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Resources and Equipment

KaiKai Lyu Medicinal ChemistryThe Center for Integrative Chemical Biology and Drug Discovery (CICBDD) was created with the mission of bringing dedicated high throughput screening and medicinal chemistry expertise to bear on biological targets of therapeutic relevance under investigation by UNC faculty. Synthetic and computational chemists, and assay development/compound profiling scientists work in the Center and create dedicated, interdisciplinary project teams to progress targets through the probe and drug discovery process. The CICBDD therefore has the staff, equipment and expertise to progress biological targets through the assay development, hit generation and hit-to-lead/probe/lead optimization phases.

The home of the CICBDD is Marsico Hall, constructed in 2014 and located in the heart of UNC’s biomedical research campus and physically connected to the Lineberger Comprehensive Cancer Center (LCCC). Laboratory accommodations for the Center consist of ~10,000 sq.ft. on the third and fourth floors of Marsico Hall. There are 25 X 6 ft fume hoods and 10 x 8 ft fume hoods, as well as 5 labs for cell culture and a dedicated lab for fluorescence microscopy in this space. The Center also has a dedicated fine chemical storeroom with a bar-coded inventory system and a walk-in -20°C freezer for storage of compound plates. The CICBDD is well equipped for state-of-the-art organic and medicinal chemistry, along with protein expression, biochemical assay development and focused or diversity-based screening.

 

Lead Discovery & Characterization, Ken Pearce, Director

Medicinal Chemistry, Xiaodong Wang, Director

The Lead Discovery and Characterization Group handles all compound management and is equipped to develop https://cicbdd.web.unc.edu/chemical-biology/screening assays using industry standard best practices and technologies. The equipment within LD&C is organized around an “islands of automation” concept where each device is capable of walk away operation sufficient to process 30-50 plates. This strategy has been proven to be maximally effective in environments where flexibility is required, and assay formats may vary significantly over time. All equipment is maintained at or above the manufacturers recommended maintenance intervals for testing and calibration. Our medicinal chemistry efforts are project based with a faculty generated lead compound. The medicinal chemistry team can support 3-5 hit to probe/lead projects concurrently.

 

Computational Biophysics and Molecular Design

Computational Biophysics and Molecular Design WorkResearch staff in CBMD are equipped with personal laptops with network access to all UNC IT resources (e-library, etc.) and have Intel Xeon workstations with Nvidia Quadro graphics cards with network access to all UNC IT resources. CBMD relies on vast resources for computational modeling available at UNC. Research Computing, a division of the Office for Information Technology Services, currently offers access to two state-of-the-art high-performance computing cluster (Longleaf) and a number of software packages to support research computing including Matlab, GROMACS, NAMD, AMBER, MBOSS, DOCK, Schrodinger, GCG, Pipeline Pilot, Discovery Studio and Gaussian.

Current Equipment Available at the CICBDD


Liquid Handling Instruments

Device Manufacturer Capabilities
Freedom EVO Tecan Liquid handler with 2 arms and integrated 96/384 well dispense and transfer head and 8 tip X-Y-Z arm.
Mosquito HTS
TTPLabtech Liquid handler capable of nanoliter dispensing and serial dilution in 96, 384, and 1536 well format, including preparation of assay ready plates
Multimek Nanoscreen 384 well liquid handler for plate replication and reagent dispensing with large and small tube dispense heads
Multidrop (5) ThermoFisher Automated reagent dispensing with large and small tube dispense heads
Preddator Redd and Whyte Non-contact bulk nanodispenser for reagents
Biomek FX Beckman Coulter 384 well liquid handler for plate replication and reagent dispensing

Plate Reading Instruments/Spectrophotometers

Device Manufacturer Capabilities
Analyst GT Molecular Devices Multi-mode plate reader; absorbance and fluorescence
Azure 600 Azure Bio Systems Fluorescence and chemiluminescence imager for analysis of Western blots, plates, gels
EnVision (3) Perkin Elmer Multilabel reader for AlphaScreen®, fluorescence intensity, fluorescence polarization, time-resolved fluorescence, luminescence (glow, flash and dual luminescence), absorbance; sample dispenser
Enspire Perkin Elmer Multilabel reader for absorbance, fluorescence, and luminescence
EZReader Caliper Life Sciences Microfluidic LabChip system utilizing mobility shift assays for enzymatic targets, real-time kinetic data, mechanism of action, kinase profiling
FLIPR (Roth lab) Molecular Devices Cell based assays including calcium flux, membrane potential and aqueorin
Glomax Promega Multimode microplate reader used for luminescence, fluorescence, UV-visible absorbance, BRET, and FRET detection; it is optimized for cell viability and genetic reporter assays
MicroBeta Trilux Perkin Elmer Plate based liquid scintillation counter/luminometer
Patch Express (Roth lab) Molecular Devices High throughput patch clamp for voltage or ligand gated ion channels
IN CELL Analyzer 2200 GE

IN CELL Analyzer 2200

High content cell imaging system with 3D deconvolution, live cell imaging, and automated sample delivery
iQue Screener Intellicyte Flow cytometry system capable of multiplexed, high-throughput analysis of cells and beads
NanoDrop Thermo Fisher Micro-volume spectrophotometer for quantification of DNA, RNA, oligos, and proteins
Paradigm Molecular Devices Multilabel reader with absorbance cassette; upgradable for fluorescence, luminescence, western blot capabilities
Patch Express (Roth lab) Molecular Devices High throughput patch clamp for voltage or ligand gated ion channels
Qubit-Flex Thermo Fisher
Benchtop fluorometer can quantify DNA, RNA or protein in 1 to 8 samples simultaneously

