A pilot single centre, double blind, placebo controlled, randomized, parallel study of Calmagen® dermaceutical cream and lotion for the topical treatment of tinea and onychomycosis.

BACKGROUND: Most of the current anti-fungal treatments are chemical-based, fungistatic, have low efficacy in the treatment of tinea and toxicity concerns, while onychomycosis remains recalcitrant to most antifungal therapies. The study aimed to establish the fungicidal, efficacy and safety profile of Calmagen® dermaceutical cream and lotion containing AMYCOT® as a topical treatment in patients with severe to very severe presentations of fungal skin (tinea) and nail infections (onychomycosis). METHODS: A randomized, placebo-controlled, double blind, parallel, single centre study was conducted on 28 subjects with severe to very severe tinea or onychomycosis. All patients were randomized in a ratio of 1:1 for treatment or placebo group. Subjects in the treatment arm received Calmagen® cream or lotion, while subjects in the placebo arm received a similar inert topical preparation. Tinea subjects were treated with cream for four weeks, while onychomycosis subjects were treated with lotion for 12 weeks. Mycological cure, the primary endpoint, was assessed by three parameters: KOH (potassium hydroxide) smear, fungal culture and live spore count. Clinical cure was defined as Investigator Global Assessment (IGA) response of 'cleared' or 'excellent'. RESULTS: All three parameters constituting mycological cure were confirmed in 92.8% (13/14) of subjects in the treatment arm, while all 14 subjects in the placebo arm remained positive for KOH smear. Calmagen® cream and lotion treatment showed a significant improvement in all three parameters: KOH smear, (95% CI (Calmagen): 79.4, 100.0; 95% CI (placebo): 0.0, 0.0; p < 0.0001); fungal culture (95% CI (Calmagen); 100.0, 100.0; 95% CI (Placebo): 17.0, 100.0; p < 0.0019); and live spore count (95% CI (Calmagen): 100.0, 100.0; 95% CI (Placebo): 17.0, 100.0; p < 0.0019). Clinical cure was achieved in all subjects in the treatment arm while none in the placebo arm were clinically cured. No treatment-related adverse effects were observed in either group. CONCLUSIONS: The Calmagen® cream and lotion containing AMYCOT® represent a potentially safe and efficacious natural alternative in the treatment of Tinea and onychomycosis. TRIAL REGISTRATION: This trial has been registered with the clinical trial registry-India (CTRI; registration number: CTRI/2012/03/002522 ).

Postprandial insulin and glucose levels are reduced in healthy subjects when a standardised breakfast meal is supplemented with a filtered sugarcane molasses concentrate.

PURPOSE: A phytochemical- and mineral-rich filtered sugarcane molasses concentrate (FMC), when added to carbohydrate-containing foods as a functional ingredient, lowers postprandial blood glucose and insulin responses. We hypothesised that this beneficial effect would also occur if FMC was administered as an oral supplement taken before a meal. METHODS: This study measured the postprandial glucose and insulin responses elicited by different doses of FMC administered immediately prior to a standard breakfast to healthy subjects. Each subject was given three or five breakfast meals once, on different days. The composition of the meals was identical, except for the addition of either placebo syrup (test meal 1) or increasing doses of FMC (test meals 2-5). RESULTS: The plasma glucose concentration curves were similar for the five test meals. Plasma insulin curves were lowered in a dose-dependent manner. Stratifying subjects based on age, BMI and insulin resistance showed greater effects of low doses of FMC on lowering insulin responses in those subjects with potentially greater insulin resistance. When insulin response is standardised to amount of carbohydrate in the meal/dose combination, the reduction in response is linear and inversely proportional to the FMC dose. CONCLUSIONS: FMC shows promise as an agent that can reduce insulin responses and lessen the load on the pancreatic beta cells.

Filtered molasses concentrate from sugar cane: natural functional ingredient effective in lowering the glycaemic index and insulin response of high carbohydrate foods.

An aqueous filtered molasses concentrate (FMC) sourced from sugar cane was used as a functional ingredient in a range of carbohydrate-containing foods to reduce glycaemic response. When compared to untreated controls, postprandial glucose responses in the test products were reduced 5-20%, assessed by accredited glycaemic index (GI) testing. The reduction in glucose response in the test foods was dose-dependent and directly proportional to the ratio of FMC added to the amount of available carbohydrate in the test products. The insulin response to the foods was also reduced with FMC addition as compared to untreated controls. Inclusion of FMC in test foods did not replace any formulation ingredients; it was incorporated as an additional ingredient to existing formulations. Filtered molasses concentrate, made by a proprietary and patented process, contains many naturally occurring compounds. Some of the identified compounds are known to influence carbohydrate metabolism, and include phenolic compounds, minerals and organic acids. FMC, sourced from a by-product of sugar cane processing, shows potential as a natural functional ingredient capable of modifying carbohydrate metabolism and contributing to GI reduction of processed foods and beverages.

