Protein and Peptide Letters - Volume 21, Issue 10, 2014

Protein and Peptide Letters has published many papers dealing with computational studies of proteins and peptides. We have recently established a new editorial policy that we will only consider manuscripts that feature a combination of computational work and experimental studies that show verification of the predictions made from computational work. For example, if bioinformatics studies are used to predict that a new protein will have a particular structure, additional work, perhaps from a collaborating laboratory, showing that the protein has some features such as a CD spectrum that agree with the prediction would be required. It is our feeling that the proliferation of computational studies with no relation to experimental work is not moving the field forward. Another point for potential authors consideration is that many manuscripts are submitted from authors in one country with a list of potential referees from a narrow geographical area, typically very near the authors home institution. In order to feature the best work in Protein and Peptide Letters, we strongly encourage authors to identify leaders in the field from around the globe to suggest as potential referees. The opinions of such individuals will help the authors to improve their manuscripts and will help us to improve the journal.

Glycopeptides, peptides containing sugar β-amino acids, have significant impact on medicinal chemistry research and pharmaceutical industr. In 1956, the discovery of one classic glycopeptide, vancomycin, broke the dawn of a new age for antibacterial research. Employing glycopeptides for the therapeutic purposes used to be regarded as proposals. Owing largely to the recent improvements in separation practices, characterization techniques, synthetic methods, and biological research, these proposals have been transformed into ongoing research projects in many laboratories around the world. Previously known as antibiotics, glycopeptides have been used as chemotherapeutic, antiviral, antitubercular, antifungal, antiproliferative and apoptotic agents. Nowadays they are even considered for the development of HIV and cancer vaccines. While several of them are in clinical trials, it could be expected that in the near future, treatment regimen of such difficult diseases might be reformed accordingly. Many interesting preliminary results are being produced in this emerging area. As witnesses and practitioners in this exciting area, however, we notice that the related communication in public domain is still limited due to the relatively small number of researchers involved. Thus, we feel the necessity to compile a timely issue about the special topic “Advances in Therapeutic Glycopeptides”, covering state-of-the-art research papers and expert reviews from this area. We are glad that Protein & Peptide Letters is willing to realize the idea with us. The opening paper of this issue by Dr. Voglmeir and coauthor discusses three types of PNGases in respect of their general properties and applications of the commercially available PNGases in glycopeptide and glycoprotein analysis. Dr. Liu and coauthors describe current techniques such as high-performance liquid chromatography (HPLC), capillary electrophoresis (CE), and mass spectrometry (MS), for the characterization of glycoproteins, with a focus on available therapeutic glycoproteins. Next three papers discuss the synthetic chemistry of glycopeptides. Dr. Zhu and coauthor describe a facile synthesis of differently protected cystathionines by the reaction of γ-bromohomoalanine with cysteine derivatives in an ethyl acetate/water biphasic system. Dr. Chen et al. report a neoglycopeptides synthesis by aqueous Suzuki-Miyaura reaction between glycosyl boronic acid and iodopeptides. Dr. Zeng et al. developed a novel strategy to prepare glycopeptide-based molecular imaging and therapy agents using fluorine-rich (fluorous) technology. The following review by Dr. Li et al. outlines a sample of mAbs currently approved for cancer treatment by the FDA, as well as antibody platforms in the research pipeline and clinic that have been engineered for greater tumor penetration, binding, and therapy efficacy. The asialoglycoprotein receptor (ASGPR) is a high-capacity C-type lectin receptor expressed on mammalian hepatocytes. Research in this field is summarized by Dr. Lu, Dr. Yin and coauthors. Recent progresses of cationic polysomes and liposomes as effective non-viral delivery system via ASGPR are also presented by these authors. Proteoglycans (PGs), a core protein and glycosaminoglycans (GAGs) chain, play important roles in amyloid-beta protein as well as tau processing, and have potential significance in Alzheimer’s disease (AD) therapy. Next, Dr. Zeng and coworkers summarized recent advances of the chemistry and biology of glycopeptides with antibiotic activity. The last review of this issue by Dr. Ding and coworker provide the progress of PGs and GAGs in AD and their therapeutic implication. In summary, experts from different fields of therapeutic glycopeptides have showcased new results and expressed their opinions in this special thematic issue of Protein & Peptide Letters. As the guest editors, we wish that this diverse collection of valuable intellectual contributions will positively influence this emerging area and gain broad readership. At the end, we would like to express our sincerest gratitude to all authors and referees for their invaluable contribution to this issue. We would also like to extend our appreciation to Editor-in-Chief, Professor Ben M. Dunn and the staffs of Protein & Peptide Letters, especially Ms Rukhshanda Rehman, for their excellent support and for providing us with the opportunity to pursue this exciting project.

