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Knut Baumann

Publications and source records attributed to Knut Baumann.

17 recordsLinked to original sources
PubMed2007

Towards a detailed understanding of bacterial metabolism--spectroscopic characterization of Staphylococcus epidermidis.

Bacteria are a major cause of infection. To fight disease and growing resistance, research interest is focused on understanding bacterial metabolism. For a detailed evaluation of the involved mechanisms, a precise knowledge of the molecular composition of the bacteria is required. In this article, various vibrational spectroscopic techniques are applied to comprehensively characterize, on a molecular level, bacteria of the strain Staphylococcus epidermidis, an opportunistic pathogen which has evolved to become a major cause of nosocomial infections. IR absorption spectroscopy reflects the overall chemical composition of the cells, with major focus on the protein vibrations. Smaller sample volumes-down to a single cell-are sufficient to probe the overall chemical composition by means of micro-Raman spectroscopy. The nucleic-acid and aromatic amino-acid moieties are almost exclusively explored by UV resonance Raman spectroscopy. In combination with statistical evaluation methods [hierarchical cluster analysis (HCA), principal component analysis (PCA), linear discriminant analysis (LDA)], the protein and nucleic-acid components that change during the different bacterial growth phases can be identified from the in vivo vibrational spectra. Furthermore, tip-enhanced Raman spectroscopy (TERS) provides insight into the surface structures and follows the dynamics of the polysaccharide and peptide components on the bacterial cells with a spatial resolution below the diffraction limit. This might open new ways for the elucidation of host-bacteria and drug-bacteria interactions.

Bacterial Proteins↗
PubMed2006

Aziridide-based inhibitors of cathepsin L: synthesis, inhibition activity, and docking studies.

A comprehensive screening of N-acylated aziridine (aziridide) based cysteine protease inhibitors containing either Boc-Leu-Caa (Caa=cyclic amino acid), Boc-Gly-Caa, or Boc-Phe-Ala attached to the aziridine nitrogen atom revealed Boc-(S)-Leu-(S)-Azy-(S,S)-Azi(OBn)(2) (18 a) as a highly potent cathepsin L (CL) inhibitor (K(i)=13 nM) (Azy=aziridine-2-carboxylate, Azi=aziridine-2,3-dicarboxylate). Docking studies, which also accounted for the unusual bonding situations (the flexibility and hybridization of the aziridides) predict that the inhibitor adopts a Y shape and spans across the entire active site cleft, binding into both the nonprimed and primed sites of CL.

Animals↗
PubMed2006

Inhibitors of cysteine proteases.

The roles of cysteine proteases (CP) as protein degrading and protein processing enzymes both in physiological and pathological processes of mammals are well known. Furthermore, the key roles of CP;s in the life cycles of infectious agents like protozoa and viruses turn them into new important targets for anti-infective drugs. Thus, the effective inhibition of pathologically relevant cysteine proteases has raised increasing interest in drug development. One strategy to create CP inhibitors is the use of electrophilic moieties, which covalently bind to the cysteine residue of the active site of the target protease. In a previous approach we have selected the aziridine-2,3-dicarboxylic acid as weak electrophilic inhibitor fragment. In order to achieve effective enzyme inhibition this electrophile was incorporated into peptidic or peptidomimetic sequences addressing the substrate binding sites of the protease. High selectivity could be obtained with compounds, which bind into both the primed and non-primed substrate binding pockets. In a second approach the alpha,beta-unsaturated ketone of the well-known diuretic drug ethacrynic acid was found to be another appropriate electrophilic moiety. Derivatives thereof turned out to be new non-peptidic CP inhibitors. Results of inhibition assays obtained with these two inhibitor series on various proteases of human, protozoan, and viral origin, theoretical studies to investigate binding modes and inhibition mechanisms, and structure-activity relationships are presented. Furthermore, the results of in vitro assays on respective pathogens as well as the results of first toxicity studies are summarized.

Animals↗
PubMed2005

A new lead for nonpeptidic active-site-directed inhibitors of the severe acute respiratory syndrome coronavirus main protease discovered by a combination of screening and docking methods.

