closo-borane conjugated regulatory peptides retain high biological affinity: synthesis of closo-borane conjugated Tyr(3)-octreotate derivatives for BNCT

Despite the improvements in cancer therapy during the past years, high-grade gliomas and many other types of cancer are still extremely resistant to current forms of therapy. Boron neutron capture therapy (BNCT) provides a promising way to destroy cancer cells without damaging healthy tissue. However, BNCT in practice is still limited due to the lack of boron-containing compounds that selectively deliver boron to cancer cells. Since many neuroendocrine tumors show an overexpression of the somatostatin receptor, it was our aim to synthesize compounds that contain a large number of boron atoms and still show high affinity toward this transmembrane receptor. The synthetic peptide Tyr (3)-octreotate (TATE) was chosen as a high-affinity and internalizing tumor targeting vector (TTV). Novel boron cluster compounds, containing 10 or 20 boron atoms, were coupled to the N-terminus of TATE. The obtained affinity data demonstrate that the use of a spacer between TATE and the closo-borane moiety is the option to avoid a loss of biological affinity of closo-borane conjugated TATE. For the first time, it was shown that closo-borane conjugated regulatory peptides retain high biological affinity and selectivity toward their transmembrane tumor receptors. The results obtained and the improvement of spacer and boron building block chemistry may stimulate new directions for BNCT.

Bacteriorhodopsin protein hybrids for chemical and biological sensing

Bacteriorhodopsin (bR), an optoelectric protein found in Halobacterium salinarum, has the potential for use in protein hybrid sensing systems. Bacteriorhodopsin has no intrinsic sensing properties, however molecular and chemical tools permit production of bR protein hybrids with transducing and sensing properties. As a proof of concept, a maltose binding protein-bacteriorhodopsin ([MBP]-bR) hybrid was developed. It was proposed that the energy associated with target molecule binding, maltose, to the hybrid sensor protein would provide a means to directly modulate the electrical output from the MBP-bR bio-nanosensor platform. The bR protein hybrid is produced by linkage between bR (principal component of purified purple membrane [PM]) and MBP, which was produced by use of a plasmid expression vector system in Escherichia coli and purified utilizing an amylose affinity column. These proteins were chemically linked using 1-ethyl-3-[3-dimethylaminopropyl]carbodiimide hydrochloride (EDC) and N-hydroxysuccinimide (NHS), which facilitates formation of an amide bond between a primary carboxylic acid and a primary amine. The presence of novel protein hybrids after chemical linkage was analyzed by SDSPAGE. Soluble proteins (MBP-only derivatives and unlinked MBP) were separated from insoluble proteins (PM derivatives and unlinked PM) using size exclusion chromatography. The putatively identified MBP-bR protein hybrid, in addition to unlinked bR, was collected. This sample was normalized for bR concentration to native PM and both were deposited onto indium tin oxide (ITO) coated glass slides by electrophoretic sedimentation. The photoresponse of both samples, activated using 100 Watt tungsten lamp at 10 cm distance, were equal at 175 mV. Testing of deposited PM with 1 mM sucrose or 1 mM maltose showed no change in the photoresponse of the xiv material, however addition of 1 mM maltose to the deposited MBP-bR linked hybrid material elicited a 57% decrease in photoresponse indicating a positive response for targeting of maltose. This chemically linked MBP-bR hybrid protein, with bacteriorhodopsin, as a photoresponsive transducing substrate, shows promise for creation of a universal sensing array by attachment of other pertinent sensing materials, in lieu of the maltose binding protein utilized. This strategy would allow significant reduction in sensor size, while increasing responsiveness and sensitivity at nano and picomolar levels.

