Propensity for spontaneous succinimide formation from aspartyl and asparaginyl residues in cellular proteins

One mechanism for the spontaneous degradation of polypeptides is the intramolecular attack of the peptide bond nitrogen on the side chain carbonyl carbon atom of aspartic acid and asparagine residues. This reaction results in the formation of succinimide derivatives and has been shown to be largely responsible for the racemization, isomerization, and deamidation of these residues in several peptides under physiological conditions (Geiger, T. & Clarke, S. J. Biol. Chem. 262, 785–794 (1987)). To determine if similar reactions might occur in proteins, I examined the sequence and conformation about aspartic acid and asparagine residues in a sample of stable, well-characterized proteins. There did not appear to be any large bias against dipeptide sequences that readily form succinimides in small peptides. However, it was found that aspartyl and asparaginyl residues generally exist in native proteins in conformations where the peptide bond nitrogen atom cannot approach the side chain carbonyl carbon to form a succinimide ring. These orientations also represent energy minimum states, and it appears that this factor may account for a low rate of spontaneous damage to proteins by succinimide-linked reactions. The presence of aspartic acid and asparagine residues in other conformations, such as those in partially denatured, conformationally flexible regions, may lead to more rapid succinimide formation and contribute to the degradation of the molecule. The possible role of isoimide intermediates, formed by the attack of the peptide oxygen atom on the side chain carboxyl group, in protein racemization, isomerization, and deamidation is also considered.     

Chemical Pathways of Peptide Degradation. III. Effect of Primary Sequence on the Pathways of Deamidation of Asparaginyl Residues in Hexapeptides

Deamidation of Asn residues can occur either by direct hydrolysis of the Asn residue or via a cyclic imide intermediate. The effects of primary sequence on the pathways of deamidation of Asn residues were studied using Val-Tyr-X-Asn-Y-Ala hexapeptides with substitution on the C-terminal side (Y) and on the N-terminal side (X) of the Asn residue. In acidic media the peptides deamidate by direct hydrolysis of the Asn residue to yield only Asp peptides, whereas under neutral or alkaline conditions, the peptides deamidate by formation of the cyclic imide intermediates which hydrolyze to yield both isoAsp and Asp peptides. At neutral to alkaline pH's the rate of deamidation was significantly affected by the size of the amino acid on the C-terminal side of the Asn residue. The amino acid on the C-terminal side of the Asn residue has no effect on the rate of deamidation at acidic pH. Changes in the structure of the amino acid on the N-terminal side of the Asn residue had no significant effect on the rate of deamidation at all the pH's studied. For peptides that underwent deamidation slowly, a reaction involving the attack of the Asn side chain on the peptide carbonyl carbon resulting in peptide bond cleavage was also observed.     

The role of the cyclic imide in alternate degradation pathways for asparagine-containing peptides and proteins

Peptides and proteins exhibit enhanced reactivity at asparagine residues due to the formation of a reactive succinimide intermediate that produces normal and isoaspartyl deamidation products along with significant racemization. This study examines the potential for attack of amine nucleophiles at the succinimide carbonyls to generate alternate decomposition products, depending on the nucleophile involved in the reaction. The reactions of the model peptides Phe-Asn-Gly (FNG) and Phe-isoAsn-Gly (FisoNG) were explored as a function of pH (8.5-10.5) in the presence and absence of ammonia buffer (0.2-2 M) using an isocratic HPLC method to monitor reactant disappearance and product formation. In addition to deamidation to form isoAsp and Asp peptides, two additional types of reactions were found to occur via the succinimide intermediate under these conditions. Back-reaction of the succinimide with ammonia led to peptide backbone isomerization while intramolecular attack by the amino terminus produced diketopiperazines. A kinetic model assuming a central role for the succinimide intermediate was derived to fit the concentration versus time data. These studies implicate the cyclic imide as a key intermediate in the formation of alternate peptide and protein degradants, including possible covalent amide-linked aggregates that may form from intermolecular attack of the cyclic imide by neighboring amino groups.     

