Abstract

Human hypoxic solid tumors overexpress carbonic anhydrase IX (CAIX), a transmembrane protein that promotes metastasis and invasiveness, helps cancer cells survive under hypoxia by acidifying the tumor microenvironment, and is a promising anticancer target (1). We designed, synthesized and measured affinities (2) of over a thousand small-molecule compounds for CA family of enzymes and determined the principles of selectivity by inhibiting the CAIX enzymatic activity. The CAIX-selective compounds helped visualize CAIX expression in cancer cells, measure dissociation constants, visualize tumors, and showed efficacy in mice xenograft models.
The data were assembled to the Protein-Ligand Binding Database (PLBD) of thermodynamics and kinetics of protein interaction with small molecules, available at https://plbd.org (3). The database contains 7247 binding datasets of 585 sulfonamides and other compounds interactions with the 12 catalytically active human CA isozymes, Hsp90, and COVID proteases, determined by the fluorescent thermal shift assay, ITC, inhibition of enzymatic activity, and SPR (4). In the PLBD, we emphasize the intrinsic thermodynamic parameters that account for the binding-linked protonation reactions. The database includes calorimetrically measured binding enthalpies, enhancing the understanding of reaction mechanisms. The binding data are linked to 127 X-ray crystal structures of six CA isozyme complexes with ligands. The database has been built using the FAIR data principles and the database schema and deposited data have revision and versioning systems providing historical traces of database evolution. The PLBD is useful for the investigations of protein-ligand recognition principles and could be applied for small molecule drug design.

References

1. Matulis, D. 2019. Carbonic anhydrase as drug target: thermodynamics and structure of inhibitor binding. Springer Nature.
2. Gedgaudas, M., D. Baronas, E. Kazlauskas, V. Petrauskas, and D. Matulis. 2022. Thermott: A comprehensive online tool for protein–ligand binding constant determination. Drug Discov. Today. 27:2076–2079.
3. Linge, D., M. Gedgaudas, etc, and D. Matulis. 2023. PLBD: Protein–Ligand Binding Database of Thermodynamic and Kinetic Intrinsic Parameters. Database.
4. Linkuvienė, V., A. Zubrienė, E. Manakova, V. Petrauskas, L. Baranauskienė, A. Zakšauskas, A. Smirnov, S. Gražulis, J.E. Ladbury, and D. Matulis. 2018. Thermodynamic, kinetic, and structural parameterization of human carbonic anhydrase interactions toward enhanced inhibitor design. Q. Rev. Biophys. 51:1–48.

Biosketch

Daumantas Matulis graduated from Vilnius University in 1993 and obtained his Ph.D in 1998 from University of Minnesota, USA. Since 2001 D. Matulis has worked for Johnson & Johnson Pharmaceutical Research and Development in the USA. In 2005 he returned to Lithuania and heads the Biothermodynamics and Drug Discovery Unit at the Institute of Biochemistry at Vilnius University Life Sciences center. Since 2022 he is the Director of Vilnius University Life Sciences center.