Fragment-based Screening by X-ray Structure Analysis

The first step of FBDD is fragment-based screening (FBS). There are various analytical methods used to perform FBS: NMR, X-rays, SPR, etc. The advantage of X-ray structure analysis in FBS is that it can cope with relatively large structural changes upon the binding of a fragment and unexpected events such as multiple binding. The first thing needed to perform FBS by X-rays is a fragment library. The library currently employed at our laboratory was designed especially for X-ray structure analysis and consists of 384 compounds. This library was built based on Ro3 and special attention was given to eliminating ambiguity when interpreting electron density. FBS by X-rays requires more than 100 times more data collection and structure analysis. Recent development of critical technologies dramatically reduced the time required for X-ray structure analysis. Additionally, development of software and the incorporation of an industrial robot to a laboratory system has enabled us to construct a fully automated structure analysis system. However, there still are some limitations to X-ray structure analysis. It demands hundreds of high quality crystals and those crystals must not only survive soaking of compounds dissolved in DMSO but also be resistant to X-ray damage. In this article, a practical example of FBS by X-rays will be presented using HSP90 along with facts on the limitations of X-rays.