Isolation of a Small‐Molecule Inhibitor of the Antiapoptotic Protein Bcl‐xL from a DNA‐Encoded Chemical Library

Bcl‐xL is an antiapoptotic member of the Bcl‐2 protein family and an attractive target for the development of anticancer agents. Here we describe the isolation of binders to Bcl‐xL from a DNA‐encoded chemical library using affinity‐capture selections and massively parallel high‐throughput sequencing of >30 000 sequence tags of library members. The most potent binder identified, compound 19 / 93 [(R)‐3‐(amido indomethacin)‐4‐(naphthalen‐1‐yl)butanoic acid], bound to Bcl‐xL with a dissociation constant (K_d) of 930 nM and was able to compete with a Bak‐derived BH3 peptide, an antagonist of Bcl‐xL function.     

6‐Substituted 2‐Aminopurine‐2′‐deoxyribonucleoside 5′‐Triphosphates that Trace Cytosine Methylation

Gene expression is extensively regulated by the occurrence and distribution of the epigenetic marker 2′‐deoxy 5‐methylcytosine (5mC) in genomic DNA. Because of its effects on tumorigenesis there is an important link to human health. In addition, detection of 5mC can serve as an outstanding biomarker for diagnostics as well as for disease therapy. Our previous studies have already shown that, by processing O⁶‐alkylated 2′‐deoxyguanosine triphosphate (dGTP) analogues, DNA polymerases are able to sense the presence of a single 5mC unit in a template. Here we present the synthesis and evaluation of an extended toolbox of 6‐substituted 2‐aminopurine‐2′‐deoxyribonucleoside 5′‐triphosphates modified at position 6 with various functionalities. We found that sensing of 5‐methylation by this class of nucleotides is more general, not being restricted to O⁶‐alkyl modification of dGTP but also applying to other functionalities.     

Mechanism‐Based Inhibitor of DNA Cytosine‐5 Methyltransferase by a SNAr Reaction with an Oligodeoxyribonucleotide Containing a 2‐Amino‐4‐Halopyridine‐C‐Nucleoside

In chromatin, 5‐methylcytosine (mC), which represents the fifth nucleobase in genomic DNA, plays a role as an inducer of epigenetic changes. Tumor cells exhibit aberrant DNA methylation patterns, and inhibition of human DNA cytosine‐5 methyltransferase (DNMT), which is responsible for generating mC in CpG sequences, is an effective strategy to treat various cancers. Here, we describe the design, synthesis, and evaluation of the properties of 2‐amino‐4‐halopyridine‐C‐nucleosides (d^XP) and oligodeoxyribonucleotides (ODNs) containing d^XP as a novel mechanism‐based inhibitor of DNMTs. The designed ODN containing ^XPpG forms a complex with DNMTs by covalent bonding through a nucleophilic aromatic substitution (S_NAr) reaction, and its cell proliferation activity is investigated. This study suggests that d^XP in a CpG sequence of DNA could serve as a potential nucleic acid drug lead in cancer chemotherapy and a useful chemical probe for studies of epigenetics. Our molecular design using a S_NAr reaction would be useful for DNMTs and other protein–DNA interactions.     

TET-Like Oxidation in 5-Methylcytosine and Derivatives: A Computational and Experimental Study

The epigenetic marker 5-methylcytosine (5mC) is an important factor in DNA modification and epigenetics. It can be modified through a three-step oxidation performed by ten-eleven-translocation (TET) enzymes and we have previously reported that the iron(IV)-oxo complex [Fe(O)(Py₅Me₂H)]²⁺ ( 1 ) can oxidize 5mC. Here, we report the reactivity of this iron(IV)-oxo complex towards a wider scope of methylated cytosine and uracil derivatives relevant for synthetic DNA applications, such as 1-methylcytosine (1mC), 5-methyl-iso-cytosine (5miC) and thymine (T/5mU). The observed kinetic parameters are corroborated by calculation of the C−H bond energies at the reactive sites which was found to be an efficient tool for reaction rate prediction of 1 towards methylated DNA bases. We identified oxidation products of methylated cytosine derivatives using HPLC-MS and GC-MS. Thereby, we shed light on the impact of the methyl group position and resulting C−H bond dissociation energies on reactivity towards TET-like oxidation.     

