Transnational Call

CHEMOPROTEOMICS

 

Chemoproteomics Call

Under this call EU-OPENSCREEN-DRIVE offers funding to enable transnational access to chemical proteomics and compound disposition study facilities. A total of 6 projects will be selected in two separate calls (scheduled May 2019 and November 2020). Users from institutions within European Member States and Associated countries and up to one user from a Non-EU country will have the possibility to apply to access 7 advanced proteomics facilities across Europe.

Chemoproteomics Call 1

The EU-OPENSCREEN-DRIVE Chemoproteomics Call 1 aims at increasing the understanding of mechanisms of action by which a tool compound or drug discovery lead compound exerts its pharmacological effect. The users are offered access to target-based and phenotype-based workflows, proteomics and related advanced mass spectrometry (MS) based technologies, including MS imaging. EU-OPENSCREEN-DRIVE chemistry partner sites together with partners with proven track-records in probe development, target deconvolution and MS imaging will support 3 successful applicants providing collaboration on target identification and compound disposition studies. Under this call, users will have the opportunity to access a broad range of experimental approaches through different chemical proteomic workflows for samples of bacterial and mammalian origin or in whole organisms (e.g. multicellular parasites).

 

EU-OPENSCREEN-DRIVE chemoproteomics pipeline offers:

  • Standard proteomics methods including the quantitative analysis of proteins and their post-translational modifications by using label-free and label-based quantification strategies.
  • Affinity-based target identification including synthesis of chemical probes, affinity purification and proteomics analysis.
  • Other advanced target ID methods based on cellular thermal shift assays (CETSA) and iso-thermal dose response (ITDR) experiments.
  • Mass Spectrometry Imaging (MSI) for compound disposition studies.
  • Data processing and bioinformatics data interpretation pipelines including statistical analysis.

Applicants will be asked to provide a detailed description of the objectives of their project, and to fulfill specific pre-requisites such as i) confirmed compound cellular or organismal activity below 1 µM; ii) ideally (but not mandatory) preliminary Structure Activity Relationships (SAR) identified; iii) ideally (but not mandatory) having a SAR-informed synthesis of linker derivatives for functional immobilization in place; iv) ideally (but not mandatory) having inactive compound from the same series available, and v) granted access to relevant biological material. All projects pre-requisites for application can be found below.

Call 1 for proposals will be open until September 30 (extended deadline!), 2019 (20:00 CET). Eligible proposals will be evaluated for technical feasibility, scientific excellence and impact. The successful projects will be allocated upon evaluation to the most appropriate EU-OPENSCREEN-DRIVE chemoproteomics pipeline according to the strengths of specific methodology and expertise of the facilities, ensuring the requirement of transnationality. Please see below to learn more about our partner sites. Proposals will be handled confidentially. Read more about the proposal submission, eligibility criteria, modality of access and evaluation processes below.

 

Call Overview / Basic Data

Topics / Keywords:

drug discovery, chemical proteomics, target identification, mass spectrometry, chemical probes

Open Time:

Start date:
May-03-2019 (20:00 CET)

Closing date:
deadline extended until
September-30-2019 (20:00 CET)

Contact:

help-desk-open-call@eu-openscreen.eu

indicating "EU-OPENSCREEN-DRIVE Chemoproteomics Call 1"

in the email subject

Involved partner sites

Within this call EU-OPENSCREEN-DRIVE offers transnational access to state-of-the-art chemical synthesis facilities for the production of conjugated probe molecules to support affinity-based studies:
 

Institute of Bioorganic Chemistry Polish Academy of Sciences, Department of Molecular Probes and Prodrugs & Center for High Throughput Screening Studies (IBCH PAS)

IBCH PAS offers support for the synthesis of 2-4  probes for studying target engagement and/or fluorescent labelling, on the basis of one  validated bioactive compound with identified activity-benign point of attachment on its scaffold.

Probes will be composed of variable length linkers connecting a ligand  (derived by the user) with a specific tag (e.g. biotin for proteomics or fluorophore for imaging). Synthesis will be performed in a convergent manner with several linker-tag adducts being synthesized in parallel and then attached through a stable moiety to the identified hit scaffold. IBCH PAS provides also advanced proteomic identification of the targets.

Contact: Jacek.kolanowski@ibch.poznan.pl

Helmholtz Centre for Infection Research, Department of Chemical Biology (HZI)

The department “Chemical Biology” at HZI aims at discovering new antibacterial and antiviral drugs, characterizing their functionality and optimizing their properties. HZI focuses on infection research and small molecules that can function as antimicrobial or antiviral agents, interfere with pathogenicity factors or stimulate the immune system.

