Influence of cation-π interactions to the structural stability of phycocyanin proteins: A computational study.

The influences of cation-π interactions in phycocyanin proteins and their environmental preferences were analyzed. The number of interactions formed by arginine showed to be higher than those formed by the lysine in the cationic group, while histidine is comparatively higher than phenylalanine and N-terminal residue in the π group. Arg-Tyr and Arg-Phe interacting pairs are predominant among the various pairs analyzed. Cation-π interactions are distance-dependent and can be realized above a wider area above the π ring. We analyzed the energy contribution resulting from cation-π interactions using ab initio calculations. The energy contribution resulting from the most frequent cation-π interactions was in the lower range of strong hydrogen bonds. The results showed that, while most of their interaction energies lay ranged from - 2 to - 8 kcal/mol, those energies could be up to -12- 12 kcal/mol. Stabilization centers for these proteins showed that all residues found in cation-π interactions are important in locating one or more of such centers. In the cation-π interacting residues, 54% of the amino acid residues involved in these interactions might be conserved in phycocyanins. From this study, we infer that cation-π forming residues play an important role in the stability of the multiply commercially used phycocyanin proteins and could help structural biologists and medicinal chemists to design better and safer drugs.

Computational Analysis of Non-covalent Interactions in Phycocyanin Subunit Interfaces.

Protein-protein interactions are an important phenomenon in biological processes and functions. We used the manually curated non-redundant dataset of 118 phycocyanin interfaces to gain additional insight into this phenomenon using a robust inter-atomic non-covalent interaction analyzing tool PPCheck. Our observations indicate that there is a relatively high composition of hydrophobic residues at the interfaces. Most of the interface residues are clustered at the middle of the range which we call "standard-size" interfaces. Furthermore, the multiple interaction patterns founded in the present study indicate that more than half of the residues involved in these interactions participate in multiple and water-bridged hydrogen bonds. Thus, hydrogen bonds contribute maximally towards the stability of protein-protein complexes. The analysis shows that hydrogen bond energies contribute to about 88 % to the total energy and it also increases with interface size. Van der Waals (vdW) energy contributes to 9.3 %±1.7 % on average in these complexes. Moreover, there is about 1.9 %±1.5 % contribution by electrostatic energy. Nevertheless, the role by vdW and electrostatic energy could not be ignored in interface binding. Results show that the total binding energy is more for large phycocyanin interfaces. The normalized energy per residue was less than -16 kJ mol-1 , while most of them have energy in the range from -6 to -14 kJ mol-1 . The non-covalent interacting residues in these proteins were found to be highly conserved. Obtained results might contribute to the understanding of structural stability of this class of evolutionary essential proteins with increased practical application and future designs of novel protein-bioactive compound interactions.

Anion-π interactions in active centers of superoxide dismutases.

We investigated 1060 possible anion-π interactions in a data set of 41 superoxide dismutase active centers. Our observations indicate that majority of the aromatic residues are capable to form anion-π interactions, mainly by long-range contacts, and that there is preference of Trp over other aromatic residues in these interactions. Furthermore, 68% of total predicted interactions in the dataset are multiple anion-π interactions. Anion-π interactions are distance and orientation dependent. We analyzed the energy contribution resulting from anion-π interactions using ab initio calculations. The results showed that, while most of their interaction energies lay in the range from -0 to -4kcalmol-1, those energies can be up to -9kcalmol-1 and about 34% of interactions were found to be repulsive. Majority of the suggested anion-π interacting residues in ternary complexes are metal-assisted. Stabilization centers for these proteins showed that all the six residues found in predicted anion-π interactions are important in locating one or more of such centers. The anion-π interacting residues in these proteins were found to be highly conserved. We hope that these studies might contribute useful information regarding structural stability and its interaction in future designs of novel metalloproteins.

Human serum albumin binding of certain antimalarials.

