From combinatorial libraries to MHC ligand motifs, T-cell superagonists and antagonists

Complete experimental data sets of HLA-ligand motifs and T-cell recognition patterns can be derived from combinatorial peptide libraries. These data provide the exact molecular basis for a fast development of synthetic vaccines, T-cell superagonists and non-peptide antagonists. Patient-specific peptides, peptidomimetics and vaccines of highest reactivity can be derived directly from the data sets via our prediction programme EPIPREDICT. The resulting lead structures may be developed into valuable diagnostics and therapeutic tools for the treatment of viral infections, autoimmune diseases and tumors. As one example, antibody and T cell recognition in the intestinal auto-immune disease, coeliac disease was investigated in more detail concerning the deamidation of gamma-gliadin peptides by tissue transglutaminase 9tTG) leading to autoreactive peptides specific for HLA-DQA1*0501, DQB1*0201.

Superoxide dismutase mutations of familial amyotrophic lateral sclerosis and the oxidative inactivation of calcineurin

Approximately 10% of all familial cases of amyotrophic lateral sclerosis (fALS) are linked to mutations in the SOD1 gene, which encodes the copper/zinc superoxide dismutase (CuZnSOD). Recently, wild-type CuZnSOD was shown to protect calcineurin, a calcium/calmodulin-regulated phosphoprotein phosphatase, from inactivation by reactive oxygen species. We asked whether the protective effect of CuZnSOD on calcineurin is affected by mutations associated with fALS. For this, we monitored calcineurin activity in the presence of mutant and wild-type SOD. We found that the degree of protection against inactivation of calcineurin by different SOD mutants correlates with the severity of the phenotype associated with the different mutations, suggesting a potential role for calcineurin-SOD1 interaction in the etiology of fALS.

Cyclofunctionalization and free-radical-based hydrogen-transfer reactions. An iterative reaction sequence applied to the synthesis of the C(7)-C(16) subunit of zincophorin

The strategy considered herein features an iodocyclofunctionalization/hydrogen-transfer reaction sequence for the elaboration of propionate motifs. Proceeding with excellent yield and diastereoselectivity, the synthetic sequence proposed gives access to the anti-anti dipropionate motif when the reduction step is performed under the control of the exocyclic effect. The tandem sequence is applied successfully to the synthesis of the C(7)-C(16) subunit of zincophorin, and iteration of the process gives the desired anti-anti-anti-anti polypropionate stereopentad. Modifications of the reaction sequence--including phenylselenocyclofunctionalization, carbonate hydrolysis, and chelation-controlled radical reduction reactions--lead to the formation of the anti-syn dipropionate motif with remarkable diastereocontrol.

Guanidine hydrochloride inhibits Hsp104 activity in vivo: a possible explanation for its effect in curing yeast prions

The presence of millimolar concentrations of guanidine hydrochloride (Gdn-HCl) in growth media causes efficient loss of the normally stable [PSI+] element from yeast cells. Although it has become common practice to include 5 mm Gdn-HCl in growth media to cure [PSI+] and other prions of yeast, the biochemical mechanism by which it cures is unknown. We find that 5 mm Gdn-HCl significantly reduces Hsp104-mediated basal and acquired thermotolerance. Gdn-HCl also reduced the ability of Hsp104 to restore activity of thermally denatured luciferase in vivo. The abundance of Hsp104 was not reduced in cells grown in the presence of Gdn-HCl, ruling out negative effects on expression or stability of Hsp104. We therefore conclude that Gdn-HCl inhibits Hsp104 activity in vivo. Since replication of yeast prions is dependent on Hsp104, our results suggest that Gdn-HCl cures prions by inhibiting Hsp104 activity.

