Synthesis and cytotoxicity of novel simplified eleutherobin analogues as potential antitumour agents.

Mixed simplified structures containing the paclitaxel and eleutherobin pharmacophore moieties were analyzed using molecular docking techniques and synthesized based on adamantane and 8-oxabicyclo[3.2.1]octane scaffolds. The crucial role of substituents' stereochemistry in biological activity is discussed. At micromolar concentrations the selected analogues interfered with tubulin dynamics in vitro and in a living organism. Furthermore, new compounds were cytotoxic against human tumour cell lines. The simplified eleutherobin analogues may be considered as prototypes of a new class of antitumour agents.

Molecular design, synthesis and biological evaluation of cage compound-based inhibitors of hepatitis C virus p7 ion channels.

The hepatitis C caused by the hepatitis C virus (HCV) is an acute and/or chronic liver disease ranging in severity from a mild brief ailment to a serious lifelong illness that affects up to 3% of the world population and imposes significant and increasing social, economic, and humanistic burden. Over the past decade, its treatment was revolutionized by the development and introduction into clinical practice of the direct acting antiviral (DAA) agents targeting the non-structural viral proteins NS3/4A, NS5A, and NS5B. However, the current treatment options still have important limitations, thus, the development of new classes of DAAs acting on different viral targets and having better pharmacological profile is highly desirable. The hepatitis C virus p7 viroporin is a relatively small hydrophobic oligomeric viral ion channel that plays a critical role during virus assembly and maturation, making it an attractive and validated target for the development of the cage compound-based inhibitors. Using the homology modeling, molecular dynamics, and molecular docking techniques, we have built a representative set of models of the hepatitis C virus p7 ion channels (Gt1a, Gt1b, Gt1b_L20F, Gt2a, and Gt2b), analyzed the inhibitor binding sites, and identified a number of potential broad-spectrum inhibitor structures targeting them. For one promising compound, the binding to these targets was additionally confirmed and the binding modes and probable mechanisms of action were clarified by the molecular dynamics simulations. A number of compounds were synthesized, and the tests of their antiviral activity (using the BVDV model) and cytotoxicity demonstrate their potential therapeutic usefulness and encourage further more detailed studies. The proposed approach is also suitable for the design of broad-spectrum ligands interacting with other multiple labile targets including various viroporins.

Substituent effects on stereoselectivity of dihalocarbene reactions with cyclohexadiene and on the reactivity of bis-dihalocyclopropanes in electrophilic nitrations en route to pyrimidine N-oxides.

Tricyclic bis-adducts of cyclohexa-1,4-diene with bromofluorocarbene and non-symmetric adducts with both bromofluoro- and dichlorocarbenes were synthesised selectively. The treatment of the bis-adducts with nitrating reagents in acetonitrile affords the products of heterocyclization of a sole dihalogenocyclopropane into 4-fluoropyrimidine N-oxide. The difference in the reactivity of bis-cyclopropanes with different sets of halogen substituents leads to selective heterocyclization of bromofluorocyclopropanes without affecting the dichlorocyclopropane moiety.

Oxindole-based intraocular pressure reducing agents.

The study represents the new findings at the crossroads of chemistry and medicine, particularly between medicinal and organic chemistry and ophthalmology. In this work we describe how the chemical reactivity of indolinone scaffold may be used to create small molecule ligands with strong biological response comparable with and larger than that of endogenous hormone. The synthesis of oxindole-based melatonin and 5-methoxycarbonylamino-N-acetyltryptamine (5-MCA-NAT) analogues was proposed and their ability to influence intraocular pressure (IOP) was studied in vivo. Time-dependent study revealed the prolonged effect (more than 6h) of the lead-compound. This effect in combination with high IOP reducing effect (41±6%) in low concentrations of the active compound (0.1wt%) and with high water solubility represents a great potential of low-cost oxindole derivatives as potent antiglaucoma agents.

Novel antimitotic agents related to tubuloclustin: synthesis and biological evaluation.