Peptide-N4-(N-acetyl-α-glucosaminyl) asparagine amidases (commonly known as PNGases) have been described in a wide variety of prokaryotic hosts and exist as an integral part of the lysosomal refolding machinery in all higher organisms. Since the discovery of this ubiquitous biological function of PNGases 15 years ago, research on PNGases has found growing attention within and outside of the glycobiology research community, with currently more than 30 eukaryotic and bacterial PNGases identified and well studied. Based on the research results of their structures, enzyme properties and functions, PNGases can be primarily divided into three different types: PNGase F–like, acidic PNGases, and cytoplasmic PNGases. In this review, a brief summary of the current knowledge of these three types of PNGases in respect of their general properties and applications of the commercially available PNGases in glycopeptide and glycoprotein analysis will be presented.

Glycoproteins are becoming increasingly relevant in therapeutics, including tissue plasminogen activator for the treatment of myocardial infarction and strokes, erythropoietin for anemia and various monoclonal antibody–based treatments for cancer. Protein N- and O-glycosylation is perhaps the most crucial and immensely complex posttranslational modification that proteins undergo, and its characterization presents a major challenge. This review will discuss current techniques for the characterization of glycoproteins, with a focus on therapeutic glycoproteins where available. The crucial analytical techniques, such as high-performance liquid chromatography (HPLC), capillary electrophoresis (CE), and mass spectrometry (MS) will be described, alongside the necessary chemical labeling methods for sensitive detection. The well-established chemical and enzymatic methods for oligosaccharide release from proteins will be discussed, as will more modern methods based on exhaustive protein hydrolysis with non-specific proteases.

A simple method for the synthesis of differently protected cystathionines is described. Reaction of γ- bromohomoalanine with cysteine derivatives in an ethyl acetate/water two-phase system, which contains TBAHS and NaHCO3, led to the desired protected cystathionines in very high to excellent yields. Apart from the high yields, the mild conditions and the ease of conducting the reactions are also attractive features for this procedure.

Suzuki-Miyaura coupling reaction was applied in the syntheses of neoglycopeptides. This work utilizes new type of glycosyl aryl boronic acid and readily accessible iodo amino acids/iodopeptides. Both carbohydrate and peptide moieties are unprotected and the final product could be isolated directly. The neoglyco amino acid and neoglycopeptide products feature an O-glycosyl biaryl linker between the carbohydrate and peptide moieties.

A novel and convenient strategy for iodine labeled glycopeptide molecular probe and purification was developed. The fluorine rich bi-functional coupling agent, 4-tris(2-perfluorohexylethyl)stannylbenzoate succinimidyl ester, was successfully synthesized via 5 steps starting from the fluorous Grignard reagent. It was purified by a simple and fast isolation using perfluorinated hexanes (FC-72). The “cold” iodine labeled yield for the coupling agent was as high as 92% within 15 min. The iodine-labeled product was only in organic fractions as we expected. It was shown that there was only one major peak in organic fractions according to HPLC. Finally, the iodine-labeled coupling agent was applied to label glycopeptide and afforded a high yield of 87% within 30 min.