Human hepatitis B virus polymerase interacts with the molecular chaperonin Hsp60

Previous studies showed that hepatitis B virus polymerase (HBV Pol) interacts with host factors such as the Hsp90 complex, which is a critical step in viral genome replication. In this report, we propose that another chaperone, Hsp60, interacts with human HBV Pol and that this is a very important step for maturation of human HBV Pol into the active state. In the immunoprecipitation of recombinant human HBV Pol expressed in insect cells with the recombinant baculovirus expression system, the 60-kDa protein was coimmunoprecipitated with Pol and the protein was identified as Hsp60 through peptide sequencing and immunogenic analysis with an anti-Hsp60 antibody. In vitro experiments showed that Hsp60 strongly affected human HBV Pol activity in that (i) blocking of Hsp60 by the protein-specific antibody reduced human HBV Pol activity, (ii) the activity was increased by addition of Hsp60 in the presence of ATP, and (iii) ATP synergistically activated human HBV Pol with Hsp60. In vivo experiments showed that inhibition of Hsp60 in cells by a mutant Hsp60, C Delta 540, resulted in the reduction of human HBV Pol activity. In summary, our results indicate that the interaction is significant for conversion of human HBV Pol into the active state.

FTICR-mass spectrometry for high-resolution analysis in combinatorial chemistry

The diversity of compound collections required for finding lead structures in pharmaceutical research can be provided by means of combinatorial organic chemistry. The resultant enormous number of single compounds but also of compound mixtures represents a challenge for the analyst. With the introduction of Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS or FT-MS), a new and, as yet, not widespread mass spectrometric technique (a means of analysis of such compound libraries with a very high mass resolution) high mass accuracy and high sensitivity has become available. Moreover, in combination with electrospray ionization (ESI), not only high-throughput measurements via flow-injection analysis (FIA) but also coupling with separation techniques such as high-performance liquid chromatography (HPLC) or capillary electrophoresis (CE) is possible. Structural verification by way of decomposing ions (MS(n); n > or = 2) using a variety of different dissociation techniques can be performed by FTICR-MS. This is the first review specifically covering applications of FTICR-MS in the field of combinatorial chemistry.

A triangle-square equilibrium of metallosupramolecular assemblies based on pd(II) and pt(II) corners and diazadibenzoperylene bridging ligands

Tetraaryloxy-substituted diazadibenzoperylene bridging ligands 1a,b were employed in transition metal-directed self-assembly with Pd(II) and Pt(II) phosphane triflates 2a,b which resulted in complex dynamic equilibria between molecular triangles 3a-d and molecular squares 4a-d in solution. Characterization of the equilibria and assignment of the metallacycles was accomplished by (1)H and (31)P[(1)H] NMR spectroscopy in combination with electrospray ionization Fourier transform ion cyclotron mass spectrometry (ESI-FTICR-MS). It was found that the equilibria depend on several factors, such as the metal ion (Pd(2+) or Pt(2+)), the solvent, and the steric demand of the phenoxy substituents of the diazadibenzoperylene ligands 1a,b. Introduction of bulky tert-butyl groups in 1b shifts the equilibrium significantly in the direction of the molecular squares. Molecular dynamics simulations of the triangle and square structures revealed critical steric effects and restricted conformational flexibilities of the phosphane and diazadibenzoperylene ligands that help explain the distinct dynamic behavior observed in variable-temperature NMR studies. Concentration-dependent UV/vis and fluorescence spectroscopy revealed the limited stability of the assemblies and confirmed the reversible nature of the dynamic equilibria.

In vitro determination of cardiac ventricular volumes using MRI at 1.0 T in a porcine heart model

PURPOSE

To determine the accuracy of a 1.0 T MR system with a standard gradient system for quantification of left and right ventricular volumes. A porcine heart model in vitro was used.

METHODS

In eight explanted porcine hearts the atria were removed and the aorta and the pulmonary truncus were cannulated. Defined volumes were injected into the ventricles. Magnetic resonance imaging (MRI): FFE-EPI (Multishot EPI) was used. Papillary muscles and trabeculae were excluded. True volumes and MR measurements were analysed separately for both ventricles and by both investigators.

RESULTS

The correlation of the true volumes and MR measurements was >0.99. MRI was found to be investigator independent in assessing right and left ventricular volumes in vitro.

CONCLUSIONS

MRI at 1.0 T using standard equipment can be used to quantitate cardiac ventricular volumes in vitro with high accuracy.

