Chemical Biology Consortium Sweden

Infrastructure Unit

Contact

Anna-Lena Gustavsson

anna-lena.gustavsson@scilifelab.se070 396 5178Stockholm

Stina Berglund Fick

stina.berglund.fick@umu.se070 340 87 21Umeå

Recent user publications

The publications in this database are the result of research conducted at the units of SciLifeLab – both in user projects and technology development.

Personnel

Anna-Lena GustavssonPlatform Scientific Director & Head of Unit (LCBKI)

In Stockholm

Hanna Axelsson

Martin Haraldsson

Brinton Seashore-Ludlow

Marianna Tampere

Francesco Massai

Tobias Koolmeister

Flavio Ballante

Compound Center

Åsa Slevin

Maria Adolfsson

Elisabeth Olsson

 

In Umeå

Stina Berglund FickHead of Unit (Umeå)

Erik Chorell, Platform Scientific Director (Umeå)

Anna Eriksson

Weixing Qian

Cecilia Lindgren

 

 

Chemical Biology Consortium Sweden

The mission of Chemical Biology Consortium Sweden (CBCS) is to provide a state-of-the-art platform and expertise for the generation of high-quality bioactive chemical tools (small organic molecules) for applications within life science research in general and with the ultimate goal to explore complex biology.  For more information, visit the CBCS external webpage.

CBCS was established in 2010 as a nation-wide infrastructure for chemical biology research consisting of two units, one at Karolinska Intitutet, LCBKI, and the other at Umeå University, LCBU. In 2012 CBCS became an integrated platform at SciLifeLab. In 2022, CBCS recieved support from the Swedish Research Council as a prioritized national infrastructure and is expanding its services to include local access nodes at Lund, Gothenburg, Linköping, and Uppsala Universities. Each university bring their own expertise in new techniques, for example phenotypic profiling using cell painting at UU, screening of ion channels at LiU, biosafety level 3 screening at KI and LiU (and UmU in the future), and increased our contacts with AstraZeneca through University of Gothenburg.

Our units comprise compound handling labs (hosting the SciLifeLab Compound Collection of ca 350,000 molecules), screening labs (microtiter format liquid handling robotics and a wide range of plate readers), and chemistry labs (equipment and instrumentation for organic chemistry synthesis and analysis). CBCS coordinates, and makes available, a powerful and integrated platform for the discovery, development and utilization of small-molecules and chemical tools for life-science application. We provide expertise support and experimental resources within assay development, computational chemistry, cheminformatics, chemical library screening and development, medicinal/synthetic chemistry, target identification.

Services

  • Access to small-molecule compound libraries and robotic instrumentation
  • Expertise in assay development and automation
  • High-throughput screening: biochemical target-based, cell-based and phenotypic
  • High-throughput imaging technology
  • Expertise in screening for antimicrobial compounds and plant-based screens
  • Hit identification and optimization
  • Computational chemistry and modelling
  • Medicinal chemistry expertise
  • Chemical proteomics & target identification of small molecule ligands
  • Mechanism of Action studies
  • The Drug Repurposing set from SPECS is now available through Compound Center

For more Information on our available services, visit our website.

Applications

CBCS works according to a collaborative research model based on mutual commitment from our group and the involved Investigator.

For more substantial projects, a formal process initiated by an application is implemented to ensure that resources are prioritized based on transparent criteria, such as scientific excellence, novelty, technical feasibility and relevance. Our Project Review Committee (PRC) consists of CBCS-independent experts in the chemical biology research field, also including industry representation.

Upcoming dates for Project Review Committee (PRC) meeting and the proposal submission deadline are published on our website www.cbcs.se

Nodes

Services provided

The KI node situated in the SciLifeLab Alpha 5 building, comprise:

  • Compound handling labs, hosting the SciLifeLab Compound Collection of ca 350,000 molecules
  • Screening labs, including microtiter format liquid handling robotics and a wide range of plate readers
  • Chemistry labs, including equipment and instrumentation for organic chemistry synthesis and analysis 

CBCS coordinates, and makes available, a powerful and integrated platform for the discovery, development and utilization of small-molecules and chemical tools for life-science application. 

We provide expertise support and experimental resources within

  • Assay development
  • Computational chemistry
  • Cheminformatics
  • Chemical library screening and development
  • Medicinal/synthetic chemistry
  • Target identification.

