Final Report Summary - DMSQD (Development of molecules for the stabilization of quadruplex DNA and regulation of oncogene expression: a potential route to novel anticancer drugs)
Project context and objectives
The interaction of small molecules with DNA has proven to be a very useful approach in the development of anti-cancer drugs. In recent years, it has become evident that a specific topology of DNA - namely quadruplex DNA - is a potentially very attractive target for drug development. The research carried out in this IEF project involved the synthesis and full characterisation of a series of metal complexes able to stabilise the formation of this quadruplex DNA structure. Considering the experience of the host group in this field, the family of molecules chosen has focused on salphen metal complexes. As previously reported by the host group, this type of complex has shown to be excellent DNA binders stabilising the formation of the quadruplex. However, some issues such as solubility in aqueous buffers or its selectivity for quadruplex over duplex DNA are still to be fully addressed.
Salphen complexes consist of three aromatic rings linked to a central metal via O,N,N,O coordination. The metal atom fixes the relative position of the aromatic rings in the ligand determining the geometry of the resulting molecule. The substituents around the aromatic ring play an important role in the solubility of the complex as well as in its selectivity as DNA binders. The research proposed in this project was scheduled over two years and was divided into four different parts as outlined in Part B of the original application.
Project work
Design of metal complexes and quadruplex DNA stabilisers: theoretical approach.
The theoretical study in this project has covered two different approaches. First, using density functional theory (DFT) calculations we investigated the core of the salphen complex using different metals. The optimised structures showed that not all salphen complexes are completely planar and this deviation of the planarity depends on the metal core. The best candidates are the metal complexes which show more planarity; therefore, the DFT-optimised structures were a useful tool in order to select the series of complexes to be synthesised.
The optimised structures were used to study their DNA interaction by molecular modelling (docking). These docking studies explained the binding mode between the metal complex and the quadruplex DNA. Results showed that p-p end-stacking interactions are the most likely possible binding between the nickel(II) salphen complex and the quadruplex, which is consistent with the experimental data.
Development of new quadruplex DNA binders: synthesis.
As outlined in the original proposal, aided by the theoretical studies a series of metal complexes were designed and synthesised. The theoretical studies indicated that nickel and platinum salphen complexes would be the best potential G-quadruplex binders. Therefore, salphen complexes with these two metals were synthesised and their DNA binding affinity compared to previously reported salphen complexes. The main aim was to improve the solubility of the metal complexes and to increase their selectivity for quadruplex over duplex DNA. In addition, the platinum(II) complexes showed they were highly emissive upon binding to DNA and therefore their potential as optical probes was also investigated.
Two different synthetic routes were used. In the first method, the salphen ligand was first synthetized and then metallated leading to the final product. In the second method, the metal complex core was first synthetized and the substituents introduced in a second step. The optimal method applied in our syntheses depended on the specific metal complex to be synthesised.
Evaluation of the interaction between the new molecules and DNA.
Three main bio-physical techniques have been applied in order to determinate the interaction between the quadruplex DNA and the metal complexes: fluorescent intercalator displacement (FID) assay, circular dichroism (CD) and UV-vis spectroscopic titrations. These three techniques are well established methodologies and were fully explained in Part B of the original proposal.
Project results
Result showed that several of these metal complexes bind strongly to quadruplex DNA finding some selectivity with respect to duplex DNA. The complexes are highly soluble in the experimental buffer conditions, solving one of the main problems of salphen complexes as DNA binders. Platinum complex 6 was found to be highly fluorescence when bonded to quadruplex DNA. This metal complex presents no fluorescence in aqueous buffered conditions; however, when quadruplex DNA is added to the solution, the metal complex becomes highly emissive fluorescence. This effect can be exploited in order to develop quadruplex DNA probes. For this purpose, a full characterisation of the fluorescence emission in the presence of quadruplex and duplex DNA was carried out.
Biological activity.
Platinum salphen complex 6 is currently being studied as a possible quadruplex probe in living cells.
The research group is involved in several international networks such as COST actions. As a result, the fellow has been directly involved in a collaboration project in the field of quadruplex DNA with the group of Prof. Janice Aldrich-Wright (University of Western Sydney, Australia) and quadruplex RNA with the group of Prof. Roland K. O. Sigel (University of Zurich, Switzerland).
