Pharmaceutical Companies have used high throughput screening as the modus operandi for drug discovery. The concept is fairly simple: screen a large number of small molecule compounds for interaction with the target system. The hope is to find at least several molecules (called “hits”) have the desired effect on the target system: protein, gene, pathway, process, organism, etc. The pharmaceutical industry’s intent is to find a chemical that can be developed into a drug. The drug development process, however, requires a heavy investment of resources: capital and personnel.
Academic researchers historically have not been in the business of developing drugs, nor did they possess the resources to do so. Nonetheless, academic researchers have superb knowledge on their target and have been in the business of finding useful probes for their systems of interest. This has changed drastically over the last few years in which big pharmaceutical companies have come to rely on academia as their source of novel targets and even starting molecules. This is where the MSSR comes into play.
The Molecular Screening Shared Resource (MSSR) offers a comprehensive range of high throughput screening (HTS) services including chemical genomics, functional genomics and drug discovery. The MSSR is an open environment and welcomes academic investigators from UCLA as well as from all over the globe. Industrial clients are equally welcome as the MSSR is set up as a fee for service entity and does not retain intellectual property. In conjunction with the Center for Environmental Implications of Nanotechnology, the MSSR is currently the only HTS facility in the nation with an ongoing, dedicated effort towards high throughput toxicity testing of nanomaterials. The MSSR is a shared resource supported in part by the Jonsson Comprehensive Cancer Center (JCCC) and works with JCCC scientists on oncology related projects.
Our compound libraries consist of over 200,000 molecules. For the purpose of chemical genomics the MSSR provides annotated small molecule libraries where the targets are known. Other sets contain over one thousand FDA approved drugs, a comprehensive set of anti-cancer agents provided by the NCI and over two thousand purified natural products. For drug discovery projects, the MSSR offers small molecule libraries which target high value classes of proteins such as kinases, proteases, ion channels as well as g-protein coupled receptors (GPCRs). The residual 140,000 compounds are contained in libraries sampling the drug-like chemical space and are filtered for any toxicological liabilities. Over 70% of our compounds are in libraries which were custom selected for the MSSR and are not likely to be found in another screening facility.
In addition to drug discovery and chemical genomics, the MSSR provides functional genomics libraries using CRISPR, inhibitory RNA (RNAi) for gene KO and the complementary cDNA overexpression methodologies. The MSSR offers three commercially available siRNA libraries covering the human and mouse druggable and the entire mouse genome. Kinases and GPCR’s are available as sub-libraries with 4 siRNA constructs per gene. This allows for advanced analysis methodologies such as redundant siRNA analysis (RSA) which allows for elimination of outliers and siRNA’s which might be off-target. Our arrayed CRISPR and shRNA libraries contain over 60,000 clones each targeting about 18,000 genes in the human genome with an emphasis in coverage on desirable target classes such as kinases, proteases, phosphatases, GPCRs and ion channels. In addition to the traditional target classes we offer various custom libraries such as a validated cancer specific sets of about 150 targets from the NCI and a cancer specific set of over 2000 clones covering 500 cancer related genes selected by the Sanger Institute. Other sublibraries cover transcription factors, ubiquitinization and de-ubiquitinization pathways, apoptosis etc. These libraries are proprietary to the MSSR as they were custom selected and arrayed at the MSSR. The capability of customizing CRISPR and shRNA libraries enables the MSSR as well to tailor shRNA libraries to the needs of a particular Principle Investigator.
