Boc Solid-phase Peptide Synthesis Research Articles

4-Methyltrityl-Protected Pyrrole and Imidazole Building Blocks for Solid Phase Synthesis of DNA-Binding Polyamides.

DNA-binding polyamides are synthetic oligomers of pyrrole/imidazole units with high specificity and affinity for double-stranded DNA. To increase their synthetic diversity, we report a mild methodology based on 4-methyltrityl (Mtt) solid phase peptide synthesis (SPPS), whose building blocks are more accessible than the standard Fmoc and Boc SPPS ones. We demonstrate the robustness of the approach by preparing and studying a hairpin with all precursors. Importantly, our strategy is orthogonal and compatible with sensitive molecules and could be readily automated.

Anhydrous Hydrogen Fluoride Cleavage in Boc Solid Phase Peptide Synthesis.

Solid phase peptide synthesis using tert-butyloxycarbonyl/benzyl chemistry (Boc-SPPS) is important for producing peptides for fundamental research as well as for clinical use. During Boc-SPPS, liquid anhydrous hydrogen fluoride (HF) is used to remove the side chain protecting groups of the assembled peptide and to release it from the resin. Here, we provide a detailed protocol for "HF cleavage," aiming to improve accessibility and the use of this valuable and well-validated technique.

Total synthesis of Crotogossamide using an on-resin concomitant cyclization/cleavage reaction

Crotogossamide, a cyclic peptide isolated from the latex of Croton gossypifolius, has been synthesized by a rapid and efficient Boc solid-phase peptide synthesis. The strategy takes advantage of the oxime resin nucleophile susceptibility and comprises the synthesis of a linear precursor followed by on-resin head-to-tail concomitant cyclization/cleavage. In addition, we report the first antimicrobial and antibiofilm investigations on Crotogossamide.

Studies on the Precise Chemical Synthesis of Human Glycoproteins

Abstract Our research group demonstrated the semi-synthesis of complex-type biantennary sialyloligosaccharide-library by means of branch-specific glycosidase and several sialyltransferase reactions toward complex-type H2N-Asn-(biantennary compex-type sialyloligosaccharide)-COOH isolated from egg yolk at over a gram scale. This methodology yielded 35 kinds of homogeneous complex-type oligosaccharides. Using this oligosaccharide library, an efficient Boc solid phase peptide synthesis (SPPS) of acid labile sialylglycopeptide-α-thioester was demonstrated. Our research group showed that the sialoside in which the carboxylic acid is protected with a phenacyl group is stable under strong acidic conditions, and this critical finding enabled us to demonstrate the first Boc-SPPS for the synthesis of a sialylglycopeptide-α-thioester. Using both a synthetic method of sialylglycopeptide-α-thioester and native chemical ligation (NCL), our research group synthesized several glycoproteins such as chemokine MCP-3, three kinds of erythropoietin analogues, and interferon-ß. Our research group also demonstrated a unique synthesis that was an intentional synthesis of homogeneous misfolded glycoproteins bearing M9-high-mannose-type oligosaccharide. This unique synthetic misfolded-glycoprotein is useful for the purpose of uncovering the mechanism of molecular recognition in glycoprotein quality control (GQC) in the endoplasmic reticulum (ER). This account discusses the function of the oligosaccharides of glycoproteins based on our research findings.

Methods, setup and safe handling for anhydrous hydrogen fluoride cleavage in Boc solid-phase peptide synthesis.

Solid-phase peptide synthesis (SPPS) using tert-butyloxycarbonyl (Boc)/benzyl (Bzl) chemistry is an indispensable technique in many laboratories around the globe, and it provides peptides to the pharmaceutical industry and to thousands of scientists working in basic research. The Boc/Bzl strategy has several advantages, including reliability in the synthesis of long and difficult polypeptides, alternative orthogonality regarding protecting groups and ease of producing C-terminal thioesters for native chemical ligation applications. In this process, anhydrous hydrogen fluoride (HF) is used to remove the side chain protecting groups of the assembled peptide and to release the peptide from the resin, a process typically described as 'HF cleavage'. This protocol describes the general methodology, apparatus setup and safe handling of HF, with the aim of providing comprehensive information on the safe use of this valuable, well-studied and validated cleavage technique. We explain the cleavage mechanism, the physicochemical properties and risks of HF, first aid measures and the correct use of the apparatus. In addition, we provide advice on scavenger selection, as well as a troubleshooting section and video material illustrating key steps of the procedure. The protocol comprises precleavage sample preparation (30 min-2.5 h), complete HF cleavage procedure (2 h) and reaction workup (30 min).

Chemical synthesis of a pore-forming antimicrobial protein, caenopore-5, by using native chemical ligation at a glu-cys site.

