Research Areas
Over 30 researchers and students with backgrounds in various scientific fields work at the Department of Biothermodynamics and Drug Design. Organic chemists design and synthesize novel compounds. Molecular biologists clone, express, and purify various target proteins (carbonic anhydrases (CA), Hsp90, HDAC isozymes, functional proteins of COVID-19 coronavirus, etc. Biothermodynamicists determine binding energies by isothermal titration calorimetry, thermal shift assay, and enzyme inhibition assay. Crystallographers determine the X-ray crystallographic structures of protein-compound complexes, while modelers perform in silico compound docking. Biologists investigate drug-candidate compounds in biological systems, including cancer cell cultures, zebrafish, and mice. Together with medical doctors, we are developing the inhibitors of anticancer target protein CA IX for tumor visualization and cancer treatment.
In our department, we measure protein-ligand binding energies and apply structure-thermodynamics correlations to design compounds of greater affinity and selectivity for target proteins. Our primary focus is on the human family of twelve catalytically active CA isozymes as protein targets in various diseases. Sometimes structurally similar compounds exhibit highly different affinities. A deep understanding of the underlying forces that determine affinity and selectivity is one of the main goals of our laboratory.
To help design compounds that bind CA isozymes and Hsp90 proteins with high affinity and selectivity, we have assembled a protein-ligand binding database – PLBD (https://plbd.org). The constantly growing database contains the thermodynamic, kinetic, and structural information of protein-compound interaction, including the standard observed and intrinsic dissociation constant, Gibbs energy, enthalpy, entropy, heat capacity changes upon binding, on- and off-rates, and X-ray structures of CA-compound complexes.
The thermal shift assay is a universal technique to determine protein-ligand affinities ranging from millimolar to picomolar levels in a single ligand dosing experiment. However, the complexity of thermodynamic data analysis leads to an underuse of this technique. We have developed a new software tool – Thermott – that provides an accurate and user-friendly way to analyze thermal shift data of protein-ligand interaction and yield a quantitative thermodynamic characterization of the binding reaction. It is solely a web-based application that does not require installation and is free of charge and open source. Thermott application, its documentation, and a tutorial can be found online at https://thermott.com.
