WO2006079364A1 - Clivage specifique et modere de peptide ou de liaison amide - Google Patents

Clivage specifique et modere de peptide ou de liaison amide Download PDF

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Publication number
WO2006079364A1
WO2006079364A1 PCT/EP2005/007233 EP2005007233W WO2006079364A1 WO 2006079364 A1 WO2006079364 A1 WO 2006079364A1 EP 2005007233 W EP2005007233 W EP 2005007233W WO 2006079364 A1 WO2006079364 A1 WO 2006079364A1
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phosphine
azide
peptide
tris
compound
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PCT/EP2005/007233
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English (en)
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Jaapwillem Back
Jan Herman Van Maarseveen
Chris Gerdinus De Koster
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Stichting Voor De Technische Wetenschappen
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    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07KPEPTIDES
    • C07K1/00General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length
    • C07K1/12General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length by hydrolysis, i.e. solvolysis in general
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07KPEPTIDES
    • C07K1/00General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length
    • C07K1/107General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length by chemical modification of precursor peptides

Definitions

  • the azide functional group is exceptionally well suited for in vivo labeling of biomolecules .
  • Azides combine a high chemical stability under biological conditions with a unique reactivity enabling mild and selective organic transformations under physiological conditions ( Saxon, E . & Bertozzi , C . R. (2000 ) Cell Surface Engineering by a Modified Staudinger Reaction . Science 287 , 2007-2010 ; Prescher, J. A. , Dube , D . H . & Bertozzi , C . R. (2004 ) Chemical remodelling of cell surfaces in living animals . Na ture 430 , 873-7 ; Kohn, M. & Breinbauer, R. (2004 ) The Staudinger Ligation - A Gift to Chemical Biology .
  • the amino acid Azido-homoalanine (Azhal ) has been shown to be effectively incorporated into proteins by the native methionyl tRNA synthase of E coli (Kiick et al . , supra) . Kiick et al . have demonstrated that proteins containing azidohomoalanine can be 5 selectively modified in the presence of other cellular proteins by means of Staudinger ligation with triarylphosphine reagents . It was thus suggested that incorporation of azide-functionalized amino acids into proteins in vivo provides opportunities for protein modification under native conditions and selective labeling of proteins in the 10 intracellular environment .
  • proteins containing azide-functionalized amino acids with azide-reducing agents in a protic environment cleavage of the amide bond C-terminal to azide-functionalized amino acid is accomplished to obtain a free amine compound and a secondary residue that varies depending on the azide-functionalized amino acid used .
  • This method may advantageously be used for cleavage of proteins or peptides , but can also be used for the cleavage of other compounds comprising an amide bond C-terminal of the azide-functionalized amino acid .
  • the present invention relates to a method for cleaving of an amide bond in a compound comprising said amide bond and at least one azide-function spaced at 3 or 4 atoms from the carbon of the amide bond to be cleaved, said compound being chosen from the compounds of formulae I-IV :
  • Ri and R 2 may be independently a hydrogen atom, a hydrocarbon group, or a heterocyclic group, which may have a substituent, and the two R ' s may be the same or different and independently a hydrogen atom, a hydrocarbon group, or a heterocyclic group, which may have a substituent
  • said method comprising the steps of : a) providing the compound of any of formulae I-IV, wherein R 1 and R 2 may be independently a hydrogen atom, a hydrocarbon group, or a heterocyclic group, which may have a substituent , and the two R ' s may be the same or different and independently a hydrogen atom, a hydrocarbon group, or a heterocyclic group, which may have a substituent; and b) subj ecting the compound of step a) to an azide-reducing agent in a protic solvent to cleave the amide bond C-terminal to the non-natural amino acid, thereby obtaining RiNH 2 and a secondary residue .
  • Detection of the presence of non-natural amino acids in a peptide chain is part of the routine work for the skilled practitioner ( see e . g . the above citations ) , and can be done by one or more of several techniques , such as mass spectrometry, EcLman degradation, amino acid analysis, or derivatization or reaction with appropriate azido specific reagents that carry a detectable label (e . g . phosphines or alkynes , labeled with fluorophores , biotins , or any other secondary label in conj unction with a suitable assay .
