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Freshwater snails of the genus Biomphalaria serve as intermediate hosts for the digenetic trematode Schistosoma mansoni, the etiological agent for the most widespread form of intestinal schistosomiasis. As neuropeptide signaling in host snails can be altered by trematode infection, a neural transcriptomics approach was undertaken to identify peptide precursors in Biomphalaria glabrata, the major intermediate host for S. mansoni in the Western Hemisphere. Three transcripts that encode peptides belonging to the FMRF-NH2 -related peptide (FaRP) family were identified in B. glabrata. One transcript encoded a precursor polypeptide (Bgl-FaRP1; 292 amino acids) that included eight copies of the tetrapeptide FMRF-NH2 and single copies of FIRF-NH2 , FLRF-NH2 , and pQFYRI-NH2 . The second transcript encoded a precursor (Bgl-FaRP2; 347 amino acids) that comprised 14 copies of the heptapeptide GDPFLRF-NH2 and 1 copy of SKPYMRF-NH2 . The precursor encoded by the third transcript (Bgl-FaRP3; 287 amino acids) recapitulated Bgl-FaRP2 but lacked the full SKPYMRF-NH2 peptide. The three precursors shared a common signal peptide, suggesting a genomic organization described previously in gastropods. Immunohistochemical studies were performed on the nervous systems of B. glabrata and B. alexandrina, a major intermediate host for S. mansoni in Egypt. FMRF-NH2 -like immunoreactive (FMRF-NH2 -li) neurons were located in regions of the central nervous system associated with reproduction, feeding, and cardiorespiration. Antisera raised against non-FMRF-NH2 peptides present in the tetrapeptide and heptapeptide precursors labeled independent subsets of the FMRF-NH2 -li neurons. This study supports the participation of FMRF-NH2 -related neuropeptides in the regulation of vital physiological and behavioral systems that are altered by parasitism in Biomphalaria.

Short peptide biomimetic affinity chromatography as a novel antibody separation chromatography is a potential alternative to protein A chromatography. However, if directly attaching ligand to matrix, the adsorption capacity and mass transfer rate would be affected by pore blockage and steric effect. Grafting resin is an effective method to solve this problem by using polymer as a bridge between matrix and ligand. In this work, a novel resin was prepared by grafting a tetrapeptide to the dextran-grafted matrix. Then, the adsorption properties for human immunoglobin G and BSA were determined. The results showed the saturation adsorption capacity could reach to 133 mg/g resin at pH 8.9 with a significantly low dissociation constant (0.03 mg/mL). The influence of flow rates to dynamic binding capacity of this resin was less than that of the non-grafted resin. The separation performance of the resin showed monoclonal antibody could be well isolated from the Chinese hamster ovary culture supernatant at pH 9.0 with the purity of 93.0% and yield of 84.7% by one step. Overall, this resin could achieve higher binding capacity by the possible of gaining higher ligand density, indicating its potential significance for separation in larger scale systems.

This study aims at analyzing complexation properties of two new short somatostatin analogues, their synthesis, radiolabeling with 44 Sc, 207 Bi, and 152 Eu and stability in vitro. Short tetrapeptide Phe-d-Trp-Lys-Thr and pentapeptide Thz-Phe-d-Trp-Lys-Thr were first conjugated with the DOTA macrocyclic chelator. These conjugates were radiolabeled with 44 Sc, 207 Bi, and 152 Eu and characterized by thin-layer chromatography (TLC) and HPLC. The radiochemical purity was measured using digital autoradiography and gamma spectrometry. Optimum conditions of DOTA-conjugate labeling were found: 0.1mM, pH 8.0 to 8.4 at 90°C for DOTA-tetrapeptide complexes with 207 Bi and 152 Eu; 0.05mM, pH 4.0 to 5.0 at 90°C for 44 Sc-DOTA-tetrapeptide; 0.2mM, pH 4.0 to 5.0 at 90°C for 44 Sc-DOTA-pentapeptide. Complexes of DOTA-pentapeptide with 207 Bi and 152 Eu of radiochemical purity more than 95% were probably unstable at temperature higher than 37°C and were obtained at 37°C, pH 8.0 to 8.4 within 4 days. Mass spectra of the Eu-DOTA-pentapeptide revealed the presence of small fragments of the pentapeptide conjugate in the complex solution. in vitro stability studies were performed in saline in the presence of serum proteins and biologically relevant metal cations. All complexes demonstrated no cation release in vitro within 1 to 4 hours.

The enzymes Csd6 and Pgp2 are peptidoglycan (PG) proteases found in the pathogenic bacteria Helicobacter pylori and Campylobacter jejuni, respectively. These enzymes are involved in the trimming of non-crosslinked PG sidechains and catalyze the cleavage of the bond between meso-diaminopimelic acid (meso-Dap) and d-alanine, thus converting a PG tetrapeptide into a PG tripeptide. They are known to be cell-shape-determining enzymes, because deletion of the corresponding genes results in mutant strains that have lost the normal helical phenotype and instead possess a straight-rod morphology. In this work, we report two approaches directed towards the synthesis of the tripeptide substrate Ac-iso-d-Glu-meso-oxa-Dap-d-Ala, which serves as a mimic of the terminus of an non-crosslinked PG tetrapeptide substrate. The isosteric analogue meso-oxa-Dap was utilized in place of meso-Dap to simplify the synthetic procedure. The more efficient synthesis involved ring opening of a peptide-embedded aziridine by a serine-based nucleophile. A branched tetrapeptide was also prepared as a mimic of the terminus of a crosslinked PG tetrapeptide. We used MS analysis to demonstrate that the tripeptide serves as a substrate for both Csd6 and Pgp2 and that the branched tetrapeptide serves as a substrate for Pgp2, albeit at a significantly slower rate.