The coronavirus main protease, M(pro), is considered to be a major target for drugs suitable for combating coronavirus infections including severe acute respiratory syndrome (SARS). An HPLC-based screening of electrophilic compounds that was performed to identify potential M(pro) inhibitors revealed etacrynic acid tert-butylamide (6a) as an effective nonpeptidic inhibitor. Docking studies suggested a binding mode in which the phenyl ring acts as a spacer bridging the inhibitor's activated double bond and its hydrophobic tert-butyl moiety. The latter is supposed to fit into the S4 pocket of the target protease. Furthermore, these studies revealed etacrynic acid amide (6b) as a promising lead for nonpeptidic active-site-directed M(pro) inhibitors. In a fluorimetric enzyme assay using a novel fluorescence resonance energy transfer (FRET) pair labeled substrate, compound 6b showed a K(i) value of 35.3 muM. Since the novel lead compound does not target the S1', S1, and S2 subsites of the enzyme's substrate-binding pockets, there is room for improvement that underlines the lead character of compound 6b.

Amides↗
PubMed2005

Screening of electrophilic compounds yields an aziridinyl peptide as new active-site directed SARS-CoV main protease inhibitor.

The coronavirus main protease, M(pro), is considered a major target for drugs suitable to combat coronavirus infections including the severe acute respiratory syndrome (SARS). In this study, comprehensive HPLC- and FRET-substrate-based screenings of various electrophilic compounds were performed to identify potential M(pro) inhibitors. The data revealed that the coronaviral main protease is inhibited by aziridine- and oxirane-2-carboxylates. Among the trans-configured aziridine-2,3-dicarboxylates the Gly-Gly-containing peptide 2c was found to be the most potent inhibitor.

Aziridines↗
PubMed2004

Probing the pharmacophore for allosteric ligands of muscarinic M2 receptors: SAR and QSAR studies in a series of bisquaternary salts of caracurine V and related ring systems.

Allosteric effects on muscarinic acetylcholine M(2) receptors were examined in a series of bisquaternary salts of the Strychnos alkaloid caracurine V (6) and related iso-caracurine V, tetrahydrocaracurine V, and bisnortoxiferine ring systems. The compounds inhibited dissociation of the orthosteric antagonist [(3)H]N-methylscopolamine (NMS) from porcine cardiac M(2) receptors with EC(0.5,diss) values from 4 to 3270 nM. The majority of compounds hardly changed [(3)H]NMS equilibrium binding, indicating similar binding affinities in free and NMS-occupied M(2) receptors. The most potent agents were found in the caracurine V, iso-caracurine V, and tetrahydrocaracurine V series and carried nonpolar alkyl groups with a maximal chain length of three carbon atoms. 3D QSAR (CoMSIA) analysis explained the wide range of binding affinities by steric and electrostatic properties of the side chains. Furthermore, the findings suggest that the spatial orientation of the "caracurine" aromatic rings compared with the bisnortoxiferine ring skeleton is favorable to optimal allostere-receptor interactions.

Alkaloids↗
PubMed2003

Mapping property distributions of molecular surfaces: algorithm and evaluation of a novel 3D quantitative structure-activity relationship technique.

A novel molecular descriptor called MaP (mapping property distributions of molecular surfaces) is presented. It combines facile computation, translational and rotational invariance, and straightforward interpretability of the computed models. A three-step procedure is used to compute the MaP descriptor. First, an approximation to the molecular surface with equally distributed surface points is computed. Next, molecular properties are projected onto this surface. Finally, the distribution of surface properties is encoded into a translationally and rotationally invariant molecular descriptor that is based on radial distribution functions (distance-dependent count statistics). The calculated descriptor is correlated with biological data through chemometric regression techniques in combination with a variable selection. The latter is used to identify variables that are highly relevant for the model and hence for its interpretation. Three applications of the new descriptor are presented, each representing a different area of 3D-QSAR. For reasons of comparability, the new descriptor was tested on the steroid "benchmark" data set. Furthermore, a highly diverse data set with potentially eye-irritating compounds was studied, and third, a set of flexible structures with a modulating effect on the muscarinic M(2) receptor were studied. Not only were all models highly predictive but interpretation of the back-projected variables into the original molecular space led to biologically and chemically relevant conclusions.

Acetates↗
PubMed2003

Determination of clotrimazole in mice plasma by capillary electrophoresis.

