Novel cyclization chemistry especially suited for biologically derive unprotected peptides

A novel method is described for the cyclization of peptides - or segments of polypeptides - which requires a free A′-terminal α-amino group and a distal amino acid residue containing a nucleophilic side chain. The reaction is conducted in two steps, both in the aqueous phase. The first step involves acylation of the N-terminal α-amino group with iodoacetic anhydride at pH 6. This acylation reaction has >90% specificity for peptide α-amino groups and gives no alkylation of Arg, His, Lys or Met by the iodoacetate side product (R. Wetzel et al, Bioconjugate Chem., 1, 114-122, 1990). In the second step, the acylation reaction mixture or the isolated iodoacetyl-peptide is incubated at room temperature to give the cyclic peptide formed by reaction of the nucleophilic side chain with the iodoacetyl moiety. The pH dependence of the cyclization reaction by Met, Lys, Arg or His is consistent with the pK_a of the nucleophilic side chain. Thus, peptides containing Met plus other nucleophilic amino acids should preferentially cyclize via Met at low pH. In this paper, preparation of cyclic peptides containing 3-6 amino acids is described; the full range of ring sizes and sequences which can undergo this cyclization has not been further explored. Preliminary results suggest that this method is also fairly general with respect to the amino acid sequence being cyclized. The reaction appears to be particularly suited for cyclization via Lys and Met side chains. All of the cyclized products are sufficiently stable for many biological applications. However, peptides cyclized via Met slowly decompose at 37° with ring cleavage to yield a C-terminal lactone peptide in which the Met methylthio-group is effectively transferred to the JV-terminus. The reactions described here have several applications which take advantage of their unique ability to efficiently cyclize naturally-derived (as well as chemically synthesized) peptides in aqueous solution with little or no protection/deprotection chemistry.     

2-Chlorotrityl chloride resin

The esterification of 2-chlorotrityl chloride resin with Fmoc-amino acids in the presence of DIEA is studied under various conditions. High esterification yields are obtained using 0.6 equiv. Fmoc-amino acid/mmol resin in DCM or DCE, in 25 min, at room temperature. The reaction proceeds without by product formation even in the case of Fmoc-Asn and Fmoc-Gln. The quantitative and easy cleavage of amino acids and peptides from 2-chlorotrityl resin, by using AcOH/TFE/DCM mixtures, is accomplished within 15-60 min at room temperature, while t-butyl type protecting groups remain unaffected. Under these exceptionally mild conditions 2-chlorotrityl cations generated during the cleavage of amino acids and peptides from resin do not attack the nucleophilic side chains of Trp. Met, and Tyr.     

Peptide Stability in Drug Development. II. Effect of Single Amino Acid Substitution and Glycosylation on Peptide Reactivity in Human Serum

The determination of peptide stability in human serum (HS) or plasma constitutes a powerful screening assay for eliminating unstable peptides from further development. Herein we report on the stability in HS of several major histocompatibility complex (MHC)-binding peptides. Some of these peptides are in development for the novel treatment of selected autoimmune disorders such as rheumatoid arthritis and insulin-dependent diabetes. For most of the 1-amino acid peptides studied, the predominant degradation mechanism is exopeptidase-catalyzed cleavage. Peptides that were protected by d-amino acids at both termini were found to be more stable than predicted, based on additivity of single substitutions. In addition, N-acetylglucosamine glycopeptides were significantly stabilized, even when the glycosylation site was several amino acids from the predominant site(s) of cleavage. This indicates that long-range stabilization is possible, and likely due to altered peptide conformation. Finally, the effect of single amino acid substitutions on peptide stability in HS was determined using a model set of poly-Ala peptides which were protected from exopeptidase cleavage, allowing the study of endopeptidase cleavage pathways.     

cDNA sequence and in vitro folding of GsMTx4, a specific peptide inhibitor of mechanosensitive channels.

