Inhibition of catechol-O-methyltransferase (COMT) by heparin oligosaccharides with specific structures

COMT inhibitors are commonly used to improve the effectiveness of levodopa in treating Parkinson's disease by inhibiting its conversion to 3-O-methyldopa. Because of the serious side effect of nitrocatechol COMT inhibitors, it is necessary to develop non-nitrocatechol COMT inhibitors with a higher safety profile. Heparin has been observed to bind to COMT. However, the exact functional significance of this interaction is not fully understood. In this study, the contribution of different substitution of heparin to its binding with COMT was investigated. In vitro and in vivo, heparin oligosaccharides can bind to COMT and inhibit its activity. Furthermore, we enriched the functional heparin oligosaccharides that bind to COMT and identified the sequence UA2S-GlcN(S/Ac)6(S/H)-UA2S-GlcNS6(S/H)-UA2(S/H)-GlcNS6S as the characteristic structural domain of these functional oligosaccharides. This study has elucidated the relationship between the structure of heparin oligosaccharides and their activity against COMT, providing valuable insights for the development of non-nitrocatechol COMT inhibitors with improved safety and efficacy.

Improving impact of heparan sulfate on the endothelial glycocalyx abnormalities in atherosclerosis as revealed by glycan-protein interactome

Endothelial dysfunction induced by oxidative stress is an early predictor of atherosclerosis, which can cause various cardiovascular diseases. The glycocalyx layer on the endothelial cell surface acts as a barrier to maintain endothelial biological function, and it can be impaired by oxidative stress. However, the mechanism of glycocalyx damage during the development of atherosclerosis remains largely unclear. Herein, we established a novel strategy to address these issues from the glycomic perspective that has long been neglected. Using countercharged fluorescence protein staining and quantitative mass spectrometry, we found that heparan sulfate, a major component of the glycocalyx, was structurally altered by oxidative stress. Comparative proteomics and protein microarray analysis revealed several new heparan sulfate-binding proteins, among which alpha-2-Heremans-Schmid glycoprotein (AHSG) was identified as a critical protein. The molecular mechanism of AHSG with heparin was characterized through several methods. A heparan analog could relieve atherosclerosis by protecting heparan sulfate from degradation during oxidative stress and by reducing the accumulation of AHSG at lesion sites. In the present study, the molecular mechanism of anti-atherosclerotic effect of heparin through interaction with AHSG was revealed. These findings provide new insights into understanding of glycocalyx damage in atherosclerosis and lead to the development of corresponding therapeutics.

Surfactant-like Additives Assisted the Lateral Growth of Pentacene Films

Lateral growth of thin films is crucial for organic electronic devices, such as field-effect transistors. Here, we report a strategy to improve the lateral growth of pentacene films using rubrene as a surfactant-like additive. Atomic force microscopy (AFM) images confirm the enhanced lateral growth with the presence of rubrene, resulting in smooth and enlarged molecule domains in the films in comparison to those without rubrene. Molecular dynamics simulations are conducted to explore the interlayer diffusion of pentacene molecules during the growth. With the rubrene molecules as surfactant-like additives, mean square displacement (MSD) analysis shows that the pentacene molecules have a descending diffusion coefficient of 2.0 × 10-5 cm2 s-1, which is greater than the ascending diffusion coefficient of 1.6 × 10-5 cm2 s-1. The more descending molecules lead to an enhanced lateral growth of pentacene films, which is in good agreement with the experiments. As a result, the pentacene films grown with rubrene exhibit a rapid increase in carrier mobility over thickness due to the well-connected domains resulting from enhanced lateral growth. This finding will provide a new strategy to modulate the morphology of organic films for high-performance devices.

Distinct mechanisms underlying the therapeutic effects of low-molecular-weight heparin and chondroitin sulfate on Parkinson's disease

Parkinson's disease (PD) is a neurodegenerative disorder influenced by various factors, including age, genetics, and the environment. Current treatments provide symptomatic relief without impeding disease progression. Previous studies have demonstrated the therapeutic potential of exogenous heparin and chondroitin sulfate in PD. However, their therapeutic mechanisms and structure-activity relationships remain poorly understood. In this study, low-molecular-weight heparin (L-HP) and chondroitin sulfate (L-CS) exhibited favorable therapeutic effects in a mouse model of PD. Proteomics revealed that L-HP attenuated mitochondrial dysfunction through its antioxidant properties, whereas L-CS suppressed neuroinflammation by inhibiting platelet activation. Two glycosaminoglycan (GAG)-binding proteins, manganese superoxide dismutase (MnSOD2) and fibrinogen beta chain (FGB), were identified as potential targets of L-HP and L-CS, and we investigated their structure-activity relationships. The IdoA2S-GlcNS6S/GlcNAc6S unit in HP bound to SOD2, whereas the GlcA-GalNAc4S and GlcA-GalNAc4S6S units in CS preferred FGB. Furthermore, N-S and 2-O-S in L-HP, and 4-O-S, 6-O-S, and -COOH in L-CS contributed significantly to the binding process. These findings provide new insights and evidence for the development and use of glycosaminoglycan-based therapeutics for PD.

Structurally defined heparin octasaccharide domain for binding to SARS-CoV-2 Omicron BA.4/BA.5/BA.5.2 spike protein RBD

Heparin, a bio-molecule with the highest negative charge density, is pharmaceutically important to prevent SARS-CoV-2 infection due to its strong competitive binding to spike protein compared with cellular heparan sulfate, which was confirmed as a co-receptor for virus-host cell interaction. Hence, the refined structural characterization of heparin targeting viral protein-HS interaction was significant for developing antiviral pharmaceuticals. In our study, heparin oligomers (dp ≥ 4) were prepared using heparinase I. The affinity oligosaccharides binding to Omicron spike protein RBD were separated by affinity chromatography and size exclusion chromatography. HILIC-ESI-FTMS was used for chain mapping analysis. The basic building blocks were analyzed and the binding domain sequence was produced by Seq-GAG software and further measured by SAX chromatography. As results, heparin octasaccharide was found with significantly higher binding ability than hexasaccharide and tetrasaccharide, and the octasaccharide [ΔUA-GlcNS6S-GlcA-GlcNS6S-IdoA2S-GlcNS6S-IdoA2S-GlcNS6S] with 12 sulfate groups showed high binding to RBD. The mechanism of this structurally well-defined octasaccharide binding to RBD was further investigated by molecular docking. The affinity energy of optimal pose was -6.8 kcal/mol and the basic amino acid residues in RBD sequence (Arg403, Arg452, Arg493 and His505) were identified as the major contribution factor to interacting with sulfate/carboxyl groups on saccharide chain. Our study demonstrated that heparin oligosaccharide with well-defined structure could be potentially developed as anti-SARS-CoV-2 drugs.