Epothilone analogues with benzimidazole and quinoline side chains: chemical synthesis, antiproliferative activity, and interactions with tubulin

A series of epothilone B and D analogues bearing isomeric quinoline or functionalized benzimidazole side chains has been prepared by chemical synthesis in a highly convergent manner. All analogues have been found to interact with the tubulin/microtubule system and to inhibit human cancer cell proliferation in vitro, albeit with different potencies (IC(50) values between 1 and 150 nM). The affinity of quinoline-based epothilone B and D analogues for stabilized microtubules clearly depends on the position of the N-atom in the quinoline system, while the induction of tubulin polymerization in vitro appears to be less sensitive to N-positioning. The potent inhibition of human cancer cell growth by epothilone analogues bearing functionalized benzimidazole side chains suggests that these systems might be conjugated with tumor-targeting moieties to form tumor-targeted prodrugs.

Adenosine Kinase of T. b. Rhodesiense identified as the putative target of 4-[5-(4-phenoxyphenyl)-2H-pyrazol-3-yl]morpholine using chemical proteomics

BACKGROUND: Human African trypanosomiasis (HAT), a major parasitic disease spread in Africa, urgently needs novel targets and new efficacious chemotherapeutic agents. Recently, we discovered that 4-[5-(4-phenoxyphenyl)-2H-pyrazol-3-yl]morpholine (compound 1) exhibits specific antitrypanosomal activity with an IC(50) of 1.0 microM on Trypanosoma brucei rhodesiense (T. b. rhodesiense), the causative agent of the acute form of HAT. METHODOLOGY/PRINCIPAL FINDINGS: In this work we show adenosine kinase of T. b. rhodesiense (TbrAK), a key enzyme of the parasite purine salvage pathway which is vital for parasite survival, to be the putative intracellular target of compound 1 using a chemical proteomics approach. This finding was confirmed by RNA interference experiments showing that down-regulation of adenosine kinase counteracts compound 1 activity. Further chemical validation demonstrated that compound 1 interacts specifically and tightly with TbrAK with nanomolar affinity, and in vitro activity measurements showed that compound 1 is an enhancer of TbrAK activity. The subsequent kinetic analysis provided strong evidence that the observed hyperactivation of TbrAK is due to the abolishment of the intrinsic substrate-inhibition. CONCLUSIONS/SIGNIFICANCE: The results suggest that TbrAK is the putative target of this compound, and that hyperactivation of TbrAK may represent a novel therapeutic strategy for the development of trypanocides.

A 6'-Fluoro-Substituent in Bicyclo-DNA Increases Affinity to Complementary RNA Presumably by CF-HC Pseudohydrogen Bonds

The synthesis of a novel bicyclic thymidine analogue carrying a β-fluoro substituent at C6' (6'F-bcT) has been achieved. Key steps of the synthesis were an electrophilic fluorination/stereospecific hydrogenation sequence of a bicyclo sugar intermediate, followed by an N-iodo-succinimide-induced stereoselective nucleosidation. A corresponding phosphoramidite building block was then prepared and used for oligonucleotide synthesis. Tm measurements of oligonucleotides with single and double incorporations showed a remarkable stabilization of duplex formation particularly with RNA as complement without compromising pairing selectivity. Increases in Tm were in the range of +1-2 °C compared to thymidine and +1-3 °C compared to a standard bc-T residue. Structural investigations of the 6'F-bcT nucleoside by X-ray crystallography showed an in-line arrangement of the fluorine substituent with H6 of thymine, however, with a distance that is relatively long for a nonclassical CF-HC hydrogen bond. In contrast, structural investigations in solution by (1)H and (13)C NMR clearly showed scalar coupling of fluorine with H6 and C6 of the nucleobase, indicating the existence of at least weak electrostatic interactions. On the basis of these results, we put forward the hypothesis that these weak CF-HC6 electrostatic interactions increase duplex stability by orienting and partially freezing torsion angle χ of the 6'F-bcT nucleoside.

