The use of fluorine-containing carboxylic acids for the large-scale isolation of highly polymerized deoxyribonucleic acids

1. The precipitation of the proteins of calf-thymus nucleohistone and herringsperm nucleoprotamine with the salts of fluorine-containing carboxylic acids has been studied. Pentadecafluoro-octanoate gave a precipitate that could be sedimented almost completely by centrifuging at 2350g for 20min. omega-H-Hexadecafluorononanoate, omega-H-eicosafluoro-undecanoate and dodecyl sulphate gave precipitates that could only be partly sedimented under these conditions. 2. A method has been developed for the isolation of highly polymerized DNA on a large scale from calf thymus and herring sperm by the use of pentadecafluorooctanoate. This is more convenient and less tedious than existing methods.     

Mixing of perfluorinated carboxylic acids with dipalmitoylphosphatidylcholine

Perfluorinated acids are emerging as an important class of persistent environmental pollutant, thus raising human health concerns. To understand the behavior of these compounds in biological systems, the mixing behavior of two perfluorinated acids, perfluorododecanoic and perfluorotetradecanoic acid, with dipalmitoylphosphatidylcholine (DPPC) was studied in monolayers at the air-water interface and in fully hydrated DPPC bilayers. The mixing behavior of both acids was indicative of an attractive interaction and partial miscibility with DPPC at the air-water interface. In the bilayer studies, the fluorinated acids cause peak broadening and elimination of the pretransition of DPPC. The onset temperature of the main phase transition remains constant in the presence of the fluorinated acids suggesting immiscibilities in the gel phase. Below X(DPPC)=0.97 significant peak broadening of the main phase transition can be observed. These results suggest strong interaction between the respective acid and DPPC, and that both acids are able to partition into the lipid bilayer. However, their mixing behavior is far from ideal, thus suggesting the presence of domains or lipid aggregates with high acid concentrations which may (adversely) impact the function of biological mono- and bilayers.     

Mixing of perfluorinated carboxylic acids with dipalmitoylphosphatidylcholine

Perfluorinated acids are emerging as an important class of persistent environmental pollutant, thus raising human health concerns. To understand the behavior of these compounds in biological systems, the mixing behavior of two perfluorinated acids, perfluorododecanoic and perfluorotetradecanoic acid, with dipalmitoylphosphatidylcholine (DPPC) was studied in monolayers at the air-water interface and in fully hydrated DPPC bilayers. The mixing behavior of both acids was indicative of an attractive interaction and partial miscibility with DPPC at the air-water interface. In the bilayer studies, the fluorinated acids cause peak broadening and elimination of the pretransition of DPPC. The onset temperature of the main phase transition remains constant in the presence of the fluorinated acids suggesting immiscibilities in the gel phase. Below X(DPPC) = 0.97 significant peak broadening of the main phase transition can be observed. These results suggest strong interaction between the respective acid and DPPC, and that both acids are able to partition into the lipid bilayer. However, their mixing behavior is far from ideal, thus suggesting the presence of domains or lipid aggregates with high acid concentrations which may (adversely) impact the function of biological mono- and bilayers.     

Thyclotides,tetrahydrofuran-modified peptide nucleic acids that efficiently penetrate cells and inhibit microRNA-21

Peptide nucleic acids (PNAs) are promising therapeutic molecules for gene modulation; however, they suffer from poor cell uptake. Delivery of PNAs into cells requires conjugation of the PNA to another large molecule, typically a cell-penetrating peptide or nanoparticle. In this study, we describe a new PNA-based molecule with cyclic tetrahydrofuran (THF) backbone modifications that in some cases considerably improve cell uptake. We refer to these THF-PNA oligomers as thyclotides. With THF groups at every position of the oligomer, the cell uptake of thyclotides targeted to miR-21 is enhanced compared with the corresponding unmodified PNA based on an aminoethylglycine backbone. An optimized thyclotide can efficiently enter cells without the use of cell-penetrating peptides, bind miR-21, its designated microRNA target, decrease expression of miR-21 and increase expression of three downstream targets (PTEN, Cdc25a and KRIT1). Using a plasmid with the PTEN-3′UTR coupled with luciferase, we further confirmed that a miR-21-targeted thyclotide prevents miR-21 from binding to its target RNA. Additionally, the thyclotide shows no cytotoxicity when administered at 200 times its active concentration. We propose that thyclotides be further explored as therapeutic candidates to modulate miRNA levels.     

