Selective kinase inhibition by exploiting differential pathway sensitivity

Protein kinase inhibitors are optimized to have high affinity for their intended target(s) to elicit the desired cellular effects. Here, we asked whether differences in inhibitory sensitivity between two kinase signaling pathways, controlled by the cyclin-dependent kinases Cdk1 and Pho85, can be sufficient to allow for selective targeting of one pathway over the other. We show the oxindole inhibitor GW297361 elicits a Pho85-selective response in cells despite having a 20-fold greater biochemical potency for Cdk1 in vitro. We provide evidence that partial inhibition of Pho85 is sufficient to activate Pho85-dependent signaling, but partial inhibition of Cdk1 is not sufficient to block Cdk1-dependent cell proliferation. Identification of highly sensitive kinases may provide a means to achieve selective perturbation of kinase signaling pathways complementary to efforts to achieve maximal differences between in vitro IC50 values.     

Selective recognition of HIV RNA by dinuclear metallic ligands

We describe the development of dinuclear metallic ligands to target specific HIV RNA structures. Two series of dipyridinyl-N bridged dinuclear metal complexes were synthesized and their binding activities toward TAR and RRE RNA were studied both experimentally and theoretically.     

Selective inhibition of USP7

The deubiquitinating enzyme USP7 is an emerging oncology and antiviral target. Reverdy et?al., in this issue of Chemistry & Biology, disclose the first small-molecule inhibitor selective for USP7, which recapitulates its knockdown in cancer cells and hence demonstrates the therapeutic feasibility of USP7 inhibitors.     

Selective surface modification of polymers by means of hydrogen and oxygen plasmas

An ESCA investigation has been made of the changes in surface functionalization for a series of polymers effected by means of low-powered inductively coupled rf plasmas excited in hydrogen and oxygen. Reactions in each case are confined to the outermost surfaces of the polymer films and the use of oxygen plasmas leads to extensive oxidative functionalization. Bisphenol-A polycarbonate and polyethylene terephthalate exhibit similar overall reactivities to both oxygen and hydrogen plasmas, while polystyrene is shown to be substantially more reactive than high-density polyethylene to the plasma treatments of interest in this work. Comparison has been made of the effects of straight hydrogen and oxygen plasmas and of sequential hydrogen/oxygen and oxygen/hydrogen plasma treatments.     

Selective intercalation of polymers in carbon nanotubes

A room-temperature, open-air method is devised to selectively intercalate relatively low-molecular-weight polymers (approximately 10-100 kDa) from dilute, volatile solutions into open-end, as-grown, wettable carbon nanotubes with 50-100 nm diameters. The method relies on a novel self-sustained diffusion mechanism driving polymers from dilute volatile solutions into carbon nanotubes and concentrating them there. Relatively low-molecular-weight polymers, such as poly(ethylene oxide) (PEO, 600 kDa) and poly(caprolactone) (PCL, 80 kDa), were encapsulated in graphitic nanotubes as confirmed by transmission electron microscopy, which revealed morphologies characteristic of mixtures in nanoconfinements affected by intermolecular forces. Whereas relatively small, flexible polymer molecules can conform to enter these nanotubes, larger macromolecules (approximately 1000 kDa) remain outside. The selective nature of this process is useful for filling nanotubes with polymers and could also be valuable in capping nanotubes.     

Selective stabilization of natively folded RNA structure by DNA constraints

Learning how native RNA conformations can be stabilized relative to unfolded states is an important objective, for both understanding natural RNAs and improving the design of artificial functional RNAs. Here we show that covalently attached double-stranded DNA constraints (ca. 14 base pairs in length) can significantly stabilize the native conformation of an RNA molecule. Using the P4-P6 domain of the Tetrahymena group I intron as the test system, we identified pairs of RNA sites where attaching a DNA duplex is predicted to be structurally compatible with only the folded state of the RNA. The DNA-constrained RNAs were synthesized and shown by nondenaturing polyacrylamide gel electrophoresis (native PAGE) to have substantial decreases in their Mg2+ midpoints ([Mg2+]1/2 values). These changes are equivalent to free energy stabilizations as large as DeltaDeltaGdegrees = -2.5 kcal/mol, which is approximately 14% of the total tertiary folding energy. For comparison, the sole modification of P4-P6 previously reported to stabilize this RNA is a single-nucleotide deletion (DeltaC209) that provides only 1.1 kcal/mol of stabilization. Our findings indicate that nature has not completely optimized P4-P6 RNA folding. Furthermore, the DNA constraints are designed not to interact directly and extensively with the RNA, but rather more indirectly to modulate the relative stabilities of folded and unfolded RNA states. The successful implementation of this strategy to further stabilize a natively folded RNA conformation suggests an important element of modularity in stabilization of RNA structure, with implications for how nature might use other molecules such as proteins to stabilize specific RNA conformations.     