Exposure to the vesicant sulfur mustard (SM) may lead to erythema and blistering. Toxicity of SM is hypothesized due to the alkylation of DNA bases and nucleophilic amino acid side chains in proteins (adducts) by forming the hydroxyethylthioethyl (HETE) moiety. Despite its prohibition by the chemical weapons convention, SM still represents a serious threat to military personnel and civilians. Therefore, development and improvement of forensic analytical methods for the verification of SM exposure is of high interest. Protein adducts have been shown to be highly suitable and beneficial biomarkers of poisoning. Herein we present methionine329 in human serum albumin (HSA) as a novel target of SM forming a HETE-methionyl sulfonium ion. The alkylated tetrapeptide LeuGlyMet329 (-HETE)Phe, LGM(-HETE)F, was detected after pepsin-mediated proteolysis and subsequent analysis by microbore liquid chromatography-electrospray ionization-high-resolution tandem-mass spectrometry. Compound identity was confirmed by a synthetic reference. Proteolysis conditions for HSA were optimized towards maximum yield of LGM(-HETE)F and its limit of identification (32.3 nM SM in serum) was similar to those of the established HSA-derived biomarkers HETE-CysPro and HETE-CysProPhe (15.6 nM SM in serum). Stability of the alkylated Met329 in vitro and in vivo was limited to 5 days making this modification a beneficial short-time biomarker. Furthermore, it was found that the HETE-methionyl sulfonium ion can transfer its HETE moiety to the side chain of cysteine and glutamic acid as well as to the N-terminus of peptides and proteins in vitro thus revealing novel insights into the molecular toxicity of SM.

From arid, high desert soil samples collected near Bend, Oregon, 19 unique bacteria were isolated. Each strain was identified by 16S rRNA gene sequencing, and their organic extracts were tested for antibacterial and antiproliferative activities. Noteworthy, six extracts (30 %) exhibited strong inhibition resulting in less than 50 % cell proliferation in more than one cancer cell model, tested at 10 μg/mL. Principal component analysis (PCA) of LC/MS data revealed drastic differences in the metabolic profiles found in the organic extracts of these soil bacteria. In total, fourteen potent antibacterial and/or cytotoxic metabolites were isolated via bioactivity-guided fractionation, including two new natural products: a pyrazinone containing tetrapeptide and 7-methoxy-2,3-dimethyl-4H-chromen-4-one, as well as twelve known compounds: furanonaphthoquinone I, bafilomycin C1 and D, FD-594, oligomycin A, chloramphenicol, MY12-62A, rac-sclerone, isosclerone, tunicamycin VII, tunicamycin VIII, and (6S,16S)-anthrabenzoxocinone 1.264-C.

Self-assembling short peptides have attracted great interest as enzyme mimics, especially if the catalytic activity resides solely in the supramolecular structure so that it can be switched on/off as needed by controlling assembly/disassembly. Among the various enzyme classes, hydrolases find wide application in biomaterials, and their mimetics often contain His residues, in addition to either divalent cations or other amino acids to mimic the catalytic site. This work reports two self-assembling tetrapeptides based on the Ser-His motif for catalysis and the Phe-Phe motif to drive amyloid structure formation. Both peptides form thermoreversible hydrogels in phosphate buffer at neutral pH that display a mild esterase-like activity, as demonstrated on the hydrolysis of 4-nitrophenyl acetate as a model substrate, although presence of Ser did not enhance catalytic activity. The systems are characterised by circular dichroism, transmission electron microscopy, oscillatory rheology and Thioflavin T fluorescence as an amyloid stain, to provide further insights that may assist the future design of improved supramolecular catalysts.

c-di-GMP is an attractive target in the fight against bacterial infections since it is a near ubiquitous second messenger that regulates important cellular processes of pathogens, including biofilm formation and virulence. Screening of a combinatorial peptide library enabled the identification of the proline-rich tetrapeptide Gup-Gup-Nap-Arg, which binds c-di-GMP selectively over other nucleotides in water. Computational and CD spectroscopic studies provided a possible binding mode of the complex and enabled the design of a pentapeptide with even higher binding strength towards c-di-GMP. Biological studies showed that the tetrapeptide inhibits biofilm growth by the opportunistic pathogen P. aeruginosa.

A combination of genomic and metabolomic approaches recently resulted in the identification of a nonribosomal tetrapeptide tambromycin, which possesses promising antiproliferative activity and several unusual structural features, including a densely substituted indole, a methyloxazoline ring, and an unusual pyrrolidine-containing amino acid called tambroline. In this work, we identify a concise synthetic route to access tambromycin, which relies on the strategic use of biocatalytic and chemocatalytic C-H functionalization methods to prepare two key precursors to the natural product in an efficient and scalable manner. The success of our study highlights the benefits of applying the principles of biocatalytic retrosynthesis as well as C-H functionalization logic to the synthesis of complex molecular scaffolds.

Supramolecular self-assembly in biological systems holds promise as a means to convert and amplify disease-specific signals to physical or mechanical signals that can direct cell fate. The approach requires programmable self-assembling systems that demonstrate tunable and predictable behavior under physiological conditions. Mixed-charge (zwitterionic) particles are considered suitable for biological applications due to favorable stability. We report on the use of zwitterionic tetrapeptide modalities to direct nanoparticle assembly. These peptides do not form specific folded structures, but they interact through self-complementary patterns of side chain interactions. We demonstrate that the self-assembly can be activated by enzymatic unveiling of zwitterionic LRGD or LRGE modalities through action of matrix metalloprotease-9 (MMP-9), which is over-expressed by cancer cells. Enzymatic activation of gold nanoparticles (AuNPs) decorated with PEGylated peptides ([EG](8)-GPKG↓LRGD-[EG](5)) reveals LRGD sequences that drive multivalent electrostatic assembly of the nanoparticles, giving rise to robust NP assembly. In the vicinity of cancer cells that over-express MMP-9 enzymes, these aggregates form in proximity of these cells and give rise to size-induced selection of cellular uptake mechanism, resulting in diminished cell growth. The enzyme-responsiveness, and therefore indirectly the uptake route, of the system can be programmed by customizing the peptide sequence: a simple inversion of the two amino acids at the cleavage site completely inactivates the enzyme-responsiveness, self-assembly and consequently changes the endocytic pathway. This robust self-complementary, zwitterionic peptide design demonstrates the use of enzyme-activated electrostatic side chain patterns as powerful and customizable peptide modalities to program NP self-assembly and alter cellular response in biological context.

