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Influenza and dengue viruses present a growing global threat to public health. Both viruses depend on the host endoplasmic reticulum (ER) glycoprotein folding pathway. In 2014, Sadat et al. reported two siblings with a rare genetic defect in ER alpha-glucosidase I (ER Glu I) who showed resistance to viral infections, identifying ER Glu I as a key antiviral target. Here we show that a single dose of UV-4B (the hydrochloride salt form of N-(9′-methoxynonyl)-1- deoxynojirimycin; MON-DNJ) capable of inhibiting Glu I in vivo is sufficient to prevent death in mice infected with lethal viral doses, even when treatment is started as late as 48 hours post-infection. The first crystal structure of mammalian ER Glu I will constitute the basis for the development of potent and selective inhibitors. Targeting ER Glu I with UV-4B derived compounds may alter treatment paradigms for acute viral disease through development of a single-dose therapeutic regime.

Liver biopsy is the reference standard for NAFLD diagnosis and staging. NAFLD can be assessed less invasively using immunoassays to detect serum biomarkers. However, biomarkers can degrade due to sample storage conditions and therefore may not be detected using these antibody-based assays. Detection of biomarkers by mass spectrometry (MS) overcomes this disadvantage.

The glycoprotein IgM is the major antibody produced in the primary immune response to antigens, circulating in the serum both as a pentamer and a hexamer. Pentameric IgM has a single J chain, which is absent in the hexamer. The mu (heavy) chain of IgM has five N-linked glycosylation sites. Asn-171, Asn-332, and Asn-395 are occupied by complex glycans, whereas Asn-402 and Asn-563 are occupied by oligomannose glycans. The glycosylation of human polyclonal IgM from serum has been analyzed. IgM was found to contain 23.4% oligomannose glycans GlcNAc2Man5-9, consistent with 100% occupancy of Asn-402 and 17% occupancy of the variably occupied site at Asn-563. Mannan-binding lectin (MBL) is a member of the collectin family of proteins, which bind to oligomannose and GlcNAc-terminating structures. A commercial affinity chromatography resin containing immobilized MBL has been reported to be useful for partial purification of mouse and also human IgM. Human IgM glycoforms that bind to immobilized MBL were isolated; these accounted for only 20% of total serum IgM. Compared with total serum IgM, the MBL-binding glycoforms contained 97% more GlcNAc-terminating structures and 8% more oligomannose structures. A glycosylated model of pentameric IgM was constructed, and from this model, it became evident that IgM has two distinct faces, only one of which can bind to antigen, as the J chain projects from the non-antigen-binding face. Antigen-bound IgM does not bind to MBL, as the target glycans appear to become inaccessible once IgM has bound antigen. Antigen-bound IgM pentamers therefore do not activate complement via the lectin pathway, but MBL might have a role in the clearance of aggregated IgM.

We propose a mass spectrometry and liquid chromatography (LC-MS) based approach for protein biomarker discovery and their quantification in human serum sample from patients with hepatitis-C virus (HCV) mediated liver fibrosis and non-alcoholic steatohepatitis (NASH). Various isotope labelling approaches like ICAT, iTRAQ and TMT have been used for protein discovery and quantification. We aim to use TMT 10-plex labelling which allows up to 10 samples to be compared at one time, resulting into higher through put sample analysis. In order to look for low abundant serum protein biomarkers we are depleting high abundant serum proteins such as albumin, IgG etc by immunoprecipitation. The depleted serum samples would be subjected to tryptic digestion and labelled with TMT 10-plex which is then analysed by LC-MS/MS to detect and find significantly changed proteins in all 10 samples. An in-solution trypsin digestion protocol was developed for undepleted serum to quantify one of our protein biomarker (lipid transfer inhibitor protein, LTIP) for HCV fibrosis in both selective reaction monitoring (SRM) and parallel reaction monitoring (PRM). In both SRM and PRM, initial studies were performed using recombinant LTIP in order to find most suitable peptides. These selected peptides and their transitions were also analysed in trypsin digested plasma samples. Using SRM, three peptides were found to be most optimal and considered for quantification. Using PRM, four peptides were selected and LOQ was found to be 308-25,000pg/uL. This study requires further validation to establish a complete method.

