Glycolipid Structure Research Articles

Glycolipopeptide biosurfactant from Bacillus pumilus SG: physicochemical characterization, optimization, antibiofilm and antimicrobial activity evaluation.

The Bacillus pumilus SG isolated from soil samples at the Persian Gulf was analyzed for its ability to produce biosurfactant. Various screening techniques were used for evaluating biosurfactant production and confirming biosurfactant presence in the culture supernatant. Most n-alkanes in the bacterial culture media were effectively degraded in the presence of biosurfactant acquired from the bacteria. The highest interfacial tension (IT) reduction (42 mN/m) was obtained at 24-h fermentation time (exponential phase) and did not change significantly afterwards. The glycolipid structure of the biosurfactant was revealed through NMR and FTIR spectroscopy analysis. Two-level factorial design was then applied for optimization of biosurfactant production, where a maximal reduction of culture broth IT (30mN/m) acquired in the presence of crude oil (0.5%, v/v), NaNO3 (1g/L), yeast extract (1g/L), peptone (2g/L) and temperature of 25°C. The produced biosurfactant that exhibited a critical micelle concentration of 0.1mg/ml was thermally stable. The glycolipid biosurfactant also displayed significant antibacterial activities against both Gram-positive and Gram-negative bacteria. The maximum inhibition of glycolipids biosurfactant was found against Acinetobacter strains (zone of inhibition, 45mm). In addition, antibiofilm activities with a 50-90% biofilm reduction percent were indicated by the glycolipid biosurfactant. In conclusion, the glycolipid biosurfactant produced by B. pumilus SG revealed a wide range of functional properties and was verified as a good candidate for biomedical application. In conclusion, the glycolipid biosurfactant produced by B. pumilus SG showed a wide range of functional properties in this study, and in the case of further in vivo studies, it can be investigated a good candidate for biomedical applications such as use against biofilm or in pharmaceutical formulations.

Synthesis and Immunological Activity of Novel Oligo(ethylene glycol) Analogues of α-Galactosylceramide.

CD1d-arbitrated activation of i-NKT cells by α-galactosylceramide results in the effective secretion of Th1 and Th2 cytokines, with adjuvanticity skewed toward Th2 immunity. However, the polarization of immune response could be achieved by suitable modification of the glycolipid structure. In the current study, novel glycolipids with an amphiphilic oligo ethylene glycol lipid moiety bearing the benzyloxy group at the terminus on the acyl arm of sphingosine, exhibited CD1d ligand binding as quantified by IL-2 cytokine production. When immunized with quadrivalent split influenza virus in BALB/c mice, the novel ceramide analogues with a longer oligo (ethylene glycol) chain length induced significant levels of antibody (IgG) with Th1-polarized immune response.

Isolation, Optimization, and Structural Characterization of Glycolipid Biosurfactant Produced by Marine Isolate Shewanella algae B12 and Evaluation of Its Antimicrobial and Anti-biofilm Activity.

Biosurfactants are microbial-derived compounds with surface and emulsifying activities. Environmental and industrial applications make glycolipid biosurfactants particularly interesting among the several categories of biosurfactants. A potential glycolipid biosurfactant resource, Shewanella algae, was isolated from marine samples at the Persian Gulf. The glycolipid biosurfactant caused a reduction in water surface tension from 72 to 43 mN/m with a 0.25mg/mL critical micelle concentration (CMC). Two-level factorial design was then applied for optimization of biosurfactant production, where a maximal reduction of culture broth surface tension (31 mN/m) acquired in the presence of crude oil (0.5%, v/v), NaNO3 (0.2g/L), NH4Cl (0.7g/L), and peptone (0.5g/L). GC-MS analysis of the culture broth showed when crude oil was used as the sole carbon source, S. algae was able to degrade most of its alkane components. Nuclear magnetic resonance (NMR) and Fourier transform infrared (FTIR) spectroscopy revealed the glycolipid structure of biosurfactant. The glycolipid biosurfactant exhibited considerable growth inhibition of clinical bacterial pathogens and disrupted the preformed biofilms of Bacillus cereus (83%), Streptococcus pneumoniae (53%), Pseudomonas aeruginosa (92%), Escherichia coli (64%), Klebsiella pneumoniae (87%), and Acinetobacter sp. (72%). In conclusion, the glycolipid biosurfactant secreted by S. algae exhibited a wide range of functional properties and was evidenced as a promising candidate for biomedical application.