Use of carboxylic acids by Thiobacillus A2

Thiobacillus A2 can grow on acetate, glycollate, succinate and citrate as sole carbon and energy sources. Results of growth and transport experiments indicated that separate transport systems existed for the four acids although acetate uptake by bacteria grown on glycollate was very rapid. Citrate was a potentially toxic substrate in that low concentrations had to be supplied to adapt organisms to growth on citrate following autotrophic culture on thiosulphate. Apparent Ks values for transport by whole organisms were around 10(-4) M. The effects of uncoupling agents, phosphate and arsenate, on acid uptake did not allow identification of the mechanisms of transport, but indicated energy-requiring processes possibly involving anion participation. The ratio of carbon assimilated from the -CH2- and the -COOH carbons of succinate was about 5:1, reflecting very rapid decarboxylation of succinate following uptake into the cell.     

Tuning hydrophobicity of highly cationic tetradecameric Gramicidin S analogues using adamantane amino acids

Ring extended Gramicidin S analogues containing adamantane amino acids and six cationic residues were designed and evaluated. Systematic replacement of the hydrophobic residues with adamantane amino acids resulted in a small set of compounds with varying amphipathic character. It was found that the amphipathicity of these compounds is correlated to their biological activity. Several bacterial strains including MRSA strains were shown to be killed by the novel peptides. The most potent antibacterial peptides are tetradecameric GS analogues containing six positives charges and two adamantane moieties.     

A novel cell-penetrating peptide TAT-A1 delivers siRNA into tumor cells selectively

siRNA is promising in anti-tumor therapy. The main challenge is lack of tumor-specific intracellular delivery. In this study, a 6 amino acids peptide (A1) with high affinity for vascular endothelial growth factor receptor-1 (VEGFR1) was conjugated with a cell penetrating peptide (CPP) TAT to form a tumor-selective CPP. To evaluate the tumor-targeted penetrate property of TAT-A1, the uptake of TAT-A1 was measured by flow cytometry. The selectivity in vitro was tested in co-cultured tumor cells and normal cells by laser confocal microscope. The internalization efficiency of TAT-A1 was significantly higher than that of TAT (p < 0.05). TAT-A1 penetrated into tumor cells selectively when added to co-cultured tumor cells and normal cells due to the recognition of VEGFR1 which is over-expressed on tumor cells. Furthermore, siRNA was successfully transferred by TAT-A1 into tumor cells in a similar way of Lipofectamine 2000, which was proved to be an efficient vector. The knockout effect of siRNA transferred by TAT-A1 was obtained at both mRNA and protein level. These results indicated that the tumor-targeted TAT-A1 can act as an excellent vehicle for specific delivery of anti-cancer agents.     

Discovery of novel BTK inhibitors with carboxylic acids

We report the design and synthesis of a series of novel Bruton’s Tyrosine Kinase (BTK) inhibitors with a carboxylic acid moiety in the ribose pocket. This series of compounds has demonstrated much improved off-target selectivities including adenosine uptake (AdU) inhibition compared to the piperidine amide series. Optimization of the initial lead compound 4 based on BTK enzyme inhibition, and human peripheral blood mononuclear cell (hPBMC) and human whole blood (hWB) activity led to the discovery of compound 40, with potent BTK inhibition, reduced off target activities, as well as favorable pharmacokinetic profile in both rat and dog.     

A leucine zipper-based peptide hybrid delivers functional Nanog protein inside the cell nucleus

We synthesized a pair of compounds containing leucine zipper peptides to deliver protein cargo into cells. One is a cell-penetrating peptide (CPP) with Lz(E), a leucine zipper peptide containing negatively charged amino acids, and the other is a Nanog protein with Lz(K), a leucine zipper peptide containing positively charged amino acids. When cells were treated with these equimolar mixtures, Nanog-Lz(K) hybridized with Lz(E)-CPP was successfully delivered into the cells. Furthermore, Nanog-Lz(K) exerted its proper function after nuclear transport.     

