The Scripps Research Institute - Lead Identification Lead ID Home Facilities



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Assay Development

Occupying 734 ft2, this laboratory, located within the clean room facility and adjacent to the HTS platform, contains capital equipment to facilitate “off-line” (pre-HTS) assay implementation and miniaturization experiments, as well as facilities for sterile cell culture and media preparation.

Compound, Reagent and Cell Dispensing: Non-contact dispensers are available for delivering reagents and cells into various well plate formats with high precision and accuracy. Collectively, these dispensers can deliver in the wide range from 0.5 to 1000 microliters. For the delivery of test compounds from compound source plates into assay plates multiple options exist: Pintools delivering from 10 to 200 nanoliters into 96-, 384- and 1536-well plates and pipettors delivering from 0.25 to 200 microliters into 96-, 384- and 1536-well plates. Pipetting is also available for preparation of control/compound source plates.

Plate Readers: Imagers capable of FLINT, FRET, TRF, TR-FRET, FP, luminescence and absorbance readings (all plate densities accepted); PMT readers capable of FLINT, FRET, TRF, TR-FRET, FP, luminescence, absorbance and AlphaScreen readings that accept 96, 384, and 1536 titer plate formats and are capable of kinetic measurements; monochromator-based readers capable of kinetic measurements in fluorescence, luminescence and absorbance mode using 96, 384, and 1536 plate densities; and a Molecular Devices FLIPRTETRA capable of real-time kinetic cell-based assays (includes 384- and 1536- liquid transfer capabilities, multi-wavelength kinetic reading, plate handling and is well suited for real-time calcium flux, membrane potential and ß-lactamase measurements). The laboratory also possesses the equipment necessary to develop High-Content Screening assays.

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HTS Robotics

High Throughput Screening (HTS) is a drug-discovery process widely used in the pharmaceutical industry. It leverages specialized automation and microfluidic devices to quickly and economically assay the biological or biochemical activity of a large collection of drug-like compounds. It is a useful for discovering ligands for receptors, enzymes, ion-channels or other pharmacological targets, or pharmacologically profiling a cellular or biochemical pathway of interest. Typically, HTS assays are performed in “automation-friendly” microtiter plates of 96, 384 or 1536 well format. Moreover, the use of robotics allows us to rapidly produce consistent, high quality data while also generating less waste since they smaller amounts of materials are used.

The robotics laboratory occupies 1452 ft2 and is shared between two Kalypsys-GNF robotic platforms: HTS and Compound Management. The HTS system is comprised of the components below:

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Figure 1: Overview of Scripps Florida's HTS Robotics Platform; [A] Stäubli Robotic Arm, [B] Kalypsys-GNF Compound Transfer Station, [C] Kalypsys-GNF Washer/Dispenser, [D] PerkinElmer ViewLux CCD Imager, [E] Molecular Devices FLIPRTETRA, [F] Thermo Cellomics CellInsight High-Content Reader, [G] Kalypsys-GNF Microplate Incubator, [H] Joaun Robotics Microplate Centrifuge, [I] PerkinElmer EnVision Multilabel Reader

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Compound Management

With a footprint of 869 ft2, this laboratory combines liquid handling automation and information management processes to support the entire compound management cycle from compound submission to delivery of assay ready compound plates. Currently, the compound management laboratory stewards more than 600,000 compounds for its small molecule HTS library and internal Medicinal Chemistry efforts as well as the 350,000 compounds from the NIH MLPCN screening file. Compounds are stored offline in an automated compound store in 96-well tube format and online in 384-well format for hitpicking operations, 1536-well for HTS operations. The facility also has a dedicated Agilent 1200 series LCMS with multimode mass spectrometry (ES, APCI, ELSD) dedicated for quality control of incoming HTS compound libraries and hit confirmation efforts. This platform is designed for automated analysis and generates database-ready reports.

The Compound Management core facility utilizes both commercial and in-house software solutions to support its operation. A suite of database products act as corporate databases and provide mechanisms for the storage and retrieval of compound, plate and assay data. One portion of the software is used as a portal to prepare and QC information before insertion to the corporate database and to retrieve the results of user-specified queries. Custom in-house software supports processes specific to Medicinal Chemistry efforts and provides streamlined interfaces to the corporate databases for hitpicking and HTS operations.

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Compound Libraries

Scripps has approximately 1 million compounds available for HTS efforts. These contain both diverse and focused sub-libraries, described in detail below:

Scripps Drug Discovery Library

Our in-house drug discovery collection consists of over 600,000 unique and drug-like compounds and is constructed from commercial sources as well as past and current internal medicinal chemistry/drug discovery efforts. The library contains several “focused” sub-libraries including: GPCR, Kinase, “Rule of 5,” Natural products, Transcription factor and “Click” chemistry collections. Over 90% of compounds can be sourced as powders.