Polymorphism of Kdo-Based Glycolipids: The Elaborately Determined Stable and Dynamic Bicelles

Polymorphism of Kdo-Based Glycolipids: The Elaborately Determined Stable and Dynamic Bicelles

Trehalose diamide glycolipids augment antigen-specific antibody responses in a Mincle-dependent manner

Many studies have investigated how trehalose glycolipid structures can be modified to improve their Macrophage inducible C-type lectin (Mincle)-mediated adjuvanticity. However, in all instances, the ester-linkage of α,ά-trehalose to the lipid of choice remained. We investigated how changing this ester-linkage to an amide influences Mincle signalling and agonist activity and demonstrated that Mincle tolerates this functional group change. In in vivo vaccination studies in murine and ovine model systems, using OVA or Mannheimia haemolytica and Mycoplasma ovipneumoniae as vaccine antigens, respectively, it was demonstrated that a representative trehalose diamide glycolipid was able to enhance antibody-specific immune responses. Notably, IgG titres against M. ovipneumoniae were significantly greater when using trehalose dibehenamide (A-TDB) compared to trehalose dibehenate (TDB). This is particularly important as infection with M. ovipneumoniae predisposes sheep to pneumonia.

Amide-Linked C4″-Saccharide Modification of KRN7000 Provides Potent Stimulation of Human Invariant NKT Cells and Anti-Tumor Immunity in a Humanized Mouse Model.

Activation of invariant natural killer T (iNKT) cells by α-galactosylceramides (α-GalCers) stimulates strong immune responses and potent anti-tumor immunity. Numerous modifications of the glycolipid structure have been assessed to derive activating ligands for these T cells with altered and potentially advantageous properties in the induction of immune responses. Here, we synthesized variants of the prototypical α-GalCer, KRN7000, with amide-linked phenyl alkane substitutions on the C4″-position of the galactose ring. We show that these variants have weak iNKT cell stimulating activity in mouse models but substantially greater activity for human iNKT cells. The most active of the C4″-amides in our study showed strong anti-tumor effects in a partially humanized mouse model for iNKT cell responses. In silico analysis suggested that the tether length and degree of flexibility of the amide substituent affected the recognition by iNKT cell antigen receptors of the C4″-amide substituted glycolipids in complex with their antigen presenting molecule CD1d. Our findings establish the use of stable C4″-amide linked additions to the sugar moiety for further exploration of the immunological effects of structural modifications of iNKT cell activating glycolipids and highlight the critical need for more accurate animal models to assess these compounds for immunotherapeutic potential in humans.

Purification and identification of surface active amphiphilic candidates produced by Geotrichum candidum MK880487 possessing antifungal property

The present study was held to optimize production, purify and identify biosurfactant from yeast strain Geotrichum candidum MK880487. Biosurfactant production was done on modified Hua medium and optimized in shake-flask method. Soybean oil (8%, v/v), KNO3 (0.75 g L−1) and yeast extract (0.3 g L−1) were the best carbon and nitrogen sources, respectively, with C:N ratio of 200:1, pH 8 at 30 °C for 168 h. Production scale-up was achieved on 2.5 L bioreactor as batch method. The resulting crude biosurfactant extract with yield of 1.75 g L−1 was purified by reversed phase column preparative HPLC. The resulting most active fraction F47 significantly reduced water surface tension by 51.92%. Chemical characterization using TLC, GC-MS, FTIR and LC-MS/MS methods revealed the biosurfactant to contain mainly glycolipid structure existing as mixture of Icariside F2, Cardenolide Di-Hexopyranoside and Di Galactosyl Di Acyl Glycerol glycolipid that collectively showed potential antifungal activity toward Macrophomina phaseolina.