Functional proteomic screens reveal an essential extracellular role for hsp90 alpha in cancer cell invasiveness.

Tumour cell invasiveness is crucial for cancer metastasis and is not yet understood. Here we describe two functional screens for proteins required for the invasion of fibrosarcoma cells that identified the molecular chaperone heat shock protein 90 (hsp90). The hsp90 alpha isoform, but not hsp90 beta, is expressed extracellularly where it interacts with the matrix metalloproteinase 2 (MMP2). Inhibition of extracellular hsp90 alpha decreases both MMP2 activity and invasiveness. This role for extracellular hsp90 alpha in MMP2 activation indicates that cell-impermeant anti-hsp90 drugs might decrease invasiveness without the concerns inherent in inhibiting intracellular hsp90.

Protein depletion using IgY from chickens immunised with human protein cocktails.

Given that proteomic analysis of complex protein mixtures may be restricted by the presence of highly abundant proteins, sample preparation to remove abundant proteins is essential for the analysis of low abundance proteins. Chickens are effective producers of antibodies (IgY) against mammalian proteins, able to produce large quantities of antibodies that can be recovered by simple non-intrusive extraction of egg yolk. The extraction procedure described uses a modification of the water dilution method (WD) to deplete lipids and lipoproteins followed by sequential precipitation with 31% ammonium sulphate and 12% poly ethylene glycol (PEG) producing IgY antibodies with greater than 95% purity and no loss in immunoreactivity. In the present study, various cocktails of the 12 most abundant human plasma proteins were used as immunogens to produce IgY antibodies. The anti-cocktail IgY antibodies were effectively used to sequentially and selectively immunodeplete abundant proteins from plasma. Also, affinity depletion (e.g., Affi-Gel Blue) was combined with immunodepletion to sequentially deplete abundant proteins from both plasma and urine. The current approach described allows the end user to mix and match sets of IgY cocktails to deplete tailored sets of targeted proteins dependent on their end use application.

Are Long-Chain Polyunsaturated Fatty Acids the Link between the Immune System and the Microbiome towards Modulating Cancer?

Three recent studies revealed synergy between immune-checkpoint inhibitors and the microbiome as a new approach in the treatment of cancer. Incidentally, there has been significant progress in understanding the role of polyunsaturated fatty acids (PUFAs) in modulating cancer and the immune system, as well as in regulating the microbiome. Inflammation seems to be the common denominator among these seemingly unrelated biological entities-immune system, the microbiome, and long-chain polyunsaturated fatty acids (LC-PUFAs). This commentary presents a hypothesis proposing the existence of an optimal level of LC-PUFAs that nurtures the suitable gut microbiota preventing dysbiosis. This synergy between optimal LC-PUFAs and gut microbiota helps the immune system overcome the immunosuppressive tumour microenvironment including enhancing the efficacy of immune checkpoint inhibitors. A model on how LC-PUFAs (such as omega(n)-3 and n-6 fatty acids) forms a synergistic triad with the immune system and the microbiome in regulating inflammation to maintain homeostasis is presented. The principles underlying the hypothesis provide a basis in managing and even preventing cancer and other chronic diseases associated with inflammation.

Functional proteomic screen identifies a modulating role for CD44 in death receptor-mediated apoptosis.

Apoptotic evasion is a hallmark of cancer and its resistance to chemotherapeutic drugs. Identification of cellular proteins that mediate apoptotic programs is a critical step toward the development of therapeutics aimed at overcoming apoptosis resistance. We developed an innovative high-throughput screen to identify proteins that modulate Fas ligand-mediated apoptosis using fluorophore-assisted light inactivation (HTS-FALIpop). The FALI protein knockdown strategy was coupled to a caspase activity assay with the ability to detect both proapoptotic and antiapoptotic surface molecules expressed by HT-1080 human fibrosarcoma cells. FALI of the Fas receptor (Fas/CD95) using a fluorescein-conjugated anti-Fas antibody abrogated Fas ligand-mediated caspase activation. Ninety-six single-chain variable fragment antibodies (scFv), selected for binding to the surface of HT-1080 cells, were screened by HTS-FALIpop. Three of the scFvs caused decreases in caspase induction after FALI of their protein targets. One of the targets of these positive scFvs was identified as CD44 and was validated by performing FALI using a CD44-specific monoclonal antibody, which resulted in similar protection from Fas apoptosis. CD44-targeted FALI was antiapoptotic in multiple human cancer cell lines, including both Fas signaling type I and II cells, and was also protective against other ligands of the tumor necrosis factor death receptor family. FALI of CD44 inhibited formation and activation of the death-inducing signaling complex, suggesting that CD44 regulates Fas at the cell surface. This mechanism of death receptor regulation represents a novel means of apoptosis modulation that could be exploited by pharmacologic agents.

