Protein affinity map of chemical space |
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Institution: | 1. Dipartimento di Informatica, Università degli Studi di Bari Aldo Moro, Via Orabona, 4 – 70125 – Bari, Italy;2. Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, P.zza L. da Vinci, 32 – 201233 – Milano, Italy\n;1. Robert Bosch GmbH, Germany;2. Ulm University, Germany;3. University of Twente, The Netherlands |
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Abstract: | Affinity fingerprinting is a quantitative method for mapping chemical space based on binding preferences of compounds for a reference panel of proteins. An effective reference panel of <20 proteins can be empirically selected which shows differential interaction with nearly all compounds. By using this map to iteratively sample the chemical space, identification of active ligands from a library of 30 000 candidate compounds has been accomplished for a wide spectrum of specific protein targets. In each case, <200 compounds were directly assayed against the target. Further, analysis of the fingerprint database suggests a strategy for effective selection of affinity chromatography ligands and scaffolds for combinatorial chemistry. With such a system, the large numbers of potential therapeutic targets emerging from genome research can be categorized according to ligand binding properties, complementing sequence based classification. |
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