Hypervalent Nonbonded Interactions of a Divalent Sulfur Atom. Implications in Protein Architecture and the Functions

Iwaoka, Michio; Isozumi, Noriyoshi

doi:10.3390/molecules17067266

Cited by 117 publications

(106 citation statements)

References 77 publications

(111 reference statements)

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“…Thus, the order of strength for the structural factors that are present in organic crystals and protein structures can be estimated to be: linearity of S-S· · · O and C-S· · · O > crystal packing force > verticality of S· · · O = C > protein structure [34,66]. This order will be useful for protein engineering and molecular design of functional organic sulfur compounds.…”

Section: Structural Controlmentioning

confidence: 99%

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Chalcogen Bonds in Protein Architecture

Iwaoka

2015

Challenges and Advances in Computational Chemistry and Physics

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Nonbonded interactions between a divalent sulfur atom and polar functional groups, i.e., S· · · X (X = O, N, and S) interactions, have recently been demonstrated to stabilize protein structures to some extent and play putative roles in their function and evolution, thanks to the interplay of statistical analysis of protein structure databases and theoretical calculation using simple molecular cluster models. The directional features observed between the interacting S and X atoms suggest that they can also be called S· · · X chalcogen bonds in analogy to halogen bonds. While the existence of chalcogen bonds in proteins may be accepted today by the protein scientist community, there are still several issues that should be addressed clearly before going forward to applications of the interactions to protein engineering and the ligand design. Herein, the current status of the research on the S· · · X chalcogen bonds in proteins is reviewed from several points of view, including the historical aspects and the analytical methods for mining chalcogen bonds in protein structures. Statistical, directional, and energetic features of four typical S· · · X chalcogen bonds in proteins are presented. Possibility of analogous Se· · · X chalcogen bonds in selenoproteins is also pointed out. Implications of S· · · X chalcogen bonds in the structural control and in the function and evolution of some particular proteins are subsequently summarized from the recent literature. Finally, it is proposed that the concept of S· · · X chalcogen bonds will be a useful tool for fully understanding not only protein structures but also the biological aspects. Thus, the chalcogen bonds, though their interaction energy is smaller than that of classical hydrogen bonds, can be an element of weak noncovalent interactions that control chemical and biological properties of protein architecture. IntroductionSulfur is involved in almost all proteins as cysteine (Cys) and methionine (Met) amino acid residues. In particular, it is contained at high concentrations in keratin

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Section: Structural Controlmentioning

confidence: 99%

“…By comparing the structural features of the S· · · X chalcogen bonds among the redundant data, the plausible roles in the protein function and evolution can be inferred [65,66].…”

Section: Protein Structure Databasementioning

confidence: 99%

Chalcogen Bonds in Protein Architecture

Iwaoka

2015

Challenges and Advances in Computational Chemistry and Physics

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“…The latter are widely distributed in proteins and crystals. 23,24 The bond H-N···H-S is formed by secondary amine nitrogen with two aromatic substituents (Fig. 3C/i).…”

Section: Analysis Of Fh Based On Hydrogen-bond Formationmentioning

confidence: 99%

Identification of Small-Molecule Frequent Hitters of Glutathione S-Transferase–Glutathione Interaction

et al. 2016

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In high-throughput screening (HTS) campaigns, the binding of glutathione S-transferase (GST) to glutathione (GSH) is used for detection of GST-tagged proteins in protein-protein interactions or enzyme assays. However, many false-positives, so-called frequent hitters (FH), arise that either prevent GST/GSH interaction or interfere with assay signal generation or detection. To identify GST-FH compounds, we analyzed the data of five independent AlphaScreen-based screening campaigns to classify compounds that inhibit the GST/GSH interaction. We identified 53 compounds affecting GST/GSH binding but not influencing His-tag/Ni 2+ -NTA interaction and general AlphaScreen signals. The structures of these 53 experimentally identified GST-FHs were analyzed in chemoinformatic studies to categorize substructural features that promote interference with GST/GSH binding. Here, we confirmed several existing chemoinformatic filters and more importantly extended them as well as added novel filters that specify compounds with anti-GST/GSH activity. Selected compounds were also tested using different antibody-based GST detection technologies and exhibited no interference clearly demonstrating specificity toward their GST/GSH interaction. Thus, these newly described GST-FH will further contribute to the identification of FH compounds containing promiscuous substructures. The developed filters were uploaded to the OCHEM website (http://ochem.eu) and are publicly accessible for analysis of future HTS results.

