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Ligand orientation target site

Figure 1 Examples of chiral metallointercalators that bind DNA with little site selectivity (above) and with high specificity for the targeted sites shown (below). In the center is shown schematically the basis for enantiomeric discrimination in stacking in the right-handed DNA helix. For the A-isomer, the ancillary ligands have a right-handed orientation in the DNA groove, whereas for the left-handed A-isomer, steric clashes between the ancillary ligands and phosphate backbone can develop. Figure 1 Examples of chiral metallointercalators that bind DNA with little site selectivity (above) and with high specificity for the targeted sites shown (below). In the center is shown schematically the basis for enantiomeric discrimination in stacking in the right-handed DNA helix. For the A-isomer, the ancillary ligands have a right-handed orientation in the DNA groove, whereas for the left-handed A-isomer, steric clashes between the ancillary ligands and phosphate backbone can develop.
A target site is characterized by different descriptors which can be used to orient a ligand in the site. Site characterization can be divided into two classes, based upon their use of geometric features and chemical functionality. Many programs have been developed we describe two examples to illustrate the different ideas SPHGEN (from the DOCK suite of programs) and Multiple Copy Simultaneous Search (MCSS). ... [Pg.1609]

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Ligand orientation

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