Abstract
Statistical analysis of data from crystal structures extracted from the Cambridge Structural Database (CSD) has shown that S and Se atoms display a similar tendency towards specific types of interaction if they are part of a fragment that corresponds to the side chains of cysteine (Cys), methionine (Met) selenocysteine (Sec) and selenomethionine (Mse). The most numerous are structures with C-H...Se and C-H...S interactions (∼80%), notably less numerous are structures with Se...Se and S...S interactions (∼5%), and Se...π and S...π interactions are the least numerous. The results of quantum-chemical calculations have indicated that C-H...Se (∼-0.8 kcal mol-1) and C-H...S interactions are weaker than the most stable parallel interaction (∼-3.3 kcal mol-1) and electrostatic interactions of σ/π type (∼-2.6 kcal mol-1). Their significant presence can be explained by the abundance of CH groups compared with the numbers of Se and S atoms in the crystal structures, and also by the influence of substituents bonded to the Se or S atom that further reduce their possibilities for interacting with species from the environment. This can also offer an explanation as to why O-H...Se (∼-4.4 kcal mol-1) and N-H...Se interactions (∼-2.2 kcal mol-1) are less numerous. Docking studies revealed that S and Se rarely participate in interactions with the amino acid residues of target enzymes, mostly because those residues preferentially interact with the substituents bonded to Se and S. The differences between Se and S ligands in the number and positions of their binding sites are more pronounced if the substituents are polar and if there are more Se/S atoms in the ligand.
Highlights
Selenium and sulfur are basic elements with closely related properties, found in nature in a vast array of active compounds, and used as reactants of numerous chemical and biochemical processes
Our search of the Cambridge Structural Database (CSD) yielded 552 structures for geometry 1, 1507 structures that correspond to geometry 2 and 2563 structures for geometry 3 (Fig. 1)
After simple elimination of all contacts that had Se/SÁ Á ÁX, Se/SÁ Á ÁY and Se/SÁ Á ÁZ distances shorter than the Se/SÁ Á ÁA distance, only 7714 contacts remained in the search results for geometry 1, 829 contacts for geometry 2 and 166 contacts for geometry 3 (Table 1)
Summary
Selenium and sulfur are basic elements with closely related properties, found in nature in a vast array of active compounds, and used as reactants of numerous chemical and biochemical processes. Selenium is an essential trace element found in selenoproteins in the form of the selenium analogue of cysteine (selenocysteine, Sec) It is toxic at higher concentrations, recent research indicates that it might be effective in preventing different types of disease (Vinceti et al, 2019; Li et al, 2019; Raygan et al, 2019), mostly because of its high chemical reactivity in metabolism. As these elements are very similar when it comes to electronegativity (2.58 for sulfur and 2.55 for selenium), number of oxidation states and ionic radius, they share many properties (Yoshizawa & Bock, 2009) a few important differences between these amino acids should be pointed out.
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