Tubuloclustin [N-(7-adamant-2-yloxy-7-oxoheptanoyl)-N-deacetylcolchicine], a highly cytotoxic anti-tubulin compound is known for its ability to promote microtubule disassembly followed by the formation of tubulin clusters of unique morphology. Three series of antimitotic agents related to tubuloclustin were designed and synthesized in order to enhance the molecular diversity of "tubuloclustin-like" family of compounds. The series of compounds with modified adamantane moiety was highly potent in cytotoxic effect on human lung carcinoma A549 cells (EC50 = 6-400 nM) and was active in affecting the microtubule arrays and induction of strong tubulin clusterization. In two other sets of compounds, the colchicine moiety of tubuloclustin was replaced by podophyllotoxin or combretastatin A-4. All combretastatin A-4 derivatives displayed noticeable cytotoxic activity ([Formula: see text]) but their effect on microtubules depended on the position of the linker attachment. Podophyllotoxin derivatives were also toxic to A549 cells ([Formula: see text]) and caused both microtubule depolymerization and some tubulin clustering. The data obtained gave additional evidence that the whole panel of C7-colchicine, podophyllotoxin and combretastatin derivatives could manifest clustering effect, and the strength of this effect correlated with cytotoxic activity of the compounds.

Threshold concentration in the nonlinear absorbance law.

A new nonlinear relationship of the absorption coefficient with the concentration was proposed, allowing the calculation of the threshold concentration, which shows that there is a deviation from the Beer-Lambert law. The nonlinear model was successfully tested on a stable dimeric phthalocyanine ligand of J-type in solvents with different polarity. It was shown that deviation from the linearity is connected with a specific association of the macrocyclic molecules, which, in the case of non-polar solvents, leads to the formation of H-aggregates composed of J-type dimeric molecules. The aggregation number was estimated to be less than 1.5, which has allowed us to conduct a series of analytical experiments in a wide range of concentrations (1 × 10-6-5 × 10-4 mol L-1).

Complex formation of albumin with tricarbocyanine dyes containing phosphonate groups.

The spectral characteristics, binding constants with bovine (BSA) and human serum albumin (HSA) and lifetimes of fluorescence in PBS and EtOH solutions and in the presence of BSA in PBS were measured for novel indotricarbocyanine dyes bearing remote phosphonate groups. These parameters are close to those for indocyanine green (ICG) indicating that the Coulomb interaction does not play a significant role in complex formation, and the binding is determined by the interaction of the dye polymethine chain with albumin. The fluorescence lifetimes of the complexes with BSA strongly indicate the formation of complexes of two types with different lifetimes. The complex with a longer fluorescence lifetime (740-800 ps) and major contribution (up to 88%) is bound to the more hydrophobic site and that with a shorter fluorescence lifetime (300-340 ps) to the more hydrophilic site.

Control of Azomethine Cycloaddition Stereochemistry by CF3 Group: Structural Diversity of Fluorinated ß-Proline Dimers.

ß-Proline-functionalized dimers consisting of homochiral monomeric units were synthesized by a non-peptidic coupling method for the first time. The applied synthetic methodology is based on 1,3-dipolar cycloaddition chemistry of azomethine ylides and provides absolute control over the ß-proline backbone stereogenic centers. An o-(trifluoromethyl)phenyl substituent contributes to appropriate stabilization of the definite acrylamide chiral cis conformation and to achieve the dipole reactivity that is not observed for aryl groups lacking strong electronegative character.

Thermally stable J-type phthalocyanine dimers as new non-linear absorbers for low-threshold optical limiters.

