Abstract: The antioxidant constituents of essential oils (EOs) of Rosmarinus officinalis L. (α-pinene chemotype) were isolated at the flowering (A), post-flowering (B), and vegetative stages (C). GC-MS was used to analyze total chemical composition, Folin-Ciocalteau and Prussian blue methods for reducing substances. Radical scavenging capacity (DPPH test, IC(50) 36.78±0.38, 79.69±1.54, 111.94±2.56μL) and anti-lipoperoxidant activity (TBARS, IC(50) 0.42±0.04, 1.20±0.06μL, 4.07±0.05μL) differed widely in the three stages. Antioxidant activity, identified after silica gel fractionation chromatography, was closely related (R(2)=0.9959) to each EO's content of hydroxilated derivatives, (containing alcohols, phenols and 1,8 cineole): 15.26±0.12%, 7.22±0.06%, and 5.09±0.10% in EOs from A, B, and C. Modeling the C, H, O terpenes in a simulated phospholipid bilayer indicated that anti-lipoperoxidant activity depended on the stability and rapidity of their interactions with the membrane bilayer components, and their positioning over its surface.
Abstract: This short review aims at summarizing the current information on Proprotein Convertase Subtilisin/Kexin type 9 (PCSK9) structure and function focusing also on the therapeutic possibilities based on the inhibition of this protein.
Abstract: A novel 5-oxa-6a,8-diazaindeno[2,1-b]phenanthren-7-one scaffold was designed and synthesized as an active analogue of the cytotoxic marine alkaloid Lamellarin D. The design was based on molecular modeling of the site of interaction of Lamellarin D with DNA-topoisomerase I cleavable complex, whereas the synthesis capitalized on a simple Friedel-Crafts cyclization of indole to a β-carbolinone nucleus. The product exhibited topoisomerase I poisoning activity and submicromolar cytotoxicity on human non-small cell lung cancer H460 cell line.
Abstract: Herein we propose the D-Trp-Phe sequence within an inverse typeâII β-turn as a new kind of pharmacophoric motif for μ-opioid receptor (MOR) cyclopeptide agonists. Initially, we observed that c[Tyr-D-Pro-D-Trp-Phe-Gly] (4), an analogue of endomorphin-1 (H-Tyr-Pro-Trp-Phe-NHâ) lacking the crucial protonatable amino group of Tyrâ1, is a MOR agonist with 10â»â¸âM affinity. Molecular docking analysis suggested that the relevant interactions with the receptor involve D-Trp-Phe. The bioactive conformation of this region was investigated by selected derivatives of 4 designed to adopt an inverse typeâII β-turn. These efforts led to c[Tyr-Gly-D-Trp-Phe-Gly] (14) and to the cyclotetrapeptide c[D-Asp-1-amide-β-Ala-D-Trp-Phe] (15), showing improved nanomolar affinity. Both 14 and 15 selectively bind MOR, as they have negligible affinity for the κ- and δ-opioid receptors. Both 14 and 15 behave as partial MOR agonists in functional assays. Conformational and docking analyses confirm the role of the inverse β-turn in binding. These results indicate that the D-Trp-Phe inverse β-turn structure can be used for designing non-endomorphin-like peptidomimetic opioid agonists in general, characterized by an atypical mechanism of interaction between ligand and receptor.
Abstract: DNA-intercalating drugs are planar molecules with several fused aromatic rings that form stacks between DNA base pairs, reducing the opening and unwinding of the double helix. Recently, interest on intercalating agents has moved in the search for new ligands to G-quadruplex structures.
Abstract: 1,2,3,4,6-Penta-O-galloyl-β-D-glucopyranose (PGG) is a polyphenolic compound found in substantial amounts in a number of medicinal herbs. We report (i) its conformational analysis by solution NMR and molecular dynamics calculation and (ii) theoretical study of its interaction with a model membrane bilayer. The galloyl groups B and E appear to play important roles in the interaction with the phospholipid bilayer.