The cryptome: a subset of the proteome, comprising cryptic peptides with distinct bioactivities.

There is increasing evidence that proteolytic cleavage gives rise to 'hidden' peptides with bioactivities that are often unpredicted and totally distinct to the parent protein. So far, the liberation of these cryptic peptides, or crypteins, has been shown to be prevalent in proteins associated with endocrine signalling, the extracellular matrix, the complement cascade and milk. A broad spectrum of proteases has been implicated in the generation of natural crypteins that appear to play a role in modulating diverse biological processes, such as angiogenesis, immune function and cell growth. The proteolytic liberation of crypteins with novel activities represents an important mechanism for increasing diversity of protein function and potentially offers new opportunities for protein-based therapeutics.

Cryptic protein fragments as an emerging source of peptide drugs.

This commentary evaluates the newly proposed concept of crypteins - peptides with embedded cryptic activity - as a source of peptide drugs. Although several crypteins are undergoing advanced clinical trials, and one cryptein, adrenocorticotropic hormone (ACTH), is already widely used as a therapeutic, crypteins remain an underappreciated class of biopharmaceuticals. The systematic exploitation of crypteins provides a novel source of peptide drugs, and may also provide templates for developing peptidomimetic compounds. In addition, crypteins appear to offer several advantages over synthetic protein libraries and other protein scaffolds.

DNA packaging intermediates of bacteriophage φX174

BACKGROUND: Like many viruses, bacteriophage phi X174 packages its DNA genome into a procapsid that is assembled from structural intermediates and scaffolding proteins. The procapsid contains the structural proteins F, G and H, as well as the scaffolding proteins B and D. Provirions are formed by packaging of DNA together with the small internal J proteins, while losing at least some of the B scaffolding proteins. Eventually, loss of the D scaffolding proteins and the remaining B proteins leads to the formation of mature virions. RESULTS: phi X174 108S 'procapsids' have been purified in milligram quantities by removing 114S (mature virion) and 70S (abortive capsid) particles from crude lysates by differential precipitation with polyethylene glycol. 132S 'provirions' were purified on sucrose gradients in the presence of EDTA. Cryo-electron microscopy (cryo-EM) was used to obtain reconstructions of procapsids and provirions. Although these are very similar to each other, their structures differ greatly from that of the virion. The F and G proteins, whose atomic structures in virions were previously determined from X-ray crystallography, were fitted into the cryo-EM reconstructions. This showed that the pentamer of G proteins on each five-fold vertex changes its conformation only slightly during DNA packaging and maturation, whereas major tertiary and quaternary structural changes occur in the F protein. The procapsids and provirions were found to contain 120 copies of the D protein arranged as tetramers on the two-fold axes. DNA might enter procapsids through one of the 30 A diameter holes on the icosahedral three-fold axes. CONCLUSIONS: Combining cryo-EM image reconstruction and X-ray crystallography has revealed the major conformational changes that can occur in viral assembly. The function of the scaffolding proteins may be, in part, to support weak interactions between the structural proteins in the procapsids and to cover surfaces that are subsequently required for subunit-subunit interaction in the virion. The structures presented here are, therefore, analogous to chaperone proteins complexed with folding intermediates of a substrate.

Functional proteomic screens in therapeutic protein drug discovery.

Biopharmaceuticals, mainly protein-based therapeutics, are rapidly being developed for several disease indications. However, most biopharmaceuticals are 'me-too' drugs or are being developed against the same handful of targets. Thus, the potential of biopharmaceuticals is not being fully exploited. The bottleneck is still the lack of validated targets and the means of implementing the appropriate target validation technology. Functional proteomic screens provide a rapid route to accelerate the discovery and development of the next generation of biopharmaceuticals.