Identifying peptide substrates that are efficiently cleaved by proteases can give insights into the substrate recognition and specificity, guide the development of inhibitors and improve the sensitivity of assays. Peptide arrays and SAMDI mass spectrometry were used to identify a tetrapeptide substrate exhibiting high activity for the bacterial outer membrane protease (OmpT). Analysis of protease activity for the preferred residues at the cleavage site (P1, P1') and nearest neighbor positions (P2, P2') and their positional interdependence revealed FRRV as the optimal peptide with the highest OmpT activity. Substituting FRRV into a fragment of LL37, a natural substrate of OmpT, led to a >400 fold improvement in OmpT's catalytic efficiency with a kcat/Km value of 6.1 x 106 M-1 s-1. Interestingly, wild-type and mutant OmpT displayed significant differences in their substrate specificities, demonstrating that even modest mutants may not be suitable substitutes for the native enzyme.

Peptidoglycan (PG) is an essential, envelope-fortifying macromolecule of eubacterial cell walls. It is a large polymer with multiple glycan strands interconnected by short peptide chains forming a sac-like structure around cytoplasmic membrane. In most bacteria, the composition of the peptide chain is well-conserved and distinctive; in E. coli, the peptide chain length varies from two to five amino acids with a tetrapeptide consisting of L-alanine - D-glutamic acid - meso-diaminopimelic acid - D-alanine. However, it is not known how bacteria conserve the composition and sequence of peptide chains of PG. Here, we find that a conserved open reading frame of unknown function, YfiH (renamed PgeF) contributes to the maintenance of peptide composition in E. coli. Using genetic, biochemical and mass spectrometrical analyses we demonstrate that absence of yfiH results in incorporation of non-canonical amino acids, L-serine or glycine in place of L-alanine in PG sacculi leading to β-lactam - sensitivity, lethality in mutants defective in PG remodelling or recycling pathways, altered cell morphology and reduced PG synthesis. yfiH orthologs from other Gram-positive genera were able to compensate the absence of yfiH in E. coli indicating a conserved pathway in bacterial kingdom. Our results suggest editing/quality control mechanisms exist to maintain composition and integrity of bacterial peptidoglycan.

The present study describes the solid-state conformation of αβ hybrid peptides, Boc-Leu-β3, 3 -Ac6 c-OH, P1; Boc-Leu-β3, 3 -Ac6 c-Leu-β3, 3 -Ac6 c-OMe, P2; and Boc-Leu-β3, 3 -Ac6 c-Leu-β3, 3 -Ac6 c-Leu-OMe, P3. The dipeptide P1 adopts extended conformations, whereas tetrapeptide P2 and pentapeptide P3 favor a helical conformation stabilized by mixed types of C11 /C9 intramolecular hydrogen bonds. In peptide P3, the amino group of β3, 3 -Ac6 c(2) and β3, 3 -Ac6 c(4) residues occupies axial orientation, whereas in P2 it occupies axial and equatorial orientations for residues β3, 3 -Ac6 c(2) and β3, 3 -Ac6 c(4), respectively. The self-assembly of P3 forms channels filled with solvent molecules that present interesting patterns.

The first 11C-labeled unmodified (“native”) peptide is described by alkylation of a tetrapeptide Schiff base, which was achieved by an automated five-step radiochemical reaction. In a proof-of-concept study, [11C]Phe-d-Trp-Lys-Thr was synthesized. This tetrapeptide is the essential pharmacophore of octreotide, an antagonist of somatostatin receptors. The asymmetric alkylation with chiral phase-transfer catalysts enabled direct labeling of a variety of isolated 11C-peptides in a highly stereoselective manner (94 % de) with acceptable radiochemical yields (9–10 %) and practical specific activities (15–35 GBq µmol–1 or 405–945 mCi µmol–1) at the end of synthesis. This novel methodology provides a powerful new radiosynthetic method to access novel, stereochemically pure carbon-11-labeled native small peptides ready for in vivo studies.

Umami substances are very important for food seasoning and healthy eating. In addition to monosodium glutamate and some nucleotides, recent investigations have revealed that several peptides also exhibit umami taste. In recent years, 52 peptides have been reported to show umami taste, including 24 dipeptides, 16 tripeptides, 5 octapeptides, 2 pentapeptides, 2 hexapeptides, 1 tetrapeptide, 1 heptapeptide, and 1 undecapeptide. Twenty of these peptides have been examined for the present of umami taste. In this review, we have listed these umami peptides based on their category, source, taste, and threshold concentration. The evidence for peptides showing umami taste, the umami taste receptors on the human tongue, and the peptides whose umami taste is controversial are also discussed.

Macrocyclic tetrapeptide analogues containing a 1,3-diyne moiety were synthesized by a Glaser–Hay-type macrocyclization. The obtained 1,3-diyne was evaluated as a handle to introduce heterocycles into the macrocyclic structure. It was shown that the macrocyclic 1,3-diynes were successfully transformed into various heterocycles by nucleophilic attack of (bis)nucleophiles to the diyne moiety. Treatment with NaHS or H2O as nucleophiles gave rise to 2,5-bridged thiophenes or furans, whereas the use of hydrazines and hydroxylamine gave rise to the corresponding pyrazole- and isoxazole-containing macrocycles. In addition, a thermoreversible Diels–Alder cycloaddition of a cyclopeptidic bridged furan was demonstrated.

Synthesis of a natural glycine-rich heptacyclopeptide - mahafacyclin A (7) was accomplished by solution-phase technique of peptide synthesis via coupling of tetrapeptide unit Boc-L-Thr-L-Ile-L-Leu-Gly-OH with tripeptide unit L-Val-L-Phe-Gly-OMe followed by cyclization of linear heptapeptide fragment. Structure of the newly synthesized cyclopolypeptide was confirmed by means of chemical, spectroscopic analyses and subjected to antibacterial, antifungal and anthelmintic activity studies. Bioactivity results showed potent antifungal and anthelmintic activities of the synthesized peptide against dermatophytes T. mentagrophytes, M. audouinii and earthworm species M. konkanensis, P. corethruses and E. eugeniea.