Abstract: The anti- and pro-oxidant effects of green tea catechins have been implicated in the alterations of cellular functions determining their chemoprotective and therapeutic potentials in toxicity and diseases. The glutathione S-transferases (GSTs; EC 2.5.1.18) family is a widely distributed phase-II detoxifying enzymes and the GST P1-1 isoenzyme has been shown to catalyze the conjugation of GSH with some alkylating anti-cancer agents, suggesting that over-expression of GST P1-1 would result in tumor cell resistance. Here we report the docking study of four green tea catechins and four alkylating anticancer drugs into the GST P1-1 model, as GSTs were found to be affected by tea catechins. The EGCG ligands exhibit higher docking potential with respect to the anticancer agents, with a ligand-receptor interaction pattern indicating an high conformational stability. Consequently, the competition mechanisms favourable for the green tea catechins could lead to enzyme(s) desensitisation with a reduction of the alkylating drugs metabolism. The results provide a useful theoretical contribution in understanding the biochemical mechanisms implicated in the chemotherapeutic use of green tea catechins in oxidative stress-related diseases.
Abstract: Antitumour activity was observed in a series of tricyclic compounds characterised by a 2-(1H-pyrrol-3-yl)-1,3,4-oxadiazole moiety with various substitutions. Their synthesis and antiproliferative activity toward a panel of human tumour cell lines is described. The most interesting compounds 1 c and 4 c were selected for further evaluation to elucidate their possible mechanism of action.Interesting antitumour activity was observed in a series of tricyclic compounds characterised by the presence of a 2-(1H-pyrrol-3-yl)-1,3,4-oxadiazole moiety that is variously substituted. Their synthesis and antiproliferative activity toward a panel of human tumour cell lines is described. The two most interesting compounds were selected for further evaluation to elucidate their possible mechanism of action. Analysis of cell cycle, tubulin polymerisation, modulation of mitotic markers of the M phase, and apoptosis showed that antimitotic activity is the primary mechanism of the cytotoxic effects of these compounds. Experiments performed on isolated tubulin confirmed that the compounds act by inducing tubulin polymerisation, like taxanes. The binding model against tubulin was also examined by molecular modelling and docking. The results support the proposed binding model, which is able to explain the activity of the oxadiazole derivatives on the basis of their docking energy.
Abstract: The availability of drug affecting neuronal nicotinic acetylcholine receptors (nAChRs) may have important therapeutic potential for the treatment of several CNS pathologies. Pursuing our efforts on the systematic structural modification of cytisine and N-arylalkyl and N-aroylalkyl cytisines were synthesized and tested for the displacement of [(3)H]-epibatidine and [(125)I]-alpha-bungarotoxin from the most widespread brain nAChRs subtypes alpha(4)beta(2) and alpha(7), respectively. While the affinity for alpha(7) subtype was rather poor (K(i) from 0.4 to >50 microM), the affinity for alpha(4)beta(2) subtype was very interesting, with nanomolar K(i) values for the best compounds. The N-substituted cytisines were docked into the rat and human alpha(4)beta(2) nAChR models based on the extracellular domain of a molluscan acetylcholine binding protein. The docking results agreed with the binding data, allowing the detection of discrete amino acid residues of the alpha and beta subunits essential for the ligand binding on rat and human nAChRs, providing a novel structural framework for the development of new alpha(4)beta(2) selective ligands.
Abstract: The mutant S64C of the short-chain flavodoxin from Desulfovibrio vulgaris has been designed to introduce an accessible and reactive group on the protein surface. Crystals have been obtained of both the monomeric and homodimeric forms of the protein, with the cofactor FMN in either the oxidized or the one electron-reduced (semiquinone) state, and the structures have been determined to high resolution. The redox properties of the different species have been investigated and the variations observed with respect to wild type have been related to the structural changes induced by the mutation and S-S bridge formation.