  • a detectable label e . g . phosphines or alkynes , labeled with fluorophores , biotins , or any other secondary label in conj unction with a suitable assay .
  • R 1 is a peptide chain (in case of the compounds of formulae III and IV) or R 1 and R 2 are both peptide chains ( in case of the compounds of formulae I and II ) , such that the non-natural azide-functionalized amino acid is incorporated in a peptide or a protein .
  • R 1 may be different from R 2 , but R 1 and R 2 may also be the same .
  • the non-natural amino acid is preferably chosen from the group, consisting of azidohomoalanine (the azide-functionalized amino acid moiety displayed in formula I wherein both R ' s are H) , azidonorvaline (the azide-functionalized amino acid moiety displayed in formula I I wherein both R' s are H) and derivates thereof (the azide- functionalized amino acid moiety displayed either in formula I or II wherein the two R ' s may be the same or different and independently a hydrogen atom, a hydrocarbon group, or a heterocyclic group, which may have a substituent; R may e . g .
  • Azidohomoalanine , azidoalanine, azidonorvaline and azidonorleucine are shown to be methionine analogs .
  • the azide group can survive cellular metabolism.
  • the incorporation of the above methionine analogs into proteins is controlled most stringently by the methionyl-tRNA synthetase of the host .
  • a methionine analog can be incorporated into the peptide chain, e .
  • Ri and R 2 may be independently a hydrogen atom, a hydrocarbon group, or a heterocyclic group, which may have a substituent, and the two R ' s may be the same or different and independently a hydrogen atom, a hydrocarbon group, or a heterocyclic group, which may have a substituent , as indicated above .
  • step b) the compound of any of formulae I-IV is subj ected to an azide-reducing agent in a protic solvent to cleave the amide bond C-terminal to the non-natural amino acid, thereby obtaining R 1 NH 2 and a secondary residue .
  • the azide-reducing agent may be any azide-reducing agent known in the art, such as LiAlH 4 , H 2 /catalyst, Cr (II ) /H + , ⁇ 3 P/NH 4 OH,
  • H 2 S/pyridine/water, H 2 /Lindlar catalyst, trivalent phosphines , and thiol-containing agents Boyley H . , Standring, D . N . and Knowles , J . R. ( 1978 ) Propane-1 , 3-dithiol : a selective reagent for the efficient reduction of alkyl and aryl azides to amines . Tetrahydr. Lett . 39, 3633-3634 ) .
  • a “protic solvent” as herein used refers to a solvent that is capable of donating a hydrogen atom for hydrogen bonding . This usually requires an NH or OH bond .
  • Non-limiting examples thereof are aqueous solutions , such as water and several types of buffer solutions , and alcohols such as ethanol , nitriles such as acetonitrile , organic acids such as acetic acid, furanes such as tetrahydrofurane , formamides such as dimethylformamide and any mixture of these solvents .
  • the protic solvent should allow for solubilisation of the peptide chain as well as the azide-reducing agent .
  • the "subj ecting the peptide chain to an azide- reducing agent in a protic solvent” refers to a reaction that occurs between the peptide chain and an azide-reducing agent, e . g . phosphine, 2-mercaptoethanol or dithiothreitol , when these are simultaneously present in the protic solvent .
  • the peptide chain will thus be subj ected to the azide-reducing agent when a sample of peptide chain in protic solvent is mixed with the azide-reducing agent in the same protic solvent or a protic solvent that is miscible with the protic solvent used to solubilise the peptide chain .
  • the amide bond C-terminal to the non-natural amino acid participates in the reaction with the triazene that results from the reaction of the azido moiety of this amino acid with the azide-reducing agent to accomplish cleavage of this amide bond, as is further exemplified using a phosphine as azide-reducing agent in Fig . 1. Due to the reaction with the azide- reducing agent, the resultant peptide C-terminal to the scissile bond becomes a peptide with an N-terminal free amine, whereas the resultant peptide N-terminal to the scissile bond becomes a so-called secondary residue ( Fig . 1 ) .
  • the secondary residue is dependent on the non-natural amino acid that is used in step a) , and is e . g . a homoserine lactone residue in the case of the non-natural amino acid being azidohomoalanine .
  • homoserine and homoserine lactone are in equilibrium, and the equilibrium is dependent on pH, as the skilled practitioner is well aware of .
  • a nucleophile e . g . a primary amine
  • Proteins may be produced in the host of choice (see e . g . Wang & Schulz, supra) if so desired as a fusion protein as to solubilise them and may accordingly undergo regular post- translational processing, and may then be cleaved from the fusion moiety to yield the desired protein in fully processed form.
  • the present invention finds further application in organic synthesis .
  • the non-natural amino acid is azidohomoalanine and the secondary residue is a homoserine lactone residue .
