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Document Page 506 Compound Width. Bulk considerations have also been examined for the phenoxy or B ring [80]. In HRV14, which has a long narrow pocket, compounds with no substituents on the phenoxy ring were the most potent. However most other serotypes were more sensitive to compounds with substituents on the phenoxy ring, either a dimethyl or a dichloro. The serotypes that preferred disubstituted compounds included HRV1A and 50, both known to have wider, shorter pockets (Table 4). This is also in agreement with the drug-clustering analysis discussed above [7]. Induced VP1 Pocket Changes. The shape constrains discussed above are by nature somewhat qualitative. The precision with which one could predict the binding energy of a compound based on its shape is limited by the ability of the pocket to conform to its occupant. Conformational changes within the pocket are most pronounced between native and drug-bound HRV14, but present to a lesser extent in both HRV1A and 16. The extent of conformational changes produced by different drugs on the same virus may differ. This observation is illustrated in a study of a compound SCH 38057 in HRV14. This compound has a substantially different structure than the WIN compounds, and when bound to HRV14, induces changes in HRV14 that are also quite different from changes resulting from the binding of a WIN compound [62]. The ability of compounds to effect conformational changes in the capsid when bound and the variability of these changes both between drug classes and viral serotypes have made a priori predictions of potency based on shape considerations very difficult. Comparative Molecular Field Analysis (CoMFA) studies has been useful, when examining similar compounds in a single serotype (HRV14), in demonstrating spatial constraints [85], but generalizing these constraints over many serotypes and drug classes is much more difficult. http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_506.html [4/9/2004 12:41:41 AM]
Document Hydrophobicity Requirements Drug binding is enhanced by hydrophobicity in that portion of the drug that binds to the pocket toe. Quantitative structure-activity relationship (QSAR) analysis of these compounds have consistently shown that the most predictive parameter of antiviral activity is a measure of hydrophobicity, the octanol:water partition coefficient (logP) [80,82,85]. These studies have also consistently shown that there is no apparent correlation between electrostatic potential or dipole moment and potency. Page 507 This evidence suggests that the drug—pocket interactions in the toe of the pocket are low-intensity hydrophobic interactions. Supporting this hypothesis is the finding that many structurally diverse molecules can be accommodated in this region, and even structurally similar molecules can bind in distinctly different conformations. Closely related structures have been shown to shift along their long axis by as much as 1.6 Å with respect to their phenoxy substituents [55]. There is even more variability with respect to the isoxazole placement (Table 5, Figure 9). No single hydrogen-bonding or electrostatic interaction appears to predominate within the pocket toe. http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_507.html [4/9/2004 12:42:05 AM]
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Structure-based Drug Design 14 Stru
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