“…Recently the cation-Tr interaction has received considerable attention as a new type of binding interaction. Besides the extensive investigations on artificial host-guest systems [16,18,[27][28][29][30], computational studies of several biolog- Table 1 c ND: no experimental data ical systems have postulated an important role in molecular recognition for such systems as ion selectivity of the potassium channel [31], binding of acetylcholine to acetylcholinesterase [16,32], and binding of choline derivatives to phospholipases A 2 [33]. The most direct evidence for biological importance has been the X-ray crystallographic determination of such an interaction in the immunoglobulin Fab McPC603-phosphocholine complex [34].…”
Factor Xa (FXa) is an important serine protease in the blood coagulation cascade. Small synthetic competitive inhibitors of FXa are under development as potential anticoagulants. To better understand FXa structural features and molecular recognition mechanisms, we have constructed three dimensional models of FXa-inhibitor complex structures via a new search approach that samples conformational space and binding space simultaneously for DABE and DX-9065a, two bis amidinoaryl derivatives that are among the most potent and selective FXa inhibitors reported to date. We find the most probable binding modes for the two inhibitors to be a folded conformation, with one distal amidino group extending into the S1 pocket, forming a salt-bridge ~ith FXa Asp-189, and the other positively charged group fitting into the $4 subsite, and stabilized by a cation-~r interaction. We propose as a hypothesis that the cavity-like $4 subsite formed by the three ~r-faces of the aromatic residues Tyr-99, Phe-174 and Trp-215 is sufficiently rich in ~r electrons that it is not only a hydrophobic pocket, but also forms a cation recognition site. This proposed cation-~r binding mechanism is one of the first proposed for enzymatic molecular recognition, and for which experimental verification can be obtained without any complicating charge compensation mechanism. Our models provide plausible explanations of the structure-activity relationships observed for these inhibitors, and suggest that cation-lr interactions may provide a novel mechanism for molecular recognition.
“…Recently the cation-Tr interaction has received considerable attention as a new type of binding interaction. Besides the extensive investigations on artificial host-guest systems [16,18,[27][28][29][30], computational studies of several biolog- Table 1 c ND: no experimental data ical systems have postulated an important role in molecular recognition for such systems as ion selectivity of the potassium channel [31], binding of acetylcholine to acetylcholinesterase [16,32], and binding of choline derivatives to phospholipases A 2 [33]. The most direct evidence for biological importance has been the X-ray crystallographic determination of such an interaction in the immunoglobulin Fab McPC603-phosphocholine complex [34].…”
Factor Xa (FXa) is an important serine protease in the blood coagulation cascade. Small synthetic competitive inhibitors of FXa are under development as potential anticoagulants. To better understand FXa structural features and molecular recognition mechanisms, we have constructed three dimensional models of FXa-inhibitor complex structures via a new search approach that samples conformational space and binding space simultaneously for DABE and DX-9065a, two bis amidinoaryl derivatives that are among the most potent and selective FXa inhibitors reported to date. We find the most probable binding modes for the two inhibitors to be a folded conformation, with one distal amidino group extending into the S1 pocket, forming a salt-bridge ~ith FXa Asp-189, and the other positively charged group fitting into the $4 subsite, and stabilized by a cation-~r interaction. We propose as a hypothesis that the cavity-like $4 subsite formed by the three ~r-faces of the aromatic residues Tyr-99, Phe-174 and Trp-215 is sufficiently rich in ~r electrons that it is not only a hydrophobic pocket, but also forms a cation recognition site. This proposed cation-~r binding mechanism is one of the first proposed for enzymatic molecular recognition, and for which experimental verification can be obtained without any complicating charge compensation mechanism. Our models provide plausible explanations of the structure-activity relationships observed for these inhibitors, and suggest that cation-lr interactions may provide a novel mechanism for molecular recognition.
“…In addition, the electrostatic binding of quaternary amines to water-soluble calixarene sulphonate derivatives has been investigated by Morozumi and Shinkai; 5 in particular, the inclusion complex formed from p-sulphonated calix [4]arene and trimethylanilinium was studied by 1 H and 13 C NMR spectroscopy. 6 However, in spite of extensive early work of the biological properties of the p-sulphonated calixarenes, 7 it is only very recently that interest in their biomedical potential has come to the fore again. 8 The charge density and size of the p-sulphonated calixarenes make them excellent candidates as heparin mimics, particularly in view of the difference in the synthetic pathways to the sulphonated derivatives (three steps) 9 as compared with the heparin pentasaccharide (over 50 steps).…”
mentioning
confidence: 99%
“…10 We have noted this heparin mimicry with respect to peptide folding and even protein-protein interactions. 11 In this work, we investigated the fundamental bases of the interactions between p-sulphonated calix [4]arene (1), calix [6]arene (2) and calix [8]arene (3) with the basic amino acid residues arginine (4) and lysine (5), known for their electrostatic anchoring of the heparin fragment 12 ( Fig. 1).…”
The interactions of calixarene sulphonates with the basic amino acids arginine and lysine were studied by 1 H NMR spectroscopy. Strong electrostatic binding occurs for calix [4]arene sulphonate with both lysine and arginine at pH 1 and 5. For the higher calixarenes, only weak interactions at the faces of the flattened macrocycles occur. This binding is in contrast to the inhibition of protein-protein interactions by the calixarenes where the calix[6]arene and calix [8]arene sulphonates show much stronger effects.
“…33 For cations derived from amines, the organic moiety introduces a significant steric factor, with the ammonium cation included in the host cavity. 34,35,36 A closely related www.intechopen.com Water-Soluble Calix [4]arene Derivatives: Binding Stoichiometry and Spectroscopic Evaluation of the Host-Guest Recognition Mechanism 37 study 37 involving a variety of ammonium guests, including acetylcholine and Nmethylquinuclidinium, reached the same conclusion that the guest is in the cavity and that its ammonium portion is closely associated with the calixarene aromatic rings. This interaction was discussed as a π-cation interaction.…”
Section: Molecular Cation Recognition and Hydrophobic Cavity Depth Ofmentioning
confidence: 91%
“…12. Aromatic neutral guests (34)(35)(36)(37), and cationic guests 38, 39. The new water-soluble aminocalix [4]arene hosts 11 and 12 with deep hydrophobic cavity facilitate hydrophilic mouth and hydrophobic mouth, respectively.…”
Section: Recognition Of Neutral Moleculesmentioning
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