Structure-Based Discovery of High-Affinity Small Molecule Ligands and Development of Tool Probes to Study the Role of Chitinase-3-Like Protein 1

  • J Med Chem. 2024 Mar 14;67(5):3959-3985. doi: 10.1021/acs.jmedchem.3c02255.
Wojciech Czestkowski  1 ,  Łukasz Krzemiński  1 ,  Michał C Piotrowicz  1 ,  Marzena Mazur  1 ,  Elżbieta Pluta  1 ,  Gleb Andryianau  1 ,  Robert Koralewski  1 ,  Krzysztof Matyszewski  1 ,  Sylwia Olejniczak  1 ,  Michał Kowalski  1 ,  Katarzyna Lisiecka  1 ,  Rafał Kozieł  1 ,  Katarzyna Piwowar  1 ,  Diana Papiernik  1 ,  Marcin Nowotny  2 ,  Agnieszka Napiórkowska-Gromadzka  2 ,  Elżbieta Nowak  2 ,  Dorota Niedziałek  1 ,  Grzegorz Wieczorek  1 ,  Anna Siwińska  1 ,  Tomasz Rejczak  1 ,  Karol Jędrzejczak  1 ,  Krzysztof Mulewski  1 ,  Jacek Olczak  1 ,  Zbigniew Zasłona  1 ,  Adam Gołębiowski  1 ,  Katarzyna Drzewicka  1 ,  Agnieszka Bartoszewicz  1
Affiliations
  • 1. Molecure S.A., Żwirki I Wigury 101, Warsaw 02-089, Poland.
  • 2. Laboratory of Protein Structure, International Institute of Molecular and Cell Biology in Warsaw, Ks. Trojdena 4, Warsaw 02-109, Poland.
PMID: 38427954 DOI: 10.1021/acs.jmedchem.3c02255
Abstract

Chitinase-3-like-1 (CHI3L1), also known as YKL-40, is a glycoprotein linked to inflammation, fibrosis, and Cancer. This study explored CHI3L1's interactions with various oligosaccharides using microscale thermophoresis (MST) and AlphaScreen (AS). These investigations guided the development of high-throughput screening assays to assess interference of small molecules in binding between CHI3L1 and biotinylated small molecules or heparan sulfate-based probes. Small molecule Binders of YKL-40 were identified in our chitotriosidase inhibitors library with MST and confirmed through X-ray crystallography. Based on cocrystal structures of potent hit compounds with CHI3L1, small molecule probes 19 and 20 were designed for an AS assay. Structure-based optimization led to compounds 30 and 31 with nanomolar activities and drug-like properties. Additionally, an orthogonal AS assay using biotinylated heparan sulfate as a probe was developed. The compounds' affinity showed a significant correlation in both assays. These screening tools and compounds offer novel avenues for investigating the role of CHI3L1.

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