Generation of a Novel Bacteriophage Library Displaying scFv Antibody Fragments from the Natural Buffalo Host to Identify Antigens from Adult Schistosoma japonicum for Diagnostic Development.

The development of effective diagnostic tools will be essential in the continuing fight to reduce schistosome infection; however, the diagnostic tests available to date are generally laborious and difficult to implement in current parasite control strategies. We generated a series of single-chain antibody Fv domain (scFv) phage display libraries from the portal lymph node of field exposed water buffaloes, Bubalus bubalis, 11-12 days post challenge with Schistosoma japonicum cercariae. The selected scFv-phages showed clear enrichment towards adult schistosomes and excretory-secretory (ES) proteins by immunofluorescence, ELISA and western blot analysis. The enriched libraries were used to probe a schistosome specific protein microarray resulting in the recognition of a number of proteins, five of which were specific to schistosomes, with RNA expression predominantly in the adult life-stage based on interrogation of schistosome expressed sequence tags (EST). As the libraries were enriched by panning against ES products, these antigens may be excreted or secreted into the host vasculature and hence may make good targets for a diagnostic assay. Further selection of the scFv library against infected mouse sera identified five soluble scFv clones that could selectively recognise soluble whole adult preparations (SWAP) relative to an irrelevant protein control (ovalbumin). Furthermore, two of the identified scFv clones also selectively recognised SWAP proteins when spiked into naïve mouse sera. These host B-cell derived scFvs that specifically bind to schistosome protein preparations will be valuable reagents for further development of a cost effective point-of-care diagnostic test.

Using the local immune response from the natural buffalo host to generate an antibody fragment library that binds the early larval stages of Schistosoma japonicum.

Antibodies isolated from the local draining inguinal lymph node of field exposed-water buffaloes following challenge with Schistosoma japonicum cercariae showed high reactivity towards S. japonicum antigen preparations and bound specifically to formaldehyde-fixed S. japonicum schistosomules. Using this specific local immune response we produced a series of single-chain antibody Fv domain libraries from the same lymph nodes. Removal of phage that cross reacted with epitopes on adult parasites yielded a single-chain antibody Fv domain-phage library that specifically bound to whole formaldehyde-fixed and live S. japonicum schistosomules. DNA sequencing indicated clear enrichment of the single-chain antibody Fv domain library for buffalo B-cell complementarity determining regions post-selection for schistosomule binding. This study also revealed that long heavy chain complementarity determining regions appear to be an important factor when selecting for antibody binding fragments against schistosomule proteins. The selected single-chain antibody Fv domain-phage were used to probe a schistosome-specific protein microarray, which resulted in the recognition of many proteins expressed across all schistosome life-cycle stages. Following absorption to adult worms, the single-chain antibody Fv domain-phage library showed significantly reduced binding to most proteins, whilst two proteins (NCBI GenBank accession numbers AY915878 and AY815196) showed increased binding. We have thus developed a unique set of host derived single-chain antibody Fv domains comprising buffalo B-cell variable regions that specifically bind to early S. japonicum life-stages.

From patenting genes to proteins: the search for utility via function.

The debate regarding the patenting of genes has extended into the post-genome era. With only approximately 35000 genes deduced from the draft sequence of the human genome, there are fears that a few companies have already gained monopoly on the potential benefits from this knowledge. Nevertheless, it is accepted that proteins determine gene function and function is not readily predicted from gene sequence. Furthermore, genes can encode multiple proteins and a single protein can have multiple functions. Here, we argue that unraveling the intrinsic complexity of proteins and their functions is the key towards determining the utility requirement for patenting protein inventions and consider the possible socioeconomic impact.

Emerging high-throughput drug target validation technologies.

Identifying the right target for drug development is a critical bottleneck in the pharmaceutical and biotech industries. The genomics revolution has shifted the problem from a scarcity of targets to a surplus of putative drug targets. As the validity of a target cannot be simply inferred from correlative data, the key is confirmation of the causative role of a gene product in a particular disease. It should therefore be recognized that an effective therapeutic strategy requires an appropriate target validation technology to verify the right target.

Direct methods for modulating protein function.

During the past few years, the drug discovery process has shifted from a chemistry- to a biology-driven paradigm. Genome sciences have made a significant contribution to this shift, leading to a plethora of potential drug targets that are mainly proteins. Genetic methods will continue to be used to characterize proteins, but more direct methods are needed to determine the suitability of these protein targets for pharmacological intervention. In addition to the use of antibodies and aptamers, technologies focusing on the direct modulation of protein activity, including chemical genetics, analog-sensitive enzyme alleles and chromophore-assisted laser inactivation, should significantly contribute to the field of post-genomic drug discovery and development.