 

QuickDrop Molecular Devices Micro-volume spectrophotometer for quantification of DNA, RNA, oligos, and proteins
qTower Analytik Jena Six-fold multiplexing Real-Time PCR System for 96 well format qPCR or thermal melt assays
Ultrasonicator LE220 Covaris Ultrasonicator for compound solutions and DNA shearing
ViiA7 Life Technologies Real-Time PCR System for 384well format qPCR or thermal melt assays

Protein Purification

Device Manufacturer Capabilities
Akta FPLC/HPLC (3) GE Lifesciences Protein purification using high pressure column chromatography

Compound Storage; Other

Device Manufacturer Capabilities
comPOUND TTPLabtech
The comPOUND chemical stores
Small tube compound storage unit with random access storage for 200,000+ compounds
Plate sealers (2) Thermo Scientific Microplate heat sealer
RS Microplate Orbitor Thermo Scientific Automated plate stacker and transporter
Twister II Perkin Elmer Automated plate mover suitable for integration with numerous instruments
Ultrasonicator LE-220 Covaris Ultrasonicator for compound solutions and DNA shearing
Ultrasonicator E-110 Covaris Ultrasonicator for compound solutions and DNA shearing

Chemistry

Device Manufacturer Capabilities
1260 Series Infinity II LC/MS Agilent Technologies Separate and detect an individual compound rapidly from a mixture; ideal for high-throughput and fast applications
1260 Infinity II (2) HPLC; Agilent Technologies Compound isolation and purification
1260 Preparative HPLC (2) Agilent Technologies Compound isolation and purification
EZ2 Evaporator (2) Genevac Remove solvents to concentrate or dry samples
L-200 Freeze Dryer Buchi Freeze drying samples
CombiFlash® Rf Automated Flash Chromatography System (3) Teledyne Isco Purification of organic compounds in normal-phase or reversed phase separations
1st Combiflash Next Gen 300+ Automated Flash Chromatography System (3) Teledyne Isco Purification of organic compounds in normal-phase or reversed phase separations
Explorer 72-position Automated Research Microwave Reactor Discover-SP (2) CEM Utilizes microwave energy (single-mode, focused technology) to accelerate organic reactions
400 MHz NMR with multiple probes and autosampler Varian Routine 1H and 13C NMR, 1D and 2D spectra (ESOP facility-co-located with CICBDD)

Computing

All faculty, research staff, students and postdoctoral fellows in the CICBDD have either personal laptops or access to a desk- based computer with network access to all UNC IT resources (e-library, etc.). The CICBDD relies on the vast resources for computational modeling available at UNC. Academic Technology & Networks (ATN), a division of the Office for Information Technology Services, currently offers a number of software packages to support research computing including EMBOSS, DOCK, Clustal, CNSsolve, GCG, Sybyl, InsightII, Genomax, Cerius2 and most InsightII modules for homology-related docking for structural searches and molecular visualization packages such as Spock and Denzo at an annual cost of over $100,000.  Recent ATN hardware commitments in support of computational biology and genomic computing include over $600,000 of the $1.3 million spent upgrading our SGI system to an Origin 3800 with 64 processors and 64 GB of memory, and $60,000 toward the installation of a 184-processor Beowulf Cluster with 184 GB of memory and a Myrinet interconnect, and the acquisition of a 44 processor SUN ES-15000 worth $2.4 million.

UNC shared facilities

UNC Research Computing provides a world-class computing infrastructure as well as other technology tools and capabilities to support the research needs of UNC researchers. The Research Computing group currently offers a number of computing services for researchers at UNC-Chapel Hill:

  • The Longleaf cluster is a Linux-based computing system available to researchers across the campus free of charge. With nearly 6500 conventional compute cores delivering 13,000 threads (hyperthreading is enabled) and a large, fast scratch disk space, it provides an environment that is optimized for memory and I/O intensive, loosely coupled workloads with an emphasis on aggregate job throughput over individual job performance.
  • The Dogwood cluster is a Linux-based computing system available to researchers across the campus free of charge. With over 11,000 computing cores, a low latency, high bandwidth Infiniband EDR switching fabric and a large scratch disk space, it provides an environment that is optimized for large, multi-node, tightly coupled computational models typically using a message passing (e.g. MPI) or hybrid (OpenMP + MPI) programming model. Most of the cluster is comprised of nodes with Intel Xeon processors with the Broadwell-EP micro-architecture and 44 cores per node. There is a partition with newer Intel Skylake nodes as well as a KNL partition, with Intel Xeon Phi processors (Knight’s Landing) and GPUs (Nvidia Tesla P100 and V100) nodes for development purposes.

Both clusters have access to a variety of statistical software packages (such as SAS and Stata), mathematical software packages (such as Matlab and Mathematica) and scientific software packages (such as Gaussian, Amber, GROMACS, Schrodinger) and deep learning frameworks (TensorFlow, PyTorch, Keras, etc).

Cloud Computing

Carolina CloudApps is a UNC managed platform for developing and deploying web applications. The managed software encompasses the underlying operating system and core software, such as web servers and development languages.