Heparin Oligosaccharides as Vasoactive Intestinal Peptide Inhibitors via their Binding Process Characterization

BACKGROUND

It has been proven that vasoactive intestinal peptide (VIP) was involved in the pathogenesis of prostate cancer. Cardin et al. found that by an alanine scan, the heparin-binding site on VIP was exactly the same sequence in VIP and its receptor. Therefore, heparin could competitively block the binding of VIP and its receptor. However, the structure-activity relationship between heparin and VIP has not been reported, especially in terms of the sequence and sulfation patterns of heparin oligosaccharides upon binding to VIP.

OBJECTIVE

The binding process between heparin oligosaccharides and VIPA variety of experiments was designed to study the structure-activity relationship between heparin oligosaccharides and VIP.

METHODS

Heparin was enzymatically digested and purified to produce heparin oligosaccharides, and the structures were characterized by NMR. The binding capacity between heparin oligosaccharides and VIP was analyzed by GMSA and ITC experiments. The binding between heparin oligosaccharides and VIP was simulated using a molecular docking program to show the complex. ELISA assay was used to investigate the effect of non-anticoagulant heparin oligosaccharides on the VIP-mediated cAMP/PKA signaling pathway in vitro.

RESULTS

The results indicated that both the length and the sulfation pattern of heparin oligosaccharides affected its binding to VIP. VIP could induce the expression of cAMP at a higher level in PC3 cells, which could be regulated by the interaction of heparin oligosaccharides and VIP.

CONCLUSION

The binding between heparin oligosaccharides and VIP could block the binding between VIP and its receptor on tumor cells. Downloading the regulation of the expression level of cAMP could possibly further affect the subsequent activation of PKA. These non-anticoagulant heparin oligosaccharides may block the VIP-mediated cAMP/PKA signaling pathway and thus exert their antitumor activity.

New insights into the binding of PF4 to long heparin oligosaccharides in ultralarge complexes using mass spectrometry

BACKGROUND

Heparin-induced thrombocytopenia (HIT) is a serious complication caused by heparin drugs. The ultralarge complexes formed by platelet factor 4 (PF4) with heparin or low molecular weight heparins (LMWHs) are important participants in inducing the immune response and HIT.

OBJECTIVES

We aim at characterizing the interaction between PF4 and long-chain heparin oligosaccharides and providing robust analytical methods for the analysis of PF4-heparin complexes.

METHODS

In this work, the characteristics of PF4-enoxaparin complexes after incubation in different molar ratios and concentrations were analyzed by multiple analytical methods, especially liquid chromatography-mass spectrometry and liquid chromatography-tandem mass spectrometry with multiple reaction monitoring were developed to qualitatively and quantitatively monitor heparin oligosaccharides and PF4 in HIT-inducing complexes.

RESULTS

The results showed that the largest proportion of ultralarge complexes formed by PF4 and enoxaparin was at a specific molar ratio, ie, a PF4/enoxaparin ratio of 2:1, while the ultralarge complexes contained PF4 tetramer and enoxaparin at a molar ratio of approximately 2:1.

CONCLUSION

A binding model of PF4 and enoxaparin in ultralarge complexes is proposed with one heparin oligosaccharide chain (∼ dp18) bound to 2 PF4 tetramers in different morphologies to form ultralarge complexes, while PF4 tetramer is surrounded by multiple heparin chains in smaller complexes. Our study provides new insights into the structural mechanism of PF4-LMWH interaction, which help to further understand the mechanism of LMWH immunogenicity and develop safer heparin products.

MsPHep: An online application for low molecular weight heparin rapid characterization based on liquid chromatography-tandem mass spectrometry

Low-molecular-weight heparins (LMWHs) are important anticoagulants widely used in clinic. Since they are comprised of complex and heterogenous glycan chains, liquid chromatography-tandem mass spectrometry (LC-MS) is commonly used for structural analysis and quality control of LMWHs to ensure their safety and efficacy. Yet, the structural complexity arising from the parent heparin macromolecules, as well as the different depolymerization methods used for preparing LMWHs, makes processing and assigning the LC-MS data of LWMHs very tedious and challenging. We therefore developed, and here report, an open-source and easy-to-use web application, MsPHep, to facilitate the LMWH analysis based on LC-MS data. MsPHep is compatible with various LMWHs and chromatographic separation methods. With the HepQual function, MsPHep is capable of annotating both the LMWH compound and its isotopic distribution from mass spectra. Moreover, the HepQuant function enables automatic quantification of LMWH compositions without prior knowledge or any database generation. To demonstrate the reliability and system stability of MsPHep, we tested various types of LMWHs that were analyzed with different chromatographic methods coupled to MS. The results show that MsPHep has its own advantages compared to another public tool GlycReSoft for LMWH analysis, and it is available online under an open-source license at https://ngrc-glycan.shinyapps.io/MsPHep.