Identification and Optimization of the First Highly Selective GLUT1 Inhibitor BAY‐876

Despite the long‐known fact that the facilitative glucose transporter GLUT1 is one of the key players safeguarding the increase in glucose consumption of many tumor entities even under conditions of normal oxygen supply (known as the Warburg effect), only few endeavors have been undertaken to find a GLUT1‐selective small‐molecule inhibitor. Because other transporters of the GLUT1 family are involved in crucial processes, these transporters should not be addressed by such an inhibitor. A high‐throughput screen against a library of ～3 million compounds was performed to find a small molecule with this challenging potency and selectivity profile. The N‐(1H‐pyrazol‐4‐yl)quinoline‐4‐carboxamides were identified as an excellent starting point for further compound optimization. After extensive structure–activity relationship explorations, single‐digit nanomolar inhibitors with a selectivity factor of >100 against GLUT2, GLUT3, and GLUT4 were obtained. The most promising compound, BAY‐876 [N⁴‐[1‐(4‐cyanobenzyl)‐5‐methyl‐3‐(trifluoromethyl)‐1H‐pyrazol‐4‐yl]‐7‐fluoroquinoline‐2,4‐dicarboxamide], showed good metabolic stability in vitro and high oral bioavailability in vivo.     

Design and Synthesis of a Series of Piperazine‐1‐carboxamidine Derivatives with Antifungal Activity Resulting from Accumulation of Endogenous Reactive Oxygen Species

In this study, we screened a library of 500 compounds for fungicidal activity via induction of endogenous reactive oxygen species (ROS) accumulation. Structure–activity relationship studies showed that piperazine‐1‐carboxamidine analogues with large atoms or large side chains substituted on the phenyl group at the R³ and R⁵ positions are characterized by a high ROS accumulation capacity in Candida albicans and a high fungicidal activity. Moreover, we could link the fungicidal mode of action of the piperazine‐1‐carboxamidine derivatives to the accumulation of endogenous ROS.     

Catalytic Conversions in Water. Part 23: Steric Effects and Increased Substrate Scope in the Palladium‐Neocuproine Catalyzed Aerobic Oxidation of Alcohols in Aqueous Solvents#

The steric influence of substituents on the 2‐ and 9‐positions of phenanthroline in the (2,9‐R₂‐1,10‐phenanthroline)palladium(II)‐catalyzed aerobic oxidation of 2‐hexanol was investigated by means of high throughput experimentation. (Neocuproine)Pd(OAc)₂ (RCH₃) was found to be a highly active catalyst for alcohol oxidation in 1 : 1 water/DMSO mixtures. The catalyst is unique in that it tolerates water, polar co‐solvents and a wide variety of functional groups in the alcohol. Turn‐over frequencies of >1500 h⁻¹ were achieved and a series of alcohols was oxidised with 0.1 to 0.5 mol % of catalyst.     

LICRED: A Versatile Drop‐In Vector for Rapid Generation of Redox‐Self‐Sufficient Cytochrome P450s

Cytochromes P450 (P450s) are a family of haem‐containing oxidases with considerable potential as tools for industrial biocatalysis. Organismal genomes are revealing thousands of gene sequences that encode P450s of as yet unknown function, the exploitation of which will require high‐throughput tools for their isolation and characterisation. In this report, a ligationindependent cloning vector “LICRED” is described that enables the high‐throughput generation of libraries of redox‐self‐sufficient P450s by fusing a range of P450 haem domains to the reductase of P450RhF (RhF‐Red) in a robust and generically applicable way. Cloning and expression of fusions of RhF‐Red with the haem domains of P450cam and P450‐XplA resulted in soluble, active, redox‐self‐sufficient, chimeric enzymes. In vitro studies also revealed that electron transfer from NADPH to haem was primarily intramolecular. The general applicability of the LICRED platform was then demonstrated through the creation of a library of RhF‐Red fusion constructs by using the diverse complement of P450 haem domains identified in the genome of Nocardia farcinica. The resultant fusion‐protein library was then screened against a panel of substrates; this revealed chimeric enzymes competent for the hydroxylation of testosterone and methyltestosterone, and the dealkylation of 7‐ethoxycoumarin.     

