Molecular recognition and physicochemical properties in the discovery of selective antibacterial minor groove binders

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Suckling, C.J. (2008) Molecular recognition and physicochemical properties in the discovery of selective antibacterial minor groove binders. Journal of Physical Organic Chemistry, 21 (7-8). pp. 575-583. ISSN 0894-3230 (http://dx.doi.org/10.1002/poc.1323)

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Abstract

The polyamide minor groove binders (MGBs), distamycin and netropsin, have been known for many years to have significant biological activities but high toxicity. Strategies are described for the development of more selective MGBs taking advantage of hydrophobic interactions with the minor groove of DNA. The introduction of branched alkyl side chain substituents, planar aromatic head groups and alkene isosteres of the amides have all been investigated. MGBs designed using these strategies and built from heterocyclic and aromatic amino acids with the ability to recognise short sequences of DNA have been found to be potent and selective antibacterial agents. Detailed structural and strength of binding investigations (NMR, capillary electrophoresis (CE), DNA footprinting, melting temperature measurement, ITC) show that their activity depends primarily upon molecular recognition in terms of both molecular shape and specific hydrogen bonding. However the lack of toxicity depends upon their basic tail group structure, the pKa of which has a major influence on access to bacterial and mammalian cells. Lead compounds are active in vivo at doses competitive with recently introduced antibacterial drugs.

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