- HTS Services
- Specialized Libraries
- Diversity Libraries
- Assay Ready Plates
- Mechanisms of Action Assays
- Seahorse Metabolism Analysis
- Mycoplasma Detection
- Modeling & Virtual Screening
- Preclinical Services
High-throughput screening or HTS technologies include robotic liquid handling and assay detection in 96-well, 384-well, and 1536-well plates and implementation of screens of over 500,000 small molecule, drug-like chemicals or 18,000 human siRNAs. Experienced staff is available to assist in assay development, assay validation, assay implementation, data analysis and chemical informatics.
The first step in initiating a high-throughput screen at Small Molecule Screening Facility (SMSF) is to contact Dr. Gene Ananiev, the co-director for HTS, or Dr. Michael Hoffmann, the Faculty Leader of the facility, to make an appointment to discuss your goals. There is no charge for these initial discussions. In addition to a primary HTS assay, it will be important to identify secondary orthogonal assays to confirm hits and counterscreens to eliminate the inevitable false positives. We strongly encourage, but do not require, a student, postdoc or technician from the client lab to assist “hands-on” with the HTS at SMSF.
A frequently asked question is “How much will it cost?” This depends on the specifics of the assay, availability of reagents from the client lab and the number of compounds or RNAi pools screened. Generally HTS assays cost from $0.10 to $1.00 per well, including reagents and the time of the SMSF scientists. Every effort will be made to provide the client with a realistic estimate of costs prior to beginning a project. This is an estimate and not a contract price.
The greatest uncertainty in staff time required and therefore costs is during the initial phases of development of a client assay that is not already in a multi-well plate format and the assay validation of the statistical properties of the assay using control compounds in a multi-well plate format. Charges for time and supplies will be billed on a frequent, usually monthly, basis thereby allowing the client to decide whether a project should be continued.
The in-house compound collection includes over 500,000 small molecules but most clients only screen a subset of the compound libraries. The number of compounds screened is a key variable in determining the overall costs of a project. Radioactive assays are currently not supported by SMSF and substances requiring a higher containment level than BSL2 are not permitted.
A terrific resource on HTS assays is the NIH-supported Assay Guidance Manual. Signal/background ratio (S/B) and well-to-well variability (CV) are key variables in HTS. See the HTS Assay Validation Chapter in the Assay Guidance Manual for a discussion of how the statistical robustness of an HTS assay will be determined by SMSF scientists.
Once HTS is demonstrated to be statistically robust, a small pilot screen of 100 – 1,000 compounds will be run in duplicate plates to confirm assay reproducibility and assess the hit rate. The client may then make a decision as to how many compounds to screen from the in-house collection.
At the completion of an HTS project, a detailed protocol of the assay as finally implemented will be provided to the client along with the raw screening data. SMSF scientists are available to assist in analysis of the data and the hits. After completing a primary HTS, clients will have many screening “positives” or hits to follow-up in secondary screens. There are several different criteria for assigning hits. Subject to compound availability, SMSF will provide clients with 1 µl of each selected screening hit (~5 µg). These are called “cherry picks.” If you require more than 1 µl of compound, SMSF scientists will assist you in ordering it directly from a commercial source. Generally, 1-5 mg of a compound can be purchased for less than $50 from the manufacturers of commercial libraries.
In addition to secondary assays, we recommend SMSF services for hit identification and triage, to evaluate the compounds, and assist in planning the follow-up procedures.
Selleck FDA Approved Drug Library
Received February 2015, the Selleck FDA Approved Drug Library is a collection of 1018 FDA-approved drugs.
- Related to oncology, cardiology, anti-inflammatory, immunology, neuropsychiatry, analgesia, etc.
- Structurally diverse, medicinally active, and cell permeable
- Documented structure, IC50, bioactivity and safety
Selleck Kinase Inhibitor Library
Received November 2013, the Selleck Kinase Inhibitor Library is a unique collection of 273 kinase inhibitors.
