A comparative study of backbone versus side chain peptide cyclization: application for HIV-1 integrase inhibitors

Peptide cyclization is an important tool for overcoming the limitations of linear peptides as drugs. Backbone cyclization (BC) has advantages over side chain (SC) cyclization because it combines N-alkylation for extra peptide stability. However, the appropriate building blocks for BC are not yet commercially available. This problem can be overcome by preparing SC cyclic peptide analogs of the most active BC peptide using commercially available building blocks. We have recently developed BC peptides that inhibit the HIV-1 integrase enzyme (IN) activity and HIV-1 replication in infected cells. Here we used this system as a model for systematically comparing the BC and SC cyclization modes using biophysical, biochemical and structural methods. The most potent SC cyclic peptide was active almost as the BC peptide and inhibited IN activity in vitro and blocked IN activity in cells even after 6 days. We conclude that both cyclization types have their respective advantages: The BC peptide is more active and stable, probably due to the N-alkylation, while SC cyclic peptides are easier to synthesize. Due to the high costs and efforts involved in preparing BC peptides, SC may be a more approachable method in many cases. We suggest that both methods are interchangeable.     

Covalent linkage of N-methyl-6-oxyquinolinium betaine to trehalose

The common route to link quinolinium and pyridinium fluorophores to biomolecules via bromoacetic acid has failed in labeling the disaccharide trehalose with N-methyl-6-oxyquinolinium betaine: the unexpected, extremely high instability of the N-carboxymethyl ester was overcome by direct N-alkylation of the quinoline derivative with trehalose triflate.     

Enhancement of solubility by temporary dimethoxybenzyl-substitution of peptide bonds. Towards the synthesis of defined oligomers of alanine and of lysyl-glutamyl-glycine

The synthesis of the model compound Aloc-Ala-Ala-Dma-Ala-Ala-OMe has been described as an illustration of the fact that a large group reversibly alkylating the amido group of an oligomer can disturb the regularity of a peptide backbone, oppose its aggregation and thus enhance its solubility greatly, affording synthons for further oligomerization. Application of such a group not only affects the solubility, but alters also the properties of the intermediates. The concomitant change in reactivity may run to such an extent that N-alkylation of oligomers has to be abandoned (this was encountered in the attempted synthesis of Lys-Glu-Dmg). Consequently, the solubility of the growing protected peptide chain will become progressively less and in the mentioned example the oligomerization had to be terminated at the dodecapeptide level, indicating the severe need for reversible "structure-breaking" functions.     

Syntheses of 6-Substituted 3-Pyridazinyl Phosphorothioates

A variety of 6-substituted-3-pyridazinyl phosphorothioates were synthesized by the reaction of O,O-dialkyl phosphorothiochloridates with corresponding 3 (2H)pyridazinones. In certain cases, N-alkylated pyridazinones were formed along with the desired phosphorothioates. The optimal condition for the phosphorylation and the mechanism of the N-alkylation were investigated.     

A convenient approach to synthesizing peptide C-terminal N-alkyl amides

Peptide C-terminal N-alkyl amides have gained more attention over the past decade due to their biological properties, including improved pharmacokinetic and pharmacodynamic profiles. However, the synthesis of this type of peptide on solid phase by current available methods can be challenging. Here we report a convenient method to synthesize peptide C-terminal N-alkyl amides using the well-known Fukuyama N-alkylation reaction on a standard resin commonly used for the synthesis of peptide C-terminal primary amides, the peptide amide linker-polyethylene glycol-polystyrene (PAL-PEG-PS) resin. The alkylation and oNBS deprotection were conducted under basic conditions and were therefore compatible with this acid labile resin. The alkylation reaction was very efficient on this resin with a number of different alkyl iodides or bromides, and the synthesis of model enkephalin N-alkyl amide analogs using this method gave consistently high yields and purities, demonstrating the applicability of this methodology. The synthesis of N-alkyl amides was more difficult on a Rink amide resin, especially the coupling of the first amino acid to the N-alkyl amine, resulting in lower yields for loading the first amino acid onto the resin. This method can be widely applied in the synthesis of peptide N-alkyl amides.     