In 2008 cancer was identified by the World Health Organization (WHO) as one of four threats to human health and development. Since the early published reports of the first chemotherapeutic, mustine, in 1946, the anti-cancer drug and development industry has grown into a multi-billion dollar business enterprise. Worldwide, the rates of new cancer cases and deaths has been steadily increasing each year, with the estimation by the WHO-sponsored GLOBOCAN cancer database, that at current rates, nearly 13 million cancer deaths will be reported in 2030. The recent successes of monoclonal antibodies (mAbs), an important class of glycoprotein, and their multivalent and drug conjugated derivatives over the past 30 years have led to the approval of 12 monoclonal antibodies for use in cancer treatment by the FDA. Modern recombinant and engineering techniques have led to an explosion of antibody platforms that can be attributed to great gains in clinical efficacy. This review discusses and outlines a sample of mAbs currently approved for cancer treatment by the FDA, as well as antibody platforms in the research pipeline and clinic that have been engineered for greater tumor penetration, binding, and efficacy.

The asialoglycoprotein receptor (ASGPR) is a high-capacity C-type lectin receptor mainly expressed on mammalian hepatic cells. The physiological function of ASGPR has not been completely clarified and is thought to be specific binding and internalization of galactose (Gal) or N-acetylgalactosamine (GalNAc)-terminating glycoproteins by hepatocytes. The human ASGPR is comprised of two homologous polypeptides, H1 and H2. ASGPR H1 has two splice variants (H1a and H1b) and ASGPR H2 has three splice variants (H2a, H2b, and H2c). These variants have been discovered to exist both in human liver tissues and in human hepatoma cells. Variant H1b, which has an in-frame deletion of exon 2 resulting in the loss of the transmembrane domain and is secreted as a soluble protein, encodes functional soluble ASGPR (s- ASGPR). Based on our previous results, we proposed the possible physiological function of s-ASGPR, which is well interpreted in the Galactosyl Homeostasis Hypothesis proposed by Weigel. ASGPR is one of the most promising targets for hepatic delivery. In this review, the recent progresses of cationic polysomes and liposomes as effective non-viral delivery system via ASGPR are also presented.

Glycopeptides with potent antibiotic activity are vital for the treatment of severe infections that caused by Gram-positive bacteria, especially methicillin-resistant Staphylococcus aureus. Recently, the glycopeptide-resistant Grampositive bacteria present a serious challenge to public health after more than decades of clinical use. Additionally, the antibacterial activity and side effect become an increasing crisis and should have to be taken into account. As a consequence, new glycopeptide antibiotics are needed to face with these problems. In the past years, with the development of natural product chemistry, more and more glycopeptide compounds with promising biological properties were discovered. In addition, the chemical modification of the known glycopeptide provides an opportunity for the discovery of new potential glycopeptide antibiotics. Considerable efforts have been made in this field in order to meet the clinical needs. In this article, we mainly focus on the advances of glycopeptide as antibiotics, including many representative glycopeptides or its analogues and derivatives. Taken together, we hope all this information is helpful for the discovery of new potential glycopeptide antibiotics.

Misfolded protein amyloid-beta protein (Aβ) and tau protein are two high hallmarks of Alzheimer’s disease (AD), representing significant targets in treating AD. Researches on mechanisms of the two proteins inducing neuron dysfunctions provide therapeutic strategies of AD, including inhibition of Aβ production and aggregation, acceleration of Aβ clearance as well as reduction of tau hyperphosphorylation. Proteoglycans (PGs) consist of a core protein and glycosaminoglycans (GAGs) chains, with enormous structural diversity due to variation in the core protein, the number of GAGs chains as well as extent and position of sulfation. Considerable evidences have indicated that PGs and GAGs play important roles in Aβ and tau processing. Numbers of GAGs and analogues have potential therapeutic function in AD. In this Review, we focus on the relationship of PGs and GAGs with misfolded proteins in AD and their potential therapeutic implications.

