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Document Figure 6 Some WIN compounds depicting different rings and linkers. Note WIN 52452 has no C ring. motions, of up to approximately 4.5 Å, are most pronounced in the region of the GH loop. In contrast, HRV1A and HRV16, a minor and major receptor group virus respectively, have their pockets in open conformations even in the absence of drug [13,15]. For these serotypes, drug binding typically shifts positions of capsid atoms a maximum of 1 to 2 Å, smaller than those shifts seen in HRV14. Drugs bind in these pockets in a fashion similar to that seen in HRV14, extended and almost entirely buried by VP1. Page 499 The structures of five HRVs have been solved to date: HRVs 1A, 3, 14, 16, and 50. In all of these HRVs, as well as the polio- and coxsackie viruses, VP1 hydrophobic pockets have been observed [5,12,13,15,17,24,70,71] (HRV3, Zhao, R. et al., personal correspondence; HRV50, Giranda V. L. et al., unpub- http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_499.html (1 of 2) [4/9/2004 12:36:54 AM]
Document Figure 7 HRV14 VP1 hydrophobic pocket schematic with WIN 61605 illustrating some of the terminology commonly used to describe this pocket. Notice the GH loop separates the pocket from the canyon floor. Page 500 lished data). These pockets all share similar features and have been described as foot shaped, with a hydrophobic toe region, a heel region capable of hydrogen bonding, and a pore region near the ankle of the foot (Figure 7). Many of the picornavirus structures have been shown to have electron density in their VP1 pockets even in the absence of any added drug. These densities have been modeled as fatty acids or similar compounds [12,15,56,70–72]. The occurrence of these pocket factors have led some to hypothesize that these factors perform a similar function as do capsid-binding inhibitors, that is, to stabilize the virions [15,24,41,73,74]. Teleologically one could argue that the virion would pick up a fatty acid in its VP1 pocket before its egress from the cell, which would then stabilize the virion in transit to new hosts. The HRVs are known to be stable for long periods of time on surfaces and the dominant mode of transmission is thought to be hand-to-hand contact [75,76]. When a new host cell is reached, the stabilization factor might exit the pocket. This would allow the necessary conformational transition (probably at the GH loop) to occur and allow productive uncoating. A. Multiple Targets The use of these structures in a traditional structure-based drug design approach has been limited by the large number of unknown target serotype structures. There have been useful studies that have grouped picornaviruses based on their susceptibility to various antiviral agents (see below) [7,77]. However, in order to design a truly broad-spectrum single drug, the structural elements common among many serotypes must be considered. http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_500.html (1 of 2) [4/9/2004 12:37:20 AM]
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