To prevent Pneumocystic carinii pneumonia (PCP) in case of patients, with weakened immune systems (ex. AIDS, cancer, inherited immune deficiencies, or organ transplants), a bis-amidine aromatic compound - pentamidine (1,5-bis(4-amidinophenoxy)pentane) is used as a drug of second choice. The acute toxicity originally associated with pentamidine, have prompted investigations for new compounds with greater potency combined with lower toxicity. The binding affinity of bis-amidines to poly(dA)-poly(dT) DNA fragment correlated well with their in vitro activity against PCP.

The DNA binding affinity could be estimated by measurements of DNA phase transition temperature T_m. The higher this temperature is, the more stable DNA - ligand complex is formed.

Our aim was to compare the theoretically estimated binding energies of bis-amidines-DNA complexes with experimental differences of T_m temperature between free and bounded DNA. Optimized at DFT level structures were also compared with crystallographic data.

The results discussed in this work were obtained using resources of Interdisciplinary Centre for Mathematical and Computational Modelling Warsaw University.

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