The 2014 report from the World Health Organization (WHO) on antimicrobial resistance revealed an alarming rise in antibiotic resistance all around the world. Unlike classical antibiotics, with the exception of a few species, no acquired resistance towards antimicrobial peptides (AMPs) has been reported. Therefore, AMPs represent leads for the development of novel antibiotics. Caenopore-5 is constitutively expressed in the intestine of the nematode Caenorhabditis elegans and is a pore-forming AMP. The protein (82 amino acids) was successfully synthesised by using Boc solid-phase peptide synthesis and native chemical ligation. No γ-linked by-product was observed despite the use of a C-terminal Glu-thioester. The folding of the synthetic protein was confirmed by (1) H NMR spectroscopy and circular dichroism and compared with data recorded for recombinant caenopore-5. The permeabilisation activities of the protein and of shortened analogues were evaluated.

Preparation of truncated orf virus entry fusion complex proteins by chemical synthesis

Members of the Chordopoxvirinae subfamily possess an unusual 11 protein entry-fusion complex (EFC) that is highly conserved and present in all species. The mode of action of this EFC is unknown, and the interactions of the constituent proteins are uncharacterised. Here, we present the chemical synthesis of membrane domain truncated linear constructs of two EFC proteins in orf virus, ORFV036 and 049. By using Boc solid phase peptide synthesis and native chemical ligation methods, these truncated proteins have been readily prepared in milligram quantities. These robust synthetic protocols allow ready access to these polypeptides to facilitate biological studies.

Total Chemical Synthesis of an Orf Virus Protein, ORFV002, an Inhibitor of the Master Gene Regulator NF-κB.

ORFV002 is a novel orf viral protein (117 Aa) that inhibits nuclear events through the regulation of the transcriptional activity of NF-κB, a master regulator of human gene expression (Diel et al., J Virol 2011, 85, 264-275). It is identified as the first nuclear inhibitor of NF-κB produced by orf virus (ORFV) and no homologues in other genera of the Chordopoxvirinae subfamily have been reported to date (Diel et al., J Virol 2011, 85, 264-275). Our molecular structure predictions suggest that ORFV002 may mimic part of IκB, an inhibitor and natural human partner of NF-κB. Recent advances in total chemical synthesis of proteins have provided solutions in overcoming challenges of current recombinant methods of protein isolation for structure elucidation. Aided by Boc solid phase peptide synthesis and native chemical ligation, ORFV002 was successfully synthesized in multimilligram amounts in good yield and high purity.

Isolation, synthesis and characterization of ω-TRTX-Cc1a, a novel tarantula venom peptide that selectively targets L-type CaV channels

Spider venoms are replete with peptidic ion channel modulators, often with novel subtype selectivity, making them a rich source of pharmacological tools and drug leads. In a search for subtype-selective blockers of voltage-gated calcium (CaV) channels, we isolated and characterized a novel 39-residue peptide, ω-TRTX-Cc1a (Cc1a), from the venom of the tarantula Citharischius crawshayi (now Pelinobius muticus). Cc1a is 67% identical to the spider toxin ω-TRTX-Hg1a, an inhibitor of CaV2.3 channels. We assembled Cc1a using a combination of Boc solid-phase peptide synthesis and native chemical ligation. Oxidative folding yielded two stable, slowly interconverting isomers. Cc1a preferentially inhibited Ba2+ currents (IBa) mediated by L-type (CaV1.2 and CaV1.3) CaV channels heterologously expressed in Xenopus oocytes, with half-maximal inhibitory concentration (IC50) values of 825nM and 2.24μM, respectively. In rat dorsal root ganglion neurons, Cc1a inhibited IBa mediated by high voltage-activated CaV channels but did not affect low voltage-activated T-type CaV channels. Cc1a exhibited weak activity at NaV1.5 and NaV1.7 voltage-gated sodium (NaV) channels stably expressed in mammalian HEK or CHO cells, respectively. Experiments with modified Cc1a peptides, truncated at the N-terminus (ΔG1–E5) or C-terminus (ΔW35–V39), demonstrated that the N- and C-termini are important for voltage-gated ion channel modulation. We conclude that Cc1a represents a novel pharmacological tool for probing the structure and function of L-type CaV channels.

Safe and efficient Boc-SPPS for the synthesis of glycopeptide-α-thioesters.

