Publications

Posters

Theses

4-Acyl Pyrrole Derivatives Yield Novel Vectors for Designing Inhibitors of the Acetyl-Lysine Recognition Site of BRD4(1). Hügle M, Lucas X, Weitzel G, Ostrovskyi D, Breit B, Gerhardt S, Einsle O, Günther S, Wohlwend D. J Med Chem. 2016;:.
PMID: 26731611 Abstract

Several human diseases, including cancer, show altered signaling pathways resulting from changes in the activity levels of epigenetic modulators. In the past few years, small-molecule inhibitors against specific modulators, including the bromodomain and extra-terminal (BET) bromodomain family of acetylation readers, have shown early promise in the treatment of the genetically defined midline carcinoma and hematopoietic malignancies. We have recently developed a novel potent inhibitor of BET proteins, 1 (XD14[ Angew. Chem., Int. Ed. 2013 , 52 , 14055 ]), which exerts a strong inhibitory potential on the proliferation of specific leukemia cell lines. In the study presented here, we designed analogues of 1 to study the potential of substitutions on the 4-acyl pyrrole backbone to occupy additional sites within the substrate recognition site of BRD4(1). The compounds were profiled using ITC, DSF, and X-ray crystallography. We could introduce several substitutions that address previously untargeted areas of the substrate recognition site. This work may substantially contribute to the development of therapeutics with increased target specificity against BRD4-related malignancies.
The Chemistry and Biological Activities of Natural Products from Northern African Plant Families: From Taccaceae to Zygophyllaceae. Fidele N, E NL, I MY, Günther S, Wolfgang S, N YJ. Nat Prod Bioprospect. 2016;:.
PMID: 26931529 Abstract

Traditional medicinal practices have a profound influence on the daily lives of people living in developing countries, particularly in Africa, since the populations cannot generally afford the cost of Western medicines. We have undertaken to investigate the correlation between the uses of plants in Traditional African medicine and the biological activities of the derived natural products, with the aim to validate the use of traditional medicine in Northern African communities. The literature is covered for the period 1959-2015 and part III of this review series focuses on plant families with names beginning with letters T to Z. The authors have focused on curating data from journals in natural products and phytomedicine. Within each journal home page, a query search based on country name was conducted. All articles "hits" were then verified, one at a time, that the species was harvested within the Northern African geographical regions. The current data partly constitutes the bases for the development of the Northern African natural compounds database. The review discusses 284 plant-based natural compounds from 34 species and 11 families. It was observed that the ethnobotanical uses of less than 40 \% of the plant species surveyed correlated with the bioactivities of compounds identified.
StreptomeDB 2.0-an extended resource of natural products produced by streptomycetes. Klementz D, Döring K, Lucas X, Telukunta KK, Erxleben A, Deubel D, Erber A, Santillana I, Thomas OS, Bechthold A, Günther S. Nucleic Acids Res. 2016;44:D509-D514.
PMID: 26615197 Abstract

Over the last decades, the genus Streptomyces has stirred huge interest in the scientific community as a source of bioactive compounds. The majority of all known antibiotics is isolated from these bacterial strains, as well as a variety of other drugs such as antitumor agents, immunosuppressants and antifungals. To the best of our knowledge, StreptomeDB was the first database focusing on compounds produced by streptomycetes. The new version presented herein represents a major step forward: its content has been increased to over 4000 compounds and more than 2500 host organisms. In addition, we have extended the background information and included hundreds of new manually curated references to literature. The latest update features a unique scaffold-based navigation system, which enables the exploration of the chemical diversity of StreptomeDB on a structural basis. We have included a phylogenetic tree, based on 16S rRNA sequences, which comprises more than two-thirds of the included host organisms. It enables visualizing the frequency, appearance, and persistence of compounds and scaffolds in an evolutionary context. Additionally, we have included predicted MS- and NMR-spectra of thousands of compounds for assignment of experimental data. The database is freely accessible via http://www.pharmaceutical-bioinformatics.org/streptomedb.
Echinocandin B biosynthesis: a biosynthetic cluster from Aspergillus nidulans NRRL 8112 and reassembly of the subclusters Ecd and Hty from Aspergillus pachycristatus NRRL 11440 reveals a single coherent gene cluster. Hüttel W, Youssar L, Grüning BA, Günther S, Hugentobler KG. BMC Genomics. 2016;17:.
Abstract

Background Echinocandins are nonribosomal lipopeptides produced by ascommycete fungi. Due to their strong inhibitory effect on fungal cell wall biosynthesis and lack of human toxicity, they have been developed to an important class of antifungal drugs. Since 2012, the biosynthetic gene clusters of most of the main echinocandin variants have been characterized. Especially the comparison of the clusters allows a deeper insight for the biosynthesis of these complex structures. Results In the genome of the echinocandin B producer Aspergillus nidulans NRRL 8112 we have identified a gene cluster (Ani) that encodes echinocandin biosynthesis. Sequence analyses showed that Ani is clearly delimited from the genomic context and forms a monophyletic lineage with the other echinocandin gene clusters. Importantly, we found that the disjunct genomic location of the echinocandin B gene cluster in A. pachycristatus NRRL 11440 on two separate subclusters, Ecd and Hty, at two loci was likely an artifact of genome misassembly in the absence of a reference sequence. We show that both sequences can be aligned resulting a single cluster with a gene arrangement collinear compared to other clusters of Aspergillus section Nidulantes. The reassembled gene cluster (Ecd/Hty) is identical to a putative gene cluster (AE) that was previously deposited at the NCBI as a sequence from A. delacroxii NRRL 3860. PCR amplification of a part of the gene cluster resulted a sequence that was very similar (97 % identity), but not identical to that of AE. Conclusions The Echinocandin B biosynthetic cluster from A. nidulans NRRL 8112 (Ani) is particularly similar to that of A. pachycristatus NRRL 11440 (Ecd/Hty). Ecd/Hty was originally reported as two disjunct sub-clusters Ecd and Hty, but is in fact a continuous sequence with the same gene order as in Ani. According to sequences of PCR products amplified from genomic DNA, the echinocandin B producer A. delacroxii NRRL 3860 is closely related to A. pachycristatus NRRL 11440. A PCR-product from the gene cluster was very similar, but clearly distinct from the sequence published for A. delacroxii NRRL 3860 at the NCBI (No. AB720074). As the NCBI entry is virtually identical with the re-assembled Ecd/Hty cluster, it is likely that it originates from A. pachycristatus NRRL 11440 rather than A. delacroxii NRRL 3860.
Preparation data of the bromodomains BRD3(1), BRD3(2), BRD4(1), and BRPF1B and crystallization of BRD4(1)-inhibitor complexes. Hügle M, Lucas X, Weitzel G, Ostrovskyi D, Breit B, Gerhardt S, Schmidtkunz K, Jung M, Schüle R, Einsle O, Günther S, Wohlwend D. Data in Brief. 2016;7:1370-1374.
Abstract

