Bis(2-sulfanylethyl)amino native peptide ligation

The reaction of a peptide featuring a bis(2-sulfanylethyl)amino (SEA) group on its C-terminus with a cysteinyl peptide in water at pH 7 and 37 °C leads to the chemoselective and regioselective formation of a native peptide bond. This method called SEA ligation enriches the native peptide ligation repertoire available to the peptide chemist. Preparation of an innovative solid support which allows the straightforward synthesis of peptide SEA fragments using standard Fmoc/tert-butyl solid phase peptide synthesis procedures is also described.     

N-Terminal peptide aldehydes as electrophiles in combinatorial solid phase synthesis of novel peptide isosteres

N-Terminal peptide aldehydes were synthesized on a solid support and utilized as electrophiles in nucleophilic reactions in order to furnish novel and diverse peptide isosteres. The aldehyde moiety of the peptide was synthesized by coupling a protected aldehyde building block to the peptide and deprotecting it quantitatively in less than 3 min. It was found that protection of the two succeeding amide nitrogens was necessary in order to avoid reaction between the aldehyde and backbone amides. The N-terminal peptide aldehydes were successfully reacted in the following way: (a) reductive amination with a large variety of amines, leading to N-alkyl-gamma-aminobutyric peptide isosteres positioned centrally in the peptide; (b) reductive amination with amino esters, leading to N-terminal 2,5-diketopiperazine peptides; (c) Horner-Wadsworth-Emmons olefination, leading to unsaturated peptide isosteres positioned centrally in the peptide; and (d) Pictet-Spengler condensations, leading to tetrahydro-beta-carbolines either positioned centrally in a peptide or fused with a diketopiperazine ring in the N-terminus of the peptide.     

A photoremovable ligation auxiliary for use in polypeptide synthesis

A photoremovable auxiliary for use in peptide synthesis via the native chemical ligation method is described. A 2-mercapto-1-(2-nitrophenyl)ethylamine (Mnpe-amine) moiety was attached to the N-terminus of a peptide via the periodate oxidation of a seryl peptide. The resulting peptide was then ligated to a peptide thioester, and UV (365 nm) irradiation resulted in the removal of the auxiliary from the peptide.     

The study of the interaction of a model alpha-helical peptide with lipid bilayers and monolayers

We studied the interaction of the alpha-helical peptide acetyl-Lys(2)-Leu(24)-Lys(2)-amide (L(24)) with tethered bilayer lipid membranes (tBLM) and lipid monolayers formed at an air-water interface. The interaction of L(24) with tBLM resulted in adsorption of the peptide to the surface of the bilayer, characterized by a binding constant K(c)=2.4+/-0.6 microM(-1). The peptide L(24) an induced decrease of the elasticity modulus of the tBLM in a direction perpendicular to the membrane surface, E(radial). The decrease of E(radial) with increasing peptide concentration can be connected with a disordering effect of the peptide to the tBLM structure. The pure peptide formed a stable monolayer at the air/water interface. The pressure-area isotherms were characterized by a transition of the peptide monolayer, which probably corresponds of the partial intercalation of the alpha-helixes at higher surface pressure. Interaction of the peptide molecules with lipid monolayers resulted in an increase of the mean molecular area of phospholipids both in the gel and liquid crystalline states. With increasing peptide concentration, the temperature of the phase transition of the monolayer shifted toward lower temperatures. The analysis showed that the peptide-lipid monolayer is not an ideally miscible system and that the peptide molecules form aggregates in the monolayer.     

Synthesis of some pseudo-peptide analogs of thiol proteinase inhibitors

Some pseudo-peptide analogs of thiol proteinase inhibitors were synthesized by a conventional solution method. Among them, Suc-Ala-Val-Val-Ala-psi-(CH2-NH)-Ala-pNA (peptide 1) and Suc-Ala-Val-Val-psi-(CH2-NH)-Ala-Ala-pNA (peptide 2) showed a stronger inhibitory activity compared with parent peptide such as Suc-Ala-Val-Val-Ala-Ala-pNA. In particular, peptide 2 was about 10-fold as active as the parent peptide (IC50 = 8 microM). Inserting psi-(CH2-NH) possibly makes the inhibitor less susceptible to papain and, as a result, produces more potent inhibition.     