EcDBS1R6: A novel cationic antimicrobial peptide derived from a signal peptide sequence

BackgroundBacterial infections represent a major worldwide health problem the antimicrobial peptides (AMPs) have been considered as potential alternative agents for treating these infections. Here we demonstrated the antimicrobial activity of EcDBS1R6, a peptide derived from a signal peptide sequence of Escherichia coli that we previously turned into an AMP by making changes through the Joker algorithm.MethodsAntimicrobial activity was measured by broth microdilution method. Membrane integrity was measured using fluorescent probes and through scanning electron microscopy imaging. A sliding window of truncated peptides was used to determine the EcDBS1R6 active core. Molecular dynamics in TFE/water environment was used to assess the EcDBS1R6 structure.ResultsSignal peptides are known to naturally interact with membranes; however, the modifications introduced by Joker transformed this peptide into a membrane-active agent capable of killing bacteria. The C-terminus was unable to fold into an α-helix whereas its fragments showed poor or no antimicrobial activity, suggesting that the EcDBS1R6 antibacterial core was located at the helical N-terminus, corresponding to the signal peptide portion of the parent peptide.ConclusionThe strategy of transforming signal peptides into AMPs appears to be promising and could be used to produce novel antimicrobial agents.General significanceThe process of transforming an inactive signal peptide into an antimicrobial peptide could open a new venue for creating new AMPs derived from signal peptides.     

Diterpene carboxylic acids and a heliangolide from Helianthus angustifolius

Two diterpene carboxylic acids, one a new kaurenoid derivative and one the previously characterized labdane, ()-cis-ozic acid, as well as a     

Kinetic resolution of alpha-acetoxy carboxylic acids with homochiral SuperQuats

Preliminary investigations focused on the kinetic resolution of (+/-)-alpha-acetoxy mandelic carboxylic acid chloride with isopropyl SuperQuat and isopropyl Evans' homochiral auxiliaries. The addition of 2 equiv. of the acid chloride to the lithium salts of the auxiliaries (SuperQuat and Evans') at -100 degrees C in the THF afforded the corresponding N-acyl auxiliaries in high chemical yields (95% and 89%) and d.e.'s of 66% and 40%, respectively. Using the same mandelic acid chloride but incorporating SuperQuat auxiliaries derived from (S)-phenylglycine and (S)-phenylalanine yielded the corresponding N-acyl SuperQuats in 86% and 90% and d.e. 's of 66% and 30%, respectively. Substituting the phenyl group within the alpha-acetoxy mandelic acid chloride for a n-butyl, tert-butyl and cyclohexyl group changed the d.e. significantly when kinetically resolved with isopropyl SuperQuat. The yields were all similar, i.e., approximately 90% but the d.e.'s varied considerably, with values of 20%, 50%, and 82%, respectively. Attempted kinetic resolution of alpha-methoxyphenylacetyl chloride using the lithium salt of isopropyl SuperQuat revealed a diasteroselectivity of 45%, significantly lower than that obtained with the corresponding alpha-acetoxy carboxylic acid chlorides.     

Improved cellular activity of antisense peptide nucleic acids by conjugation to a cationic peptide-lipid (CatLip) domain

Conjugation to cationic cell penetrating peptides (such as Tat, Penetratin, or oligo arginines) efficiently improves the cellular uptake of large hydrophilic molecules such as oligonucleotides and peptide nucleic acids, but the cellular uptake is predominantly via an unproductive endosomal pathway and therefore mechanisms that promote endosomal escape (or avoid the endosomal route) are required for improving bioavailability. A variety of auxiliary agents (chloroquine, calcium ions, or lipophilic photosensitizers) has this effect, but improved, unaided delivery would be highly advantageous in particular for future in vivo applications. We find that simply conjugating a lipid domain (fatty acid) to the cationic peptide (a CatLip conjugate) increases the biological effect of the corresponding PNA (CatLip) conjugates in a luciferase cellular antisense assay up to 2 orders of magnitude. The effect increases with increasing length of the fatty acid (C8-C16) but in parallel also results in increased cellular toxicity, with decanoic acid being optimal. Furthermore, the relative enhancement is significantly higher for Tat peptide compared to oligoarginine. Confocal microscopy and chloroquine enhancement indicates that the lipophilic domain increases the endosomal uptake as well as promoting significantly endosomal escape. These results provide a novel route for improving the (cellular) bioavailability of larger hydrophilic molecules.     