Synthesis of photo-crosslinking probes and their application for the site-selective chemical modification of the 5-HT3 receptor

The 5-HT3 receptor (5-HT3R) is an important ion channel responsible for the transmission of nerve impulses in the CNS and PNS that is activated by the endogenous agonist serotonin (5-hydroxytryptamine, 5-HT). 5-HT3R is the only serotonin receptor belonging to the Cys-loop superfamily of neurotransmitter receptors. Different structural biology approaches can be applied, such as crystallization and x-ray analysis. Nonetheless, characterizing the exact ligand binding site(s) of these dynamic receptors is still challenging. The use of photo-crosslinking probes is an alternative validated approach allowing identification of regions in the protein that are important for the binding of small molecules. We designed our probes based on the core structure of the 5-HT3R antagonist granisetron, a FDA approved drug used for the treatment of chemotherapy-induced nausea and vomiting. We synthesized a small library of photo-crosslinking probes by conjugating diazirines and benzophenones via various linkers to granisetron. We were able to obtain several compounds with diverse linker lengths and different photo-crosslinking moieties that show nanomolar binding affinity for the orthosteric binding site. Furthermore we established a stable h5-HT3R expressing cell line and a purification protocol to yield the receptor in a high purity. Several experiments showed unambiguously that we are able to photo-crosslink our probes with the receptor site-specifically. The functionalised protein was analysed by Western blot and MS-analysis. This yielded the exact covalent modification site, corroborating current ligand binding models derived from mutagenesis and docking studies.

Age and chemical composition of magmatic rocks from the Belkovsky Island, New Siberian Islands

The study was inspired by information on Paleozoic andesites, dacites, and diabases on the Belkovsky Island in the 1974 geological survey reports used to reconstruct tectonic evolution of the continental block comprising the New Siberian Islands and the bordering shelf. We did not find felsic volcanics or Middle Paleozoic intrusions in the studied area of the island. Igneous rocks are mafic subvolcanic intrusions including dikes, randomly shaped bodies, explosion breccias, and peperites. They belong to the tholeiitic series and are similar to Siberian traps in petrography and trace-element compositions, with high LREE and LILE and prominent Nb negative anomalies. The island arc affinity is due to continental crust contamination of mantle magma and its long evolution in chambers at different depths. K-Ar biotite age (252+/-5 Ma) of magmatism indicates that it was coeval to the main stage of trap magmatism in the Siberian craton at the Permian-Triassic boundary. The terrane including the New Siberian Islands occurred on the periphery of the Siberian trap province where magmatism acted in rifting environment. Magma intruded into semiliquid wet sediments at shallow depths shortly after their deposition. Therefore, the exposed Paleozoic section in Belkovsky Island may include Permian or possibly Lower Triassic sediments of younger ages than it was believed earlier.

Chemical and Sr isotopic compositions of pore fluids and marine carbonates from ODP Hole 130-807A

The 87Sr/86Sr ratios and Sr concentrations in sediment and pore fluids are used to evaluate the rates of calcite recrystallization at ODP Site 807A on the Ontong Java Plateau, an 800-meter thick section of carbonate ooze and chalk. A numerical model is used to evaluate the pore fluid chemistry and Sr isotopes in an accumulating section. The deduced calcite recrystallization rate is 2% per million years (%/Myr) near the top of the section and decreases systematically in older parts of the section such that the rate is close to 0.1/age (in years). The deduced recrystallization rates have important implications for the interpretation of Ca and Mg concentration profiles in the pore fluids. The effect of calcite recrystallization on pore fluid chemistry is described by the reaction length, L, which varies by element, and depends on the concentration in pore fluid and solid. When L is small compared to the thickness of the sedimentary section, the pore fluid concentration is controlled by equilibrium or steady-state exchange with the solid phase, except within a distance L of the sediment-water interface. When L is large relative to the thickness of sediment, the pore fluid concentration is mostly controlled by the boundary conditions and diffusion. The values of L for Ca, Sr, and Mg are of order 15, 150, and 1500 meters, respectively. L_Sr is derived from isotopic data and modeling, and allows us to infer the values of L_Ca and L_Mg. The small value for L_Ca indicates that pore fluid Ca concentrations, which gradually increase down section, must be equilibrium values that are maintained by solution-precipitation exchange with calcite and do not reflect Ca sources within or below the sediment column. The pore fluid Ca measurements and measured alkalinity allow us to calculate the in situ pH in the pore fluids, which decreases from 7.6 near the sediment-water interface to 7.1+/-0.1 at 400-800 mbsf. While the calculated pH values are in agreement with some of the values measured during ODP Leg 130, most of the measurements are artifacts. The large value for L_Mg indicates that the pore fluid Mg concentrations at 807A are not controlled by calcite-fluid equilibrium but instead are determined by the changing Mg concentration of seawater during deposition, modified by aqueous diffusion in the pore fluids. We use the pore fluid Mg concentration profile at Site 807A to retrieve a global record for seawater Mg over the past 35 Myr, which shows that seawater Mg has increased rapidly over the past 10 Myr, rather than gradually over the past 60 Myr. This observation suggests that the Cenozoic rise in seawater Mg is controlled by continental weathering inputs rather than by exchange with oceanic crust. The relationship determined between reaction rate and age in silicates and carbonates is strikingly similar, which suggests that reaction affinity is not the primary determinant of silicate dissolution rates in nature.

