31/12-2004 (funds carried forward to 2005) 'DNA Interactions of Polynuclear Platinum. Mechanistic NMR Studies Probing the Origin of the Unique Antitumour Activity of BBR3464'.
Australian Research Council, Discovery Project DP0662817, Berners-Price and Farrell 1/1/2006-31/12-8 'Second Generation Polynuclear Platinum Compounds. Mechanistic NMR Studies Probing DNA Binding and Pharmacokinetics'.
Australian Research Council, Discovery Project DP35400100, Berners-Price and Baker 1/1/2003-31/12-2006. 'Gold Phosphine and Carbene Complexes as Potential Antimitochondrial Anticancer Agents: Design, Synthesis and Biological Chemistry'.
Australian Research Council, Linkage International Project LX0346972, Berners-Price and Farrell, 1/1/2002-31/12-2004 (funds carried forward to 2005) 'NMR Studies on DNA Interactions of Polynuclear Platinum'.
Australian Research Council, Linkage International Project LX0667281, Berners-Price and Farrell, 1/1/2006-31/12-2008. 'NMR Studies of Second Generation Polynuclear Platinum Compounds'.
Publications
Effects of geometric isomerism in dinuclear platinum anticancer complexes on aquation reactions in the presence of perchlorate, acetate and phosphate. J. Zhang, D. S. Thomas, M. S. Davies, S. J. Berners-Price and N. Farrell J. Biol. Inorg. Chem. 10, (2005), 652-666.