On-sequencer pyridylethylation of cysteine residues after protection of amino groups by reaction with phenylisothiocyanate

Cysteine residues in polypeptides are not easily identified during automated N-terminal sequence analysis. Reaction of cysteine side chains with 4-vinylpyridine and identification as the pyridylethylated phenylthiohydantion derivative (PE-PTH-Cys) were proposed. However, after this reaction a desalting step is necessary. If limited sample amounts do not allow this desalting step, on-sequencer pyridylethylation is an alternative, although preview of the consecutive amino acid is usually observed in this case. We describe an on-sequencer procedure that avoids such preview formation by derivatizing the peptide with phenylisothiocyanate (PITC) prior to reaction with 4-vinylpyridine. The pyridylethylation is performed in the cartridge of the sequencer after immobilization of the protein or peptide on a polybrene-coated glass fiber filter and thiocarbamylation with PITC. Preview caused by N-alkylation is not observed and PE-PTH-Cys is detected in much higher yields than usual. The procedure reported here is significantly shortened, optimized to reduce side products, and avoids losses during sample handling. It can easily be adapted to any automated version of the sequencers.     

Protected peptide p-nitroanilides by solid-phase synthesis

Peptide p-nitroanilides (peptide p> NAs) have found wide application as chromogenic substrates. An improved SPPS method to synthesize rapidly and in good yield a broad range of peptide pNAs under mild conditions will be presented here. To obtain a suitable carrier, the (4-aminophenyl)aminocarbonyloxy derivatives of Wang resin and Sasrin were synthesized. SPPS employing Fmoc/tBu-based protection followed by acidolytic cleavage yielded the (protected) peptide p-aminoanilide which was oxidized with sodium perborate in acetic acid to yield the(protected) peptide pNA. Side-chain protectionproved to be advantageous. Acid-labile peptide pNAs such as the proteasome substrate Z-Glu(OtBu)-Ala-Leu-pNA thus can be obtaineddirectly. The behavior of Cys, Met, Tyr and Trp being susceptible towards oxidation was studied more closely.     

Cyclic enediyne–amino acid chimeras as new aminopeptidase N inhibitors

Enediyne–peptide conjugates were designed with the aim to inhibit aminopeptidase N, a widespread ectoenzyme with a variety of functions, like protein digestion, inactivation of cytokines in the immune system and endogenous opioid peptides in the central nervous system. Enediyne moiety was embedded within the 12-membered ring with hydrophobic amino acid alanine, valine, leucine or phenylalanine used as carriers. Aromatic part of the enediyne bridging unit and the amino acid side chains were considered as pharmacophores for the binding to the aminopeptidase N (APN) active site. Additionally, the fused enediyne–amino acid “heads” were bound through a flexible linker to the l-lysine, an amino group donor. The synthesis included building the aromatic enediyne core at the C-terminal of amino acids and subsequent intramolecular N-alkylation. APN inhibition test revealed that the alanine-based derivative 9a inhibits the APN with IC₅₀ of 34 ± 11 μM. Enediyne–alanine conjugate 12 missing the flexible linker was much less effective in the APN inhibition. These results show that enediyne-fused amino acids have potential as new pharmacophores in the design of APN inhibitors.     

The importance of the amino acid in position 32 of cholecystokinin in determining its interaction with cholecystokinin receptors on pancreatic acini