Isotopic and chemical compositions of lower crust rocks and minerals from ODP Hole 176-735B

The composition of gabbroic rocks from the drill core of Hole 735B (ODP Leg 176) at the 11 Ma Atlantis II bank close to the slow spreading Southwest Indian Ridge (SWIR) has been analyzed for major and trace elements and Sr, Nd and Pb isotopic composition. The samples are thought to represent much of the mineralogical and geochemical variation in a vertical 1-km section (500-1500 m below the sea floor) of the lower ocean crust. Primitive troctolitic gabbros, olivine gabbros and gabbros that have Mg#=84-70, Ca#>61 and low Na# (Na/(Na+Al)) (8-17) are intruded by patches or veins of more evolved FeTi-oxide rich gabbroic and dioritic rocks with Mg# to 20, Ca# to 32, Na#=14-23, TiO2<7 wt.% and FeOtotal<18 wt.%. All rocks are acdcumulates, and incompatible element concentrations are low, e.g. Pb=0.1-0.7 ppm and Uaffinity to old depleted mantle (DM). The isotopic composition of the magmas parental to the FeTi-oxide rich rocks cannot be distinguished from the magmas parental to the primitive gabbros and an intimate relationship is indicated. The small-scale inhomogeneity indicated for the SWIR MORB-mantle at the Atlantis II Fracture Zone was probably inherited by the lower crustal rocks due to small-scale melting and monogenetic magma chambers at this slow spreading ridge.

Petrographic and chemical characteristics of diabases at DSDP Holes 63-469 and 63-471

Diabasic rocks were recovered at Sites 469 and 471 on IPOD/DSDP Leg 63. The diabasic rocks are composed mainly of Plagioclase, clinopyroxene, and low-temperature alteration products. In addition to these phases, a considerable amount of primary biotite and lesser colorless amphibole are observed in some of the Site 471 diabases. Major and trace element data suggest that these rocks are tholeiitic; however, their highly altered nature obscures their petrologic affinity with the DSDP Leg 63 tholeiitic basalts and others from the nearby Pacific ocean floor. It is likely that the Site 469 and 471 diabasic rocks represent products of off-ridge intrusive activity.

Phage display of a catalytic antibody to optimize affinity for transition-state analog binding

Catalytic antibodies have shown great promise for catalyzing a tremendously diverse set of natural and unnatural chemical transformations. However, few catalytic antibodies have efficiencies that approach those of natural enzymes. In principle, random mutagenesis procedures such as phage display could be used to improve the catalytic activities of existing antibodies; however, these studies have been hampered by difficulties in the recombinant expression of antibodies. Here, we have grafted the antigen binding loops from a murine-derived catalytic antibody, 17E8, onto a human antibody framework in an effort to overcome difficulties associated with recombinant expression and phage display of this antibody. “Humanized” 17E8 retained similar catalytic and hapten binding properties as the murine antibody while levels of functional Fab displayed on phage were 200-fold higher than for a murine variable region/human constant region chimeric Fab. This construct was used to prepare combinatorial libraries. Affinity panning of these resulted in the selection of variants with 2- to 8-fold improvements in binding affinity for a phosphonate transition-state analog. Surprisingly, none of the affinity-matured variants was more catalytically active than the parent antibody and some were significantly less active. By contrast, a weaker binding variant was identified with 2-fold greater catalytic activity and incorporation of a single substitution (Tyr-100aH → Asn) from this variant into the parent antibody led to a 5-fold increase in catalytic efficiency. Thus, phage display methods can be readily used to optimize binding of catalytic antibodies to transition-state analogs, and when used in conjunction with limited screening for catalysis can identify variants with higher catalytic efficiencies.