This article presents detailed purification procedures for the bromodomains BRD3(1), BRD3(2), BRD4(1), and BRPF1B. In addition we provide crystallization protocols for apo BRD4(1) and BRD4(1) in complex with numerous inhibitors. The protocols described here were successfully applied to obtain affinity data by isothermal titration calorimetry (ITC) and by differential scanning fluorimetry (DSF) as well as structural characterizations of BRD4(1) inhibitor complexes (PDB codes: PDB: 4LYI, PDB: 4LZS, PDB: 4LYW, PDB: 4LZR, PDB: 4LYS, PDB: 5D24, PDB: 5D25, PDB: 5D26, PDB: 5D3H, PDB: 5D3J, PDB: 5D3L, PDB: 5D3N, PDB: 5D3P, PDB: 5D3R, PDB: 5D3S, PDB: 5D3T). These data have been reported previously and are discussed in more detail elsewhere [1,2].
Target Fishing by Cross-Docking to Explain Polypharmacological Effects. Patel H, Lucas X, Bendik I, Günther S, Merfort I. ChemMedChem. 2015;10:1209-1217.
PMID: 26033840 Abstract

Drugs may have polypharmacological phenomena, that is, in addition to the desired target, they may also bind to many undesired or unknown physiological targets. As a result, they often exert side effects. In some cases, off-target interactions may lead to drug repositioning or to explaining a drug's mode of action. Herein we present an in silico approach for target fishing by cross-docking as a method to identify new drug-protein interactions. As an example and proof of concept, this method predicted the peroxisome proliferator-activated receptor (PPAR)-γ as a target of ethacrynic acid, which may explain the hyperglycemic effect brought on by this molecule. The antagonistic effect of ethacrynic acid on PPAR-γ was validated in a transient transactivation assay using human HEK293 cells. The cross-docking approach also predicted the potential mechanisms of many other drug side effects and discloses new drug repositioning opportunities. These putative interactions are described herein, and can be readily used to discover therapeutically relevant drug effects.
The Purchasable Chemical Space: A Detailed Picture. Lucas X, Grüning BA, Bleher S, Günther S. J Chem Inf Model. 2015;55:915-924.
PMID: 25894297 Abstract

The screening of a reduced yet diverse and synthesizable region of the chemical space is a critical step in drug discovery. The ZINC database is nowadays routinely used to freely access and screen millions of commercially available compounds. We collected ∼125 million compounds from chemical catalogs and the ZINC database, yielding more than 68 million unique molecules, including a large portion of described natural products (NPs) and drugs. The data set was filtered using advanced medicinal chemistry rules to remove potentially toxic, promiscuous, metabolically labile, or reactive compounds. We studied the physicochemical properties of this compilation and identified millions of NP-like, fragment-like, inhibitors of protein–protein interactions (i-PPIs) like, and drug-like compounds. The related focused libraries were subjected to a detailed scaffold diversity analysis and compared to reference NPs and marketed drugs. This study revealed thousands of diverse chemotypes with distinct representations of building block combinations among the data sets. An analysis of the stereogenic and shape complexity properties of the libraries also showed that they present well-defined levels of complexity, following the tendency: i-PPIs-like < drug-like < fragment-like < NP-like. As the collected compounds have huge interest in drug discovery and particularly virtual screening and library design, we offer a freely available collection comprising over 37 million molecules under: http://pbox.pharmaceutical-bioinformatics.org, as well as the filtering rules used to build the focused libraries described herein.
Regio- and Stereoselective Intermolecular Oxidative Phenol Coupling in Streptomyces. Präg A, Grüning BA, Häckh M, Lüdeke S, Wilde M, Luzhetskyy A, Richter M, Luzhetska M, Günther S, Müller M. J Am Chem Soc. 2014;136:6195-6198.
PMID: 24746278 Abstract

Intermolecular oxidative phenol coupling is the main process in nature for the formation of atroposelective biaryl compounds. Although well defined in plants and fungi, this type of dimerization reaction in bacteria is poorly understood. Therefore, the biosynthesis of julichromes, spectomycins, and setomimycin was investigated. The monomeric subunits of these biarylic pre-anthraquinones are derived from a common polyketidic precursor, yet the coupling reaction proceeds in a regioselective manner, with the position of attachment of the two subunits depending on the specific streptomycete strain. By using genome analysis and deletion experiments, the biosynthetic gene clusters were identified. Furthermore, it was established that cytochrome P450 enzymes are fundamentally involved during dimerization of the polyketide monomers.
PyWATER: A PyMOL plugin to find conserved water molecules in proteins by clustering. Patel H, Grüning BA, Günther S, Merfort I. Bioinformatics. 2014;30:2978-2980.
PMID: 24990608 Abstract

SUMMARY: Conserved water molecules play a crucial role in protein structure, stabilization of secondary structure, protein activity, flexibility and ligand binding. Clustering of water molecules in superimposed protein structures, obtained by x-ray crystallography at high resolution is an established method to identify consensus water molecules in all known protein structures of the same family. PyWATER is an easy to use PyMOL plugin and identifies conserved water molecules in the protein structure of interest. PyWATER can be installed via the user interface of PyMOL. No programming or command line knowledge is required for its use. AVAILABILITY AND IMPLEMENTATION: PyWATER and a tutorial are available at https://github.com/hiteshpatel379/PyWATER. PyMOL is available at http://www.pymol.org or http://sourceforge.net/projects/pymol.
Using chiral molecules as an approach to address low-druggability recognition sites. Lucas X, Günther S. J Comput Chem. 2014;35:2114-2121.
PMID: 25223950 Abstract

The content of chiral carbon atoms or structural complexity, which is known to correlate well with relevant physicochemical properties of small molecules, represents a promising descriptor that could fill the gap in existing drug discovery between ligand library filtering rules and the corresponding properties of the target's recognition site. Herein, we present an in silico study on the yet unclear underlying correlations between molecular complexity and other more sophisticated physicochemical and biological properties. By analyzing thousands of protein–ligand complexes from DrugBank, we show that increasing molecular complexity of drugs is an approach to addressing particularly low-druggability and polar recognition sites. We also show that biologically relevant protein classes characteristically bind molecules with a certain degree of structural complexity. Three distinct behaviors toward drug recognition are described. The reported results set the basis for a better understanding of protein–drug recognition, and open the possibility of including target information in the filtering of large ligand libraries for screening.
Targeting the BET family for the treatment of leukemia. Lucas X, Günther S. Epigenomics. 2014;6:153-155.
PMID: 24811781
Metabolic Pathway Monitoring of Phenalinolactone Biosynthesis from Streptomyces sp. Tü6071 by LC-MS coupling. Kiske C, Erxleben A, Lucas X, Willmann L, Klementz D, Günther S, Römer W, Kammerer B. Rapid Commun Mass Spectrom. 2014;28:1459-1467.
PMID: 24861595 Abstract