BSL3 Biomedicum is a fully equipped facility performing a wide range of research activities with any pathogens that require biosafety level 3 laboratory. The facility is equipped with state-of-the-art equipment such as liquid-handling robotics, plate reader and flow cytometry and expertise staff specialized in high-throughput screening, as exemplified in Figure 1.

Figure 1. An example of high-throughput antiviral assays available at BSL3 Biomedicum. An image-based screening assay was developed in collaboration with Dr Charlotte Stadler (Kaimal et al. biorxiv, 2022) and cell viability assay in collaboration with Dr Marianna Tampere.

Contact

Antonio Gigliotti Rothfuchs, BSL3 Director
antonio.rothfuchs@ki.se

Marjo-Riitta Puumalainen,BSL3 coordinator
marjo-riitta.puumalainen@ki.se

Services provided

CBCS Umeå is located in the Chemistry Biology Building at the Department of Chemistry, Umeå University. We offer a range of labs and equipment, including

  • Screening lab, including microtiter format liquid handling robotics and several plate readers
  • Biology labs – a clean cell lab, an infection cell lab for BSL-2 organisms and a high content screening cell lab (Including Molecular Devises ImageXpress and Intellicyte IQue3).
  • Chemistry labs, including equipment and instrumentation for organic chemistry synthesis and analysis

CBCS Umeå (former LCBU) has since 2006 assisted academic research groups, research institutes, and SMEs with the identification and development of bioactive small molecules. 

We have long expertise in phenotypic screening and have recently invested in a High Throughput Flow Cytometry instrument, the Intellicyte IQue3. The IQue3 is an advanced flow cytometry platform that allows researchers to acquire and analyze high content, multiplexed assays needed to assess immune cell function by combining cell immuno-phenotyping, cell health, and secreted protein (cytokine) analysis in every well of a microtiter plate.

We provide expertise support and experimental resources within biology as well as chemistry:

  • Assay development
  • Computational chemistry
  • Cheminformatics
  • Chemical library screening
  • Medicinal/synthetic chemistry
  • Target identification

Personnel

Stina Berglund Fick, Head of Unit (Umeå)

Erik Chorell, Platform Scientific Director (Umeå)

Anna Eriksson

Weixing Qian

Cecilia Lindgren

Contact

  • Stina Berglund Fick, stina.berglund.fick@umu.se
  • Erik Chorell, erik.chorell@umu.se

Services provided

  • Consulting with compound screening and drug
  • Assay development
  • Small molecule screening (phenotypic and target based)
  • Fragment based screens using NMR spectroscopy
  • Hit confirmation and guidance for hit molecule optimization
  • Hit complex assessment: macromolecular target structure and dynamics

Infrastructure Gothenburg

  • NMR spectrometers for fragment based screens: 800 MHz, 3 mm TCI probe; 700 MHz, 5 mm 19F probe; 600 MHz, 5 mm TCI, 19F and 1H detection optimized, cooled SampleJets
  • NMR spectrometers for hit conformation with macromolecular targets: 400 – 900 MHz
  • Pipetting robots: Bruker SamplePro Tube L., Single channel, four cooled positions; Agilent Bravo, 96 channels, one cooled position, shaker, magnet position; Opentrons OT-2, multiple dispense, Two single channel pipettes, two cooled positions,
  • Plate reader (96), SpectraMax® iD5
  • Cell culture lab, CO2 incubator, light microscope, centrifure, cell dispenser etc.
  • Maybridge and Bionet small molecule libraries with NMR annotation. In total 1200 compounds.
  • CBCS compounds libraries on demand.

Contact

Mail/Visiting address

Swedish NMR Centre at the University of Gothenburg
Medicinaregatan 5C
413 90 Gothenburg
Sweden

Mail address

Weixiao Yuan Wahlgren
Swedish NMR Centre at the University of Gothenburg
Box 465
405 30 Gothenburg
Sweden

Parcel delivery address

Weixiao Yuan Wahlgren
Swedish NMR Centre at the University of Gothenburg
Medicinaregatan 1G
413 90 Gothenburg
Sweden

Personnel

Göran Karlsson, Director
goran.karlsson@nmr.gu.se

Weixiao Yuan Wahlgren, contact person
weixiao.yuan.wahlgren@gu.se
Telephone 0706-296074

Ulrika Brath, staff scientist
ulrika.brath@nmr.gu.se

Phenotypic Profiling using Cell Painting

Phenotypic profiling of cells by high-throughput high-content microscopy allows for the identification of morphological changes in the cell that are indicative, for instance, of the mode of action (MoA) of a drug, novel compound or biological.

