October 1, 2012 (Vol. 32, No. 17)
The advent of high-throughput screening (HTS) and robotic automation also saw an evolution in compound-management tools.
New technologies, as well as steady increases in available compounds, have made organizing and managing the libraries of chemicals, compounds, and other reagents used by research labs a major challenge. More than ever before, labs are incorporating automated solutions for liquid handling, compound retrieval, and sample barcoding, for example.
“Whether it is preparing millions of compounds for screening, or a few for lead optimization, compound management is now heavily reliant on automation that is directly connected to inventory management software for quick and accurate delivery of requested compounds,” said Dan Hascall, senior scientific manager at Genentech.
What are the effects of new, automated, and faster technologies on compound management? Do labs need them, and are they helping? Last month in Boston, several experts spoke about innovative compound-management practices at the IQPC conference on “Compound Management and Integrity”. Their insights hold promise for those trying to understand the issues and possible solutions in compound management today.
Software Holds It All Together
Recently, a group from the University of Michigan developed a new, secure, web-based open-source application called MScreen, that is designed to organize and run HTS and compound management. Described in an application note in this month’s issue of the Journal of Biomolecular Screening, MScreen is free to academic and nonprofit institutions, and available by license for industry.
Though its main focus is HTS, it also facilitates compound management, governing standard tasks such as debiting volumes while loading screening plates, for example. But MScreen can also accomplish other jobs, such as making and handling mixture plates for screening multiple compounds simultaneously. It shows you views of each well and the compounds contained within the well, with thumbnails of each compound’s structure, to which is linked the complete information on the individual compounds.
An MScreen author Richard Neubig, M.D., Ph.D., professor of pharmacology, and co-director of the Center for Chemical Genomics at the University of Michigan, says that MScreen also has a unique ability to handle compounds and extracts.
“[This is useful] if you have an unknown mixture,” said Dr. Neubig. “MScreen has a large collection of natural extracts. We can also link those to the constituents [of your mixture] once you’ve identified what the chemical constituents are. So we’ve got substances and compounds, and you can link a compound well, or a compound structure, to a particular substance so that you can see how those fit.”
Mscreen also helps you keep track of chemicals’ sources, using different sets of daughter plates made with different concentrations, or made at different times.
“If you order in a new stock of something, we can keep good track of which lot it was, and we also can keep track of the different daughter plates,” said Dr. Neubig. “We make sure that when we do a screen, we know exactly which daughter plate the compound came from. So if we see discrepancies between two assays on a single compound, we can track those easily to make sure there wasn’t a difference in the two daughter plates that were used.”
MScreen also features a specially designed infrastructure for managing nucleic acid reagents. “We have a very specific structure set up for the siRNAs, where we have links to sequences of the siRNAs in the collection, and links to the genes that are targeted by the siRNAs,” continued Dr. Neubig.
This framework within MScreen is also easily adaptable to work for shRNAs or micro RNAs as well, he added.
Errors and Quality Control
Though automation is meant to prevent human error, it can also inadvertently result in more errors—which could have potentially profound effects on compound management. For example, even increases in sample throughput and plate densities in HTS can increase the frequency of errors.
“[In addition to error frequency,] these technologies also introduce opportunities for [entirely] new types of errors, some of which may not be obvious until the technology is used routinely,” said Pierre Baillargeon, compound manager at Scripps Florida.
“At the same time, new technologies often allow tighter integration between software and hardware automation, leading to reduced potential for human error.”
He recommended that tools for quality control and quality assurance be in place to check for errors that might originate from new technologies. “This means identifying bottlenecks and weaknesses in existing laboratory practices, and finding ways to mitigate error without negating the efficiency gains from the technology being used,” said Baillargeon.
For example, his group uses an automated volume checking device to verify that the amount of solubilized sample in a container matches the electronic record of that sample. This eliminates the potential error that might result from discrepancies between actual sample amounts, and those recorded in the management system.
To help prevent further errors, Baillargeon’s group also developed a novel machine vision based instrument called the Plate Auditor, which automatically inspects plates for insufficient volume, precipitate, and sample color.