A single chiral cyclic α,α-disubstituted amino acid with side-chain methoxymethyl (MOM) protecting groups, (3S,4S)-1-amino-(3,4-dimethoxymethoxy)cyclopentanecarboxylic acid [(S, S)-Ac5 c(dOMOM) ], or side-chain hydroxy groups, (3S,4S)-1-amino-(3,4-dihydroxy)cyclopentanecarboxylic acid [(S, S)-Ac5 c(dOH) ], was attached to the N-terminal or C-terminal position of α-aminoisobutyric acid (Aib) tetrapeptide segments; i.e., we designed and synthesized four pentapeptides, Cbz-[(S, S)-Ac5 c(dOMOM) ]-(Aib)4 -OEt (1), Cbz-[(S, S)-Ac5 c(dOH) ]-(Aib)4 -OEt (2), Cbz-(Aib)4 -[(S, S)-Ac5 c(dOMOM) ]-OMe (3), and Cbz-(Aib)4 -[(S, S)-Ac5 c(dOH) ]-OMe (4). We then analyzed the peptides' structures in the crystalline state. The four peptides all folded into 310 -helical structures; 1 formed a left-handed (M) 310 -helix, 2 formed a mixture of right-handed (P) and (M) 310 -helices, 3 formed a mixture of (P) and (M) 310 -helices, and 4 formed a (P) 310 -helix, respectively. In packing mode, the molecules of peptides 1 and 3, which both possessed an Ac5 c(dOMOM) residue, were connected by intermolecular hydrogen bonds along the peptide backbone (NH···O type). On the other hand, the packing of peptides 2 and 4, which both contained an Ac5 c(dOH) residue, was based on intermolecular hydrogen bonds derived from both the peptide backbone and the side-chain hydroxy groups of the amino acid Ac5 c(dOH) (OH···O type). © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 757-768, 2016.

In this research, the synthesis, biological evaluation, and conformational analysis of an apratoxin C oxazoline analog (3) have been demonstrated. The preparation of synthetic key intermediate 9 was achieved using an improved strategy that involves commercially available 3-methylglutaric anhydride (12), an enzymatic enantioselective alcoholysis, and a diastereoselective reduction. The Pro-Dtrina (3,7-dihydroxy-2,5,8-trimethylnonanoic acid) moiety 8 was successfully synthesized in a similar manner as our previously reported synthesis of apratoxin C (1). The cyclization precursor 5 was formed after the coupling of Pro-Dtrina 8 with a known tetrapeptide 7 to afford a linear peptide 6, the formation of an oxazoline, and the removal of the protecting groups. Finally, the macrolactamization of 5 with O-(7-aza-1H-benzotriazol-1-yl)-N,N,N',N'-tetramethyluronium hexafluorophosphate (HATU)/N,N-diisopropylethylamine (DIEA) furnished an apratoxin C oxazoline analog (3), which exhibited a potent cytotoxicity against HeLa cells (IC50 value of 22 nM) that was comparable with the cytotoxicity of apratoxin C (1) (IC50 value of 4.2 nM). Conformational analyses of 1 and 3 through NMR experiments showed that oxazoline analog 3 formed a tertiary structure that was similar to the apratoxin C (1) structure in CD3 CN, which provided a probable explanation for their comparable cytotoxicities. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 404-414, 2016.

Constrained azapeptides were designed based on the Ala-Val-Pro-Ile sequence from the second mitochondria-derived activator of caspases (Smac) protein and tested for ability to induce apoptosis in cancer cells. Diels-Alder cyclizations and Alder-ene reactions on azopeptides enabled construction of a set of constrained aza-valine dipeptide building blocks, that were introduced into mimics using effective coupling conditions to acylate bulky semicarbazide residues. Evaluation of azapeptides 7-11 in MCF-7 breast cancer cells indicated aza-cyclohexanylglycyine analog 11 induced cell death more efficiently than the parent tetrapeptide likely by a caspase-9 mediated apoptotic pathway. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 235-244, 2016.

Chlorambucil is a classic nitrogen mustard drug that has been used in the treatment of cancers. It may induce neutropenia, thrombocytopenia and other side effects because of its short lifetime and off-target effect. In this report, chlorambucil-tetrapeptide (AAAK, A3K) conjugate vesicles were developed to improve the stability and bioactivity of chlorambucil. First of all, chlorambucil-A3K conjugate was synthesized by solid phase synthesis strategy. Secondly, the chlorambucil-A3K conjugate was assembled and characterized by critical aggregation concentration, circular dichroism, dynamic light scattering and transmission electron microscopy. The results indicated that the chlorambucil-A3K conjugate can be assembled to form spherical vesicles with an average diameter of 390.5 nm, and high drug loading about 47.1% is reached. Surprisingly, the preliminary biological evaluation of the chlorambucil-A3K conjugate vesicles revealed the best in vitro anticancer activity against HeLa, HepG-2 and MCF-7 cell lines compared with chlorambucil and chlorambucil-A3K conjugate free drugs. Furthermore, conjugate vesicles showed excellent in vivo antitumoral activity. It can be partly attributed to their vesicular structure which isolates chlorambucil active moiety from aqueous solution to retard degradation before killing cancer cells. Therefore, chlorambucil-peptide (A3K) conjugate vesicles may be an alternative delivery system of chlorambucil.

Peptides are attracting increasing interest from the pharmaceutical industry because of their specificity and ability to address novel targets, including protein-protein interactions. However, typically they require stabilization for therapeutic applications owing to their susceptibility to degradation by proteases. Advances in the ability to chemically synthesize peptides and the development of new side-chain and backbone ligation strategies provide new tools to stabilize bioactive peptide epitopes. Two such epitopes are LyP1, a nine residue peptide that localizes to tumor cells and has potential as an anticancer therapeutic, and RGDS, a tetrapeptide shown to bind to survivin and induce apoptosis. Here we applied a variety of strategies for the stabilization of LyP1 and RGDS, including side-chain cyclization using "click" chemistry and "grafting" the epitopes into two naturally occurring cyclic peptide scaffolds, i.e., θ-defensins and cyclotides. NMR data showed that the three-disulfide θ-defensin and cyclotide scaffolds accommodated the LyP1 and RGDS epitopes but that scaffolds with fewer disulfide bonds were structurally compromised by inclusion of the LyP1 epitope. LyP1, LyP1-, and RGDS-grafted peptides that were largely unstructured also had reduced resistance to degradation in human serum, showing that grafting into a stable cyclic scaffold is an effective strategy for increasing the stability of a bioactive peptide epitope. Overall, the study demonstrates several methods for stabilizing peptide epitopes using side-chain or backbone cyclization and illustrates their potential in peptide drug design.

