Supramolecular insight into the substitution of sulfur by selenium, based on crystal structures, quantum-chemical calculations and biosystem recognition

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-HÁ Á ÁSe and C-HÁ Á ÁS interactions ($80%), notably less numerous are structures with SeÁ Á ÁSe and SÁ Á ÁS interactions ($5%), and SeÁ Á Á and SÁ Á Á interactions are the least numerous. The results of quantum-chemical calculations have indicated that C-HÁ Á ÁSe ($À0.8 kcal mol À1 ) and C-HÁ Á ÁS interactions are weaker than the most stable parallel interaction ($À3.3 kcal mol À1 ) and electrostatic interactions of / type ($À2.6 kcal mol À1 ). 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-HÁ Á ÁSe ($À4.4 kcal mol À1 ) and N-HÁ Á ÁSe interactions ($À2.2 kcal mol À1 ) 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.

Zero-, one-, two- and three-dimensional supramolecular architectures sustained by Se…O chalcogen bonding: A crystallographic survey

“…This percentage is an underestimate as in the present survey as crystals where Se … O interactions were acting in concert with other identifiable intermolecular forces, the notable example being hydrogen bonding, were omitted. This percentage compares favourably to the 6% of selenium(lone-pair) … π(arene) interactions in crystals where these interactions can potentially form [248] , [249] . Over and above different chemical composition, as alluded to above, secondary bonding interactions, including chalcogen bonding interactions, are notoriously subject to steric effects in that these interactions are mitigated when bulky metal-bound and/or ligand-bound substituents are present [54] , [56] , [57] , [58] , [59] , [60] , [61] , [62] , [63] .…”

Adaptive Laboratory Evolution Reveals the Selenium Efflux Process To Improve Selenium Tolerance Mediated by the Membrane Sulfite Pump in Saccharomyces cerevisiae

“…Fzf1p is composed of five zinc fingers (ZFs) and plays a positive role in the transcription of ssu1 ( 26 ). Given the tight regulatory relationship between ssu1 and fzf1 and that they were both mutated in most evolved groups within several positions coincidentally, these results suggested that ssu1 and fzf1 are likely to perform homogeneous functions in selenium metabolism combined with the chemical similarity between selenium and sulfur ( 27 – 29 ). Therefore, we investigated the latent functions of ssu1 and fzf1 in the selenium tolerance of yeasts and then confirmed that both ssu1 and fzf1 indeed play vital roles, while the other four most frequently mutated genes ( fcy21 , cos9 , mnn4 , and bio3 ) screened by sequencing analysis were found to be irrelevant for selenium tolerance (Fig.…”

Supramolecular aggregation patterns featuring Se⋯N secondary-bonding interactions in mono-nuclear selenium compounds: A comparison with their congeners

“…for delocalised [97] selenium(lone-pair) … π(arene) interactions [45,198]; both these surveys allowed for the presence of multi-nuclear selenium compounds. As performed for the recent survey of Se … O secondary-bonding interactions [50], specific classes of compounds were evaluated for their propensity to form secondary-bonding interactions.…”