Biosynthesis of the orthosomycin antibiotic avilamycin A: deductions from the molecular analysis of the avi biosynthetic gene cluster of Streptomyces viridochromogenes Tü57 and production of new antibiotics

BACKGROUND

Streptomyces viridochromogenes Tü57 is the producer of avilamycin A. The antibiotic consists of a heptasaccharide side chain and a polyketide-derived dichloroisoeverninic acid as aglycone. Molecular cloning and characterization of the genes governing the avilamycin A biosynthesis is of major interest as this information might set the direction for the development of new antimicrobial agents.

RESULTS

A 60-kb section of the S. viridochromogenes Tü57 chromosome containing genes involved in avilamycin biosynthesis was sequenced. Analysis of the DNA sequence revealed 54 open reading frames. Based on the putative function of the gene products a model for avilamycin biosynthesis is proposed. Inactivation of aviG4 and aviH, encoding a methyltransferase and a halogenase, respectively, prevented the mutant strains from producing the complete dichloroisoeverninic acid moiety resulting in the accumulation of new antibiotics named gavibamycins.

CONCLUSIONS

The avilamycin A biosynthetic gene cluster represents an interesting system to study the formation and attachment of unusual deoxysugars. Several enzymes putatively responsible for specific steps of this pathway could be assigned. Two genes encoding enzymes involved in post-PKS tailoring reactions were deleted allowing the production of new analogues of avilamycin A.

Synthesis of linear and comb-like peptide constructs containing up to four copies of a T cell epitope and their capacity to stimulate T cells

Polypeptide constructs containing up to four copies of the T cell epitope 306-318 of influenza virus haemagglutinin have been synthesized on solid phase. Between the copies, a non-natural PEG-based spacer amino acid has been introduced. The oligomeric epitopes were analysed by RP-HPLC and ES-MS. The arrangement of the epitopes within the peptide constructs was either linear or comb-like. The proliferative response in a T helper cell assay induced by these oligomerized epitopes has been tested, showing that the linearly arranged epitopes are more effective than the comb-like oligomers.

Staphylococcus aureus resistance to human defensins and evasion of neutrophil killing via the novel virulence factor MprF is based on modification of membrane lipids with l-lysine

Defensins, antimicrobial peptides of the innate immune system, protect human mucosal epithelia and skin against microbial infections and are produced in large amounts by neutrophils. The bacterial pathogen Staphylococcus aureus is insensitive to defensins by virtue of an unknown resistance mechanism. We describe a novel staphylococcal gene, mprF, which determines resistance to several host defense peptides such as defensins and protegrins. An mprF mutant strain was killed considerably faster by human neutrophils and exhibited attenuated virulence in mice, indicating a key role for defensin resistance in the pathogenicity of S. aureus. Analysis of membrane lipids demonstrated that the mprF mutant no longer modifies phosphatidylglycerol with l-lysine. As this unusual modification leads to a reduced negative charge of the membrane surface, MprF-mediated peptide resistance is most likely based on repulsion of the cationic peptides. Accordingly, inactivation of mprF led to increased binding of antimicrobial peptides by the bacteria. MprF has no similarity with genes of known function, but related genes were identified in the genomes of several pathogens including Mycobacterium tuberculosis, Pseudomonas aeruginosa, and Enterococcus faecalis. MprF thus constitutes a novel virulence factor, which may be of general relevance for bacterial pathogens and represents a new target for attacking multidrug resistant bacteria.

Solution structure, backbone dynamics and chitin binding of the anti-fungal protein from Streptomyces tendae TÜ901 1 1Edited by M. F. Summers