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“…CB is usually defined as non-covalent interactions between localized positive regions on Nowadays, one of the vigorously investigating types of such interactions is chalcogen bonding (CB). CB is usually defined as non-covalent interactions between localized positive regions on a chalcogen atom in the extension of the covalent bonds (σ-holes) and electron donor species serving as CB acceptors [11][12][13][14][15][46][47][48][49][50]. Unlike halogens a chalcogen atom possess two σ-holes at the same time and is prone to the formation of bifurcated chalcogen bonding (BCB) (Figure 1) [51][52][53][54][55][56][57].…”

Section: Introductionmentioning

confidence: 99%

“…The hydrogen [1,2], halogen [3][4][5][6][7][8][9][10], chalcogen [11][12][13][14][15][16][17][18][19][20][21][22][23][24], pnictogen [25][26][27][28][29][30][31], tetrel [32] bonding, stacking [33][34][35][36][37], cation/anion-π [38][39][40][41][42], and metallophilic interactions [43][44][45] play key roles in many chemical, physical, and biochemical processes, due to their ability to control structures and properties of associates and supramolecular systems.…”

Section: Introductionmentioning

confidence: 99%

Intra-/Intermolecular Bifurcated Chalcogen Bonding in Crystal Structure of Thiazole/Thiadiazole Derived Binuclear (Diaminocarbene)PdII Complexes

et al. 2018

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The coupling of cis-[PdCl2(CNXyl)2] (Xyl = 2,6-Me2C6H3) with 4-phenylthiazol-2-amine in molar ratio 2:3 at RT in CH2Cl2 leads to binuclear (diaminocarbene)PdII complex 3c. The complex was characterized by HRESI+-MS, 1H NMR spectroscopy, and its structure was elucidated by single-crystal XRD. Inspection of the XRD data for 3c and for three relevant earlier obtained thiazole/thiadiazole derived binuclear diaminocarbene complexes (3a EYOVIZ; 3b: EYOWAS; 3d: EYOVOF) suggests that the structures of all these species exhibit intra-/intermolecular bifurcated chalcogen bonding (BCB). The obtained data indicate the presence of intramolecular S•••Cl chalcogen bonds in all of the structures, whereas varying of substituent in the 4th and 5th positions of the thiazaheterocyclic fragment leads to changes of the intermolecular chalcogen bonding type, viz. S•••π in 3a,b, S•••S in 3c, and S•••O in 3d. At the same time, the change of heterocyclic system (from 1,3-thiazole to 1,3,4-thiadiazole) does not affect the pattern of non-covalent interactions. Presence of such intermolecular chalcogen bonding leads to the formation of one-dimensional (1D) polymeric chains (for 3a,b), dimeric associates (for 3c), or the fixation of an acetone molecule in the hollow between two diaminocarbene complexes (for 3d) in the solid state. The Hirshfeld surface analysis for the studied X-ray structures estimated the contributions of intermolecular chalcogen bonds in crystal packing of 3a–d: S•••π (3a: 2.4%; 3b: 2.4%), S•••S (3c: less 1%), S•••O (3d: less 1%). The additionally performed DFT calculations, followed by the topological analysis of the electron density distribution within the framework of Bader’s theory (AIM method), confirm the presence of intra-/intermolecular BCB S•••Cl/S•••S in dimer of 3c taken as a model system (solid state geometry). The AIM analysis demonstrates the presence of appropriate bond critical points for these interactions and defines their strength from 0.9 to 2.8 kcal/mol indicating their attractive nature.

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Hypervalent Nonbonded Interactions of a Divalent Sulfur Atom. Implications in Protein Architecture and the Functions

Cited by 117 publications

References 77 publications

Chalcogen Bonds in Protein Architecture

Chalcogen Bonds in Protein Architecture

Identification of Small-Molecule Frequent Hitters of Glutathione S-Transferase–Glutathione Interaction

Intra-/Intermolecular Bifurcated Chalcogen Bonding in Crystal Structure of Thiazole/Thiadiazole Derived Binuclear (Diaminocarbene)PdII Complexes

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