Within this call, HZI offers expertise in the area of drug conjugates to synthesize functionalized chemical probes. HZI has ample experience in the synthesis of bacteria-targeted conjugates that combine a targeting and an effector moiety (an antibiotic, a fluorophore, etc) through various cleavable and non-cleavable linkers. HZI will support preparation of probes for affinity-based target identification using chemoproteomics.

Contact: mark.broenstrup@helmholtz-hzi.de

Leibniz Research Institute for Molecular Pharmacology (FVB-FMP)

Within this call, Medicinal Chemistry group at FMP offers chemical probe optimization (activity, selectivity, linker attachment exploration) and follow-up modification towards labeled chemical probes for target deconvolution, fluorescent labeling, and crosslinking.

Contact: Marc Nazare nazare@fmp-berlin.de

 
Within this call EU-OPENSCREEN-DRIVE offers transnational access to advanced proteomics facilities for the prosecution of affinity-based studies and MALDI-Imaging for compound disposition studies:

Partners operate state-of-the-art quantitative mass spectrometry readout capable of interrogating thousands of potential drug-protein interactions simultaneously along with the required bioinformatics tools for data analysis and QC.

       

SINTEF Trondheim, Department of Biotechnology and Nanomedicine (SIN)

SINTEF provides access to advanced mass spectrometry-based proteomics facilities for drug target interaction studies. This includes facilities for quantitative proteomics to support non-targeted and targeted screening of drug-protein interactions. Using robotic handling SINTEF offers high-throughput sample preparation (extraction, lysis, in solution digestion, FASP, SPE clean-up) for both targeted and shotgun proteomics analysis. For shotgun proteomics to support non-targeted screening of drug-protein interaction, QExactive-HF-X mass spectrometer is employed (at a Core facility). For targeted screening of identified interactions, LC-MS/MS (Agilent QQQ) analysis is offered for highly sensitive analysis of multiple peptides, and targeted screening of identified interactions in a high-throughput manner is offered using Rapidfire-MS/MS (Agilent). In targeted analysis, isotope-labelled peptide standards are employed. 

Data processing and bioinformatics data interpretation pipelines are also offered including statistical analysis. Moreover, within this call SINTEF offers Mass Spectrometry Imaging (MSI) for compound disposition studies. MSI facilities at SINTEF include sample preparation set-ups (cryostat sectioning, ImagePrep for matrix and reagent deposition), and sample analysis using ultra-high-resolution mass spectrometry on a Bruker Solarix XR 12T FTICR. Analysis of resulting imaging data by multivariate statistical analysis tools is also provided (SCiLS software). The facilities offered by SINTEF using MSI support the determination of discrete tissue distribution of the parent compound, its metabolites, synthetic derivatives, as well as endogenous molecules linked to pharmacological and toxicological mechanisms of the compound, and thus, investigations of i) the relative compound disposition of close structural analogues and ii) the target activation and thus possibly modes of action for compounds at their site of action.

Contact: Geir.Klinkenberg@sintef.no; Hanne.Haslene-Hox@sintef.no; Anna.Nordborg@sintef.no

University of Santiago de Compostela, Biofarma (USC)

USC offers a proteomic facility and expertise for target identification with chemical proteomics methods. Established chemical proteomics workflows include gel-based affinity based protein profiling and target-based screening methodologies. Specialized chemical probes to enrich proteomes (e.g. protein kinases, proteases, GPCR) are readily available for selectivity profiling of inhibitors. Fluorescence scanner, MALDI-TOF and Triple TOF LC/MS equipment is available.

Our bioinformatics infrastructure includes supercomputing and data storage capabilities (a heterogeneous cluster, with an Infiniband FDR low latency network interconnecting 317 computing nodes based on Intel Xeon Hasswell processors. Together, these nodes are able to provide a computing power of 328 TFLOPS, 44,8 TB of RAM and 1,5 PB of disk capacity. The system includes a high-performance parallel storage system able to achieve a speed of more than 20 GB/s) and can be implemented for the real-time analysis of genomics and proteomics data.