Interactions between eight in-house synthesized aminoquinolines, along with well-known chloroquine, and human serum albumin (HSA) have been studied by fluorescence spectroscopy. The synthesized aminoquinolines, despite being structurally diverse, were found to be very potent antimalarials. Fluorescence measurements indicate that three compounds having additional thiophene or benzothiophene substructure bind more strongly to HSA than other studied compounds. Competitive binding experiments indicate that these three compounds bind significantly stronger to warfarin compared to diazepam binding site. Fluorescence quenching at three temperatures (20, 25, and 37°C) was analyzed using classical Stern-Volmer equation, and a static quenching mechanism was proposed. The enthalpy and entropy changes upon sulphur-containing compound-HSA interactions were calculated using Van't Hoff equation. Positive values of enthalpy and entropy changes indicate that non-specific, hydrophobic interactions are the main contributors to HSA-compound interaction. Molecular docking and calculated lipophilicity descriptors indicate the same, pointing out that the increased lipophilicity of sulphur-containing compounds might be a reason for their better binding to HSA. Obtained results might contribute to design of novel derivatives with improved pharmacokinetic properties and drug efficacy.

α-Glucosidase inhibitory activity and cytotoxic effects of some cyclic urea and carbamate derivatives.

The inhibitory activities of selected cyclic urea and carbamate derivatives (1-13) toward α-glucosidase (α-Gls) in in vitro assay were examined in this study. All examined compounds showed higher inhibitory activity (IC50) against α-Gls compared to standard antidiabetic drug acarbose. The most potent was benzyl (3,4,5-trimethoxyphenyl)carbamate (12) with IC50 = 49.85 ± 0.10 µM. In vitro cytotoxicity of the investigated compounds was tested on three human cancer cell lines HeLa, A549 and MDA-MB-453 using MTT assay. The best antitumour activity was achieved with compound 2 (trans-5-phenethyl-1-phenylhexahydro-1H-imidazo[4,5-c]pyridin-2(3H)-one) against MDA-MB-453 human breast cancer cell line (IC50 = 83.41 ± 1.60 µM). Cyclic ureas and carbamates showed promising anti-α-glucosidase activity and should be further tested as potential antidiabetic drugs. The PLS model of preliminary QSAR study indicated that, in planing the future synthesis of more potent compounds, the newly designed should have the substituents capable of polar interactions with receptor sites in various positions, while avoiding the increase of their lipophilicity.

Anion-π interactions in complexes of proteins and halogen-containing amino acids.

We analyzed the potential influence of anion-π interactions on the stability of complexes of proteins and halogen-containing non-natural amino acids. Anion-π interactions are distance and orientation dependent and our ab initio calculations showed that their energy can be lower than -8 kcal mol(-1), while most of their interaction energies lie in the range from -1 to -4 kcal mol(-1). About 20 % of these interactions were found to be repulsive. We have observed that Tyr has the highest occurrence among the aromatic residues involved in anion-π interactions, while His made the least contribution. Furthermore, our study showed that 67 % of total interactions in the dataset are multiple anion-π interactions. Most of the amino acid residues involved in anion-π interactions tend to be buried in the solvent-excluded environment. The majority of the anion-π interacting residues are located in regions with helical secondary structure. Analysis of stabilization centers for these complexes showed that all of the six residues capable of anion-π interactions are important in locating one or more of such centers. We found that anion-π interacting residues are sometimes involved in simultaneous interactions with halogens as well. With all that in mind, we can conclude that the anion-π interactions can show significant influence on molecular organization and on the structural stability of the complexes of proteins and halogen-containing non-natural amino acids. Their influence should not be neglected in supramolecular chemistry and crystal engineering fields as well.

Interaction of arylpiperazine ligands with the hydrophobic part of the 5-HT1A receptor binding site.

A flexible docking of a series of arylpiperazine derivatives with structurally different aryl part to the binding site of a model of human 5-HT1A receptor was exercised. The influence of structure and hydrophobic properties of aryl moiety on binding affinities was discussed and a model for ligand binding in the hydrophobic part of the binding site was proposed.