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Fragment-based drug design has introduced a bottom-up process for drug development, with improved sampling of chemical space and increased effectiveness in early drug discovery. Here, we combine the use of pharmacophores, the most general concept of representing drug-target interactions with the theory of protein hotspots, to develop a design protocol for fragment libraries. The SpotXplorer approach compiles small fragment libraries that maximize the coverage of experimentally confirmed binding pharmacophores at the most preferred hotspots. The efficiency of this approach is demonstrated with a pilot library of 96 fragment-sized compounds (SpotXplorer0) that is validated on popular target classes and emerging drug targets. Biochemical screening against a set of GPCRs and proteases retrieves compounds containing an average of 70% of known pharmacophores for these targets. More importantly, SpotXplorer0 screening identifies confirmed hits against recently established challenging targets such as the histone methyltransferase SETD2, the main protease (3CLPro) and the NSP3 macrodomain of SARS-CoV-2.

Original publication




Journal article


Nature communications

Publication Date





Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary.


Vero Cells, Animals, Humans, Histone-Lysine N-Methyltransferase, Receptors, G-Protein-Coupled, Ligands, Crystallography, X-Ray, Cell Survival, Protein Binding, Drug Design, Hydrogen Bonding, Databases, Protein, Small Molecule Libraries, Drug Discovery, High-Throughput Screening Assays, HEK293 Cells, Hydrophobic and Hydrophilic Interactions, Drug Development, Computational Chemistry, Chlorocebus aethiops, SARS-CoV-2, Coronavirus 3C Proteases, Coronavirus Papain-Like Proteases