The Radical Ion Chemistry of S-Nitrosylated Peptides

The radical ion chemistry of a suite of S-nitrosopeptides has been investigated. Doubly and triply-protonated ions of peptides NYCGLPGEYWLGNDK, NYCGLPGEYWLGNDR, NYCGLPGERWLGNDR, NACGAPGEKWAGNDK, NYCGLPGEKYLGNDK, NYGLPGCEKWYGNDK and NYGLPGEKWYGCNDK were subjected to electron capture dissociation (ECD), and collision-induced dissociation (CID). The peptide sequences were selected such that the effect of the site of S-nitrosylation, the nature and position of the basic amino acid residues, and the nature of the other amino acid side chains, could be interrogated. The ECD mass spectra were dominated by a peak corresponding to loss of ^?NO from the charge-reduced precursor, which can be explained by a modified Utah-Washington mechanism. Some backbone fragmentation in which the nitrosyl modification was preserved was also observed in the ECD of some peptides. Molecular dynamics simulations of peptide ion structure suggest that the ECD behavior was dependent on the surface accessibility of the protonated residue. CID of the S-nitrosylated peptides resulted in homolysis of the S?CN bond to form a long-lived radical with loss of ^?NO. The radical peptide ions were isolated and subjected to ECD and CID. ECD of the radical peptide ions provided an interesting comparison to ECD of the unmodified peptides. The dominant process was electron capture without further dissociation (ECnoD). CID of the radical peptide ions resulted in cysteine, leucine, and asparagine side chain losses, and radical-induced backbone fragmentation at tryptophan, tyrosine, and asparagine residues, in addition to charge-directed backbone fragmentation.     

Fast and Cysteine-Specific Modification of Peptides,Proteins and Bacteriophage Using Chlorooximes

This work reports a novel chlorooxime mediated modification of native peptides and proteins under physiologic conditions. This method features fast reaction kinetics (apparent k₂=306±4 M⁻¹s⁻¹ for GSH) and exquisite selectivity for cysteine residues. This cysteine conjugation reaction can be carried out with just single-digit micromolar concentrations of the labeling reagent. The conjugates show high stability towards acid, base, and external thiol nucleophiles. A nitrile oxide species generated in situ is likely involved as the key intermediate. Furthermore, a bis-chlorooxime reagent is synthesized to enable facile Cys-Cys stapling in native peptides and proteins. This highly efficient cysteine conjugation and stapling was further implemented on bacteriophage to construct chemically modified phage libraries.     

Biomimetic studies on the mechanism of stereoselective lanthionine formation

Selenocysteine derivatives are useful precursors for the synthesis of peptide conjugates and selenopeptides. Several diastereomers of Fmoc-3-methyl-Se-phenylselenocysteine (FmocMeSec(Ph)) were prepared and used in solid phase peptide synthesis (SPPS). Once incorporated into peptides, the phenylselenide functionality provides a useful handle for the site and stereospecific introduction of E- or Z-dehydrobutyrine residues into peptide chains via oxidative elimination. The oxidation conditions are mild, can be performed on a solid support, and tolerate functionalities commonly found in peptides, including variously protected cysteine residues. Dehydropeptides containing unprotected cysteine residues undergo intramolecular stereoselective conjugate addition to afford cyclic lanthionines and methyllanthionines, which have the same stereochemistry as found in lantibiotics, a family of ribosomally synthesized and post-translationally modified peptide antibiotics. The observed stereoselectivity is shown to originate from a kinetic rather than a thermodynamic preference.     

Iodine Oxidation of S-Trityl- and S-Acetamidomethyl-cysteine-peptides Containing Tryptophan: Conditions Leading to the Formation of Tryptophan-2-thioethers

Cystine peptides are conveniently prepared from S-acetamidomethyl- or S-trityl-protected cysteine derivatives by direct oxidation with iodine. Since the reaction proceeds through the formation of sulfenyl iodides, these highly reactive groups may substitute the indole ring of tryptophan residues, resulting in the formation of 2-thioethers. During the synthesis of the peptide hormone somatostatin, we investigated this possible side reaction. By-products of the tryptophan-2-thioether type can be produced under conditions which lead to a marked retardation of the disulfide bond formation. The largest amount of these compounds were formed when the oxidation was carried out in 90% aqueous trifluoroethanol. In model peptides in which tryptophan and cysteine residues were separated by 1 to 4 glycine residues, the ring size of the resulting thioether exerted a strong influence on the yield: in peptides with 1 and 2 glycines, only dimeric disulfides were formed. Incorporation of 3 and 4 glycine residues gave thioethers in yields of about 40% and 70% respectively. Conversely, under normal conditions of iodine oxidation, when disulfides are rapidly formed from the S-acetamidomethyl- or S-tritylcysteine residues, tryptophan-2-thioethers are produced only in insignificant amounts or not at all.     