A terminally protected acyclic tetrapeptide has been synthesized, and the crystal structure of its hydrated form, Boc-Tyr-Aib-Tyr-Ile-OMe·2H2O (1), has been determined directly from powder X-ray diffraction data. The backbone conformation of tetrapeptide (1) exhibiting two consecutive β-turns is stabilized by two 4 → 1 intramolecular N-H · · · O hydrogen bonds. In the crystalline state, the tetrapeptide molecules are assembled through water-mediated O-H · · · O hydrogen bonds to form two-dimensional molecular sheets, which are further linked by intermolecular C-H · · · O hydrogen bonds into a three-dimensional supramolecular framework. The molecular electrostatic potential (MEP) surface of (1) has been used to supplement the crystallographic observations. The nature of intermolecular interactions in (1) has been analyzed quantitatively through the Hirshfeld surface and two-dimensional fingerprint plot. The DFT optimized molecular geometry of (1) agrees closely with that obtained from the X-ray structure analysis. The present structure analysis of Boc-Tyr-Aib-Tyr-Ile-OMe·2H2 O (1) represents a case where ab-initio crystal structure of an acyclic tetrapeptide with considerable molecular flexibility has been accomplished from laboratory X-ray powder diffraction data.

The conformation of the N-amino-imidazolidin-2-one (Aid) peptidomimetic was investigated using NMR spectroscopy and X-ray crystallography. In solution, the tetrapeptide model p-bromobenzoyl-Aid-l-Phe-N′-iso-propylamide (1) exhibited shielded and solvent exposed amide protons indicative of a turn conformation. In the crystal lattice of 1, four turn conformers were present in the unit cell differing primarily by the ring puckering of the Aid residue. Two pairs of β-turn conformers were observed each possessing an intramolecular ten-member hydrogen bond between the benzamide carbonyl and iso-propylamine NH moieties. The pairs had types II and II′ β-turn geometry that differed slightly about the ϕ and ψ torsion angles. Moreover, the X-ray analysis of 1 has been compared with that of the related unsaturated N-amino-imidazolin-2-one (Nai) analogs indicating the influences of ring flattening and substituents on conformation. Insertion of the preorganized Aid structure into biologically active peptides has thus been shown to offer a potentially valuable means for exploring the importance of turn geometry for activity, particularly in drug discovery. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 104: 629–635, 2015.

At their C-termini, cytosolic Hsp70s have an EEVD tetrapeptide that interacts with J-protein co-chaperones of the B, but not A, class. This interaction is required for partnering with yeast B-type J-proteins in protein folding. Here we report conservation of this feature. Human B-type J-proteins also have a stringent EEVD requirement. Human A-type J-proteins function less well than their yeast orthologs with Hsp70ΔEEVD. Changes in the zinc binding domain, a domain absent in B-type J-proteins, overcomes this partial EEVD dependence. Our results suggest that the structurally similar A- and B-class J-proteins of the cytosol have evolved conserved, yet distinct, features that enhance specialized functionality of Hsp70 machinery.

The tetrapeptide segment LVFF from the central hydrophobic core of amyloid β-peptide, Aβ17-20 , based methacrylate monomer was polymerized via reversible addition-fragmentation chain transfer (RAFT) polymerization to afford well-defined side-chain peptide polymers. The polymer was transformed to carry primary amino groups in the peptide terminals, depicting pH-responsiveness and was further modified to provide amphiphilic graft copolymer-based nanocarriers with pH-triggered dynamic dye release capability. The polymers acquired α-helical conformation guided by Aβ17-20 peptide. Computational studies were performed to investigate the secondary interactions of the peptide-based materials.

The voltage-gated potassium channel Kv1.3 is an important target for the treatment of autoimmune diseases and asthma. Blockade of Kv1.3 by the sea anemone peptide K+-channel toxin from Stichodactyla helianthus (ShK) inhibits the proliferation of effector memory T lymphocytes and ameliorates autoimmune diseases in animal models. However, the lack of selectivity of ShK for Kv1.3 over the Kv1.1 subtype has driven a search for Kv1.3-selective analogues. In the present study, we describe N-terminally extended analogues of ShK that contain a negatively-charged Glu, designed to mimic the phosphonate adduct in earlier Kv1.3-selective analogues, and consist entirely of common protein amino acids. Molecular dynamics simulations indicated that a Trp residue at position [-3] of the tetrapeptide extension could form stable interactions with Pro377 of Kv1.3 and best discriminates between Kv1.3 and Kv1.1. This led to the development of ShK with an N-terminal Glu-Trp-Ser-Ser extension ([EWSS]ShK), which inhibits Kv1.3 with an IC50 of 34 pm and is 158-fold selective for Kv1.3 over Kv1.1. In addition, [EWSS]ShK is more than 2900-fold more selective for Kv1.3 over Kv1.2 and KCa3.1 channels. As a highly Kv1.3-selective analogue of ShK based entirely on protein amino acids, which can be produced by recombinant expression, this peptide is a valuable addition to the complement of therapeutic candidates for the treatment of autoimmune diseases.

Actinonin is a pseudotripeptide that displays a high affinity towards metalloproteases including peptide deformylases (PDFs) and M1 family aminopeptidases. PDF and M1 family aminopeptidases belong to thermolysin-metzincin superfamily. One of the major differences in terms of substrate binding pockets between these families is presence (in M1 aminopeptidases) or absence (in PDFs) of an S1 substrate pocket. The binding mode of actinonin to PDFs has been established previously; however, it is not clear how the actinonin, without a P1 residue, would bind to the M1 aminopeptidases. Here we describe the crystal structure of Escherichia coli aminopeptidase N (ePepN), a model protein of the M1 family aminopeptidases in complex with actinonin. For comparison we have also determined the structure of ePepN in complex with a well-known tetrapeptide inhibitor, amastatin. From the comparison of the actinonin and amastatin ePepN complexes, it is clear that the P1 residue is not critical as long as strong metal chelating head groups, like hydroxamic acid or α-hydroxy ketone, are present. Results from this study will be useful for the design of selective and efficient hydroxamate inhibitors against M1 family aminopeptidases.

