Scientific research
Scientific areas
Computational biology; molecular dynamics; protein engineering; medicinal chemistry; bioinorganic and bioorganic chemistry.
Current research
Currently, my main research topic is focused on utilizing molecular modelling tools for protein engineering. I am working on several projects involving the optimization of various properties of enzymes (e.g., haloalkane dehalogenases and dioxygenases) for different practical purposes. I also collaborate with other research groups to understand the catalytic properties of their proteins of interest or design improved variant using computational biology methods.
More recently, I have been involved in applying computational methods for understanding the mechanisms of Alzheimer's disease at the molecular level and the protective effects of small molecules.
COZYME action
I have been part of the COST action CA21162 - "Establishing a Pan-European Network on Computational Redesign of Enzymes (COZYME)" since October 2022. In this action, I am the leader of working group 1, WG1 - Computational optimization of global enzyme properties.
Technical skills
Computational biology: MM and QM/MM molecular dynamics (AMBER, GROMACS, ACEMD); metadynamics (GROMACS); adaptive sampling (ACEMD), tunnel calculation and analysis (CAVER, Caver Analyst 2); molecular docking (AutoDock Vina, AutoDock 4, GOLD); protein design and mutagenesis (ROSETTA); molecular and quantum mechanics (GAUSSIAN); computer scripting (BASH), Jupyter notebooks
Organic synthesis: preparation and characterization of organic compounds
Characterization techniques: 1H and 13C NMR; IV; ESI-MS
Analytical chemistry: potentiometry, UV/Vis spectrophotometry, NMR, IV spectroscopy, calculation of protonation constants (pKa) and stability constants of metal complexes (log β) (HYPERQUAD).
Enzymology: enzyme inhibition assays using spectrofluorimetric methods or stopped flow
Computational biology; molecular dynamics; protein engineering; medicinal chemistry; bioinorganic and bioorganic chemistry.
Current research
Currently, my main research topic is focused on utilizing molecular modelling tools for protein engineering. I am working on several projects involving the optimization of various properties of enzymes (e.g., haloalkane dehalogenases and dioxygenases) for different practical purposes. I also collaborate with other research groups to understand the catalytic properties of their proteins of interest or design improved variant using computational biology methods.
More recently, I have been involved in applying computational methods for understanding the mechanisms of Alzheimer's disease at the molecular level and the protective effects of small molecules.
COZYME action
I have been part of the COST action CA21162 - "Establishing a Pan-European Network on Computational Redesign of Enzymes (COZYME)" since October 2022. In this action, I am the leader of working group 1, WG1 - Computational optimization of global enzyme properties.
Technical skills
Computational biology: MM and QM/MM molecular dynamics (AMBER, GROMACS, ACEMD); metadynamics (GROMACS); adaptive sampling (ACEMD), tunnel calculation and analysis (CAVER, Caver Analyst 2); molecular docking (AutoDock Vina, AutoDock 4, GOLD); protein design and mutagenesis (ROSETTA); molecular and quantum mechanics (GAUSSIAN); computer scripting (BASH), Jupyter notebooks
Organic synthesis: preparation and characterization of organic compounds
Characterization techniques: 1H and 13C NMR; IV; ESI-MS
Analytical chemistry: potentiometry, UV/Vis spectrophotometry, NMR, IV spectroscopy, calculation of protonation constants (pKa) and stability constants of metal complexes (log β) (HYPERQUAD).
Enzymology: enzyme inhibition assays using spectrofluorimetric methods or stopped flow
Previous research
Biogate project
The BIOGATE project was focused on the study of molecular gates based on theoretical simulations, in order to get a deep understanding of their mechanisms. Our model enzymes are the haloalkane dehalogenases (HLDs), which are are bacterial enzymes that catalyze the hydrolysis of a wide variety of halogenated organic compounds into the corresponding alcohols. This ability makes them very interesting for a number of biotechnological applications, such as bioremediation, biocatalysis, and biosensing. The ultimate goal of this project is to operate rational design on those gates and optimize their functions, in order to produce new enzymes with improved properties (catalytic activity and stability).
This project was awarded by the SoMoPro II program for distinguished researchers, which is co-financed by the South Moravian Region and the 7th Framework Programme for Research and Development, the Marie Skłodowska-Curie Actions.
Multi-functional enzyme inhibitors
Molecular design, synthesis and study of new compounds with potential anticancer activity, with perspective for further medicinal application. The aim was to inhibit the action of certain metalloenzymes involved in this pathology (e.g. matrix metalloproteinases, carbonic anhydrases, etc.).
The field of research also extended to the development of polyfunctional antineurodegenerative agents against Alzheimer's disease. The target was the inhibition of neurological enzymes, such as acetylcholinesterase (AChE), while also providing antioxidant activity and inhibition of β-amyloid aggregation.
Chelating agents with medical applications
Another important work topic was the synthesis and study of chelating agents. The aim of this research was the development of new compounds for radiodiagnosis (e.g. carriers of gallium or lanthanide radioisotopes) or metal detoxication (e.g. iron and alluminium).
Biogate project
The BIOGATE project was focused on the study of molecular gates based on theoretical simulations, in order to get a deep understanding of their mechanisms. Our model enzymes are the haloalkane dehalogenases (HLDs), which are are bacterial enzymes that catalyze the hydrolysis of a wide variety of halogenated organic compounds into the corresponding alcohols. This ability makes them very interesting for a number of biotechnological applications, such as bioremediation, biocatalysis, and biosensing. The ultimate goal of this project is to operate rational design on those gates and optimize their functions, in order to produce new enzymes with improved properties (catalytic activity and stability).
This project was awarded by the SoMoPro II program for distinguished researchers, which is co-financed by the South Moravian Region and the 7th Framework Programme for Research and Development, the Marie Skłodowska-Curie Actions.
Multi-functional enzyme inhibitors
Molecular design, synthesis and study of new compounds with potential anticancer activity, with perspective for further medicinal application. The aim was to inhibit the action of certain metalloenzymes involved in this pathology (e.g. matrix metalloproteinases, carbonic anhydrases, etc.).
The field of research also extended to the development of polyfunctional antineurodegenerative agents against Alzheimer's disease. The target was the inhibition of neurological enzymes, such as acetylcholinesterase (AChE), while also providing antioxidant activity and inhibition of β-amyloid aggregation.
Chelating agents with medical applications
Another important work topic was the synthesis and study of chelating agents. The aim of this research was the development of new compounds for radiodiagnosis (e.g. carriers of gallium or lanthanide radioisotopes) or metal detoxication (e.g. iron and alluminium).