In the C-terminal heptapeptide of cholecystokinin, replacement of the penultimate residue, aspartic acid, by β-alanine caused a 300-fold decrease in potency with which the peptide stimulated enzyme secretion, whereas replacement by glutamic acid caused a 1000-fold decrease in potency. The β-alanine-substituted peptide was approximately ten times more potent when the N terminus was blocked with t-butyloxycarbonyl than when it was blocked with benzyloxycarbonyl, and the glutamic acid-substituted peptide was approximately twice as potent when the N terminus was blocked with t-butyloxycarbonyl than when it was blocked with benzyloxycarbonyl. Changes in the ability of the peptide to stimulate amylase secretion were acompanied by corresponding changes in the ability of the peptide to inhibit binding of ¹²⁵I-labeled cholecystokinin. The magnitude of stimulation of enzyme secretion caused by a maximally effective peptide concentration was the same with each analogue as it was with the unaltered peptide. Rpelacing the aspartyl by β-alanine or glutamic acid or replacing of N-terminal t-butyloxycarbonyl moiety by benzyloxycarbonyl caused an equivalent decrease in the ability of the peptide to stimulate enzyme secretion and its ability to cause residual stimulation of enzyme secretion. In contrast, the N-terminal desamino analogue of cholecystokinin heptapeptide was ten times less potent than the unaltered peptide in stimulating amylase secretion, but 100 times less potent that the unaltered peptide in causing residual stimulation of enzyme secretion.     

An approach to peptide-based ATP receptors by a combination of random selection, rational design, and molecular imprinting

Random selection, rational design and molecular imprinting were cooperatively utilized to develop peptide-based ATP synthetic receptors. In this fusion strategy, combinatorial chemistry was utilized for screening a precursor peptide useful for construction of ATP receptors, and rational design was employed in modification of the selected precursor peptide for higher affinity and selectivity. Finally, molecular imprinting was used for pre-organizing the conformation of the precursor peptide as complementary to a target molecule ATP. The fusion strategy appeared to have advantage to sole use of the individual strategy: (1) a low hit-rate of combinatorial chemistry will be improved by customizing a higher order structure of a selected peptide by molecular imprinting, (2) combinatorial chemistry allows us to semi-automatically select components of water-compatible synthetic receptors, (3) rational design improves the selected peptide sequence for better molecularly imprinted receptors.A peptide consisting of a randomly selected sequence and a rationally designed sequence (Resin-Lys-Gly-Arg-Gly-Lys-Gly-Gly-Gly-Glu-Lys-Tyr-Leu-Lys-NHAc) was designed and synthesized as a precursor peptide. The rational design was made according to the sequence of the adenine binding site of biotin carboxylase. The on-beads peptide was cross-linked with dimethyl adipimidate in the presence of ATP. In the saturation binding tests, the cross-linked on-beads peptide showed 5.3 times higher affinity compared to the non-cross-linked peptide with the same sequence. Furthermore, the cross-linked peptide showed improved selectivity; the ratios of binding constants, K_(ATP)/K_(ADP) and K_(ATP)/K_(GTP), were increased from 2.4 to 19, and from 0.8 to 10, respectively. It would be notable that the peptide without the rationally designed sequence showed no discrimination between ATP and GTP (K_(ATP)/K_(GTP) as 0.9), suggesting that the rationally designed site was successfully engaged for recognition of the adenine base.     

Functional expression,purification, and antimicrobial activity of a novel antimicrobial peptide MLH in Escherichia coli

In this study, a novel heterozygous antimicrobial peptide MLH was synthesized, expressed, purified, and characterized. The peptide Md-cec-LL-37_Hp (MLH) was selected through bioinformatic analysis using musca domestica antimicrobial peptide (Cec-Med), human antimicrobial peptide LL-37, and helicobacter pylori antimicrobial peptide (Hp) as parent peptides. The target gene was synthesized by overlap extension PCR (SOE-PCR) and connected to the expression vector pET-32a (+), and the recombinant plasmid pET-32a-MLH was transformed to Escherichia coli for constructing pET-32a-MLH/BL21 (DE3). Isopropyl β-D-thiogalactoside (IPTG) was used to induce protein expression, and SDS-PAGE and western blot were adopted to test the target protein. And fermentation condition was optimized to get the mass expression of the fusion protein. The Ni²⁺ affinity chromatographic column was used to purify. Active heterozygous peptide was obtained after renaturation. Finally, the activity of the heterozygous antimicrobial peptide was identified. The fusion peptide showed significant antimicrobial effect on both E. coli and Staphylococcus aureus.     

