Synthesis of novel 9-O-N-aryl/aryl-alkyl amino carbonyl methyl substituted berberine analogs and evaluation of DNA binding aspects

This manuscript describes the design and synthesis of three 9-O substituted analogs of plant alkaloid berberine to enhance the DNA binding affinity. Three analogs of berberine with aryl/aryl-alkyl amino carbonyl methyl substituent at the 9-position of the isoquinoline chromophore were synthesized and characterized by NMR (1HNMR and 13C NMR) and mass spectroscopy. The products were evaluated for their binding to calf thymus DNA by a wide variety of techniques like spectrophotometry, spectrofluorimetry, circular dichroism, thermal melting, viscosity and isothermal titration calorimetry. The results revealed that these analogs showed more than six times higher binding affinity to DNA compared to berberine. From fluorescence and absorbance studies it was inferred that all the analogs bound to DNA non-cooperatively in contrast to the cooperative binding of the parent alkaloid berberine. The viscosity and ferrocyanide quenching experiments confirmed that the analogs are stronger intercalative binders to DNA useful for potential biological applications. Stronger binding of the analogs was also inferred from circular dichroism studies and thermal melting experiments. Thermodynamics of the binding from isothermal titration calorimetry experiments revealed an entropy driven binding for these analogs compared to the enthalpy driven binding of berberine. The small but negative heat capacity change of the analogs along with the significant enthalpy-entropy compensation phenomenon observed established the involvement of multiple weak noncovalent interactions in the binding process. A comparative study also revealed that the spacer length is also significant in modulating the DNA binding affinities.