Biochips beyond DNA: technologies and applications.

Technological advances in miniaturization have found a niche in biology and signal the beginning of a new revolution. Most of the attention and advances have been made with DNA chips yet a lot of progress is being made in the use of other biomolecules and cells. A variety of reviews have covered only different aspects and technologies but leading to the shared terminology of "biochips." This review provides a basic introduction and an in-depth survey of the different technologies and applications involving the use of non-DNA molecules such as proteins and cells. The review focuses on microarrays and microfluidics, but also describes some cellular systems (studies involving patterning and sensor chips) and nanotechnology. The principles of each technology including parameters involved in biochip design and operation are outlined. A discussion of the different biological and biomedical applications illustrates the significance of biochips in biotechnology.

CD155/PVR plays a key role in cell motility during tumor cell invasion and migration.

BACKGROUND: Invasion is an important early step of cancer metastasis that is not well understood. Developing therapeutics to limit metastasis requires the identification and validation of candidate proteins necessary for invasion and migration. METHODS: We developed a functional proteomic screen to identify mediators of tumor cell invasion. This screen couples Fluorophore Assisted Light Inactivation (FALI) to a scFv antibody library to systematically inactivate surface proteins expressed by human fibrosarcoma cells followed by a high-throughput assessment of transwell invasion. RESULTS: Using this screen, we have identified CD155 (the poliovirus receptor) as a mediator of tumor cell invasion through its role in migration. Knockdown of CD155 by FALI or by RNAi resulted in a significant decrease in transwell migration of HT1080 fibrosarcoma cells towards a serum chemoattractant. CD155 was found to be highly expressed in multiple cancer cell lines and primary tumors including glioblastoma (GBM). Knockdown of CD155 also decreased migration of U87MG GBM cells. CD155 is recruited to the leading edge of migrating cells where it colocalizes with actin and alphav-integrin, known mediators of motility and adhesion. Knockdown of CD155 also altered cellular morphology, resulting in cells that were larger and more elongated than controls when plated on a Matrigel substrate. CONCLUSION: These results implicate a role for CD155 in mediating tumor cell invasion and migration and suggest that CD155 may contribute to tumorigenesis.

Developments in modulating protein function for effective target validation.

The targets of more than 95% of clinically approved drugs are proteins. Thus, the plethora of targets derived from genomics and proteomics efforts must be validated at the protein level. However, most of the preferred target validation technologies are gene- or transcript-based. Protein-based or proteinetic approaches, which are more relevant to determine target druggability, are now emerging.:

The anti-cancer IgM monoclonal antibody PAT-SM6 binds with high avidity to the unfolded protein response regulator GRP78.

The monoclonal IgM antibody PAT-SM6 derived from human tumours induces apoptosis in tumour cells and is considered a potential anti-cancer agent. A primary target for PAT-SM6 is the unfolded protein response regulator GRP78, over-expressed externally on the cell surface of tumour cells. Small angle X-ray scattering (SAXS) studies of human GRP78 showed a two-domain dumbbell-shaped monomer, while SAXS analysis of PAT-SM6 revealed a saucer-shaped structure accommodating five-fold symmetry, consistent with previous studies of related proteins. Sedimentation velocity analysis of GRP78 and PAT-SM6 mixtures indicated weak complex formation characterized by dissociation constants in the high micromolar concentration range. In contrast, enzyme-linked immunosorbant assays (ELISAs) showed strong and specific interactions between PAT-SM6 and immobilized GRP78. The apparent binding constant estimated from a PAT-SM6 saturation curve correlated strongly with the concentration of GRP78 used to coat the microtiter tray. Experiments using polyclonal antiGRP78 IgG antibodies or a monoclonal IgG derivative of PAT-SM6 did not show a similar dependence. Competition experiments with soluble GRP78 indicated more effective inhibition of PAT-SM6 binding at low GRP78 coating concentrations. These observations suggest an avidity-based binding mechanism that depends on the multi-point attachment of PAT-SM6 to GRP78 clustered on the surface of the tray. Analysis of ELISA data at high GRP78 coating concentrations yielded an apparent dissociation constant of approximately 4 nM. We propose that the biological action of PAT-SM6 in tumour cell apoptosis may depend on the multivalent nature of PAT-SM6 and the high avidity of its interaction with multiple GRP78 molecules clustered on the tumour cell surface.