Weak affinity chromatography as a new approach for fragment screening in drug discovery

• Published in: Analytical biochemistry Vol. 414; no. 1; pp. 138 - 146
• Main Authors: Duong-Thi, Minh-Dao, Meiby, Elinor, Bergström, Maria, Fex, Tomas, Isaksson, Roland, Ohlson, Sten
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.07.2011
• Subjects: affinity chromatography; amidines; Amidines - chemistry; Amidines - pharmacology; Animals; Biochemistry; Biokemi; Biomedical Sciences; Biomedicinsk vetenskap; Cattle; Chromatography, Affinity - methods; dissociation; Drug design; Drug discovery; Drug Discovery - methods; drugs; Fragment screening; Fragment-based drug discovery; high performance liquid chromatography; Humans; Mass spectrometry; screening; Small Molecule Libraries; thrombin; Thrombin - antagonists & inhibitors; Thrombin - metabolism; trypsin; Trypsin - metabolism; Trypsin Inhibitors - chemistry; Trypsin Inhibitors - pharmacology; Weak affinity chromatography; Weak affinity chromatography; Fragment screening; Drug design; Drug discovery; Mass spectrometry; Fragment-based drug discovery
• ISSN: 0003-2697; 1096-0309; 1096-0309
• DOI: 10.1016/j.ab.2011.02.022

Fragment-based drug design (FBDD) is currently being implemented in drug discovery, creating a demand for developing efficient techniques for fragment screening. Due to the intrinsic weak or transient binding of fragments (mM–μM in dissociation constant ( K D)) to targets, methods must be sensitive enough to accurately detect and quantify an interaction. This study presents weak affinity chromatography (WAC) as an alternative tool for screening of small fragments. The technology was demonstrated by screening of a selected 23-compound fragment collection of documented binders, mostly amidines, using trypsin and thrombin as model target protease proteins. WAC was proven to be a sensitive, robust, and reproducible technique that also provides information about affinity of a fragment in the range of 1 mM–10 μM. Furthermore, it has potential for high throughput as was evidenced by analyzing mixtures in the range of 10 substances by WAC–MS. The accessibility and flexibility of the technology were shown as fragment screening can be performed on standard HPLC equipment. The technology can further be miniaturized and adapted to the requirements of affinity ranges of the fragment library. All these features of WAC make it a potential method in drug discovery for fragment screening.