The possibility of developing new advanced optical limiters of laser radiation at 532 nm with low limiting thresholds has been demonstrated on thermally stable phthalocyanine J-type dimeric complexes of Mg, Zn, Cu, Ni, and Co. A new "threshold" model based on radiative transfer phenomena in nonlinear optical media was suggested for the exact definition of nonlinear absorption coefficient ß and optical limiting threshold Ic. This model allows the determination of the optical characteristics of the limiter in the same active material with layers of different thicknesses, as well as the use of different parameters of laser radiation, such as cross-sectional spatial profiles of the laser beam and shapes of the laser pulse over time. The maximum value of the nonlinear absorption coefficient (ß = 360 cm GW(-1)) and the lowest limiting threshold (Ic = 0.03 J cm(-2)) were estimated for a J-type zinc phthalocyanine dimer.

Design of Broad-Spectrum Inhibitors of Influenza A Virus M2 Proton Channels: A Molecular Modeling Approach.

BACKGROUND: The influenza A virus M2 proton channel plays a critical role in its life cycle. However, known M2 inhibitors have lost their clinical efficacy due to the spread of resistant mutant channels. Thus, the search for broad-spectrum M2 channel inhibitors is of great importance. OBJECTIVE: The goal of the present work was to develop a general approach supporting the design of ligands interacting with multiple labile targets and to propose on its basis the potential broad-spectrum inhibitors of the M2 proton channel. METHOD: The dynamic dimer-of-dimers structures of the three primary M2 target variants, wild-type, S31N and V27A, were modeled by molecular dynamics and thoroughly analyzed in order to define the inhibitor binding sites. The potential inhibitor structures were identified by molecular docking and their binding was verified by molecular dynamics simulation. RESULTS: The binding sites of the M2 proton channel inhibitors were analyzed, a number of potential broad-spectrum inhibitors were identified and the binding modes and probable mechanisms of action of one promising compound were clarified. CONCLUSION: Using the molecular dynamics and molecular docking techniques, we have refined the dynamic dimer-ofdimers structures of the WT, S31N and V27A variants of the M2 proton channel of the influenza A virus, analyzed the inhibitor binding sites, identified a number of potential broad-spectrum inhibitor structures targeting them, and clarified the binding modes and probable mechanisms of action of one promising compound. The proposed approach is also suitable for the design of ligands interacting with other multiple labile targets.

Synthesis and biological evaluation of novel 5-hydroxylaminoisoxazole derivatives as lipoxygenase inhibitors and metabolism enhancing agents.

A versatile synthesis of novel 5-hydroxylaminoisoxazoles bearing adamantane moieties has been accomplished using the heterocyclization reactions of readily available unsaturated esters by the treatment with tetranitromethane in the presence of triethylamine and subsequent reduction of resulting 5-nitroisoxazoles by SnCl2 with the participation of THF. A number of obtained isoxazole derivatives were evaluated for their antioxidative activity, inhibition of lipoxygenases and impact on the rat liver mitochondria. The majority of tested compounds demonstrated moderate antiradical activity in DPPH test (up to EC50 16µM). The same compounds strongly inhibited soybean lipoxygenase (up to IC50 0.4µM) and Fe(2+)- and Fe(3+)-induced lipid peroxidation (LP) of rat brain cortex homogenate (up to IC50 0.3µM). All tested isoxazole derivatives promoted the phosphorylating respiratory activity simultaneously with maximal stimulated respiratory activity of mitochondria and do not reveal any toxicity towards the primary culture of rat cortex neurons.

Beyond the Dimer and Trimer: Tetraspiro[2.1.2(5).1.2(9).1.2(13).1(3)] hexadecane-1,3,5,7-tetraone--the Cyclic Tetramer of Carbonylcyclopropane.

Tetraspiro[2.1.2(5).1.2(9).1.2(13).1(3)]hexadecane-1,3,5,7-tetraone 4, a unique tetraketone containing a cyclooctane core and four spiroannelated cyclopropane moieties, represents the previously unknown cyclotetramer of carbonylcyclopropane. For this purpose oxidation of the parent polyspirocyclic hydrocarbon was examined under various oxidative conditions, and the reactivity of oxidants towards methylene groups of the eight-membered cycle, activated by adjacent spirocyclopropane rings, was evaluated and contrasted. Whereas the treatment of tetraspirohexadecane with ozone resulted in monooxidation, its reaction with methyl(trifluoromethyl)dioxirane afforded the product of four-fold oxidation, triketoalcohol 10. Subsequent oxidation of the latter with Dess-Martin periodinane gave the target tetraketone 4.