The synthesis of a series of N-guanidinylated cyclic ureidopeptides, analogues of 1,4-ureido-deltorphin/dermorphine tetrapeptide is described. The δ- and μ-opioid receptor affinity of new guanidinylated analogues and their non-guanidinylated precursors was determined by the displacement radioligand binding experiments. Our results indicate that the guanidinylation of cyclic 1,4-ureidodeltorphin peptide analogues does not exhibit a uniform influence on the opioid receptor binding properties, similarly as reported earlier for some linear peptides. All analogues were also tested for their in vitro resistance to proteolysis during incubation with large excess of chymotrypsin, pepsin, and papain by means of mass spectroscopy. Guanidinylated ureidopeptides 1G–4G showed mixed μ agonist/δ agonist properties and high enzymatic stability indicating their potential as therapeutic agents for treatment of pain. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd.

The tetrapeptide, l-Phe-l-Leu-l-Pro-l-Ser (FLPS), alleviates pain in a rat model of post-surgery pain. The crystal structure of the tetrapeptide is solved at high resolution (0.54 A). The asymmetric unit contains two FLPS molecules, one Zn ion, and four molecules of water with a formula of [Zn(C23H33N4O6)2(H2O)4]. Each Zn ion is octahedrally coordinated with Phe and Ser residues from four peptide molecules [2N+4O]. The linking of Phe and Ser residues of one FLPS molecule to three other FLPS molecules by Zn ion forms a complex consisting of chains of metal ions and FLPS molecules oriented along the b axis. Analysis of molecular packing reveals the coexistence of two FLPS conformers in the same crystal. The crystallographic parameters for [Zn(C23H33N4O6)2(H2O)4] are as follows: space group P212121, a = 9.8698(2) A, α = 90°, b = 20.1844(4) A, β = 90°, c = 25.9302(6) A, γ = 90°. Volume = 5165.71(19) A3, Z = 4, density (calc) = 1.364 Mg/cm3, and agreement factor R1 = 4.13%. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 104: 84–90, 2015.

WSXWS motif is a conserved amino acid sequence that is present in type I cytokine receptors. This motif that can be found both in the ligand binding chains and signal transducer molecule of the receptors with different amino acids at the position “X” plays a role in the receptor folding, ligand binding and signal transduction as well. Structural analysis proved that WSEWS motif of IL-6R is located in a highly accessible location in the protein. Structural properties and chemotaxis of a tetrapeptide library with SXWS sequence, where X was the 19 proteinogenic amino acids except cystein were systematically studied earlier. It has been proved that C-terminal amidation and the identity of amino acid X had a pronounced influence on the chemotactic properties but less of the structure of the peptides. Here, we present our findings on the effect of a tetrapeptide and a pentapeptide library with the sequence of SXWS and WSXWS on the chemotaxis and adhesion of J774 murine macrophage cell line. We studied the effect of the presence/absence of N-terminal tryptophan and the different amino acids at the X position on these physiological responses. Results indicated that amino acid X had a marked influence on chemotaxis, adhesion as well as on proliferation induced by (W)SXWS peptides. Elongation of SXWS sequence with a tryptophan at the N terminus also altered pronouncedly all the physiological responses of the cells studied. A good correlation could be observed between the chemotaxis and the proliferation and physicochemical parameters of the amino acid X.

Arginine-rich cell-penetrating peptides are widely utilized as vectors for gene delivery. However, their transfection efficacy still needs to be optimized. To accomplish this, guanidinocarbonylpyrrole groups, which are tailor-made anion binding sites, were introduced into the side chains of tetralysine to obtain the peptide analogue 1. In contrast to the common strategy of adding a lipophilic tail to peptide vectors, this novel method most likely enhances transfection efficacy through more specific interactions between the binding motifs and DNA or the cell membrane. Tetrapeptide analogue 1 is thus the smallest peptidic transfection vector that has been reported to date. The transfection efficacy of 1, which on average has less than two positive charges under physiological conditions, is even better than that of polyethylenimine (PEI). Furthermore, 1 exhibits only negligible cytotoxicity, which makes it an interesting candidate for further development.

A good understanding of gas-phase fragmentation chemistry of peptides is important for accurate protein identification. Additional product ions obtained by sodiated peptides can provide useful sequence information supplementary to protonated peptides and improve protein identification. In this work, we first demonstrate that the sodiated a3 ions are abundant in the tandem mass spectra of sodium-cationized peptides although observations of a3 ions have rarely been reported in protonated peptides. Quantum chemical calculations combined with tandem mass spectrometry are used to investigate this phenomenon by using a model tetrapeptide GGAG. Our results reveal that the most stable [a3 + Na − H]+ ion is present as a bidentate linear structure in which the sodium cation coordinates to the two backbone carbonyl oxygen atoms. Due to structural inflexibility, further fragmentation of the [a3 + Na − H]+ ion needs to overcome several relatively high energetic barriers to form [b2 + Na − H]+ ion with a diketopiperazine structure. As a result, low abundance of [b2 + Na − H]+ ion is detected at relatively high collision energy. In addition, our computational data also indicate that the common oxazolone pathway to generate [b2 + Na − H]+ from the [a3 + Na − H]+ ion is unlikely. The present work provides a mechanistic insight into how a sodium ion affects the fragmentation behaviors of peptides. Copyright © 2015 John Wiley & Sons, Ltd.

A rare new cyclic tetrapeptide, 5,5′-epoxy-MKN-349A (1), featured by a MKN-349A (5) skeleton and containing an uncommon ether bridge between C(5) and C(5′), and a new steroid, named 11-O-acetyl-NGA0187 (2), together with two known steroids, 3 and 4, were isolated from an endophytic fungus Penicillium sp. GD6 associated with the Chinese mangrove Bruguiera gymnorrhiza. The structures of the new compounds were elucidated on the basis of extensive spectroscopic analyses and by comparison with the data of related compounds reported in literature. Neither of the compounds 3 and 4, isolated in this study, showed obvious bioactivities in the antibacterial bioassay experiments.

Natural tetrapeptide Goralatide inhibits primitive hematopoietic cell proliferation but reported to be rather unstable in solution (half-life 4.5 min). In this work, we report the synthesis of an aminoxy analog of Goralatide. Aminoxy moiety is expected to provide increased stability and bioavailability of the Goralatide analog. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.

