Hydroquinone-O,O'-diacetic acid ('Q-linker') as a replacement for succinyl and oxalyl linker arms in solid phase oligonucleotide synthesis.

When hydroquinone-O,Ooffiacetic acid is used as a linker arm in solid phase oligonucleotide synthesis, the time for NH4OH cleavage of oligodeoxy- or oligoribonucleotides is reduced to only 2 min. This allows increased productivity on automated DNA synthesizers without requiring any other modifications to existing reagents or synthesis and deprotection methods. The Q-linker may also be rapidly cleaved by milder reagents such as 5% NH4OH, potassium carbonate, anhydrous ammonia, t-butylamine or fluoride ion. However, the Q-linker is sufficiently stable for long-term storage at room temperature without degradation and no loss of material occurs during synthesis. The linker is also reasonably resistant to 20% piperidine/DMF, 0.5 M DBU/pyridine and 1:1 triethylamine/ethanol. The Q-linker can therefore serve as a general replacement for both succinyl and oxalyl linker arms.     

A solid support with a hydroxyallyl linker, full parts of which are potentially reusable for the synthesis of oligonucleotides

This paper describes a solid support with a hydroxyallyl linker that is regenerated without loss of any parts after having used for the synthesis of nucleotides. Reproduction of the solid support can be achieved through detachment of the oligonucleotide by treatment with an organopalladium catalyst in the presence of triethylammonium acetate and subsequent methanolysis of the resulting allyl acetate.     

Multiple peptide synthesis using a single support (MPS3)

An automated multiple peptide synthesis method to synthesize, cleave, and purify several peptides simultaneously in a single batch has been developed. The technique is based on the synthesis of multiple peptides on a single solid phase support and is easily adapted to manual or to automated methods. The approach relies on coupling of amino acid mixtures to the resin and it has been found that DCC/HOBt gives the best coupling performance. Fast Atom Bombardment Mass Spectrometry (FAB-MS) was used to rapidly and efficiently identify the peptides in each synthetic mixture which significantly assisted the purification process by HPLC. The method has been successfully applied to the synthesis of magainin 2 and angiotensinogen peptides.     

Laccase-poly(lactic-co-glycolic acid) (PLGA) nanofiber: highly stable, reusable, and efficacious for the transformation of diclofenac

Nanobiocatalysis has received growing attention for use in commercial applications. We investigated the efficiency, stability, and reusability of laccase-poly(lactic-co-glycolic acid) (PLGA) nanofiber for diclofenac transformation. NH stretching vibrations (3400-3500 cm(-1) and 1560 cm(-1)) in FT-IR spectra confirmed immobilization of laccase on PLGA nanofibers. The relative activity of immobilized laccase was 82% that of free laccase. Immobilized laccase had better storage, pH, and thermal stability than free laccase. The immobilized laccase produced complete diclofenac transformation in three reuse cycles, which was extended to 6 cycles in the presence of syringaldehyde. Results suggest that laccase-PLGA nanofiber may be useful for removing diclofenac from aqueous sources and has potential for other commercial applications.     

Backbone amide linker (BAL) strategy for Nalpha-9-fluorenylmethoxycarbonyl (Fmoc) solid-phase synthesis of peptide aldehydes.

A rapid and efficient strategy has been developed for the general synthesis of complex peptide aldehydes. N(alpha)-Benzyloxycarbonylamino acids were converted to protected aldehyde building blocks for solid-phase synthesis in four steps and moderate overall yields. The aldehydes were protected as 1,3-dioxolanes except for one case where a dimethyl acetal was used. These protected amino aldehyde monomers were then incorporated onto 5-[(2 or 4)-formyl-3,5-dimethoxyphenoxy]butyryl-resin (BAL-PEG-PS) by reductive amination, following which the penultimate residue was introduced by HATU-mediated acylation. The resultant resin-bound dipeptide unit, anchored by a backbone amide linkage (BAL), was extended further by routine Fmoc chemistry procedures. Several model peptide aldehydes were prepared in good yields and purities. Some epimerization of the C-terminal residue occurred (10% to 25%), due to the intrinsic stereolability conferred by the aldehyde functional group, rather than any drawbacks to the synthesis procedure.     

