6S15

Pyridine derivative of the natural alkaloid Berberine as Human Telomeric G-quadruplex Binder


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.268 

wwPDB Validation 3D Report Full Report



Literature

Pyridine Derivative of the Natural Alkaloid Berberine as Human Telomeric G4-DNA Binder: A Solution and Solid-State Study.

Papi, F.Bazzicalupi, C.Ferraroni, M.Ciolli, G.Lombardi, P.Khan, A.Y.Kumar, G.S.Gratteri, P.

(2020) ACS Med Chem Lett 11: 645-650

  • DOI: 10.1021/acsmedchemlett.9b00516
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Telomerase is an enzyme deputed to the maintenance of eukaryotic chromosomes; however, its overexpression is a recognized hallmark of many cancer forms. A viable route for the inhibition of telomerase in malignant cells is the stabilization of G-quad ...

    Telomerase is an enzyme deputed to the maintenance of eukaryotic chromosomes; however, its overexpression is a recognized hallmark of many cancer forms. A viable route for the inhibition of telomerase in malignant cells is the stabilization of G-quadruplex structures (G 4 ) at the 3' overhang of telomeres. Berberine has shown in this regard valuable G 4 binding properties together with a significant anticancer activity and telomerase inhibition effects. Here, we focused on a berberine derivative featuring a pyridine containing side group at the 13th position. Such modification actually improves the binding toward telomeric G-quadruplexes and establishes a degree of selectivity in the interaction with different sequences. Moreover, the X-ray crystal structure obtained for the complex formed by the ligand and a bimolecular human telomeric quadruplex affords a better understanding of the 13-berberine derivatives behavior with telomeric G 4 and allows to draw useful insights for the future design of derivatives with remarkable anticancer properties.


    Organizational Affiliation

    Department NEUROFARBA - Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via U. Schiff 6, 50019 Sesto Fiorentino, Florence, Italy.



Macromolecules
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
DNA TAGGGTTAGGGTA, B12synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KQT
Query on KQT

Download CCD File 
A
Berberine
C28 H27 N2 O4
QVKHJFYKHMGTFF-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.268 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.25α = 90
b = 41.25β = 90
c = 68.6γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-06-03
    Type: Initial release