Previous projects

Rational Drug Design

The emergence of multi-drug resistant strains is one of the most challenging problems of modern pharmacology that prompts interdisciplinary studies in quest for new antibiotics. We participate in such studies in collaboration with the Medical University of Lublin. Within these studies a few families of heterocyclic molecules are evaluated for their biological activity, and their physico-chemical properties evaluated experimentally and theoretically are used to guide future rational synthesis of effective antibacterials. Quantum-chemical calculations are used to find a reasonably robust and inexpensive theory level that allows SAR-like descriptors such as geometries, partial atomic charges, ionization potentials, electron affinities, HOMO, LUMO, HOMO-LUMO gaps, logP, hydration energy, refractivity, and polarizability to be calculated for large number of compounds. Furthermore, in order to understand interactions of the synthesized inhibitors with the active site of target enzymes (such as for example topoisomerase and HIV reverse transcriptase) docking, MD, and QM/MM calculations are carried out. We also try to employ isotope effects, and in particular binding isotope effects in these studies.

The increasing resistance of pathogens to the drugs used induces constant search for new biologically active substances that could effectively replace them. The process of searching for such substances is extremely difficult and expensive, which is why it is increasingly preceded by in-depth scientific research, the purpose of which is to provide information on the mechanism of their operation to limit the range of searches to a group of highly promising compounds.

A large part of pharmaceuticals are compounds blocking the action of specific enzymes (so-called inhibitors), which consequently lead to inhibition of pathogen development. Therefore, research aimed at the development of new drugs focuses on the detailed recognition of the mechanisms of enzymatic reactions and understanding the interactions between the drug molecule and the enzyme. One of the most subtle kinetic methods of studying the mechanisms of enzymatic reactions is the observation of the impact on the dynamics of changes in the isotopic composition – these are the so-called isotopic effects. It is believed that the extraordinary efficiency of enzymes results mainly from the stabilization of the structure with the lowest energy necessary to react (this structure is referred to as the transition state). Interactions between the transition state and the place where the enzyme reacts in the so-called active site are responsible for stabilization. In recent years, however, frequently the second, no less important, source of enzymatic catalysis is suggested – the destabilization of the inhibitor as a result of binding to the enzyme. However, the use of isotopic effects to study the enzyme-inhibitor interactions has been significantly limited so far because the isotopic effects associated with this process are usually small and their measurement is difficult and expensive.

Our research has focused on the use of isotope effects on the inhibitor-enzyme binding for a detailed understanding of the interactions between them and on this basis for the rational design of compounds with high biological activity. As a model enzyme, we chose HIV-1 reverse transcriptase, one of the three enzymes responsible for the proliferation of this virus. This enzyme shows a high tendency to mutation, which makes it necessary to constantly search for new inhibitors.

In the initial phase, based on the known structures of this enzyme, we determined the binding strength of a given compound with the enzyme (this process is called docking) and then we performed a structure-activity relationship study in the tested class of compounds that allowed us to indicate the directions of beneficial structural changes. The next step was to perform theoretical calculations proposed on the basis of the above tests, which allowed to determine the molecular basis of the interaction between these compounds and the enzyme and to calculate the expected values ​​of isotopic effects. During the study it turned out that these inhibitors can bind to reverse transcriptase in more than one place. We performed theoretical calculations of the isotopic effects values ​​associated with these alternative binding sites and showed that the isotopic effect of the oxygen atom of the carbonyl group can allow to experimentally determine where the enzyme actually binds the inhibitor. In the final step, we developed a method to determine the experimental values of this isotope effect. Our studies have demonstrated the usefulness of isotopic effects to determine the binding site of the inhibitor to the enzyme and the nature of interactions determining the binding strength of molecules by enzymes. In addition, we have synthesized a non-toxic inhibitor that exceeds in biological activity the compounds currently used in clinical practice and is characterized by significantly higher solubility, due to which it could be used in much lower doses. This compound is an excellent starting point for further exploration of an even more effective drugs for use in anti AIDS therapy.

Funding:

NCN (National Science Centre) Poland, Maestro grant, 2012-2017, Binding isotope effects as a new, unique tool for studies of receptor – ligand interactions (PI: Piotr Paneth)

Degradation of Nitroaromatics

Within the studies of environmental pollutants we worked on isotopic fractionation of nitroaromatic compounds. These studies were carried out with a group at Eawag, Zurich which delivered experimental measurements of deuterium, carbon and nitrogen signatures which were predicted theoretically in our laboratory for the relevant chemical and enzyme-catalyzed processes.

Funding:

  1. Polish-Swiss Joint Research Project (2011-2015), Novel stable isotope-based approaches for assessing the biodegradation of soil and groundwater contaminants (PI: Piotr Paneth)
  2. FP7 Maria Curie Action ITN (2010-2015), CSI: Environment—Isotope forensics meets biogeochemistry – linking sources and sinks of organic contaminants by compound-specific isotope investigation