May 6, 2025 | Lexington, MA

Purification of target compounds from crude synthetic mixtures has always been a rate limiting step in the new molecular entity discovery process. Typical technologies employed either have limited resolving power, but simple guiding principles (Flash Chromatography, TLC) or high resolving power but no simple universal rules (Mass-directed HPLC). Incorporating Agilent’s state-of-the-art Analytical-to Prep software in our purification process resulted in dramatic increase in throughput and significant decrease in turnaround time. Our overall process draws on the years of experience of our staff and has been utilized to purify thousands of compounds. This presentation describes the steps from prepurification to FinalQC and the best practices to obtain the preparative conditions to isolate the target molecules from a wide variety of synthetic mixtures. Several case studies will be presented.

Fully automated solid-phase peptide synthesis (SPPS) can produce hundreds, if not thousands, of peptides to propel medicinal chemistry programs in early drug discovery against targets of interest.  Due to substantial bottlenecks associated with manual purification, when using these high-throughput synthesis techniques, molecules are tested as crude mixtures ranging from 20-70% purities depending on peptide length and synthesis efficiency.  This can lead to confounded rank-ordering of active molecules, as well as preventing analysis of other key aspects of ‘drug-likeness’ such as solubility, biophysical characteristics, stability, etc.  Mass-guided, automated purification provides a dramatic benefit to exploration of structure-activity relationships and drug-like properties by expanding the purification bottleneck.  This presentation will describe the instrumentation, methods, and workflows associated with a typical peptide medicinal chemistry program, and how mass-guided auto-purification expands the screening funnel to provide more high-quality data for lead molecule discovery.

This talk will focus on enhancing efficiency and productivity within a high throughput separations lab. The presentation will explore equipment suggestions, lab optimization strategies, and 'best practices' to enhance the day-to-day operation of Agilent Preparative LCMS systems. Additionally, an alternative 'run engine' will be discussed for controlling Agilent ChemStation software, which facilitates the seamless interpretation of analytical datafiles and the generation of optimized preparative gradients.

Compound purification by liquid chromatography is part of an industrial process with the aim of obtaining ideally highly pure compounds after their separation from a crude mixture. But there is also a need of including aspects which will lead to more efficiency and cost reduction. The selection of the right column dimensions for your task, strategies for upscaling, the selection of the most affordable solvents, sample throughput and automation are often the variables which must be set with due diligence in advance. In this lesson we will learn how to differentiate between three selected common purification workflows, therefore I will guide you through the basics of method development from each of them.