脂多糖模拟肽13L诱导对小鼠内毒素休克的保护反应

为研究LPS 2630表位模拟肽13L是否能诱导抗脂多糖（LPS）抗体的产生、对细菌攻击及内毒素休克的保护性反应,合成了模拟LPS表位的短肽13L．用合成肽13L-蓝载体（blue carrier,BC）交联物免疫Balb／C小鼠,观察小鼠体内抗LPS抗体产生的规律,并观察免疫小鼠细菌感染存活时间,用颈总动脉插管测定技术观察免疫小鼠内毒素休克的血压变化．结果显示,合成肽13L-BSA交联物能与兔抗鼠伤寒和大肠杆菌LPS抗血清及抗鼠伤寒LPS单抗结合,证明短肽13L可模拟LPS的抗原性．用13L-BC交联物免疫可诱发小鼠体内针对大肠杆菌LPS 2630和鼠伤寒沙门氏菌LPS 7261的抗体反应,该反应可被灭活大肠杆菌及两种LPS所加强,其抗体亚类主要为IgG2a,其次为IgG2b与IgM,而IgG1与IgG3含量极低．免疫13L-BC小鼠显示对细菌攻击的抵抗,与免疫BC对照小鼠比较,其存活时间分别为（12±1．3）天和（5．3±0．4）天（P〈0．01）．免疫13L-BC小鼠对静脉注射LPS诱发内毒素休克的保护作用体现在血压下降幅度明显低于对照动物,在LPS 2630攻击后1、2、3及4h时两组动物血压明显差别（P〈0．05、P〈0．01、P〈0．05及P〈0．01）,而LPS 7261攻击后1、2、3及4h时两组动物血压差别则略小于LPS 2630组（P〉0．05、P〈0．05、P〈0．05及P〈0．01）．上述结果证明,LPS表位模拟肽13L交联物免疫小鼠可产生针对细菌攻击及内毒素休克的保护性效应,提示该模拟肽作为LPS交叉保护性疫苗候选的可行性．     

Characterization of the secretion efficiency of a plant signal peptide in Bacillus subtilis.

Summary The ability of the Bacillus subtilis secretion machinery to interact with a heterologous signal peptide was studied using a plant (wheat -amylase) signal peptide. The plant signal peptide was capable of mediating secretion of Escherichia coli alkaline phosphatase and B. amyloliquefaciens levansucrase from B. subtilis. This secretion was dependent on the plant signal peptide, as deletion of five amino acids from the hydrophobic core resulted in a block of secretion. Attempts to improve the efficiency of the plant signal peptide in B. subtilis were made by increasing the length of the hydrophobic core from 10 to 16 residues by insertion of 2, 4, 5 or 6 amino acids. None of the alterations improved the secretion efficiency relative to the wild-type plant signal peptide.     

Expression of Biologically Active Crustacean Hyperglycemic Hormone (CHH) of <Emphasis Type="Italic">Penaeus monodon</Emphasis> in <Emphasis Type="Italic">Pichia pastoris</Emphasis>

Crustacean hyperglycemic hormone (CHH), molt-inhibiting hormone (MIH), and gonad-inhibiting hormone (GIH) are members of a major peptide family produced from the X-organ sinus gland complex in the eyestalk of crustaceans. This peptide family plays important roles in controlling several physiologic processes such as regulation of growth and reproduction. In this study the complementary DNA encoding a peptide related to the CHH/MIH/GIH family (so-called Pem-CMG) of the black tiger prawn Penaeus monodon was successfully expressed in the yeast Pichia pastoris under the control of the AOX1 promoter. The recombinant Pem-CMG was secreted into the culture medium using the -factor signal sequence; of Saccharomyces cerevisiae without the Glu-Ala-Glu-Ala spacer peptide. The amino terminus of the recombinant Pem-CMG was correctly processed as evidenced by amino-terminal peptide sequencing. The recombinant Pem-CMG was purified by reverse-phase high-performance liquid chromotography and used in a biological assay for CHH activity. The final yield of the recombinant Pem-CMG after purification was 260 µg/L of the culture medium. Both crude and purified recombinant Pem-CMG produced from P. pastoris showed the ability to elevate the glucose level in the hemolymph of eyestalk-ablated P. monodon, which demonstrates that Pem-CMG peptide functions as hyperglycemic hormone in P. monodon.     

