Pentamidine

A major impetus for studies on aromatic bis-amidinium compounds has been the finding that 1,5-bis(4-amidinophenoxy)pentane 22 (“pentamidine”) has clinical activity in the treatment of Pneumocystis carinii pneumonia, the commonest opportunistic life-threatening infection in AIDS patients. Pentamidine is one of the drugs of choice in treating this pathogen, although its effectiveness is limited and it causes a number of side-effects such as leucopenia and hypoglycaemia. Pentamidine and a number of closely-related analogues have been shown to bind to duplex DNA, with a preference for A/T sequences. Footprinting studies have shown that the binding site size for both pentamidine and its short-chain analogue propamidine is approximately four base pairs, with neither drug tolerating a G:C base pair within the site. These conclusions are in agreement with X-ray crystallographic studies of propamidine and pentamidine complexes with the sequence d(CGCGAATTCGCG).

In an effort to elucidate the binding mode of complexes 4–6, fluorescence quenching (Qvalues) of duplex adenine–thymine (A–T) and guanine–cytosine (G–C) polymers were conducted. Under conditions of limited Et bound to an excess of DNA, exogenous intercalating agents (e.g. actinomycin D) demonstrate high affinities toward G–C base pairs, while minor groove binding species (e.g. pentamidine) prefer A–T base paired regions. Complexes 4–6 display greater affinities toward poly[d(A–T)] ₂ than pentamidine but low Q values are also evident within poly[d(G–C)]₂, possibly indicating flexible or multimodal binding.

This work arouse in the context of our recent studies on the development of fluorogenic aza-bisbenzamidines DNA binders. Bisbenzamidines like pentamidine (1b) are attractive drugs from the clinical point of view, as they display antiparasitic and antifungal activities. Indeed pentamidine is indicated for treatment of Pneumocystis carinii, Leishmaniasis or early-phase African sleeping sickness, among other diseases. It is believed that the biological activity results from its binding to short stretches of A/T-rich DNA sequences, binding which requires the presence of the amidinium groups because they establish hydrogen bonds with the edges of the bases and make electrostatic contacts with the bottom of the minor groove.

Increasing the sodium concentration in the sample to the physiological level cancels the ICD signals of PNT but a small UV hypochromism still can be observed (ESI,† Fig. S7). The physiological sodium concentration used here (140 mM) is characteristic to the extracellular space. However, intracellular organelles such as lysosomes are featured with lower cationic contents, ~60 mM Na⁺ and ~20 mM K⁺, that is very close to the ionic strength used in the present study (80–100 mM Na⁺, see Table 1). Importantly, the catabolism of GAGs is intimately related to lysosomes and pentamidine was shown to be selectively accumulated in these subcellular compartments. Accordingly, by non-covalent association with GAGs, pentamidine (and presumably berenil) may perturb a lysosome function.