Acetyl coenzyme A synthetase catalyzed reactions of coenzyme A with alpha, beta-unsaturated carboxylic acids

alpha, beta-Unsaturated coenzyme A (CoA) thioesters including acrylyl CoA, methacrylyl CoA, and propiolyl CoA were synthesized by catalysis with acetyl CoA synthetase (EC 6.2.1.1.). After isolation from the enzymatic reactions, the products were found to be the result of 1,4 addition of CoASH to the double bond and addition of water to the triple bond of the initial acyl CoA adducts. Structural determinations of these products by 1H NMR, 13C NMR, and the chemical reactions leading to their formation are described.     

Polystyrene-bound Mn(T4PyP): A highly efficient and reusable catalyst for biomimetic oxidative decarboxylation of carboxylic acids with sodium periodate

In this report, highly efficient oxidative decarboxylation of carboxylic acids with sodium periodate catalyzed by a supported manganese(III) porphyrin is described. In the presence of manganese(III) tetra(4-pyridyl)porphyrin supported on cross-linked chloromethylated polystyrene, [Mn(T4PyP)-CMP], as catalyst, carboxylic acids were converted to their corresponding carbonyl compounds via oxidative decarboxylation with sodium periodate using imidazole as axial ligand. The oxidation of anti-inflammatory drugs such Indomethacin and Ibuprofen was carried out successfully and the decarboxylated products were obtained. This catalyst can be reused several times without loss of its catalytic activity in the oxidation reactions.     

A second activation peptide from bovine cationic trypsinogen.

1. Although only one activation peptide of bovine cationic trypsinogen has been reported previously, the peptide fraction obtained from activation mixtures shows several bands on paper electrophoresis at pH 6.5. 2. The major band was the peptide previously described. The band second in intensity of staining with ninhydrin (10-20% of that of the main band, as judged by eye) had an electrophoretic mobility consistent with its being related to the main peptide. It appeared on activation both of bulk commercial samples of trypsinogen and, as the Appendix shows, of samples prepared from pancreases obtained at the local abattoir. 3. The second peptide proved to be Phe-Pro-Val-Asp-Asp-Asp-Asp-Lys, and we conclude that it is another activation peptide. We discuss briefly the genetic and phylogenetic implications of our findings.     

A peptide with alternating lysines can act as a highly specific Z-DNA binding domain

Many nucleic acid binding proteins use short peptide sequences to provide specificity in recognizing their targets, which may be either a specific sequence or a conformation. Peptides containing alternating lysine have been shown to bind to poly(dG–d5meC) in the Z conformation, and stabilize the higher energy form [H. Takeuchi, N. Hanamura, H. Hayasaka and I. Harada (1991) FEBS Lett., 279, 253–255 and H. Takeuchi, N. Hanamura and I. Harada (1994) J. Mol. Biol., 236, 610–617.]. Here we report the construction of a Z-DNA specific binding protein, with the peptide KGKGKGK as a functional domain and a leucine zipper as a dimerization domain. The resultant protein, KGZIP, induces the Z conformation in poly(dG–d5meC) and binds to Z-DNA stabilized by bromination with high affinity and specificity. The binding of KGZIP is sufficient to convert poly(dG–d5meC) from the B to the Z form, as shown by circular dichroism. The sequence KGKGKGK is found in many proteins, although no functional role has been established. KGZIP also has potential for engineering other Z-DNA specific proteins for future studies of Z-DNA in vitro and in vivo.     

Phosphono peptide nucleic acids with a constrained hydroxyproline-based backbone

DNA mimics representing negatively charged analogues of peptide nucleic acids (PNAs), particularly hetero-oligomers constructed from alternating phosphono-PNA residues (pPNA) and monomers on the base of trans-4-hydroxy-L-proline (HypNA) as well as mimics composed of phosphono-HypNA monomers (pHypNA) were tested in a set of in vitro and in vivo assays, and they demonstrated a high potential for the use in nucleic acid based diagnostic, isolation of nucleic acids and antisense experiments.