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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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Induced circular dichroism results for (A) compound 1 and (B) compound 2. (A) Spectra are shown for a ligand concentration of 45 μM in the presence of triplex DNA ranging from 5 μM to 450 μM triplets. (B) Spectra are shown for a ligand concentration of 22.5 μM in the presence of triplex DNA ranging from 2.25 μM to 225 μM triplets.
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Figure 3: Induced circular dichroism results for (A) compound 1 and (B) compound 2. (A) Spectra are shown for a ligand concentration of 45 μM in the presence of triplex DNA ranging from 5 μM to 450 μM triplets. (B) Spectra are shown for a ligand concentration of 22.5 μM in the presence of triplex DNA ranging from 2.25 μM to 225 μM triplets.

Mentions: The interaction of compounds 1 and 2 with DNA was studied by circular dichroism (Figure 3). Both compounds show pronounced induced circular dichroism (ICD) in the presence of triplex DNA. The ICD is in a spectral range where the compounds absorb light but the DNA does not. This ICD is unambiguous proof of the ligand binding to triplex DNA. For both compounds 1 and 2, the ICD is negative in sign, and relatively weak in magnitude. Such behavior is consistent with an intercalative binding mode, although the mode of binding can only be definitively established by high-resolution experimental structural analysis (50).Figure 3.


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)

Induced circular dichroism results for (A) compound 1 and (B) compound 2. (A) Spectra are shown for a ligand concentration of 45 μM in the presence of triplex DNA ranging from 5 μM to 450 μM triplets. (B) Spectra are shown for a ligand concentration of 22.5 μM in the presence of triplex DNA ranging from 2.25 μM to 225 μM triplets.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 3: Induced circular dichroism results for (A) compound 1 and (B) compound 2. (A) Spectra are shown for a ligand concentration of 45 μM in the presence of triplex DNA ranging from 5 μM to 450 μM triplets. (B) Spectra are shown for a ligand concentration of 22.5 μM in the presence of triplex DNA ranging from 2.25 μM to 225 μM triplets.
Mentions: The interaction of compounds 1 and 2 with DNA was studied by circular dichroism (Figure 3). Both compounds show pronounced induced circular dichroism (ICD) in the presence of triplex DNA. The ICD is in a spectral range where the compounds absorb light but the DNA does not. This ICD is unambiguous proof of the ligand binding to triplex DNA. For both compounds 1 and 2, the ICD is negative in sign, and relatively weak in magnitude. Such behavior is consistent with an intercalative binding mode, although the mode of binding can only be definitively established by high-resolution experimental structural analysis (50).Figure 3.

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