  • azidohomoalanine is most efficiently incorporated into a protein by means of the cell ' s native translational apparatus (Kiick et al . , supra and Link et al . , supra) .
  • the method according to the invention can be very efficiently carried out as is shown below in the examples and in figure 1.
  • the protic solvent is an aqueous solution .
  • protons are available for the reaction that is depicted in fig . 1.
  • the phosphine of formula V may be any phosphine of formula V
  • R 4 , R 5 and R 6 are independently optionally substituted alkyl or aryl chains and may be the same or different .
  • R 4 , R 5 and R 6 groups that render the phosphine soluble in a protic solvent, in particular in water .
  • Non- limiting examples of R 4 , R 5 and R 6 include carboxylic acids (e . g . propionic acid, acetic acid) , alkylamines (e . g . propylamine , ethylamine ) , alkylhydroxyls (e . g .
  • the thiol-containing agent may be any thiol-containing agent known in the art, particular one of formulae VII or VIII
  • R 7 is an independently optionally substituted alkyl or aryl chain .
  • Non-limiting examples thereof include hydroxylalkylthiols , e . g . (2- ) mercaptoethanol , mercaptopropanol , mercaptobutanol , dithiothreitol , dithioerytol ; aminoalkylthiols , e . g . cysteine , cystamine ; alkylthiols , e . g . ethanedithiol , propanedithiol , butanedithiol ; and carboxyalkylthiols , e . g . thioglycolic acid, 2 , 3- dimercaptosuccinic acid.
  • Such thiol-containing agents are readily soluble in protic solvents in the applicable pH ranges and are therefore the preferred thiol-containing agents to be used .
  • the azide-reducing agent is water-soluble such that reaction between the azide-reducing agent and the peptide chain according to the method of the invention is facilitated and most efficient .
  • R 4 , R 5 and R 6 are independently optionally substituted alkyl or aryl chains and may be the same or different . It was found that such phosphines are particularly suitable for use in the method of the invention .
  • the phosphine is chosen from the group, consisting of tris (carboxyethyl ) phosphine , tris (carboxypropyl ) phosphine , tris (hydroxyethyl ) phosphine , tris (hydroxypropyl ) phosphine , tris (ethylamine ) phosphine , tris (propylamine) phosphine .
  • These phosphines are readily soluble in protic solvents in the applicable pH values and are therefore the preferred phosphines to be used .
  • the phosphine is tris (carboxyethyl ) - phosphine, as this compound is readily available at a relatively low cost price . It is expected that the trisalkylaminephosphines and the trisalkylhydroxylphosphines will be particularly effective at low pH .
  • the thiol-containing agent is a dithiol-containing agent, as it was found that dithiol-containing agents are 300-1 , 000 times more efficient in the reduction of the azide than monothiol-containing agents . It was found that dithiol- containing agents are about equally efficient in comparison to trivalent phosphines .
  • dithiothreitol butanedithiol or propanedithiol is used, as these compounds are readily available on the market, the latter two at a relatively low cost price .
  • the compound of step a) is peptide chain, which peptide chain is obtained by in vivo incorporation of at least one non-natural azide-functionalized amino acid, since this in particular allows for post-translational processing as indicated above .
  • the azide-functionalized amino acid may be any amino acid as disclosed above , such as azidohomoalanine and azidonorvaline and derivatives thereof .
  • step b) of the method according to the present invention is carried out at a pH in the range of 3-10.
  • the preferred pH is dependent on the protic solvent used and the solubility of the azide-reducing agent used.
  • One skilled in the art will readily be capable of determining a suitable system for carrying out the invention .
  • One example of such system is the system set forth below in example 2.
  • the present invention relates to a peptide obtained by a method according to the present invention .
  • This peptide may originate from a larger peptide from which it was liberated by the method according to the present invention .
  • the peptide C-terminal to the scissile bond may closely or fully resemble a native peptide or protein .
  • Figure 1 shows the mechanism proposed for the reaction :
  • Phosphines add to the electron deficient centre of the azide 1 initially forming intermediate 2 , that may either hydrolyze through postulated intermediate 3 into the triazene 4 or fragment into aza- ylide 5.
  • Triazenes have previously been shown react through an S N 2 reaction with suitable nucleophiles of either intra- or intermolecular origin . It is worthy to mention that at elevated pH conversion of 1 to homoserine without peptide cleavage occurs , indicative of S N 2 attack by OH " .
  • the protonated triazene 6 enables an energetically favorable five-membered membered ring closure resulting in cyclic imido ester 7 , a pathway analogous to the cyanogen bromide induced cleavage of the methionine peptide bond.