Abstract: The wound-healing properties of honey are well established and it has been suggested that, among its pharmaco-active constituents, kynurenic acid (KA) exerts antinociceptive action on injured tissue by antagonizing NMDA at peripheral GABA receptors. The aim of this study was to investigate the quantitative profile of KA and of two recently identified, structurally related derivatives, 3-pyrrolidinyl-kynurenic acid (3-PKA) and its gamma-lactamic derivative (gamma-LACT-3-PKA), by examining their mass spectrometric behavior, in honeys from different botanical sources. We used a combination of HPLC-DAD-ESI-MS and NMR techniques (one-dimensional (1)H NMR and diffusion-ordered spectroscopy NMR). Chestnut honey constantly contained KA (2114.9-23 g/kg), 3-PKA (482.8-80 mg/kg) and gamma-LACT-3-PKA (845.8-32 mg/kg), confirming their reliability as markers of origin. A new metabolite, 4-quinolone (4-QUIN), was identified for the first time in one chestnut honey sample (743.4 mg/kg). Small amounts of KA were found in honeydew, sunflower, multifloral, almond and eucalyptus honeys, in the range of 23.1-143 mg/kg, suggesting contamination with chestnut honey. Total phenol content (TPC) was in the range from 194.9 to 1636.3 mg(GAE)/kg and total antiradical activity (TAA) from 61 to 940 mg/(GAE)/kg), depending on the botanical origin. Principal component analysis (PCA) was then done on these data. The three different clusters depicted: (i) antinociceptive activity from KA and/or its derivatives, typical of chestnut honey; (ii) antioxidant/radical scavenging activity by antioxidants responsible for the antiinflammatory action (dark honeys); (iii) peroxide-dependent antibacterial activity due to H(2)O(2) production by glucose oxidase in honey. The PCA findings provide useful indications for the dermatologist for the treatment of topical diseases, and the profiling of KA and its derivatives may shed light on new aspects of the kynurenine pathway involved in tryptophan metabolism.
Abstract: The human serum albumin (HSA) secondary structure modifications induced by the chrysotile surface have been investigated via computational molecular dynamics (MD) and experimental infrared spectroscopy (FTIR) on synthetic chrysotile nanocrystals coated with different amount of HSA. MD simulations, conducted by placing various albumin subdomains close to the fixed chrysotile surface, show an initial adsorption phase, accompanied by local rearrangements of the albumin motifs in contact with the chrysotile layer. Next, large-scale rearrangements follow with consequent secondary structure modifications. Gaussian curve fitting of the FTIR spectra obtained for HSA-coated synthetic chrysotile nanocrystals has allowed the quantification of HSA structural modifications as a function of the amount of protein adsorbed. The experimental results support the atomistic computer simulations providing a realistic description of the adsorption of plasma proteins onto chrysotile and unravelling a key step in the understanding of asbestos toxicity.
Abstract: Acrolein (ACR) is a well-known carbonyl toxin produced by lipid peroxidation of polyunsaturated fatty acids, which is involved in several life-threatening pathologies such as Alzheimer disease, arteriosclerosis, diabetes, and nephropathy. The aim of this work was to study the quenching ability of the endogenous tripeptide glycyl-histidyl-lysine (GHK), a liver cell growth factor isolated from human plasma, towards the electrophilic aldehyde ACR and to characterize the reaction products by electrospray mass spectrometry (ESI-MS/MS infusion experiments; positive ion mode). The reaction of ACR (30 microM) with GHK (0.1, 0.25, 0.5, 1.0 mM) was followed by measuring aldehyde consumption by reverse-phase HPLC (phosphate buffer, pH 7.4); after 4h, when the aldehyde had completely disappeared; the reaction products were checked by ESI-MS/MS. Several products were detected in the GHK+ACR reaction (1:1). This indicates a complex reaction cascade involving the sequential addition of ACR (up to 3 mol) to the tripeptide GHK and, in particular, to the epsilon-amino group of the lysine residue and to the N(tau) and N(pi) of the histidine moiety. The Michael addition of two molecules of ACR to the epsilon-amino group of the lysine residue is followed by aldol condensation and dehydration to give the N-(3-formyl-3,4-dehydropiperidino) derivative. The results confirm that the ESI-MS/MS approach in a direct infusion experiment permits rapid profiling of the products of the GHK+ACR reaction. They firstly point to the potential medicinal use of GHK in the prevention of carbonyl stress-linked pathologies, and--second--help shed light on the physiological role of this histidine-containing tripeptide which is claimed to be an endogenous growth factor, but has never been shown to be an ACR quencher.