Interactions of heparin with key glycoproteins of human respiratory syncytial virus

Introduction: The unexpected surge of respiratory syncytial virus (RSV) cases following pandemic phase of COVID-19 has drawn much public attention. Drawing on the latest antiviral research, revisiting this heightened annual outbreak of respiratory disease could lead to new treatments. The ability of sulfated polysaccharides to compete for a variety of viruses binding to cell surface heparan sulfate, suggests several drugs that might have therapeutic potential for targeting RSV-glycosaminoglycan interactions. Methods: In the current study, the binding affinity and kinetics of two RSV glycoproteins (RSV-G protein and RSV-F protein) to heparin were investigated by surface plasmon resonance. Furthermore, solution competition studies using heparin oligosaccharides of different lengths indicated that the binding of RSV-G protein to heparin is size-dependent, whereas RSV-F protein did not show any chain length preference. Results and discussion: The two RSV glycoproteins have slightly different preferences for heparin sulfation patterns, but the N-sulfo group in heparin was most critical for the binding of heparin to both RSV-G protein and RSV-F protein. Finally, pentosan polysulfate and mucopolysaccharide polysulfate were evaluated for their inhibition of the RSV-G protein and RSV-F protein-heparin interaction, and both highly negative compounds showed strong inhibition.

The Alterations and Roles of Glycosaminoglycans in Human Diseases

Glycosaminoglycans (GAGs) are a heterogeneous family of linear polysaccharides which are composed of a repeating disaccharide unit. They are also linked to core proteins to form proteoglycans (PGs). GAGs/PGs are major components of the cell surface and the extracellular matrix (ECM), and they display critical roles in development, normal function, and damage response in the body. Some properties (such as expression quantity, molecular weight, and sulfation pattern) of GAGs may be altered under pathological conditions. Due to the close connection between these properties and the function of GAGs/PGs, the alterations are often associated with enormous changes in the physiological/pathological status of cells and organs. Therefore, these GAGs/PGs may serve as marker molecules of disease. This review aimed to investigate the structural alterations and roles of GAGs/PGs in a range of diseases, such as atherosclerosis, cancer, diabetes, neurodegenerative disease, and virus infection. It is hoped to provide a reference for disease diagnosis, monitoring, prognosis, and drug development.

A Cluster Sequencing Strategy To Determine the Consensus Affinity Domains in Heparin for Its Binding to Specific Proteins

Glycosaminoglycans (GAGs) have high negative charge and are biologically and pharmaceutically important because their high charge promotes a strong interaction with many proteins. Due to the inherent heterogeneity of GAGs, multiple oligosaccharides, containing certain common domains, often can interact with clusters of basic amino acid residues on a target protein. The specificity of many GAG-protein interactions remains undiscovered since there is insufficient structural information on the interacting GAGs. Herein, we establish a cluster sequencing strategy to simultaneously deduce all major sequences of the affinity GAG oligosaccharides, leading to a definition of the consensus sequence they share that corresponds to the specific binding domain for the target protein. As a proof of concept, antithrombin III-binding oligosaccharides were examined, resulting in a heptasaccharide domain containing the well-established anticoagulant pentasaccharide sequence. Repeating this approach, a new pentasaccharide domain was discovered corresponding to the heparin motif responsible for binding interferon-γ (IFNγ). Our strategy is fundamentally important for the discovery of saccharide sequences needed in the development of novel GAG-based therapeutics.

Kinetic and Structural Aspects of Glycosaminoglycan-Monkeypox Virus Protein A29 Interactions Using Surface Plasmon Resonance

Monkeypox virus (MPXV), a member of the Orthopoxvirus genus, has begun to spread into many countries worldwide. While the prevalence of monkeypox in Central and Western Africa is well-known, the recent rise in the number of cases spread through intimate personal contact, particularly in the United States, poses a grave international threat. Previous studies have shown that cell-surface heparan sulfate (HS) is important for vaccinia virus (VACV) infection, particularly the binding of VACV A27, which appears to mediate the binding of virus to cellular HS. Some other glycosaminoglycans (GAGs) also bind to proteins on Orthopoxviruses. In this study, by using surface plasmon resonance, we demonstrated that MPXV A29 protein (a homolog of VACV A27) binds to GAGs including heparin and chondroitin sulfate/dermatan sulfate. The negative charges on GAGs are important for GAG-MPXV A29 interaction. GAG analogs, pentosan polysulfate and mucopolysaccharide polysulfate, show strong inhibition of MPXV A29-heparin interaction. A detailed understanding on the molecular interactions involved in this disease should accelerate the development of therapeutics and drugs for the treatment of MPXV.

Evaluating the immunogenicity of heparin and heparin derivatives by measuring their binding to platelet factor 4 using biolayer interferometry

Heparin (HP) is a polysaccharide that is widely used in the clinic as an anticoagulant. A major side effect associated with HP is the heparin-induced thrombocytopenia (HIT), which is initiated by the immune response to complex formed by HP and platelet factor 4 (PF4). Low molecular weight heparins (LMWHs) are the depolymerized version of HP, which have reduced risks of inducing HIT. However, it is still necessary to evaluate the immunogenicity of LMWHs to ensure their drug safety. Since HIT involves very complicated processes, the evaluation of HP and LMWH immunogenicity requires experiments from multiple aspects, of which the binding affinity between HP and PF4 is a key property to be monitored. Herein, we developed a novel competitive biolayer interferometry (BLI) method to investigate the binding affinity between HP and PF4. The influence of different domains in HP on its immunogenicity was compared for better understanding of the molecular mechanism of HP immunogenicity. Furthermore, the half maximal inhibitory concentration (IC50) of HP and LMWH can be measured by competitive combination, which is important for the quality control during the developing and manufacturing of HP and LMWH drugs.

O021 Evaluating the impact of neurosurgical rotation experience in Africa on the interest and perception of medical students towards a career in neurosurgery: a continental, multi-centre, cross-sectional study

Introduction

Africa has the second-highest neurosurgical workforce deficit globally, and many medical students in Africa lack exposure to the field. This study aims to assess the impact of a neurosurgical rotation during medical school in shaping the perception and interest of students towards a career in neurosurgery.

Methods

This is a continental, multi-centre, cross-sectional study. A Google Form e-survey was disseminated to African clinical medical students between February 21st and March 20th, 2021. Data was analysed using descriptive statistics and adjusted logistic regression modelling.

