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Biomedical subjects

Beat Ernst

Publications and source records attributed to Beat Ernst.

11 recordsLinked to original sources
PubMed2007

Simulating alpha/beta selectivity at the human thyroid hormone receptor: consensus scoring using multidimensional QSAR.

We present a consensus-scoring study on the human thyroid hormone receptor alpha and beta using two receptor-modeling concepts (software Quasar and Raptor) that are based on multidimensional QSAR and allow for the explicit simulation of induced fit. The binding mode of 82 agonists and indirect antagonists, spanning an activity range of seven orders of magnitude in K(i), was identified through flexible docking to the respective X-ray crystal structures (Yeti software) and represented by a 4D data set with up to four conformations per compound. The receptor surrogates for the thyroid alpha receptor converged at a cross-validated r(2) of 0.846/0.919 (64 training compounds; for Quasar and Raptor, respectively) and yielded a predictive r(2) of 0.812/0.814 (18 test compounds); the models for the thyroid beta receptor resulted in a cross-validated r(2) of 0.823/0.909 and a predictive r(2) of 0.665/0.796, respectively. Consensus was achieved as, on average, the calculated activities of the training set differ only by a factor of 2.2 in K(i) and those of the test set by a factor of 2.8 when predicted by Quasar and Raptor, respectively.

Binding Sites↗
PubMed2006

Antagonists of the myelin-associated glycoprotein: a new class of tetrasaccharide mimics.

The tetrasaccharide substructure 1 of the ganglioside GQ1balpha shows a remarkable affinity for the myelin-associated glycoprotein (MAG). In the search for structurally simplified and pharmacokinetically improved mimics of 1, biphenyl was identified as a feasible replacement for the core disaccharide Galbeta(1-3)GalNAc according to saturation transfer difference (STD) NMR and molecular modeling investigations. Using Suzuki coupling, a convergent synthesis of the mimics was achieved. To optimize the yields of the coupling reactions, the catalytic effects of microwave irradiation and conventional heating were compared. The biological evaluation of mimics 3 and 4 was performed in a competitive target-based assay. It was found that the relative inhibitory potency (rIP) of antagonist 3 was clearly enhanced in comparison to the reference trisaccharide 2, despite the former having a much simpler structure. In addition to the improved synthetic feasibility, an increase of the partition coefficient between octanol and water (logP), and therefore a beneficial change in the pharmacokinetic properties of 3 and 4 was achieved.

Animals↗
PubMed2005

Comparative epitope mapping with saturation transfer difference NMR of sialyl Lewis(a) compounds and derivatives bound to a monoclonal antibody.

The monoclonal antibody GSLA-2 recognizes the sialyl Lewis(a) (sLe(a)) epitope, which has an increased occurrence on mucin type glycoproteins of patients with colorectal carcinoma. GSLA-2 is therefore used in tumor diagnosis. To advance the understanding of this highly specific molecular recognition reaction, we have analyzed the binding epitope of sLe(a) at atomic resolution using saturation transfer difference NMR. To compare, the binding epitopes of sialyl Lewis(x) (sLe(x)) and of four synthetic derivatives of sLe(a) were explored. Surface plasmon resonance experiments furnished thermodynamic and kinetic data. It is observed that all pyranose rings of sLe(a) are in contact with the protein surface, with the neuramic acid residue receiving the largest fraction of saturation transfer. In contrast, sLe(x) binds very weakly, though specifically to GSLA-2, with a different binding epitope. This study provides a comprehensive picture of the recognition sLe(a) and explains the exquisite specificity of the antibody.

Antibodies, Monoclonal↗
PubMed2005

Impact of induced fit on ligand binding to the androgen receptor: a multidimensional QSAR study to predict endocrine-disrupting effects of environmental chemicals.

We investigated the influence of induced fit of the androgen receptor binding pocket on free energies of ligand binding. On the basis of a novel alignment procedure using flexible docking, molecular dynamics simulations, and linear-interaction energy analysis, we simulated the binding of 119 molecules representing six compound classes. The superposition of the ligand molecules emerging from the combined protocol served as input for Raptor, a receptor-modeling tool based on multidimensional QSAR allowing for ligand-dependent induced fit. Throughout our study, protein flexibility was explicitly accounted for. The model converged at a cross-validated r(2) = 0.858 (88 training compounds) and yielded a predictive r(2) = 0.792 (26 test compounds), thereby predicting the binding affinity of all compounds close to their experimental value. We then challenged the model by testing five molecules not belonging to compound classes used to train the model: the IC(50) values were predicted within a factor of 4.5 compared to the experimental data. The demonstrated predictivity of the model suggests that our approach may well be beneficial for both drug discovery and the screening of environmental chemicals for endocrine-disrupting effects, a problem that has recently become a cause for concern among scientists, environmental advocates, and politicians alike.

Benzhydryl Compounds↗
PubMed2005

Molecular cloning and functional expression of a novel Helicobacter pylori alpha-1,4 fucosyltransferase.