High-affinity binding of bioactive glycosylation-inhibiting factor to antigen-primed T cells and natural killer cells

High-affinity binding was demonstrated between suppressor-T-cell-derived bioactive glycosylation-inhibiting factor (GIF) and helper T hybridomas and natural killer cell line cells. Inactive GIF present in cytosol of suppressor T cells and Escherichia coli-derived recombinant human GIF (rhGIF) failed to bind to these cells. However, affinity of rhGIF for the target cells was generated by replacement of Cys-57 in the sequence with Ala or of Asn-106 with Ser or binding of 5-thio-2-nitrobenzoic acid to Cys-60 in the molecule. Such mutations and the chemical modification of rhGIF synergistically increased the affinity of GIF molecules for the target cells. The results indicated that receptors on the target cells recognize conformational structures of bioactive GIF. Equilibrium dissociation constant (Kd) of the specific binding between bioactive rGIF derivatives and high-affinity receptors was 10–100 pM. Receptors for bioactive GIF derivatives were detected on Th1 and Th2 T helper clones and natural killer NK1.1+ cells in normal spleen but not on naive T or B cells. Neither the inactive rGIF nor bioactive rGIF derivatives bound to macrophage and monocyte lines or induced macrophages for tumor necrosis factor α production.

High-Affinity Binding Of The AP-1 Adaptor Complex to Trans-Golgi Network Membranes Devoid Of Mannose 6-Phosphate Receptors

The GTP-binding protein ADP-ribosylation factor (ARF) initiates clathrin-coat assembly at the trans-Goli network (TGN) by generating high-affinity membrane-binding sites for the AP-1 adaptor complex. Both transmembrane proteins, which are sorted into the assembling coated bud, and novel docking proteins have been suggested to be partners with GTP-bound ARF in generating the AP-1-docking sites. The best characterized, and probably the major transmembrane molecules sorted into the clathrin-coated vesicles that form on the TGN, are the mannose 6-phosphate receptors (MPRs). Here, we have examined the role of the MPRs in the AP-1 recruitment process by comparing fibroblasts derived from embryos of either normal or MPR-negative animals. Despite major alterations to the lysosome compartment in the MPR-deficient cells, the steady-state distribution of AP-1 at the TGN is comparable to that of normal cells. Golgi-enriched membranes prepared from the receptor-negative cells also display an apparently normal capacity to recruit AP-1 in vitro in the presence of ARF and either GTP or GTPγS. The AP-1 adaptor is recruited specifically onto the TGN and not onto the numerous abnormal membrane elements that accumulate within the MPR-negative fibroblasts. AP-1 bound to TGN membranes from either normal or MPR-negative fibroblasts is fully resistant to chemical extraction with 1 M Tris-HCl, pH 7, indicating that the adaptor binds to both membrane types with high affinity. The only difference we do note between the Golgi prepared from the MPR-deficient cells and the normal cells is that AP-1 recruited onto the receptor-lacking membranes in the presence of ARF1·GTP is consistently more resistant to extraction with Tris. Because sensitivity to Tris extraction correlates well with nucleotide hydrolysis, this finding might suggest a possible link between MPR sorting and ARF GAP regulation. We conclude that the MPRs are not essential determinants in the initial steps of AP-1 binding to the TGN but, instead, they may play a regulatory role in clathrin-coated vesicle formation by affecting ARF·GTP hydrolysis.