AFP1 is a recently discovered anti-fungal, chitin-binding protein from Streptomyces tendae Tü901. Mature AFP1 comprises 86 residues and exhibits limited sequence similarity to the cellulose-binding domains of bacterial cellulases and xylanases. No similarity to the Cys and Gly-rich domains of plant chitin-binding proteins (e.g. agglutinins, lectins, hevein) is observed. AFP1 is the first chitin-binding protein from a bacterium for which anti-fungal activity was shown. Here, we report the three-dimensional solution structure of AFP1, determined by nuclear magnetic resonance spectroscopy. The protein contains two antiparallel beta-sheets (five and four beta-strands each), that pack against each other in a parallel beta-sandwich. This type of architecture is conserved in the functionally related family II of cellulose-binding domains, albeit with different connectivity. A similar fold is also observed in other unrelated proteins (spore coat protein from Myxococcus xanthus, beta-B2 and gamma-B crystallins from Bos taurus, canavalin from Jack bean). AFP1 is therefore classified as a new member of the betagamma-crystallin superfamily. The dynamics of the protein was characterized by NMR using amide 15N relaxation and solvent exchange data. We demonstrate that the protein exhibits an axially symmetric (oblate-like) rotational diffusion tensor whose principal axis coincides to within 15 degrees with that of the inertial tensor. After completion of the present structure of AFP1, an identical fold was reported for a Streptomyces killer toxin-like protein. Based on sequence comparisons and clustering of conserved residues on the protein surface for different cellulose and chitin-binding proteins, we postulate a putative sugar-binding site for AFP1. The inability of the protein to bind short chitin fragments suggests that certain particular architectural features of the solid chitin surface are crucial for the interaction.

Streptocidins A-D, novel cyclic decapeptide antibiotics produced by Streptomyces sp. Tü 6071. II. Structure elucidation

The structures of the new antibiotics streptocidins A approximately D were elucidated as cyclic decapeptides cyclo[L-Val1-L-Orn2-L-Leu3-D-Phe4-L-Pro5-L-Leu6-X7-L-Asn8-L-Gln9-X10] with X7=D-Trp (A, B, C) or D-Phe (D) and X10=L-Tyr (A), L-Trp (B, D), or D-Trp (C). The amino acid composition (including the configuration) of the substances was determined by chiral-phase GC-MS of the hydrolysates. The sequences were established by EDMAN degradation following linearisation of the cyclic peptides upon treatment with LiAlH4. NMR spectroscopic studies of streptocidins C and D confirmed the proposed sequences and provided conformational data which indicate a molecular topology of streptocidins C and D similar to those of tyrocidine A and gramicidin S.

Lipidation of T helper sequences from hepatitis C virus core significantly enhances T-cell activity in vitro

Successful elimination of the hepatitis C virus (HCV) during acute infection has been linked to strong HCV-specific in vitro T-cell proliferation, whereas T cells from patients with chronic hepatitis C respond only weakly to HCV antigens. Lipid-coupled peptides are immunostimulants, which might provide a basis for novel therapeutic strategies against HCV. Therefore, in 20 patients with chronic hepatitis C, we studied whether tri-palmitoyl-S-cysteine-coupled peptides could modify in vitro T-cell proliferation (by [3H]thymidine uptake) in response to virus core and NS4. The lipopeptides corresponded to five immunodominant T helper epitopes of HCV core. Contrary to unmodified peptides, the lipopeptides specifically enhanced [3H]thymidine uptake in response to HCV antigens but not to a non-HCV related control antigen. They increased the frequency of responders (stimulation index, SI > or = 4) to core (13/20 versus 2/20; p = 0.0008) and NS4 (20/20 versus 7/20; p < 0.0001) among our patients with chronic hepatitis C. This immunostimulatory effect was dose-dependent, and was observed specifically with lipopeptides corresponding to the HCV epitopes. Our data demonstrate that the poor in vitro T-cell proliferation of patients with chronic hepatitis C can be improved when T cells are co-stimulated with HCV core-derived T helper lipopeptides, while the same peptides in unlipidated form had no effects. Thus, lipopeptides corresponding to HCV T-cell epitopes may offer novel immunomodulatory strategies against HCV.

