Peptide-biphenyl hybrid-capped AuNPs: stability and biocompatibility under cell culture conditions.

In this study, we explored the biocompatibility of Au nanoparticles (NPs) capped with peptide-biphenyl hybrid (PBH) ligands containing glycine (Gly), cysteine (Cys), tyrosine (Tyr), tryptophan (Trp) and methionine (Met) amino acids in the human hepatocellular carcinoma cell line Hep G2. Five AuNPs, Au[(Gly-Tyr-Met)2B], Au[(Gly-Trp-Met)2B], Au[(Met)2B], Au[(Gly-Tyr-TrCys)2B] and Au[(TrCys)2B], were synthesised. Physico-chemical and cytotoxic properties were thoroughly studied. Transmission electron micrographs showed isolated near-spherical nanoparticles with diameters of 1.5, 1.6, 2.3, 1.8 and 2.3 nm, respectively. Dynamic light scattering evidenced the high stability of suspensions in Milli-Q water and culture medium, particularly when supplemented with serum, showing in all cases a tendency to form agglomerates with diameters approximately 200 nm. In the cytotoxicity studies, interference caused by AuNPs with some typical cytotoxicity assays was demonstrated; thus, only data obtained from the resazurin based assay were used. After 48-h incubation, only concentrations ≥50 µg/ml exhibited cytotoxicity. Such doses were also responsible for an increase in reactive oxygen species (ROS). Some differences were observed among the studied NPs. Of particular importance is the AuNPs capped with the PBH ligand (Gly-Tyr-TrCys)2B showing remarkable stability in culture medium, even in the absence of serum. Moreover, these AuNPs have unique biological effects on Hep G2 cells while showing low toxicity. The production of ROS along with supporting optical microscopy images suggests cellular interaction/uptake of these particular AuNPs. Future research efforts should further test this hypothesis, as such interaction/uptake is highly relevant in drug delivery systems.

Chemical applications of neural networks: aromaticity of pyrimidine derivatives.

Neural networks are computational tools able to apprehend non-linear relationships between different parameters, having the capacity to order a large amount of input data and transform them into a graphical pattern of output data. We have previously reported their use for the quantification of the aromaticity through the Euclidean distance between neurons. In this article, we apply the method to a variety of pyrimidine derivatives with electron-donor and electron-withdrawing groups as substituents, with capacity to produce push-pull compounds. We have calculated the aromaticity of benzene (as a reference molecule), parent pyrimidine and other 11 pyrimidine derivatives having amino, dimethylamino and tricyanovinyl substitution. The neural network has been generated using ASE, Λ, NICS(zz)(1) and HOMA as aromaticity descriptors, since our previous work showed that the combination of these indices provided the best performance of the network. On studying the influence of the substituent on the aromaticity of the molecule, we have found that, opposite to benzene derivatives, all the substituents decrease the aromaticity of the ring. The interplay between aromaticity, planarity and push-pull properties of all the substituted pyrimidines has also been addressed. An interesting feature of the neural network to quantify aromaticity is that the importance of the reference reaction used to evaluate energy stabilization and magnetic susceptibility exaltation is minimized.

Preparation and characterization of gold nanoparticles capped by peptide-biphenyl hybrids.

Gold nanoparticles were prepared using peptide-biphenyl hybrids (PBHs) as capping agents. AuNPs were characterized by different techniques including UV-Vis, TEM, EDX, FT-IR, elemental analysis, (1)H NMR and (13)C CP/MAS NMR spectroscopy. TEM analysis showed that AuNPs present diameters in the range of 1.8-3.7 nm, depending on the structure and the amount of the capping PBH used. FT-IR spectroscopy and solid-state (13)C NMR revealed that the carboxylic group of PBHs, especially in the case of the acid ligands, interacts with the gold surface (in the form of carboxylate). The results confirm that PBHs are excellent stabilizers of AuNPs, being one of the first examples on the use of peptidomimetics-gold hybrid materials.

Biological and chemical studies on aryl hydrocarbon receptor induction by the p53 inhibitor pifithrin-α and its condensation product pifithrin-ß.