One of the hallmarks of male germ cell development is the formation of a specialized secretory organelle, the acrosome. This process can be pharmacologically disturbed in C57BL/6 mice, and thus infertility can be induced, by small molecular sugar-like compounds (alkylated imino sugars). Here the biochemical basis of this effect has been investigated. Our findings suggest that in vivo alkylated imino sugars primarily interact with the non-lysosomal glucosylceramidase. This enzyme cleaves glucosylceramide into glucose and ceramide, is sensitive to imino sugars in vitro, and has been characterized as beta-glucosidase 2 (GBA2). Imino sugars raised the level of glucosylceramide in brain, spleen, and testis, in a dose-dependent fashion. In testis, multiple species of glucosylceramide were similarly elevated, those having long acyl chains (C16-24), as well as those with very long polyunsaturated acyl chains (C28-30:5). Both of these GlcCer species were also increased in the testes from GBA2-deficient mice. When considering that the very long polyunsaturated sphingolipids are restricted to germ cells, these results indicate that in the testis GBA2 is present in both somatic and germ cells. Furthermore, in all mouse strains tested imino sugar treatment caused a rise in testicular glucosylceramide, even in a number of strains, of which the males remain fertile after drug administration. Therefore, it appears that acrosome formation can be derailed by accumulation of glucosylceramide in an extralysosomal localization, and that the sensitivity of male germ cells to glucosylceramide is genetically determined.

Reversible infertility can be induced in male mice by oral administration of the alkylated imino sugars N-butyldeoxynojirimycin (NB-DNJ) and N-butyldeoxygalactonojirimycin (NB-DGJ). Spermatozoa of these mice have grossly misshapen heads and reduced motility. Because NB-DNJ and related compounds may hold promise as nonhormonal male contraceptives, a comprehensive examination of their effects on male reproduction is necessary. To this end, we further examined reproductive properties of the dysmorphic spermatozoa that are produced after short-term imino sugar administration at the minimal dose that completely abolishes the ability of male C57BL/6 mice to produce offspring by natural mating. Here, we report that, in vitro, the abnormal spermatozoa from the NB-DNJ- and NB-DGJ-treated mice were unable to fertilize oocytes. In addition, we investigated whether the imino sugars damage the genetic integrity of spermatozoa. To test this, we microsurgically injected deformed spermatozoa from imino sugar-treated males into oocytes. The deformed spermatozoa from the testis were able to activate oocytes very efficiently, but those from the cauda epididymis often failed to do so. This problem was overcome when the sperm-injected oocytes were treated with a parthenogenetic agent, Sr(2+). Oocytes injected with the misshapen spermatozoa from NB-DNJ- and NB-DGJ-treated mice developed (with or without Sr(2+) treatment) into live offspring that grew normally and were normally fertile. This indicates that during short-term administration, alkylated imino sugars alter sperm morphology and physiology but do not diminish the genetic potential of spermatozoa.

HCV morphogenesis is a key step of the viral cycle and represents an original target for the development of new antivirals that could complement more conventional antiviral strategies based on inhibition of viral enzymes. As proof of concept, the inhibition of morphogenesis was demonstrated using the BVDV, a pestivirus related to HCV, as a surrogate model. Using this model, it was shown that alpha-glucosidase inhibitors, i.e. deoxynojirimycin (DNJ) derivatives, could inhibit viral morphogenesis in cellulo via the perturbation of the N-glycosylation pathway. Due to the importance of N-glycosylation for HCV glycoprotein folding and assembly, it was hypothesized that such inhibitors could also affect HCV morphogenesis.