The interaction of small molecules with DNA has proven to be a very useful approach in the development of anti-cancer drugs. In recent years, it has become evident that a specific topology of DNA - namely quadruplex DNA - is a potentially very attractive target for drug development. The research carried out in this IEF project involved the synthesis and full characterisation of a series of metal complexes able to stabilise the formation of this quadruplex DNA structure. Considering the experience of the host group in this field, the family of molecules chosen has focused on salphen metal complexes. As previously reported by the host group, this type of complex has shown to be excellent DNA binders stabilising the formation of the quadruplex. However, some issues such as solubility in aqueous buffers or its selectivity for quadruplex over duplex DNA are still to be fully addressed.
Salphen complexes consist of three aromatic rings linked to a central metal via O,N,N,O coordination. The metal atom fixes the relative position of the aromatic rings in the ligand determining the geometry of the resulting molecule. The substituents around the aromatic ring play an important role in the solubility of the complex as well as in its selectivity as DNA binders. The research proposed in this project was scheduled over two years and was divided into four different parts as outlined in Part B of the original application.
Project work
Design of metal complexes and quadruplex DNA stabilisers: theoretical approach.
The theoretical study in this project has covered two different approaches. First, using density functional theory (DFT) calculations we investigated the core of the salphen complex using different metals. The optimised structures showed that not all salphen complexes are completely planar and this deviation of the planarity depends on the metal core. The best candidates are the metal complexes which show more planarity; therefore, the DFT-optimised structures were a useful tool in order to select the series of complexes to be synthesised.
The optimised structures were used to study their DNA interaction by molecular modelling (docking). These docking studies explained the binding mode between the metal complex and the quadruplex DNA. Results showed that p-p end-stacking interactions are the most likely possible binding between the nickel(II) salphen complex and the quadruplex, which is consistent with the experimental data.
Development of new quadruplex DNA binders: synthesis.
As outlined in the original proposal, aided by the theoretical studies a series of metal complexes were designed and synthesised. The theoretical studies indicated that nickel and platinum salphen complexes would be the best potential G-quadruplex binders. Therefore, salphen complexes with these two metals were synthesised and their DNA binding affinity compared to previously reported salphen complexes. The main aim was to improve the solubility of the metal complexes and to increase their selectivity for quadruplex over duplex DNA. In addition, the platinum(II) complexes showed they were highly emissive upon binding to DNA and therefore their potential as optical probes was also investigated.
Two different synthetic routes were used. In the first method, the salphen ligand was first synthetized and then metallated leading to the final product. In the second method, the metal complex core was first synthetized and the substituents introduced in a second step. The optimal method applied in our syntheses depended on the specific metal complex to be synthesised.
Evaluation of the interaction between the new molecules and DNA.
Three main bio-physical techniques have been applied in order to determinate the interaction between the quadruplex DNA and the metal complexes: fluorescent intercalator displacement (FID) assay, circular dichroism (CD) and UV-vis spectroscopic titrations. These three techniques are well established methodologies and were fully explained in Part B of the original proposal.
Project results
Result showed that several of these metal complexes bind strongly to quadruplex DNA finding some selectivity with respect to duplex DNA. The complexes are highly soluble in the experimental buffer conditions, solving one of the main problems of salphen complexes as DNA binders. Platinum complex 6 was found to be highly fluorescence when bonded to quadruplex DNA. This metal complex presents no fluorescence in aqueous buffered conditions; however, when quadruplex DNA is added to the solution, the metal complex becomes highly emissive fluorescence. This effect can be exploited in order to develop quadruplex DNA probes. For this purpose, a full characterisation of the fluorescence emission in the presence of quadruplex and duplex DNA was carried out.
Biological activity.
Platinum salphen complex 6 is currently being studied as a possible quadruplex probe in living cells.
The research group is involved in several international networks such as COST actions. As a result, the fellow has been directly involved in a collaboration project in the field of quadruplex DNA with the group of Prof. Janice Aldrich-Wright (University of Western Sydney, Australia) and quadruplex RNA with the group of Prof. Roland K. O. Sigel (University of Zurich, Switzerland).