Selective enrichment and separation of phosphotyrosine peptides by thermosensitive molecularly imprinted polymers

Novel thermosensitive molecularly imprinted polymers were successfully prepared using the epitope imprinting approach in the presence of the mimic template phenylphosphonic acid, the functional monomer vinylphosphonic acid‐Ti⁴⁺, the temperature‐sensitive monomer N‐isopropylacrylamide and the crosslinker N,N′‐methylenebisacrylamide. The ratio of the template/thermosensitive monomers/crosslinker was optimized, and when the ratio was 2:2:1, the prepared thermosensitive molecularly imprinted polymers had the highest imprinting factor. The synthetic thermosensitive molecularly imprinted polymers were characterized by Fourier transform infrared spectroscopy to reveal the combination and elution processes of the template. Then, the adsorption capacity and thermosensitivity was measured. When the temperature was 28°C, the imprinting factor was the highest. The selectivity and adsorption capacity of the thermosensitive molecularly imprinted polymers for phosphotyrosine peptides from a mixture of three tailor‐made peptides were measured by high‐performance liquid chromatography. The results showed that the thermosensitive molecularly imprinted polymers have good selectivity for phosphotyrosine peptides. Finally, the imprinted hydrogels were applied to specifically adsorb phosphotyrosine peptides from a sample mixture containing phosphotyrosine and a tryptic digest of β‐casein, which demonstrated high selectivity. After four rebinding cycles, 78.9% adsorption efficiency was still retained.     

RNA cleavage and inhibition of protein synthesis by bleomycin

Bleomycin is a clinically used antitumor antibiotic long thought to function therapeutically at the level of DNA cleavage. Recently, it has become clear that bleomycin can also cleave selected members of all major classes of RNA. Using the computer program COMPARE to search the database established by the Anticancer Drug Screening Program of the National Cancer Institute, a possible mechanism-based correlation was found between onconase, an antitumor ribonuclease currently being evaluated in phase III clinical trials, and the chemotherapeutic agent bleomycin. Following these observations, experimentation revealed that bleomycin caused tRNA cleavage and DNA-independent protein synthesis inhibition in rabbit reticulocyte lysate and when microinjected into Xenopus oocytes. The correlation of protein synthesis inhibition to the previously reported site-specific RNA cleavage caused by bleomycin supports the thesis that RNA cleavage may constitute an important element of the mechanism of action of bleomycin.     

Selective sample treatment using molecularly imprinted polymers

The molecularly imprinted polymers (MIPs) are synthetic polymers possessing specific cavities designed for a target molecule. By a mechanism of molecular recognition, the MIPs are used as selective sorbents for the solid-phase extraction of target analytes from complex matrices. MIPs are often called synthetic antibodies in comparison with immuno-based sorbents; they offer some advantages including easy, cheap and rapid preparation and high thermal and chemical stability. This review describes the use of MIPs in solid-phase extraction with emphasis on their synthesis, the various parameters affecting the selectivity of the extraction, their potential to selectively extract analytes from complex aqueous samples or organic extracts, their on-line coupling with LC and their potential in miniaturized devices.     

Selective extraction of antioxidants with molecularly imprinted polymers

Molecular imprinting technology can be used to generate specific artificial polymeric receptors, i.e., high affinity stationary phases, as already shown for peptides and many other food ingredients. In this work, polymers have been molecularly imprinted with three exemplary antioxidants, butylated hydroxyanisole (BHA), butylated hydroxytoluene (BHT) and propyl gallate (PG). Results of chromatographic evaluations are presented, demonstrating the specificity of the imprinted polymers (MIP) compared to non-specific control polymers (CP). For a BHA imprinted polymer and the respective analyte BHA a separation factor of α=k_BHA-MIP′/k_CP′=1.12 was found, whereas for the BHT-MIP a higher selectivity was determined with α=k_BHT-MIP′/k_CP′=1.47. Using the PG selective MIP for PG as analyte a value of α=k_PG-MIP′/k_CP′=1.24 could be achieved. Furthermore, results of extraction procedures based on MIP and CP phases are presented, demonstrating for instance a higher selectivity of the BHA-MIP in comparison with its CP when using methanol or acetonitrile as analyte solvent, and of the PG-MIP when performing the extraction in acetonitrile.     

