No abstract

Four new ligands that bind to the minor groove of DNA have been designed, synthesized, and evaluated by DNA footprinting. Two of the ligands are polyamides containing central regions with five or six N-methylpyrrole units, conferring hydrophobicity and good binding affinity but without retaining the correct spacing for hydrogen bonding in the base of the minor groove. The two remaining ligands have central regions which are head-to-head-linked polyamides, in which the linker is designed to improve the phasing of hydrogen bonding of the ligand with the floor of the minor groove. The highest affinity was obtained with the two polypyrroles without headgroup spacers, indicating that H-bond phasing is secondary in determining affinity compared to the major hydrophobic driving force. With a dimethylaminoalkyl group, representing a moiety with modest base strength, at both ends, water solubility is good and pH-partition theory predicts that penetration through lipid membranes will be enhanced, compared to strongly basic amidine analogues of the alkaloid precursors. All four compounds bind to DNA, with strong selectivity for AT sequences but some tolerance of GC base pairs and subtle individual preferences. The data show that very high affinities can be anticipated for future compounds in this series, but drug design must take account of overall physicochemical properties as well as the details of hydrogen bonding between ligands and the floor of the minor groove.

Molecular modelling studies showed that indole dicarboxylic acids are potential linkers for the synthesis of bis-netropsin analogues with a good fit to the minor groove of DNA. To test this hypothesis, 2-carboxyindole-6-acetic acid, indole-2,6-dicarboxylic acid, 6-(2-carboxyethyl)indole-2-carboxylic acid, 6-(2-carboxy-1-ethenyl)indole-2-carboxylic acid were prepared and coupled to 3-[1-methyl-4-(1-methyl-4-aminopyrrole-2-carboxamido)pyrrole-2-carboxamido]dimethylaminopropane. Similarly indole-2,5-dicarboxylic acid was prepared and coupled to 3-[1-methyl-4-(1-methyl-4-aminopyrrple-2-carboxamido)pyrrole-2-carboxamido]propionamidine hydrochloride. The derivatives of 26–28 showed especially strong binding to AT rich regions as shown by footprinting studies.

An analogue of LHRH containing an extension of Gly‐Cys at the carboxyl‐terminus has been designed to permit reproducible coupling to a suitably modified carrier via a thioether bond. Potential energy calculations indicated that this analogue adopted a conformation in solution virtually identical to the type II′ turn around Gly‐6—Leu‐7 predicted for native LHRH. Intradermal administration of a conjugate of this analogue with purified protein derivative of tuberculin to male rats previously primed with BCG vaccine rapidly led to complete testicular regression. This adjuvant‐free immunisation protocol may represent an alternative to castration for the veterinary control of reproductive function.