The peptide GsMTx4 from the tarantula venom (Grammostola spatulata) inhibits mechanosensitive ion channels. In this work, we report the cDNA sequence encoding GsMTx4. The gene is translated as a precursor protein of 80 amino acids. The first 21 amino acids are a predicted signal sequence and the C-terminal residues are a signal for amidation. An arginine residue adjacent to the N-terminal glycine of GsMTx4 is the cleavage site for release. The resulting peptide is 34 amino acids in length with a C-terminal phenylalanine and not a serine-alanine previously identified [J. Gen. Physiol. 115 (2000) 583]. We chemically synthesized this peptide and folded it in 0.1 M Tris, pH 7.9 with oxidized/reduced glutathione (1/10). Properties of the synthetic peptide were identical to the wild type for high performance liquid chromatography (HPLC), mass spectrometry, CD, and NMR. We also cloned GsMTx4 in a thioredoxin fusion protein system containing six histidines. Nickel affinity columns allowed rapid purification and folding occurred in conditions described above with 0.5 M guanidiniumHCl present. Thrombin cleavage liberated GsMTx4 with three extra amino acids at the N-terminus. The retention time in HPLC analysis and the CD spectrum was similar to wild type. Both the synthetic and cloned peptides were active in the patch clamp assay.     

Development of conformationally restricted analogues of bradykinin and somatostatin using constrained amino acids and different types of cyclization

The structure-based design of peptide drugs requires the knowledge of the bioactive conformation. Studies on this receptor-bound 3D structure require linear or cyclic analogues with strongly reduced flexibility, but high biological activity, since only analogues with retained potency have preserved the bioactive conformation. Constrained amino acids containing double bonds or bulky substituents at the N(alpha)-, C(alpha)- and C(beta)-atom as well as at the aromatic ring atom were successfully applied to obtain potent and stable analogues of bradykinin and somatostatin, which due to their restricted conformation were suitable objects for conformational studies. Besides the generation of constrained cyclic analogues with improved biological and pharmacological properties, cyclic peptides were used as convenient models for the study of turn formations. Cyclization of the linear peptide bradykinin was performed by linking the N-terminus and the C-terminus, and in both bradykinin and somatostatin by cyclization using the amino acid side chains and by backbone cyclization. The later requires the introduction of N(alpha)-functionalised amino acids for ring closure which can be performed either through incorporation of N(alpha)-functionalised amino acids or dipeptide building units. Conformational analysis of a cyclic bradykinin analogue by means of NMR-studies together with molecular dynamics simulation led to a quasicyclic 3D structure with two turns and together with other 3D structures provided a pharmacophore model of bradykinin antagonists.     

Effect of adjacent histidine and cysteine residues on the spontaneous degradation of asparaginyl- and aspartyl-containing peptides

Aspartate and asparagine residues in polypeptides are subject to nonenzymatic reactions that lead to deamidation, isomerization, peptide bond cleavage and racemization. Much of this reactivity is due to the propensity for the initial formation of a cyclic succinimide intermediate. We have been interested in determining the effect of the side chains of neighboring histidine and cysteine residues in facilitating these reactions, particularly in the possibility that they can act as general acids and bases. In this study, we found little or no effect of histidine residues preceding an asparagine residue in hexapeptides derived from the sequence of adrenocorticotropic hormone, while a histidine residue preceding an aspartic acid residue was found to increase the rate of succinimide formation 8- to 11-fold. The presence of a histidine residue following either an asparagine or aspartic acid residue did not effect the rate of succinimide formation by peptide-bond nitrogen attack, but did increase the rate of the competing side-chain nitrogen attack leading to cleavage in the asparaginyl-containing peptide. We found that the effect of a cysteine residue following an asparagine or aspartic acid residue was in general similar to that of a serine residue, although the cleavage reaction appeared to be enhanced. These results suggest that His-Asp sequences may be particularly labile to spontaneous degradation in proteins and peptides, possibly owing to the ability of the histidine residue to facilitate succinimide formation by protonating the OH^? leaving group on the side chain carboxylic acid of the aspartic acid residue. Finally, we have also utilized these results, along with previously accumulated data on succinimide formation in related peptides, to correlate the rate of succinimide formation with the predicted acidity of the peptide bond nitrogen atom that is involved in the initial nucleophilic attack. © Munksgaard 1995.     