RATIONALE: A rapid and precise analytical method for the investigation of natural products is required for pathway monitoring of the biosynthesis of secondary metabolites. Phenalinolactones, used in antibiotic research, are produced by Streptomyces sp. Tü6071. For the analysis of those compounds, prior to mass spectrometric analysis, an efficient separation technique is required. METHODS: For the identification of phenalinolactones from liquid cultures of Streptomyces sp. Tü6071, a new method comprising the combination of solid-phase extraction (SPE) prior to liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) was established. MS/MS product ion scans were applied for phenalinolactone detection and structure elucidation, performed in negative mode and optimized for sensitivity and specificity. For the discovery of new intermediates, a MS/MS precursor ion scan was applied. RESULTS: Analysis of the extracts revealed that the Oasis® MAX cartridge, containing a quaternary amine functionality, is the most efficient SPE material for purification of phenalinolactones, since it allowed sufficient enrichment and detection of intermediates from the biosynthetic pathway by LC/ESI-MS/MS. Using the precursor ion scan technique, two new secondary metabolites, PL IM1 with m/z 672.6 and PL IM2 with m/z 433.3, have been detected. The structures of the new intermediates are postulated and arranged into the biosynthetic pathway of phenalinolactones. CONCLUSIONS: A precise analytical method was established for the identification of phenalinolactones by combining purification from Streptomyces using SPE prior to LC/ESI-MS/MS. By optimising LC/ESI-MS/MS settings, this method has been successfully applied for pathway monitoring of secondary metabolites. Application of a precursor ion scan allowed for the identification of unknown intermediates in biosynthetic pathways.
Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease. Gilsbach R, Preissl S, Grüning BA, Schnick T, Burger L, Benes V, Würch A, Bönisch U, Günther S, Backofen R, Fleischmann BK, Schübeler D, Hein L. Nat Commun. 2014;5:5288.
PMID: 25335909 Abstract

The heart is a highly specialized organ with essential function for the organism throughout life. The significance of DNA methylation in shaping the phenotype of the heart remains only partially known. Here we generate and analyse DNA methylomes from highly purified cardiomyocytes of neonatal, adult healthy and adult failing hearts. We identify large genomic regions that are differentially methylated during cardiomyocyte development and maturation. Demethylation of cardiomyocyte gene bodies correlates strongly with increased gene expression. Silencing of demethylated genes is characterized by the polycomb mark H3K27me3 or by DNA methylation. De novo methylation by DNA methyltransferases 3A/B causes repression of fetal cardiac genes, including essential components of the cardiac sarcomere. Failing cardiomyocytes partially resemble neonatal methylation patterns. This study establishes DNA methylation as a highly dynamic process during postnatal growth of cardiomyocytes and their adaptation to pathological stress in a process tightly linked to gene regulation and activity.
Characterization and Phylogenetic Analysis of the Mitochondrial Genome of Glarea lozoyensis Indicates High Diversity within the Order Helotiales. Youssar L, Grüning BA, Günther S, Hüttel W. PLoS ONE. 2013;8:e74792.
PMID: 24086376 Abstract

Background: Glarea lozoyensis is a filamentous fungus used for the industrial production of non-ribosomal peptide pneumocandin B0. In the scope of a whole genome sequencing the complete mitochondrial genome of the fungus has been assembled and annotated. It is the first one of the large polyphyletic Helotiaceae family. A phylogenetic analysis was performed based on conserved proteins of the oxidative phosphorylation system in mitochondrial genomes. Results: The total size of the mitochondrial genome is 45,038 bp. It contains the expected 14 genes coding for proteins related to oxidative phosphorylation,two rRNA genes, six hypothetical proteins, three intronic genes of which two are homing endonucleases and a ribosomal protein rps3. Additionally there is a set of 33 tRNA genes. All genes are located on the same strand. Phylogenetic analyses based on concatenated mitochondrial protein sequences confirmed that G. lozoyensis belongs to the order of Helotiales and that it is most closely related to Phialocephala subalpina. However, a comparison with the three other mitochondrial genomes known from Helotialean species revealed remarkable differences in size, gene content and sequence. Moreover, it was found that the gene order found in P. subalpina and Sclerotinia sclerotiorum is not conserved in G. lozoyensis. Conclusion: The arrangement of genes and other differences found between the mitochondrial genome of G. lozoyensis and those of other Helotiales indicates a broad genetic diversity within this large order. Further mitochondrial genomes are required in order to determine whether there is a continuous transition between the different forms of mitochondrial genomes or G. lozoyensis belongs to a distinct subgroup within Helotiales.
4-Acyl Pyrroles: Mimicking Acetylated Lysines in Histone Code Reading. Lucas X, Wohlwend D, Hügle M, Schmidtkunz K, Gerhardt S, Schüle R, Jung M, Einsle O, Günther S. Angew Chem Int Ed Engl. 2013;52:14055-14059.
PMID: 24272870 Abstract

Bromodomains are acetyllysine epigenetic mark reader proteins. Small molecules inhibiting them have potential as anti-inflammatory, antiviral, and anticancer agents. A 4-acyl pyrrole derivative (see yellow structure in recognition pocket) has been identified that potently inhibits specific bromodomains and exhibits antiproliferative activity against leukemia cell lines.
Discovery of the Inhibitory Effect of a Phosphatidylinositol Derivative on P-Glycoprotein by Virtual Screening Followed by In Vitro Cellular Studies. Lucas X, Simon S, Schubert R, Günther S. PLoS One. 2013;8:e60679.
PMID: 23593281 Abstract

P-glycoprotein is capable of effluxing a broad range of cytosolic and membrane penetrating xenobiotic substrates, thus leading to multi-drug resistance and posing a threat for the therapeutic treatment of several diseases, including cancer and central nervous disorders. Herein, a virtual screening campaign followed by experimental validation in Caco-2, MDKCII, and MDKCII mdr1 transfected cell lines has been conducted for the identification of novel phospholipids with P-gp transportation inhibitory activity. Phosphatidylinositol-(1,2-dioctanoyl)-sodium salt (8∶0 PI) was found to significantly inhibit transmembrane P-gp transportation in vitro in a reproducible-, cell line-, and substrate-independent manner. Further tests are needed to determine whether this and other phosphatidylinositols could be co-administered with oral drugs to successfully increase their bioavailability. Moreover, as phosphatidylinositols and phosphoinositides are present in the human diet and are known to play an important role in signal transduction and cell motility, our finding could be of substantial interest for nutrition science as well.
StreptomeDB: a resource for natural compounds isolated from Streptomyces species. Lucas X, Senger C, Erxleben A, Grüning BA, Döring K, Mosch J, Flemming S, Günther S. Nucleic Acids Res. 2013;41:D1130-D1136.
PMID: 23193280 Abstract

