Investigations on the role of cation–pi interactions in active centres of superoxide dismutase

In this study, we have analysed the influence of cation–π interactions on stability and properties of superoxide dismutase (SOD) active centres. The number of interactions formed by arginine is higher than by lysine in the cat­ionic group, while those formed by histidine are comparatively higher in the π group. The energy contribution resulting from most frequent cation–π interact­ions was in the lower range of strong hydrogen bonds. The cation–π interact­ions involving transition metal ions as cation have energy more negative than –418.4 kJ mol-1. The stabilization centres for these proteins showed that all the residues involved in cation–π interactions were important in locating one or more of such centres. The majority of the residues involved in cation–p inter­actions were evolutionarily conserved and might have a significant contribution towards the stability of SOD proteins. The results presented in this work can be very useful for understanding the contribution of cation–π interactions to the stability of SOD active centres

Application of Hybrid Density Functional Theory in Calculation of Edge-to-Face Interactions of Receptor-Ligand System

Our previously described research on docking analysis of a series of isosteric N4-arylpiperazines on a model of 5-HT1A receptor was used earlier to investigate interactions of different ligands with the receptor binding site. Due to the limitations of molecular mechanics (MM) methods, docking analysis failed to give precise results about interactions that influence binding affinity of the ligands, but we presumed that aromatic-aromatic interactions, or edge-to-face, to be more precise, play an important role in the binding process. In order to further elaborate on this hypothesis, ab initio approach was used to calculate possible edge-to-face interactions on a model system and correlate them to ligand affinity. Obtained results indicate that those dispersive interactions can show notable influence on the binding of the ligands to 5-HT1A receptor. Stabilization energies of modeled receptor-ligand complex, calculated using Becke's "half-and-half" hybrid DFT method showed strong correlation with the affinity of investigated ligands towards 5-HT1A receptor

Interactions of cytotoxic amino acid derivatives of tert-butylquinone with DNA and lysozyme

The interactions of nine amino acid derivatives of tert-butylquinone with biomacromolecules were studied. Sodium dodecyl sulphate (SDS) gel electrophoresis and mass spectrometry confirmed the absence of modifications of lysozyme by any of the synthesized compounds. Spectrophotometric studies demonstrated hyperchromism, i.e., the existence of interactions between the quinones and calf thymus DNA (CT-DNA). Determination of the binding constants by absorption titration indicated weak interactions between the quinone derivatives and CT-DNA. The quenching of fluorescence of the intercalator ethidium bromide (EB) from the EB-CT-DNA system and of the minor groove binder Hoechst 33258 (H) from the H-CT-DNA system by the synthesized derivatives indicated interactions of the compounds and CT-DNA. Circular dichroism (CD) spectra demonstrated a non-intercalative binding mode of the quinone derivatives to CT-DNA. Molecular docking results confirmed binding to the minor groove. The electrophoretic pattern showed no cleavage of the pUC19 plasmid in the presence of any of the synthesized compounds. The ability of the derivatives to scavenge radicals was confirmed by the 2,2-diphenyl-1-picrylhydrazyl (DPPH) test. All the presented results suggest that the DNA minor groove binding is the principal mechanism of action of the examined amino acid derivatives

Human serum albumin binding of certain antimalarials

Tested compounds, previously synthesized, are derivatives of chloroquine, drug commonly used in the treatment and prevention of malaria. Human serum albumin (HSA) has the role in transport of endogenous (fatty acids, hormones, bile acids, amino acids) and exogenous compounds (drug molecules and nutrients). Interaction between tested compounds and HSA has been studied by fluorescence spectroscopy in phosphate buffered saline (1× PBS, pH 7.4) [1]. Results show that among tested compounds, all positively charged at pH 7.4, derivatives with thiophene substructure bind to HSA. Molecular docking studies were used to determine HSA–compound binding mode. Fluorescence quenching data were processed using Stern-Volmer (S-V) equation [2]. Almost linear S-V plot for binding of 1 to HSA (Fig. 1a) indicates single type of quenching mechanism. Results show that Ksv decreases (20C: (2.60±0.07)×105 M -1 ; 25C: (2.33±0.07)×105 M -1 and 37C: (2.18±0.08)×105 M -1 ) as temperature increases indicating static quenching mechanism. Downward curvature in S-V plots of 2 and 3 (Fig. 1b and 1c) indicates that tryptophan residues are not fully accessible to the drug and that dynamic quenching dominates over static. Fraction of tryptophan residues that are buried and inaccessible to the quencher and effective quenching constants can be determined by modified S-V equation. The effective quenching constant for 2 and 3 increases as temperature increases, this is another indication that dynamic quenching process is dominant in binding of 2 and 3 to HSA. Effective quenching constants of all three compounds are in the order of 10 5 M-1, meaning that these compounds can be effectively carried and stored by HSA in the human body