Contact: mabel.loza@usc.es; pepo.brea@usc.es; eduardo.dominguez@usc.es

Technical University of Munich, Chair of Proteomics and Bioanalytics (TUM)

TUM Proteomics offers a broad range of advanced mass spectrometry based proteomic methods and expertise on specialized chemical proteomics technologies for drug target deconvolution. Established chemical proteomics workflows include the generation and application of affinity matrices from small molecules as well as natural compound derivatives. Specialized affinity matrices enriching subproteomes (protein kinases, HDACs) are readily available at TUM and allow for selectivity profiling of small molecule kinase and HDAC inhibitors.

In addition, TUM infrastructure provides facilities for cellular thermal shift assays (CETSA) and iso-thermal dose response (ITDR) experiments. It also provides bioinformatics infrastructure (400 TB online data storage, about 20 server computers totaling 300 CPUs and about 1 TB memory, 6 GPUs) and operates ProteomicsDB, a powerful in-memory database for the real-time analysis of proteomic data.

Contact: Stephanie.heinzlmeir@tum.de

Mannheim University of Applied Sciences, Center for Mass Spectrometry and Optical Spectroscopy (MUAS-CeMOS)

CeMOS combines expertise in development of measurement devices, in optics and spectroscopy and in mass spectrometry with substantial expertise in application development for the chemical, pharmaceutical, MedTech and Biotech industries. Within this call, CeMOS will provide access to Mass Spectrometry Imaging (MSI) for (quantitative) compound disposition studies, discovery and imaging of response markers and evaluation of toxicology findings. Focus areas include lipid/metabolite as well as infrared microscopy-guided MSI in fresh-frozen tissue sections, mainly in the therapy areas of oncology, neurodegeneration and metabolic diseases. MUAS offers state-of-the-art instrumentation for MSI sample preparation (HTX M5 and SunChrom sprayers) and analysis using high-resolution mass spectrometry on a Bruker solariX XR 7T FTICR and high-speed mass spectrometry on a Bruker rapifleX. Suitable data analysis tools are available (SCiLSlab and in-house bioinformatics).

Moreover, MUAS offers access to MALDI MS-based assays for drug discovery. Assay facilities include an Analytik Jena CyBio Felix pipetting robot for sample preparation and a high-speed Bruker rapifleX mass spectrometer for measurements. Assays are currently run in 384-well format and can be either biochemical assays with enzymes causing mass changes or cell-based assays where enzyme inhibition causes an accumulation of the substrate.

Contact: Sandra Schulz s.schulz@hs-mannheim.de; Carsten Hopf c.hopf@hs-mannheim.de

Application requirements and submission

Pre-requisites for application

Applicants are required to provide the following pre-requisites for application:

  • Confirmed phenotypically determined concentration-dependent cellular/ or organismal activity of at least 1 µM or lower;
  • Ideally, preliminary results regarding structure-activity-relationships (SAR);
  • Information on Pan-assay interference (PAIN) analysis of the structure;
  • Availability of sufficient amounts of isolated compound with purity > 95% (amount indicated by the user will restrict or expand the possible options for target deconvolution);
  • If available, (bio)synthetic protocol for the preparation of HIT compounds (preferentially bearing functional groups for further modification, which would not interfere with activity);
  • If available, preliminary hypotheses around mode of action or target protein for compound to be tested;
  • Sufficient amount ofbiological material of interest or cell lysateor other lysates thereof.

Specific additional requirements for MSI experiments:

  • Collected tissues from animal studies, stored and transported to EU-OPENSCREEN-DRIVE facility(ies) accordingly, providing necessary documentation (if needed). Access to available embedding protocols (if needed) upon request.
  • Knowledge of pharmacokinetic parameters of the test drug (e.g. half-life, bioavailability, maximum tolerated dose, dosing route, initial formulation).

Proposal submission

  • Applicants are invited to submit their proposals via EU-OPENSCREEN-DRIVE website, by connecting to the ARIA online proposal submission system (online system will be available by May 3rd 2019 (20:00 CET). Applicants are required to register upon their first visit to ARIA, or login directly if they are already registered with an ARIA account. Once registered, the applicants are required to follow ARIA instructions.
  • The ARIA application system for EU-OPENSCREEN-DRIVE is handled by Instruct-ERIC. Although potential EU-OPENSCREEN-DRIVE users are requested to register with the ARIA system, the application, review, and reporting process will be handled by EU-OPENSCREEN ERIC.
  • Guidelines for the application form for this call can be downloaded here.
  • The online proposal submission will be open until September 30 (extended deadline!), 2019 (20:00 CET).
  • Applicants will be notified about acceptance or rejection of their proposal within 12 weeks after the closure of the chemoproteomics call 1.
  • If you have any doubt or question relating to the submission process within ARIA please contact us at aria@eu-openscreen.eu (indicating “EU-OPENSCREEN-DRIVE Chemoproteomics Call 1” within the subject).