The relative rates of glutamine and asparagine deamidation in glucagon fragment 22-29 under acidic conditions

Our objective was to compare the relative rates of asparaginyl and glutaminyl deamidation in fragment 22-29 of the polypeptide hormone glucagon in acidic aqueous solutions. Reaction mixtures containing 22-29 (FVQWLMNT) or its degradation products were degraded at 60 degrees C in dilute hydrochloric acid or phosphate buffer in the pH range 1-3. Degradation products were separated by high-performance liquid chromatography and identified by amino acid sequencing, amino acid analysis, liquid chromatography-mass spectrometry (LC-MS), and matrix-assisted laser desorption and ionization (MALDI). Nine major degradation products were identified, including asparaginyl and glutaminyl deamidated forms, aspartyl peptide cleavage of the asparaginyl deamidated products, and a cyclic imide intermediate. The pH dependences of rate constants for individual pathways were consistent with acid catalysis. Previous investigators have reported a greater susceptibility of asparagine residues to deamidation in neutral and alkaline solutions due to the formation of a more stable five-membered succinimide intermediate. It has been suggested that asparagine may be more labile under acidic conditions also. We have observed a more facile deamidation for the glutamine residue under the acidic condition studied. It is proposed that the lower reactivity of the asparagine residue may be due to a decreased electrophilicity of its side chain carbonyl carbon imparted by a parallel cleavage pathway at this residue.     

USE OF CYCLOPENTYL ESTER PROTECTION FOR ASPARTIC ACID TO REDUCE BASE CATALYZED SUCCINIMIDE FORMATION IN SOLID-PHASE PEPTIDE SYNTHESIS

A study was conducted to determine the effect of amino acid sequence and aspartyl protecting group on the rate of base catalyzed succinimide formation in the solid-phase synthesis of aspartyl peptides. The peptides H-Ala-Asp-Gly-Phe-OH and H-Ala-Asp-Leu-Phe-OH were synthesized by the solid-phase method with cyclopentyl or benzyl protection for the β-carboxyl of aspartic acid. The results showed that the cyclopentyl ester was notably less susceptible to succinimide formation by treatment with tertiary amine than was the benzyl ester, and that the difference could have significant consequences for the synthesis of large peptides which contain reactive sequences such as Asp-Gly.     

Solution stability of linear vs. cyclic RGD peptides

Abstract: Arg-Gly-Asp (RGD) peptides contain an aspartic acid residue that is highly susceptible to chemical degradation and leads to the loss of biological activity. Our hypothesis is that cyclization of RGD peptides via disulphide bond linkage can induce structural rigidity, thereby preventing degradation mediated by the aspartic acid residue. In this paper, we compared the solution stability of a linear peptide (Arg-Gly-Asp-Phe-OH; 1 ) and a cyclic peptide (cyclo-(1, 6)-Ac-Cys-Arg-Gly-Asp-Phe-Pen-NH_2; 2 ) as a function of pH and buffer concentration. The decomposition of both peptides was studied in buffers ranging from pH 2–12 at 50°C. Reversed-phase HPLC was used as the main tool in determining the degradation rates and pathways of both peptides. Fast atom bombardment mass spectrometry (FAB-MS), electrospray ionization mass spectrometry (ESI-MS), matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry, liquid chromatography-mass spectrometry (LC-MS), and one- and two-dimensional nuclear magnetic resonance spectroscopy (NMR) were used to characterize peptides 1 and 2 and their degradation products. In addition, co-elution with authentic samples was used to identify degradation products. Both peptides displayed pseudo-first-order kinetics at all pH values studied. The cyclic peptide 2 appeared to be 30-fold more stable than the linear peptide 1 at pH 7. The degradation mechanisms of linear ( 1 ) and cyclic ( 2 ) peptides primarily involved the aspartic acid residue. However, above pH 8 the stability of the cyclic peptide decreased dramatically due to disulphide bond degradation. Both peptides also exhibited a change in degradation mechanism upon an increase in pH. The increase in stability of cyclic peptide 2 compared to linear peptide 1 , especially at neutral pH, may be due to decreased structural flexibility imposed by the ring. This rigidity would prevent the Asp side chain carboxylic acid from orientating itself in the appropriate position for attack on the peptide backbone.     