Synthesis and electrochemical studies of disubstituted ferrocene/dipeptide conjugates with sulfur-containing side chains

A series of 1,1′-disubstituted ferrocenoyl peptides incorporating dipeptide sidearms has been synthesized and studied electrochemically. The target peptides include ferrocene as an electrochemical reporter, sulfur-containing amino acids (l-methionine, S-methyl-l-cysteine, S-trityl-l-cysteine, S-benzhydryl-l-cysteine) as metal binding agents, and amino acids with non-polar side chains (l-alanine, l-valine, l-phenylalanine) as spacers between reporter and metal binding groups. Ferrocene/dipeptide conjugates were prepared using solution phase peptide synthesis methods employing a BOC-protecting group strategy and HBTU- (O-(benzotriazol-1-yl)-N,N,N′,N′-tetramethyluronium hexafluorophosphate) mediated peptide coupling. The electrochemical properties of these 1,1′-substituted ferrocenoyl peptides have been characterized using cyclic voltammetry. All exhibit fully reversible one electron oxidation steps; forward sweep half wave peaks (E_F), reverse sweep half wave peaks (E_R), peak separations (ΔE_P) and half wave potentials (E_1/2) are reported. Finally, towards the goal of utilizing ferrocenoyl peptides to detect heavy metals in solution, the response of these ferrocene/dipeptide conjugates to metal cations (zinc(II), mercury(II), cadmium(II), lead(II), silver(I)) has been examined. Monitoring changes in the potential of the Fe(II)/Fe(III) redox couple to follow peptide/metal interactions, we have probed the influence of the spacer unit between the redox reporter and the metal-binding amino acid, and shown that these systems respond to mercury(II) more strongly than to other heavy metal ions.     

Analysis of Fragmentation Pathways of Peptide Modified with Quaternary Ammonium and Phosphonium Group as Ionization Enhancers

Peptide modification by a quaternary ammonium group containing a permanent positive charge is a promising method of increasing the ionization efficiency of the analyzed compounds, making ultra-sensitive detection even at the attomolar level possible. Charge-derivatized peptides may undergo both charge remote (ChR) and charge-directed (ChD) fragmentation. A series of model peptide conjugates derivatized with N,N,N-triethyloammonium (TEA), 1-azoniabicyclo[2.2.2]octane (ABCO), 2,4,6-triphenylopyridinium (TPP) and tris(2,4,6-trimetoxyphenylo)phosphonium (TMPP) groups were analyzed by their fragmentation pathways both in collision-induced dissociation (CID) and electron-capture dissociation (ECD) mode. The effect of the fixed-charge tag type and peptide sequence on the fragmentation pathways was investigated. We found that the aspartic acid effect plays a crucial role in the CID fragmentation of TPP and TEA peptide conjugates whereas it was not resolved for the peptides derivatized with the phosphonium group. ECD spectra are mostly dominated by c_n ions. ECD fragmentation of TMPP-modified peptides results in the formation of intense fragments derived from this fixed-charge tag, which may serve as reporter ion.     

Stereodivergent approach to both syn- and anti-isomers of γ-amino-β-hydroxy acids: (3S,4S)- and (3R,4S)-AHPPA derivatives

A stereodivergent approach employing an N-hydroxymethyl group has been utilized to produce both diastereomeric derivatives of (3S,4S)-AHPPA 3 and (3R,4S)-AHPPA 4, via an intramolecular conjugate addition and an intramolecular epoxidation, respectively. The selectivity of the intramolecular conjugate addition was more than 10:1 while that of the intramolecular epoxidation was more than 1:20.     

Copper(I)-catalyzed amination of halothiophenes with polyamines

Copper(I)-catalyzed hetarylation of a series of polyamines and of 4,7,10-trioxatridecane-1,13-diamine with halothiophenes has been studied with a view to obtaining the corresponding N,N′-dihetaryl derivatives. The target products can be obtained using both 3-iodothiophene in the presence of CuI/L-proline/EtCN or CuI/N,N-dimethylglycine/EtCN as catalytic system and 3-bromothiophene in the system CuI/2-(2-methyl-1-oxopropyl)cyclohexanone/DMF. The latter system is also suitable for the hetarylation of 4,7,10-trioxatridecane-1,13-diamine with 3-iodothiophene. In some cases, N-(thiophen-3-yl) derivatives have also been isolated.     