Везивање неких антималарика за хумани серум албумин

Human serum albumin (HSA) is the most abundant protein in blood plasma and it transports endogenous (fatty acids and bilirubin) and exogenous compounds (drugs) through the blood. In the present study binding of several derivatives of our new antimalarials, and chloroquine, to HSA was investigated by fluorescence spectroscopy (in 0.15 М HEPES, pH 7.35). Results show that among ten studied compounds only those with additional thiophene substructure bind to HSA, with moderate binding constants (comp. 1 logKb = 4.33(±0.46) and comp. 2 logKb = 3.81(±0.29)), representative spectra shown on Fig. 1. Competitive binding method with site specific probes (warfarin for Sudlow site I and ibuprofen for Sudlow site II) indicate that compounds 1 and 2 compete with both site probes, with slight preference toward Sudlow site I. Molecular docking studies were used to determine the binding mode of compounds 1 and 2 to HSA.Хумани серум албумин (ХСА) је најзаступљенији протеин у крвној плазми који преноси ендогенe (масне киселине и билирубин) и егзогенe супстанце (лекове) кроз крв. Флуоресцентном спектроскопијом je проучавано везивање ХСА са хлорокином и неколико наших нових аминохинолинских антималарика (у 0,15 М HEPES пуферу, pH 7,35). Показано је да се од испитиваних једињења за ХСА везују само једињења која садрже тиофенско језгро (logKb = 4,33(±0,46) за једињење 1 и logKb = 3,81(±0,29) за једињење 2). Методом компетитивног везивања са специфичним пробама (варфарин и ибупрофен) показано је да се 1 и 2 везују за оба места, уз нешто већи афинитет према варфаринском месту. Докинг студије су коришћене у циљу утврђивања начина везивања једињења 1 и 2 за ХСА

Second Generation Steroidal 4-Aminoquinolines Are Potent, Dual-Target Inhibitors of the Botulinum Neurotoxin Serotype A Metalloprotease and P. falciparum Malaria

Significantly more potent second generation 4-amino-7-chloroquinoline (4,7-ACQ) based inhibitors of the botulinum neurotoxin serotype A (BoNT/A) light chain were synthesized. Introducing an amino group at the C(3) position of the cholate component markedly increased potency (IC50 values for such derivatives ranged from 0.81 to 2.27 mu M). Two additional subclasses were prepared: bis(steroidal)-4,7-ACQ derivatives and bis(4,7-ACQ)cholate derivatives; both classes provided inhibitors with nanomolar-range potencies (e.g., the K-i of compound 67 is 0.10 mu M). During BoNT/A challenge using primary neurons, select derivatives protected SNAP-25 by up to 89%. Docking simulations were performed to rationalize the compounds' in vitro potencies. In addition to specific residue contacts, coordination of the enzyme's catalytic zinc and expulsion of the enzyme's catalytic water were a consistent theme. With respect to antimalarial activity, the compounds provided better IC90 activities against chloroquine resistant (CQR) malaria than CQ, and seven compounds were more active than mefloquine against CQR strain W2

The influence of dispersive interactions on the binding affinities of ligands with an arylpiperazine moiety to the dopamine D2 receptor

Several isosteric 1,3-dihydro-5-[2-(4-aryl-1-piperazinyl)ethyl]-2H-benzimidazole-2-thiones were used to investigate the interactions of different ligands with the binding site of the D2 receptor. Due to limitations of the simulation methods, docking analysis failed to show precisely the interactions that influence the binding affinity of the ligands. It is presumed that dispersive forces or more precisely edge-to-face interactions play an important role in the binding process, especially for the lipophilic part of the ligands. In order to confirm this hypothesis, ab initio calculations were applied on a model system in order to find the stabilization energies of potential edge-to-face interactions and then to correlate them with the ligand affinity. The obtained results indicate that there is a significant correlation between the strength of dispersive inter-actions and ligand affinity. It was shown that for the calculation of stabilization energies of modeled receptor–ligand complexes the Becke “half-and-half” hybrid DFT method can be used, thus speeding up the usually long calculation time and reducing the required computer strength

JSCS–3899

The influence of dispersive interactions on the binding affinities of ligands with an arylpiperazine moiety to the dopamine D2 recepto

Interactions of cytotoxic amino acid derivatives of tert-butylquinone with DNA lysozyme

The interactions of nine amino acid derivatives of tert-butylquinone with biomacromolecules were studied. SDS electrophoresis and mass spectrometry confirmed the absence of modifications of lysozyme by any of the synthesized compounds. Spectrophotometric studies demonstrated hyperchromism, i.e. existence of interactions between the quinones and CT-DNA. Determination of binding constant by absorption titration indicates weak interactions between quinone derivatives and CT-DNA. The quenching of fluorescence of intercalator ethidium bromide from EB-CT-DNA system and of minor groove binder Hoechst 33258 from H-CT-DNA system by the synthesized derivatives indicates interactions of compounds and CT-DNA. CD spectra demonstrate non-intercalative binding mode of quinone derivaties to CT-DNA. Molecular docking results confirm binding to the minor groove. Electrophoretic pattern showed no cleavage of pUC19 plasmid in the presence of any of the synthesized compounds. The ability of the derivatives to scavenge radicals was confirmed by DPPH test. All the presented results suggest that the DNA minor groove binding is the principal mechanism of action of the examined amino acid derivatives. [Projekat Ministarstva nauke Republike Srbije, br. 172055

Human serum albumin binding of certain antimalarials

Tested compounds, previously synthesized, are derivatives of chloroquine, drug commonly used in the treatment and prevention of malaria. Interaction between tested compounds and Human serum albumin (HSA) has been studied by fluorescence spectroscopy in phosphate buffered saline (1× PBS, pH 7.4) . Molecular docking studies were used to determine HSA–compound binding mode