MSSR services rely on an extensive machine park supplying the advanced enabling technologies necessary for transformative research. At the center of its screening operations are four integrated robotic HTS systems with a per diem capacity exceeding a total of 100K samples in 384 well plate format. These systems also feature robotic vision allowing for automatic teaching of equipment stations which streamlines the maintenance process and integration of novel equipment. MSSR is able to address any plate format or read-mode such as optical density, fluorescence, luminescence, time resolve fluorescence, fluorescence polarization and Alpha screening with multiple plate readers in excellent sensitivity. The Resource also offers kinetic readouts for Calcium or cAMP flux GPCR assays using a monochromator based plate reader built-in injectors. Non-contact plate dispensing and washing are also supported. Automated compound transfers are executed using a Biomek FX with custom V&P pin tool sets addressing volumes from 50-500nl with 90 second cycle time. MSSR also has a large park of ancillary equipment that enables high throughput preparation of plasmid DNA, lentiviral libraries under BSL2+ conditions and maintenance of compound libraries. Of particular note are the high content screening capabilities: The MSSR boast three imaging systems, a true spinning disk ImageXpressConfocal microscopy system, an ImageXpressXL widefield microscopy system and an Acumen Explorer laser scanning imager. These systems are also available to faculty for walk-up use when not occupied with high throughput screening campaigns. The MSSR upgraded its image analysis capabilities with the PowerCore image analysis platform and paired it with additional servers with 300 TB hard drive space
How we work
The MSSR works in close conjunction with each Principle Investigator. In addition to infrastructure and chemical or biological libraries the MSSR provides the necessary expertise to guide a given HTS project towards fruition. We have adopted a collaborative workmodel in which typically one member of the Principle Investigator’s laboratory is working with the MSSR team on a given project. This ensures that a person with detailed knowledge of the biology which stands behind each project is available at all times as well as high quality results and value added to the project.
Scheduling: Instrument time and library screens must be scheduled at least a day in advance, with two or more days strongly preferred. This allows time to consult, adapt the assay to high throughput mode and run controls, if necessary. Scheduling a consultation appointment well in advance (2 weeks or more) of the projected screen date is advised.
Cancelling: Cancellations should be made at least 24 hours in advance. Chemical libraries have to be de-sealed in order to perform a screen. Each cycle has the potential to damage chemical entities in the libraries. By canceling before the libraries are opened, we avoid unnecessary risk to the libraries. In addition, by canceling in advance, other users can schedule to use instruments and to perform screens. So, please be considerate.
Hours of operation: Typically, the facility will be open for consultation from 9:00 am-5:00 pm, Monday through Friday. Screens may begin earlier and run longer than this allotted time as needed.
Library handling: By MSSR personnel only.
Instrument operation: Liquid handlers, plate readers and microscopes by MSSR personnel and trained users only upon approval by MSSR Director and only for the purpose discussed with MSSR Director. Echo system and robotic arm systems are used and handled by MSSR personnel only.
Acknowledgements/Grants: If you plan to write a grant or write a paper including the screening you plan to perform at the MSSR, please let us know. We need to keep records of these. Such records are needed when we apply for money to support the MSSR. Recharge does not cover the entire cost of running a screen. Please help us to keep the costs to users as low as possible. Inclusion of MSSR members in papers and patents is expected according to commonly used standards and is not negated by fee-for-service arrangements.
Access Prioritization: The MSSR has so far been able to accommodate all requests. Should the need arise, the MSSR advisory board will resolve prioritization conflicts.
Screening Data and Library Composition
The MSSR delivers screening results as hit lists, comprising hits with a z-score of >3 or <−3. Upon completion of testing and analysis, investigators receive, for each hit, the compound identity, its target or mechanism annotation where annotated in our databases, and the associated activity values. Some proprietary compound decks require a memorandum of understanding, as these compounds have no CAS numbers and public disclosure of the set would forfeit our ability to file composition-of-matter patents. Additional terms apply as per end user agreements.
Full per-well result tables and MSSR compound sets are not distributed. The collections are assembled and curated by Dr. Damoiseaux of the MSSR and are made available for screening rather than for redistribution; several sublibraries also carry terms from their originating sources. On occasion, analysis is also run by students from the originating laboratory. Such analysis is performed blinded to compound identity; hits are unblinded by the MSSR Director following counter-analysis, once confirmed and, where appropriate, corrected.
Where an analysis requires knowing what was screened — for example, a claim that hits are enriched or depleted for a given mechanism — Dr. Damoiseaux provides summary composition on request: total compounds screened, the breakdown by target class, and as needed the number of compounds in any specified class together with how they scored. This supports enrichment and depletion claims without release of the collection.
Chemists who contribute compounds to the MSSR deck receive read-only access to full per-well results for the sublibrary they contributed to.
Requests for data beyond the above, including requests arising under industry-sponsored agreements, are directed to the MSSR Director, Dr. Damoiseaux, and are decided by the Director.