S-Trityl protection of bis-amino bis-thiol (BAT) chelator enables flexible derivatisation and facile labelling with technetium-99m

We have coupled S,S′-bis-trityl N-BOC protected 1,2-ethylenedicysteamine, a bis-amino bis-thiol (BAT) tetraligand, via a propylene or ethylene spacer to several biologically active molecules including 2-nitroimidazole, desethylflumazenil, a beta-CIT analogue, glucose and 2-(2′-hydroxy-4′-aminophenyl)-1,3-benzothiazole. The conjugates were efficiently labelled with technetium-99m by consecutive heating of the S,S′-bis-trityl protected ligand in hydrochloric acid followed by neutralisation and heating in the presence of ^99mTc-tartrate. The S,S′-bis-trityl BAT chelator is an interesting synthon that allows both flexible derivatisation with various biologically active molecules and facile labelling with technetium-99m.     

Luminol anchors improve the electrochemical-tyrosine-click labelling of proteins

New methods for chemo-selective modifications of peptides and native proteins are important in chemical biology and for the development of therapeutic conjugates. Less abundant and uncharged amino-acid residues are interesting targets to form less heterogeneous conjugates and preserve biological functions. Phenylurazole (PhUr), N-methylphenylurazole (NMePhUr) and N-methylluminol (NMeLum) derivatives were described as tyrosine (Y) anchors after chemical or enzymatic oxidations. Recently, we developed the first electrochemical Y-bioconjugation method coined eY-click to activate PhUr in biocompatible media. In this work, we assessed the limitations, benefits and relative efficiencies of eY-click conjugations performed with a set of PhUr, NMePhUr and NMeLum derivatives. Results evidenced a high efficiency of NMeLum that showed a complete Y-chemoselectivity on polypeptides and biologically relevant proteins after soft electrochemical activation. Side reactions on nucleophilic or heteroaromatic amino-acids such as lysine or tryptophan were never observed during mass spectrometry analysis. Myoglobine, bovine serum albumin, a plant mannosidase, glucose oxidase and the therapeutically relevant antibody trastuzumab were efficiently labelled with a fluorescent probe in a two-step approach combining eY-click and strain-promoted azide–alkyne cyclization (SPAAC). The proteins conserved their structural integrity as observed by circular dichroism and the trastuzumab conjugate showed a similar binding affinity for the natural HER2 ligand as shown by bio-layer interferometry. Compared to our previously described protocol with PhUr, eY-click with NMeLum species showed faster reaction kinetics, higher (complete) Y-chemoselectivity and reactivity, and offers the interesting possibility of the double tagging of solvent-exposed Y.

We assessed the relative efficiencies of tyrosine anchors in the electrochemical conjugation of peptides and proteins. Luminol derivatives showed faster reaction kinetics, complete tyrosine-chemoselectivity, and possible double modification.     

Guanidine Additive Enabled Intermolecular ortho-Phthalaldehyde-Amine-Thiol Three-Component Reactions for Modular Constructions

Recently, ortho-phthalaldehyde (OPA) is experiencing a renascence for the modification of proteins and peptides through OPA-amine two-component reactions for bioconjugation and intramolecular OPA-amine-thiol three-component reactions for cyclization. Historically, small thiol molecules were used in large excess to allow for the intermolecular OPA-amine-thiol reaction forming 1-thio-isoindole derivatives. In this study, we discovered that guanidine could serve as an effective additive to switch the intermolecular OPA-amine-thiol three-component reaction to a stoichiometric process and enable the modular construction of peptide-peptide, and peptide-drug conjugate structures. Thus, 12 model peptide-peptide conjugates have been synthesized from unprotected peptides featuring all proteinogenic residues. Besides, 6 peptide-drug conjugates have been prepared in one step, with excellent conversions and isolated yields. In addition, a conjugate product has been further functionalized by utilizing a premodified OPA derivative, demonstrating the versatility and flexibility of this reaction.     