AIMS: Pifithrin α (PFTα), an inhibitor of the p53 protein, is regarded as a lead compound for cancer and neurodegenerative disease therapy. There is some evidence that this compound activates the aryl hydrocarbon receptor (AhR) in a complete independent way of the p53 inhibition and that it is easily converted to its condensation product pifithrin ß (PFTß). The aim of this study was to explore the ability of PFTα and of PFTß to induce a variety of AhR mediated processes. MAIN METHODS: Computational analysis using quantum chemical calculations and chemical analysis have been used to study the conformation of the compounds as well as the cyclization reaction. The AhR mediated processes of these compounds have been studied in a rainbow trout cell line (RTG-2) and in a rat hepatoma cell line (H4IIE). KEY FINDINGS: PFTα molecule could not take a planar conformation required for AhR activation whereas PFTß showed a conformation similar to those of the prototypical AhR ligand ß-naphthoflavone. In both cell lines, PFTα and PFTß provoked different responses related with AhR activation. However, when cyclization of PFTα to PFTß was hampered by acetylation of the exocyclic nitrogen, all these responses were not observed. These results lead to the conclusion that the activation of the AhR is probably caused by PFTß instead of PFTα. SIGNIFICANCE: Since PFTα is a promising compound for the development of new pharmaceuticals inhibiting p53, the chemical instability of this compound as well as the capacity of its transformation product should be taken into account.

Substituent effects on the aromaticity of carbocyclic five-membered rings.

The influence of the substituent nature, as well as the number and position of the substituents, on the aromaticity/antiaromaticity of a comprehensive set of derivatives of cyclopentadienyl anion, cyclopentadiene and cyclopentadienyl cation has been analyzed. The aromaticity/antiaromaticity of substituted cyclopentadienyl derivatives has been measured using energetic, magnetic and structural criteria to take into account the multidimensional character of aromaticity. Furthermore, the Euclidean distance values (d(j)) for all compounds have been estimated using the neural network developed previously. It has been demonstrated that the d(j) as a scale of aromaticity overcomes the particular limitations of the ASE, Lambda, NICS and HOMA indices to describe the changes in the aromaticity of cyclopentadiene ring due to substituent effects. Additionally, it is shown that neural networks are useful tools for establishing structure-property relationships. The results indicate that mostly the aromaticity of cyclopentadiene ring and cyclopentadienyl anion ring decrease upon substitution irrespective of the electronic character of the substituent. The electron-donating groups, especially hydroxyl groups, destabilize carbanion to a larger extent than electron-accepting ones. On the other hand, all the substituents reduce strongly the antiaromaticity of the cyclopentadienyl cation. These results can be useful for the design of new cationic ligands with lowered instability and new cyclopentadienyl ligands with improved stability and reactivity.

A universal scale of aromaticity for pi-organic compounds.

Aromaticity is an essential concept in chemistry, invented to account for the stability, reactivity, molecular structure, and properties of many organic and inorganic compounds. In recent years, numerous methods to quantify aromaticity based on the energetic, magnetic, structural, and electronic properties of molecules have been proposed but none of them is universal. The inability of establishing a universal scale of aromaticity based on a single parameter is due to the multidimensional character of this phenomenon. Consequently, aromaticity analyses should be carried out by employing a set of aromaticity descriptors on the basis of different physical manifestations of aromaticity. Here, we report a universal scale of aromaticity for pi-organic compounds based on the Euclidean distance between neurons in a self-organizing map. The most widely used aromaticity indicators have been used as molecular descriptors, and so our approach provides the first scale of aromaticity which contains the energetic, magnetic, and structural aspects of this property. The method is applicable to a wide variety of unsaturated organic compounds and allows quantification of both aromaticity and antiaromaticity. Additionally, the position of a compound on the bidimensional map determinates immediately the following: (a) the group (aromatic, nonaromatic, or antiaromatic) to which the system belongs, (b) their degree of pi-electronic delocalization, and (c) the similarity in aromaticity/antiaromaticity between different compounds. This new scale of aromaticity is able to indicate the expected order of aromaticity of analogues of fulvene and heptafulvene, heteroaromatic species, substituted benzenes, and functionalized cyclopentadienyl compounds.

X-ray diffraction, solution structure, and computational studies on derivatives of (3-sec-butyl-2,3-dihydro-1H-isoquinolin-4-ylidene)acetic acid: compounds with activity as calpain inhibitors.