In addition to its antifungal activity, clotrimazole attracts interest as an anti-inflammatory drug. In order to correlate this effect with plasma concentrations in mice, a capillary electrophoretic method was developed. Sample preparation was carried out by protein precipitation using methanol. Quantification of clotrimazole was achieved by means of capillary electrophoresis using ketoconazole as an internal standard (IS). The background electrolyte (BGE) composed of a Tris buffer solution (100 mM, pH 3.0, adjusted with acetic acid) and methanol (8:2, v/v). Injection was carried out electrokinetically with 10 kV over a time period of 20 s. A special rinsing procedure utilizing a sequence of a SDS/methanol solution, a sodium hydroxide solution, water and BGE, was applied to enhance the reproducibility. With this procedure, an intermediate precision (day-to-day precision) of the area ratios of clotrimazole and IS of 5.0% for 0.5 microg ml(-1) and 2.6% for 10 microg ml(-1) was obtained. In summary, with the described capillary zone electrophoresis (CZE) method it is possible to handle small sample volumes of 60 microl, to detect clotrimazole concentrations of 0.3 microg ml(-1) (limit of detection), and to quantify clotrimazole down to concentrations of 0.5 microg ml(-1) (limit of quantification).

Animals↗
PubMed2003

Synthesis, biological activity, and docking studies of new acetylcholinesterase inhibitors of the bispyridinium type.

A novel series of acetylcholinesterase (AChE) inhibitors of the bispyridinium type was synthesized and the inhibitory activity against AChE and butyrylcholinesterase (BChE) measured. In essence, the substitution pattern influenced the inhibitory potency against AChE, where the most active bispyridiniumoxime (TMB-4) was bisbenzyl substituted followed by monobenzyl substituted, bismethyl substituted, and unsubstituted derivatives of TMB-4. Hence, the bisbenzyl ether of TMB-4 was further investigated. In order to obtain diverse lipophilic and electronic properties for these bisbenzyl bispyridinium derivatives (so-called DUO series), the lateral ring substitution was systematically varied. The lowest IC(50) value against AChE found thus far in the DUO series was 0.34 microM. Docking studies were carried out to elucidate the differences in biological activity. A general binding mode for nearly all compounds could be identified by these investigations. In this binding mode, the docked ligands span the narrow, deeply buried active-site gorge, interacting with Trp84 at the bottom of the gorge, Tyr334 or Phe331 halfway down the gorge, and Trp279 at the peripheral anionic site at the mouth of the gorge. For specific ligands, additional interactions were found which helped to explain their deviating activity. Based on the promising characteristics of the novel acetylcholinesterase inhibitors presented, a series of structurally related, optimized candidates will be developed.

Acetylcholinesterase↗
PubMed2003

Synthesis and biological activity of pyridinium-type acetylcholinesterase inhibitors.

A novel series of bispyridinium-type acetylcholinesterase (AChE) inhibitors derived from obidoxime, being active in the lower micromolar range, has been reported recently. According to the hypothesis that shorter pyridinium compounds should exhibit higher activity, a new series of compounds was synthesized that has 2,6-dichlorobenzyl, 2-chlorobenzyl and phthalimidomethyl moieties, respectively, at one end of the molecule and that are systematically shortened from the contralateral end. The concentration inhibiting the AChE and butyrylcholinesterase (BChE) by 50% (IC50) was evaluated by means of Ellman's test. Compounds characterized by a phenylpropyl residue at the contralateral end (3) were found to have IC50 values comparable with tacrine. In addition, the affinity of 3c toward the BChE was lower, indicating a lower degree of side effects.

Acetylcholinesterase↗
PubMedDate not supplied

Validation tools for variable subset regression.

Variable selection is applied frequently in QSAR research. Since the selection process influences the characteristics of the finally chosen model, thorough validation of the selection technique is very important. Here, a validation protocol is presented briefly and two of the tools which are part of this protocol are introduced in more detail. The first tool, which is based on permutation testing, allows to assess the inflation of internal figures of merit (such as the cross-validated prediction error). The other tool, based on noise addition, can be used to determine the complexity and with it the stability of models generated by variable selection. The obtained statistical information is important in deciding whether or not to trust the predictive abilities of a specific model. The graphical output of the validation tools is easily accessible and provides a reliable impression of model performance. Among others, the tools were employed to study the influence of leave-one-out and leave-multiple-out cross-validation on model characteristics. Here, it was confirmed that leave-multiple-out cross-validation yields more stable models. To study the performance of the entire validation protocol, it was applied to eight different QSAR data sets with default settings. In all cases internal and external model performance was good, indicating that the protocol serves its purpose quite well.