Peptide vaccines and peptide libraries

Synthetic immunogens, containing built-in adjuvanticity, B cell, T helper cell and CTL epitopes or mimotopes, are ideal and invaluable tools to study the immune response with respect to antigen processing and presentation. This serves as a basis for the development of complete and minimal vaccines which do not need large carrier proteins, further adjuvants, liposome formulations or other delivery systems. Combinatorial peptide libraries, either completely random or characterized by one or several defined positions, are useful tools for the identification of the critical features of B cell epitopes and of MHC class I and class II binding natural and synthetic epitopes. The complete activity pattern of an O/Xn library with hundreds of peptide collections, each made up from billions of different peptides, represents the ranking of amino acid residues mediating contact to the target proteins of the immune system. Combinatorial libraries support the design of peptides applicable in vaccination against infectious agents as well as therapeutic tumour vaccines. Using the principle of lipopeptide vaccines, strong humoral and cellular immune responses could be elicited. The lipopeptide vaccines are heat-stable, non-toxic, fully biodegradable and can be prepared on the basis of minimized epitopes by modern methods of multiple peptide synthesis. The lipopeptides activate the antigen-presenting macrophages and B cells and have been recently shown to stimulate innate immunity by specific interaction with receptors of the Toll family.

Stereocontrol in Radical Processes through the Exocyclic Effect: Dual Role of Triethylboron as Radical Initiator and in Situ Derivatization Agent

[structure in text] The diastereoselectivity of radical processes involving 1,3-diols is increased significantly with a simple and efficient strategy using the exocyclic effect. Boronate derivatives are successfully formed in situ by treatment of an equimolar amount of Et(3)B in the presence of oxygen. This step is followed by the mediation of a carbon-centered radical alpha to the cyclic boronate to give the anti reduced product with high stereocontrol. The sequence is also extended to beta-amino alcohols.

Target cell-restricted triggering of the CD95 (APO-1/Fas) death receptor with bispecific antibody fragments

Like many other cell surface receptors, the CD95 (APO-1/Fas) molecule needs to be cross-linked by its physiological ligand or by immobilized or multimeric antibodies to mediate biological activity, that is, induction of apoptotic cell death. Monomeric CD95 antibodies of the IgG2a or IgG1 subtype block rather than induce apoptosis. We report here that such antibodies, hybridized to a second antibody directed against a different target antigen on the same cell, effectively induce apoptosis of the cells if the expression of the target antigen exceeds a certain threshold level. It appears that this effect is due to bicellular binding of bispecific antibodies resulting in mutual cross-linking of the CD95 death receptor and the target antigen. Using bispecific reagents, it may therefore be possible to restrict the activation of death receptors to a given target site, e.g., a tumor. In general terms, our findings illustrate a principle according to which the triggering of a cell surface receptor may be confined to a given target cell using bispecific reagents with target X cell surface receptor specificity.

Ligand motif of the autoimmune disease-associated mouse MHC class II molecule H2-A(s)

The MHC class II molecule H2-A(s), expressed in the SJL mouse strain, is the principle restriction element of autoreactive CD4(+) T cells mediating experimental autoimmune encephalomyelitis, an animal model of multiple sclerosis. We deduced the H2-A(s) ligand motif from the analysis of naturally processed self peptides and from peptide binding studies. Major anchor residues were identified using various sets of substituted and truncated peptides, derived from natural peptide ligands and known H2-A(s) binders like myelin basic protein 81 - 99. The nine-residue H2-A(s) core binding motif comprises an arrangement of anchors in relative positions P1, P4, P6, P7, and P9. The P1 pocket is relatively unspecific and the P6 pocket favors hydrophobic-aliphatic side chains. The P1 pocket contributes little to peptide binding. Primary anchors were identified in P4, P7, and in particular in P9. The preferred anchor residues are Lys (P4), His/Arg (P7), and Pro (P9), respectively. Ala-polysubstituted peptides containing only one of these dominant anchor residues still retain the capacity to bind to H2-A(s). Thus, the presence of only one suitable anchor side chain in P4, P7, or P9 is sufficient for high-affinity peptide binding, at least in the absence of negatively charged side chains nearby. The identified ligand motif facilitates the analysis of immunogenic peptides interacting with H2-A(s) and will allow a better prediction of pathogenetically relevant peptide antigens in the autoimmune mouse model.