- Targets kinases such as RTKs, PI3K, Aurora Kinase, CDK, and MEK
- Most are ATP competitive
- Structurally diverse, medicinally active and cell permeable
- Documented structure, IC50 and customer reviews
Selleck Epigenetics Compound Library
Received April 2015, the Selleck Epigenetics Library is a collection of 128 compounds
- Contains inhibitors of epigenetic enzymes including:
- Histone Deacetylase (HDACs)
- Lysine demethylases
- Histone Acetyltransferases (HATs)
- DNA Methyltransferase (Dnmts)
- SIRTs activators
- Structurally diverse, medicinally active, and cell permeable
Enzo Screen-Well Bioactive Lipid Library
Received November 2013, the Screen-Well™ Bioactive Lipid Library contains 195 bioactive lipids. This includes:
- Farnesyl/geranylgeranly derivatives
- Polyunsaturated fatty acids
- LPA and phosphatidic acids
- Prostaglandins and thromboxanes
- Vitamin D metabolites
GlaxoSmithKline (GSK) Protein Kinase Inhibitor Set
Received March 2031, July 2014, the Protein Kinase Inhibitor Set (PKIS1 and PKIS2) consists of 868 small molecule kinase inhibitors that have been published by GSK
- Representing a range of chemotypes as well as multiple exemplars within a given chemotype
- Broad coverage of kinase targets, characterized across a panel of 220 kinase assays.
Received October 2012
- The NCI04 “Diversity Set III” library consists of 1597 compounds.
- The NCI05 “Mechanistic Diversity Set” library consists of 879 compounds which have represent a broad range of structural diversity and patterns of growth inhibition in the NCI 60 cell line screen.
- The NCI06 “Natural Product Set II” library consists of 117 natural products that were selected from the NCI open repository.
- The NCI07 “Approved Oncology Set IV” library includes 101 compounds.
More information about these libraries can be found on the NCI/NIH Developmental Therapeutics Program website for Synthetics and Pure National Products Repositories and Basic Chemical Data.
Received July 2014, the Anti-Infectives Library includes 960 molecules and contains low molecular weight, drug-like molecules with scaffolds found in antiseptic agents with anti-bacterial (Gram+ve and Gram-ve), anti-fungoid, anti-microbial activities.
Prestwick Chemical Library
Received January 2011, the Prestwick Chemical Library® contains 1280 marketed drugs.
The Spectrum Collection
The Spectrum Library contains 2000 structurally diverse compound selected by medicinal chemists and biologists for a wide range of biological activities
(received #1- January 2009, #2- October 2009, #3- November 2015, #4 – October 2016)
The Life Chemicals diversity libraries (LC-1, LC-2, LC-3, LC-4) total 100,000 diverse compounds, arrayed in subsets of 25,000. Each set was selected for diverse coverage of chemical space and general drug-likeness. Available for screening as each subset or the full library.
(received October 2008)
The Maybridge HitFinder collection consists of 14,400 compounds representing the drug-like diversity of the Maybridge compound catalog.
MLPCN: NIH Molecular Libraries Probe Production Centers Network Diversity Library
(received May 2014)
The MLPCN library consists of 340,364 small molecule probes, covering a wide range of chemical space.
NCI NExT Diversity Library
(requested as needed from NCI for oncology-related HTS campaigns that received funding through a peer-viewed process)
The set contains a variety of chemical scaffolds across ten commercial suppliers, while keeping within the boundaries of drug-like chemical space (e.g. Lipinski’s Rule of 5, high QED scores). The collection includes a total of 83,536 compounds.
Tip-less acoustic liquid handling using the Labcyte ECHO can transfer as little as 2.5nL of DMSO compound solution between plates. This capability allows us to offer assay ready plates for screening at low cost. The resulting plates are ready to accept reagents for screening in your lab or ours. Control wells can be formatted as desired. The SMSF Diversity and Specialized libraries are available in 96-well, 384-well and 1536-well formats in a wide range of plate styles. For additional details or prices, please contact Dr. Gene Ananiev (email@example.com).
The Small Molecule Screening Facility (SMSF) offers a broad range of biological profiling assays to help identify a chemical compound’s biological activity and potency including:
- AlphaLisa and AlphaScreen Assays for Biomarkers, Cytokines, Phospho-proteins and more
- AKT Phosphorylation
- Anti-microbial Assays
- Apoptosis Assays
- Cell Migration
- Cytotoxicity and Cell Proliferation Assays
- DNA Damage Assays
- Enzyme Activity
- ERK1/2 Phosphorylation
- Phosphatase Assays (PP1A and PP2A)
- Protein-DNA Binding
- Protein-Protein Binding
- Reporter Gene Expression
- Signal Transduction
- TGF-beta signaling
- Tubulin Polymerization
- Viral Entry
- WNT -Beta Catenin (Super Topflash Assay)
- Wound Healing and Chamber Migration Assays
Custom assay development services are also available.