Different glycolipids in sperm from different freshwater fishes – A high‐performance thin‐layer chromatography/electrospray ionization mass spectrometry study

Glycolipids play important roles in many physiological processes - despite their commonly low abundance. This study summarizes selected data on the (glyco)lipid composition of sperm from different fish species. Lipid extraction of fish sperm was performed according to the procedure by Bligh and Dyer. The lipid composition of the organic extracts was analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) and electrospray ionization ion trap (ESI-IT)MS coupled to high-performance thin-layer chromatography (HPTLC). It was shown that sperm from carp, northern pike, rainbow trout and burbot contain high amounts of neutral and acidic glycosphingolipids as well as sulfoglycolipids. These particular lipids are presumably involved in reproduction requirements. Phospholipids and glycolipids in crude lipid extracts can be analyzed in parallel by MS coupled to TLC. The direct application of tandem mass spectrometry (MS/MS) helps to elucidate the glycolipid structure. Thus, compositional analysis can be performed very rapidly.

Age-dependent membrane release and degradation of full-length glycosylphosphatidylinositol-anchored proteins in rats

Glycosylphosphatidylinositol (GPI)-anchored proteins (GPI-APs) are associated with the surface of eucaryotic cells only through a covalently coupled carboxy-terminal GPI glycolipid structure which is anchored at the outer leaflet of plasma membranes. This mode of membrane association may be responsible for the recent observations that full-length GPI-APs harbouring the complete GPI anchor are (i) released from isolated rat adipocytes in vitro and (ii) expressed in rat and human serum. The upregulation of the adipocyte release in response to increased cell size and blood glucose/insulin levels of the donor rats and downregulation of the expression in serum of insulin resistant and diabetic rats have been reconciled with enhanced degradation of the full-length GPI-APs released into micelle-like complexes together with (lyso) phospholipids and cholesterol by serum GPI-specific phospholipase D (GPI-PLD).Here by using a sensitive and reliable sensing method for full-length GPI-APs, which relies on surface acoustic waves propagating over microfluidic chips, the upregulation of (i) the release of the full-length GPI-APs CD73, alkaline phosphatase and CD55 from isolated adipocyte plasma membranes monitored in a “lab-on-the-chip” configuration, (ii) their release from isolated rat adipocytes into the incubation medium and (iii) the lipolytic cleavage of their GPI anchors in serum was demonstrated to increase with age (3–16 weeks) and body weight (87−477 g) of (healthy) donor rats. In contrast, the amount of full-length GPI-APs in rat serum, as determined by chip-based sensing, turned out to decline with age/body weight. These correlations suggest that age-/weight-induced alterations (in certain biophysical/biochemical characteristics) of plasma membranes are responsible for the release of full-length GPI-APs which becomes counteracted by elevated GPI-PLD activity in serum. Thus, sensitive and specific measurement of these GPI-AP-relevant parameters may be useful for monitoring of age-related cell surface changes, in general, and diseases, in particular.

Potential Food Application of a Biosurfactant Produced by Saccharomyces cerevisiae URM 6670.