Results

Data was received from 539 students in 30 African countries (n=30/54, 55.6%). The majority of participants were male (n=289/539, 53.6%) and were from Kenya (n=83/539, 15.4%). Most students had undertaken a clinical neurosurgery rotation (n=278/539, 51.6%); the majority reported a rotation length of four weeks or less (n=181/278, 65.1%). Students with clinical experience were less likely to pursue the specialty (p=0.02) and had a stronger perception that it is more difficult for women to pursue neurosurgery (p=0.0001) when compared to those without clinical experience. However, after adjusting for other factors, students with greater than four weeks of neurosurgical exposure were more likely to express a career interest in neurosurgery (odds ratio [OR]=1.75, p<0.04) and men were more likely to express interest in a neurosurgical career compared to women (OR=3.22, p<0.001).

Conclusion

Our findings support standardised, continent-wide, curriculum development, and advocacy supporting improved gender inclusivity in education and policy-making to improve the quality of neurosurgical exposure during medical school and tackle the workforce deficit across Africa.

Take-home message

A continent-wide, standardised curriculum guide to neurosurgical rotations, and advocacy for gender inclusivity in education and policy-making efforts across the African continent is required to shape the perception and interest of medical students towards a career in neurosurgery.

Chondroitin Sulfate/Dermatan Sulfate-Protein Interactions and Their Biological Functions in Human Diseases: Implications and Analytical Tools

Chondroitin sulfate (CS) and dermatan sulfate (DS) are linear anionic polysaccharides that are widely present on the cell surface and in the cell matrix and connective tissue. CS and DS chains are usually attached to core proteins and are present in the form of proteoglycans (PGs). They not only are important structural substances but also bind to a variety of cytokines, growth factors, cell surface receptors, adhesion molecules, enzymes and fibrillary glycoproteins to execute series of important biological functions. CS and DS exhibit variable sulfation patterns and different sequence arrangements, and their molecular weights also vary within a large range, increasing the structural complexity and diversity of CS/DS. The structure-function relationship of CS/DS PGs directly and indirectly involves them in a variety of physiological and pathological processes. Accumulating evidence suggests that CS/DS serves as an important cofactor for many cell behaviors. Understanding the molecular basis of these interactions helps to elucidate the occurrence and development of various diseases and the development of new therapeutic approaches. The present article reviews the physiological and pathological processes in which CS and DS participate through their interactions with different proteins. Moreover, classic and emerging glycosaminoglycan (GAG)-protein interaction analysis tools and their applications in CS/DS-protein characterization are also discussed.

Glycosaminoglycan-Protein Interactions and Their Roles in Human Disease

Glycosaminoglycans (GAGs) are a family of linear and negatively charged polysaccharides that exist ubiquitously on the human cell surface as well as in the extracellular matrix. GAGs interact with a wide range of proteins, including proteases, growth factors, cytokines, chemokines and adhesion molecules, enabling them to mediate many physiological processes, such as protein function, cellular adhesion and signaling. GAG-protein interactions participate in and intervene in a variety of human diseases, including cardiovascular disease, infectious disease, neurodegenerative diseases and tumors. The breakthrough in analytical tools and approaches during the last two decades has facilitated a greater understanding of the importance of GAG-protein interactions and their roles in human diseases. This review focuses on aspects of the molecular basis and mechanisms of GAG-protein interactions involved in human disease. The most recent advances in analytical tools, especially mass spectrometry-based GAG sequencing and binding motif characterization methods, are introduced. An update of selected families of GAG binding proteins is presented. Perspectives on development of novel therapeutics targeting specific GAG-protein interactions are also covered in this review.

Discovery of exolytic heparinases and their catalytic mechanism and potential application

Heparinases (Hepases) are critical tools for the studies of highly heterogeneous heparin (HP)/heparan sulfate (HS). However, exolytic heparinases urgently needed for the sequencing of HP/HS chains remain undiscovered. Herein, a type of exolytic heparinases (exoHepases) is identified from the genomes of different bacteria. These exoHepases share almost no homology with known Hepases and prefer to digest HP rather than HS chains by sequentially releasing unsaturated disaccharides from their reducing ends. The structural study of an exoHepase (BIexoHep) shows that an N-terminal conserved DUF4962 superfamily domain is essential to the enzyme activities of these exoHepases, which is involved in the formation of a unique L-shaped catalytic cavity controlling the sequential digestion of substrates through electrostatic interactions. Further, several HP octasaccharides have been preliminarily sequenced by using BIexoHep. Overall, this study fills the research gap of exoHepases and provides urgently needed tools for the structural and functional studies of HP/HS chains.

Coupling Liquid Chromatography and Tandem Mass Spectrometry to Electrophoresis for In-Depth Analysis of Glycosaminoglycan Drugs: Heparin and the Multicomponent Sulodexide

Glycosaminoglycans (GAGs) contribute to the treatment of many human diseases, especially in the field of thrombosis, because of their anticoagulant activity. GAGs interrupt the coagulation process by interacting with multiple coagulation factors through defined sequences within their linear and negatively charged chains, which are not fully elucidated. Numerous methods have been developed to characterize the structure of pharmaceutical GAGs, including intravenously or subcutaneously administered heparin and orally administered sulodexide. However, most currently available methods only focus on the oligosaccharide portion or analyze the whole mixture because longer-chain polysaccharides are extremely difficult to resolve by chromatographic separation. We have established two novel electrophoresis-mass spectrometry methods to provide a panoramic view of the structures of pharmaceutical GAGs. In the first method, an in-gel digestion procedure was developed to recover GAGs from the polyacrylamide gels, while in the second method, a strong anion exchange ultrafiltration procedure was developed to extract multiple GAG species from the agarose gels. Both procedures are compatible with liquid chromatography-tandem mass spectrometry, and structural information, such as disaccharide composition and chain length, can be revealed for each GAG fraction. The applications of these two methods on analysis of two different GAG drugs, heparin and sulodexide, were demonstrated. The current study offers the first robust tool to directly elucidate the structure of larger GAG chains with more biological importance rather than obtaining a vague picture of all chains as a mixture, which is fundamental for better understanding the structure-activity relationship and quality control of the GAG drugs.