  • hydrolysis of the imido ester 7 produces the homoserine lactone 8 and amine 9. This mechanism is supported by the 18 O labeling experimental results described below which allow the carbonyl oxygen to be conserved in the lactone .
  • the phosphine activated azide , aza-ylide 5 can be reduced to amine or may become protonated generating intermediate 11 which via intramolecular S N 2 displacement involving the amide oxygen atom yields the common intermediate imido-ester 7 , that will then again hydrolyze into 8 and 9.
  • A Coomassie Blue stained gel of equal amounts (23 ⁇ g) of Azhal-PYP either mock incubated or incubated with 2ME, DTT, or TCEP in the absence and presence of urea as indicated .
  • B MALDI-FTMS spectrum of TCEP cleaved Azhal-PYP .
  • C sequence of His- tagged PYP from E. halophila , in which X denotes azidohomoalanine . Intact molecule mass and tryptic peptide mapping confirmed >95% incorporation of azidohomoalanine at methionine coded residues .
  • a coverage map obtained with TCEP (above the sequence ) and DTT (below the sequence) is presented . Solid lines indicate peptides resulting from cleavage that were detected with MALDI-TOF; dashed lines indicate peptides that were detected with ESI-FTMS .
  • Figure 3 shows a comparison of the cleavage of Azhal-PYP (all methionines replaced with Azhal ) with TCEP and methionine containing PYP with cyanogen bromide .
  • Digests were loaded onto an LCMSMS system.
  • B Deconvoluted MSMS fragmentation spectra of the doubly charged ion indicated in panel A with annotation of fragment ions and parent ion (par) . Identical fragment spectra prove the identicity of both peptides .
  • C sequence of the peptide and annotation of retrieved fragment ions .
  • U denotes homoserine lactone .
  • HIS- tagged recombinant Photoactive Yellow Protein ( PYP) from Ectothiorhodospira halophila was produced in methionine auxotrophic E. coli grown on L-Azhal containing media as follows .
  • L-Azhal was synthesized from L-BOC-2 , 4-diaminobutyric acid (Chem-Impex, Wood Dale, USA) by diazo transfer using Triflic-azide (TfN 3 ) (Lundquist, J. T . & Pelletier, J. C . (2001 ) Improved solid- phase peptide synthesis method utilizing alpha-azide-protected amino acids . Org. Lett . 3, 781-783 ) , followed by BOC deprotection with dioxane/HCl in dichloromethane .
  • Optimal cleavage of peptides and protein was achieved with a peptide concentration of about 0.2 mg/ml in 50 mM Na-acetate buffer pH 4.4 and 1-100 mM of Tris-carboxy-ethyl-phosphine (TCEP) .
  • TCEP Tris-carboxy-ethyl-phosphine
  • For hydrolysis of homoserine lactone an excess of unbuffered IM tris (hydroxymethyl ) amine was added and left for 48 h before sample cleanup with ZipTip Ci 8 (Millipore, Bedford, USA) .
  • TCEP-induced reduction and cleavage of purified Azhal-labelled PYP was analysed by SDS-PAGE ( figure 2a) and mass spectrometry ( figure 2b) .
  • MALDI-TOF MS or ESI-FTMS we were able to detect fragments N- or C- terminal to all Azhal residues (figure 2b) of TCEP treated protein . All fragments carried a free amine at the N-terminus and all , except the C-terminal peptide that ended in valine, having a homoserine lactone residue at the C-terminus . This was confirmed by tandem mass spectrometry using collision induced dissociation on ESI-FTMS .
  • the cleavage process disclosed in example 2 was performed in a broad range of pH values (tested from 3 to 10 ) .
  • the rate of reaction is slow at pH below 4 , due to decreased solubility of TCEP .
  • the highest ratio of cleavage : reduction occurs at pH 4.5 - 5. Under these conditions approximately only 5% of PYP is still intact and fully or partially reduced .
  • Peptide FFRXGFRF wherein X denotes a Azhal residue
  • TCEP TCEP at pH 5.
  • the products of this cleavage were FFRO, wherein 0 denotes a homoserine lactone residue , and GFRF as a free amine .
  • Example 5 Mass spectrometry
  • Reflectron MALDI-TOF mass spectra were recorded on a Micromass TofSpec 2EC (Micromass, Whyttenshawe, UK) .
  • ESI-FTMS spectra were acquired on an APEX-Q FTMS (Bruker Daltonics, Billerica, USA) , for low energy CID the ions were activated in the external collision cell or produced by SORI-CID in the FTMS cell.

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Abstract

La présente invention a trait à un procédé pour le clivage d'une liaison amide dans une chaîne peptidique, permettant d'obtenir un peptide N-terminal sous la forme d'une amine libre et un résidu secondaire, ainsi qu'à un peptide obtenu par un tel procédé.
PCT/EP2005/007233 2005-01-31 2005-07-01 Clivage specifique et modere de peptide ou de liaison amide WO2006079364A1 (fr)

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Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20030199084A1 (en) * 2000-03-16 2003-10-23 Eliana Saxon Chemoselective ligation

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20030199084A1 (en) * 2000-03-16 2003-10-23 Eliana Saxon Chemoselective ligation

Non-Patent Citations (15)

* Cited by examiner, † Cited by third party
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