A single replacement of histidine to arginine in EGFR-lytic hybrid peptide demonstrates the improved anticancer activity

We previously reported that novel targeted “hybrid peptide” in which epidermal growth factor receptor (EGFR) binding peptide was conjugated with lytic-type peptide had selective cytotoxic activity to EGFR expressing cancer cell lines, and in vivo analysis revealed that this EGFR-lytic peptide displayed significant antitumor activity in a xenograft model of human breast cancer which was resistant to tyrosine kinase inhibitor drugs. As an attempt to improve the selective anticancer activity of EGFR-lytic peptide, we modified the EGFR-binding peptide through introducing the mutation of amino acid according to biophysical analysis by biomolecular interaction and circular dichroism (CD) spectra. When cytotoxic activity of EGFR-lytic or EGFR(2R)-lytic hybrid peptides was investigated in various human cancer and normal cell lines, it was demonstrated that EGFR(2R)-lytic, in which second histidine (H) of EGFR-binding peptide was replaced to arginine (R) had 1.2–1.9-fold higher cytotoxic activity than that of original EGFR-lytic peptide. In vivo analysis also revealed that this modified peptide displayed significant antitumor activity at as low as 1 mg/kg dosage. These results suggest that mutated arginine on EGFR-lytic peptide produces higher binding ability to EGFR on cancer cells, and thereby the improved anticancer activity.     

Applying Proteolytic Enzymes on Soybean

The soybean cold-insoluble protein was hydrolyzed with pepsin and the hydrolyzate was dialyzed. The diffusate was submitted to gel permeation chromatography of Sephadex G-10 and thin layer chromatography of silica gel G. A ninhydrin-negative bitter peptide was detected by chlorine-starch-iodine test and was purified by paper electrophoresis and by rechromatography on the silica gel. Azeotropic HCl hydrolysis of the peptide gave equal molar ratio of Ala, Glu, Gly, Ile, Leu, Phe, Ser and Val. N-Terminal residue was composed of pyrrolidone carboxylic acid, which was tentatively identified in comparison with the authentic sample by paper electrophoresis and thin layer chromatography. Hydrazinolysis of the peptide, followed by the 2,4-dinitrophenylation, produced α,α,γ-tri-DNP-glutamic acid-α,γ-dihydrazide and DNP-pyrrolidone carboxylic acid hydrazide, also supporting the N-terminal structure. Hydrolysis of the peptide by carboxypeptidase A gave Leu, Val, Phe, Ile, Ala, etc. in the order of the liberation rate. As the peptide fragments remaining in this hydrolyzate were detected pyrrolidone carboxyl-Gly·OH, pyrrolidone carboxyl-Gly-Ser·OH, pyrrolidone carboxyl-Gly-Ser-Ala·OH, etc. In conclusion, the structure of this peptide was proposed as: pyrrolidone carboxyl-Gly-Ser-Ala-Ile-Phe-Val-Leu·OH. Quantitative information about the total amount of pyrrolidone carboxyl residue contained in the peptic hydrolyzate of the soybean protein and sensory study on the bitterness of the peptide as referred by standard solution of phenylthiourea, were demonstrated.     

Design of a Tumor Homing Cell-Penetrating Peptide for Drug Delivery

The major drawbacks with conventional cancer chemotherapy are the lack of satisfactory specificity towards tumor cells and poor antitumor activity. In order to improve these characteristics, chemotherapeutic drugs can be conjugated to targeting moieties e.g. to peptides with the ability to recognize cancer cells. We have previously reported that combining a tumor homing peptide with a cell-penetrating peptide yields a chimeric peptide with tumor cell specificity that can carry cargo molecules inside the cells. In the present study, we have used a linear breast tumor homing peptide, CREKA, in conjunction with a cell-penetrating peptide, pVEC. This new chimeric peptide, CREKA–pVEC, is more convenient to synthesize and moreover it is better in translocating cargo molecules inside cancer cells as compared to previously published PEGA–pVEC peptide. This study demonstrates that CREKA–pVEC is a suitable vehicle for targeted intracellular delivery of a DNA alkylating agent, chlorambucil, as the chlorambucil–peptide conjugate was substantially better at killing cancer cells in vitro than the anticancer drug alone.     