Delayed Comparison and Apriori Algorithm (DCAA): A Tool for Discovering Protein-Protein Interactions From Time-Series Phosphoproteomic Data

Analysis of high-throughput omics data is one of the most important approaches for obtaining information regarding interactions between proteins/genes. Time-series omics data are a series of omics data points indexed in time order and normally contain more abundant information about the interactions between biological macromolecules than static omics data. In addition, phosphorylation is a key posttranslational modification (PTM) that is indicative of possible protein function changes in cellular processes. Analysis of time-series phosphoproteomic data should provide more meaningful information about protein interactions. However, although many algorithms, databases, and websites have been developed to analyze omics data, the tools dedicated to discovering molecular interactions from time-series omics data, especially from time-series phosphoproteomic data, are still scarce. Moreover, most reported tools ignore the lag between functional alterations and the corresponding changes in protein synthesis/PTM and are highly dependent on previous knowledge, resulting in high false-positive rates and difficulties in finding newly discovered protein–protein interactions (PPIs). Therefore, in the present study, we developed a new method to discover protein–protein interactions with the delayed comparison and Apriori algorithm (DCAA) to address the aforementioned problems. DCAA is based on the idea that there is a lag between functional alterations and the corresponding changes in protein synthesis/PTM. The Apriori algorithm was used to mine association rules from the relationships between items in a dataset and find PPIs based on time-series phosphoproteomic data. The advantage of DCAA is that it does not rely on previous knowledge and the PPI database. The analysis of actual time-series phosphoproteomic data showed that more than 68% of the protein interactions/regulatory relationships predicted by DCAA were accurate. As an analytical tool for PPIs that does not rely on a priori knowledge, DCAA should be useful to predict PPIs from time-series omics data, and this approach is not limited to phosphoproteomic data.

Role of the head-stalk linker region (aa115-122) of Newcastle disease virus haemagglutinin-neuraminidase in regulating fusion triggering

To gain insights into the role of the head-stalk linker region in the fusion triggering, we constructed mutants by deleting or substituting the linker region (115-NGAANNSG-122) of Newcastle disease virus (NDV) haemagglutinin-neuraminidase (HN) with the corresponding sequences of other paramyxoviruses. The results showed that these HN mutants exhibited different levels of fusion-triggering activity, but most of them maintained comparable levels with wide-type HN in both receptor recognition and neuraminidase activity. We tried to figure out reasons for fusion alteration through assessing the expression and the oligomeric state of HN mutants. Moreover, four mutants with significant fusion changes were introduced into the headless HN stem (HN1-123) to intensively investigate the role of the linker region in fusion triggering. Consequently, the stability of HN oligomers and the structural integrity of the 4 helical-bundle of stalk have complicated influences on the alteration of fusion-triggering activities for different mutants. These data suggested that the head-stalk linker could regulate the fusion triggering at both full-length and headless HN levels.

Comprehensive Glycomic Analysis Reveals That Human Serum Albumin Glycation Specifically Affects the Pharmacokinetics and Efficacy of Different Anticoagulant Drugs in Diabetes

Long-term hyperglycemia in patients with diabetes leads to human serum albumin (HSA) glycation, which may impair HSA function as a transport protein and affect the therapeutic efficacy of anticoagulants in patients with diabetes. In this study, a novel mass spectrometry approach was developed to reveal the differences in the profiles of HSA glycation sites between patients with diabetes and healthy subjects. K199 was the glycation site most significantly changed in patients with diabetes, contributing to different interactions of glycated HSA and normal HSA with two types of anticoagulant drugs, heparin and warfarin. An in vitro experiment showed that the binding affinity to warfarin became stronger when HSA was glycated, while HSA binding to heparin was not significantly influenced by glycation. A pharmacokinetic study showed a decreased level of free warfarin in the plasma of diabetic rats. A preliminary retrospective clinical study also revealed that there was a statistically significant difference in the anticoagulant efficacy between patients with diabetes and patients without diabetes who had been treated with warfarin. Our work suggests that larger studies are needed to provide additional specific guidance for patients with diabetes when they are administered anticoagulant drugs or drugs for treating other chronic diseases.

microRNA-155 attenuates profibrotic effects of transforming growth factor-beta on human lung fibroblasts

Transforming growth factor-beta (TGF-β) functions in fibrogenesis as a profibrotic mediator, regulating cell proliferation, migration, apoptosis and collagen production of fibroblasts. microRNA-155 (miR-155), the expression of which has been related to bleomycin-induced idiopathic pulmonary fibrosis, has been involved in TGF-β induced epithelial-mesenchymal transition. Here, we found that miR-155 expression was decreased in human pulmonary fibroblasts by TGF-β treatment. We overexpressed miR-155 in fibroblasts to investigate the functional impact of miR-155 on TGF-β-induced fibrotic phenotype of fibroblasts. It is suggested that miR-155 overexpression attenuated the stimulatory effect of TGF-β on fibroblast proliferation, migration and collagen synthesis, by evidence from assessment of cell cycle, viability, apoptosis, migration and collagen content. Furthermore, quantitative measurement showed that SMAD1 gene expression was decreased following miR-155 inhibition, thereby demonstrating an indirect miRNA-SMAD interaction that links miR-155 to TGF-β signaling. Our work helped uncover an miRNA-mediated mechanism of fibroblast response to TGF-β. Moreover, it will help to achieve a better understanding of the regulatory roles of miR-155 in fibrogenesis.