Selective adsorption of metronidazole on conjugated microporous polymers

Conjugated microporous polymers (CMPs) have recently received extensive attention in oil/organic solvent-water separation field as a kind of ideal porous absorbents with tunable porosity, large surface areas, and super-hydrophobicity. However, reports on the application of CMPs in adsorption of hydrophilic contaminants from water are very few. In this work, we studied the adsorption of metronidazole (MNZ), a polar antibiotic, by two kinds of CMPs. The adsorption characteristics of MNZ by the CMPs, including adsorption kinetics, mechanism, and isotherm parameters were calculated. The adsorption kinetics of MNZ was well expressed by the pseudo-second-order model, and the adsorption process was found to be mainly controlled by film diffusion. The adsorption isotherm data agreed well with the Langmuir isotherm model, and the values of free energy E indicated that the adsorption nature of MNZ on the CMPs was physisorption. Increasing dispersion degree of the CMPs in MNZ solution resulted in greater adsorption. This work may provide fundamental guidance for the removal of antibiotics by CMPs.     

Selective inhibition of Trypanosoma cruzi GAPDH by "bi-substrate" analogues

A new series of "bi-substrate" analogues have been synthesized as potential inhibitors of the glyceraldehyde-3-phosphate dehydrogenase and one lead compound has been identified that inhibits the enzyme from Trypanosoma cruzi with good affinity and very high (50-fold) specificity.     

Application of DNA-binding polymers for preparation of DNA for analysis by matrix-assisted laser desorption/ionization mass spectrometry

The susceptibility of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) to the presence of salts in a sample, especially salts of alkali metals, requires careful and often tedious desalting procedures which complicate and slow the throughput of MS-based methods. A novel approach to sample preparation was developed based on the extraction of DNA out of solution onto a solid surface with an attached DNA-binding polymer, such as polyethyleneimine or polyvinylpyrrolidone. The observed binding is strong enough to sustain washing, and, as a result, desalting and concentration can be performed in a single fast step. After DNA has been immobilized on the surface and supernatant solution removed, subsequent addition of MALDI matrix releases material from the surface, which co-crystallizes with matrix. The mass spectrometric analysis is then performed directly from this support. Analysis of oligonucleotides and three-fold multiplexed SNP typing reactions performed by this method shows improved sensitivity and excellent resolution for various DNA fragments, together with high tolerance to various buffer components, such as alkali metals and surfactants. Simplicity and speed make it attractive for high-throughput sample preparation and analysis of oligonucleotide mixtures by MALDI-MS.     

Selective piezoelectric odor sensors using molecularly imprinted polymers

Molecular imprinting technique has been used to create sensors with a predetermined selectivity for molecules in the gas phase. Piezoelectric quartz crystals coated with a 2-methylisoborneol (MIB) imprinted polymer gave responses which were consistently 5–10 Hz (1.1–1.3 times) higher than those of sensors coated with a non-imprinted polymer. Geosmin, another tertiary alcohol odorant with an earthy odor resembling, and often accompanying MIB, produced almost equal responses on either imprinted- or non-imprinted sensors. A number of other odorants were examined and their responses to the non-imprinted sensors were found to be similar to or greater than their responses to the imprinted sensors. The responses of MIB to the imprinted sensors were always the highest, while other odorants produced equal or higher responses using the non-imprinted sensor. The sensor has a detection limit of ca. 5 mg l⁻¹ and a dynamic range of at least 1000 mg l^−l. When the time taken for the sensor to stabilize is used as the response, instead of the frequency change, the detection limit is lowered to ca. 200 μg l^−l.     

Selective separation of lambdacyhalothrin by porous/magnetic molecularly imprinted polymers prepared by Pickering emulsion polymerization

Porous/magnetic molecularly imprinted polymers (PM‐MIPs) were prepared by Pickering emulsion polymerization. The reaction was carried out in an oil/water emulsion using magnetic halloysite nanotubes as the stabilizer instead of a toxic surfactant. In the oil phase, the imprinting process was conducted by radical polymerization of functional and cross‐linked monomers, and porogen chloroform generated steam under the high reaction temperature, which resulted in some pores decorated with easily accessible molecular binding sites within the as‐made PM‐MIPs. The characterization demonstrated that the PM‐MIPs were porous and magnetic inorganic–polymer composite microparticles with magnetic sensitivity (M_s = 0.7448 emu/g), thermal stability (below 473 K) and magnetic stability (over the pH range of 2.0–8.0). The PM‐MIPs were used as a sorbent for the selective binding of lambdacyhalothrin (LC) and rapidly separated under an external magnetic field. The Freundlich isotherm model gave a good fit to the experimental data. The adsorption kinetics of the PM‐MIPs was well described by pseudo‐second‐order kinetics, indicating that the chemical process could be the rate‐limiting step in the adsorption of LC. The selective recognition experiments exhibited the outstanding selective adsorption effect of the PM‐MIPs for target LC. Moreover, the PM‐MIPs regeneration without significant loss in adsorption capacity was demonstrated by at least four repeated cycles.