Biosurfactants have aroused considerable interest due to the possibility of acquiring useful products that are tolerant to processing techniques used in industries. Some yeasts synthesize biosurfactants that offer antioxidant activity and thermal resistance and have no risk of toxicity or pathogenicity, demonstrating potential use in food formulations. The aim of the present study was to assess the use of a biosurfactant produced by Saccharomyces cerevisiae URM 6670 to replace egg yolk in a cookie formulation. The yeast was grown in a medium containing 1% waste soybean oil and 1% corn steep liquor. The biosurfactant was isolated using a novel method and was structurally characterized using FT-IR, NMR, and GC/FID. Thermal stability was determined using thermogravimetry (TG)/differential scanning calorimetry (DSC) and antioxidant activity was investigated using three methods. Cytotoxicity tests were performed using the MTT assay with mouse fibroblast and macrophage lines. In the final step, the biosurfactant was incorporated into the formulation of a cookie dough replacing egg yolk. The physical properties and texture profile were analyzed before and after baking. The surface and interfacial tensions of the culture medium after the production process were 26.64 ± 0.06 and 9.12 ± 0.04 mN/m, respectively, and the biosurfactant concentration was 5.84 ± 0.17 g/L after isolation. In the structural characterization by NMR and FT-IR, the biosurfactant from S. cerevisiae exhibited a glycolipid structure, with the fatty acid profile revealing a high percentage of linoleic acid (50.58%). The thermal analysis demonstrated stability at the industrial application temperature, with the negligible loss of mass at temperatures of up to 200°C. The biosurfactant was non-toxic to the fibroblast and macrophage cell lines, with cell inhibition less than 15%. The incorporation of the biosurfactant into the cookie dough did not alter the physical or physicochemical properties of the product after baking. In the analysis of the texture profile before baking, the substitution of egg yolk with the biosurfactant did not alter the properties of firmness, cohesiveness, or elasticity compared to the standard formulation. Therefore, the biosurfactant produced by S. cerevisiae URM 6670 has potential applications in the food industry as a replacement for egg yolk.

Antibodies to Protein but Not Glycolipid Structures Are Important for Host Defense against Mycoplasma pneumoniae.

Antibody responses to Mycoplasma pneumoniae correlate with pulmonary M. pneumoniae clearance. However, M. pneumoniae-specific IgG antibodies can cross-react with the myelin glycolipid galactocerebroside (GalC) and cause neurological disorders. We assessed whether antiglycolipid antibody formation is part of the physiological immune response to M. pneumoniae We show that antibodies against M. pneumoniae proteins and glycolipids arise in serum of M. pneumoniae-infected children and mice. Although antibodies to M. pneumoniae glycolipids were mainly IgG, anti-GalC antibodies were only IgM. B-1a cells, shown to aid in protection against pathogen-derived glycolipids, are lacking in Bruton tyrosine kinase (Btk)-deficient mice. M. pneumoniae-infected Btk-deficient mice developed M. pneumoniae-specific IgG responses to M. pneumoniae proteins but not to M. pneumoniae glycolipids, including GalC. The equal recovery from M. pneumoniae infection in Btk-deficient and wild-type mice suggests that pulmonary M. pneumoniae clearance is predominantly mediated by IgG reactive with M. pneumoniae proteins and that M. pneumoniae glycolipid-specific IgG or IgM is not essential. These data will guide the development of M. pneumoniae-targeting vaccines that avoid the induction of neurotoxic antibodies.

Isolation and genetic identification of yeast producing biosurfactants, evaluated by different screening methods

The present study, investigated the potential application of yeast isolates for extracellular biosurfactant production. Twenty-five yeast isolates are primarily evaluated for their biosurfactant activity using ten screening analytical methods. Isolates 263, 27(1), 20(2) and 24(1) achieved maximum emulsification indexes of 59.65, 56.14, 52.63 and 47.37%, maximum diameters of oil free clearing zone at 2.25, 2.15, 2.03 and 1.89 cm, largest diameters of liquid droplets on the hydrophobic surface and significantly reduced surface tension of MSM from 90.93 to 51.64, 54.07, 57.45 and 62.40 mN m−1, respectively. The four isolates were hydrocarbon utilizers, lipase producers, showed no hemolytic activity while gave positive results in CTAB and phenol‑sulfuric acid tests, indicating that they produced anionic biosurfactant with possible glycolipid structure. Those promising isolates were identified by 18S rRNA gene amplification and sequencing analysis. Yeast isolates 263 and 27(1) were identified as Geotrichum candidum, 20(2) was Galactomyces pseudocandidum and 24(1) was Candida tropicalis.

Metabolic Labeling and Structural Analysis of Glycosylphosphatidylinositols from Parasitic Protozoa.

