Minor binding mode

The most important aspect of coralyne is its ability to inhibit DNA relaxation in a fashion significantly similar to the most potent antitumour alkaloid camptothecin, which is known to exert this property [242], Presumably, the most notable biological action of these alkaloids appears to be topoisomerase inhibition [238-242], which has direct relevance to their DNA intercalating property. In this context. Pilch et al. [167] described a mixed binding mode model (Fig. 16) in which the protoberberine structure constitutes portions that can intercalate or bind to the minor groove of DNA. Wang et al. [240] demonstrated that coralyne (Ci) and several of its derivatives (Ce to Ch) (Scheme 5), including the partial saturated... 

Interestingly, all ligands reported in Table 7.4 revealed the same binding mode to DNA. In detail, 6-18 bind to the dodecamer s minor groove from the fourth pair of nucleotides until the ninth pair. This feature permits the investi-... 

Fig. 4.2.2. Binding modes of typical stains used for homogenous detection of double stranded DNA. Binding to the minor groove or intercalation between base pairs can lead to fluorescence enhancement.

The difference in the preferred binding mode observed for the Pd- and Ni-based catalysts can be the crucial factor determining activity/inactivity of these two systems in polar copolymerization. However, the question arises about the stability of the alternative binding modes at finite temperature. If the minima were separated by relatively low barriers and fast interconversion between the two isomer complexes could occur, then this difference would be of minor importance. In order to check the stability of the two modes and get the insight into the mechanism of possible interconversions, a series of molecular dynamics simulations was performed. 

Table I shows examples of the steady-state and time-resolved emission characteristics of [Ru(phen)2(dppz)]2+ upon binding to various DNAs. The time-resolved luminescence of DNA-bound Ru(II) is characterized by a biexponential decay, consistent with the presence of at least two binding modes for the complex (47, 48). Previous photophysical studies conducted with tris(phenanthroline)ruthenium(II) also showed biexponential decays in emission and led to the proposal of two non-covalent binding modes for the complex (i) a surface-bound mode in which the ancillary ligands of the metal complex rest against the minor groove of DNA and (ii) an intercalative stacking mode in which one of the ligands inserts partially between adjacent base pairs in the double helix (36, 37). In contrast, quenching studies using both cationic quenchers such as [Ru(NH3)6]3+ and anionic quenchers such as [Fe(CN)6]4 have indicated that for the dppz complex both binding modes...

A different example is provided by a set of elastase inhibitors. These ligands are also related by continuous SARs. This is reflected by the presence of highly potent inhibitors with diverse structures and, in addition, structurally similar ligands that display only minor potency differences. However, in contrast to factor Xa, 3D analysis reveals a more complex picture. Specifically, elastase accepts multiple binding modes, each of which is adopted by structurally... 

Multiple Binding Modes. Realistically, congeneric series that can be a useful construct exist only in the mind of the medicinal chemist. The orientation of the drug in the active site depends on a multitude of interactions and a minor perturbation in structure can destabilize the predominant binding mode, in favor of another. As examples, detailed... 

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