A thorough experimental and computational study of derivatives of (3-sec-butyl-2,3-dihydroisoquinolin-4-ylidene)acetic acid was performed. Some of these compounds are calpain inhibitors and could be useful as therapeutic agents, since this enzyme is a Ca(2+)-dependent cysteine protease involved in a wide variety of metabolic and physiological processes, whose over-activation is associated to several pathological conditions. To gain a better understanding of the structure-activity relationships, a structural analysis was carried out with (1)H and (13)C NMR spectroscopy and DFT calculations together with the X-ray diffraction data of three compounds. The solid state structures showed that the crystal packing as well as the intermolecular interactions depend on the substituent nature of the COOR group. Also, the reactivity of the exocyclic double bond was theoretically evaluated, finding that the more reactive compound is the most potent inhibitor of calpain (IC(50) = 25 nM).

Decabromobiphenyl (PBB-209) activates the aryl hydrocarbon receptor while decachlorobiphenyl (PCB-209) is inactive: experimental evidence and computational rationalization of the different behavior of some halogenated biphenyls.

In rat H4IIE cells permanently transfected with a luciferase gene under the control of AhR, incubation with PBB-209 led to a statistically significant increase of luminescence. In this system, PCB-209 only caused a small induction of luciferase activity. In a fish cell line, only PBB-209 was able to provoke an induction of ethoxyresorufin- O-deethylase activity. Ligand binding to the AhR was studied by means of a cell-free in vitro system in which the activation of AhR is very unlikely to occur without ligand binding. None of the biphenyls studied provoked any activation of AhR in this system. To rationalize the results and to get insight into the molecular mechanism of activation of AhR by PBB-209 as compared with PCB-209, a comprehensive computational study was carried out on these congeners as well as on PCB-126 and PCB-169, two potent AhR activators through ligand binding. The calculations include (i) conformational analysis and dipole moments of each conformer, (ii) aromaticity indices, (iii) molecular electrostatic potentials, (iv) quadrupole moments, (v) electronic and reactivity descriptors, and (vi) dissociation energies of C-Cl and C-Br bonds in model aromatic compounds. It was found that some molecular features of PBB-209, such as the electrostatic potential (EP) and EP-derived descriptors (Politzer's parameters), indicate that PBB-209 is more similar to PCB-126 and PCB-169 than to PCB-209, which share quite similar geometries based on the substitution pattern. The similarity between PBB-209, PCB-126, and PCB-169 seems to hint that these three compounds can share, at least partially, similar mechanisms of activation of AhR. It is unquestionable that PCB-126 and PCB-169 directly bind AhR and PBB-209 does not. We hypothesize that there are several simultaneous mechanisms for activation of AhR, and the most active compounds act for more than one mechanism.

Neural networks as a tool to classify compounds according to aromaticity criteria.

Aromaticity is a fundamental concept in chemistry, with many theoretical and practical implications. Although most organic compounds can be categorized as aromatic, non-aromatic, or antiaromatic, it is often difficult to classify borderline compounds as well as to quantify this property. Many aromaticity criteria have been proposed, although none of them gives an entirely satisfactory solution. The inability to fully arrange organic compounds according to a single criterion arises from the fact that aromaticity is a multidimensional phenomenon. Neural networks are computational techniques that allow one to treat a large amount of data, thereby reducing the dimensionality of the input set to a bidimensional output. We present the successful applications of Kohonen's self-organizing maps to classify organic compounds according to aromaticity criteria, showing a good correlation between the aromaticity of a compound and its placement in a particular neuron. Although the input data for the training of the network were different aromaticity criteria (stabilization energy, diamagnetic susceptibility, NICS, NICS(1), and HOMA) for five-membered heterocycles, the method can be extended to other organic compounds. Some useful features of this method are: 1) it is very fast, requiring less than one minute of computational time to place a new compound in the map; 2) the placement of the different compounds in the map is conveniently visualized; 3) the position of a compound in the map depends on its aromatic character, thus allowing us to establish a quantitative scale of aromaticity, based on Euclidean distances between neurons, 4) it has predictive power. Overall, the results reported herein constitute a significant contribution to the longstanding debate on the quantitative treatment of aromaticity.

Activation of the aryl hydrocarbon receptor by carbaryl: Computational evidence of the ability of carbaryl to assume a planar conformation.