Glycosylphosphatidylinositol (GPI) is a complex glycolipid structure that acts as a membrane anchor for many cell-surface proteins of eukaryotes. GPI-anchored proteins are particularly abundant in protozoa and represent the major carbohydrate modification of many cell-surface parasite proteins. A minimal GPI-anchor precursor consists of core glycan (ethanolamine-PO4-Manα1-2Manα1-6Manα1-4GlcNH2) linked to the 6-position of the D-myo-inositol ring of phosphatidylinositol. Although the GPI core glycan is conserved in all organisms, many differences in additional modifications to GPI structures and biosynthetic pathways have been reported. The preassembled GPI-anchor precursor is post-translationally transferred to a variety of membrane proteins in the lumen of the endoplasmic reticulum in a transamidase-like reaction during which a C-terminal GPI attachment signal is released. Increasing evidence shows that a significant proportion of the synthesized GPIs are not used for protein anchoring, particularly in protozoa in which a large amount of free GPIs are being displayed at the cell surface. The characteristics of GPI biosynthesis are currently being explored for the development of parasite-specific inhibitors. Especially this pathway, at least for Trypanosoma brucei, has been validated as a drug target. Furthermore, thanks to an increase of new innovative strategies to produce pure synthetic carbohydrates, a novel era in the use of GPIs in diagnostic, anti-GPI antibody production, as well as parasitic protozoa GPI-based vaccine approach is developing fast.

Physicochemical characterization and optimization of glycolipid biosurfactant production by a native strain of Pseudomonas aeruginosa HAK01 and its performance evaluation for the MEOR process.

In this study, a glycolipid type of biosurfactant (BS) was produced, its characteristics were evaluated and several flooding tests were conducted in a micromodel to investigate its potential for enhancing oil recovery. A rhamnolipid BS producer strain was identified as a bacterium belonging to the genus Pseudomonas aeruginosa. This BS showed good stability at temperatures of 40–121 °C, pH values of 3–10 and salinity up to 10% (w/v) NaCl which is important in Microbial Enhanced Oil Recovery (MEOR). The rhamnolipid decreased the surface tension of water from 72 to 28.1 mN m−1 with a critical micelle concentration of 120 ppm. Thin layer chromatography, FTIR spectroscopy, 1H-NMR and 13C-NMR spectroscopy revealed the glycolipid structure of the BS. Response surface methodology was applied to optimize BS production. Several micromodel flooding tests were conducted to study the capability of the produced rhamnolipid in enhanced oil recovery for the first time. An oil recovery factor of 43% was obtained at 120 ppm of BS solution whereas the recovery factor obtained for water flooding was 16%. Contact angle measurements showed that BS solutions altered the wettability of a glass surface from oil wet to a strongly water wet state. Also the results illustrated that all BS solutions were impressive in microbial enhanced oil recovery (MEOR) and using the produced BS a considerable amount of trapped oil can be extracted due to interfacial tension reduction, wettability alteration towards water wet conditions and improving the mobility ratio.

CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans.

Glycolipids (such as glycoglycerolipids, glycosphingolipids, and glycosylphosphatidylinositol) and lipoglycans (such as lipopolysaccharides (LPS), lipooligosaccharides (LOS), mycobacterial lipoarabinomannan, and mycoplasma lipoglycans) are typically found on the surface of cell membranes and play crucial roles in various cellular functions. Characterizing their structure and dynamics at the molecular level is essential to understand their biological roles, but systematic generation of glycolipid and lipoglycan structures is challenging because of great variations in lipid structures and glycan sequences (i.e., carbohydrate types and their linkages). To facilitate the generation of all-atom glycolipid/LPS/LOS structures, we have developed Glycolipid Modeler and LPS Modeler in CHARMM-GUI ( http://www.charmm-gui.org ), a web-based interface that simplifies building of complex biological simulation systems. In addition, we have incorporated these modules into Membrane Builder so that users can readily build a complex symmetric or asymmetric biological membrane system with various glycolipids and LPS/LOS. These tools are expected to be useful in innovative and novel glycolipid/LPS/LOS modeling and simulation research by easing tedious and intricate steps in modeling complex biological systems and shall provide insight into structures, dynamics, and underlying mechanisms of complex glycolipid-/LPS-/LOS-containing biological membrane systems.

