J Chem Inf Model - Scaffold hopping by fragment replacement.

Tópicos

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Resumo

This work describes a data driven method for scaffold hopping by fragment replacement. A search database of scaffolds is created by cutting bonds of existing compounds in a combinatorial fashion. Three-dimensional structures of the scaffolds are then generated and made searchable based on the relative orientation of the broken bonds using an auxiliary index file. The retrieved scaffolds are ranked using volume overlap and electrostatic similarity scores. A similar approach has been used before in the program CAVEAT and others. The present work introduces a novel indexing scheme for the attachment vector geometry, which allows for fast searching. A scaffold shape descriptor is defined, which allows for queries with a single attachment vector (R-groups) and improves the shape similarity between the query and the suggested replacement fragments. The program, called Scaffold Hopping, is shown to retrieve relevant bioisosteric replacement scaffolds for a set of example queries in a reasonable time frame, making the program suitable to be used in drug design work.

Resumo Limpo

work describ data driven method scaffold hop fragment replac search databas scaffold creat cut bond exist compound combinatori fashion threedimension structur scaffold generat made searchabl base relat orient broken bond use auxiliari index file retriev scaffold rank use volum overlap electrostat similar score similar approach use program caveat other present work introduc novel index scheme attach vector geometri allow fast search scaffold shape descriptor defin allow queri singl attach vector rgroup improv shape similar queri suggest replac fragment program call scaffold hop shown retriev relev bioisoster replac scaffold set exampl queri reason time frame make program suitabl use drug design work

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