Bacteria from the genus Streptomyces are very important for the production of natural bioactive compounds such as antibiotic, antitumour or immunosuppressant drugs. Around two-thirds of all known natural antibiotics are produced by these bacteria. An enormous quantity of crucial data related to this genus has been generated and published, but so far no freely available and comprehensive database exists. Here, we present StreptomeDB (http://www.pharmaceutical-bioinformatics.de/streptomedb/). To the best of our knowledge, this is the largest database of natural products isolated from Streptomyces. It contains >2400 unique and diverse compounds from >1900 different Streptomyces strains and substrains. In addition to names and molecular structures of the compounds, information about source organisms, references, biological role, activities and synthesis routes (e.g. polyketide synthase derived and non-ribosomal peptides derived) is included. Data can be accessed through queries on compound names, chemical structures or organisms. Extraction from the literature was performed through automatic text mining of thousands of articles from PubMed, followed by manual curation. All annotated compound structures can be downloaded from the website and applied for in silico screenings for identifying new active molecules with undiscovered properties.
Rapid degradation of solid-phase bound peptides by the 20S proteasome. Hovestädt M, Kuckelkorn U, Niewienda A, Keller C, Goede A, Ay B, Günther S, Janek K, Volkmer R, Holzhütter H. J Pept Sci. 2013;19:588-597.
PMID: 23893543 Abstract

Proteasomes are cellular proteases involved in the degradation of numerous cellular proteins. The 20S proteasome is a cylindrical 28-mer protein complex composed of two outer heptameric α-rings forming the entrance for the protein substrate and two inner heptameric β-rings carrying the catalytic sites. Numerous in vitro studies have provided evidence that the 20S proteasome may degrade peptides of various lengths and even unfolded full-length polypeptide chains. However, a direct demonstration that the 20S proteasome may also cleave surface-attached immobilized peptides is lacking so far. To this end, we used a model system by coupling peptides from different source proteins covalently to the surface of glass beads and applied nanoLC/MS analysis to monitor the generation of proteolytic fragments in the presence of the 20S proteasome. Detectable amounts of cleavage products occurred within a few minutes indicating a much higher cleavage rate than observed with the same substrates in solution. Our finding lends support to the idea that proteasomes may directly degrade segments of membrane-bound proteins protruding into the aqueous phase. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd.
Draft Genome Sequence of Streptomyces viridochromogenes Strain Tu57, Producer of Avilamycin. Grüning BA, Erxleben A, Hähnlein A, Günther S. Genome Announc. 2013;1:.
PMID: 23788550 Abstract

Here we present the draft genome sequence of Streptomyces viridochromogenes Tü57. This strain is a producer of avilamycin A, an oligosaccharide antibiotic from the orthosomycin group, which is active against Gram-positive bacteria.
Genome Sequence of the Fungus Glarea lozoyensis: the First Genome Sequence of a Species from the Helotiaceae Family. Youssar L, Grüning BA, Erxleben A, Günther S, Hüttel W. Eukaryot Cell. 2012;11:250.
PMID: 22302591 Abstract

The anamorphic fungus Glarea lozoyensis mutant strain 74030 is an overproducer of pneumocandin B(0), which is chemically converted into Cancidas, a potent antibiotic against clinically important fungal pathogens. Pneumocandins are acylated, cyclic hexapeptides with unusual hydroxylated amino acids. With the Glarea lozoyensis genome, the first species from the large polyphyletic family Helotiaceae has been sequenced.
Mining and evaluation of molecular relationships in literature. Senger C, Grüning BA, Erxleben A, Döring K, Patel H, Flemming S, Merfort I, Günther S. Bioinformatics. 2012;28:709-714.
PMID: 22247277 Abstract

Specific information on newly discovered proteins is often difficult to find in literature. Particularly if only sequences and no common names of proteins or genes are available, preceding sequence similarity searches can be crucial for the process of information collection. In drug research, it is important to know whether a small molecule targets only one specific protein or whether similar or homologous proteins are also influenced that may account for possible side effects.prolific (protein-literature investigation for interacting compounds) provides a one-step solution to investigate available information on given protein names, sequences, similar proteins or sequences on the gene level. Co-occurrences of UniProtKB/Swiss-Prot proteins and PubChem compounds in all PubMed abstracts are retrievable. Concise 'heat-maps' and tables display frequencies of co-occurrences. They provide links to processed literature with highlighted found protein and compound synonyms. Evaluation with manually curated drug-protein relationships showed that up to 69\% could be discovered by automatic text-processing. Examples are presented to demonstrate the capabilities of prolific.The web-application is available at http://prolific.pharmaceutical-bioinformatics.de and a web service at http://www.pharmaceutical-bioinformatics.de/prolific/soap/prolific.wsdl.stefan.guenther@pharmazie.uni-freiburg.deSupplementary data are available at Bioinformatics online.
Tetrahydroxynaphthalene reductase: catalytic properties of an enzyme involved in reductive asymmetric naphthol dearomatization. Schätzle MA, Flemming S, Husain SM, Richter M, Günther S, Müller M. Angew Chem Int Ed Engl. 2012;51:2643-2646.
PMID: 22308069 Abstract

In reduced circumstances: tetrahydroxynaphthalene reductase shows a broad substrate range including alternate phenolic compounds and cyclic ketones. Structural modeling reveals major enzyme-substrate interactions; C-terminal truncation of the enzyme causes an altered substrate preference, in accordance with stabilization of the substrate by the C-terminal carboxylate. This effect allows the identification of a homologous enzyme.
Regio- and Stereoselective Oxidative Phenol Coupling in Aspergillus niger. Girol CG, Fisch KM, Heinekamp T, Günther S, Hüttel W, Piel J, Brakhage AA, Müller M. Angew Chem Int Ed Engl. 2012;51:9788-9791.
PMID: 22945023 Abstract

Piecing it together: Aspergillus niger produces kotanin by dimerization of the monomeric, polyketide-synthase-derived (PKS) 7-demethylsiderin. A combined approach, comprising bioinformatics and gene-deletion experiments, identified the biosynthetic cluster responsible for kotanin production. Homology modeling and substrate docking provide a rationale for the regio- and stereoselective phenol coupling reaction.
Abietane diterpenes induce cytotoxic effects in human pancreatic cancer cell line MIA PaCa-2 through different modes of action. Fronza M, Lamy E, Günther S, Heinzmann B, Laufer S, Merfort I. Phytochemistry. 2012;78:107-119.
PMID: 22436445 Abstract