It has long been thought that iminosugar antiviral activity is a function of inhibition of endoplasmic reticulum-resident α-glucosidases, and on this basis, many iminosugars have been investigated as therapeutic agents for treatment of infection by a diverse spectrum of viruses, including dengue virus (DENV). However, iminosugars are glycomimetics possessing a nitrogen atom in place of the endocyclic oxygen atom, and the ubiquity of glycans in host metabolism suggests that multiple pathways can be targeted via iminosugar treatment. Successful treatment of patients with glycolipid processing defects using iminosugars highlights the clinical exploitation of iminosugar inhibition of enzymes other than ER α-glucosidases. Evidence correlating antiviral activity with successful inhibition of ER glucosidases together with the exclusion of alternative mechanisms of action of iminosugars in the context of DENV infection is limited. Celgosivir, a bicyclic iminosugar evaluated in phase Ib clinical trials as a therapeutic for the treatment of DENV infection, was confirmed to be antiviral in a lethal mouse model of antibody-enhanced DENV infection. In this study we provide the first evidence of the antiviral activity of celgosivir in primary human macrophages in vitro, in which it inhibits DENV secretion with an EC50 of 5 μM. We further demonstrate that monocyclic glucose-mimicking iminosugars inhibit isolated glycoprotein and glycolipid processing enzymes and that this inhibition also occurs in primary cells treated with these drugs. By comparison to bicyclic glucose-mimicking iminosugars which inhibit glycoprotein processing but do not inhibit glycolipid processing and galactose-mimicking iminosugars which do not inhibit glycoprotein processing but do inhibit glycolipid processing, we demonstrate that inhibition of endoplasmic reticulum-resident α-glucosidases, not glycolipid processing, is responsible for iminosugar antiviral activity against DENV. Our data suggest that inhibition of ER α-glucosidases prevents release of virus and is the primary antiviral mechanism of action of iminosugars against DENV., Author Summary Current treatment of dengue virus infection is supportive; however, iminosugars have been widely investigated as an antiviral strategy. The means by which these molecules are thought to exert their antiviral effects is through inhibition of host-resident glycoprotein processing enzymes, the endoplasmic reticulum-resident α-glucosidases, but many iminosugars are also capable of inhibiting host glycolipid processing and are utilized clinically for the treatment of lysosomal storage disorders such as Gaucher’s and Niemann-Pick type C diseases. The work presented here is the first to conclusively differentiate the antiviral properties of these two major mechanisms of action of iminosugars, and our data support the long-standing hypothesis that inhibition of glycoprotein processing is the essential antiviral property of iminosugars in the case of dengue virus infection. These results indicate that further development of iminosugars as dengue antivirals should focus on optimization of glycoprotein inhibition efficacy with reduction or elimination of glycolipid modulating properties to minimize off-target effects. These results are supported by the in vitro and in vivo efficacy of the bicyclic iminosugar, celgosivir, which we demonstrate to lack capacity for inhibition of glycosphingolipid processing.

One can treat a viral infection such as hepatitis B (HBV), hepatitis C (HCV), and bovine viral diarrhea virus (BVDV) infections via the delivery of pH sensitive liposomes directly into the endoplasmic reticulum (ER) membrane. Two exemplary liposome formulations are DOPE/CHEMS (DC liposomes) and DOPE/CHEMS/PEG-PE (DCPP liposomes). DC and DCPP liposomes can optimize the intracellular delivery of N -butyl deoxynojirimycin (NB-DNJ), and consequently increase the in vivo activity of this iminosugar several orders of magnitude, and could be used in combination with other therapeutic agents such as interferon and/or ribavirin. The optimized release of N B-DNJ directly into the ER can be also applied for the treatment of other viruses, for which NB-DNJ is known to be an effective antiviral, such as human immunodeficiency virus (HIV).

Provided are compositions that include lipid particles, such as liposomes, that can fuse with the ER membrane of a cell. The lipid particles can also deliver a cargo, such as a therapeutic or an imaging agent, encapsulated inside the particles inside the ER lumen of the cell. The compositions can be useful for treating and/or preventing diseases or conditions caused by or associated with a virus, such as viral infections, including HIV and HCV infections.