Total synthesis of microcin B17 via a fragment condensation approach

The total synthesis of the 43 amino acid antibacterial peptide Microcin B17 (MccB17) is described. The natural product was synthesized via a convergent approach from a heterocycle-derived peptide and peptide thioester fragments prepared via Fmoc-strategy solid phase peptide synthesis (SPPS). Final assembly was achieved in an efficient manner using two Ag(I)-assisted peptide ligation reactions to afford MccB17 in excellent overall yield.     

Peptide bond formation mediated by 4,5-dimethoxy-2-mercaptobenzylamine after periodate oxidation of the N-terminal serine residue

[reaction in text] A thiol linker-attached peptide was prepared from a nonprotected peptide via an N(alpha)()-alpha-oxoacyl peptide. Selective oxidation of the N-terminal serine with sodium periodate gave the N(alpha)-glyoxyloyl peptide, reductive amination of which with 4,5-dimethoxy-2-(triphenylmethylthio)benzylamine gave an N(alpha)-4,5-dimethoxy-2-mercaptobenzyl glycyl peptide after removal of the trityl group. The N(alpha)-4,5-dimethoxy-2-mercaptobenzyl peptide can be condensed with a peptide thioester, and the linker is removable. This strategy provides a useful method for the synthesis of peptides using recombinant proteins.     

Spectroscopic investigations of metalloporphyrin-oligopeptide systems: evidence for peptide aggregation

Anionic pentapeptides consisting of a string of four glutamic acid residues terminated by either tyrosine (Glu4Tyr) or tryptophan (Glu4Trp) were synthesized, and their aggregation properties in buffered (pH = 7.0) aqueous solutions were investigated using two different approaches. In the first approach, the effects of the concentration of peptide used as its own probe (intrinsic probe) on its fluorescence emission, circular dichroism, surface tension, and solution pH yielded similar critical peptide concentrations of around 175 microM. This particular concentration was taken as evidence for peptide aggregation. In the second approach, peptide aggregation was investigated using cationic metalloporphyrins, tetrakis(N-methyl-4-pyridyl)porphyrin (Pd(II)TMPyP(4+) and Zn(II)TMPyP(4+)), as extrinsic probes. The effect of peptide concentration on porphyrin ground-state absorption confirmed peptide aggregation, but at a lower critical peptide concentration near 125 microM. This difference was attributed to the possible distortion introduced by the association of one (or more) large metalloporphyrin molecule with the peptide aggregates. Evidence for peptide aggregation was also demonstrated from the effect of peptide concentration on Pd(II)TMPyP(4+) triplet-state decay. The fast component (k(f), associated with electron transfer from the target Tyr and Trp residues to the porphyrin triplet state) was found to be independent of peptide concentration, implying no noticeable effect of peptide aggregation on the electron-transfer event. This was attributed to the fact that species formed by excitation of porphyrin associated with ion-pair complexes or bound to peptide aggregates and the diffusion together of the separate T(1) and peptide entities in the bulk phase are kinetically similar. On the other hand, the slower component (k(s)) of the decay, which is associated with the diffuse formation of an encounter complex between the free peptide and T(1) porphyrin (bulk phase), was peptide-dependent and displayed a critical peptide concentration near 125 microM, above which it became practically independent of peptide concentration. This invariance of k(s) was taken as an indication that the free peptide concentration in the bulk phase remains constant above 125 microM, the concentration at which peptide molecules prefer to associate as aggregates.     

Screening of inhibitors for influenza A virus using high-performance affinity chromatography and combinatorial peptide libraries

The affinity inhibitor of fusion peptide of influenza A virus has been studied using a combination of high-performance affinity chromatography (HPAC) and combinatorial peptide libraries. Fusion peptide (FP) (1-11) of influenza A virus was used as the affinity ligand and immobilized onto the poly(glycidyl methacrylate) (PGMA) beads. Positional scanning peptide libraries based on antisense peptide strategy and extended peptide libraries were designed and synthesized. The screening was carried out at acidic pH (5.5) in order to imitate the environment of virus fusion. A hendecapeptide FHRKKGRGKHK was identified to have a strong affinity to the FP (1-11). The dissociation constant of the complex of the hendecapeptide and the FP (1-11) is 3.10 x 10(-6) mol l(-1) in a physiological buffer condition. The polypeptide has a fairly inhibitory effect on three different strains of influenza A virus H1N1 subtype.     