MLPCN Library

The Molecular Libraries Small Molecule Repository (MLSMR) library provided through the Molecular Libraries Initiative. In summary, the MLSMR library is a highly diversified collection of more than 350,000 small molecules (more that 50% of compounds exhibit molecular weights between 350 and 410 g/mol) comprising both synthetic and natural products, from either commercial or academic sources, that can be grouped into the three following categories: (1) specialty sets of known bioactive compounds such as drugs and toxins, (2) focused libraries aimed at specific target classes and (3) diversity sets covering a large area of the chemical space.

Scripps Approved Drug Library

A collection of 1280 drugs that have reached clinical trial stages in the USA or that are marketed in Europe and/or Asia. Compound have been assigned USAN, USP INN, BAN and/or JAN designations and are included in the USP Dictionary (U.S. Pharmacopeia), the authorized list of established names for drugs in the USA and/or are listed in the Index Nominum, the International Drug Directory.

Scripps Clinically Relevant Collection

Our in-house clinically relevant collection consists of over 1000 commercial bioactive compounds identified from the MDL® Comprehensive Medicinal Chemistry database (over 7500 bioactive compounds used or studied as medicinal agents in humans) or DrugBank database (detailed drug data for nearly 4800 bioactives tested in humans).

Scripps Pilot Screen Libraries

  • LOPAC (1280 compounds): A collection of pharmacologically-active compounds useful for HTS validation. The library contains high purity, small molecule ligands with well-documented pharmacological activities in areas such as apoptosis, phosphorylation and well-characterized compounds against orphan receptors.
  • The Prestwick Chemical Library (1120 compounds): A library containing off-patent small molecules, with 90% being marketed drugs and 10% being bioactive alkaloids or related substances. The set is selected for structural diversity, broad spectrum activity covering several therapeutic areas (e.g. neuropsychiatry to cardiology, immunology, anti-inflammatory, analgesia and more) and for known safety and bioavailability profiles in humans.
  • Tocriscreen (979 compounds): A collection of unique and diverse bioactive compounds.
  • The Nuclear Receptor Signaling Ligand Set (55 compounds): Includes the latest endogenous and synthetic ligands for well-characterized receptors in the field of Nuclear Receptor Signaling including: Androgen (AR), Estrogen (ER), Glucocorticoid (GR), Mineralocorticoid (MR), Peroxisome proliferator-activated (PPARα, PPARχ or PPARδ), Progesterone (PR), Liver X (LXR), Retinoic acid (RAR), Retinoid X (RXR), Thyroid hormone.


All contents have been tested for purity and structural confirmation via LC-MS or NMR (or both), allowing for rapid follow-up studies by our collaborators after completion of HTS effort (LC-MS reports also available from Scripps).

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Lead Identification also encompasses a microbiology laboratory which is capable of handling bacterial pathogens up to and including Biosafety Level 2, contained within 275ft2 of lab space. The lab is fully equipped with standard items for microbial and molecular biology including Class II hoods, refrigerators and freezer storage, bulk reagent dispensing, microplate reading and is even capable of HTS screening BSL-2 organisms in 1536-well microplates. Temperature controlled and humidified shaker incubators are located within the facility, allowing for large scale culture or plate based growth. For molecular research PCR machines and post-PCR equipment is available allowing for cloning and expression work to be done. For large scale protein purification we have an Akta FPLC installed inside a double glass door refrigerator. Time kill and bacteria kinetic assays are facilitated by Spiral Biotech spiral platers and Qcount imaging colony counters. In addition, all of our microbiology efforts conform to the Clinical Laboratory Standards Institute (CLSI) methods for all antibacterial experiments which include MIC determination, phenotypic characterization, time kill and checkerboard synergy assays. We have cutting edge imaging apparatus to allow visual inspection of membrane active compounds and have implemented one of the most advanced and sensitive methods for the early detection of anti-proliferative effects by inhibitors.

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Tissue Culture


The Tissue Culture Unit produces large amounts of cells (classically over 2 billion cells) to support screening activities. Utilizing 640 ft2 of laboratory space, it is articulated around HEPA-filtered laminar air flow biosafety cabinets, which allow multiple cell biologists to work safely at the same time. For HTS cell production and scale-up, cell biologists are assisted in their repetitive tasks by automated reagent dispensing units. Plates and tubes can be centrifuged by dedicated centrifuges. Cell cultures are monitored with inverted phase-contrast microscopes with fluorescence capability. Cell culture flasks and plates are stored in humidity/temperature/CO2-controlled, dual chamber, self-sterilizing incubators. Reagents are stored in 4°C refrigerators and -20°C or -80°C dual chamber freezers. Dedicated 37°C and 25ºC water baths and Millipore Ultrapure water production units are also available for cell culture. Our facility hosts a large variety of commonly used mammalian cell lines as well as insect cells, both adherent and non-adherent. Depending on the needs, cells are maintained in regular flasks, high-density flasks, roller bottles or bags.

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