It has been accepted that aryl hydrocarbon receptor (AhR) ligands are compounds with two or more aromatic rings in a coplanar conformation. Although general agreement exists that carbaryl is able to activate the AhR, it has been proposed that such activation could occur through alternative pathways without ligand binding. This idea was supported by studies showing a planar conformation of carbaryl as unlikely. The objective of the present work was to clarify the process of AhR activation by carbaryl. In rat H4IIE cells permanently transfected with a luciferase gene under the indirect control of AhR, incubation with carbaryl led to an increase of luminescence. Ligand binding to the AhR was studied by means of a cell-free in vitro system in which the activation of AhR can occur only by ligand binding. In this system, exposure to carbaryl also led to activation of AhR. These results were similar to those obtained with the AhR model ligand beta-naphthoflavone, although this compound exhibited higher potency than carbaryl in both assays. By means of computational modeling (molecular mechanics and quantum chemical calculations), the structural characteristics and electrostatic properties of carbaryl were described in detail, and it was observed that the substituent at C-1 and the naphthyl ring were not coplanar. Assuming that carbaryl would interact with the AhR through a hydrogen bond, this interaction was studied computationally using hydrogen fluoride as a model H-bond donor. Under this situation, the stabilization energy of the carbaryl molecule would permit it to adopt a planar conformation. These results are in accordance with the mechanism traditionally accepted for AhR activation: Binding of ligands in a planar conformation.

Induction of cytochrome P4501A (CYP1A) by clotrimazole, a non-planar aromatic compound. Computational studies on structural features of clotrimazole and related imidazole derivatives.

The classical pathway for induction of cytochrome P4501A (CYP1A) by xenobiotics is ligand binding to the aryl hydrocarbon receptor (AhR). High-affinity AhR ligands are planar polyaromatic molecules such as the prototypic ligand, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). The present work investigated the ability of the imidazole derivative, clotrimazole [1-(2'chlorotrityl)imidazole, CLO], to induce CYP1A in cultured rainbow trout (Oncorhynchus mykiss) hepatocytes at the catalytic activity (determined as 7-ethoxyresorufin-O-deethylase, EROD) and at the transcriptional level. CLO resulted in a significant increase of hepatocyte EROD activity and CYP1A mRNA at a concentration of 1.56 microM. Computational studies on the molecular structure of CLO show that CLO is unlikely to take a planar conformation. Further indications that CLO does not behave like a planar AhR ligand come from the experimental observation that co-incubation of trout hepatocytes with CLO and the AhR antagonist, alpha-naphthoflavone (alpha-NF), did not result in an inhibition of CLO induction of CYP1A mRNA, whereas alpha-NF was able to inhibit CYP1A induction by the prototpyic, planar AhR ligand, beta-naphthoflavone. The experimental findings on CLO agree with previous results obtained for another non-planar imidazole derivative, 1-benzylimidazole (BIM). Further, computational studies showed that the non-planar imidazoles, BIM and CLO, are highly similar with respect to some electrostatic properties, namely the dipole moment and the molecular electrostatic potential (MEP). Overall our experimental and computational studies suggest that transcriptional activation of CYP1A by the imidazole derivatives CLO and BIM is mediated by a mechanism different to that of prototypic CYP1A inducers such as the planar AhR-ligands.

Differences in retention of dioxin-like compounds and organochlorinated insecticides on an immunochromatographic column. Interpretation and applicability.

The retention of organochlorinated compounds on an immunochromatographic column is studied. The compounds considered are usually found together in real samples of environmental concern, and include chlorinated biphenyls, chlorinated dibenzo-p-dioxins, chlorinated dibenzofurans, and organochlorinated insecticides. The different retention observed for different compounds is interpreted in light of the structural similarities of the compound studied with that used as a hapten to raise the antibodies employed as ligands in the immunochromatographic column. Differences in retention of the organochlorinated compounds on the immunocolumn make it possible to fractionate them. Mixtures of phosphate buffer solution and ACN in different ratios were used as desorption agents. Depending on the percentage of ACN employed, different fractionations of the organochlorinated compounds are obtained. The use of 20% ACN allows fractionation of most insecticides from chlorinated biphenyls, dioxins, and furans. Besides, chlorinated biphenyls of different chlorination degree can be separated. Moreover, pentachlorinated dioxins and pentachlorinated furans are separated from hexachlorinated biphenyls. Fractionation is of critical importance from a practical point of view, as it avoids some of the interferences that otherwise take place during the subsequent gas chromatography/mass spectrometry (GC/MS) analysis of these compounds. In this way, immunochromatography makes it possible to perform in a single step all the processes (extraction, clean-up, concentration, and fractionation) that are needed prior to the GC/MS analysis of these analytes in aqueous samples. An additional advantage of this method is the reusability of the immunoaffinity chromatography column for more than 500 times.