Surface-enhanced Raman scattering has been employed to characterize the adsorption of an oligopeptide containing histidine residues on colloidal nanoparticles of metals as Ag and Cu obtained by laser ablation. The title molecule consists of two histidine and glycine residues alternating along the chain and terminating with an acetyl on one side and an amide group on the other. Histidine residues are found to act as docking sites of the molecule to the surface of the metal nanoparticles. Semiempirical parameterized model number 3 (PM3) calculations performed on molecule/metal model complexes suggest possible different adsorption geometries depending on the metallic substrate. This investigation could provide useful information to address the interaction of protein systems with metal ions, which is often related to fundamental biological process in living systems and can play an important role in different neuropathological diseases. Copyright © 2014 John Wiley & Sons, Ltd.

Alternating copolymers of an oligopeptide (N-3-GVGV-N-3, where G: glycine; V: valine) and an oligothiophene (5,5'-bis(ethynyl)-3,3'-dioctyltetrathiophene) are prepared by click chemistry. The experimental results discover that these copolymers exhibit strong molecular-weight-dependent self-assembly behaviors. The copolymer P1 with the lowest weight-average molecular weight ((M) over bar (w) = 7400 g mol(-1)), assembles into well-ordered fibrous nanostructures. P3 ((M) over bar (w) = 16 980 g mol(-1)) assembles into nanoballs. P2, which has the medium (M) over bar (w) between P1 and P3, ((M) over bar (w) = 14 800 g mol(-1)), exhibits more-complicated self-assembly behaviors, more like a transition state between the other two. All of the results suggest the self-assembly ability of these oligopeptide segments might be the major reason for the nano-structure evolution.

We have in the present study explored the anticancer activity against human Burkitt's lymphoma cells (Ramos) of a series of small linear and cyclic tetrapeptides containing a β2,2-amino acid with either two 2-naphthyl-methylene or two para-CF3-benzyl side chains, along with their interaction with the main plasma protein human serum albumin (HSA). The cyclic and more amphipathic tetrapeptides revealed a notably higher anticancer potency against Ramos cells [50% inhibitory concentration (IC50) 11–70 μM] compared to the linear tetrapeptide counterparts (IC50 18.7 to >413 μM). The most potent cyclic tetrapeptide c3 had a 16.5-fold preference for Ramos cells compared to human red blood cells, whereas the cyclic tetrapeptide c1 both showed low hemolytic activity and displayed the overall highest (2.9-fold) preference for Ramos cells (IC50 23 μM) compared to healthy human lung fibroblast cells (MRC-5). Investigating the interaction of selected tetrapeptides and recently reported hexapeptides with HSA revealed that the peptides bind to drug site II of HSA in the 22–28 μM range, disregarding size and overall structure. NMR and in silico molecular docking experiments identified the lipophilic residues as responsible for the interaction, but in vitro studies showed that the anticancer potency of the peptides varied in the presence of HSA and that c3 remained the most potent peptide. Based on our findings, we call for implementing serum albumin binding in development of anticancer peptides, as it may have implications for future administration and systemic distribution of peptide-based cancer drugs. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.

N-Amino-imidazolin-2-ones, a new class of turn mimics onto which side chains of different amino acids may be added conveniently, have been analyzed by X-ray crystallography. 4-Methyl and 4-benzyl N-amino-imidazolin-2-one tetrapeptide models 2 and 3 were examined to study the influence of the 4-position substituent on turn conformation and the chi dihedral angle of the neighbouring C-terminal residue side-chain. The nature of the 4-position substituent caused substantial effects on the ψi + 2 main chain and C-terminal Phe χ1 side-chain dihedral angle values, giving a preference for β- and γ-turn conformers for the methyl- and benzyl-substituted imidazolin-2-ones, respectively. Conformational analysis in the solid state has provided insight to guide application of N-amino-imidazolin-2-ones in peptide mimicry. © 2013 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 102: 7–15, 2014.

Carbon-donated hydrogen bonds (CDHBs) are weak forms of hydrogen bonding (0.5-1.0 kcal mol(-1) ) that are difficult to detect, and thus their roles in the structure and functionality of chemical systems often go unrecognized. Utilizing a computational approach, the existence of a structurally significant CDHB in the medically relevant protein Streptococcus pneumoniae hyaluronate lyase (SpnHL) is affirmed. The structure of a tetrapeptide fragment model containing the CDHB was optimized with second-order perturbation theory. From this, a CDHB with bond distance and angle consistent with previously discovered CDHBs and comparable to neighboring traditional HBs in the fragment model was found. The CDHB competes with another donor T253 OH, whereby the two alternate in strength between protein conformations, imbuing αHelix 3 appreciable flexibility. The CDHB seems to exist in spite of torsional and steric strain on the donor methyl group. It is postulated that the CDHB could aid in either counteracting the macrodipole of αHelix 3 or protecting the A249 CO from destabilizing interactions with the adjacent solvent. Employing the energy gradients from the optimization, the torque generated by the fragment model was computed, which accurately predicts the direction of rotation of αHelix 3 observed from experiment. A strongly correlated motion between αHelix 3 and αHelices 2, 4, and 5 was noted, which the interactions of the fragment model help drive by generating a torque much larger than necessary to rotate just αHelix 3. Considering these results, we conclude that CDHBs should be considered as possible beneficial components of chemical and biological phenomena.

The conformational preferences of helix foldamers having different sizes of the H-bonded pseudocycles have been studied for di- to octa-γ2,3-peptides based on 2-(aminomethyl)cyclohexanecarboxylic acid (γAmc6) with a cyclohexyl constraint on the Cα–Cβ bond using density functional methods. The helical structures of the γAmc6 oligopeptides with homochiral configurations are known to be much stable than those with heterochiral configurations in the gas phase and in solution (chloroform and water). In particular, it is found that the (P/M)−2.514-helices are most preferred in the gas phase and in chloroform, whereas the (P/M)−2.312-helices become most populated in water due to the larger helix dipole moments. As the peptide sequence becomes longer, the helix propensities of 14- and 12-helices are found to increase both in the gas phase and in solution. The γAmc6 peptides longer than octapeptide are expected to exist as a mixture of 12- and 14-helices with the similar populations in water. The mean backbone torsion angles and helical parameters of the 14-helix foldamers of γAmc6 oligopeptides are quite similar to those of 2-aminocyclohexylacetic acid oligopeptides and γ2,3,4-aminobutyric acid tetrapeptide in the solid state, despite the different substituents on the backbone. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 87–95, 2014.

