Streamlined Approach to the Crude Compound Purification to Assay Process

Abstract

Purification of medicinal chemistry compounds is often the slow step in the drug‐discovery process, particularly for compounds generated through parallel synthesis. To address this bottleneck we have developed a fully automated purification platform using a preparative‐LC/MS with a customized compound analysis requestor and a data tracking‐handling program. The six workstations that comprise the platform are an 8‐channel MUX, a mass‐directed Prep‐LC/MS, a liquid handling system, a balance automator, an evaporation system, and a central PC that runs the core program. The first step involved in the library purification, following the electronic submission of the dry crude synthetic material submitted in a barcoded plate, consists of automatic dissolution of the material and transfer of an aliquot for pre‐purification QC. Subsequent steps involve generation of a sequence list consisting of the methods for the analysis and processing, automatic generation of a sequence of the confirmed wells for LC/MS purification, evaporation, fraction dissolution and pooling, automatic weighing, and calculation of the amount needed to make a specified concentration. The final step involves compound distribution into a solubilization tube for the biochemical assay and plates for post‐purification QC by LC/MS and NMR. Functions incorporated into the core program were written in CSharp (C#) and Microsoft.NET to create a sample sequence list, annotate wells, track purification status, and to enable on‐line retrieval of pre‐ and post‐purification data. This platform enables a complete informatics solution from crude compound in a plate to purified compound ready for storage and assay. The processes and results for compounds purified at the multi‐milligram level by automated Prep‐LC/MS will be described.

Keywords:

• Streamlined approach
• Purification
• Process

Acknowledgments

The authors thank Zheng Hua, Doug Overland, and Wyeth Jones who were the members of the previous version of this platform. We are also grateful for the invaluable discussions and brainstorming sessions we had with Yining Zhao before transitioning to Pfizer, La Jolla CA. In addition, we thank Adrian Smith for the initial set up of the purification system and Scott Harried for his trust in the use of his library as a first purified batch with this new program.