Eligibility criteria

  • Applicants may come from academia or industry (including SMEs).
  • Applicants may be working in an institution of a European Member State or Associated State or Associated country. Up to 1 project will be open to applicants from outside Europe.
  • Principal investigators and members of their research groups from EU-OPENSCREEN-DRIVE beneficiaries are not eligible to apply.
  • Applicants commit to have legal and ethical consent regarding their research, their samples and/or their data prior to submitting their application.
  • Applicants must agree to comply with the access, IP and dissemination policies described in the statutes of EU-OPENSCREEN ERIC.
  • Applicants must agree to comply with EU-OPENSCREEN ERIC/EU-OPENSCREEN-DRIVE privacy policy and terms of submission.
  • If you have any doubt or question relating to the eligibility criteria for this call please contact us at help-desk-open-call@eu-openscreen.eu (indicating “EU-OPENSCREEN-DRIVE Chemoproteomics Call 1” within the subject).

Modality of access

  • The successful projects will be allocated to the most appropriate EU-OPENSCREEN-DRIVE chemoproteomics pipeline according to the strengths of specific methodology and expertise of the facilities upon technical and scientific evaluation.
  • Successful projects could require up to 12 months of work and could involve 2 or more partners (for example access for chemical probe preparation at one site followed by proteomics at a second site and compound distribution studies at a third site).
  • User access is transnational only. Users are not allowed to access facility(ies) in their home country.
  • Users are expected to contribute with scientific insight, relevant know-how and protocols and provide access to key reagents normally found in user labs, including physical samples of lead compounds under study.
  • The experimental work will be run as a remote service; however, users can plan medium-term visits to familiarize themselves with data evaluation aided by experienced scientists. Users are invited to apply for potential reimbursements of individual travel and accommodation expenses at the access facility directly in accordance with the facility´s rules for external user’s reimbursements. Each visit (if applicable) must be discussed and agreed with the EU-OSPENSCREEN-DRIVE management team (help-desk-open-call@eu-openscreen.eu) and access facility contact.
  • Costs of successful projects (consumables, personnel) required at the facilities offering the access will be funded by EU-OPENSCREEN-DRIVE.
  • Project-related costs (personnel, consumables, and other costs) at the user laboratory are not funded under this call.
  • EU-OPENSCREEN-DRIVE chemoproteomics experts will work closely with users in identifying the optimal approach and experimental plan. After the approval of the successful project, a specific work plan will be requested from the user before the start of the research activities. Each access project will involve multiple experimental procedures and diverse items of equipment used in a multi-disciplinary manner. EU-OPENSCREEN-DRIVE recommends users to contact EU-OPENSCREEN-DRIVE team by email at help-desk-open-call@eu-openscreen.eu to discuss the feasibility of the project prior to the submission of proposal (indicating “EU-OPENSCREEN-DRIVE Chemoproteomics Call 1” within the subject).

Proposal evaluation

The review process of applications consists of 2 steps of evaluation (technical and scientific).The application will remain strictly confidential throughout the review process. Reviewers will be bound by a non-disclosure agreement.

Technical evaluation of submitted proposals will be performed by a minimum of 2 internal EU-OPENSCREEN-DRIVE members involved in the chemoproteomics activities. Technical evaluation will ensure the necessary alignment between user proposals and the technical capabilities of each partner site in terms of technical feasibility. EU-OPENSCREEN-DRIVE technical reviewers will ensure that the eligibility criteria and pre-requisites for applicants are met. Moreover, they will assess that appropriate resources for the technical implementation of the projects are available.

Scientific evaluation of submitted proposals will be performed by 2 external experts in the field of chemical proteomics. Proposals will be assessed based on the scientific excellence of the proposal, the scientific quality of the research, and impact and innovation potential of the proposed study. Societal impact and gender aspects of the project-specific research questions and method will also be considered.

Publication

Open access (gold or green) is required for any publication of access results. EU-OPENSCREEN-DRIVE funding must be clearly acknowledged by: “This project has received funding from the European Union´s Horizon 2020 research and innovation programme under grant agreement No 823893.”


Chemoproteomics call 2

Call text and access topics will be published here in due time before call opening in November 2020 (tentative date).

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