All experimental procedures discussed could be treated as a screening tool for probing the existence of molecular association among the chiral molecules and the solvent system. The molecular association phases of a racemic conglomerate solution (CS) and a racemic compound solution (RCS), and the templating effect of aspartic acid solid surface were observed to minimize the chance of redissolving racemic conglomerate and racemic compound aspartic acid in water and reforming an RCS in crossovers experiments. Only 1 %wt% of l-aspartic acid was adequate enough to induce a transformation from a racemic compound aspartic acid to a racemic conglomerate aspartic acid. This would make the propagation of biochirality more feasible and sound. However, tetrapeptide, (l-aspartic acid)4 , failed to induce enantioseparation as templates purely by crystallization. Nonclassical crystallization theory was needed to take into account the existence of a CS. Fundamental parameters of the crystallization kinetics such as the induction time, interfacial energy, Gibbs energetic barrier, nucleation rate, and critical size of stable nuclei of: (i) racemic compound aspartic acid, (ii) racemic compound aspartic acid seeded with 1 %wt% l-aspartic acid, (iii) racemic conglomerate aspartic acid, and (iv) l-aspartic acid were evaluated and compared with different initial supersaturation ratios. Morphological studies of crystals grown from the crystallization kinetics were also carried out.

Isomerization and enantiomerization of Asp in the tetrapeptide Ala-Phe-Asp-GlyOH are studied at pH 10 and 80°C as well as 25°C. CE-MS allowed the distinction between α-Asp and β-Asp linkages in degradation products based on the ratio of the b and y fragment ions. Besides isomerization and enantiomerization of Asp, enantiomerization of Ala and Phe was also observed at both temperatures by chiral amino acid HPLC analysis using Marfey's reagent for derivatization. The rate of enantiomerization of the amino acids proceeded in the order Asp > Ala > Phe. The CE assay was validated with respect to linearity, LOQ, LOD, and precision and employed to characterize the time course of the degradation of the tetrapeptide upon incubation in borate buffer, pH 10. Isomerization to β-Asp peptides was identified as the major degradation reaction. The configuration of Asp or Ala affected the half-life of the starting peptide to a minor extent but did not influence the distribution of the individual products under equilibrium conditions at 80°C. Degradation at 25°C proceeded very slowly so that the equilibrium was not reached after 245 days.

Biomedical polyurethane (BPU) and silk fibroin have similarly molecular architecture in their primary and aggregate structure, both of which have amide bonds and microphase separation, and they have been employed as scaffold materials for biomedical applications. Based on this, as the featured peptide sequence of silkworm silk fibroin, GlycineAlanineGlycineAlanine (GlyAlaGlyAla) tetrapeptide was synthesized by using traditional liquid-phase peptide synthesis method with Boc-protected glycine and alanine as starting materials, and was transformed to its derivative with two amine-terminated functional groups. The derivative was introduced as a chain extender into the backbone to form the hard segment of a silk-inspired PU with urea-linkage. Related measurements show that molecular weight of the synthesized silk-inspired PU ranged from 13,000 to 15,000. Fourier transform infrared (FTIR) absorption bands of Amides I and II are at 1651 cm−1 and 1534 cm−1, and Raman absorption band of Amide III is at 1302 cm−1. UV-Vis absorption peak of the silk-inspired PU is at 266 nm. This new concept and strategy may allow the fabrication of a new class of thermoplastic polyurethane elastomers to mimic the structure and properties of silk fibroin of silkworms and spiders. Information provided by this study may be used to better understand the correlation between the natural and man-made materials. © 2013 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2013

This thesis describes the design and synthesis of small molecule derivatives and their polypeptide conjugates as high affinity binders for proteins: the D-dimer protein (D-dimer), a biomarker for diagnosis of thromboembolic diseases; human myeloperoxidase (MPO), a biomarker for cardiovascular diseases; and chitinases, potential targets for asthma therapy. The interactions between the synthetic binder molecules and those proteins were evaluated by surface plasmon resonance (SPR) biosensor analysis and fluorescence spectroscopy. Competition SPR experiments or other methods proved that the small molecule components of the binder molecules were critical for binding and specifically bound to the original binding site of small molecules. The binder molecules consisted of a 42-residue helix-loop-helix polypeptide conjugated to a small molecule via aliphatic spacers of suitable length. The small molecules could be any type of moderately binding structure. In the binder development for the D-dimer, the tetrapeptide GPRP with a dissociation constant Kd of 25 μM was used and the affinity of 4C15L8GPRP obtained was estimated to be approximately 3 nM. In the binder development for MPO, salicylhydroxamic acid (SHA) with Kd of 2 μM was used and the affinity of 4C37L34C11SHA obtained was estimated to be approximately 0.4 nM. In the binder development for chitinases, a theobromine derivative (pentoxifylline) with a Kd of 43±10 μM was used and the affinity of 4C37L34-P obtained was estimated to be considerably higher than that of pentoxifylline. The binder molecules were identified from a 16-membered pool of candidates obtained by conjugating the small molecules to each member of a set of 16 designed polypeptides. The affinities were greatly enhanced by 2-3 orders of magnitude, compared to the small molecule. The polypeptides did not bind to the proteins with measurable affinities. The discovery of these new synthetic binders for protein targets can pave the way to diagnostic tests in vivo or in vitro, independent of antibodies.

β-Amino acids containing α,β-hybrid peptides show great potential as peptidomimetics. In this paper, we describe the synthesis and affinity to μ-opioid and δ-opioid receptors of α,β-hybrids, analogs of the tetrapeptide Tyr- d-Ala-Phe-Phe-NH(2) (TAPP). Each amino acid was replaced with an l- or d-β(3) -h-amino acid. All α,β-hybrids of TAPP analogs were synthesized in solution and tested for affinity to μ-opioid and δ-opioid receptors. The analog Tyr-β(3) h- d-Ala-Phe-PheNH(2) was found to be as active as the native tetrapeptide.