Abstract: Endogenous and exogenous opiates are currently considered the drugs of choice for treating different kinds of pain. However, their prolonged use produces several adverse symptoms, and in addition, many forms of pain are resistant to any kind of therapy. Therefore, the discovery of compounds active towards mu-opioid receptors (MORs) by alternative pharmacological mechanisms could be of value for developing novel classes of analgesics. There is evidence that some unusual molecules can bind opioid receptors, albeit lacking some of the typical opioid pharmacophoric features. In particular, the recent discovery of a few compounds that showed agonist behavior even in the absence of the primary pharmacophore, namely a protonable amine, led to a rediscussion of the importance of ionic interactions in stabilizing the ligand-receptor complex and in activating signal transduction. Very recently, we synthesized a library of cyclic analogs of the endogenous, MOR-selective agonist endomorphin-1 (YPWF-NH(2)), containing a Gly5 bridge between Tyr1 and Phe4. The cyclopeptide c[YpwFG] showed good affinity and agonist behavior. This atypical MOR agonist does not have the protonable Tyr amine. In order to gain more information about plausible mechanisms of interaction between c[YpwFG] and the opioid receptor, we synthesized a selected set of derivatives containing different bridges between Tyr1 and Phe4, and tested their affinities towards mu-opioid receptors. We performed conformational analysis of the cyclopeptides by NMR spectroscopy and molecular dynamics, and investigated plausible, unprecedented modes of interaction with the MOR by molecular docking. The successive quantum mechanics/molecular mechanics investigation of the complexes obtained by the molecular docking procedure furnished a more detailed description of the binding mode and the electronic properties of the ligands. The comparison with the binding mode of the potent agonist JOM-6 seems to indicate that the cyclic endomorphin-1 analogs interact with the receptor by way of an alternative mechanism, still maintaining the ability to activate the receptor.
Abstract: Three cytisine derivatives, (-)-(7R,9S)-1-phenyl-3-(cytisin-12-yl)propan-1-one (1), (-)-(7R,9S)-1-phenyl-2-(cytisin-12-yl)ethane (2), and (-)-(7R,9S)-1,2-bis(cytisin-12-yl)ethane (3), with different electronic and steric features have been characterized by X-ray analysis and theoretical calculations in order to evaluate how structural modulations affect the intrinsic binding affinity at the neuronal nicotinic receptors (nAChRs). The crystal structures of 1 and 2, which display comparable affinities, are characterized by the same conformation of the cytisine moiety with different orientations of the substituent at N2. In 3, two independent molecules have the pyridinone rings diversely oriented. This compound has a lower affinity with respect to 1 and 2, but it increases the expression of neuronal nAChRs. Compounds 1, 2, and 3 retain the key prerequisite of the classical pharmacophoric models, with sp(3)-N-atom--HBA distances close to the expected value, both in solid state and in solution (theoretical calculations), where, in contrast with the extended in the crystal state, a curled-up conformation has been found, though maintaining the N-substituent in equatorial position.
