From fragments to high affinity binders interfacing integrated structural biology, medicinal chemistry and artificial intelligence

Research InfrastructuresHORIZON-RIAID: 101094131
EC Contribution
€82,651
Consortium Size
26 orgs
Start Year
2023
Summary

Fragment-Screen will develop innovative instrumentation, workflows and experimental and computational methodologies for fragment-based drug discovery (FBDD) enabling access to early phase structure-based drug discovery for all biological targets and for scientists both in industry and academia. The established workflows will use structural biology insights and associated data to feed artificial intelligence (AI) methodology to guide medicinal chemistry in drug development. Fragment-Screen brings together scientists from four ESFRI Landmark research infrastructures (RIs): ESRF (the European synchrotron) and the distributed RIs EU-OPENSCREEN ERIC (medicinal chemistry), ELIXIR (data resources for life science) under the coordination of Instruct-ERIC (integrated structural biology) and seven industry partners in scientific instrumentation and computational and AI sectors including SMEs to remove crucial bottlenecks in early phase drug discovery. The new instrumentation and workflows will be available at European RIs, while the new instruments will be commercialised to increase the technological competitiveness of European industry in drug design and the attractiveness of structural biology RIs for the pharmaceutical and biotech sectors. Fragment-Screen will implement open science approaches in early drug discovery to maximise the impact of screening campaigns. Generated data will be made accessible so that iterative cycles applying AI will improve response times for drug discovery. We will create a framework for the objective and independent evaluation of AI in drug design to identify critical developments in this thriving research field. Methodologies for rigorous cross-validation will be established through demonstrator and pilot studies and results will be disseminated to the large scientific communities affiliated to the European RIs and beyond.

Consortium (26)

Project Results (27)

Source: CORDIS, the EU research results database.

Publications (14)
The future of integrated structural biology
Structure· 2025DOI
Harald Schwalbe, Pauline Audergon, Natalie Haley, Claudia Alen Amaro, Jon Agirre, Marc Baldus, Lucia Banci, Wolfgang Baumeister, Martin Blackledge, Jose Maria Carazo, Kristina Djinovic Carugo, Patrick Celie, Isabella Felli, Darren J. Hart, Thomas Hauß, Lari Lehtiö, Kresten Lindorff-Larsen, José Márquez, André Matagne, Roberta Pierattelli, Antonio Rosato, Frank Sobott, Sridhar Sreeramulu, Jan Steyaert, Joel L. Sussman, Lukas Trantirek, Manfred S. Weiss, Matthias Wilmanns
Controlling the incorporation of fluorinated amino acids in human cells and its structural impact
Protein Science· 2024DOI
Azzurra Costantino, Lan B. T. Pham, Letizia Barbieri, Vito Calderone, Gili Ben-Nissan, Michal Sharon, Lucia Banci, Enrico Luchinat
Design, quality and validation of the EU-OPENSCREEN fragment library poised to a high-throughput screening collection
RSC Medicinal Chemistry· 2024DOI
Jalencas, Xavier and Berg, Hannes and Espeland, Ludvik Olai and Sreeramulu, Sridhar and Kinnen, Franziska and Richter, Christian and Georgiou, Charis and Yadrykhinsky, Vladyslav and Specker, Edgar and Jaudzems, Kristaps and Miletić, Tanja and Harmel, Robe
EasyGrid: A versatile platform for automated cryo-EM sample preparation and quality control
bioRXiv· 2024DOI
Olivier Gemin, Victor Armijo, Michael Hons, Caroline Bissardon, Romain Linares, View ORCID ProfileMatthew W. Bowler, Georg Wolff, View ORCID ProfileKirill Kovalev, Anastasiia Babenko, Veijo T. Salo, Sarah Schneider, Christopher Rossi, Léa Lecomte, Thiba
Language Models in Molecular Discovery
Drug Development Supported by Informatics· 2024DOI
Nikita Janakarajan, Tim Erdmann, Sarath Swaminathan, Teodoro Laino, Jannis Born
Machine Learning-Enhanced Quantum Chemistry-Assisted Refinement of the Active Site Structure of Metalloproteins
Inorganic Chemistry· 2024DOI
Lucia Gigli, José Malanho Silva, Linda Cerofolini, Anjos L. Macedo, Carlos F. G. C. Geraldes, Elizaveta A. Suturina, Vito Calderone, Marco Fragai, Giacomo Parigi, Enrico Ravera, Claudio Luchinat
NMR 1H,19F-based screening of the four stem-looped structure 5_SL1–SL4 located in the 5′-untranslated region of SARS-CoV 2 RNA
RSC Medicinal Chemistry· 2024DOI
Daniel Hymon, Jason Martins, Christian Richter, Sridhar Sreeramulu, Anna Wacker, Jan Ferner, Neeraj N. Patwardhan, Amanda E. Hargrove, and Harald Schwalbe
Targeting the Main Protease (Mpro, nsp5) by Growth of Fragment Scaffolds Exploiting Structure-Based Methodologies
ACS Chemical Biology· 2024DOI
Nadide Altincekic, Nathalie Jores, Frank Löhr, Christian Richter, Claus Ehrhardt, Marcel J. J. Blommers, Hannes Berg, Sare Öztürk, Santosh L. Gande, Verena Linhard, Julien Orts, Marie Jose Abi Saad, Matthias Bütikofer, Janina Kaderli, B. Göran Karlsson, U
Biomacromolecules
Biomacromolecules· 2023DOI
Fallarini S.; Cerofolini L.; Salobehaj M.; Rizzo D.; Gheorghita G. R.; Licciardi G.; Capialbi D. E.; Zullo V.; Sodini A.; Nativi C.; Fragai M.
Combining Solid‐State NMR with Structural and Biophysical Techniques to Design Challenging Protein‐Drug Conjugates
Angewandte Chemie International Edition· 2023DOI
Linda Cerofolini, Kristian Vasa, Elisa Bianconi, Maria Salobehaj, Giulia Cappelli, Alice Bonciani, Giulia Licciardi, Anna Pérez‐Ràfols, Luis Padilla‐Cortés, Sabrina Antonacci, Domenico Rizzo, Enrico Ravera, Caterina Viglianisi, Vito Calderone, Giacomo Parigi, Claudio Luchinat, Antonio Macchiarulo, Stefano Menichetti, Marco Fragai
eLife
eLife· 2023DOI
Isabelle Petit-Härtlein; Annelise Vermot; Michel Thépaut; Anne Sophie Humm; Florine Dupeux; Jérôme Dupuy; Vincent Chaptal; José A. Marquez; Susan M.E. Smith; Franck Fieschi
The rise of automated curiosity-driven discoveries in chemistry
Chemical Science· 2023DOI
Latimah Bustillo, Teodoro Laino, and Tiago Rodrigues
Regression Transformer enables concurrent sequence regression and generation for molecular language modelling
Nature Machine Intelligence· 2022DOI
Jannis Born, Matteo Manica
Chemical Communications
The synthesis of specifically isotope labelled fluorotryptophan and its use in mammalian cell-based protein expression for 19F-NMR applicationsDOI
Giorgia Toscano, Martina Rosati,Letizia Barbieri, Katharina Maier, Lucia Banci, Enrico Luchinat, Robert Konrat, Roman J. Lichtenecker
Deliverables (12)
Other Results (1)
Periodic Reporting for period 2 - Fragment-Screen (From fragments to high affinity binders interfacing integrated structural biology, medicinal chemistry and artificial intelligence)