Abietane diterpenes, especially those containing quinone moieties, are often reported to have cytotoxic effects on cancer cell lines. They deserve greater attention because several cancer chemotherapeutic agents also possess the quinone structural feature. To date, very little is known about their cytotoxic molecular modes of action. In the present study, five diterpenes, 7 alpha-acetoxyroyleanone, horminone, royleanone, 7-ketoroyleanone and sugiol which have been previously isolated from the medicinal plant Peltodon longipes were shown to possess cytotoxic activity against the human pancreatic cancer cell line MIA PaCa-2. 7 alpha-Acetoxyroyleanone, horminone and royleanone were demonstrated to possess alkylating properties using the nucleophile 4-(4-nitrobenzyl)pyridine. However, no clear correlation between the alkylating properties and cytotoxicity of these diterpenes was observed. Furthermore, the relaxation activity of human DNA topoisomerases I and II was found to be influenced by these compounds, with 7-ketoroyleanone and sugiol being the most active. These two diterpenes preferentially inhibited topoisomerase I and exhibited lower IC(50) values than the classical topoisomerase I inhibitor camptothecin. Molecular docking studies revealed possible interactions of diterpenes with topoisomerase I, indicating that these compounds do not form the drug-enzyme-DNA covalent ternary complex as observed with camptothecin. A binding pocket located at the surface of the DNA-interaction site was proposed. Moreover, the ability of the five diterpenes to generate DNA-strand breaks in single cells was confirmed using the alkaline comet assay. As expected, these diterpenes also influenced cell cycle progression and arrested cells in different phases of the cell cycle, primarily the G1/G0 and S-phases. Interestingly, the diterpenes only exhibited a slight ability to induce apoptotic cell death and failed to generate intracellular reactive oxygen species. These results provide additional understanding of the cytotoxic effects of abietane diterpenes. Depending on their functional groups, we propose that abietane diterpenes utilise different mechanisms to induce cell death.
Binding sites in membrane proteins - Diversity, druggability and prospects. Adams R, Worth CL, Günther S, Dunkel M, Lehmann R, Preissner R. Eur J Cell Biol. 2012;91:326-339.
PMID: 21872966 Abstract

The identification of novel drug targets is one of the major challenges in proteomics. Computational methods developed over the last decade have enhanced the process of drug design in both terms of time and quality. The main task is the design of selective compounds, which bind targets more specifically, dependent on the desired mode of action of the particular drug. This makes it necessary to create compounds, which either exhibit their functions on one single protein to exclude undesired cross-reactivity or to use the advantageous effect of less selective drugs that target numerous proteins and therefore exhibit their functions on whole protein classes. Main aspects in the assignment of interactions between ligands and putative targets involve the amino acid composition of the binding site, evolutionary conservation and similarity in sequence and structure of known targets. Similarities or differences within classified protein families can be the key to their function and give first hints to functional drug design. Hereby, binding site-based classification outnumbers sequence-based classifications since similar binding sites can also be found in more distant proteins. Membrane proteins are 'difficult targets', because of their special physicochemical characteristics and the general lack of structural information. Here, we describe recent advances in modeling methods dedicated to membrane proteins. Different descriptors of similarity between compounds and the similarity between binding sites are under development and elucidate important aspects like dynamics or entropy. The importance of computational drug design is undisputable. Nevertheless, the process of design is complicated by increasing complexity, which underlines the importance of accurate knowledge about the addressed target class(es) and particularly their binding sites. One main objective by considering named topics is to predict putative side effects and errant functions (off-target effects) of novel drugs, which requires a holistic (systems biology) view on drug-target-pathway relations. In the following, we give a brief summary about the recent discussion on drug-target interactions with emphasis on membrane proteins.
Rational design of an aryl-C-glycoside catalyst from a natural product o-glycosyltransferase. Härle J, Günther S, Lauinger B, Weber M, Kammerer B, Zechel DL, Luzhetskyy A, Bechthold A. Chem Biol. 2011;18:520-530.
PMID: 21513888 Abstract

Because the sugar moieties of natural products are primarily O-linked, the hydrolytic sensitivity of the glycosidic linkage limits their therapeutic application. One potential solution to this problem is to replace the labile O-glycosidic bond with an enzymatically and chemically stable C-glycosidic bond. In this study, computational analysis of the O-glycosyltransferase LanGT2 and the C-glycosyltransferase UrdGT2 was used to predict the changes necessary to switch the O-glycosylating enzyme to a C-glycosyltransferase. By screening rationally designed LanGT2 mutants a number of LanGT2 variants with C-glycosyltransferase activity were identified. One variant, having 10 amino acid substitutions, revealed the primary region that determines O- versus C-glycosylation. By modeling the active site of this mutant and probing the role of active site residues with alanine substitutions, this work also illuminates the mechanistic features of O- and C-glycosylation.
Compounds In Literature (CIL): screening for compounds and relatives in PubMed. Grüning BA, Senger C, Erxleben A, Flemming S, Günther S. Bioinformatics. 2011;27:1341-1342.
PMID: 21414988 Abstract

Searching for certain compounds in literature can be an elaborate task, with many compounds having several different synonyms. Often, only the structure is known but not its name. Furthermore, rarely investigated compounds may not be described in the available literature at all. In such cases, preceding searches for described similar compounds facilitate literature mining. Highlighted names of proteins in selected texts may further accelerate the time-consuming process of literary research. Compounds In Literature (CIL) provides a web interface to automatically find names, structures, and similar structures in over 28 million compounds of PubChem and more than 18 million citations provided by the PubMed service. CIL's pre-calculated database contains more than 56 million parent compound-abstract relations. Found compounds, relatives and abstracts are related to proteins in a concise 'heat map'-like overview. Compounds and proteins are highlighted in their respective abstracts, and are provided with links to PubChem and UniProt.An easy-to-use web interface with detailed descriptions, help and statistics is available from http://cil.pharmaceutical-bioinformatics.de.stefan.guenther@pharmazie.uni-freiburg.de.
Genome Sequence of Streptomyces sp. Strain Tu6071. Erxleben A, Wunsch-Palasis J, Grüning BA, Luzhetska M, Bechthold A, Günther S. J Bacteriol. 2011;193:4278-4279.
PMID: 21705604 Abstract

Streptomyces sp. Tü6071 is a soil-dwelling bacterium which has a highly active isoprenoid biosynthesis. Isoprenoids are important precursors for biopharmaceutical molecules such as antibiotics or anticancer agents, e.g., landomycin. Streptomyces sp. Tü6071 produces the industrially important terpene glycosides phenalinolactones, which have antibacterial activity against several Gram-positive bacteria. The availability of the genome sequence of Streptomyces sp. Tü6071 allows for understanding the biosynthesis of these pharmaceutical molecules and will facilitate rational genome modification to improve industrial use.
Small-molecule conversion of toxic oligomers to nontoxic β-sheet-rich amyloid fibrils. Bieschke J, Herbst M, Wiglenda T, Friedrich RP, Boeddrich A, Schiele F, Kleckers D, Amo JMLD, Grüning BA, Wang Q, Schmidt MR, Lurz R, Anwyl R, Schnoegl S, Fändrich M, Frank RF, Reif B, Günther S, Walsh DM, Wanker EE. Nat Chem Biol. 2011;8:93-101.
PMID: 22101602 Abstract