Boc-solid phase peptide synthesis is useful for the preparation of peptide-α-thioesters. However, this strategy usually employs hydrogen fluoride for the final deprotection step. These strongly acidic conditions cannot be applied for the synthesis of acid-labile glycopeptide-α-thioesters. The protocol presented here is a modified in situ neutralization Boc-solid phase peptide synthesis employing 10% sulfuric acid/dioxane conditions for intermediate Boc removal and TfOH for the final side-chain deprotection step. These conditions were found to be applicable for the synthesis of acid-labile glycopeptide-α-thioesters. In this protocol, a glycopeptide is synthesized as α- thioester on a thiol linker, and the product glycopeptide-α-thioester is released from the resin by thiolysis after side-chain deprotection step with an acid cocktail containing TfOH instead of hydrogen fluoride.

Evaluation of COMU as a coupling reagent for in situ neutralization Boc solid phase peptide synthesis

Benzotriazole-based coupling reagents have dominated the last two decades of solid phase peptide synthesis. However, a growing interest in synthesizing complex peptides has stimulated the search for more efficient and low-cost coupling reagents, such as COMU which has been introduced as a nonexplosive alternative to the classic benzotriazole coupling reagents. Here, we present a comparative study of the coupling efficiency of COMU with the benzotriazole-based HBTU and HCTU for use in in situ neutralization Boc-SPPS. Difficult sequences, such as ACP(65-74), Jung-Redeman 10-mer, and HIV-1 PR(81-99), were used as model target peptides on polystyrene-based resins, as well as polyethylene glycol-based resins. Coupling yields obtained using fast in situ Boc-SPPS cycles were determined with the quantitative ninhydrin test as well as via LC-MS analysis of the crude cleavage products. Our results demonstrate that COMU coupling efficiency was less effective compared to HBTU and HCTU with HCTU ≥ HBTU > COMU, when polystyrene-based resins were employed. However, when the PEG resin was employed in combination with a safety catch amide (SCAL) linker, more comparable yields were observed for the three coupling reagents with the same ranking HCTU ≥ HBTU > COMU.

Chemical Synthesis and Structure of the Prokineticin Bv8

Bv8, a 77-residue protein isolated from frogs, is the prototypic member of the prokineticin family of cytokines. Prokineticins (PKs) have only recently been identified in vertebrates (including humans), and they are believed to be involved in a number of key physiological processes, such as angiogenesis, neurogenesis, nociception, and tissue development. We used a combination of Boc solid-phase peptide synthesis, native chemical ligation, and in vitro protein folding to establish robust chemical access to this molecule. Synthetic Bv8 was obtained in good yield and exhibited full activity in a human neuroblastoma cell line and rat dorsal root ganglion (DRG) neurons. The 3D structure of the synthetic protein was determined by using NMR spectroscopy and it was found to be homologous with that of mamba intestinal toxin 1, which is the only other known prokineticin structure. Analysis of a truncated mutant lacking five residues at the N terminus that are critical for receptor binding and activation showed no perturbation to the core protein structure. Together with the functional data, this suggests that receptor binding is likely to be a highly cooperative process possibly involving major allosterically driven structural rearrangements. The facile and efficient synthesis presented here will enable preparation of unique chemical analogues of prokineticins, which should be powerful tools for modulating the structure and function of prokineticins and their receptors, and studying the many physiological processes that have been linked to them.

Toward the total chemical synthesis of the cancer protein NY‐ESO‐1

During the course of developing a synthetic route for the cancer protein NY-ESO-1 using native chemical ligation, a number of the required thioester polypeptide fragments were unable to be synthesized effectively using Boc solid phase peptide synthesis. Modification of the SPPS protocols to include an arginine tag at the C terminus linked via the thioester resulted in a better purity profile and enhanced solubility, facilitating purification by HPLC. During preparation of another reactive partner for ligation that contained an internal Cys(Acm) residue by Fmoc SPPS, extensive loss of the Acm group occurred during cleavage from the resin while substitution with Cys(tBu) resulted in no loss of protecting group. It was shown that native chemical ligation of N-terminal cysteine peptide 155-180 containing the Cys(tBu) residue with thioester 140-154 was slow, incomplete and led to extensive HPLC column fouling. Subsequent incorporation of a C-terminal arginine tag into the N-terminal NY-ESO-1 155-180 fragment joined by a base labile 4-hydroxymethylbenzoic acid (HMBA) linker facilitated rapid quantitative ligation. The HMBA linker was demonstrated to be stable to the conditions required for native chemical ligation, subsequent transformations and final purification. Importantly it was effectively removed at pH=10.

Microwave‐assisted Boc‐solid phase peptide synthesis of cyclic cysteine‐rich peptides

In this study we describe the first protocols for the synthesis of cystine-rich peptides in the presence of microwave radiation with Boc-solid phase peptide synthesis (SPPS). This method is exemplified for macrocyclic peptides known as cyclotides, which comprise approximately 30 amino acids and incorporate a cystine knot arrangement of their three disulfide bonds. However, the method is broadly applicable for a wide range of peptides using Boc-SPPS, especially for SPPS of large peptides via native chemical ligation. Microwave radiation produces peptides in high yield and with high purity, and we were able to reduce the time for the assembly of approximately 30 mer peptide chains to an overnight reaction in the automated microwave-assisted synthesis.