Quantitative structure-activity relationships of the bitter thresholds of amino acids, peptides, and their derivatives

Bitter thresholds of a total of 93 amino acids, peptides, and their derivatives were analyzed quantitatively by use of hydrophobicity parameters reported for amino acid side chains and those for the whole molecules estimated from partition coefficients obtained experimentally. We also explored the steric parameters that best explained the variation in the intensity of bitterness attributable to the molecular shape. The results showed that the total length along the zigzag peptide backbone chain of the molecule is an important factor. The bitterness of nonzwitterionic N-acyl and ester derivatives and that of neutral N-acyl ester derivatives were expressed by a single, common equation together with those of zwitterionic amino acids and peptides. Thus the interaction via the charge with the receptor site was probably not an indispensible factor for triggering of the bitter sensation. This study, together with earlier ones, may serve as a prototype of approaches toward unraveling structure-activity relationships of complex molecules like amino acids, peptides, and their derivatives that are of medicinal or agricultural importance.     

Efficient macrocyclization for cyclicpeptide using solid-phase reaction

Cyclicpeptides are important targets in peptide synthesis because of their interesting biological properties. Constraining highly flexible linear peptides by cyclization is one of the mostly widely used approaches to define the bioactive conformation of peptides. Cyclic peptides often have increased receptor affinity and metabolic stability over their linear counterparts. We carried out virtual screening experiment via docking in order to understand the interaction between HLE-Human Leukocyte Elastase and ligand peptide and to identify the sequence that can be a target in various ligand peptides. We made cyclic peptides as a target base on Met-Ile-Phe sequence having affinity for ligand and receptor active site docking. There are three ways to cyclize certain sequences of amino acids such as Met-Ile-Phe-Gly-Ile. First is head-to-tail cyclization method, linking between N-terminal and C-terminal. Second method utilizes amino acid side chain such as thiol functional group in Cys, making a thioether bond. The last one includes an application of resin-substituted amino acids in solid phase reaction. Among the three methods, solid phase reaction showed the greatest yield. Macrocyclization of Fmoc-Met-Ile-Phe-Gly-Ile-OBn after cleavage of Fmoc protection in solution phase was carried out to give macrocyclic compound 5 in about 7% yield. In the contrast with solution phase reaction, solid phase reaction for macrocyclization of Met-Ile-Phe-Gly-Ile-Asp-Tentagel in normal concentrated condition gave macrocyclic compound 7 in more than 35% yield.     

Large fragments of nef-protein and gp110 envelope glycoprotein from HIV-1

Chemical synthesis of large peptide fragments (from 18 to 66 amino acid residues long) of the gp110 envelope glycoprotein and of nef-protein from HIV-1 was achieved by the solid phase method. Stepwise assembling of the peptide chains was carried out automatically on 4-(oxymethyl)-phenylacetamidomethyl resin using the N-α-butyloxycarbonyl amino acids with benzyl-based side chain protecting groups. Two elongation protocols were used depending on the peptide chain length: a standard cycle, mainly characterized by a single coupling step (Boc-amino acid symmetrical anhydride in dimethylformamide), and an optimized one for large peptides, based on a double coupling strategy (Boc-amino acid symmetrical anhydride first in dimethylformamide, then in dichloromethane). Final cleavage of the peptide from the solid support was carried out by anhydrous hydrogen fluoride and crude peptides were purified by C₁₈ reverse phase medium pressure liquid chromatography after molecular filtration. Characterization of the purified peptides was done by analytical HPLC, amino acid content determination, and circular dichroism analysis both in polar (H₂O) and in non-polar (TFE) environments. Immunoreactivity of anti-nef positive sera from HIV-1 infected patients by ELISA with the synthetic peptides was investigated. The results showed four major antigenic regions of nef-protein and mainly the immunodominance of the N- and C-termini of the molecule. Several of these peptides should prove to be useful for both diagnosis and vaccination purposes.     