An efficient peptide ligation using azido-protected peptides via the thioester method

Azido-protected Fmoc-Lys-OH (Fmoc-Lys(N₃)-OH) was synthesized from Fmoc-Lys-OH by the copper(II)-catalyzed diazo transfer method, and introduced to a peptide by the ordinary Fmoc-based solid-phase peptide synthesis. This azido peptide could be condensed with a peptide thioester by the Ag⁺-free thioester method without any significant side reactions. The azido group was easily reduced to an amino group by Zn powder after peptide condensation.     

One‐Pot/Sequential Native Chemical Ligation Using N‐Sulfanylethylanilide Peptide

N‐Sulfanylethylanilide (SEAlide) peptides were developed with the aim of achieving facile synthesis of peptide thioesters by 9‐fluorenylmethyloxycarbonyl (Fmoc)‐based solid‐phase peptide synthesis (Fmoc SPPS). Initially, SEAlide peptides were found to be converted to the corresponding peptide thioesters under acidic conditions. However, the SEAlide moiety was proved to function as a thioester in the presence of phosphate salts and to participate in native chemical ligation (NCL) with N‐terminal cysteinyl peptides, and this has served as a powerful protein synthesis methodology. The reactivity of a SEAlide peptide (anilide vs. thioester) can be easily tuned with or without the use of phosphate salts. This interesting property of SEAlide peptides allows sequential three‐fragment or unprecedented four‐fragment ligation for efficient one‐pot peptide/protein synthesis. Furthermore, dual‐kinetically controlled ligation, which enables three peptide fragments simultaneously present in the reaction to be ligated in the correct order, was first achieved using a SEAlide peptide. Beyond our initial expectations, SEAlide peptides have served in protein chemistry fields as very useful crypto‐peptide thioesters. DOI 10.1002/tcr.201200007     

Strategies for generating peptide radical cations via ion/ion reactions

Several approaches for the generation of peptide radical cations using ion/ion reactions coupled with either collision induced dissociation (CID) or ultraviolet photo dissociation (UVPD) are described here. Ion/ion reactions are used to generate electrostatic or covalent complexes comprised of a peptide and a radical reagent. The radical site of the reagent can be generated multiple ways. Reagents containing a carbon–iodine (C―I) bond are subjected to UVPD with 266‐nm photons, which selectively cleaves the C―I bond homolytically. Alternatively, reagents containing azo functionalities are collisionally activated to yield radical sites on either side of the azo group. Both of these methods generate an initial radical site on the reagent, which then abstracts a hydrogen from the peptide while the peptide and reagent are held together by either electrostatic interactions or a covalent linkage. These methods are demonstrated via ion/ion reactions between the model peptide RARARAA (doubly protonated) and various distonic anionic radical reagents. The radical site abstracts a hydrogen atom from the peptide, while the charge site abstracts a proton. The net result is the conversion of a doubly protonated peptide to a peptide radical cation. The peptide radical cations have been fragmented via CID and the resulting product ion mass spectra are compared to the control CID spectrum of the singly protonated, even‐electron species. This work is then extended to bradykinin, a more broadly studied peptide, for comparison with other radical peptide generation methods. The work presented here provides novel methods for generating peptide radical cations in the gas phase through ion/ion reaction complexes that do not require modification of the peptide in solution or generation of non‐covalent complexes in the electrospray process. Copyright © 2015 John Wiley & Sons, Ltd.     

Gas-phase anionic complexes of alkali metal ions and peptides: Structure and collision activated decompositions

Alkali metal ions and anionic peptides can be desorbed into the gas phase to give metal-bound peptides and bis(peptide) complexes bearing a ? 1 charge. Although amide nitrogens of peptide bonds are deprotonated in the gas phase by alkali metal ions, this reacion does not occur in solution. Metal-bound dipeptide anions exist as a single structure, whereas those of tripeptide complexes have three structures as revealed by tandem mass spectrometric studies. Ions of bis(peptide) complexes of alkali metals decompose upon collisional activation principally to form deprotonated peptides, in contrast to bis(peptide) complexes of alkaline earth metal ions, which undergo elimination of a neutral peptide.     

