Supramolecular insight into the substitution of sulfur by selenium, based on crystal structures, quantum-chemical calculations and biosystem recognition
Authors
Đorđević, Ivana S.Popadić, Marko
Sarvan, Mirjana
Petković-Benazzouz, Marija
Janjić, Goran V.
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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 substitu...ents 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. © 2020 International Union of Crystallography.
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Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials, 2020, 76, 1, 122-136Publisher:
- Wiley
Funding / projects:
- Studies of enzyme interactions with toxic and pharmacologically active molecules (RS-172023)
- Rational design and synthesis of biologically active and coordination compounds and functional materials, relevant for (bio)nanotechnology (RS-172035)
- Graphitic and Inorganic Low-dimensional Nanostructures (RS-171035)
DOI: 10.1107/S2052520619016287
ISSN: 2052-5206
WoS: 000513005400015
Scopus: 2-s2.0-85079570171
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Hemijski fakultetTY - JOUR AU - Đorđević, Ivana S. AU - Popadić, Marko AU - Sarvan, Mirjana AU - Petković-Benazzouz, Marija AU - Janjić, Goran V. PY - 2020 UR - https://cherry.chem.bg.ac.rs/handle/123456789/3877 AB - 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. © 2020 International Union of Crystallography. PB - Wiley T2 - Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials T1 - Supramolecular insight into the substitution of sulfur by selenium, based on crystal structures, quantum-chemical calculations and biosystem recognition VL - 76 IS - 1 SP - 122 EP - 136 DO - 10.1107/S2052520619016287 ER -
@article{ author = "Đorđević, Ivana S. and Popadić, Marko and Sarvan, Mirjana and Petković-Benazzouz, Marija and Janjić, Goran V.", year = "2020", 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. © 2020 International Union of Crystallography.", publisher = "Wiley", journal = "Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials", title = "Supramolecular insight into the substitution of sulfur by selenium, based on crystal structures, quantum-chemical calculations and biosystem recognition", volume = "76", number = "1", pages = "122-136", doi = "10.1107/S2052520619016287" }
Đorđević, I. S., Popadić, M., Sarvan, M., Petković-Benazzouz, M.,& Janjić, G. V.. (2020). Supramolecular insight into the substitution of sulfur by selenium, based on crystal structures, quantum-chemical calculations and biosystem recognition. in Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials Wiley., 76(1), 122-136. https://doi.org/10.1107/S2052520619016287
Đorđević IS, Popadić M, Sarvan M, Petković-Benazzouz M, Janjić GV. Supramolecular insight into the substitution of sulfur by selenium, based on crystal structures, quantum-chemical calculations and biosystem recognition. in Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials. 2020;76(1):122-136. doi:10.1107/S2052520619016287 .
Đorđević, Ivana S., Popadić, Marko, Sarvan, Mirjana, Petković-Benazzouz, Marija, Janjić, Goran V., "Supramolecular insight into the substitution of sulfur by selenium, based on crystal structures, quantum-chemical calculations and biosystem recognition" in Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials, 76, no. 1 (2020):122-136, https://doi.org/10.1107/S2052520619016287 . .