Polyclonal anti-desmosine antiserum is specific to desmosine molecule: no cross-reaction to pyridinoline

Inhibition ELISA assay was used to examine the cross-reaction of the polyclonal anti-desmosine antiserum produced in rabbit against molecules possessing a "pyridinium ring" as their core structure i.e. isodesmosine, pentasine, pyridinoline and 2'-deoxypyridinoline, highly purified with column chromatography, and structurally unrelated substances, i.e. cysteic acid, taurine and 2-aminopyridine (core structure of desmosine). No cross-reaction was observed to the pyridinoline, 2'-deoxypyridinoline possessing "pyridinium ring" and derived from collagen cross-links, structurally unrelated cysteic acid and taurine, nor core structure of 2-aminopyridine. The antiserum specifically recognized the molecules derived from the elastin cross-links. Using the ELISA assay system with antisera and amino acids analysis, 10 micrograms of desmosine were extracted from 1.0 mg of the hydrolysate of commercial elastin.     

Efficient peptide ladder sequencing by MALDI-TOF mass spectrometry using allyl isothiocyanate

A new modification of the peptide ladder sequencing technique is described in which allyl isothiocyanate (AITC) replaces trifluoroethyl isothiocyanate as the volatile amine-modification reagent. AITC is commercially available, readily purified, stable up to 80 °C and reacts cleanly and rapidly with all amino groups of polypeptides. Several model peptides and two side chain-modified peptides were sequentially degraded using AITC and the cleavage reagent heptafluorobutyric acid (HFBA) up to seven amino acids from the TV-terminus. Matrix-assisted laser-desorption and ionization coupled with time-of-flight (MALDITOF) mass spectroscopy of the peptide mixture provided a clear ladder-like mass profile with consecutive molecular ions corresponding to each shortened peptide at picomole range. The results indicate the general utility of this analytical protocol by the use of AITC as the amine-coupling reagent.     

The remarkable sensitivity to acid-catalyzed peptolysis of peptide chains (endopeptolysis) having a succession of three N-alkylated amino acid residues

An investigation on the resistance against acids of over 30 peptides containing a repetition of N-alkylated amino acids has revealed the extremely facile cleavage of the peptide bond (endopeptolysis; ranking from a few minutes to 1 hour in Tfa) between the second and third residue in a sequence of three l -imino acid residues (called “triad”)- This is pronouncedly so if Pro is the head member of the triad. Triads become resistant against hydrolysis, however, when both the first and second positions are occupied by Pro, and even more so if the second member is d -MePhe. On the other hand, as an exception, diads of iminoacids preceded by Gly also are sensitive to hydrolysis. Two possible mechanisms are proposed, among which the one that is characterized by an intramolecular attack of the N-nucleophilic site of the first residue on the peptide bond between the second and third unit and thus forming a diketopiperazine-onium intermediate, is our preference. This sensitivity towards acidolysis and acid-catalyzed hydrolysis should not be overlooked, not only during the planning of peptide syntheses (having especially implications during acidic deprotection protocols), but it will compromise any strategy that makes use of strong acid conditions, e.g. in chiral determinations of N-alkylated amino acids in peptide hydrolysates, because acidic peptide breakdown is accompanied by appreciable stereo-mutation. Finally, the weakened resistance of iminoacid peptide chains is obviously related to trans-cis isomerization about the first peptide bond within the triads and suggests that endopeptidases may well act initially through a trans-cis isomerase stage.     

Circular dichroism studies on synthetic peptides corresponding to the cleavage site region of precursor proteins

The conformations of synthetic peptides which span the region in which the precursor part of proteins (signal sequences) destined for export are cleaved by signal peptidases, were investigated by circular dichroism spectroscopy. Pentapeptides comprising amino acids only from the carboxy-terminus of signal sequences or the amino terminus of the mature protein do not have any preferred conformation in a variety of solvents. Octa- and nonapeptides containing amino acids from the carboxy-terminal protion of signal sequences and the amino-terminus of the mature portions of precursor proteins tend to adopt β-turn conformations in trifluoroethanol and micelles of sodium dodecylsulphate. Hence, in addition to the distribution of amino acids with small side chains at the carboxy terminus of signal sequences, it is conceivable that signal peptidases also recognize a β-turn conformation in the cleavage site region of precursor proteins.     