Menthols as Chiral Auxiliaries for Asymmetric Cycloadditive Oligomerization: Syntheses and Studies of ß-Proline Hexamers.

To produce a novel class of structurally ordered poly-ß-prolines, an emergent method for synthesizing chiral ß-peptide molecular frameworks was developed based on 1,3-dipolar cycloaddition chemistry of azomethine ylides. Functionalized short ß-peptides with up to six monomeric residues were efficiently synthesized in homochiral forms using a cycloadditive oligomerization approach. X-ray, NMR, and CD structural analyses of the novel ß-peptides revealed secondary structure features that were generated primarily by Z/E-ß-peptide bond isomerism. Anticancer in cellulo activity of the new ß-peptides toward hormone-refractory prostate cancer cells was observed and was dependent on the absolute configuration of the stereogenic centers and the chain length of the ß-proline oligomers.

meso-Phenyltetrabenzotriazaporphyrin based double-decker lanthanide(III) complexes: synthesis, structure, spectral properties and electrochemistry.

A series of half-sandwich and sandwich-type lanthanide(III) complexes have been prepared using tetrabenzotriazaporphyrin ligands. Reaction of 27-phenyl-29H,31H-tetrabenzo[b,g,l,q][5,10,15]-triazaporphyrin (PhTBTAPH2, 1) with salts [LnX3]·nH2O (Ln = Eu (a), Lu (b); X = OAc, acac) afforded the single- and homoleptic double-deckers (PhTBTAP)LnOAc (2) and (PhTBTAP)2Ln (3) respectively. Heteroleptic double-decker compounds (PhTBTAP)LnPc (4a,b) were obtained upon interaction of 1 with the corresponding Ln mono(phthalocyaninates). An unexpected formation of partially and completely dephenylated co-products 5 and 6 has been detected in the synthesis of sandwich 3, while the possibility of the dearylation of the half-sandwich compound 2 has been demonstrated as well. A more predictable yet firstly observed formation of the triple-decker compound (PhTBTAP)3Eu2 (7) has also been found. Structural studies of 3 supported by 1H NMR spectra, XRD analysis and DFT theoretical calculations reveal that the Eu complex 3a is formed as a single isomer, while the lutetium compound 3b represents an inseparable mixture of two rotational isomers with virtually identical spectral characteristics. The double-decker compounds 3 and 4 reveal intrinsic UV-Vis/NIR absorption as well as peculiar electrochromic behavior. The heteroleptic derivatives 4 generally show intermediate spectral and electrochemical properties with respect to their homoleptic relatives.

Progress in visual representations of chemical space.

INTRODUCTION: The concept of 'chemical space' reveals itself in two forms: the discrete set of all possible molecules, and multi-dimensional descriptor space encompassing all the possible molecules. Approaches based on this concept are widely used for the analysis and enumeration of compound databases, library design, and structure-activity relationships (SAR) and landscape studies. Visual representations of chemical space differ in their applicability domains and features and require expert knowledge for choosing the right tool for a particular problem. AREAS COVERED: In this review, the authors present recent advances in visualization of the chemical space in the framework of current general understanding of this topic. Attention is given to such methods as van Krevelen diagrams, descriptor plots, principal components analysis (PCA), self-organizing maps (SOM), generative topographic mapping (GTM), graph and network-based approaches. Notable application examples are provided. EXPERT OPINION: With the growth of computational power, representations of large datasets are becoming more and more common instruments in the toolboxes of chemoinformaticians. Every scientist in the field can find the method of choice for a particular task. However, there is no universal reference representation of the chemical space currently available and expert knowledge is required.

