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Rational design, synthesis, and verification of affinity ligands to a protein surface cleft
Author(s) -
Baumann Herbert,
Öhrman Sara,
Shinohara Yasuro,
Ersoy Oguz,
Choudhury Devapriya,
Axén Andreas,
Tedebark Ulf,
Carredano Enrique
Publication year - 2003
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.0236603
Subject(s) - chemistry , ligand (biochemistry) , sepharose , docking (animal) , elution , combinatorial chemistry , in silico , small molecule , active site , affinity chromatography , rational design , binding site , enzyme , stereochemistry , chromatography , biochemistry , nanotechnology , materials science , receptor , nursing , gene , medicine
The structure‐based design, synthesis, and screening of a glucuronic acid scaffold library of affinity ligands directed toward the catalytic cleft on porcine pancreas α‐amylase are presented. The design was based on the simulated docking to the enzyme active site of 53 aryl glycosides from the Available Chemicals Directory (ACD) selected by in silico screening. Twenty‐three compounds were selected for synthesis and screened in solution for binding toward α‐amylase using nuclear magnetic resonance techniques. The designed molecules include a handle outside of the binding site to allow their attachment to various surfaces with minimal loss of binding activity. After initial screening in solution, one affinity ligand was selected, immobilized to Sepharose (Amersham Biosciences), and evaluated as a chromatographic probe. A column packed with ligand‐coupled Sepharose specifically retained the enzyme, which could be eluted by a known inhibitor.