title: Sequence specific binding of beta carboline alkaloid harmalol with deoxyribonucleotides: binding heterogeneity, conformational, thermodynamic and cytotoxic aspects.
abstract: BACKGROUND
  Base dependent binding of the cytotoxic alkaloid harmalol to four synthetic polynucleotides, poly(dA).poly(dT), poly(dA-dT).poly(dA-dT), poly(dG).poly(dC) and poly(dG-dC).poly(dG-dC) was examined by various photophysical and calorimetric studies, and molecular docking.
  
  
  RESULTS
  Binding data obtained from absorbance according to neighbor exclusion model indicated that the binding constant decreased in the order poly(dG-dC).poly(dG-dC)>poly(dA-dT).poly(dA-dT)>poly(dA).poly(dT)>poly(dG).poly(dC). The same trend was shown by the competition dialysis, change in fluorescence steady state intensity, stabilization against thermal denaturation, increase in the specific viscosity and perturbations in circular dichroism spectra. Among the polynucleotides, poly(dA).poly(dT) and poly(dG).poly(dC) showed positive cooperativity where as poly(dG-dC).poly(dG-dC) and poly(dA-dT).poly(dA-dT) showed non cooperative binding. Isothermal calorimetric data on the other hand showed enthalpy driven exothermic binding with a hydrophobic contribution to the binding Gibbs energy with poly(dG-dC).poly(dG-dC), and poly(dA-dT).poly(dA-dT) where as harmalol with poly(dA).poly(dT) showed entropy driven endothermic binding and with poly(dG).poly(dC) it was reported to be entropy driven exothermic binding. The study also tested the in vitro chemotherapeutic potential of harmalol in HeLa, MDA-MB-231, A549, and HepG2 cell line by MTT assay.
  
  
  CONCLUSIONS
  Studies unequivocally established that harmalol binds strongly with hetero GC polymer by mechanism of intercalation where the alkaloid resists complete overlap to the DNA base pairs inside the intercalation cavity and showed maximum cytotoxicity on HepG2 with IC50 value of 14 µM. The results contribute to the understanding of binding, specificity, energetic, cytotoxicity and docking of harmalol-DNA complexation that will guide synthetic efforts of medicinal chemists for developing better therapeutic agents.
authors.affiliation: Department of Zoology, University of Kalyani, Nadia, West Bengal, India.
authors.forename: Sarita
authors.initials: S
authors.lastname: Sarkar
authors.affiliation: Department of Zoology, University of Kalyani, Nadia, West Bengal, India.
authors.forename: Prateek
authors.initials: P
authors.lastname: Pandya
authors.affiliation: Department of Zoology, University of Kalyani, Nadia, West Bengal, India.
authors.forename: Kakali
authors.initials: K
authors.lastname: Bhadra
mesh_terms: D045744:Cell Line, Tumor; D002942:Circular Dichroism; D006246:Harmaline / Q000031:analogs & derivatives* / Q000378:metabolism; D006801:Humans; D008968:Molecular Conformation
chemical_list: C007904:harmalol; D006246:Harmaline