Distamycin

To 17 C of a culture obtained by submerged fermentation as mentioned above, siliceous earth is added and the batch is filtered. The mixture of mycelium and the siliceous earth are agi-tatedforl hour with 2.5 Cof butanol. This treatment is repeated twice. Thebutanolic extracts are combined, washed with water, evaporated to dry ness (about 10 g) and boiled with acetone (80 ml). The residue (5.41 g of yellowish powder) is distamycin. 

Fig. 3.1 Schematic representation of the two modes of distamycin DNA complexes with putative hydrogen bonds shown as dashed lines. Circles with dots represent lone pairs of N(3) of purines and 0(2) of pyrimidines...

SCHUHMANN, E., I. HaUPT, H. ThRUM, U. Taubeneck, and U. May. Effect of distamycin A and netropsin on normal cells and wall-less cells of Escherichia coli W 1655 F+. Zeitschrififot Allg. Mikrobiologie 1974, 14, 321-327. 

Verini, M.A. and M. Ghione. Activity of distamycin A on vaccinia virus infection of cell cultures. Chemotherapia 1964, 9, 144-157. 

Mars, G. and U. Regoli. Su di Un. Me-todo clinico-farmacologico per valutare I attivia antivirale della distamycin A. ain. Ter. 1968, 30, 573-580. 

Lombardi, P. and A. Crisanti. Antima-larial activity of synthetic analogues of distamycin. Pharmacol. Then 1997, 76, 125-133. 

Kopka, M.L, C. Yoon, D. Goodsell, P. Pjura, and R.E. Dickerson. The molecular origin of DNA drug specificity in ne-tropsin and distamycin. Proc. Natl. Acad. Sci. USA 1985, 82, 1376-1380. 

Coll, M., C. A. Erederick, A. H. J. Wang, and A. Rich. A bifurcated hydrogen-bonded conformation in the D(A-T) base-pairs of the DNA dodecamer D(CGCAAATTTGCG) and its complex with distamycin. Proc. Natl. Acad. Sci. USA 1987, 84, 8385-8389. 

Nature provides examples of sequence-selective minor groove binding, such as antibiotics including netropsin, distamycin, anthelvencin, and kikumycin. 

Dolenc, J. Oostenbrink, C. Koller, J. van Gunsteren, W.F., Molecular dynamics simulations and free energy calculations of netropsin and distamycin binding to an AAAAA DNA binding site, Nucl. Acids Res. 2005, 33, 725-733. 

Some of the best characterized ligands that bind in the minor groove of DNA are distamycin and netropsin. Both these molecules are long and flat and are sterically and electrostatically complementary to the characteristics of the minor groove of DNA. Distamycin and netropsin are known to have specific affinity towards the minor groove of AT rich regions of B-DNA. 

The electrostatic potential calculations have shown that the minor groove of AT rich B-DNA sequence has the lowest negative potential.15 This led to the implication that the cationic drugs will exhibit binding specificity to the minor groove regions of AT rich sequences. The crystal structure of a DNA distamycin complex showed that there is only one molecule bound to the minor groove of an AATT DNA site.2 However, experimental studies... 

The free energy calculations with complexes of oligomeric DNA with distamycin and netropsin presented in this chapter were carried out using the AMBER force field2 and the AMBER software.21 The associated potential energy function is ... 

The MD simulations were carried out under standard temperature and pressure. A 1 fs time step was used with SHAKE25 applied to bonds. A 2 fs time step with SHAKE was used in the d(IC)6 d(IC)6 —> d(GC)6 d(GC)6 calculations. The non-bonded interactions for DNA complexes were subject to 10 -12 A spherical cutoff whereas no cutoff was applied to solute-solute interactions to avoid cutoff artifacts on coulombic interactions between sodium ions with phosphates. In the case of d(IC)6 d(IC)6 —> d(GC)6 d(GC)6 calculations an 8 A spherical cutoff was applied to non-bonded interactions. A weak harmonic restraint of 5.0 kcal/mol was imposed to avoid the disruption of terminal base pairs during FEP simulations of netropsin —> 0 and 2-imidazole-distamycin —> distamycin calculations. 

Relative Free Energy of Binding of [d(CGCAAGTTGGC)]219 to 2-Imidazole-distamycin versus Distamycin... 

Figure 5. Solution structure16 of 2 1 complex 2-imidazole-distamycin bound to [d(CGCAAGTTGGC)]2 shown in stereo.

The mutation of 2-ImD to distamycin at site I led to a free energy difference of 0.65 kcal/mol (AG4- AG3) (Table 3). This calculation showed that distamycin has weaker affinity for [d(CGCAAGTTGGC)]2 at site I relative to that of 2-ImD. The NMR experiments carried out in Wemmer s... 

Figure 6A. Thermodynamic cycles for the calculation of the free energy difference of the binding of distamycin relative to 2-imidazoIe-distamycin at two adjacent sites of d(CGCAAGTTGGC>2.

TableRelative free energy differences between the binding of distamycin and 2-imidazole-distamycin to [d(CGCAAGTTGGC)]2...

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