• Aqeel Khan

Student thesis: Phd


Benzimidazoles are heterocyclic compounds. Symmetrical and unsymmetrical benzimidazoles/ oligomers are minor groove DNA sequence selective binding compounds. Distamycin A and netropsin are examples of naturally occurring DNA binders. Hoechst 33258 (Bis-benzimidazole) is a synthetic minor groove A-T sequence selective reagent and has in vivo activity by inhibiting the topoisomerase II enzyme.The targets in this research work were to synthesise extended analogues of Hoechst with structural modifications (amide bond) or amide-linked dimers with a view to identifying new potential ligands. To synthesise a library of novel bis-benzimidazoles (analogues of Hoechst) several methods were used. For C5-C2 direct linkage aldehyde synthesis via ester, Weinreb amide reduction, condensation of acids with diamine by Eaton's reagent were applied. Cyclization of amide-linked benzimidazoles (amide bond between carboxylic acid of C5 benzimidazole and diamine), an indirect method of bis-benzimidazole synthesis was also used to prepare a library of novel bis-benzimidazoles giving a series of novel intermediates. Higher molecular weight oligomeric structures (Linked by amide bond either between C5-C5 or C5-C2) were prepared by using (EDCI / HOBt) or (HBTU / DIPEA). A library of novel amide-linked, oligomeric analogues of Hoechst were also synthesised by coupling bis-benzimidazole building blocks bearing reactive groups at positions 2 or 5. Amine (by the reduction of a nitro precursor) or carboxylic acid (from ester hydrolysis) was coupled with monomeric amino or carboxylic acid benzimidazole derivatives using different peptide coupling reagents. Further structural modifications were performed either by reduction of an ester on a bis-benzimidazole or by the reaction of hydrazine with the ester or acid to have an additional flexible spacer (amide bond) with reactive amine to address the issue of solubility.SPR (Surface Plasmon Resonance) was employed to evaluate more than 30 different analogues in comparison with Hoechst 33258 in terms of their DNA binding affinity using three different oligonucleotides having A2T2, A3T3, A4T4 sequences. The data revealed that compounds with charged specie at peripheral groups are better binders in the grooves of DNA.
Date of Award31 Dec 2010
Original languageEnglish
Awarding Institution
  • The University of Manchester
SupervisorJohn Gardiner (Supervisor)

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