Controlled porous glass (CPG) with reactive epoxy groups as support for affinity chromatography I. Optimization of CPG modification and the binding of glucose with modified surface

The selective and complementary interaction between the ligand bound to support surface and isolated substance is the key of the affinity chromatography. This is the reason of the research in the field of certain sorbents. They are obtained by chemical reaction of matrix with proper ligands. It is carried out mainly by using bifunctional substances which make the reaction with the ligand in question possible. This paper deals with the preparation of controlled porosity glass with reactive epoxy groups. In order to obtain such support and avoid application of a proper epoxy silane compound, the double-step reaction using simple agents was employed. The sorbent syntheses were optimized. The prepared sorbents were applied for coupling some carbohydrates and amino acids.     

A support for affinity chromatography that covalently binds amino groups via a cleavable connector arm.

The preparation of a new succinimidyl ester agarose derivative (SEPE-Agarose) is described. This agarose derivative can be used for covalently linking proteins and other ligands containing amino groups to agarose via phenyl ester linkages that can later be broken under mild conditions which should not alter other groups which may be present in proteins such as cystinyl residues and glycosyl residues. SEPE-Agarose is prepared by the reaction of bis[4-[2-(N-succinimidoxycarbonyl)ethyl]phenyl]succinate with an aminoethylcarbamylmethyl derivative of agarose. Studies of the covalent binding and release of trypsin and myoglobin to SEPE-Agarose indicate that gels containing 0.1 to 0.6 μmol protein/ml of gel are obtained by reacting protein (0.5–5 mg/ml) with the N-succinimidyl ester groups in SEPE-Agarose. Protein-linked gel is reasonably stable in dilute phosphate buffers (pH ≤ 7.4, ≤ 25 °C). Protein is released from the gel, however, by treatment at 25 °C with solutions containing nucleophiles such as 1 m imidazole-glycine, pH 7.4, for 4 h, or 1 m hydroxylamine, pH 7, for 10 min. Protein is also released from the gel by treatment with 1 m Tris pH 8.2 for 24 h. SEPE-Agarose should prove useful in affinity chromatography and immunoabsorption when it is difficult or impractical to elute material bound to conventional affinity supports.     

Solvent-free synthesis of a Pd(II) coordination networked complex as reusable catalyst based on 3,5-bis(diphenylphosphino)benzoic acid

3,5-bis(diphenylphosphino)benzoic acid (LH) reacted with Pd(COD)Cl₂ to give [Pd(μ-LH)Cl₂]₂ (1) in which the Cl ligands are trans. Solventless grinding of 1 and ferric nitrate yielded an insoluble networked Pd-phosphine complex [LPdCl₂Fe_2/3]_∞ (2), in which Fe atom bonds to the carboxylate group of LH. The networked complex 2 has been characterized by using FT-IR, X-ray photoelectron spectroscopy (XPS), scanning electron microscope (SEM), and BET surface area analysis. Complex 2 efficiently catalyzed the Suzuki coupling reactions and could be reused under ambient atmosphere.     

Allosteric kidney-type glutaminase (GLS) inhibitors with a mercaptoethyl linker

A series of allosteric kidney-type glutaminase (GLS) inhibitors possessing a mercaptoethyl (SCH₂CH₂) linker were synthesized in an effort to further expand the structural diversity of chemotypes derived from bis-2-(5-phenylacetamido-1,3,4-thiadiazol-2-yl)ethyl sulfide (BPTES), a prototype allosteric inhibitor of GLS. BPTES analog 3a with a mercaptoethyl linker between the two thiadiazole rings was found to potently inhibit GLS with an IC₅₀ value of 50 nM. Interestingly, the corresponding derivative with an n-propyl (CH₂CH₂CH₂) linker showed substantially lower inhibitory potency (IC₅₀ = 2.3 μM) while the derivative with a dimethylsulfide (CH₂SCH₂) linker showed no inhibitory activity at concentrations up to 100 μM, underscoring the critical role played by the mercaptoethyl linker in the high affinity binding to the allosteric site of GLS. Additional mercaptoethyl-linked compounds were synthesized and tested as GLS inhibitors to further explore SAR within this scaffold including derivatives possessing a pyridazine as a replacement for one of the two thiadiazole moiety.     