Helicobacter pylori is an important human pathogen which causes both gastric and duodenal ulcers and is associated with gastric cancer and lymphoma. This microorganism synthesizes fucosylated oligosaccharides, predominantly the Galb-1,4GlcNAc (Type II) blood group antigens Lewis X and Y, whereas a small population also expresses the Galb-1,3GlcNAc (Type I) blood group antigens Lewis A and B. These carbohydrate structures are known to mimic host cell antigens and permit the bacteria to escape from the host immune response. Here, we report the cloning and characterization of a novel H. pylori alpha-1,4 fucosyltransferase (FucT). In contrast to the family members characterized to date, this enzyme shows exclusively Type I acceptor substrate specificity. The enzyme consisting of 432 amino acids (MW 50,502 Da) was cloned using a polymerase chain reaction (PCR)-based approach. It exhibits a high degree of identity (75-87%) and similar structural features, for example, in the heptamer repeat pattern, with other H. pylori FucTs. The kinetic characterization revealed a very efficient transferase (k(cat)/Km = 229 mM(-1) s(-1)) for the Type I acceptor substrate (Gal)-1,3 GlcNAc-Lem (1). Additionally, the enzyme possesses a broad tolerance toward nonnatural Type I acceptor substrate analogs and therefore represents a valuable tool for the chemoenzymatic synthesis of Lewis A, sialyl Lewis A as well as mimetics thereof.

Amino Acid Sequence↗
PubMed2005

Systemic administration of a TLR7 ligand leads to transient immune incompetence due to peripheral-blood leukocyte depletion.

Toll-like receptor (TLR) ligands lead to the induction of proinflammatory cytokines and are potent enhancers of specific immune responses. We show here that a single systemic dose of R-848, a ligand for TLR7, potently enhanced hapten sensitization during the induction of contact hypersensitivity (CHS). However, R-848 administration also resulted in a rapid and almost complete depletion of leukocytes from the blood. This effect was transient and was associated with general induction of endothelial adhesiveness. In response to R-848, endothelial cells up-regulated adhesion molecules in vitro and in vivo and leukocytes exhibited increased rolling on endothelia in R-848-treated animals. Adhesion molecule induction appeared to be a direct effect, because endothelial cells expressed TLR7 in vitro and in vivo. After R-848 treatment, the tissue residence time of leukocytes was markedly prolonged in all major peripheral organs. The resulting transiently reduced availability of peripheral-blood leukocytes (PBLs) (TRAP) significantly inhibited otherwise potent CHS responses until the effector cells returned. Thus, although TLR7 ligands are effective adjuvants for the induction of cell-mediated immunity, they can transiently inhibit the elicitation of localized immune responses, possibly due to a systemic endothelial activation throughout the vasculature.

Adaptor Proteins, Signal Transducing↗
PubMed2004

Synthesis of aryl sialosides using Mitsunobu conditions.

Mitsunobu conditions for the efficient synthesis of aryl alpha/beta-sialosides were developed. An oxidative work-up procedure was employed to avoid a cumbersome chromatographic separation from the 2,3-dehydro derivative of sialic acid, which is formed as a side-product.

Glycosides↗
PubMed2003

Epitope mapping of sialyl Lewis(x) bound to E-selectin using saturation transfer difference NMR experiments.

A complex between sialyl Lewisx (alpha-D-Neu5Ac-[2-->3]- beta-D-Gal-[1-->4]-[alpha-L-Fuc-(1-->3)]-beta-D-GlcNAc-O-[CH2]8 COOMe) and E-selectin was studied using saturation transfer difference (STD) nuclear magnetic resonance (NMR) experiments. These experiments allow the identification of the binding epitope of a ligand at atomic resolution. A semiquantitative analysis of STD total correlation spectroscopy spectra provides clear evidence that the galactose residue receives the largest saturation transfer. The protons H4 and H6 of the galactose residue are in especially close contact to the amino acids of the E-selectin binding pocket. The fucose residue also receives a significant saturation transfer. The GlcNAc and Neu5Ac residues, with the exception of H3 and H3' of Neu5Ac, were found to interact weakly with the protein surface. These findings are in excellent agreement with a recently published X-ray structure and with the earlier findings from syntheses and activity assays. To further characterize the binding pocket of E-selectin, an inhibitory peptide, Ac-TWDQLWDLMK-CONH2, was synthesized and the binding to E-selectin studied utilizing transfer nuclear Overhauser effect spectroscopy (trNOESY) experiments. Finally, competitive trNOESY experiments were performed, showing that the synthetic peptide is a competitive inhibitor of sialyl Lewisx.

Carbohydrate Conformation↗
PubMed2003

Drug discovery today.

In recent years, tools for the development of new drugs have been dramatically improved. These include genomic and proteomic research, numerous biophysical methods, combinatorial chemistry and screening technologies. In addition, early ADMET studies are employed in order to significantly reduce the failure rate in the development of drug candidates. As a consequence, the lead finding, lead optimization and development process has gained marked enhancement in speed and efficiency. In parallel to this development, major pharma companies are increasingly outsourcing many components of drug discovery research to biotech companies. All these measures are designed to address the need for a faster time to market. New screening methodologies have contributed significantly to the efficiency of the drug discovery process. The conventional screening of single compounds or compound libraries has been dramatically accelerated by high throughput screening methods. In addition, in silico screening methods allow the evaluation of virtual compounds. A wide range of new lead finding and lead optimization opportunities result from novel screening methods by NMR, which are the topic of this review article.

Animals↗