Synthesis of N-protected peptides by the o-nitrophenylsulfenyl group using o-nitrophenylsulfenyl N-carboxy α-amino acid anhydrides

N-protected peptides, which are important intermediates as a carboxyl component in the fragment condensation method, have been prepared in high yields by the reaction of o-nitrophenylsulfenyl (Nps) N-carboxy α-amino acid anhydrides with unprotected peptides and amino acids in aqueous organic systems. An Nps hexapeptide ester was prepared by the fragment condensation of an Nps tripeptide with a tripeptide ester. It was demonstrated that the synthesis of unprotected peptides by the NCA method, followed by N-protection by the Nps-NCA, is a rapid and very useful method for preparing Nps peptides.     

Solid-phase peptide synthesis using tert.-butyloxycarbonylamino acid pentafluorophenyl esters

Boc-amino acid pentafluorophenyl esters have been successfully used in solid-phase peptide synthesis. The coupling rates and the purity of the products are comparable to those with the symmetrical anhydrides. These active esters require modified Merrifield resin, polar medium for coupling and in some cases, base catalysis.     

Potentially prebiotic syntheses of condensed phosphates

In view of the importance of a prebiotic source of high energy phosphates, we have investigated a number of potentially prebiotic processes to produce condensed phosphates from orthophosphate and cyclic trimetaphosphate from tripolyphosphate. The reagents investigated include polymerizing nitriles, acid anhydrides, lactones, hexamethylene tetramine and carbon suboxide. A number of these processes give substantial yields of pyrophosphate from orthophosphate and trimetaphosphate from tripolyphosphate. Although these reactions may have been applicable in local areas, they are not sufficiently robust to have been of importance in the prebiotic open ocean.     

Synthesis of the oligodeoxyribonucleotide, d(CpTpGpGpApTpCpCpApG), and its substrate activity with the restriction endonuclease, BamHI

The synthesis of the DNA fragment, d(CpTpGpGpApTpCpCpApG), using a long-chain alkylamine-controlled pore glass bead polymer support, crystalline (9-phenyl-9-xanthenyl) nucleosides, and the bifunctional phosphorylating reagent, bis(1-benzotriazolyl)-2-chlorophenyl phosphate is described. For high coupling yields a mixed catalyst (1-methyl-imidazole + diisopropylethylamine) is required. The oligodeoxyribonucleotide shows activity with the DNA restriction endonuclease, BamHI. Kinetic parameters have been determined for the reaction.     

Stepwise synthesis of oligopeptides with N-carboxy alpha-amino acid anhydrides

Oligopeptides were synthesized in high yields by the controlled coupling reaction of N-carboxy α-amino acid anhydrides (NCA's) with amino acid and peptide sodium salts in the heterogeneous reaction medium of acetonitrile–water which contained sodium carbonate. In this solvent, it could be considered that the reaction could occur at the interface of acetonitrile and aqueous layers, and that NCA's could be protected by the organic layer from side reactions such as hydrolysis and polymerization. The careful control of reaction conditions such as pH of the solution was not necessary when the heterogeneous mixed solvent was used. Sodium carbonate which had not been used for a reaction of this kind could be satisfactorily used for stabilizing the carbamate intermediates in the aqueous layer of the heterogeneous reaction medium.     

Derivatization of controlled pore glass beads for solid phase oligonucleotide synthesis

An improved and simplified procedure for the attachment of nucleosides onto long chain alkylamine controlled pore glass beads (LCAA-CPG) is presented. This procedure uses 1-(3-dimethylamino-propyl)-3-ethylcarbodiimide (DEC) to couple nucleoside 3'-succinates directly to the LCAA-CPG. The preparation of nucleoside 3'-succinate anhydrides, p-nitrophenyl, or pentachlorophenyl esters and the use of highly toxic dicyclohexylcarbodiimide (DCC) is no longer required. Procedures involving acidic activation of the LCAA-CPG before derivatization and a pre-synthesis capping are also described, which prevent the formation of oligonucleotides linked by 3'-phosphates to the LCAA-CPG. Evidence is presented indicating that this type of linkage is responsible for the apparently greater than 100% coupling yields observed for the first coupling cycle.     

Homogeneous catalytic dehalodimerization of 17-iodo-Δ steroids

17-Iodo-Δ¹⁶ steroids undergo selective dimerization and carbonylative dimerization in the presence of palladium catalysts in dimethylformamide which result in 16–17′-coupled dienes and 17-carboxylic anhydrides, respectively. Moderate to good yields have been obtained for both types of dimers.     

Studies Towards the Synthesis of Peptide-Oligonucleotide Conjugates

Abstract

We describe a peptide fragment, solid-phase coupling strategy for synthesis of peptide-oligonucleotide conjugates. Model conjugates contained a hydrophobic tetrapeptide, a hydrophobic influenza virus fusion nonapeptide, or a basic octapeptide of the HIV-1 Tat protein coupled to either dT₁₂ or a 16-mer anti-Tat oligodeoxyribonucleotide. Conjugation yields were improved by removal of internucleotide 2-cyanoethyl groups prior to peptide coupling and by use of a C12 spacer between peptide and oligonucleotide.     

