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Bioorg Med Chem Lett. 2004 Oct 4;14(19):4843-6.

Modeling the binding affinities of beta-secretase inhibitors: application to subsite specificity.

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Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, PO Box 776, Spring House, PA 19477-0776, USA.


A new linear binding affinity model has been developed for hydroxyethylene based inhibitors of beta-secretase (BACE). This model is an improvement over a previously published model, and has been applied to a series of analogs not included in the training set. The linear model has been used to study subsite specificity for the P(2) through P(2)' positions, and to evaluate a small number of C-terminal analogs. The predicted rankings are in good agreement with experiment and support using this model for structure-based design of BACE inhibitors.

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