Chimeric Antigen Receptor T-Cell Therapy: A Beacon of Hope in the Fight Against Cancer.

Despite significant advancements, relapses, and persistent malignancies are still a major challenge faced by the oncologists. Immunotherapy has shown remarkable potential in induction of sustained remission in refractory malignancies. Chimeric antigen receptor T-cell (CAR-T) therapy is a newer treatment methodology approved by the Food and Drug Administration (FDA). The chimeric pairing of an antigen receptor with the T-cell receptor (TCR) intracellular signaling domain allows cluster of designation 8 (CD8) cytotoxic T-cells to target cell surface makers independent of major histocompatibility complex (MHC) activation. Another essential feature which contributes to the broad applicability of CARs and expanding their potential targets is their ability to bind not only to proteins but also to carbohydrate and glycolipid structures. Their antigen-specific and targeted immune responses have shown promising outcomes in clinical trials particularly involving B-cell malignancies and solid tumors. High remission rates and low percentages of relapses have caused a paradigm shift in the treatment of relapsed or refractory cancers. Challenges include side effects such as cytokine release syndrome, on-target off-tumor toxicities, and replication of its success in treating solid tumors. The burden of side effects and hefty cost of treatment are major obstacles which could hinder its progress globally. Nevertheless, ongoing research would only result in a maximized therapeutic potential in addition to more patient- and cost-friendly treatment. In this review, we aim to provide the readers an overview of chimeric antigen receptor T-cell therapy, a relatively new advancement in the world of immuno-oncology and thereby also discussing its advantages, side effects and future challenges.

Synthesis of Branched Trehalose Glycolipids and Their Mincle Agonist Activity.

The macrophage inducible C-type lectin (Mincle) is a pattern recognition receptor that recognizes trehalose dimycolate (TDM), and trehalose dibehenate (TDB) and related trehalose diesters, and thus represents a promising target for the development of vaccine adjuvants based on the trehalose glycolipid scaffold. To this end, we report on the synthesis of a series of long-chain α-branched, β-modified trehalose monoesters and diesters to explore how glycolipid structure affects signaling through Mincle. Key steps in our synthetic strategy include a Fráter-Seebach α-alkylation to install the C20 aliphatic lipid on a malic acid derivative, and the formation of a β,γ-epoxide as an intermediate from which modifications to the β-position of the lipid can be made. Biological evaluation of the derivatives using nuclear factor of activated T cells (NFAT)-green fluorescent protein (GFP) reporter cell lines expressing mMincle or hMincle revealed that the hMincle agonist activity of all diesters was superior to that of the current lead trehalose glycolipid adjuvant TDB, while the activity of several monoesters was similar to that of their diester counterparts for mMincle, but all showed reduced hMincle agonist activity. Taken together, diesters 2d-g are thus potent Mincle agonists and promising vaccine adjuvants.

Isolation and purification of glycosylphosphatidylinositols (GPIs) in the schizont stage of Theileria annulata and determination of antibody response to GPI anchors in vaccinated and infected animals