Several lines of evidence indicate that prefibrillar assemblies of amyloid-β (Aβ) polypeptides, such as soluble oligomers or protofibrils, rather than mature, end-stage amyloid fibrils cause neuronal dysfunction and memory impairment in Alzheimer's disease. These findings suggest that reducing the prevalence of transient intermediates by small molecule-mediated stimulation of amyloid polymerization might decrease toxicity. Here we demonstrate the acceleration of Aβ fibrillogenesis through the action of the orcein-related small molecule O4, which directly binds to hydrophobic amino acid residues in Aβ peptides and stabilizes the self-assembly of seeding-competent, β-sheet-rich protofibrils and fibrils. Notably, the O4-mediated acceleration of amyloid fibril formation efficiently decreases the concentration of small, toxic Aβ oligomers in complex, heterogeneous aggregation reactions. In addition, O4 treatment suppresses inhibition of long-term potentiation by Aβ oligomers in hippocampal brain slices. These results support the hypothesis that small, diffusible prefibrillar amyloid species rather than mature fibrillar aggregates are toxic for mammalian cells.
SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions. Preissner S, Kroll K, Dunkel M, Senger C, Goldsobel G, Kuzman D, Günther S, Winnenburg R, Schroeder M, Preissner R. Nucleic Acids Res. 2010;38:D237-D243.
PMID: 19934256 Abstract

Much of the information on the Cytochrome P450 enzymes (CYPs) is spread across literature and the internet. Aggregating knowledge about CYPs into one database makes the search more efficient. Text mining on 57 CYPs and drugs led to a mass of papers, which were screened manually for facts about metabolism, SNPs and their effects on drug degradation. Information was put into a database, which enables the user not only to look up a particular CYP and all metabolized drugs, but also to check tolerability of drug-cocktails and to find alternative combinations, to use metabolic pathways more efficiently. The SuperCYP database contains 1170 drugs with more than 3800 interactions including references. Approximately 2000 SNPs and mutations are listed and ordered according to their effect on expression and/or activity. SuperCYP (http://bioinformatics.charite.de/supercyp) is a comprehensive resource focused on CYPs and drug metabolism. Homology-modeled structures of the CYPs can be downloaded in PDB format and related drugs are available as MOL-files. Within the resource, CYPs can be aligned with each other, drug-cocktails can be 'mixed', SNPs, protein point mutations, and their effects can be viewed and corresponding PubMed IDs are given. SuperCYP is meant to be a platform and a starting point for scientists and health professionals for furthering their research.
Structural features and evolution of protein-protein interactions. Eichborn JV, Günther S, Preissner R. Genome Inform. 2010;22:1-10.
PMID: 20238414 Abstract

Solved structures of protein-protein complexes give fundamental insights into protein function and molecular recognition. Although the determination of protein-protein complexes is generally more difficult than solving individual proteins, the number of experimentally determined complexes increased conspicuously during the last decade. Here, the interfaces of 750 transient protein-protein interactions as well as 2,000 interactions between domains of the same protein chain (obligate interactions) were analyzed to obtain a better understanding of molecular recognition and to identify features applicable for protein binding site prediction. Calculation of knowledge-based potentials showed a preference of contacts between amino acids having complementary physicochemical properties. The analysis of amino acid conservation of the entire interface area showed a weak but significant tendency to a higher evolutionary conservation of protein binding sites compared to surface areas that are permanently exposed to solvent. Remarkably, contact frequencies between outstandingly conserved residues are much higher than expected confirming the so-called "hot spot" theory. The comparisons between obligate and transient domain contacts reveal differences and point out that structural diversification and molecular recognition of protein-protein interactions are subjected to other evolutionary aspects than obligate domain-domain interactions.
JAIL: a structure-based interface library for macromolecules. Günther S, Eichborn Jv, May P, Preissner R. Nucleic Acids Res. 2009;37:D338-D341.
PMID: 18832369 Abstract

The increasing number of solved macromolecules provides a solid number of 3D interfaces, if all types of molecular contacts are being considered. JAIL annotates three different kinds of macromolecular interfaces, those between interacting protein domains, interfaces of different protein chains and interfaces between proteins and nucleic acids. This results in a total number of about 184,000 database entries. All the interfaces can easily be identified by a detailed search form or by a hierarchical tree that describes the protein domain architectures classified by the SCOP database. Visual inspection of the interfaces is possible via an interactive protein viewer. Furthermore, large scale analyses are supported by an implemented sequential and by a structural clustering. Similar interfaces as well as non-redundant interfaces can be easily picked out. Additionally, the sequential conservation of binding sites was also included in the database and is retrievable via Jmol. A comprehensive download section allows the composition of representative data sets with user defined parameters. The huge data set in combination with various search options allow a comprehensive view on all interfaces between macromolecules included in the Protein Data Bank (PDB). The download of the data sets supports numerous further investigations in macromolecular recognition. JAIL is publicly available at http://bioinformatics.charite.de/jail.
SuperSite: dictionary of metabolite and drug binding sites in proteins. Bauer RA, Günther S, Jansen D, Heeger C, Thaben PF, Preissner R. Nucleic Acids Res. 2009;37:D195-D200.
PMID: 18842629 Abstract

The increasing structural information about target-bound compounds provide a rich basis to study the binding mechanisms of metabolites and drugs. SuperSite is a database, which combines the structural information with various tools for the analysis of molecular recognition. The main data is made up of 8000 metabolites including 1300 drugs, bound to about 290,000 different receptor binding sites. The analysis tools include features, like the highlighting of evolutionary conserved receptor residues, the marking of putative binding pockets and the superpositioning of different binding sites of the same ligand. User-defined compounds can be edited or uploaded and will be superimposed with the most similar co-crystallized ligand. The user can examine all results online with the molecule viewer Jmol. An implemented search algorithm allows the screening of uploaded proteins, in order to detect potential drug binding sites, which are similar to known binding pockets. The huge data set of target-bound compounds in combination with the provided analysis tools allow to inspect the characteristics of molecular recognition, especially for drug target interactions. SuperSite is publicly available at: http://bioinformatics.charite.de/supersite.
NAIP and Ipaf control Legionella pneumophila replication in human cells. Vinzing M, Eitel J, Lippmann J, Hocke AC, Zahlten J, Slevogt H, N'guessan PD, Günther S, Schmeck B, Hippenstiel S, Flieger A, Suttorp N, Opitz B. J Immunol. 2008;180:6808-6815.
PMID: 18453601 Abstract