The effects of a histidine residue on the C-terminal side of an asparaginyl residue on the rate of deamidation using model pentapeptides

The effects of a histidine (His) residue located on the C-terminal side of an asparaginyl (Asn) residue on the rate of deamidation were studied using Gly-Gln-Asn-X-His pentapeptides. The rates of deamidation of the pentapeptides were determined at 37 degrees C (I = 0.5) as function of pH, buffer species, and buffer concentration. A capillary electrophoresis stability-indicating assay was developed to monitor simultaneously the disappearance of the starting peptides and the appearance of the degradation products. The rates of degradation of the peptides were pH dependent, increasing with pH, and followed apparent first-order kinetics. At pH values <6.5, Gly-Gln-Asn-His-His degraded faster than Gly-Gln-Asn-Gly-His, suggesting that the N+1 His residue is catalyzing the deamidation of the Asn residue. The His side chain at these pH values could function as a general acid catalyst, stabilizing the oxyanionic transition state of the cyclic imide intermediate formation. In contrast, at pH values >6.5, Gly-Gln-Asn-Gly-His deamidates more rapidly than Gly-Gln-Asn-His-His. The bulk of the side chain of the N+1 His residue versus the N+1 Gly residue apparently inhibits the flexibility of the peptide around the reaction site and, consequently, reduces the rate of the reaction. The significance of this steric hindrance effect of the N+1 His residue on the rate of deamidation was examined further. It was observed that at pH >6.0, Gly-Gln-Asn-His-His undergoes deamidation faster than Gly-Gln-Asn-Val-His. This observation indicated that, at the higher pH values, the N+1 His residue is also acting as a catalyst. Thus, at basic pH, the N+1 His residue influences the rate of deamidation via two opposing effects; that is, general base catalysis and steric interference. The pentapeptide Gly-Gln-Asn-His-His, in addition to undergoing the deamidation reaction, also undergoes bond cleavage at the Asn-His peptide bond. The enhanced rate of Asn-His peptide bond cleavage can be attributed to the general base behavior of the His residue, leading to increased nucleophilicity of the Asn side-chain amide group. Finally, we have shown that the His residue that is two amino acids removed from the Asn, the N+2 position, has little or no effect on the rate of deamidation.     

A cleavage cocktail for methionine-containing peptides

Abstract: A new cocktail has been developed for cleavage and deprotection of methionine-containing peptides synthesized by 9-fluorenylmethoxycarbonyl (Fmoc)-based solid-phase peptide synthesis methodology. The cocktail (trifluoroacetic acid 81%, phenol 5%, thioanisole 5%, 1,2-ethanedithiol 2.5%, water 3%, dimethylsulphide 2%, ammonium iodide 1.5% w/w) was designed to minimize methionine side-chain oxidation. Application of the new cocktail (Reagent H) is demonstrated with the synthesis of a model pentadecapeptide from the active site of DsbC, a periplasmic protein involved in protein disulphide bond formation. The model peptide, which contains one methionine and two cysteine residues, was cleaved with several cleavage cocktails, including Reagent H. The crude peptides obtained with the widely used cocktails K, R and B were found to be 15% to 55% in the methionine sulphoxide form, whereas no methionine sulphoxide was detected in the crude peptide obtained by cleavage and deprotection with Reagent H. Also, no methionine sulphoxide was detected when 1.5% w/w NH₄I was added to cocktails K, R and B; however, the yield of the desired peptide was less than with Reagent H. A second 28 amino acid model peptide of the active site of DsbC was also cleaved and deprotected with Reagent H. The reduced dithiol form of the peptide was found to be the major component (51% yield) of the crude peptide obtained by cleavage for 3 h. When the cleavage time was extended to 10 h, the peptide was converted to the intramolecular disulphide form (35% yield). A proposed mechanism for the in situ oxidation of cysteine with Reagent H is presented.     