Versatile signal peptide of Flavobacterium‐originated organophosphorus hydrolase for efficient periplasmic translocation of heterologous proteins in Escherichia coli

Organophosphorus hydrolase (OPH) from Flavobacterium species is a membrane‐associated homodimeric metalloenzyme and has its own signal peptide in its N‐terminus. We found that OPH was translocated into the periplasmic space when the original signal peptide‐containing OPH was expressed in recombinant Escherichia coli even though its translocation efficiency was relatively low. To investigate the usability of this OPH signal peptide for periplasmic expression of heterologous proteins in an E. coli system, we employed green fluorescent protein (GFP) as a cytoplasmic folding reporter and alkaline phosphatase (ALP) as a periplasmic folding reporter. We found that the OPH signal peptide was able to use both twin‐arginine translocation (Tat) and general secretory (Sec) machineries by switching translocation pathways according to the nature of target proteins in E. coli. These results might be due to the lack of Sec‐avoidance sequence in the c‐region and a moderate hydrophobicity of the OPH signal peptide. Interestingly, the OPH signal peptide considerably enhanced the translocation efficiencies for both GFP and ALP compared with commonly used TorA and PelB signal peptides that have Tat and Sec pathway dependences, respectively. Therefore, this OPH signal peptide could be successfully used in recombinant E. coli system for efficient periplasmic production of target protein regardless of the subcellular localization where functional folding of the protein occurs. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:848–854, 2016     

Analysis of ER stress in developing rice endosperm accumulating β‐amyloid peptide

The common neurodegenerative disorder known as Alzheimer’s disease is characterized by cerebral neuritic plaques of amyloid β (Aβ) peptide. Plaque formation is related to the highly aggregative property of this peptide, because it polymerizes to form insoluble plaques or fibrils causing neurotoxicity. Here, we expressed Aβ peptide as a new causing agent to endoplasmic reticulum (ER) stress to study ER stress occurred in plant. When the dimer of Aβ_1–42 peptide was expressed in maturing seed under the control of the 2.3‐kb glutelin GluB‐1 promoter containing its signal peptide, a maximum of about 8 μg peptide per grain accumulated and was deposited at the periphery of distorted ER‐derived PB‐I protein bodies. Synthesis of Aβ peptide in the ER lumen severely inhibited the synthesis and deposition of seed storage proteins, resulting in the generation of many small and abnormally appearing PB bodies. This ultrastructural change was accounted for by ER stress leading to the accumulation of aggregated Aβ peptide in the ER lumen and a coordinated increase in ER‐resident molecular chaperones such as BiPs and PDIs in Aβ‐expressing plants. Microarray analysis also confirmed that expression of several BiPs, PDIs and OsbZIP60 containing putative transmembrane domains was affected by the ER stress response. Aβ‐expressing transgenic rice kernels exhibited an opaque and shrunken phenotype. When grain phenotype and expression levels were compared among transgenic rice grains expressing several different recombinant peptides, such detrimental effects on grain phenotype were correlated with the expressed peptide causing ER stress rather than expression levels.     

Heterologous expression of a synthetic gene encoding a novel hevein-type antimicrobial peptide of <Emphasis Type="Italic">Leymus arenarius</Emphasis> in <Emphasis Type="Italic">Escherichia coli</Emphasis> cells

A novel antifungal peptide, LAMP-1a, was isolated from sand-elymus (Leymus arenarius) seeds. Expression of a synthetic gene encoding this peptide in Escherichia coli cells was obtained. The target peptide was expressed as a fusion with thioredoxin. Identity of the recombinant peptide to native LAMP-1a was confirmed by chromatography, mass spectrometry, and amino acid sequencing. LAMP-1a displayed a high inhibitory activity in respect of a number of phytopathogenic fungi in in vitro assays, which opens up possibilities for the gene encoding it to be used for genetic transformation of plants and for engineering pathogen-resistant crops