Tri(propylene glycol) glycerolate diacrylate cross-linked polystyrene: a new resin support for solid-phase peptide synthesis.

A highly flexible, mechanically and chemically stable copolymer, tri(propylene glycol) glycerolate diacrylate cross-linked polystyrene (PS-TRPGGDA), was synthesized by the suspension polymerization and employed as a solid support for peptide synthesis. The beaded polymer support containing secondary hydroxyl functional groups in the cross-linker was used as the growth site for peptide synthesis. The procedure is unique and cost-effective in that it avoids the initial functionalization steps required for most of the styrene-based polymer supports. The resin was characterized by 13C-CP-MAS NMR spectroscopy and the morphologic features of the resin were investigated using scanning electron microscopy. Swelling studies conducted on the new support revealed that the PS-TRPGGDA resin undergoes more effective swelling and solvation than PS-DVB resin in all solvents used in peptide synthesis. The efficiency of the new support was demonstrated by synthesizing a 'difficult' sequence Ala-Arg-(Ala)6-Lys and comparing it with commercially available Merrifield and Sheppard resins. The synthetic efficiency was further demonstrated by the synthesis of a 24-residue NR 2A peptide substrate of calcium/calmodulin-binding peptide. The high yield and purity of the peptide synthesized on the novel support indicates the positive role of the flexible and hydrophilic cross-linking agent in the solid support.     

A study on the effects of linker flexibility on acid phosphatase PhoC-GFP fusion protein using a novel linker library

Fusion strategy has been widely used to construct artificial multifunction proteins. The flexibility or rigidity of linkers between two fused partners is an important parameter that affects the function of fusion proteins. By combining the flexible unit GGGGS (F) and rigid unit EAAAK (R), ten linkers consisting of five elementary units that cover the fully rigid RRRRR linker to the fully flexible FFFFF linker were used to construct acid phosphatase-green fluorescence protein fusion protein (PhoC-GFP). By varying the linker flexibility in PhoC-GFPs, the relative specific activity of phosphotransferase and phosphatase varied from ∼19.0% to 100% and ∼9.35% to 100%, respectively. There exists an optimal linker capable of achieving the highest phosphotransferase/phosphatase activity and GFP fluorescence intensity. We found that the highest activities were achieved neither with the rigid RRRRR linker nor with the flexible FFFFF linker, but with the FFFRR linker. Linker flexibility could adjust the activity ratio between phosphotransferase and phosphatase and varied between ∼30% to 100%. PhoC-GFP with FRRRR linker achieved the highest relative specific phosphotransferase activity/relative specific phosphatase activity (T/P) value. Our results show that applying a linker library with controllable flexibility to the fusion proteins will be an efficient way to adjust the function of fusion enzymes.     

The binding of zinc (II) to a double-stranded oligodeoxyribonucleotide. A voltammetric study

Binding of zinc to a 19 mer double-stranded oligodeoxyribonucleotide was investigated by anodic stripping voltammetry and cyclic voltammetry in order to understand the roles of zinc in DNA cleavage catalyzed by mung bean nuclease. These methods rely on the direct monitoring of zinc oxidation current in the absence and in the presence of the oligo. Zinc titration curves with the ds-oligodeoxyribonucleotide were obtained in concentrations ranging from 3.62 x 10(-9) to 3.62 x 10(-8) M and 4.06 x 10(-10) to 5.25 x 10(-9) M. The acquired data were used to determine the dissociation constant, stoichiometry and zinc binding sites of the complex and to understand the specific changes of ds-oligodeoxyribonucleotide secondary structure by zinc binding. The oxidation-reduction process of zinc was also investigated by cyclic voltammetry through I (oxidation current) versus v(1/2) (square root of scan rate) curves in the absence and in the presence of the double-stranded oligodeoxyribonucleotide.     

Application of Mitsunobu reaction to solid-phase peptide nucleic acid (PNA) monomer synthesis

PNA type I monomer backbone with a reduced peptide bond was synthesized on a Merrifield resin in Mitsunobu reaction of Boc-aminoethanol with resin-bound o-nitrobenzenesulfonylglycine. The pseudodipeptide secondary amine group was deprotected by thiolysis and acylated with thymin-1-ylacetic acid. The monomer was released as a methyl ester. The procedure seems to be of general applicability and allows various modifications of PNA structure by using diverse alcohols and amino acid esters.     