THERMITASE,A THERMOSTABLE SERINE PROTEASE FROM THERMOACTINOMYCES VULGARIS

Studies on the amino acid composition, chemical modifications, and characterization of the cyanogen bromide cleavage peptides of a thermostable serine protase (thermitase) from Thermoactinomyces vulgaris were performed. The amino acid analysis shows that the enzyme contains a single cysteine and methionine residue. From the amino acid composition as well as a partial sequence determination around the single methionine residue it is concluded that thermitase belongs to the subtilisin-type proteases. The two peptides obtained by cyanogen bromide cleavage were further characterized by amino acid analysis and molecular weight determination yielding 25 000 and 6 000 daltons, respectively. Chemical modification experiments show that in addition to the active site serine and histidine residue the cysteine as well as the methionine residue are essential for activity of the enzyme. The alignment of these amino acids in the polypeptide chain of the thermitase is supposed.     

Easy cleavage of C′-terminal iminoacids from peptide acids through acidic hydrolysis

Evidence is presented for the facile acid-hydrolytic cleavage of C-terminal N-alkylated amino acid residues in peptide acids. A mechanism (defined as “back-biting”) is proposed in which the process is initiated by a nucleophilic attack of the conjugated base of the terminal acid on the (protonated) preceding cis-peptide bond.     

Kinetics of Aspartic Acid Isomerization and Enantiomerization in Model Aspartyl Tripeptides under Forced Conditions

The aim of the present study was the determination of the isomerization and enantiomerization of aspartic acid (Asp) in tripeptides. Capillary electrophoresis (CE) assays were developed and validated allowing the simultaneous determination of the diastereomeric α- D/L-Asp and β-D/L-Asp peptides. Rapid isomerization and enantiomerization were noted for peptides with the Phe-Asp-GlyOH sequence at pH 10 and 80 °C while Gly-Asp-PheOH proved to be more stable due to the steric influence of the phenyl side chain. A kinetic model assuming a central role of the succinimide intermediate was used to fit the concentration versus time data. In incubations of L-Phe-a-L-Asp-GlyOH the ratio of α-Asp/β-Asp peptides was about 1:4 in agreement with literature data. With regard to L-Asp and D-Asp peptides an α-Asp/β-Asp ratio of about 1:3 and 1:5, respectively, was observed. The stereochemistry of Phe at the X — 1 position affected the ratio of L-Asp/D-Asp implying an effect of the stereochemistry of neighboring amino acids on Asp enantiomerization. Modeling only overall Asp enantiomerization rate constants in accordance to literature data were observed for Asp peptides. In case of the asparagine (Asn) peptide the data could only be fitted to the models considering a direct conversion of L-Asn to a D-configured succinimide via an alternative pathway. © 2010 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm SciJ. Pharm. Sci. 99:4162-4173, 2010     

Effect of conformation on the conversion of cyclo-(1,7)-Gly-Arg-Gly-Asp-Ser-Pro-Asp-Gly-OH to its cyclic imide degradation product

Abstract: The objective of this study was to explain the increased propensity for the conversion of cyclo-(1,7)-Gly-Arg-Gly-Asp-Ser-Pro-Asp-Gly-OH ( 1 ), a vitronectin-selective inhibitor, to its cyclic imide counterpart cyclo-(1,7)-Gly-Arg-Gly-Asu-Ser-Pro-Asp-Gly-OH ( 2 ). Therefore, we present the conformational analysis of peptides 1 and 2 by NMR and molecular dynamic simulations (MD). Several different NMR experiments, including COSY, COSY-Relay, HOHAHA, NOESY, ROESY, DQF-COSY and HMQC, were used to: (a) identify each proton in the peptides; (b) determine the sequential assignments; (c) determine the cis–trans isomerization of X–Pro peptide bond; and (d) measure the NH–HC^α coupling constants. NOE- or ROE-constraints were used in the MD simulations and energy minimizations to determine the preferred conformations of cyclic peptides 1 and 2 . Both cyclic peptides 1 and 2 have a stable solution conformation; MD simulations suggest that cyclic peptide 1 has a distorted type I β-turn at Arg2-Gly3-Asp4-Ser5 and cyclic peptide 2 has a pseudo-type I β?turn at Ser5-Pro6-Asp7-Gly1. A shift in position of the type I β-turn at Arg2-Gly3-Asp4-Ser5 in peptide 1 to Ser5-Pro6-Asp7-Gly1 in peptide 2 occurs upon formation of the cyclic imide at the Asp4 residue. Although the secondary structure of cyclic peptide 1 is not conducive to succinimide formation, the reaction proceeds via neighbouring group catalysis by the Ser5 side chain. This mechanism is also supported by the intramolecular hydrogen bond network between the hydroxyl side chain and the backbone nitrogen of Ser5. Based on these results, the stability of Asp-containing peptides cannot be predicted by conformational analysis alone; the influence of anchimeric assistance by surrounding residues must also be considered.     

