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Discovery of novel triple helical DNA intercalators by an integrated virtual and actual screening platform.

Holt PA, Ragazzon P, Strekowski L, Chaires JB, Trent JO - Nucleic Acids Res. (2009)

Bottom Line: Further molecular docking studies using compounds with high structural similarity resulted in two compounds that were then demonstrated by competition dialysis to have a superior affinity and selectivity for the triplex nucleic acid than MHQ-12.Biophysical characterization of these compounds by circular dichroism and thermal denaturation studies confirmed their binding mode and selectivity.These studies provide a proof-of-principle for our integrated screening strategy, and suggest that this platform may be extended to discover new compounds that target therapeutically relevant nucleic acid morphologies.

View Article: PubMed Central - PubMed

Affiliation: James Graham Brown Cancer Center, Department of Biochemistry and Molecular Biology, University of Louisville, 529 S. Jackson Street, Louisville, KY 40202, USA.

ABSTRACT
Virtual Screening is an increasingly attractive way to discover new small molecules with potential medicinal value. We introduce a novel strategy that integrates use of the molecular docking software Surflex with experimental validation by the method of competition dialysis. This integrated approach was used to identify ligands that selectively bind to the triplex DNA poly(dA)-[poly(dT)](2). A library containing approximately 2 million ligands was virtually screened to identify compounds with chemical and structural similarity to a known triplex intercalator, the napthylquinoline MHQ-12. Further molecular docking studies using compounds with high structural similarity resulted in two compounds that were then demonstrated by competition dialysis to have a superior affinity and selectivity for the triplex nucleic acid than MHQ-12. One of the compounds has a different chemical backbone than MHQ-12, which demonstrates the ability of this strategy to 'scaffold hop' and to identify small molecules with novel binding properties. Biophysical characterization of these compounds by circular dichroism and thermal denaturation studies confirmed their binding mode and selectivity. These studies provide a proof-of-principle for our integrated screening strategy, and suggest that this platform may be extended to discover new compounds that target therapeutically relevant nucleic acid morphologies.

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Competition dialysis results for MHQ-15, OZ-85H, compounds 1 and 2. The concentration of bound ligand to each nucleic acid structure in the array is shown.
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Figure 2: Competition dialysis results for MHQ-15, OZ-85H, compounds 1 and 2. The concentration of bound ligand to each nucleic acid structure in the array is shown.

Mentions: The results of the competition dialysis experiments are shown in Figure 2. It is visually apparent that compounds 1 and 2 have a much higher affinity for the TAT triplex than the two positive control reference compounds, MHQ-15 and OZ-85H. The competition dialysis results for MHQ-12 have previously been described in detail (18), and this compound has an SS of 1.32 and a Cmax/SS ratio of 8.93. Determination of the SS (Table 1) for compounds 1 and 2 demonstrates superior triplex selectivity compared to OZ-85H but slightly less selectivity than MHQ-12 and MHQ-15. However, the significantly higher binding affinities of compounds 1 and 2 translate to much higher Cmax/SS values than MHQ-12, MHQ-15 or OZ-85H. The Cmax/SS ratio for compounds 1 and 2 is significant as it suggests that compounds 1 and 2 have a superior combination of binding affinity and selectivity compared to the reference compounds. These results validate the virtual screening approach, and show that the method can be used to identify compounds with high affinity and selectivity for a target nucleic acid, in this case the DNA TAT triplex.Figure 2.


Discovery of novel triple helical DNA intercalators by an integrated virtual and actual screening platform.

Holt PA, Ragazzon P, Strekowski L, Chaires JB, Trent JO - Nucleic Acids Res. (2009)

Competition dialysis results for MHQ-15, OZ-85H, compounds 1 and 2. The concentration of bound ligand to each nucleic acid structure in the array is shown.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2651796&req=5

Figure 2: Competition dialysis results for MHQ-15, OZ-85H, compounds 1 and 2. The concentration of bound ligand to each nucleic acid structure in the array is shown.
Mentions: The results of the competition dialysis experiments are shown in Figure 2. It is visually apparent that compounds 1 and 2 have a much higher affinity for the TAT triplex than the two positive control reference compounds, MHQ-15 and OZ-85H. The competition dialysis results for MHQ-12 have previously been described in detail (18), and this compound has an SS of 1.32 and a Cmax/SS ratio of 8.93. Determination of the SS (Table 1) for compounds 1 and 2 demonstrates superior triplex selectivity compared to OZ-85H but slightly less selectivity than MHQ-12 and MHQ-15. However, the significantly higher binding affinities of compounds 1 and 2 translate to much higher Cmax/SS values than MHQ-12, MHQ-15 or OZ-85H. The Cmax/SS ratio for compounds 1 and 2 is significant as it suggests that compounds 1 and 2 have a superior combination of binding affinity and selectivity compared to the reference compounds. These results validate the virtual screening approach, and show that the method can be used to identify compounds with high affinity and selectivity for a target nucleic acid, in this case the DNA TAT triplex.Figure 2.

Bottom Line: Further molecular docking studies using compounds with high structural similarity resulted in two compounds that were then demonstrated by competition dialysis to have a superior affinity and selectivity for the triplex nucleic acid than MHQ-12.Biophysical characterization of these compounds by circular dichroism and thermal denaturation studies confirmed their binding mode and selectivity.These studies provide a proof-of-principle for our integrated screening strategy, and suggest that this platform may be extended to discover new compounds that target therapeutically relevant nucleic acid morphologies.

View Article: PubMed Central - PubMed

Affiliation: James Graham Brown Cancer Center, Department of Biochemistry and Molecular Biology, University of Louisville, 529 S. Jackson Street, Louisville, KY 40202, USA.

ABSTRACT
Virtual Screening is an increasingly attractive way to discover new small molecules with potential medicinal value. We introduce a novel strategy that integrates use of the molecular docking software Surflex with experimental validation by the method of competition dialysis. This integrated approach was used to identify ligands that selectively bind to the triplex DNA poly(dA)-[poly(dT)](2). A library containing approximately 2 million ligands was virtually screened to identify compounds with chemical and structural similarity to a known triplex intercalator, the napthylquinoline MHQ-12. Further molecular docking studies using compounds with high structural similarity resulted in two compounds that were then demonstrated by competition dialysis to have a superior affinity and selectivity for the triplex nucleic acid than MHQ-12. One of the compounds has a different chemical backbone than MHQ-12, which demonstrates the ability of this strategy to 'scaffold hop' and to identify small molecules with novel binding properties. Biophysical characterization of these compounds by circular dichroism and thermal denaturation studies confirmed their binding mode and selectivity. These studies provide a proof-of-principle for our integrated screening strategy, and suggest that this platform may be extended to discover new compounds that target therapeutically relevant nucleic acid morphologies.

Show MeSH