Abstract: Histidine-containing oligopeptides are currently studied as detoxifying agents against cytotoxic alpha,beta-unsaturated aldehydes (prototype: 4-hydroxy-2-nonenal, HNE), electrophilic end products formed by decomposition of omega-6 polyunsaturated fatty acids, associated with severe pathologies such as diabetes, nephropathy, retinopathy, and neurodegenerative diseases. This study evaluated the quenching reaction against HNE of the endogenous tripeptide l-glycyl- l-histidyl- l-lysine (GHK), an oligopeptide discovered to be a growth-modulating factor and also a strong activator of wound healing. We first evaluated the HNE consumption (50 microM, HPLC-UVDAD method) in the presence of GHK (1 mM) in physiomimetic conditions (phosphate buffer, pH 7.4) and confirmed GHK/HNE adduct formation by mass spectrometric analysis (ESI-MS/MS) and (1)H NMR analyses. These results indicated that GHK was an effective quencher of HNE, although significantly less potent than the reference compound carnosine, and that HNE modulation by GHK can contribute to the satisfactory outcome of the wound-healing process. In the second part of the study, we investigated the quenching reaction between GHK and HNE, in parallel to carnosine, using (1)H NMR and computational analyses. At a mechanistic level, this explained the different reactivity of the two peptides: (i) The greater stability of the macrocyclic intermediate HNE/carnosine was compared to HNE/GHK. (ii) GHK in solution has a quasi-folded conformation due to the interaction of four intramolecular hydrogen bonds, three of which need to be broken for the transition state to form (energy barrier, approximately 20 kcal/mol). By contrast, carnosine, with an extended conformation and only one hydrogen bond, requires less energy to reach the transition state ( approximately 7 kcal/mol). (iii) The different stereoelectronic features of the transition state lead to the intramolecular Michael reaction, that is, the favorable superimposition of carnosine highest occupied molecular orbital and the HNE lowest unoccupied molecular orbital, in relation to the unfavorable orbital configuration of GHK. The overall findings provide interesting and useful insights into the mechanisms of interaction of both GHK and carnosine with HNE and illustrate the utility of computational studies for defining the (optimal) chemical and structural parameters for an optimal quenching of alpha,beta-unsaturated aldehydes.
Abstract: Among the many receptor classes of the GPCR family, ORs constitute a privileged drug target for their involvement in pain modulation and in a number of physiological functions and behavioural effects. Endogenous and exogenous opioid agonists have been the subject of intense investigations aiming to develop safe and potent analgesics for clinical practice; however, despite the large number of highly selective opioid agonists so far discovered, there is no convincing alternative to the use of morphine, fentanyls, and their derivatives. Alternative compounds could be very useful for treating pain forms "resistant" to the usual therapeutic agents. The recent discovery of a small number of atypical opioid agonists can furnish promising candidates for the development of alternative analgesic. In particular, a few molecules exist that can bind and activate ORs even deprived of the "minimal pharmacological requisites" generally considered to be necessary. In these cases it appears that receptor activation must be based on different ligand-receptor interaction mechanisms. Taken together, the data discussed in the review suggest that the prevailing assumptions about OR binding need revision. In particular, they strengthen the evidence that ORs can bind ligands via diverse binding modes, and in some cases an electrostatic interaction is not an absolute requirement.
Abstract: A novel pyridine-containing DTPA-like ligand, carrying additional hydroxymethyl groups on the pyridine side-arms, was synthesized in 5 steps. The corresponding Gd(III) complex, potentially useful as an MRI contrast agent, was prepared and characterized in detail by relaxometric methods and its structure modeled by computational methods.
Abstract: A 2.0 ns unrestrained Molecular Dynamics was used to elucidate the geometric and dynamic properties of the HSA binding sites. The structure is not stress affected and the rmsds calculated from the published crystallographic data are almost constant for all the simulation time, with an averaged value of 2.4A. The major variability is in the C-terminus region. The trajectory analysis of the IIA binding site put in evidence fast oscillations for the Cgamma@Leu203...Cgamma@Leu275 and Cgamma@Leu219...Cgamma@Leu260 distances, with fluctuations around 250 ps, 1000 ps and over for the first, while the second is smoothly increasing with the simulation time from 7 to 10A. These variations are consistent with a volume increase up to 20% confirmed by the inter-domain contacts analysis, in particular for the pair O@Pro148...Ogamma@Ser283, representing the change of distance between IB-h9 and IIA-h6, O@Glu149...Ogamma@Ser189 for sub-domains IB-h9/IIA-h1 and N@Val339...Odelta2@Asp447 sub-domains IIB-h9/IIIA-h1. These inter-domain motions confirm the flexibility of the unfatted HSA with possible binding site pre-formation.