Chemical Conversion of Ribonucleoside 5′-S-Methyl Phosphorothiolates into Ribonucleotide Anhydrides Including Adenosine 5′-Triphosphate and Uridine Diphosphate Glucose

Ribonucleotide anhydrides have been prepared from corresponding ribonucleoside 5′-S-methyl phosphorothiolates by demethylthiolation with iodine in dry pyridine at room temperature in the presence of appropriate phosphates such as inorganic orthophosphate, inorganic pyrophosphate or glucose 1-phosphate. Thus synthesis of ribonucleotide anhydrides have been achieved and three ribonucleoside 5′-triphosphates (ATP, CTP and UTP), three ribonucleoside 5′-diphosphates (ADP, CDP and UDP) and a pyrophosphate coenzyme (UDPG) have been synthesized and isolated as lithium salts by charcoal treatment followed by ion exchange chromatography.     

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.     

An efficient synthesis of mixed acid phospholipids using 1-palmitoyl-sn-glycerol-3-phosphoric acid bromoalkyl esters

The preparation of mixed-acid phospholipids is possible in high yields from 1.2-dipalmitoyl-sn-glycerol-3-phosphoric acid bromoalkyl esters. The fatty acid in the 2-position of these general intermediates for phospholipid synthesis was completely removed by hyrolysis with phospholipase A₂. The resulting 1-palmitoyl-sn-glycerol-3-phosphoric acid bromoalkyl esters were reacylated in high yields with fatty acid anhydrides in the presence of perchloric acid. Transformation of the mixed-acid phosphatidic acid bromoalkyl esters to the respective phosphatidyl cholines or -ethanolamines was possible by direct amination.     

Real time monitoring of acylations during solid phase peptide synthesis: a method based on electrochemical detection

Monitoring of acylation reactions during solid phase peptide synthesis is important to ensure high coupling yields in all steps of the synthesis. We describe in this paper a simple and reliable method for monitoring the time course of the acylation steps as well as the washing and deprotection steps during computer-controlled solid phase peptide synthesis. The method is based on the continuous measurement of electrical conductivity in the reaction vessel. It is shown that there is a close correspondence between the degree of acylation (as determined from the amount of 9-fluorenylmethoxycarbonyl- (Fmoc) groups released during deprotection) and the conductivity profile obtained during coupling of the amino acids to the growing peptide chain. The measurements are fed back to the computer providing data for software control of the duration of the acylation, deprotection and washing steps. The method is demonstrated with pentafluorophenol esters, but is equally applicable to dihydroxybenzotriazole esters and symmetric anhydrides using the Fmoc-polyamide strategy in a continuous flow set-up with dimethylformamide (DMF) as the general solvent.     

Peptide synthesis using o-nitrophenylsulfenyl N-carboxy alpha-amino acid anhydrides. Sequential oligopeptides having alternate gamma-methyl L-glutamyl and L-phenylalanyl residues.

A series of sequential oligopeptides having the sequence alternating γ-methyl L -glutamyl and L -phenylalanyl residues have been successfully prepared by a rapid method involving the reaction of o-nitrophenylsulfenyl N-carboxy α-amino acid anhydrides with amino acid and peptide esters. The sequential oligopeptides, which are interesting from a conformational aspect, were obtained in optical pure forms above 74% yields. This result demonstrates that the o-nitrophenylsulfenyl N-carboxy α-amino acid anhydride method is especially useful for easy synthesis of protected oligopeptides with o-nitrophenylsulfenyl group.     

Estimation of apparent quadrupolar coupling constants for complexes of magnesium ions with mono- and dicarboxylic acid ligands. Applications to magnesium ion: protein interactions

25Mg+2 ion NMR studies of complexes of magnesium ions with acetate and malonate ligands have yielded apparent quadrupolar coupling constants, chi, of approximately 1.5 MHz. The aquo magnesium ion yields a smaller chi value of 0.12 MHz, consistent with its expected higher symmetry. chi values for magnesium ion: acetate and magnesium ion: malonate complexes are utilized to calculate observed linewidths for magnesium ion: bovine prothrombin fragment 1 and magnesium ion: human Factor XII interactions. These calculated values are compared with observed values and implications of the agreement are discussed.     