Structural and dynamical analysis of the hydration of the Alzheimer's beta-amyloid peptide

An analysis of the water molecules in the first solvation shell obtained from the molecular dynamics simulation of the amyloid beta(10-35)NH2 peptide and the amyloid beta(10-35)NH2E22Q "Dutch" mutant peptide is presented. The structure, energetics, and dynamics of water in the hydration shell have been investigated using a variety of measures, including the hydrogen bond network, the water residence times for all the peptide residues, the diffusion constant, experimentally determined HN amide proton exchange, and the transition probabilities for water to move from one residue to another or into the bulk. The results of the study indicate that: (1) the water molecules at the peptide-solvent interface are organized in an ordered structure similar for the two peptide systems but different from that of the bulk, (2) the peptide structure inhibits diffusion perpendicular to the peptide surface by a factor of 3 to 5 relative to diffusion parallel to the peptide surface, which is comparable to diffusion of bulk water, (3) water in the first solvation shell shows dynamical relaxation on fast (1-2 ps) and slow (10-40 ps) time scales, (4) a novel solvent relaxation master equation is shown to capture the details of the fast relaxation of water in the peptide's first solvation shell, (5) the interaction between the peptide and the solvent is stronger in the wild type than in the E22Q mutant peptide, in agreement with earlier results obtained from computer simulations [Massi, F.; Straub, J. E. Biophys J 2001, 81, 697] correlated with the observed enhanced activity of the E22Q mutant peptide.     

UV Raman spatially resolved melting dynamics of isotopically labeled polyalanyl peptide: slow alpha-helix melting follows 3(10)-helices and pi-bulges premelting

We used UV resonance Raman (UVRR) to examine the spatial dependence of the T-jump secondary structure relaxation of an isotopically labeled 21-residue mainly Ala peptide, AdP. The AdP penultimate Ala residues were perdeuterated, leaving the central residues hydrogenated, to allow separate monitoring of melting of the middle versus the end peptide bonds. For 5 to 30 degrees C T-jumps, the central peptide bonds show a approximately 2-fold slower relaxation time (189 +/- 31 ns) than do the exterior peptide bonds (97 +/- 15 ns). In contrast, for a 20 to 40 degrees C T-jump, the central peptide bond relaxation appears to be faster (56 +/- 6 ns) than that of the penultimate peptide bonds (131 +/- 46 ns). We show that, if the data are modeled as a two-state transition, we find that only exterior peptide bonds show anti-Arrhenius folding behavior; the middle peptide bonds show both normal Arrhenius-like folding and unfolding. This anti-Arrhenius behavior results from the involvement of pi-bulges/helices and 3(10)-helix states in the melting. The unusual temperature dependence of the (un)folding rates of the interior and exterior peptide bonds is due to the different relative (un)folding rates of 3(10)-helices, alpha-helices, and pi-bulges/helices. Pure alpha-helix unfolding rates are approximately 12-fold slower (approximately 1 micros) than that of pi-bulges and 3(10)-helices. In addition, we also find that the alpha-helix is most stable at the AdP N-terminus where eight consecutive Ala occur, whereas the three hydrophilic Arg located in the middle and at the C-terminus destabilize the alpha-helix in these regions and induce defects such as pi-bulges and 3(10)-helices.     

Conformation and Self-Association of Peptide Amphiphiles Based on the KTTKS Collagen Sequence

Studying peptide amphiphiles (PAs), we investigate the influence of alkyl chain length on the aggregation behavior of the collagen-derived peptide KTTKS with applications ranging from antiwrinkle cosmetic creams to potential uses in regenerative medicine. We have studied synthetic peptides amphiphiles C(14)-KTTKS (myristoyl-Lys-Thr-Thr-Lys-Ser) and C(18)-KTTKS (stearoyl-Lys-Thr-Thr-Lys-Ser) to investigate in detail their physicochemical properties. It is presumed that the hydrophobic chain in these self-assembling peptide amphiphiles enhances peptide permeation across the skin compared to KTTKS alone. Subsequently C(n)-KTTKS should act as a prodrug and release the peptide by enzymatic cleavage. Our results should be useful in the further development of molecules with collagen-stimulating activity.     

Synthesis and purification of aggregation-prone hydrophobic peptides by the incorporation of an Fmoc dipeptide with the peptide bond protected with a modified 2-hydroxy-4-methoxybenzyl (Hmb) group

The dipeptide Fmoc-Val-(2-hydroxy-4-methoxybenzyl)Gly-OBzl was synthesized and the 2-hydroxyl group carbamoylated to give a Boc-N(CH₃)CH₂CH₂N(CH₃)CO–, (Boc-Nmec-) modification of the 2-hydroxy-4-methoxybenzyl (Hmb) group. After catalytic hydrogenation and purification, the resulting dipeptide Fmoc-Val-(Boc-Nmec-Hmb)Gly-OH was used in solid phase peptide synthesis. During treatment with TFA, the peptide was released from the resin and the Boc group cleaved. The peptide could then be purified with an alkylated peptide bond carrying a cationic charge that both increased the solubility of the peptide during the purification steps and facilitated analysis by MALDI-TOF mass spectrometry. The Nmec group was cleaved by intramolecular cyclization under slightly alkaline conditions, followed by cleavage of the Hmb group by TFA to give the fully deprotected peptide.     