BackgroundTropical theileriosis is widely distributed from North Africa to East Asia. It is a tick-borne disease caused by Theileria annulata, an obligate two-host intracellular protozoan parasite of cattle. Theileria annulata use leukocytes and red blood cells for completion of the life-cycle in mammalian hosts. The stage of Theileria annulata in monocytes and B lymphocytes of cattle is an important step in pathogenicity and diagnosis of the disease. Glycosylphosphatidylinositols (GPIs) are a distinct class of glycolipid structures found in eukaryotic cells and are implicated in several biological functions. GPIs are particularly abundant in protozoan parasites, where they are found as free glycolipids or attached to proteins in the plasma membrane.ResultsIn this study we first isolated and purified schizonts of Theileria annulata from infected leukocytes in Theileria annulata vaccine cell line (S15) by aerolysin-percoll technique. Then, the free GPIs of schizont stage and isolated GPI from cell membrane glycoproteins were purified by high performance liquid chromatography (HPLC) and confirmed by gas chromatography-mass spectrometry (GC-MS). Furthermore, enzyme linked immunosorbent assay (ELISA) on the serum samples obtained from naturally infected, as well as Theileria annulata-vaccinated animals, confirmed a significant (P < 0.01) high level of anti-GPI antibody in their serum.ConclusionsThe results presented in this study show, to our knowledge for the first time, the isolation of GPI from the schizont stage of Theileria annulata and demonstrate the presence of anti-GPI antibody in the serum of naturally infected as well as vaccinated animals. This finding is likely to be valuable in studies aimed at the evaluation of chemically structures of GPIs in the schizont stage of Theileria annulata and also for pathogenicity and immunogenicity studies with the aim to develop GPI-based therapies or vaccines.

CHARMM-GUI 10 years for biomolecular modeling and simulation.

CHARMM-GUI, http://www.charmm-gui.org, is a web-based graphical user interface that prepares complex biomolecular systems for molecular simulations. CHARMM-GUI creates input files for a number of programs including CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. Since its original development in 2006, CHARMM-GUI has been widely adopted for various purposes and now contains a number of different modules designed to set up a broad range of simulations: (1) PDB Reader & Manipulator, Glycan Reader, and Ligand Reader & Modeler for reading and modifying molecules; (2) Quick MD Simulator, Membrane Builder, Nanodisc Builder, HMMM Builder, Monolayer Builder, Micelle Builder, and Hex Phase Builder for building all-atom simulation systems in various environments; (3) PACE CG Builder and Martini Maker for building coarse-grained simulation systems; (4) DEER Facilitator and MDFF/xMDFF Utilizer for experimentally guided simulations; (5) Implicit Solvent Modeler, PBEQ-Solver, and GCMC/BD Ion Simulator for implicit solvent related calculations; (6) Ligand Binder for ligand solvation and binding free energy simulations; and (7) Drude Prepper for preparation of simulations with the CHARMM Drude polarizable force field. Recently, new modules have been integrated into CHARMM-GUI, such as Glycolipid Modeler for generation of various glycolipid structures, and LPS Modeler for generation of lipopolysaccharide structures from various Gram-negative bacteria. These new features together with existing modules are expected to facilitate advanced molecular modeling and simulation thereby leading to an improved understanding of the structure and dynamics of complex biomolecular systems. Here, we briefly review these capabilities and discuss potential future directions in the CHARMM-GUI development project. © 2016 Wiley Periodicals, Inc.

Structure–activity relationship studies on acremomannolipin A, the potent calcium signal modulator with a novel glycolipid structure 4: Role of acyl side chains on d-mannose

As part of an ongoing study on the structure–activity relationship of acremomannolipin A (1)—the novel glycolipid isolated from Acremonium strictum possessing potent calcium signal-modulating activity—the role of acyl substituents on the d-mannose moiety was examined. Three partially deacylated homologs (2a–2c) and 20 homologs (2d–2w) bearing different acyloxy side chains were synthesized via the stereoselective β-mannosylation of appropriately protected mannosyl sulfoxides (3) with d-mannitol derivatives (4), and their calcium signal-modulating activities were examined. The activities of 2a–2c were completely lost. Homologs bearing relatively short acyloxy groups at C-3, C-4, and C-6 positions (2t–2v) exhibited less activity than 1, whereas a heptanoyl homolog (2w: C7) maintained activity nearly equal to that of 1. When the acyl groups at these three positions were substituted by an octanoyl group (2i: C8), the activity was completely lost. On the other hand, of the 10 homologs in which the octanoyl at C-2 was substituted by other acyloxy moieties (2j–2s), three (2m: C7, 2n: C9, 2o: C10) maintained potent activity. These results suggested that peracylated mannose structure is critical for calcium signal-modulating activity, and this activity is precisely dependent on the length of four acyl side chains on d-mannose.