Synthesis and characterization of oligonucleotides containing conformationally constrained bicyclo[3.1.0]hexane pseudosugar analogs

Oligodeoxyribonucleotides containing pseudorotationally locked sites derived from bicyclo[3.1.0]hexane pseudosugars have been synthesized using adenosine, thymidine and abasic versions of North- and South-methanocarba nucleosides. The reaction conditions for coupling and oxidation steps of oligonucleotide synthesis have been investigated and optimized to allow efficient and facile solid-phase synthesis using phosphoramidite chemistry. Our studies demonstrate that the use of iodine for P(III) to P(V) oxidation leads to strand cleavage at the sites where the pseudosugar is North. In contrast, the same cleavage reaction was not observed in the case of South pseudosugars. Iodine oxidation generates a 5′-phosphate oligonucleotide fragment on the resin and releases the North pseudosugar into the solution. This side reaction, which is responsible for the extremely low yields observed for the incorporation of the North pseudosugar analogs, has been studied in detail and can be easily overcome by replacing iodine with t-butylhydroperoxide as oxidant.     

Solid-phase peptide synthesis by fragment condensation: Coupling in swelling volume

Summary The condensation of short peptides to resin-bound fragments was examined with respect to high coupling yields with only a small molar excess of a peptide in the reaction solution. The best results were achieved by the addition of reactants (C-unprotected peptide, DIC, and HOBt) dissolved in a so-called swelling volume of an appropriate solvent to a dry resin with an attached N-deprotected peptide chain. Each coupling step was followed by the end-capping of unreacted resin-bound peptide with 2,4-dinitrofluorobenzene. The substituted dinitroaniline chromophore formed in this reaction made the detection and separation of deletion peptides easy. Both conventional and ‘swelling volume’ methods were compared on parallel syntheses of the HIV-1 protease C-terminal 78–99 fragment. The yields of the isolated heneicosapeptide were 21 and 81% in favor of the ‘swelling volume’ procedure.     

Biomedicals from a soil bug: expanding scFv production host range

Recombinant antibody fragments have a wide range of applications from research to diagnostics and therapy. Of special interest are small fragments like fragment antigen binding (Fab) or single chain fragment variables (scFv) fragments as they can be produced inexpensively in bacterial expression systems. However, recombinant production efficiencies from established production hosts vary significantly leading to inadequate yields. Gene sequences that have been synthetically adapted to match the codon preferences and respective genomic tRNA pool of the host have been used to improve yields but cannot resolve the principal problem. The development of inducible broad host range scFv expression plasmid constructs leads the way to an easy and efficient screening method for the identification of the optimal bacterial expression host.     

Semisynthesis and purification of homogeneous plasmenylcholine molecular species.

Methods for the efficient use of limiting amounts of fatty acid probes in the synthesis of individual molecular species of plasmenylcholine have been developed. Plasmenylcholine molecular species were synthesized through acylation of homogeneous 1-O-(Z)-hexadec-1'-enyl-sn-glycero-3-phosphocholine utilizing fatty acid anhydrides generated in situ from combined pools of reactant and recycled fatty acids by repeated addition of small amounts (10 mol%) of N,N'-dicyclohexylcarbodiimide. The efficient generation of reactive anhydrides was accomplished through minimizing irreversible formation of N-acyl urea adducts by maintaining a persistent molar excess of fatty acid (with respect to carbodiimide) during the entire reaction time course. The synthesis of multiple different sn-2 labeled plasmenylcholine probes for utilization in fluorescence, ESR, or 2H NMR spectroscopy as well as isotopically labeled plasmenylcholines for metabolic studies has been achieved in good yield (40-50% of theoretical yield based on fatty acid) by these methods. Rapid and effective purification methods utilizing high-performance liquid chromatography were developed for both large- and small-scale purifications of individual reaction mixtures which collectively resulted in the isolation of homogeneous plasmenylcholine molecular species in high yield from limiting amounts of fatty acid probes.     

Synthesis of protected peptides with the sequence 8-13-1-3 and 4-13-1-3 of mycobacillin and their analogs

We have synthesized both a protected nonapeptide of the mycobacillin 8-13-1-3 amino acid sequence and a protected tridecapeptide of the 4-13-1-3 sequence, which are a fragment and a open chain analog of this antibiotic, respectively. Some of their analogs with a reversed configuration of the amino acids at fixed positions have also been synthesized. The nonapeptides were obtained by coupling partially protected mycobacillin fragments with the sequence 8-10 and 11-13-1-3 while the tridecapeptides were synthesized by coupling partially protected fragments 4-7 and 8-13-1-3. Configuration analogs of these fragments were also used. The coupling methods applied were DCCI/HONSu or DCCI/HOBt. The purification of the synthesized peptides was achieved by means of recrystallization or column chromatography on silica gel. They were characterized mainly by m.p., degree of optical rotation, elemental and amino acid analysis.     

Nucleoside H-Phosphonates. V. The Mechanism of Hydrogenphosphonate Diester Formation Using Acyl Chlorides as Coupling Agents in Oligonucleotide Synthesis by the Hydrogenphosphonate Approach

Abstract

The H-phosphono-acyl mixed anhydrides of type III were found to be the main intermediates during H-phosphonate diester formation using acyl chlorides as coupling agents in the reaction of hydrogenphosphonate monoesters with hydroxylic components.