Local immunotherapy of glioma patients with a combination of 2 bispecific antibody fragments and resting autologous lymphocytes: evidence for in situ t-cell activation and therapeutic efficacy

After adoptive transfer of pre-activated lymphocytes into the operation cavity of glioma patients, tumor regression and improved survival have been reported in some patients. Results were most impressive when bispecific antibodies with tumor x CD3 specificity were also applied. In this study, we attempted to avoid time-consuming pre-activation procedures for adoptively transferred cells by using a combination of bispecific antibodies directed to the EGF receptor (EGFR) on tumor cells and to CD3 and CD28 on T cells. Eleven patients with high-grade malignant glioma received 3 injections of 2 bispecific antibody fragments (EGFR x CD3 and EGFR x CD28) together with freshly isolated autologous lymphocytes via an Ommaya reservoir. Intracavitary fluid aspirated during immunotherapy was examined for markers of T-cell activation. Increased levels of soluble IL-2 receptor and TNF-alpha were detected in the intracavitary fluid of all patients tested. Two of the 11 treated patients experienced a beneficial response to therapy as defined by a transient contrast enhancement in subsequent MRI scans and prolonged survival. Side effects were transient and consisted of fever, nausea, headache and aggravation of pre-existing neurologic deficits. These adverse effects were most likely due to the antibody construct containing anti-CD3 specificity. Two patients developed cerebral edema and required steroid treatment.

The treatment of lacrimal apparatus obstruction with the use of an inner canthal Jones tube insertion via a transcaruncular route

BACKGROUND AND OBJECTIVE

To evaluate the clinical utility of the lacrimal bypass surgery using Bowman's probe in treatment of obstruction of the lacrimal apparatus.

PATIENTS AND METHODS

This study evaluated 124 cases of obstruction of the lacrimal passage systems with mean epiphora of 2.7 years. An incision was made on the side of the caruncle, and the lacrimal bone was penetrated between the lacrimal sac and the nasal mucosa by Bowman #0. Insertion of a Jones tube was made at the new lacrimal pathway, a puctum dilator or scissors was introduced through the caruncle and dilated across the lacrimal bone into the nasal cavity. The Jones tube was introduced over the probe into the nasal cavity, and fixed at the caruncle with nonabsorbable suture material.

RESULTS

Complete resolution of epiphora was accomplished in 120 (96.8%) of 124 eyes; only 4 (3.2%) eyes failed during a mean of 17.1 months of follow-up.

CONCLUSION

This procedure is simple and safe with no facial scarring, short operation time, high success rate, and can be performed under local anesthesia. Therefore, the clinical utility of this procedure seems to be of value in treatment of complicated obstruction of the lacrimal apparatus.

HLA-DR53 molecules restrict glutamic acid decarboxylase peptide presentation to T cells of a Type I diabetes patient: specification of the trimolecular HLA-peptide/T-cell receptor complex

AIMS/HYPOTHESIS

Our aim was to define the molecular specificity of glutamic acid decarboxylase-specific T-cells isolated from a patient (patient 40) with recent onset Type I (insulin-depent) diabetes mellitus.

METHODS

The peptide epitope was defined using synthetic peptides to identify the minimal sequence required for T-cell activation and to determine the amino acids that contribute either to MHC binding or T-cell receptor signaling. The MHC class II-restricted peptide presentation was determined using a panel of allogeneic antigen-presenting cells and murine fibroblast-cell lines transfected to express individual human class II alleles and by blocking studies with monoclonal antibodies. The T-cell receptor was also molecularly characterized.

RESULTS

Despite that patient 40 carries high-risk alleles of the DRB1 and DQB1 loci, his T-cells recognize a glutamic acid decarboxylase-derived peptide in association with class II, DR53, molecules. Although anchor residues for DR53 molecules have not yet been determined, it was possible to model epitope binding based on sequence comparisons with other class II molecules associated with susceptibility or protection for Type I diabetes.

CONCLUSION/INTERPRETATION

The complete molecular specification of the MHC-peptide ligand and the T-cell receptor complex of glutamic acid decarboxylase-specific T-cells will enable analysis of strategies designed to alter T-cell function. For example, the role of altered peptide ligands or T-cell receptor-specific peptides can be studied using a model whose components reflect the natural affinities of MHC-peptide and T-cell receptor-ligand interactions selected in response to this important autoantigen.