Colonization of the stomach by Helicobacter pylori can result in such gastrointestinal illnesses as chronic gastritis, peptic ulcer and gastric cancer. Antimicrobial peptides (AMPs) are expressed in the stomach and play a key role in the innate immune responses to H. pylori in humans. During H. pylori infections, AMP expression mediated by NOD-1, NF-kB and/or ERK, functions to eradicate the bacteria, thereby preventing the gastritis and gastric cancer. This suggests that the use of synthetic AMPs could be one component of an effective therapeutic strategy to combat H. pylori. In addition, it appears that some peptides, and combinations of peptides, act synergistically with conventional drugs, thereby enhancing therapeutic efficacy. Our aim in this article was to review what is currently known about gastric AMP expression in response to H. pylori infection, and to briefly discuss the potential use of AMPs, either alone or in combination with conventional antibiotics, for the treatment of H. pylori infection.

Abstract: Elastin-like polypeptides (ELPs) have been widely used to promote the development of a variety of smart biomaterials. Transition temperature is a key attribute of ELPs central to ELPs researches. Therefore, it is essential to establish predictive models of transition temperature that are both computationally efficient and reliable by employing simple parameters. Back propagation neural network (BPNN), a powerful feed-forward algorithm designed to solve problems with overwhelming complexity, has been successfully used in non-linear predictor model. In this study, two pH-sensitive ELPs were expressed, purified and determined for temperature transition across a range of pH. The pH, concentration and molecular weight (MW) as well as isoelectric point (PI) and pseudo amino acid (PseAA) of these two ELPs were adopted as input parameters. Support vector machine (SVM) and back propagation neural network (BPNN) were performed respectively. We selected Lamda ( λ) value by training set and evaluated predictor model by jackknife test that combined with Uniform Design (UD). According to the results of BPNN and SVM, whose mean absolute error (MAE) of BPNN model jackknife test were 4.80 and 4.95 respectively, the predictive ability of BPNN is a minor improvement over SVM. Applying Mackay’s data, MAE of BPNN jackknife test was 2.02, while the MAE between experimental and predicted transition temperature was 2.30 in Mackay’s predictor model. Compared with Mackay predictor model, the enhancement in the accuracy indicates that the proposed BPNN method could play a complementary role to predict ELPs transition temperature.

Protein derived from the oyster (Saccostrea cucullata) was hydrolyzed using protease from Bacillus cereus SU12 for isolation of antioxidant peptides. The oyster hydrolysate exhibited a strong antioxidant potential in DPPH (85.7±0.37%) followed by Hydrogen peroxide radical scavenging activity (81.6±0.3%), Hydroxyl radical-scavenging activity (79.32±0.6%), Reducing power assay (2.63±0.2 OD at 700nm). Due to the high antioxidant potential, hydrolysate was fractionated in Sephadex G-25 gel filtration chromatography. The active peptide fraction was further purified by UPLC-MS. Totally 7 antioxidant peptides were collected. Among 7 peptides (SCAP 1-7), 3 peptides (SCAP 1, 3 and 7) had highest scavenging ability on DPPH radicals. The amino acid sequence and molecular mass of purified antioxidant peptides (SCAP1, SCAP3 and SCAP7) were determined by Q-TOF ESI mass spectroscopy and structures of the peptides were Leu-Ala-Asn-Ala-Lys (MW=515.29Da), Pro-Ser-Leu-Val-Gly-Arg-Pro-Pro-Val-Gly-Lys-Leu-Thr-Leu (MW=1432.89Da) and Val-Lys-Val-Leu-Leu-Glu-His-Pro-Val-Leu (MW=1145.75Da), respectively. The unique amino acid composition and sequence in the peptides might play an important role in expression of their antioxidant activity. The results of this study suggest that oyster protein hydrolysate is good source of natural antioxidants.