Conserved amino acids around the DIII-DI linker region of the Newcastle disease virus fusion protein are critical for protein folding and fusion activity

Newcastle disease virus (NDV), an avian paramyxovirus, causes Newcastle disease (ND) which is a highly contagious and fatal viral disease affecting poultry and most species of birds. The fusion (F) protein of NDV mediates membrane fusion, which is essential to the processes of viral entry, replication, and dissemination. Although several domains of NDV F are known to have important effects on regulating the membrane fusion activity, the role of the region around domain III (DIII) and domain I (DI) still remains ill-defined. Site-directed mutagenesis was utilized to change the conserved amino acids at 269, 274, 277, 286, 287, 290, 295, and 297 to alanine in order to investigate the effects of these conserved amino acids around the DIII and DI linker region of the NDV F protein on fusion activity. It was found that five of these substitutions almost abolished fusion activity except for mutants I269A, Q286A, and N297A, which showed 57.1%, 161.1%, and 97.7% of the wt F level, respectively. Four (I274A, D277A, V287A, and P290A) of these five mutants likely result in interfering with folding or transporting of the molecule since these proteins were minimally expressed at the cell surface, formed aggregates, or not proteolytically cleaved. However, mutant L295A almost abolished fusion activity even with a similar level of cell surface expression. These data indicated that conserved amino acids around the DIII-DI linker region are critical for the folding of the F protein and have an important influence on fusion activity.

Self-assembly of 5,6-dihydroxyindole-2-carboxylic acid: polymorphism of a eumelanin building block on Au(111)

Investigating two-dimensional (2D) self-assembled structures of biological monomers governed by intermolecular interactions is a prerequisite to understand the self-assembly of more complex biomolecular systems. 5,6-Dihydroxyindole carboxylic acid (DHICA) is one of the building blocks of eumelanin - an irregular heteropolymer and the most common form of melanin which has potential applications in organic electronics and bioelectronics. By means of scanning tunneling microscopy, density functional theory and Monte Carlo calculations, we investigate DHICA molecular configurations and interactions underlying the multiple 2D patterns formed on Au(111). While DHICA self-assembled molecular networks (SAMNs) are dominated by the hydrogen bonding of carboxylic acid dimers, a variety of 2D architectures are formed due to the multiple weak interactions of the catechol group. The hydroxyl group also allows for redox reactions, caused by oxidation via O2 exposure, resulting in molecular rearrangement. The susceptibility of the molecules to oxidation is affected by their SAMNs architectures, giving insights on the reactivity of indoles as well as highlighting non-covalent assembly as an approach to guide selective oxidation reactions.

The protein S-nitrosylation of splicing and translational machinery in vascular endothelial cells is susceptible to oxidative stress induced by oxidized low-density lipoprotein

Oxidized low-density lipoprotein (ox-LDL) can impair endothelial function and lead to the atherosclerosis development. Protein S-nitrosylation is sensitive to cellular redox state and acts as a crucial regulator and executor of nitric oxide (NO) signaling pathways. Aberrant S-nitrosylation contributes to the pathogenesis of cardiovascular and cerebrovascular diseases. However, the effect of ox-LDL on S-nitrosylation and its significance for endothelial dysfunction have not been studied at proteome level. Herein, the combined quantitative analysis of proteome and S-nitrosoproteome was performed using an integrated biotin switch and iTRAQ labeling approach in EA.hy926 cell line derived from human umbilical vein endothelial cell (HUVEC) treated with ox-LDL. A total of 2204 S-nitrosylated (SNO) peptides of 1318 SNO-proteins were quantified. Notably, 352 SNO-peptides of 262 SNO-proteins were significantly regulated after excluding S-nitrosylation changes caused by protein expression alterations. Many of them belonged to mRNA splicing, ribosomal structure and translational regulatory proteins, covering the entire translation process. The results indicated that S-nitrosylation of the splicing and translational machinery in vascular endothelial cells was susceptible to ox-LDL. Abnormal protein S-nitrosylation may be one pivotal mechanism underlying endothelial dysfunction induced by ox-LDL. This study potentially enriches the present understanding of pro-atherogenic effect of ox-LDL from the perspective of S-nitrosylation. SIGNIFICANCE: The role of ox-LDL in endothelial dysfunction and atherosclerosis development has been recognized from the aspect of impaired NO production. However, its effect on S-nitrosylation, which is directly related to NO signaling pathway, still remains largely unexplored. Our work initially provided a systematic characterization of S-nitrosoproteome in ox-LDL-treated endothelial cells after ruling out the changes of S-nitrosylation modification caused by protein expression alone. MS-based approach coupled with iTRAQ technique indicated 262 SNO-proteins were significantly regulated. Functional enrichment and interaction network analysis revealed that proteins involved in mRNA splicing and translational machinery were susceptible to abnormal S-nitrosylation under ox-LDL treatment. This achievement suggested one potential mechanism underlying endothelial dysfunction induced by ox-LDL from the perspective of S-nitrosoproteome.

Preparation of low molecular weight heparins from bovine and ovine heparins using nitrous acid degradation

Low molecular weight heparins (LMWHs) are important anticoagulant drugs. Nitrous acid degradation is a major approach to produce LMWHs, such as dalteparin. Due to the foreseeable shortage of porcine intestinal mucosa heparin and other potential risks, expansion of other animal tissues for heparin preparation is necessary. Heparins from different tissues differ in structure and bioactivity potency, and these variations may be carried over to the LMWH products. Sophisticated analytical techniques have been applied to compare various versions of dalteparins produced from porcine intestinal, bovine lung and ovine intestinal heparins to elucidate the effects of different animal tissues starting materials and processing conditions on the properties of final dalteparin products. With adjusted depolymerization conditions, versions of dalteparins that qualify under the European Pharmacopeia (EP) specifications were manufactured using non-porcine heparins. Dissimilarities among the three interspecies animal tissue heparin-derived dalteparins regarding fine structures are also disclosed, and their origins are discussed.