Synthesis of Arg-Gly-Asp (RGD) sequence conjugated thermo-reversible gel via the PEG spacer arm as an extracellular matrix for a pheochromocytoma cell (PC12) culture

Adhesion molecules composed of Gly-Arg-Gly-Asp-Ser (GRGDS) peptides and cell recognition ligands were inculcated into thermo-reversible hydrogel composed of N-isopropylacrylamide, with a small amount of succinyl poly(ethylene glycol) (PEG) acrylate (MW 3400) used as a biomimetic extracellular matrix (ECM). The GRGDS-containing p(NiPAAm-co-PEG) copolymer gel was studied in vitro for its ability to promote cell spreading and to increase the viability of cells by introducing PEG spacers. Hydrogel lacking the adhesion molecules proved to be a poor ECM for adhesion, permitting only a 20% spread of the seeded cells after 10 days. When PEG spacer arms, immobilized by a peptide linkage, had been integrated into the hydrogel, conjugation of RGD promoted cell spread by 600% in a 10-day trial. In addition, in a serum-free medium, only GRGDS peptides conjugated with the spacer arm were able to promote cell spread. In terms of the cell viability, GRGDS peptides conjugated with the PEG-carrying copolymer gel specifically mediated cell spread. This result supports the theory that specific recognition is the result of interaction between the integrin families on the fibroblast, and the RGD sequence on the p(NiPAAm-co-PEG) copolymer gel.     

A novel and efficient method for synthetic carbohydrate conjugate vaccine preparation: synthesis of sialyl Tn-KLH conjugate using a 4-(4-N-maleimidomethyl) cyclohexane-1-carboxyl hydrazide (MMCCH) linker arm

STn (NeuAc26GalNAc-O-Ser/Thr) is a carbohydrate epitope overexpressed in various human carcinomas. Clinical trials are underway using synthetic STn or STn trimeric glycopeptides [STn, cluster; STn(c) conjugated with keyhole limpet hemocyanin (KLH) as active specific immunotherapy for these cancers. These vaccines have been prepared by conjugating a crotyl ethyl amide derivative of STn or STn(c) to KLH by direct reductive amination after ozonolysis. In the case of STn(c) the conjugation efficiency and the resulting epitope ratios were low. This may be due to steric hinderance of the short spacer arm. To overcome these difficulties, without resynthesis, the STn(c) glycopeptide was modified by attachment of an MMCCH (4-(4-N-maleimidomethyl) cyclohexane-1-carboxyl hydrazide) spacer arm to the aldehyde derivative, and then conjugated with thiolated KLH. This method gave a higher epitope ratio and yield than the direct method. The STn(c)-MMCCH-KLH conjugate induced high titer antibodies in mice against STn(c). This method may be generally applicable for large synthetic oligosaccharides.     

Comparison of two solid-phase peptide syntheses of a 32-amino acid carboxyl-terminal fragment of human parathyroid hormone,hPTH-(53–84)

Two approaches were employed in separate syntheses of the carboxyl-terminal third of human parathyroid hormone, hPTH-(53–84). The standard N,N′-dicychohexylcarbodiimide coupling method was compared to amino acid incorporation using in situ and preformed symmetrical anhydrides of tert-butoxycarbonyl-amino acids. Also, protection of the δ-carboxyl function of glutamic acid by the benzyl group was compared to protection by the chlorobenzyl group. The products of both synthetic strategies were chemically evaluated. The purified synthetic hormone fragment prepared by standard methods was found to be homogeneous and virtually identical to the native carboxyl-terminal region of the hormone by the analytical criteria employed. However, the synthetic product resulting from use of symmetrical anhydrides was heterogeneous. Also, several practical advantages were noted for amino acid incorporation by the standard method. Since the symmetrical anhydride method has been found to be extremely successful as an approach to the synthesis of other peptides, this report indicates that the choice of symmetrical anhydride versus standard coupling methods may in part be determined by the sequence selected for synthesis. In addition, both approaches produced a large number of side products. Hence, methods selected for purification of the desired product were essential to the successful preparation of this synthetic peptide.