Calixarene‐Derived Mono‐Iminophosphoranes: Highly Efficient Ligands for Palladium‐ and Nickel‐Catalysed Cross‐Coupling

The first mono‐iminophosphoranes based on a calix[4]arene skeleton have been synthesised and tested in the arylation of aryl bromides and aryl chlorides. Combining these ligands with [Pd(OAc)₂] or [Ni(cod)₂] resulted in highly active Suzuki–Miyaura and Kumada–Tamao–Corriu cross‐coupling catalysts, respectively. TOFs up to ca. 4×10⁵ mol(ArBr)⋅mol(M)⁻¹⋅h⁻¹ were obtained in each case. The remarkable activities observed probably arise from the ligands’ ability to form complexes with cavity‐entrapped “MArX” moieties (endo‐complexes), their highly crowded metal environment favouring formation of mono‐ligated intermediates over that of less reactive bis‐ligated ones. Possible supramolecular interactions within the cavity involving the receptor wall and the aromatic substrate may also significantly influence the reaction rates, notably by increasing the proportion of endo‐complexes.     

Monitoring Binding of HIV‐1 Capsid Assembly Inhibitors Using 19F Ligand‐and 15N Protein‐Based NMR and X‐ray Crystallography: Early Hit Validation of a Benzodiazepine Series

The emergence of resistance to existing classes of antiretroviral drugs underlines the need to find novel human immunodeficiency virus (HIV)‐1 targets for drug discovery. The viral capsid protein (CA) represents one such potential target. Recently, a series of benzodiazepine inhibitors was identified via high‐throughput screening using an in vitro capsid assembly assay (CAA). Here, we demonstrate how a combination of NMR and X‐ray co‐crystallography allowed for the rapid characterization of the early hits from this inhibitor series. Ligand‐based ¹⁹F NMR was used to confirm inhibitor binding specificity and reversibility as well as to identify the N‐terminal domain of the capsid (CA_NTD) as its molecular target. Protein‐based NMR (¹H and ¹⁵N chemical shift perturbation analysis) identified key residues within the CA_NTD involved in inhibitor binding, while X‐ray co‐crystallography confirmed the inhibitor binding site and its binding mode. Based on these results, two conformationally restricted cyclic inhibitors were designed to further validate the possible binding modes. These studies were crucial to early hit confirmation and subsequent lead optimization.     

Substrate Hunting for the Myxobacterial CYP260A1 Revealed New 1α‐Hydroxylated Products from C‐19 Steroids

Cytochromes P450 catalyze a variety of synthetically useful reactions. However, it is difficult to determine their physiological or artificial functions when a plethora of orphan P450 systems are present in a genome. CYP260A1 from Sorangium cellulosum So ce56 is a new member among the 21 available P450s in the strain. To identify putative substrates for CYP260A1 we used high‐throughput screening of a compound library (ca. 17 000 ligands). Structural analogues of the type I hits were searched for biotechnologically relevant compounds, and this led us to select C‐19 steroids as potential substrates. We identified efficient surrogate redox partners for CYP260A1, and an Escherichia coli‐based whole‐cell biocatalyst system was developed to convert testosterone, androstenedione, and their derivatives methyltestosterone and 11‐oxoandrostenedione. A detailed ¹H and ¹³C NMR characterization of the product(s) from C‐19 steroids revealed that CYP260A1 is the very first 1α‐steroid hydroxylase.     

Ozonation of the reactive dye intermediate 2‐naphthylamine 3,6,8‐trisulphonic acid (K‐Acid): kinetic assessment,ozonation products and ecotoxicity

Ozonation of the commercially important, recalcitrant reactive dye intermediate 2‐naphthylamine 3,6,8‐trisulphonic acid (K‐Acid) was investigated. Ozonation performance was examined by following ozone absorption rates and K‐Acid, chemical oxygen demand and total organic carbon removals. Mean oxidation states and unidentified organic products were also determined. At pH 3, where direct ozone reactions are dominant, the second‐order rate constant between K‐Acid and molecular ozone was determined as 20 m ^?1 s^?1 for steady‐state aqueous ozone concentration. The competition kinetics approach was also adopted where a reference compound, phenol, and K‐Acid were subjected to ozonation. By applying this method, the second‐order reaction rate constant was found to be 76 m ^?1 s^?1. Common oxidation products formed during ozonation at pH 3, pH 7 and pH 7 with 1 mm hydrogen peroxide were identified as methoxy‐phenyl‐oxime, phenol, benzene, benzaldehyde and oxalic acid via high‐performance liquid chromatography and gas chromatography/mass spectrometry analyses. Continuous nitrate and sulphate evolution were observed during K‐Acid ozonation as a consequence of the abrupt release and subsequent oxidation of its amino and sulphonate groups. The number and amount of reaction products were most intensive for K‐Acid ozonation at pH 7 with 1 mm hydrogen peroxide. According to the acute toxicity tests conducted with Vibrio fischeri, ozonation products were not less toxic than the original K‐Acid solution that caused only 15% inhibition.     