Facile production of mono‐substituted urea side chains in solid phase peptide synthesis

A method is reported for the straightforward generation of urea-containing peptides during Boc solid phase peptide synthesis. Primary amine side chains are converted to mono-alkyl ureas in two steps via an intermediate p-nitrophenyl carbamate. Use of p-methoxybenzyl amine as an ammonia equivalent affords mono-alkyl final products from standard resin cleavage methods, without the need for additional steps. The reaction is highly efficient and applicable to variable length side chains and peptides.

Solid-phase synthesis of backbone-cyclized β-helical peptides

This paper describes the synthesis and purification of two 22-residue cyclic peptides, cyclo{[( l-Val- d-Val) 4-( l-Val- d-Pro-Gly)] 2-} 3 and cyclo{[( d-Leu- l-Leu) 4-( d-Leu- l-Pro-Gly)] 2-} 4, that were designed to fold into double-stranded antiparallel β-helical structures. Due to intramolecular hydrogen bonding and the conformational constraints imposed by the two reverse-turn segments ( d-Pro-Gly and l-Pro-Gly, respectively), the linear precursors to 3 and 4 (lin- 3 and lin- 4) were expected to adopt preorganized conformations that would bring the N and C termini close together and thereby favor ring closure. Precursors lin- 3 and lin- 4 were constructed by stepwise Boc solid-phase peptide synthesis using the commercially available alkanesulfonamide ‘safety-catch’ linker and cyclized head-to-tail via the method of cleavage-by-cyclization. The crude cyclic peptides were highly hydrophobic and contained minor impurities that could not be removed solely by reversed-phase HPLC (RP-HPLC); however, two-step purification—first by RP-HPLC with i-PrOH/water gradients, followed by gel-permeation chromatography (GPC) on Sephadex LH-20 with CHCl 3/MeOH—afforded both peptides in pure form (≥95% by 1H NMR) and in acceptable yield (23%). Subsequent 1H NMR experiments supported the expected structures of 3 and 4. The successful formation of the 66-membered rings of 3 and 4 is consistent with the notion of conformational preorganization in the linear precursors; furthermore, the protocols for synthesis and purification described should prove useful for preparing additional cyclic β-helical peptides, including longer peptides and peptides having polar residues.

Efficient introduction of protected guanidines in boc solid phase peptide synthesis.

[reaction: see text] Reaction of primary amines with pyrazole 1 results in rapid and efficient guanidinylation, either in solution or on solid phase. The reaction affords sulfonamide-protected products required for BOC solid phase peptide synthesis (SPPS) in a single step under mild conditions. Incorporation of orthogonally protected side chain amines permits the synthesis of peptides containing arginine analogues, one of which could not be prepared by coupling of preformed amino acids.

3] Cleavage methods following Boc-based solid-phase peptide synthesis

[3] Cleavage methods following Boc-based solid-phase peptide synthesis In solid-phase peptide synthesis (SPPS) using Boc (tert-butyloxycar bonyl) amino acids, peptide chains are linked to the resin supports as benzyl esters or by bonds of similar chemical stability, and side-chain functional groups are protected by groups of similar reactivity. Although anhydrous hydrogen fluoride (HF) is an inconvenient (it dissolves glass, is volatile) and toxic reagent, it has been used successfully in SPPS and is the cleavage reagent of choice in most cases. Methods have been developed to overcome the limitations of HF cleavage—such as unwanted side reactions with certain amino acids. If equipment for handling HF is not available, peptide-resins may be cleaved by using trifluoromethanesulfonic acid (TFMSA) or trifluoromethanesulfonic acid trimethylsilyl ester (TMSOTf), although these reagents may cause serious side reactions with some peptides. Much of the versatility of the Merrifield system of Boc SPPS lies in the fact that different reagents can be used to cleave the finished peptide from the resin, thus, yielding a variety of final products.

Protection of the indole ring of tryptophan by the nucleophile-stable, acid-cleavable Nin-2,4-dimethylpent-3-yloxycarbonyl (Doc) protecting group

The Nin-2,4-dimethylpent-3-yloxycarbonyl (Doc) group is presented as a new protecting group for tryptophan that is stable to nucleophiles and trifluoroacetic acid, suppresses alkylation side reactions and is cleaved by strong acid among with other protecting groups used in Boc solid phase peptide synthesis.