A method for characterising human intervertebral disc glycosaminoglycan disaccharides using liquid chromatography-mass spectrometry with multiple reaction monitoring

Intervertebral disc (IVD) degeneration results in the depletion of proteoglycans and glycosaminoglycans (GAGs), which can lead to structural and mechanical loss of IVD function, ingrowth of nociceptive nerve fibres and eventually discogenic pain. Specific GAG types as well as their disaccharide patterns can be predictive of disease and degeneration in several tissues but have not been comprehensively studied within the IVD. A highly sensitive mass spectrometry based technique with multiple reaction monitoring (MRM) was used to provide characterisation of chondroitin sulphate (CS), hyaluronic acid (HA), heparan sulphate (HS) and their disaccharide sulphation patterns across different anatomical regions of human IVDs. Principal component analysis further distinguished important regional variations and proposed potential ageing variations in GAG profiles. CS was the GAG in greatest abundance in the IVD followed by HA and HS. Principal component analysis identified clear separation of GAG profiles between nucleus pulposus and annulus fibrosus in young and old specimens. Distinct patterns of predominantly expressed disaccharides of CS and HS between young and old IVD samples, provided preliminary evidence that important alterations in disaccharides occur within IVDs during ageing. This technique offered a novel approach to identify and quantify specific GAG disaccharides in human IVDs and the data presented were the first to offer insight into the spatial distribution as well as association with ageing of GAGs and GAG disaccharide sulphation patterns across the human IVD.

Characterization of structural motifs for interactions between glycosaminoglycans and proteins

Glycosaminoglycans (GAGs) are a family of linear and anionic polysaccharides that play essential roles in many biological and physiological processes. Interactions between GAGs and proteins regulate function in many proteins and are related to many human diseases and disorders. The structural motifs and mechanisms for interactions between GAGs and proteins are not fully understood. Specific bindings, including minor but unique sequences sporadically distributed along the GAG chains or variably sulfated domains interspersed by undersulfated regions, may be specifically recognized by defined domains of a variety of proteins. Understanding the molecular basis of these interactions will provide a template for developing novel glycotherapeutic agents. The present article reviews recent methodologies and progress on the characterization of structural motifs in both GAGs and proteins involved in GAG-protein interactions. The analytical approaches are categorized into three groups: affinity-based methods; molecular docking, nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography; and mass spectrometry (MS) techniques. The advantages and limitations of each category of methods are discussed and are based on examples of using these techniques to investigate binding between GAGs and proteins.

Validation, Identification, and Biological Consequences of the Site-specific O-GlcNAcylation Dynamics of Carbohydrate-responsive Element-binding Protein (ChREBP)

O-GlcNAcylation of carbohydrate-responsive element-binding protein (ChREBP) is believed as an important modulator of ChREBP activities, however little direct evidence of O-GlcNAcylation on ChREBP and no exact O-GlcNAcylation sites have been reported so far. Here, we validate O-GlcNAcylation on ChREBP in cell-free coupled transcription/translation system and in cells by chemoenzymatic and metabolic labeling, respectively. Moreover, for the first time, we identify O-GlcNAcylation on Ser614 in the C-terminus of ChREBP by mass spectrometry and validate two important sites, Thr517 and Ser839 for O-GlcNAcylation and their function via molecular and chemical biological method. Under high glucose conditions, Ser514 phosphorylation enhances ChREBP O-GlcNAcylation, maintaining the transcriptional activity of ChREBP; Ser839 O-GlcNAcylation is essential for Mlx-heterodimerization and DNA-binding activity enhancement, consequently inducing transcriptional activity. Ser839 O-GlcNAcylation is also crucial for ChREBP nuclear export partially by strengthening interactions with CRM1 and 14-3-3. This work is a detailed study of ChREBP O-GlcNAcylation and highlights the biological consequences of the site-specific O-GlcNAcylation dynamics of ChREBP.

Species-specific identification of collagen components in Colla corii asini using a nano-liquid chromatography tandem mass spectrometry proteomics approach

Colla corii asini (CCA) is a protein-based traditional Chinese medicine made from donkey skins. Because it has the ability to nourish blood, its demand is increasing rapidly. The shortage of donkey skins increases the risk of the adulteration of CCA products with other animal skins. To ensure the drug efficacy and safety of CCA products, a proteomics technique was applied to reveal proteins in the skins of donkey, horse, cattle, and pig. Species-specific peptides for each animal species were predicted using bioinformatics, and their presence in the skins and gelatin samples was examined by nano-liquid chromatography-tandem mass spectrometry (nano-LC-MS/MS). One unique marker peptide for each animal species was selected to develop an LC-MS/MS multiple reaction monitoring method. The capability of this method to identify donkey, horse, cattle, and pig materials was demonstrated by analyzing in-house-made donkey gelatins containing different amounts of other animal skins and commercial CCA products. The adulteration of non-donkey species could be sensitively detected at a low level of 0.5%. Hybrid animals, such as mules and hinnies, were also differentiated from donkeys. We provide a practical tool for the quality control of CCA products. The strategy can also be used to study other important traditional Chinese medicines which contain animal proteins.

Synthesis of 3-O-Sulfated Oligosaccharides to Understand the Relationship between Structures and Functions of Heparan Sulfate

The sulfation at the 3-OH position of glucosamine is an important modification in forming structural domains for heparan sulfate to enable its biological functions. Seven 3-O-sulfotransferase isoforms in the human genome are involved in the biosynthesis of 3-O-sulfated heparan sulfate. As a rare modification present in heparan sulfate, the availability of 3-O-sulfated oligosaccharides is very limited. Here, we report the use of a chemoenzymatic synthetic approach to synthesize six 3-O-sulfated oligosaccharides, including three hexasaccharides and three octasaccharides. The synthesis was achieved by rearranging the enzymatic modification sequence to accommodate the substrate specificity of 3-O-sulfotransferase 3. We studied the impact of 3-O-sulfation on the conformation of the pyranose ring of 2-O-sulfated iduronic acid using NMR, and on the correlation between ring conformation and anticoagulant activity. We identified a novel octasaccharide that interacts with antithrombin and displays anti factor Xa activity. Interestingly, the octasaccharide displays a faster clearance rate than fondaparinux, an FDA-approved pentasaccharide drug, in a rat model, making this octasaccharide a potential short-acting anticoagulant drug candidate that could reduce bleeding risk. Having access to a set of critically important 3-O-sulfated oligosaccharides offers the potential to develop new heparan sulfate-based therapeutics.