“By integrating this new instrument into our existing workflows, we have enabled errors to be detected and corrected much earlier in the sample lifecycle,” said Baillargeon. “Detecting problems earlier in the sample lifecycle simultaneously reduces the cost of errors and increases the quality of data produced downstream.” The Plate Auditor was recently licensed by Brooks Life Science Systems.
Monitoring for Aggregates
The issue of precipitates or aggregates in solutions is one that vexes nearly every lab. The Plate Auditor, cameras to look for precipitates in samples, and devices to measure the amount of water in a DMSO solvent, are some solutions that researchers use.
Robert Damoiseaux, scientific director of the Molecular Screening Shared Resource at UCLA’s Jonsson Comprehensive Cancer Center, uses dynamic light scattering to look for particles or aggregates in solutions using 384 and 1,536 well plates. Wells containing particles are flagged for further inspection.
“We use this for nanoformulations quite a bit,” said Damoiseaux. “For example, the compound Abraxane® is nanoparticles made of Taxol particles with an albumin shell. It’s a great concept, because Taxol is very hydrophobic and precipitates out really easily.”
The albumin shell renders it less hydrophobic, making it more potent and easier to infuse into patients.
“The vasculature around cancers actually actively recruits albumin because it’s bound to many nutrients,” explained Damoiseaux. “So basically the tumor loads itself up with the albumen-coated nanoparticles by the active transport mechanism, resulting in enrichment of Taxol where it needs to be.”
In compound management, nanoparticles are more needy than their chemical cousins. They are less stable than small molecules, which can exist happily in DMSO in a desiccator.
“But with nanoparticles, even if they’re in powder, they clump, they aggregate, they re-precipitate, there are templating effect. It’s a very complicated picture,” said Damoiseaux. “That’s something that dynamic light scattering is very useful for.”
Challenge of Dry Compounds
Recent progress in compound management has not, however, included the transfer of dry compounds, despite the high demand for automation of this common task.
“The physical transfer of dry compound from source to destination is still a very manual process, mainly because the industry has not developed an acceptable automated solution due to the extreme complexities of transferring dry compounds,” says Genentech’s Hascall.
“Although weighing compounds is one of the least desired tasks in the lab, it is a critical first step to preparing the sample for testing. Whether compound management is weighing a large library, or newly synthesized compounds from chemistry, it has historically required human manipulation of the compound for the transfer to occur.”
One of the challenges of automating this process is the type of solid—powders are much easier for robots to work with. Hascall’s group uses a fully automated weighing system called the Nova, from Innovate Engineering, to transfer dry, free-flowing powders.
Other solids such as dry films, oils, globular material, or chunks of crystals, still present challenges. For powder transfer, the Nova uses a stainless steel collector pin charged with static electricity, to which the powder clings.
The Nova changes the collector pin each time to avoid cross contamination, and uses powder level detection (similar to liquid level sensing) to calculate the static charge, and the right level at which to place the collector into the vial.
“Fully automated weighing holds many challenges that the Nova has been designed to handle,” says Hascall. “With a greater than 85% success rate in our study of over 4,000 compounds, the Nova can be considered to be one of the first fully automated compound transfer robots.”
It is also integrated into Titian’s Mosaic compound-management software to eliminate manual data entry.
Even though compound management is evolving quickly, new challenges are directly ahead. For example, nucleic acid reagents such as plasmids, siRNA, microRNA, and shRNA are increasingly stored and require a special kind of management.
A repository that stores plasmids, which are typically purified using RNases, and also stores siRNA must have separate, dedicated liquid-handling systems to avoid destruction of the siRNA.
“These are the strategies,” says Damoiseaux. “You have to be very careful to set up your equipment in such a way that the workflows are parallel, and the overlaps are such that you are not damaging reagents.”
Whether for nucleic acid reagents or other compounds, no doubt parallel advances in software and automated instrumentation, such as MScreen, the Plate Auditor, and the Nova, will pave the way to progress, with labs running more smoothly than ever.