Solid-phase combinatorial synthesis of peptide-biphenyl hybrids as calpain inhibitors.

[structure: see text] The combinatorial parallel synthesis of peptide-biphenyl hybrids on solid support using state of the art of peptide synthesis is reported. Key steps were the N to C addition of an amino moiety, hydrolysis of the methyl ester, and the absence of cross-linked compounds when the 2,2'-diamino-1,1'-biphenyl was incorporated. When tested for activity as calpain inhibitors, some of the compounds exhibited IC(50) values in the nanomolar range.

Studies on aromatic compounds: inhibition of calpain I by biphenyl derivatives and peptide-biphenyl hybrids.

With the objective to understand structural features responsible for the biological activity, novel nonelectrophilic biphenyl derivatives and peptide-biphenyl hybrids have been synthesized and evaluated as calpain I inhibitors. The preliminary results indicate that the presence of additional aromatic rings (besides the biphenyl system) makes these compounds potent calpain inhibitors with IC50 values in the nanomolar range.

Peptide-biphenyl hybrids as calpain inhibitors.

Calpain is a cysteine protease that is activated by Ca2+. The over-activation of calpain, which occurs on increasing Ca2+ concentration, causes a variety of diseases. This paper reports experimental results on the inhibition of calpain I (mu-calpain) by peptide-biphenyl hybrids. We have found that some peptide-biphenyl hybrids, with aromatic amino acids in the peptide chains, inhibit calpain with IC50 values in the nanomolar range. Since the peptide-biphenyl hybrids reported in the present paper do not possess a reactive electrophilic functionality, we hypothesize that they interfere with the activation of calpain by Ca2+, and present experimental and computational results on the binding of peptide-biphenyl hybrids to Ca2+.

Induction of CYP1A by the N-imidazole derivative, 1-benzylimidazole.

Xenobiotics can induce cytochrome P4501A (CYP1A) by ligand binding to the aryl hydrocarbon receptor (AhR). Typical AhR ligands are polycyclic aromatic compounds with planar molecular conformation. The present work investigated the ability of the N-imidazole derivative, 1-benzylimidazole (BIM), to induce CYP1A in rainbow trout hepatocytes. Benzylimidazole increased hepatocellular CYP1A catalytic activity (determined as 7-ethoxyresorufin-O-deethylase [EROD] activity) and CYP1A mRNA in a concentration-dependent way. Computational studies on the molecular structure of BIM indicated that the energetically most stable BIM conformer has the imidazole ring and the phenyl ring in different planes, i.e., does not take a planar conformation. This property of BIM does not agree with the structural requirements of a typical AhR ligand. In line with this observation, we found that the AhR antagonist, alpha-naphthoflavone (alphaNF), was not able to inhibit BIM induction of EROD activity and CYP1A mRNA, although it inhibited the induction of CYP1A by the prototypic AhR ligand, beta-naphthoflavone (betaNF). The results suggest that transcriptional activation of CYP1A by the N-imidazole derivative, BIM, is not mediated through direct ligand binding to the AhR.

Computational studies on biphenyl derivatives. Analysis of the conformational mobility, molecular electrostatic potential, and dipole moment of chlorinated biphenyl: searching for the rationalization of the selective toxicity of polychlorinated biphenyls (PCBs).

With the objective to understand how the pattern and degree of chlorination influence on the properties of the title molecules, a computational study on biphenyl and all the chlorinated biphenyls (from 1 to 10 chlorine atoms, 209 congeners) has been undertaken. The study includes conformational searches (and further refinement by molecular dynamics simulations) and the ab initio calculation of the molecular electrostatic potential (MEP) and the dipole moments for all the congeners. The most significant property is the MEP, finding a good correlation between the MEPs and the substitution pattern on chlorinated biphenyls. The most toxic congeners possess highly positive values of electrostatic potential on the aromatic rings and highly negative values of electrostatic potential on the chlorine atoms. Additionally, we have found that the toxic congeners possess conformations with low dipole moments, a fact that may be linked to the ready accumulation on the adipose tissue. The results on the geometry and electrostatic properties of chlorinated biphenyls can be useful to rationalize their selective toxicities.