In mice, different alleles of the mNAIP5 (murine neuronal apoptosis inhibitory protein-5)/mBirc1e gene determine whether macrophages restrict or support intracellular replication of Legionella pneumophila, and whether a mouse is resistant or (moderately) susceptible to Legionella infection. In the resistant mice strains, the nucleotide-binding oligomerization domain (Nod)-like receptor (NLR) family member mNAIP5/mBirc1e, as well as the NLR protein mIpaf (murine ICE protease-activating factor), are involved in recognition of Legionella flagellin and in restriction of bacterial replication. Human macrophages and lung epithelial cells support L. pneumophila growth, and humans can develop severe pneumonia (Legionnaires disease) after Legionella infection. The role of human orthologs to mNAIP5/mBirc1e and mIpaf in this bacterial infection has not been elucidated. Herein we demonstrate that flagellin-deficient L. pneumophila replicate more efficiently in human THP-1 macrophages, primary monocyte-derived macrophages, and alveolar macrophages, and in A549 lung epithelial cells compared with wild-type bacteria. Additionally, we note expression of the mNAIP5 ortholog hNAIP in all cell types examined, and expression of hIpaf in human macrophages. Gene silencing of hNAIP or hIpaf in macrophages or of hNAIP in lung epithelial cells leads to an enhanced bacterial growth, and overexpression of both molecules strongly reduces Legionella replication. In contrast to experiments with wild-type L. pneumophila, hNAIP or hIpaf knock-down affects the (enhanced) replication of flagellin-deficient Legionella only marginally. In conclusion, hNAIP and hIpaf mediate innate intracellular defense against flagellated Legionella in human cells.
Hydrogen-bonding and packing features of membrane proteins: functional implications. Hildebrand PW, Günther S, Goede A, Forrest L, Frömmel C, Preissner R. Biophys J. 2008;94:1945-1953.
PMID: 17921213 Abstract

The recent structural elucidation of about one dozen channels (in which we include transporters) has provided further evidence that these membrane proteins typically undergo large movements during their function. However, it is still not well understood how these proteins achieve the necessary trade-off between stability and mobility. To identify specific structural properties of channels, we compared the helix-packing and hydrogen-bonding patterns of channels with those of membrane coils; the latter is a class of membrane proteins whose structures are expected to be more rigid. We describe in detail how in channels, helix pairs are usually arranged in packing motifs with large crossing angles (|tau| approximately 40 degrees ), where the (small) side chains point away from the packing core and the backbones of the two helices are in close contact. We found that this contributes to a significant enrichment of Calpha-H...O bonds and to a packing geometry where right-handed parallel (tau = -40 degrees +/- 10 degrees ) and antiparallel (tau = +140 degrees +/- 25 degrees ) arrangements are equally preferred. By sharp contrast, the interdigitation and hydrogen bonding of side chains in helix pairs of membrane coils results in narrowly distributed left-handed antiparallel arrangements with crossing angles tau = -160 degrees +/- 10 degrees (|tau| approximately 20 degrees ). In addition, we show that these different helix-packing modes of the two types of membrane proteins correspond to specific hydrogen-bonding patterns. In particular, in channels, three times as many of the hydrogen-bonded helix pairs are found in parallel right-handed motifs than are non-hydrogen-bonded helix pairs. Finally, we discuss how the presence of weak hydrogen bonds, water-containing cavities, and right-handed crossing angles may facilitate the required conformational flexibility between helix pairs of channels while maintaining sufficient structural stability.
SuperTarget and Matador: resources for exploring drug-target relationships. Günther S, Kuhn M, Dunkel M, Campillos M, Senger C, Petsalaki E, Ahmed J, Urdiales EG, Gewiess A, Jensen LJ, Schneider R, Skoblo R, Russell RB, Bourne PE, Bork P, Preissner R. Nucleic Acids Res. 2008;36:D919-D922.
PMID: 17942422 Abstract

The molecular basis of drug action is often not well understood. This is partly because the very abundant and diverse information generated in the past decades on drugs is hidden in millions of medical articles or textbooks. Therefore, we developed a one-stop data warehouse, SuperTarget that integrates drug-related information about medical indication areas, adverse drug effects, drug metabolization, pathways and Gene Ontology terms of the target proteins. An easy-to-use query interface enables the user to pose complex queries, for example to find drugs that target a certain pathway, interacting drugs that are metabolized by the same cytochrome P450 or drugs that target the same protein but are metabolized by different enzymes. Furthermore, we provide tools for 2D drug screening and sequence comparison of the targets. The database contains more than 2500 target proteins, which are annotated with about 7300 relations to 1500 drugs; the vast majority of entries have pointers to the respective literature source. A subset of these drugs has been annotated with additional binding information and indirect interactions and is available as a separate resource called Matador. SuperTarget and Matador are available at http://insilico.charite.de/supertarget and http://matador.embl.de.
SuperPred: drug classification and target prediction. Dunkel M, Günther S, Ahmed J, Wittig B, Preissner R. Nucleic Acids Res. 2008;36:W55-W59.
PMID: 18499712 Abstract

The drug classification scheme of the World Health Organization (WHO) [Anatomical Therapeutic Chemical (ATC)-code] connects chemical classification and therapeutic approach. It is generally accepted that compounds with similar physicochemical properties exhibit similar biological activity. If this hypothesis holds true for drugs, then the ATC-code, the putative medical indication area and potentially the medical target should be predictable on the basis of structural similarity. We have validated that the prediction of the drug class is reliable for WHO-classified drugs. The reliability of the predicted medical effects of the compounds increases with a rising number of (physico-) chemical properties similar to a drug with known function. The web-server translates a user-defined molecule into a structural fingerprint that is compared to about 6300 drugs, which are enriched by 7300 links to molecular targets of the drugs, derived through text mining followed by manual curation. Links to the affected pathways are provided. The similarity to the medical compounds is expressed by the Tanimoto coefficient that gives the structural similarity of two compounds. A similarity score higher than 0.85 results in correct ATC prediction for 81\% of all cases. As the biological effect is well predictable, if the structural similarity is sufficient, the web-server allows prognoses about the medical indication area of novel compounds and to find new leads for known targets. Availability: the system is freely accessible at http://bioinformatics.charite.de/superpred. SuperPred can be obtained via a Creative Commons Attribution Noncommercial-Share Alike 3.0 License.
Superhaptens and their potential role in contact dermatitis. Günther S, Weiser AA, Ahmed J, Preissner R. Drug Discovery Today: Therapeutic Strategies. 2007;4:11-17.
Abstract

Allergic contact dermatitis occurs with increasing incidence and is a common environmental health problem. The undesirable immune response is triggered by small molecules denoted as haptens. Known haptens are synthetic or natural compounds that are present in everyday items like cosmetics or textiles. Certain compounds ([`]superhaptens') are of particular importance because of their outstanding immunogenic potential. In this article, the processes underlying such hypersensitivities are summarized and therapeutic options will be discussed.
Cellular Fingerprints: A Novel Concept for the Integration of Experimental Data and Compound-Target-Pathway Relations. Günther S, Neumann S, Ahmed J, Preissner R. LNBI. 2007;4643:167-70.
Docking without docking: ISEARCH--prediction of interactions using known interfaces. Günther S, May P, Hoppe A, Frömmel C, Preissner R. Proteins. 2007;69:839-844.
PMID: 17803236 Abstract