酶解鱼可溶性肽分子组成结构及营养评价

本文叙述了用胃蛋白酶、胰蛋白酶水解的鱼可溶性肤类水解物,经凝胶高效液相色谱和氨基酸分析仪分析测定其肤类分子组成结构和氨基酸组成成分.测得水解产物中肽类相对分子质量在7400以下,其中相对分子质量6600～7400、由52～58个氨基酸组成的较长肽链占1.74%;相对分子质量2500～5300、由20～41个氨基酸组成的中长肽链占29.75%;相对分子质量在1000以下的由2～10个氨基酸组成的寡肽占50%.水解物的总氮与氨基酸态氮比为25.91,约有96%的氨基酸以肽类形式存在,4%为游离氨基酸.测得可溶性肽的总氨基酸含量为73.98%,必需氨基酸为32.39%,占总氮基酸的43.78%,与FAO/WHO相比,苯丙氨酸为第一限制性氨基酸,氨基酸分值为61.根据分析结果,深入探讨了鱼可溶性肽氨基酸组成的平衡性及其有关寡肽在动物机体的生理功能作用.     

Ligand‐presenting assembly: a method for C‐ and N‐terminal antigen presentation

Abstract: Achiral dicarboxylic acids were coupled with 2 eq. of the free α‐amino groups of two fully side‐chain protected peptide chains while these were still attached to a synthesis resin. Cleavage from the resin with simultaneous side‐chain deprotection afforded two assembled peptide chains with free C‐terminals. Suitable functionalization of the achiral dicarboxylic acid alternatively permited continued peptide synthesis in a C to N orientation leading to a final peptide assembly which, after cleavage from the resin, may have multiple N to C and C to N presentation of one or more epitopes.     

Recent advances in the medicinal chemistry of alpha-aminoboronic acids, amine-carboxyboranes and their derivatives

This article describes recent developments in the synthesis and biological activity of alpha-aminoboronic acids, amine-carboxyboranes and their derivatives as potential therapeutic agents. alpha-Amino acid analogues are of considerable interest as inhibitors of enzymes involved in amino acid and peptide metabolism. In particular, alpha-amino alkylphosphonic acids and alpha-amino alkylboronic acids, in which the carboxyl group of amino acids is replaced by a phosphonic acid or boronic acid function, respectively, constitute a unique class of amino acid mimics from which a number of potent enzyme inhibitors have been synthesized. The inhibitory activity mainly stems from the fact that the tetrahedral phosphonic moiety or the tetrahedral adduct of electrophilic boronic acid is a good mimic of the putative tetrahedral transition state or intermediate encountered in the enzymatic hydrolysis or formation of peptides. Since the peptide hydrolysis and formation invariably involves the tetrahedral high energy species in the course of the reaction, these amino acid mimics serve as a general key element for inhibitors of a broad spectrum of proteases and peptide ligases. Serine protease inhibitors provide promising compounds having a P site binding moiety and a boronic acid chelating moiety. The compounds have been shown to have high inhibitory activity.     

固相法合成心肌兴奋肽及其类似物

用Boc-和Tos-基团分别保护氨基和侧链胍基,以1%交联度聚苯乙烯二苯甲氨基树脂为载体,用DCC固相法合成肽,HF断裂肽树脂键和去除侧链保护基团,粗产物经高效液相层析纯化,合成了心肌兴奋肽Phe-Met-Arg-Phe-NH_2及其类似物Phe-Pro-Arg-Phe-NH_2,并观察了此二种肽对大鼠血压和心率的影响。     

Chemical mechanism to account for artifactual formation of shortened peptides with free alpha-amino groups in solid phase peptide synthesis

