Fragment-based Screening by X-ray Structure Analysis

Abstract

Theˆrst 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. Theˆrst 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.Key words-X-ray structure analysis; fragment-based screening; fragment library

Technical Capabilities and Limitations of Optical Spectroscopy and Calorimetry Using Water-Miscible Solvents: The Case of Dimethyl Sulfoxide, Acetonitrile, and 1,4-Dioxane

“…For dissolving poorly soluble drug substances, it is customary to use a water-miscible solventddimethyl sulfoxide (DMSO); the drug substances dissolved in DMSO are then diluted into aqueous solution containing target macromolecules to induce drug-protein interactions. [1][2][3][4] However, DMSO can affect the performance of analytical techniques, such as signal/noise ratios and baseline stability, on account of its optical absorption and heat capacity. 5,6 Other water-miscible solvents should thus be tested as alternatives; for their successful application to drug-protein interaction analyses, it is necessary to clarify their applicability to the analytical techniques, that is, their technical capabilities and limitations, and their solubilization capacity for drug substances.…”