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Synthesis of Substituted Derivatives of Plant Alkaloid Berberine And Studies on Their dna And Rna Binding Aspects

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Title Synthesis of Substituted Derivatives of Plant Alkaloid Berberine And Studies on Their dna And Rna Binding Aspects
 
Creator Basu, Anirban
 
Subject Chemistry
 
Description Berberine is one of the most widely distributed alkaloids in the plant kingdom. Berberine and related alkaloids have remarkable biological activity ranging from antileishmanial, antimalarial, antifungal to anticancer activity. More recently the antidiabetic activity and novel cholesterol lowering activity have also been revealed. DNA and RNA are believed to be the primary cellular target of this alkaloid in manifesting its biological activity particularly the anticancer activity. More efficient derivatives of this alkaloid with enhanced DNA and RNA binding efficacy are essential for effective biological applications. There are few reports that 9-position is an important determinant in the DNA and topoisomerase I binding of berberine. But no detailed studies exist on the interaction of 9-substituted analogs with DNA and RNA. Hence in this thesis a series of new 9-O-substituted berberine analogs have been synthesized and their DNA and poly(A) binding studies investigated using various biophysical technique.In the second chapter these analogs were evaluated for their binding to double stranded 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. The viscosity and ferrocyanide quenching experiments confirmed that the analogs are stronger intercalative binders to DNA, useful for further 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. A comparative study also revealed that the spacer length is also of significant importance in modulating the DNA binding affinities.
In the third and fourth chapters the novel analogs of berberine with aryl/arylalkyl amino carbonyl methyl substituent at the 9-position of the isoquinoline chromophore were evaluated for their binding to single (ss) and double stranded(ds) poly(A) by a wide variety of biophysical techniques. The results suggested that these analogs exhibited several fold higher binding affinity to ss poly(A) relative to berberine. Optical melting and the unique dilution experiments revealed that berberine analogs induced self-structure formation in ss poly(A) and the nature of the substituent was important for the ease of formation of self-structure. Energetics of the binding suggested an entropy driven binding for the analogs in sharp contrast to the enthalpy driven binding of berberine. The study also revealed that the spacer length at the 9-position had an important role in the self-structure formation.In the fifth chapter absorption, fluorescence, circular dichroism and microcalorimetry tchniques were employed to study the interaction of five 9-O-(ω-amino) alkyl ether analogs of berberine with double-stranded calf thymus DNA. The C-9 derivatization resulted in dramatic enhancements in the fluorescence emission of these compounds. Interaction of these analogs, which have an additional recognition motif with DNA, were evaluated through different spectroscopic and calorimetric titration experiments. The analogs remarkably enhanced the DNA binding affinity and the same was directly dependent on the alkyl chain length. The analog with six –CH2 groups enhanced the DNA binding affinity by about thirty three times compared to berberine. The binding became more entropically driven with increasing chain length.
In the sixth and seventh chapters the interaction of berberine and these five 9-O-(ω-amino) alkyl ether analogs with single and double stranded polyadenylic acid has been studied to understand the role of an additional anchoring module in the formation and/or amplification of self-structure in poly(A). The binding was characterized by absorption and fluorescence titration, Job plot and isothermal titration calorimetry. Self-structure formation was confirmed by circular dichroic melting, optical melting, and dilution experiments. Energetics of the interaction revealed that as the alkyl chain length increased, the binding was more entropy dominated. The results showed that berberine and all the analogs induced self-structure formation in poly(A). The length of the alkyl chain had a significant influence on the ease of formation of self-structure. New insights in terms of structural and thermodynamic aspects into self-structure formation in poly(A) by berberine analogs are revealed from these studies. Finally, the significant conclusions from these studies have been summarized at the end of the thesis.
 
Date 2012
 
Type Thesis
NonPeerReviewed
 
Format application/pdf
 
Identifier http://www.eprints.iicb.res.in/1986/1/Anirban_thesis.pdf
Basu, Anirban (2012) Synthesis of Substituted Derivatives of Plant Alkaloid Berberine And Studies on Their dna And Rna Binding Aspects. PhD thesis, Jadavpur University.
 
Relation http://www.eprints.iicb.res.in/1986/