Study of intramolecular aminolysis in peptides containing N-alkylamino acids at position 2

Many peptides and proteins, containing N^α-alkylamino acids (including proline) at the second position, are prone to intramolecular aminolysis (IA) with elimination of N-terminal dipeptide sequence as 2,5-diketopiperazines (DKP). We synthesized a series of short peptides, containing N-alkylamino acids at position 2, and studied their stability in the presence of acetic acid and amines. The presence of side chains in the second and the third amino acid residues and alkylation at N^α of the third amino acid residue slowed down IA. N^α-Alkyl residue in the first amino acid residue impeded IA only in peptides, containing three or more residues. Side chains of the first amino acids did not affect significantly the cleavage rates. Acetic acid promoted IA more strongly than aqueous ammonia, while tertiary amines were less effective. Peptides with methionine-S-oxide residues were more labile than the unoxidized analogs, suggesting intramolecular assistance of the S-oxide group in aminolysis. Surprisingly, intermediate compounds of the formula Boc–Met-MeXaa-Sar–NHR underwent rapid cleavage (endopeptolysis) upon attempted acidolytic deprotection.     

Chromatographic methods for determination of S-substituted cysteine derivatives—A comparative study

A novel HPLC method for determination of a wide variety of S-substituted cysteine derivatives in Allium species has been developed and validated. This method allows simultaneous separation and quantification of S-alk(en)ylcysteine S-oxides, γ-glutamyl-S-alk(en)ylcysteines and γ-glutamyl-S-alk(en)ylcysteine S-oxides in a single run. The procedure is based on extraction of these amino acids and dipeptides by methanol, their derivatization by dansyl chloride and subsequent separation by reversed phase HPLC. The main advantages of the new method are simplicity, excellent stability of derivatives, high sensitivity, specificity and the ability to simultaneously analyze the whole range of S-substituted cysteine derivatives. This method was critically compared with other chromatographic procedures used for quantification of S-substituted cysteine derivatives, namely with two other HPLC methods (derivatization by o-phthaldialdehyde/tert-butylthiol and fluorenylmethyl chloroformate), and with determination by gas chromatography or capillary electrophoresis. Major advantages and drawbacks of these analytical procedures are discussed. Employing these various chromatographic methods, the content and relative proportions of individual S-substituted cysteine derivatives were determined in four most frequently consumed alliaceous vegetables (garlic, onion, shallot, and leek).     

2-Nitroferrocenyloxazolines: precursors to nitrofulvalenes and derivatives of (pS)- and (pR)-2-aminoferrocenecarboxylic acids

Diastereoselective lithiation of (S)-2-ferrocenyl-4-(1-methylethyl)oxazoline, followed by addition of N₂O₄, gave (S)-2-[(_pS)-2-nitroferrocenyl]-4-(1-methylethyl)oxazoline which was subsequently converted into derivatives of (_pS)-2-aminoferrocenecarboxylic acid. The corresponding (_pR)-derivatives were obtained through use of a removable TMS blocking group. The 2-nitroferrocenyloxazolines produced in this work underwent facile photo-decomplexation to give 2-nitrocyclopentadienyliden-1,3-oxazolidenes.     

Asymmetric synthesis of cyclic β-amino acids and cyclic amines via sequential diastereoselective conjugate addition and ring closing metathesis

Diastereoselective conjugate addition of lithium (S)-N-allyl-N-α-methylbenzylamide to a range of α,β-unsaturated esters followed by ring closing metathesis is used to afford efficiently a range of substituted cyclic β-amino esters in high d.e. Alternatively, conjugate addition to α,β-unsaturated Weinreb amides, functional group conversion and ring closing metathesis affords cyclic amines in high d.e. The further application of this methodology to the synthesis of a range of carbocyclic β-amino esters via conjugate addition, enolate alkylation and ring closing metathesis is also described. Application of this methodology affords, after deprotection, (S)-homoproline, (S)-homopipecolic acid, (S)-coniine and (1S,2S)-trans-pentacin.     

Synthesis of [60]fullerene-glycopyranosylaminopyrimidin-4-one conjugates

The synthesis of several C₆₀ derivatives containing a 6-(β-d-glycopyranosylamino)pyrimidin-4-one unit and a C₆₀-uridine conjugate is described. The fullerene derivatives bearing a 4-(β-d-glycopyranosylamino)pyrimidin-4-one moiety were synthesised by 1,3-dipolar cycloaddition reactions of C₆₀ with azomethine ylides generated in situ from the corresponding 5-formylpyrimidin-4-one derivatives and N-methylglycine. The synthesis of the C₆₀-uridine conjugate involved the selective protection of the 2′- and 3′-hydroxyl groups of uridine, esterification, cyclopropanation of C₆₀ and, finally, the deprotection of the hydroxyl groups. One of the fullerene-glycopyranosylaminopyrimidin-4-one conjugates was characterised by single-crystal X-ray crystallography. Differentiation between pairs of diastereoisomers, for several fullerene derivatives, was achieved through the study of their gas-phase fragmentations.     