[The value of different antibodies detection in diagnosis of rheumatism with uveitis]

Objective: To investigate the value of HLA-B27 antigen, antinuclear antibody (ANA), anti-dsDNA and Anti-Neutrophil Cytoplasmic Antibodies (ANCA) detection in diagnosis of rheumatism with uveitis. Methods: Seven hundred and twenty four newly diagnosed patients with non-infection uveitis in Beijing Tongren Hospital from March 2012 to March 2016 who long-term lived in Beijing and its surrounding areas were continuously enrolled. HLA-B27 antigen expressions in peripheral blood lymphocytes and ANA, anti-dsDNA and ANCA levels in serum were tested. The detailed clinical data, imaging examinations and pathological examinations were recorded to define whether the patients had rheumatism and the types of rheumatism. Results: There were 285 patients were diagnosed with rheumatism in 724 patients (39.4%), with 135 male (47.4%) and 150 female (52.6%). The mean age of male (41±14) was lower than that of female (44±14), with statistically significant (t=2.18, P<0.05). There were 176 patients with Spondyloarthropathies, 48 patients with primary systemic vasculitis, 22 patients with systemic lupus erythematosus, 18 patients with primary Sjogren's syndrome, 16 patients with rheumatoid arthritis and 5 patients with juvenile idiopathic arthritis in 285 rheumatism patients. The positive rate of HLA-B27(57.2%), ANA(15.8%), anti-dsDNA (5.3%) and ANCA(9.1%) in rheumatic uveitis patients were obviously higher than those of non-rheumatic uveitis patients [HLA-B27(1.1%), ANA(1.6%), anti-dsDNA (0.0%) and ANCA(0.9%)], with statistically significant (Fisher's exact test, P<0.01). The HLA-B27 positive antigen were mainly in patients with Spondyloarthropathies, rate was 92.1%; the positive ANA were mainly in patients with systemic lupus erythematosus, rate was 95.5%; the positive anti-dsDNA were mainly in patients with systemic lupus erythematosus, rate was 59.1%; the positive ANCA were mainly in patients with primary systemic vasculitis (besides Behcet disease), rate was 57.1%. Conclusions: The detections of HLA-B27 antigen, ANA, anti-dsDNA and ANCA are valuable for primary screening of some rheumatic uveitis. There fore, clinicians should select targeted laboratory examination combine with the patients' clinical manifestations. This will be helpful in the auxiliary diagnosis of some types of rheumatic uveitis.

Comparison of Low-Molecular-Weight Heparins Prepared From Bovine Heparins With Enoxaparin

Heparin and its low-molecular-weight heparin (LMWH) derivatives are widely used clinical anticoagulants. These drugs are critical for the practice of medicine in applications including kidney dialysis, cardiopulmonary bypass, and in the management of venous thromboembolism. Currently, these drugs are derived from livestock, primarily porcine intestine. The worldwide dependence on a single animal species has made the supply chain for this critical drug quite fragile, leading to the search for other sources of these drugs, including bovine tissues such as bovine intestine or lung. A number of laboratories are currently examining the similarities and differences between heparins prepared from porcine and bovine tissues. The current study is designed to compare LMWH prepared from bovine heparins through chemical β-elimination, a process currently used to prepare the LMWH, enoxaparin, from porcine heparin. Using top-down, bottom-up, compositional analysis and bioassays, LMWHs, derived from bovine lung and intestine, are shown to closely resemble enoxaparin.

GlycCompSoft: Software for Automated Comparison of Low Molecular Weight Heparins Using Top-Down LC/MS Data

Low molecular weight heparins are complex polycomponent drugs that have recently become amenable to top-down analysis using liquid chromatography-mass spectrometry. Even using open source deconvolution software, DeconTools, and automatic structural assignment software, GlycReSoft, the comparison of two or more low molecular weight heparins is extremely time-consuming, taking about a week for an expert analyst and provides no guarantee of accuracy. Efficient data processing tools are required to improve analysis. This study uses the programming language of Microsoft Excel™ Visual Basic for Applications to extend its standard functionality for macro functions and specific mathematical modules for mass spectrometric data processing. The program developed enables the comparison of top-down analytical glycomics data on two or more low molecular weight heparins. The current study describes a new program, GlycCompSoft, which has a low error rate with good time efficiency in the automatic processing of large data sets. The experimental results based on three lots of Lovenox®, Clexane® and three generic enoxaparin samples show that the run time of GlycCompSoft decreases from 11 to 2 seconds when the data processed decreases from 18000 to 1500 rows.

A meta-analysis of serum p16 gene promoter methylation for diagnosis of nonsmall cell lung cancer

OBJECTIVES

To evaluate the diagnostic value of serum p16 gene promoter methylation for diagnosis of nonsmall cell lung cancer (NSCLC).

MATERIALS AND METHODS

By searching the databases of PubMed and CNKI, we included all the published articles related serum p16 gene promoter methylation and nonsmall lung cancer. The true positive, false positive, false negative, and true negative data for each included publication were extracted by the reviewers. The diagnostic sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, and area under the receiver operating characteristic (ROC) were pooled by MetaDiSc1.4 software.

RESULTS

Finally, 13 manuscripts with 1440 subjects were involving in this diagnostic meta-analysis. The pooled sensitivity and specificity were 0.25 (95% confidence interval [CI]: 0.18-0.32) and 0.95 (95% CI: 0.93-0.97), respectively, with randomized effect model. The pooled positive likelihood ratio and negative likelihood ratio were 5.08 (95% CI: 3.00-8.62) and 0.69 (95% CI: 0.62-0.77) with fixed effect model and randomized effect model, respectively. The diagnostic ROC curve for the included 13 publications was pooled by statistical software MetaDiSc14.0 according to the Bayes theorem. The pooled area under the ROC was 0.72 with its standard error of 0.10.

CONCLUSION

According to the published articles, high specificity and low sensitivity were found in this meta-analysis for the p16 gene promoter methylation in the diagnosis of NSCLC.