The energy landscape of a selective tumor-homing pentapeptide

Recently, a potentially powerful strategy based on phage-display libraries has been presented to target tumors via homing peptides attached to nanoparticles. The Cys-Arg-Glu-Lys-Ala (CREKA) peptide sequence has been identified as a tumor-homing peptide that binds to clotted plasmas proteins present in tumor vessels and interstitium. The aim of this work consists of mapping the conformational profile of CREKA to identify the bioactive conformation. For this purpose, a conformational search procedure based on modified simulated annealing combined with molecular dynamics was applied to three systems that mimic the experimentally used conditions: (i) the free peptide; (ii) the peptide attached to a nanoparticle; and (iii) the peptide inserted in a phage display protein. In addition, the free peptide was simulated in an ionized aqueous solution environment, which mimics the ionic strength of the physiological medium. Accessible minima of all simulated systems reveal a multiple interaction pattern involving the ionized side chains of Arg, Glu, and Lys, which induces a beta-turn motif in the backbone observed in all simulated CREKA systems.     

Computational study on nonenzymatic peptide bond cleavage at asparagine and aspartic acid

Nonenzymatic peptide bond cleavage at asparagine (Asn) and glutamine (Gln) residues has been observed during peptide deamidation experiments; cleavage has also been reported at aspartic acid (Asp) and glutamic acid (Glu) residues. Although peptide backbone cleavage at Asn is known to be slower than deamidation, fragmentation products are often observed during peptide deamidation experiments. In this study, mechanisms leading to the cleavage of the carboxyl-side peptide bond of Asn and Asp residues were investigated using computational methods (B3LYP/6-31+G**). Single-point solvent calculations at the B3LYP/6-31++G** level were carried out in water, utilizing the integral equation formalism-polarizable continuum (IEF-PCM) model. Mechanism and energetics of peptide fragmentation at Asn were comparatively analyzed with previous calculations on deamidation of Asn. When deamidation proceeds through direct hydrolysis of the Asn side chain or through cyclic imide formationvia a tautomerization routeit exhibits lower activation barriers than peptide bond cleavage at Asn. The fundamental distinction between the mechanisms leading to deamidationvia a succinimideand backbone cleavage was found to be the difference in nucleophilic entities involved in the cyclization process (backbone versus side-chain amide nitrogen). If deamidation is prevented by protein three-dimensional structure, cleavage may become a competing pathway. Fragmentation of the peptide backbone at Asp was also computationally studied to understand the likelihood of Asn deamidation preceding backbone cleavage. The activation barrier for backbone cleavage at Asp residues is much lower (approximately 10 kcal/mol) than that at Asn. This suggests that peptide bond cleavage at Asn residues is more likely to take place after it has deamidated into Asp.     

Ab Initio Design of Potent Anti-MRSA Peptides Based on Database Filtering Technology

To meet the challenge of antibiotic resistance worldwide, a new generation of antimicrobials must be developed. (1) This communication demonstrates ab initio design of potent peptides against methicillin-resistant Staphylococcus aureus (MRSA). Our idea is that the peptide is very likely to be active when the most probable parameters are utilized in each step of the design. We derived the most probable parameters (e.g., amino acid composition, peptide hydrophobic content, and net charge) from the antimicrobial peptide database (2) by developing a database filtering technology (DFT). Different from classic cationic antimicrobial peptides usually with high cationicity, DFTamP1, the first anti-MRSA peptide designed using this technology, is a short peptide with high hydrophobicity but low cationicity. Such a molecular design made the peptide highly potent. Indeed, the peptide caused bacterial surface damage and killed community-associated MRSA USA300 in 60 min. Structural determination of DFTamP1 by NMR spectroscopy revealed a broad hydrophobic surface, providing a basis for its potency against MRSA known to deploy positively charged moieties on the surface as a mechanism for resistance. Our ab initio design combined with database screening (3) led to yet another peptide with enhanced potency. Because of the simple composition, short length, stability to proteases, and membrane targeting, the designed peptides are attractive leads for developing novel anti-MRSA therapeutics. Our database-derived design concept can be applied to the design of peptide mimicries to combat MRSA as well.