Studies on the mechanism of aspartic acid cleavage and glutamine deamidation in the acidic degradation of glucagon

In this study, the polypeptide hormone glucagon was used as a model to investigate the mechanisms of aspartic acid cleavage and glutaminyl deamidation in acidic aqueous solutions. Kinetic studies have shown that cleavage at Asp-21 occurred at significantly slower rates than at Asp-9 and Asp-15 while deamidation rates were similar at the three Gln residues. The role of side-chain ionization in the cleavage mechanism was investigated by determining the pK(a) values of the three Asp residues using TOCSY and NOESY NMR methods. The role of proton transfer was investigated using kinetic solvent isotope effect studies (KSIE). The pK(a) values for the sidechains of Asp-9, Asp-15, and Asp-21 were found to be 3.69, 3.72, and 4.05 respectively. No kinetic solvent isotope effect was observed for the cleavage reaction whereas an inverse effect was observed for deamidation. Based on the lack of sequence effects, pH-rate behavior, and KSIE, the deamidation mechanism was proposed to involve direct hydrolysis of the amide side-chain by water. Based on substrate ionization, pH-rate profiles, and KSIE, the proposed mechanism for Asp cleavage involved nucleophilic attack of the ionized side-chain carboxylate on the protonated carbonyl carbon of the peptide bond to give a cyclic anhydride intermediate.     

Early Engineering Approaches to Improve Peptide Developability and Manufacturability

Downstream success in Pharmaceutical Development requires thoughtful molecule design early in the lifetime of any potential therapeutic. Most therapeutic monoclonal antibodies are quite similar with respect to their developability properties. However, the properties of therapeutic peptides tend to be as diverse as the molecules themselves. Analysis of the primary sequence reveals sites of potential adverse posttranslational modifications including asparagine deamidation, aspartic acid isomerization, methionine, tryptophan, and cysteine oxidation and, potentially, chemical and proteolytic degradation liabilities that can impact the developability and manufacturability of a potential therapeutic peptide. Assessing these liabilities, both biophysically and functionally, early in a molecule’s lifetime can drive a more effective path forward in the drug discovery process. In addition to these potential liabilities, more complex peptides that contain multiple disulfide bonds can pose particular challenges with respect to production and manufacturability. Approaches to reducing the disulfide bond complexity of these peptides are often explored with mixed success. Proteolytic degradation is a major contributor to decreased half-life and efficacy. Addressing this aspect of peptide stability early in the discovery process increases downstream success. We will address aspects of peptide sequence analysis, molecule complexity, developability analysis, and manufacturing routes that drive the decision making processes during peptide therapeutic development.KEY WORDS: developability, peptide, proteolysis, PTM risk     

Ammonia cleaves polypeptides at asparagine proline bonds

Abstract: Polypeptides that contain the sequence Asn‐Pro undergo complete cleavage at this amide bond with ammonia. One cleavage product possesses Pro as the new amino terminus and the other Asn or isoAsn as the new C‐terminus, the formation of the latter probably arising by way of a cyclic succinimide intermediate. Other Asn‐X bonds where X = Tyr, Gln, Ile, Glu, Ala, Gly, Asn or Phe did not exhibit any peptide bond cleavage, whereas when X = Leu, Thr and Ser partial cleavage was observed. Asn residues not involved in chain‐cleavage underwent deamidation to Asp as shown by MALDI‐ToF mass spectrometry (MS) analysis. The partial conversion of in‐chain Asp residues to isoAsp under the reaction conditions was inferred from RP‐HPLC and MS analysis of reaction mixtures.     