Heteroleptic naphthalo-phthalocyaninates of lutetium: synthesis and spectral and conductivity properties.

Novel heteroleptic naphthalo-phthalocyaninates of lutetium possessing a symmetrical substituted naphthalocyanine deck were synthesized on the basis of two preformed synthetic blocks: naphthalocyanine ligand and lutetium phthalocyaninates. The compounds obtained were characterized by (1)H NMR and high-resolution MALDI-TOF/TOF mass spectrometry. The correlation between the nature of the substituents and the spectral properties of the target complexes was determined by the introduction of electron-donating (aryl-, aryloxy-) or electron-withdrawing (chloro-) substituents into the phthalocyanine deck. In addition, the nature of peripheral substituents was shown not to affect drastically the phthalocyanine conductivity and activation energy. Conductivity properties depend on thin film morphology which, in turn, relies on intermolecular π-π interactions.

Synthesis and assessment of 4-aminotetrahydroquinazoline derivatives as tick-borne encephalitis virus reproduction inhibitors.

Tick-borne encephalitis virus (TBEV) belonging to Flavivirus genus causes severe infection in humans. The search for therapeutically relevant compounds targeting TBEV requires the exploration of novel chemotypes. A versatile synthesis of previously unknown 4-aminopyrimidines and 4-aminopyrimidine N-oxides based on a fluorosubstituted heterocyclic core is described. A representative series of 4-aminotetrahydroquinazoline derivatives, containing aliphatic and aromatic substituents as well as the adamantane framework, was obtained and their activity against tick-borne encephalitis virus reproduction was studied. Nine compounds were found to inhibit TBEV entry into the host cells. A bulky hydrophobic adamantyl group was identified to be important for the antiviral activity. The developed synthetic route allowed an easy access to a consistent compound library for further structure-activity relationship studies.

Structural studies and anticancer activity of a novel class of ß-peptides.

Functionalized oligomeric organic compounds with well-defined ß-proline scaffold have been synthesized by a cycloadditive oligomerization approach in racemic and enantiopure forms. The structure of the novel ß-peptides was investigated by NMR spectroscopic and X-ray methods determining the conformational shapes of the ß-proline oligomers in solution and solid states. The main structural elements subject to conformational switches are ß-peptide bonds between 5-arylpyrrolidine-2-carboxylic acid units existing in Z/E configurations. The whole library of short ß-peptides and intermediate acrylamides has been tested on antiproliferative activity towards the hormone-refractory prostate cancer cell line PC-3 revealing several oligomeric compounds with low micromolar and submicromolar activities. Bromine-substituted dimeric and trimeric acrylamides induced caspase-dependent apoptosis of PC-3 cells through cell-cycle arrest and mitochondrial damage.

Perspectives of Halogen Bonding Description in Scoring Functions and QSAR/QSPR: Substituent Effects in Aromatic Core.

Halogen bonding (XB) is a new promising interaction pattern in medicinal chemistry. It has predominantly electrostatic nature - high electrostatic potential anisotropy. However to fully unleash the potential of XB in rational drug design fast and robust empirical methods of XB description should be developed. Current approaches rely heavily on ab initio calculation for each molecule studied. Thus fast prediction of electrostatic parameters for description of XB for arbitrary organic molecules is of paramount importance to promptly establish QSAR/QSPR, virtual screening and molecular docking pipelines suitable for today's agile development requirements. The two most promising approaches to describe anisotropic electrostatic models - the extra point (EP) charge model and the multipole expansion (ME) model - were studied on their ability (1) to describe ab initio molecular electrostatic potential (MEP) and (2) to produce parameters that can be predicted for each molecule empirically rather than estimated via ab initio calculations. The reference ab initio MEP was calculated for a set of 730 substituted halobenzenes. Parameters for anisotropic electrostatics of both empirical models (EP and ME) studied were extracted from ab initio MEP. The FreeWilson and Hansch type QSPR models relating XB parameters with aromatic substituents were built and analyzed, providing the guidelines for further development.