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EU-OPENSCREEN extends its capacities in the field of fragment-based drug discovery (FBDD)

Sep. 15, 2020

In FBDD low-molecular-weight fragments (<250 Da) are screened using structural biology and biophysical techniques to identify hits, which commonly have lower binding affinities (in the range of several mM down to about 100 μM) due to their smaller size, but form high-quality interactions with sites on biologically important macromolecules. Those can be efficiently optimized into potent lead molecules. In fact, the fragment-based approach to drug discovery is today considered an excellent tool in the search for new drugs complementing the HTS, and using smaller libraries of around 1.000 compounds or even less.[1,2]

To embark into this new capacity, EU-OPENSCREEN, within the H2020 funded project EU-OPENSCREEN-DRIVE, is closely collaborating with Instruct-ERIC (https://instruct-eric.eu/), the European Research Infrastructure Consortium for Structural Biology, and the iNEXT-Discovery consortium (https://inext-discovery.eu/). iNEXT-Discovery/ Instruct-ERIC sites are specialized in X-Ray crystallography, NMR spectroscopy and cryo-Electron Microscopy, among other structure-based techniques. Such expertise in structural biology, combined with EU-OPENSCREEN’s strong medicinal chemistry expertise, will allow us to build a complete FBDD pipeline from the design of a novel fragment library, to fragment screening campaigns all the way to hit evolution.

Recently, our partner sites Fraunhofer IME in Hamburg and IMIM in Barcelona, in collaboration with iNEXT-Discovery/ Instruct-ERIC partners, designed the first EU-OPENSCREEN-DRIVE fragment library composed of 968 low-molecular-weight fragments and 88 ultra-low-molecular-weight compounds (so called minifrags).[3] Deriving from the fragment space of the EU-OPENSCREEN small molecule diversity library (100k commercial compounds),[4] this designed set of compounds facilitates the hit follow-up with a rapid availability of parent molecules from the EU-OPENSCREN small molecule collection, of which the fragments and minifrags are substructures.

The EU-OPENSCREEN fragment library is now available for structure-based fragment screening projects at several EU-OPENSCREEN-DRIVE facilities for biophysical experiments, and at five iNEXT-Discovery/ Instruct-ERIC sites for X-Ray and NMR screens. EU-OPENSCREEN medicinal chemistry sites can support further hit optimization campaigns. In fact, the current use of the EU-OPENSCREEN fragment library in screens on SARS-CoV-2 targets at iNEXT-Discovery/ Instruct-ERIC and EU-OPENSCREEN sites underlines the importance of a joint research effort exploiting competences from different fields of the life sciences for a prompt contribution to a global endeavor in understanding and combat COVID-19.

This project was fully funded by the EU under the grant agreement No 823893 (EU-OPENSCREEN-DRIVE) and its realization was possible thanks to the lead of Aigars Jirgensons, from our partner site the Latvian Institute of Organic Synthesis (OSI), in close collaboration with EU-OPENSCREEN chemoinformaticians Andrea Zaliani (Fraunhofer IME) and Jordi Mestres (IMIM), together with EU-OPENSCREEN-DRIVE partners at the HZI, CIPF, DTU, CSCI, FVB-FMP, UiB, MTA TTK and EMBL-Grenoble. Five iNEXT-Discovery sites, EMBL (Grenoble, France), University of Frankfurt (Germany), Helmholtz Center Berlin (Germany), Diamond Light Source (Didcot, United Kingdom) and Netherlands Cancer Institute (Amsterdam, the Netherlands) will make available their extensive expertise and facilities for X-ray crystallography and NMR spectroscopy-based experiments. The EU-OPENSCREEN fragment library was acquired at Specs, which also performed the 1536-well formatting for the iNEXT-Discovery partner Diamond Light Source.

For more information on access to these compounds please contact the EU-OPENSCREEN team at fragment-screening@eu-openscreen.eu.

References [1] C. W. Murray, D. C. Rees, Nat. Chem. 2009, 1, 187–192. [2] D. A. Erlanson, S. W. Fesik, R. E. Hubbard, W. Jahnke, H. Jhoti, Nat. Rev. Drug Discov. 2016, 15, 605–619. [3] M. O’Reilly, A. Cleasby, T. G. Davies, R. J. Hall, R. F. Ludlow, C. W. Murray, D. Tisi, H. Jhoti, Drug Discov. Today 2019, 24, 1081–1086. [4] D. Horvath, M. Lisurek, B. Rupp, R. Kühne, E. Specker, J. von Kries, D. Rognan, C. D. Andersson, F. Almqvist, M. Elofsson, et al., ChemMedChem 2014, 9, 2309–2326.