2-Imidazole distamycin

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.

Figure 6B. Thermodynamic cycles for the calculation of the free energy difference of the binding of distamycin relative to 2-imidazole-distamycin at both sites of d(CGCAAGTTGGC)2.

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

The simultaneous mutation of 2-imidazole-distamycin to distamycin at both the sites I and II led to a free energy change of -1.8 kcal/mol (AGg - 2 AG3). The NMR experiments showed that the relative populations of Dst Dst DNA and 2-ImD 2-ImD DNA are 50 1 giving an experimental free energy difference of -2.3 kcal/mol (AG7 - AG2). This indicates that the favorable van der Waals interactions between distamycin and DNA at sites I and II and the stacking interactions between the two distamycin molecules stabilize the 2 1 Dst DNA complex over the 2 1 2-ImD DNA complex. The major destabilization factor for the 2 1 2-ImD DNA complex is the lack of... 

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