Morphological changes in the cell can be measured using two major approaches: 1) making use of image analysis software (e.g. Cell Profiler) to identify and segment the cells, and subsequently extracting selected cellular features, and 2) using Deep Learning (DL) to extract relevant cellular features in an unbiased manner. Upon the extraction and selection of the morphological features, morphological profiles are generated that are unique per each cell type or perturbation. This is achieved through extensive analysis of the vast number of features extracted at a single cell level.

Figure: a) Overview of cell profiling using the Cell Painting methodology. Cells are exposed to perturbations in the form of chemical substances in multi well plates. Images of cells are acquired and used to generate morphological cell profiles describing a wide range of the cells’ properties. These cell profiles or the original images can then be used in predictive modeling with e.g. Deep Learning methods. 

b) Experiments are carried out in our automated cell profiling lab.

Our node has extensive experience in large scale data handling and analysis, and we have built a complete IT infrastructure capable of storing and analyzing the large quantities of images and subsequent data generated from Cell Painting experiments. 

We offer morphological profiling using Cell Painting as a service, including:

  • Cell Painting protocol optimization for a given cell line.
  • Cell Painting experiments carried out using our automated lab.
  • The necessary cell culture work.
  • Automated imaging, image and data analysis, and visualization.

Personnel

  • Jordi Carreras-Puigvert, Head of Unit
  • Ola Spjuth, Platform Scientific Director Uppsala
  • Malin Jarvius, Node Manager
  • Martin Johansson, Researcher

Contact

Services provided

  • Consulting within drug discovery and medicinal chemistry
  • Assay development
  • Small molecule screening (phenotypic and target based)
  • HTS imaging
  • Hit confirmation and analysis and guidance for further development
  • Nova cell transfection method using in house developed NanoStraw technique for gene editing of sensitive cells

Infrastructure Lund

  • Agilent screening system with Bravo pipetting robotic (96 and 384 wells plate format), BenchCel and PlateLoc.
  • Multidrop dispenser
  • HTS-imaging and plate reader Tecan Spark Cyto 400 with incubator function
  • Small molecule libraries of approved drugs, annotated tool compounds and commercial none-biased compounds. In total 8000 compounds.
  • CBCS compounds libraries on demand.

Contact

Mail/Visiting address

Lund University
Chemical Biology & Therapeutics
BMC D10, Sölvegatan 19
22184 Lund
Sweden

Parcel/delivery address

Lunds universitet – BMC godsmottagning D09                  
Fredrik Ek, D10                                                                  
Baravägen 18                                                                                             
222 41 Lund
Sweden

Personnel

Roger Olsson, Platform Scientific Director
Roger.Olsson@med.lu.se

Fredrik Ek, contact person
Fredrik.ek@med.lu.se
Telephone 0727-172205

Martin Hjort
Martin.Hjort@med.lu.se

The CBCS Linköping unit offers services within two areas: Electrophysiology and Screening in biosafety level 2 and 3 environments.

Electrophysiology

Automated patch clamp, current equipment Qpatch 48

Services offered: Cardiac toxicity (hERG, Nav1.5, Cav1.2), Compound screening on a selection voltage-gated ion channels, Electrophysiological characterization of channel/cell lines.

Contact

  • Prof. Fredrik Elinder, fredrik.elinder@liu.se
  • Dr. Nina Ottosson, staff scientist and expert in automated patch clamp, nina.ottosson@liu.se

BSL-2 and BSL-3

  • Guidance from the assay development phase through hit validation
  • Automated live-cell imaging inside the BSL-3 facility
  • A variety of BSL-2 and 3 pathogens avaliable
  • Mode of operation: Users come and visit the lab to start experiments

Contact

  • Prof. Maria Lerm, Head of Unit, maria.lerm@liu.se

Last updated: 2023-01-19

Content Responsible: Scilifelab Administration()