One can treat a viral infection by first administering at least one first antiviral compound for a first time period and then, after the end of the first time period, concurrently or subsequently administering the at least one first antiviral compound and at least one second antiviral compound for a second period. In some cases, after the end of the second period, the same at least one second antiviral compound that was administered during the second time period may be administered for a third time period without concurrent or subsequent administration of the at least one first antiviral compound.

The inventors have proposed a novel panel of human serum protein biomarkers for diagnosing hepatic fibrosis and cirrhosis. Presently there is no reliable non-invasive way of assessing liver fibrosis. A 2D-P AGE based proteomics study was used to identify potential fibrosis biomarkers. Serum from patients with varying degrees of hepatic scarring induced by infection with the hepatitis C virus (HCV) was analysed. Several proteins associated with liver scarring and/or viral infection were identified. These proteins include the inter-α-trypsin inhibitor heavy chain H4 fragments, complement factor H-related protein 1, CD5L, Apo Ll, and β2GPI. Increased and decreased thiolester cleavage of a2M and Complement C3, respectively, was also detected. The concentrations of these novel biomarkers can be determined using an immunoassay where the concentrations would reflect the extent of fibrosis. A fibrosis scoring scale for each of the novel biomarkers is proposed. The additive result from the scores of all the novel biomarkers would give a more reliable indication of the degree of fibrosis rather than examining individual biomarkers.

A method of determining one or more glycosylation markers of disease comprises obtaining a diseased sample and a control sample, wherein the diseased sample is a sample from a patient diagnosed with disease and the control sample is a sample from a healthy control; releasing a diseased glycan pool of total glycoproteins from the diseased sample and a control glycan pool of total glycoproteins from the control sample without purifying the glycoproteins and without exposing the diseased sample and the control sample to hydrazinolysis wherein the total glycoproteins from the disease and the total glycoproteins from the control sample are immobilized in a high throughput format; measuring a diseased glycoprofile of the diseased glycan pool and a control glycoprofile of the control glycan pool using chromatography, mass spectrometry or a combination thereof; comparing the diseased glycoprofile and the control glycoprofiles to determine said one or more glycosylation markers of disease. A method for diagnosing and monitoring disease in a subject comprising obtaining a sample of body fluid or a body tissue of the subject; releasing a glycan pool of total glycoproteins from the sample without purifying the glycoproteins and exposing the sample to hydrazinolysis; measuring a glycoprofile of the glycan pool. Also provided are methods of glycan releasing compatible with a high throughput format and for analysis of glycosylation from 2D-PAGE spots.

Compositions and methods are provided for treating hepatitis, flavivirus or pestivirus infections, especially hepatitis B or C virus infections, in mammals, especially humans.

Long chain N-alkyl amino and imino compounds, oxa-substituted derivatives thereof, and pharmaceutical compositions including such compounds are described. The long chain N-alkyl group is a C¿8?-C¿16? alkyl group. The long chain N-alkyl compounds and oxa-substituted derivatives thereof can be used in the treatment of viral infections, in particular hepatitis B virus or hepatitis C virus, in a cell or an individual. For example, the long chain N-alkyl compounds or oxa-substituted derivatives thereof can be derived from piperidines, pyrrolidines, phenylamines, pyridines, pyrroles, or amino acids.

One can identify and quantify one or more glycosylation markers of cancer by utilizing quantitative HPLC analysis of glycans which have been released from unpurified glycoproteins. The unpurified glycoproteins can be total glycoproteins or a selection of the total glycoproteins. The identified glycosylation marker can be a native glycan or a digestion product which has been segregated and amplified by exoglycosidase digestions. One can utilize the identified glycosylation marker, for example, for diagnosing and/or monitoring cancer in a subject. One can also use the glycosylation marker to identify glycoprotein biomarkers that carry the glycosylation marker. Such biomarkers can also be used for monitoring and/or diagnosing cancer. The biomarker may also be a subset of glycoforms of a glycoprotein that are separated in trains of spots on 2D gel.