Electrocatalytic Oxidation of Formaldehyde onto Carbon Paste Electrode Modified with Nickel Decorated Nanoporous Cobalt‐Nickel Phosphate Molecular Sieve for Fuel Cell

Nanoporous cobalt‐nickel phosphate VSB‐5 molecular sieve (CoVSB‐5) was synthesized by conventional heating for 48 h in the presence of (2‐hydroxyethyl) trimethylammonium hydroxide as template. Then, a novel, cheap and efficient catalyst was developed for formaldehyde electrooxidation by decorating Ni²⁺ ions on the surface of CoVSB‐5 modified carbon paste electrode (CoVSB‐5/CPE). The electrochemical behavior of the Ni‐CoVSB‐5/CPE electrode towards the formaldehyde oxidation was evaluated by cyclic voltammetry (CV) as well as chronoamperometry methods. An oxidation peak was observed at 0.60 V in 0.1M NaOH solution for electrocatalytic oxidation of formaldehyde with EC′ mechanism. It has been observed that CoVSB‐5 at the surface of CPE can improve catalytic efficiency of the dispersed nickel ions toward oxidation of formaldehyde. The values of electron transfer coefficient, the mean value of catalytic rate constant and diffusion coefficient for formaldehyde and redox sites were obtained to be 0.66, 1.80 × 10⁵ cm³ mol⁻¹ s⁻¹ and 3.62 × 10⁻⁴ cm² s⁻¹, respectively. Obtained results from cyclic voltammetry (CV) and chronoamperometry techniques specified that the electrode reaction is a diffusion‐controlled process. The good catalytic activity, high sensitivity, good selectivity and stability and easy in preparation rendered the Ni‐CoVSB‐5/CPE to be a capable electrode for formaldehyde electrooxidation.     

Energetic Salts of 5‐(5‐Azido‐1H‐1,2,4‐triazol‐3‐yl)tetrazole

Several metal and nitrogen‐rich salts of the recently presented 5‐(5‐azido‐1H‐1,2,4‐triazol‐3‐yl)tetrazole (AzTT), including silver ( 1 ), copper(I) ( 2 ), potassium ( 3 ), cesium ( 4 ), copper(II) ( 7 ), ammonium ( 8 ), and guanidinium ( 9 ), as well as the respective double‐salts of 3 , 4 , 8 and 9 , were prepared and well characterized by IR and multinuclear (¹H, ¹³C, ¹⁴N) NMR spectroscopy, DSC, mass spectrometry, elemental analysis and one ( 4 ) additionally by single‐crystal X‐ray diffraction. The sensitivities towards impact, friction and electrostatic discharge were determined according to BAM standards, revealing most of the metal salts as highly sensitive and the nitrogen‐rich salts as insensitive. The metal salts were further tested for their ability of being primary explosives.     

Synthesis of 2‐(9H‐carbazole‐9‐yl)ethyl methacrylate: Electrochemical impedance spectroscopic study of poly(2‐(9H‐carbazole‐9‐yl)ethyl methacrylate) on carbon fiber

In this contribution, 2‐(9H‐carbazol‐9‐yl) ethyl methacrylate (CzEMA) monomer was chemically synthesized. The monomer characterization was performed by FT‐IR, ¹H‐NMR, ¹³C‐NMR, and melting point analysis. The electropolymerization of CzEMA was studied onto carbon fiber microelectrodes (CFMEs) as an active electrode material in 0.1M sodium perchlorate (NaClO₄)/acetonitrile (ACN) solution. The electropolymerization experiments were done from 1 mM to 10 mM. The detailed characterization of the resulting electrocoated Poly (CzEMA)/CFME thin films was studied by various techniques, i.e., cyclic voltammetry (CV), Scanning electron microscopy (SEM) and electrochemical impedance spectroscopy (EIS). The effects of initial monomer concentrations (1, 3, 5, and 10 mM) during the preparation of modified electrodes were examined by EIS. Capacitive behaviors of modified CFMEs were defined via Nyquist, Bode‐magnitude, and Bode‐phase plots. Variation of capacitance values by initial monomer concentration and specific capacitance values are presented. The highest specific capacitance value electrocoated polymer thin film by CV method in the initial monomer concentration of 5 mM with a charge of 52.74 mC was obtained about 424.1 μF cm^?2. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011