SMSF is the home of a new Seahorse Bioscience XFe96 Extracellular Flux Analyzer which simultaneously interrogates mitochondrial respiration and glycolysis – in a microplate, in real-time. The XFe96 Analyzer determines in vitro oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) in order to assess cellular functions such as oxidative phosphorylation, glycolysis and fatty acid oxidation.
- Real-time Results- this integrated system reports metabolic rates in just minutes, without sample extraction or labeling. Wave software controls the instrument and performs rate measurements on the fly for same day results.
- Live-Cell Responses – detect responses to substrates, inhibitors, and other compounds in real time via the 4-port injection system and automated mixing while maintaining physiologic temperature (37°C).
- Flexible Assay Design- the 96-well plate format accommodates many conditions in a single run and is best for dose-response studies and compound screening.
- High Sensitivity- analyze as few as 5000 cells per well in the custom 96-well plate. Cell number requirements vary by cell type; consult the Cell Reference Database for details.
- Compatible with a variety of samples due to the precision-controlled heating tray, which can maintain 16-42oC (12oC-20oC above ambient conditions).
- Measure mitochondrial function with the Seahorse XF Cell Mito Stress Test
- Generate a metabolic phenotype within one hour with the Seahorse XF Cell Energy Phenotype Test
- Assess glycolytic rates in live cells with the Seahorse XF Glycolytic Rate Assay
- Quickly determine dependency of cellular energy production on mitochondrial substrates with the Seahorse XF Mito Fuel Flex Test
Analyze 3D samples such as spheroids and islets with the Seahorse XFe96 Spheroid Plate
- Easily create assay protocols and analyze data with Seahorse Wave software
- For Research Use Only. Not for use in diagnostic procedures.
Mycoplasma contamination is one of the most common and serious problems in culturing eukaryotic cells because it alters the phenotypic characteristics of the cells and can negatively impact results. Since mycoplasma is typically not visible and does not respond to antibiotics, an alternative sensitive and reliable detection method is required. Small Molecule Screening Facility (SMSF) uses the R&D Systems Mycoprobe Mycoplasma Detection Kit. This assay is capable of detecting the eight mycoplasma species known to cause 95% of eukaryotic cell culture contamination: M. hyorhinis, M. arginini, M. fermentans, M. orale, M. pirum, M. hominis, M. salivarium and Acholeplasma laidlawii.
The SMSF staff scientists test each client-provided sample in triplicate along side positive and negative controls.
Assays are usually run the week that samples are submitted and data are available within 48 hours of assay completion.
The SMSF can provide a variety of molecular modeling services to guide the identification of small molecules that bind to protein targets of interest.
Docking and Scoring
HTS Data Analysis and Compound Selection
Structure-based or Ligand-based molecular design
Protein Molecular Dynamics
We will work with researchers to determine the methods that are most appropriate for each particular project.
Our virtual screening techniques can be applied to most projects where either a protein target or potent ligand is known. Docking and scoring is most commonly applied in conjunction with synthetic chemistry effort.
We are actively involved in optimization of methods for virtual screening and machine learning approaches for drug discovery. We collaborate with investigators from Biostatistics, Computer Science, Engineering, Biochemistry, and the Center for Predictive Computational Phenotyping on these efforts, and use these novel techniques on our discovery projects.
Our computation resources include 5 Dell servers and workstations with a total of 48 CPUs, including NVIDIA 3D graphics capabilities. We make extensive use of computational resources at the UW Center for High Throughput Computing (CHTC) through HTCondor. Common software includes Autodock (Scripps), Vina (Scripps), ROCS and FRED (OpenEye), Sybyl (Tripos), Surflex (UCSF), MOE (CCG). An additional workstation is available for researchers who wish to actively participate under the supervision of our team.
Hands-on Course in Molecular Modeling and Drug Docking
The SMSF also sponsors a “hands on” 8-week course on molecular modeling with an emphasis on drug design called “Molecular Modeling and Drug Docking” for the UW community to learn how to model the drugs in their targets. The course covers the basics of protein and small molecule modeling using the commercial software Sybyl from Tripos. Several docking programs, such as SurFlex, DOCK and Autodock4, are examined with real examples from the literature.