Asymmetric synthesis of α-mercapto-β-amino acid derivatives: application to the synthesis of polysubstituted thiomorpholines

Tandem conjugate addition of homochiral lithium N-benzyl-N-(α-methyl-p-methoxybenzyl)amide to tert-butyl cinnamate and enolate trapping with TsS^tBu proceeds with high diastereoselectivity to give a homochiral anti-α-tert-butylthio-β-amino ester. Stepwise deprotection gives the corresponding free α-tert-butylthio-β-amino acid without epimerisation. Tandem conjugate addition of homochiral lithium N-allyl-N-(α-methylbenzyl)amide to tert-butyl cinnamate and enolate trapping with TsS^tBu followed by conversion of the S-tert-butyl group to a disulphide, and reduction with Lalancette’s reagent generates polysubstituted thiomorpholine derivatives.     

Amino acid bromides: their utilization for difficult couplings in solid-phase peptide synthesis

Use of N-protected-α-amino acid bromides for facile solid-phase synthesis of peptides (SPPS) containing extremely sterically hindered non-proteinogenic amino acids is presented. Amino acid bromides (Aaa-Br), generated in situ, were used for the synthesis of long chain homopeptides containing up to eight successive α-MeVal or Aib residues. SPPS of a heteropeptide containing a very bulky amino acid building block is also described. The choice of suitable N-protections is discussed.     

Synthesis of polyglutamine conjugates of lysine dendrimers in solution and polymer gel

The synthesis of polyglutamine conjugates of lysine dendrimers, in which carboxyl groups of polyglutamine chains are linked via one point to the amino groups of N-terminal lysine fragments of dendrimers, is studied. Lysine dendrimers of third, fourth, and fifth generations are preliminarily prepared via the solid-phase synthesis on a polymer support, crosslinked p-methylbenzohydrylaminopolystyrene. The first approach to the synthesis of polyglutamine conjugates of dendrimers consisted in that, after the synthesis of lysine dendrimers, their removal from the polymer support, their full unblocking, and their purification, γ-benzyl glutamate N-carboxyadhydride is involved in solution polymerization at the amino groups of lysine of the outer sphere of dendrimers. The second approach includes the polymerization of γ-benzyl glutamate N-carboxyadhydride on the amino groups of N-terminal lysine residues of lysine dendrimers performed before dendrimer removal from the polymer support. The structural study of star-shaped conjugate of lysine dendrimers makes it possible to for the first time estimate the similarities and differences in these two approaches to the synthesis of polyglutamine conjugates of lysine dendrimers.     

Novel Cysteine Tags for the Sequencing of Non-Tryptic Disulfide Peptides of Anurans: ESI-MS Study of Fragmentation Efficiency

Mass spectrometry faces considerable difficulties in de novo sequencing of long non-tryptic peptides with S–S bonds. Long disulfide-containing peptides brevinins 1E and 2Ec from frog Rana ridibunda were reduced and alkylated with nine novel and three known derivatizing agents. Eight of the novel reagents are maleimide derivatives. Modified samples were subjected to MS/MS studies on FT-ICR and Orbitrap mass spectrometers using CAD/HCD or ECD/ETD techniques. Procedures, fragmentation patterns, and sequence coverage for two peptides modified with 12 tags are described. ECD/ETD and CAD fragmentation revealed complementary sequence information. Higher-energy collisionally activated dissociation (HCD) sufficiently enhanced y-ions formation for brevinin 1E, but not for brevinin 2Ec. Some novel tags [N-benzylmaleimide, N-(2,6-dimethylphenyl)maleimide] along with known N-phenylmaleimide and iodoacetic acid showed high total sequence coverage taking into account combined ETD and HCD fragmentation. Moreover, modification of long (34 residues) brevinin 2Ec with N-benzylmaleimide or N-(2,6-dimethylphenyl)maleimide yielded high sequence coverage and full C-terminal sequence determination with ECD alone.