Abstract: The crystal structure of Acetylcholine Binding Protein (AChBP), homolog of the ligand binding domain of nAChR, has been used as model for computational investigations on the ligand-receptor interactions of derivatives of 6-chloropyridazine substituted at C3 with 3,8-diazabicyclo[3.2.1]octane, 2,5-diazabicyclo[2.2.1]heptane and with piperazine and homopiperazine, substituted or not at N4. The ligand-receptor complexes have been analyzed by docking techniques using the binding site of HEPES complexed with AChBP as template. The good relationship between the observed binding affinity and the calculated docking energy confirms that this model provides a good starting point for understanding the binding domain of neuronal nicotinic receptors. An analysis of the possible factors significant for the ligand recognition has evidenced, besides the cation-pi interaction, the distance between the chlorine atom of the pyridazinyl group and the carbonylic oxygen of Leu B112 as an important parameter in the modulation of the binding energy.
Abstract: The crystallographic structure of an engineered flavodoxin mutant from Desulfovibrio vulgaris has been analysed. Site-directed mutagenesis was used to substitute serine 35 with a cysteine to provide a possible covalent linkage. The crystal structure of the semiquinone form of this mutant is similar to the corresponding oxidation state of the wild-type flavodoxin. Analysis of the structural changes reveals the interaction between N(5)H of the flavin and the carbonyl O atom of Gly61 to be critical for modulation of the electrochemical properties of the protein.
Abstract: The reactions of iodoflavone with 3-methyl-3-hydroxybut-1-yne and 3-methylbut-3-en-2-yne are described and the antimicrobial and cytotoxic activities of the obtained compounds have been tested. The molecular structures of 6-(3-hydroxy-3-methylbut-1-ynyl)-flavone (1a) and 6-(3-methylbut-3-en-1-ynyl) flavone (1b) have been determined by X-ray crystallography. The planar configuration of the two compounds has been attributed to intramolecular hydrogen bond interactions. In 1a, the presence of the hydroxyl group determines a dimeric arrangement of the molecules. In both compounds in the crystal state, molecular stacking has been observed.
Abstract: The structural characteristics of an immunostimulating agent (3-(5-thioxo-L-prolyl)-L-thiazolidine-4-carboxylic acid) have been established using a combination of 1H and 13C NMR spectroscopy, molecular mechanic calculations (in vacuo and in solution) and X-ray crystallographic analyses. Conformational calculations and NMR spectra identify two classes of conformers, cis and trans, around the peptide bond between the rings, while in the solid state only the cis form has been found.
Abstract: Engineered flavodoxins in which a surface residue has been replaced by an exposed cysteine are useful modules to link multi-domain redox proteins obtained by gene fusion to electrode surfaces. In the present work, the crystal structure of the S35C mutant of Desulfovibrio vulgaris flavodoxin in the oxidized state has been determined and compared with a refined structure of the wild type (wt). The structure of wt flavodoxin (space group P4(3)2(1)2, unit-cell parameters a = 50.52, b = 50.52, c = 138.59 A) at 1.34 A resolution has been refined to R = 0.16 and R(free) = 0.18. The structure of the S35C mutant (space group P4(3)2(1)2, unit-cell parameters a = 50.55, b = 50.55, c = 138.39 A) at 1.44 A resolution has been refined to R = 0.13 and R(free) = 0.16. Data sets were collected with synchrotron radiation at 100 K. In the S35C mutant, the Cys35 thiol group points towards a hydrophobic region, whilst in the wt the Ser35 hydroxyl group points towards a more polar region. The solvent exposure of Cys35 is 43 A(2), of which 8 A(2) is for the sulfur. This is comparable to the exposure of 48 A(2) found for the wt Ser35, where that of the hydroxyl oxygen is also 8 A(2).