Quantitative Structure-Activity Relationship↗
PubMedDate not supplied

Structure-based validation of the 3D-QSAR technique MaP.

For three target proteins with different binding pocket characteristics (size and shape, hydrophobicity, hydrogen-bonding) a structure-based validation of the translationally and rotationally invariant 3D-QSAR technique MaP is performed (MaP: Mapping Property distributions of molecular surfaces). The structure-based validation procedure comprises two steps: first, QSAR models are derived without using the information of the target protein. Second, the models are back-projected into the crystal structure of the binding pockets and interpreted. It is demonstrated that MaP is able to identify characteristics important for ligand binding in the cases studied here. Moreover, it is demonstrated that MaP is a versatile 3D-QSAR technique since good, predictive models could be obtained for all three data sets showing distinct characteristics.

Cholinesterase Inhibitors↗
PubMedDate not supplied

ErG: 2D pharmacophore descriptions for scaffold hopping.

An extended reduced graph approach (ErG) is presented that uses pharmacophore-type node descriptions to encode the relevant molecular properties. The basic idea of the method can be described as a hybrid approach of reduced graphs (Gillet et al. J. Chem. Inf. Comput. Sci. 2003, 43, 338-345) and binding property pairs (Kearsley et al. J. Chem. Inf. Comput. Sci. 1996, 36, 118-127). However, specific extension modifications to correctly describe the pharmacophoric properties, size, and shape of the molecules under study result in a very stable and good performance as compared to DAYLIGHT fingerprints (DFP). This is exemplified for 11 activity classes of the MDL Drug Data Report database, for which ErG performs as well or better than DFP in 10 cases. On the basis of the example data sets, the ability of ErG to switch from one chemotype to another (often referred to as "scaffold hopping") is highlighted. Additionally, possible pitfalls of reduced graph approaches as well as suitable solutions are discussed with the help of example structures. Overall, it is shown that ErG is a widely applicable method capable of identifying structurally diverse actives for a given active search query. This diversity is achieved by a high degree of molecular abstraction, which in turn results in a low dimensional descriptor vector that allows very low computation times for similarity searches.

Journal Article↗
PubMedDate not supplied

An alignment-independent versatile structure descriptor for QSAR and QSPR based on the distribution of molecular features.

A molecular descriptor based upon a count statistic of the topological distance matrix is described and evaluated for use in QSAR studies. Encoding a molecule is done by computing many selective count statistics (histograms) reflecting the distribution of different atom types and bond types in the molecule. The descriptor was also extended to incorporate geometric features of molecules by weighting the topological distance counts with the geometric distance. It is invariant to both translation and rotation. As a result, it does not require the alignment of the structures under study. The method was applied to several QSAR data sets and performed equally well or better than CoMFA and the EVA descriptor. Compared to the latter two methods, it is computationally easier.

Algorithms↗
PubMedDate not supplied

Evaluation of extended parameter sets for the 3D-QSAR technique MaP: implications for interpretability and model quality exemplified by antimalarially active naphthylisoquinoline alkaloids.

The 3D-QSAR technique MaP (Mapping Property distributions of molecular surfaces) characterises biologically active compounds in terms of the distribution of their surface properties (H-bond donor, H-bond acceptor, hydrophilic, weakly hydrophobic, strongly hydrophobic). The MaP descriptor is alignment-independent and yields chemically intuitive models. In this study, the impact of different operational parameters on the interpretability and model quality was investigated. Based on a set of antimalarially active naphthylisoquinoline alkaloids the effect of hydrophobicity assignment as well as the differentiation of H-bond propensity was evaluated according to a full factorial design. It turns out, that including different categories for H-bond donor strength significantly improved interpretability, reduced model complexity, and made possible the derivation of a novel pharmacophore hypothesis for this dataset. Further analysis of the factorial design reveals, that MaP models are robust to parameter changes and generate consistent models for different parameter settings.

Algorithms↗