The formation of terminated peptides with free α-amino groups has often been observed in stepwise solid phase peptide synthesis. This has been attributed to variable accessibility in regions of the swollen crosslinked resin supports. It is now shown that impurities in the amino acid reagents are responsible for these by-products. Thus, sec. -butyloxycarbonylamino acids were isolated from tert. -butyloxycarbonylamino acids after treatment with trifluoroacetic acid under standard deprotection conditions for the removal of the tert. -butyloxycarbonyl (Boc) group. Direct reverse phase HPLC analysis of Boc-amino acids from commercial sources also showed the sec. -Boc-amino acids as impurities present at varying levels. The sec. -Boc group was stable to treatment at room temperature with trifluoroacetic acid in dichloromethane (1:1, v/v) (half-life 7 years), but was removed by HF-anisole under the standard conditions of cleavage and deprotection of assembled peptides. In model syntheses, the level of terminated free peptides corresponded to the level of preexisting sec. -Boc-amino acid impurities present in the Boc-amino acid reagents. Use of Boc-amino acids with no detectable sec. -Boc resulted in negligible levels (< 0.05%) of terminated peptides. The problem is thus readily overcome by the use of pure Boc-amino acid starting materials and is not a reflection of a shortcoming inherent to the polymer supported nature of solid phase syntheses as has been previously suggested.     

Buforin I, a natural peptide, inhibits botulinum neurotoxin B activity in vitro

Botulinum neurotoxin B (BoNT/B) serotype specifically cleaves between the amino acids glutamine and phenylalanine (Q and F bond) in position 76-77 of synaptobrevin (VAMP2). We evaluated peptides that contain the QF cleavage site but are not identical in primary structure to the VAMP2 sequence surrounding the QF site for both inhibition of BoNT/B proteolytic activity and as substrates for BoNT/B. A reverse-phase high-performance liquid chromatography (RP-HPLC) method was used to measure digested peptides. A dose as high as 600 microM of substance P, and 11-amino acid peptide containing the QF bond, was neither a substrate nor inhibitor of BoNT/B in our assay, suggesting that more than the QF bond is required to be recognized by BoNT/B. Buforin I (B-I, QF site 24-25) is 39 amino acids in length, and sequence comparison of B-I and VAMP2 indicated a similarity of 18% for conserved amino acids around the QF site. Furthermore, computer-aided secondary structure computations predict alpha-helical structures flanking the QF site for VAMP2 and for the upstream sequence of B-I. Although predictions for the downstream sequence give nearly equal tendencies for alpha-helical and beta-sheet structures, Yi et al. showed that the downstream sequence is likely to be the alpha-helix based on their examination of buforin II (B-II, a 21-amino acid subset of B-I (16-36)), which includes the QF site and the downstream sequence of B-I. Buforin I was found not to be a substrate for BoNT/B; however, B-I dose dependently and competitively inhibited BoNT/B activity, yielding IC(50) = 1 x 10(-6) M. In contrast, B-II was not a substrate for BoNT/B and exhibited only 25% of the B-I inhibition of BoNT/B. Two additional B-I deletion peptides were tested for inhibition of BoNT/B proteolysis: peptide 36 (36 mer; containing B-I amino acids 1-36) and peptide 24 (24 mer; B-I amino acids 16-39). Peptide 24 had a similar inhibitory effect to B-II (ca. 25% of B-I) but peptide 36 was almost 50% as potent as B-I. These findings suggest that the buforin tertiary structure is important for the inhibitory activity of these peptides for BoNT/B.     

Solid-phase peptide synthesis on proteins

A new method for solid-phase peptide synthesis in which a protein is used as the solid support has been developed. Two aspects of the method have been demonstrated. The peptides H-Phe-Leu-Glu-Glu-Val-OH (1) and H-Leu-Leu-Ala-Glj-Val-OH (2), respectively, were synthesized on the amino groups of BSA via a cleaveable linker, using the Fmoc group protecting scheme. The free peptides were obtained by cleavage from the protein with 95% TFA. precipitation in diethyl ether and additional work-up by either dialysis or centrifugation through a membrane followed by gel filtration. The identity of the products was determined by amino acid analysis and HPLC. The peptide-protein conjugates, H-Ser-Met-Asp-Thr-Ser-Asn-Lys-Glu-Glu-Lys-BSA (3) and H-Thr-Val-Leu-BTG (4), were obtained in the same manner, omitting the cleavable linker group. It was found that 35-50 peptide chains were conjugated per molecule BSA and BTG, respectively. Immunization of rabbits with conjugate 3 gave rise to peptide specific antibodies. This method will be useful for generation of sequence specific antibodies, since the peptide is conjugated to the carrier protein exclusively via its C-terminus, and will allow synthesis of highly specific peptide-protein conjugates.