The course is held in the Digital Media Center teaching lab in the Biochemical Sciences Building, 420 Henry Mall. Each student runs Sybyl on a Linux server thru a Macintosh interface. There is no UW credit for this course. The course has been taught the last five years by Dr. Ken Satyshur from the SMSF during the Spring semester.
Preclinical in vitro Pharmacology Assays
The SMSF staff can assist users with characterizing the pharmacological properties of compounds through contracts maintained with external CROs.
- Aqueous Solubility (pH 5.0,6.2,7.4) Assay
- Lipophilicity, LogD7.4 Assay
- Plasma Stability Assay
- Microsome Stability Assay
- S9 Stability Assay
- Permeability (PAMPA) Assay
- Blood Brain Barrier Permeability (BBB-PAMPA) Assay
- Plasma Protein Binding Assay
- Cytotoxicity (Human Hepatocytes) Assay
- CYP Inhibition (1A2, 2B6, 2C9, 2D6, 3A4) Assay by LC-MS (single conc)
- CYP Inhibition (1A2, 2B6, 2C9, 2D6, 3A4) Assay by LC-MS (dose response)
- Chemical Stability
Preclinical Pharmacokinetics in Mice
The SMSF staff can assist users with obtaining PK results in mice through contracts maintained with external CROs.
- Single compound, 1dose, 1 route, 0.5hr and 2hr
- Brain tissue penetration study, Single compound, 1dose, 1 route, 0.5hr and 2hr
- Single compound, 1dose, 1 routes, 0.5 h, 2h, 4h, and 7h
- Single compound, 1 group, 2 routes, 0, 0.5, 1, 2, 4, 8, 24 hrs
- Five test compounds per mouse, 1dose, 1 route, 0.5hr and 2hr
- Five test compounds per mouse, 1dose, 1 route, 0.5 h, 2h, 4h, and 7h
- Single Dose Tolerability (1 day), Five dose levels, 1 route, 7 Blood sampling times up to 24h post dosing per animal
- Multi- Dose Tolerability (5 days), Five dose levels, 1 route, Animals will receive repeat dose once daily for five days, 7 Blood sampling times up to 24h post dosing per animal
HTS and Profiling Assay Equipment
Training and Scheduled Walk-up Use Available
$60/hour; minimum time 15 minutes
Liquid Handling (available in Biosafety Cabinet if sterile transfers needed)
- Beckman Biomek 2000 eight-channel liquid handler
- Benchtop Pipetter 96 and Benchtop Pipetter 96-low volume
- Biotek Microflo peristaltic reagent dispensers
- Biotek ELx405 96-pin plate washer
- Thermo Scientific Hydra 96-channel liquid handler
Plate Readers and Scanners
- BMG Pherastar Multimode plate reader
- LI-COR Odyssey imaging system (scanner)
- PerkinElmer Enspire plate reader for AlphaScreen
- BMG Clariostar plate reader
- Wallac/PE 1420 VICTOR3 V plate reader
Walk-up Use Not Available
- Beckman fX Liquid Handling (96 and 384)
- Beckman 96-channel Multimek liquid handler
- EVOS® FL Auto Cell Imaging System
Seahorse Metabolism Analysis
$100 / experiment
- Consumables extra, available at cost at SMSF
The Small Molecule Screening Facility (SMSF) operates on a fee-for-service model. User fees pay for staff scientist salaries, consumables and reagents. UWCCC Members receive subsidized rates.
The broad range of services and the individually tailored projects preclude a simple fee schedule. To obtain an estimate for your specific project, please contact us to discuss your needs. There is no charge for meetings or conference calls to discuss project details. Staff scientists will provide an estimate for the project; this is not a contract price, but a conservative estimate based on experience. Projects may include intermediate evaluations of progress and costs to permit clients to make “go/no go” decisions about continuing a project, especially in the event of unexpected complications that increase the cost of the project.
Before SMSF initiates a project, the client must provide a UW fund number, or a purchase order number for off-campus clients. Costs will be billed monthly. Detailed invoices showing time logged by staff scientists on the project and all supply costs are prepared monthly and available to the client or their departmental administrator.
All clients should acknowledge the participation of the SMSF in publications of project results. See Acknowledging UWCCC in Publications, Posters and Presentations. An electronic or hard copy of any publications should be sent to the SMSF.
Users can now pay by credit card using our online bill pay option