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SHOP: Scaffold HOPping by GRID-Based Similarity Searches
Umeå University, Faculty of Science and Technology, Chemistry.
2007 (English)In: Journal of Medicinal Chemistry, Vol. 50, no 11, 2708-2717 p.Article in journal (Refereed) Published
Abstract [en]

A new GRID-based method for scaffold hopping (SHOP) is presented. In a fully automatic manner, scaffolds were identified in a database based on three types of 3D-descriptors. SHOP's ability to recover scaffolds was assessed and validated by searching a database spiked with fragments of known ligands of three different protein targets relevant for drug discovery using a rational approach based on statistical experimental design. Five out of eight and seven out of eight thrombin scaffolds and all seven HIV protease scaffolds were recovered within the top 10 and 31 out of 31 neuraminidase scaffolds were in the 31 top-ranked scaffolds. SHOP also identified new scaffolds with substantially different chemotypes from the queries. Docking analysis indicated that the new scaffolds would have similar binding modes to those of the respective query scaffolds observed in X-ray structures. The databases contained scaffolds from published combinatorial libraries to ensure that identified scaffolds could be feasibly synthesized.

Place, publisher, year, edition, pages
2007. Vol. 50, no 11, 2708-2717 p.
URN: urn:nbn:se:umu:diva-16156DOI: doi:10.1021/jm061259gOAI: diva2:155829
Available from: 2007-08-21 Created: 2007-08-21 Last updated: 2011-01-11Bibliographically approved

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