Estimation of the deamidation rate of asparagine side chains

Abstract: Statistical analysis of data from the literature concerning the deamidation reaction of asparagine side‐chains in short peptides reveals that the logarithm of rate constants can be solved into a constant plus contributions from the residues closest to asparagine. A table of amino acid contributions has been derived, from which deamidation rate constants can be estimated with good approximation. Assuming the contribution of glycine to be zero, the mean of the absolute values of the contributions for the residues following aspagine is approximatley seven times that for the preceding residues. In both positions residues with no bulk side chains or with functional side groups contribute markedly to the increase in the rate constant.     

Ethylcarbamoyl protection for cysteine in the preparation of peptide-conjugate immunogens

During the solid-phase synthesis of over 100 peptides, we have observed that the ethylcarbamoyl group is useful for the side chain protection of cysteine in peptides containing a single cysteine residue. The ethylcarbamoyl group is stable to the conditions of acidolytic cleavage, purification and long term storage. Brief treatment of peptides containing an S-ethylcarbamoylcysteine residue with aqueous sodium hydroxide gives the deprotected cysteine peptide that can be coupled to carrier molecules such as proteins to give immunogen conjugates.     

Design and NMR studies of cyclic peptides targeting the N-terminal domain of the protein tyrosine phosphatase YopH

We report on the design and evaluation of novel cyclic peptides targeting the N-terminal domain of the protein tyrosine phosphatase YopH from Yersinia. Cyclic peptides have been designed based on a short sequence from the protein SKAP-HOM [DE(pY)DDPF (pY=phosphotyrosine)], and they all contain the motif DEZXDPfK (where Z is a phosphotyrosine or a non-hydrolyzable phosphotyrosine mimetic, X is an aspartic acid or a leucine and f is a d-phenylalanine). These peptides present a 'head to tail' architecture, enabling cyclization through formation of an amide bond in between the side chains of the first aspartic acid and the lysine residues. Chemical shift perturbation studies have been carried out to monitor the binding of these peptides to the N-terminal domain of YopH. Peptides containing a phosphotyrosine moiety exhibit binding affinities in the low micromolar range; substitution of the phosphotyrosine with one of its non-hydrolyzable derivatives dramatically reduces the binding affinities. These preliminary studies may pave the way for the discovery of more potent and selective peptide-based ligands of the YopH N-terminal domain which could be further investigated for their ability to inhibit Yersiniae infections.     

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 micro-proteins and mechanisms of cyclization

Transpeptidation reactions result in the formation of new peptide bonds and this can occur between two separate peptides or within the one peptide. These reactions are catalyzed by enzymes and when the N- and C-terminus of the one peptide are joined it results in the formation of cyclic proteins. Cyclization via head-to-tail linkage of the termini of a peptide chain occurs in only a small percentage of proteins but gives the resultant cyclic proteins exceptional stability. The mechanisms are not well understood and this review documents what is known of the events that lead to cyclization. Gene encoded cyclic proteins are found in both prokaryotic and eukaryotic species. The prokaryotic circular proteins include the bacteriocins and pilins. The eukaryotic circular proteins in mammals include the θ-defensins and retrocyclins. Small cyclic proteins are also found in fungi and a large range of cyclic proteins are expressed in cyanobacteria. Three types of cyclic proteins have been found in plants, the small cyclic proteins of 5-12 amino acids, the cyclic proteins from sunflower which are made up of 12-14 amino acids, and the larger group known as cyclotides which contain 28-37 amino acids. Three classes of enzymes are able to catalyse transpeptidation reactions, these include the cysteine, serine and threonine proteases. However only cysteine and serine proteases have been documented to cyclize proteins. The cyclotides from Oldenlandia affinis, the plant in which cyclotides were first discovered, are processed by an asparaginyl endopeptidase which is a cysteine protease. These proteases cleave an amide bond and form an acyl enzyme intermediate before nucleophilic attack of the amine group of the N-terminal residue to form a peptide bond, resulting in a cyclic peptide.