All decisions should be made “as a team, driven by data and tools,” said Grieco. “The goal is to take the subjectivity out of library production decisions.”
Complete QC of one sample library at Infinity showed that only about 45% of the library had a target purity of 75% or higher (compared to the predicted and desired 90%). A review of QC testing revealed that the process was marred by inconsistent judgments, subjective decisions, limited standardization, and lack of data and consistency regarding the use of analytical systems and methods.
Changes instituted at Infinity gave the CM group responsibility for processing all pathway tests and QC data and for controlling the flow of data back to the chemists. Additionally, analytical methods were standardized, and recorded and analytical data was preserved in databases.
Grieco identified several specific strategies designed to improve workflow. For example, to minimize lost time for methods optimization, the company uses a small subset of early compounds to develop and optimize analytical methods. For compound encoding, Infinity uses a combination of radio-frequency identification and AC tags—lantern and transtem assemblies—and scans each tag as individual compounds are processed and moved from one microplate to another. After the chemistry group performs synthesis reactions, it sends the QC compounds to the analytical group for LCMS and the QC lanterns to the CM group. The chemistry group then reviews the LCMS results to determine whether the reactions proceeded as planned and to check the yields.
To preserve QC compound tracking during the cleavage steps, the cleavage reaction solutions are transferred from 96-well array plates to weighed, barcoded glass tubes, and then they are transferred to 384-well plates arrayed in four quadrants. The process of arraying, cleaving, and formatting about 10,000 compounds takes approximately three weeks.
High-throughput compound analysis at Infinity involves annotation of all chromatograms using tools and interfaces designed by the IT group. CM cherry-picks compounds based on the annotations and formats them for delivery to the customer.
A subsequent panel discussion, which focused on evaluating the value added by analytical analysis, emphasized the importance, at the outset, of defining the goals of analytical studies—to determine purity, concentration, and/or solubility, for example—and ensuring that the results contribute to the decision-making process.
The panelists were asked how to manage archives of older compounds, how to monitor their quality, and whether to periodically QC entire libraries. The response differed depending on the intended use of the compounds. For libraries used in high-throughput screening it might be sufficient to QC a subset of the collection, perhaps selecting compound sets based on chemical diversity.
“For lead optimization, you might want to know that what you have is the right stuff,” responded Rodney Bednar, Ph.D., senior investigator for pain research and chief drug discovery engineer for the facility for automation and screening technology at Merck Research Laboratories(www.merck.com).
QC analysis is a good idea “before sending a compound forward into development,” said Greg Nagy, Ph.D., research operations manager for materials management at Amgen (www.amgen.com). It is a matter of weighing the cost of a full analytical analysis with the cost and risk of moving ahead with a compound that may not be what you think it is. Consensus estimates for QC testing ranged from $2–3 per sample for in-house, high-throughput LCMS to $5–10 per sample for outsourcing to a CRO.
Dr. Nagy described Amgen’s tiered approach to the organization of libraries based on the purity of compounds. The company is in the process of converting from an archival approach to compound collection to a split storage strategy. One question is when to introduce online, high-throughput analytical technology, either at the point of use or earlier, when building a compound inventory. Dr. Nagy emphasized the importance of having in place a parallel IT initiative to look at the analytical data and provide real-time information on changes in a compound’s structure or activity.
In response to a query about whether to perform IC50 tests on HTS hits in liquid or powder form, Marybeth Burton, associate director for chemical technologies at Schering-Plough Research Institute (www.schering-plough.com), suggested QC analysis of hits in liquid form by the HTS group, and eventually, if the compound moves forward in development, the therapy group would QC the solid form.
When testing an historical library, there is no one ideal LCMS method or set of conditions for all compounds. Developing an LCMS strategy for high-throughput QC analysis “is a delicate balance between throughput and methodology,” said Burton.