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Molecules 2013, 18(10), 12051-12070; doi:10.3390/molecules181012051
Article

Identification of New Natural DNA G-Quadruplex Binders Selected by a Structure-Based Virtual Screening Approach

, , ,  and *
Received: 4 September 2013; in revised form: 18 September 2013 / Accepted: 22 September 2013 / Published: 30 September 2013
(This article belongs to the Special Issue G-Quadruplexes & i-Motif DNA)
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Abstract: The G-quadruplex DNA structures are mainly present at the terminal portion of telomeres and can be stabilized by ligands able to recognize them in a specific manner. The recognition process is usually related to the inhibition of the enzyme telomerase indirectly involved and over-expressed in a high percentage of human tumors. There are several ligands, characterized by different chemical structures, already reported in the literature for their ability to bind and stabilize the G-quadruplex structures. Using the structural and biological information available on these structures; we performed a high throughput in silico screening of commercially natural compounds databases by means of a structure-based approach followed by docking experiments against the human telomeric sequence d[AG3(T2AG3)3]. We identified 12 best hits characterized by different chemical scaffolds and conformational and physicochemical properties. All of them were associated to an improved theoretical binding affinity with respect to that of known selective G-binders. Among these hits there is a chalcone derivative; structurally very similar to the polyphenol butein; known to remarkably inhibit the telomerase activity.
Keywords: DNA; G-quadruplex; PDB; pharmacophore; natural compounds; virtual screening; docking DNA; G-quadruplex; PDB; pharmacophore; natural compounds; virtual screening; docking
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

Artese, A.; Costa, G.; Ortuso, F.; Parrotta, L.; Alcaro, S. Identification of New Natural DNA G-Quadruplex Binders Selected by a Structure-Based Virtual Screening Approach. Molecules 2013, 18, 12051-12070.

AMA Style

Artese A, Costa G, Ortuso F, Parrotta L, Alcaro S. Identification of New Natural DNA G-Quadruplex Binders Selected by a Structure-Based Virtual Screening Approach. Molecules. 2013; 18(10):12051-12070.

Chicago/Turabian Style

Artese, Anna; Costa, Giosuè; Ortuso, Francesco; Parrotta, Lucia; Alcaro, Stefano. 2013. "Identification of New Natural DNA G-Quadruplex Binders Selected by a Structure-Based Virtual Screening Approach." Molecules 18, no. 10: 12051-12070.


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