The increasing number of solved protein structures provides a solid number of interfaces, if protein-protein interactions, domain-domain contacts, and contacts between biological units are taken into account. An interface library gives us the opportunity to identify surface regions on a target molecule that are similar by local structure and residue composition. If both unbound components of a possible protein complex exhibit structural similarities to a known interface, the unbound structures can be superposed onto the known interfaces. The approach is accompanied by two mathematical problems. Protein surfaces have to be quickly screened by thousands of patches, and similarity has to be evaluated by a suitable scoring scheme. The used algorithm (NeedleHaystack) identifies similar patches within minutes. Structurally related sites are recognized even if only parts of the template patches are structurally related to the interface region. A successful prediction of the protein complex depends on a suitable template of the library. However, the performed tests indicate that interaction sites are identified even if the similarity is very low. The approach complements existing ab initio methods and provides valuable results on standard benchmark sets.
SuperHapten: a comprehensive database for small immunogenic compounds. Günther S, Hempel D, Dunkel M, Rother K, Preissner R. Nucleic Acids Res. 2007;35:D906-D910.
PMID: 17090587 Abstract

The immune system protects organisms from foreign proteins, peptide epitopes and a multitude of chemical compounds. Among these, haptens are small molecules, eliciting an immune response when conjugated with carrier molecules. Known haptens are xenobiotics or natural compounds, which can induce a number of autoimmune diseases like contact dermatitis or asthma. Furthermore, haptens are utilized in the development of biosensors, immunomodulators and new vaccines. Although hapten-induced allergies account for 6-10\% of all adverse drug effects, the understanding of the correlation between structural and haptenic properties is rather fragmentary. We have developed a manually curated hapten database, SuperHapten, integrating information from literature and web resources. The current version of the database compiles 2D/3D structures, physicochemical properties and references for about 7500 haptens and 25,000 synonyms. The commercial availability is documented for about 6300 haptens and 450 related antibodies, enabling experimental approaches on cross-reactivity. The haptens are classified regarding their origin: pesticides, herbicides, insecticides, drugs, natural compounds, etc. Queries allow identification of haptens and associated antibodies according to functional class, carrier protein, chemical scaffold, composition or structural similarity. SuperHapten is available online at http://bioinformatics.charite.de/superhapten.
A structural genomics approach to the regulation of apoptosis: chimp vs. human. Ahmed J, Günther S, Möller F, Preissner R. Genome Inform. 2007;18:22-34.
PMID: 18546471 Abstract

After the sequencing of the human genome, the publication of the genome of our nearest relative, the chimpanzee (Pan troglodytes) provided groundbreaking data improving the understanding of the recent human evolution. There are about forty million changes, most of them single nucleotide substitutions, which teach us about ourselves, both in terms of similarities and differences with chimpanzees. From a medical point of view differences in incidence and severity of diseases are of special importance to pinpoint novel targets and to develop innovative therapies. This analysis focuses on the cognition that chimpanzees rarely suffer from cancer. To elucidate possible reasons for this finding, we compare differences regarding apoptosis and DNA-repair on different levels of chromosome organization, gene structure, post-transcriptional and post-translational modifications to functional changes in protein structures. The result is a complex pattern of subtle variances and a few large-scale changes.
Legionella pneumophila induces IFNbeta in lung epithelial cells via IPS-1 and IRF3, which also control bacterial replication. Opitz B, Vinzing M, Laak Vv, Schmeck B, Heine G, Günther S, Preissner R, Slevogt H, N'Guessan PD, Eitel J, Goldmann T, Flieger A, Suttorp N, Hippenstiel S. J Biol Chem. 2006;281:36173-36179.
PMID: 16984921 Abstract

Legionella pneumophila, a Gram-negative facultative intracellular bacterium, causes severe pneumonia (Legionnaires' disease). Type I interferons (IFNs) were so far associated with antiviral immunity, but recent studies also indicated a role of these cytokines in immune responses against (intracellular) bacteria. Here we show that wild-type L. pneumophila and flagellin-deficient Legionella, but not L. pneumophila lacking a functional type IV secretion system Dot/Icm, or heat-inactivated Legionella induced IFNbeta expression in human lung epithelial cells. We found that factor (IRF)-3 and NF-kappaB-p65 translocated into the nucleus and bound to the IFNbeta gene enhancer after L. pneumophila infection of lung epithelial cells. RNA interference demonstrated that in addition to IRF3, the caspase recruitment domain (CARD)-containing adapter molecule IPS-1 (interferon-beta promoter stimulator 1) is crucial for L. pneumophila-induced IFNbeta expression, whereas other CARD-possessing molecules, such as RIG-I (retinoic acid-inducible protein I), MDA5 (melanoma differentiation-associated gene 5), Nod27 (nucleotide-binding oligomerization domain protein 27), and ASC (apoptosis-associated speck-like protein containing a CARD) seemed not to be involved. Finally, bacterial multiplication assays in small interfering RNA-treated cells indicated that IPS-1, IRF3, and IFNbeta were essential for the control of intracellular replication of L. pneumophila in lung epithelial cells. In conclusion, we demonstrated a critical role of IPS-1, IRF3, and IFNbeta in Legionella infection of lung epithelium.
Representation of target-bound drugs by computed conformers: implications for conformational libraries. Günther S, Senger C, Michalsky E, Goede A, Preissner R. BMC Bioinformatics. 2006;7:293.
PMID: 16764718 Abstract

BACKGROUND: The increasing number of known protein structures provides valuable information about pharmaceutical targets. Drug binding sites are identifiable and suitable lead compounds can be proposed. The flexibility of ligands is a critical point for the selection of potential drugs. Since computed 3D structures of millions of compounds are available, the knowledge of their binding conformations would be a great benefit for the development of efficient screening methods. RESULTS: Integration of two public databases allowed superposition of conformers for 193 approved drugs with 5507 crystallised target-bound counterparts. The generation of 9600 drug conformers using an atomic force field was carried out to obtain an optimal coverage of the conformational space. Bioactive conformations are best described by a conformational ensemble: half of all drugs exhibit multiple active states, distributed over the entire range of the reachable energy and conformational space.A number of up to 100 conformers per drug enabled us to reproduce the bound states within a similarity threshold of 1.0 angstroms in 70\% of all cases. This fraction rises to about 90\% for smaller or average sized drugs. CONCLUSION: Single drugs adopt multiple bioactive conformations if they interact with different target proteins. Due to the structural diversity of binding sites they adopt conformations that are distributed over a broad conformational space and wide energy range. Since the majority of drugs is well represented by a predefined low number of conformers (up to 100) this procedure is a valuable method to compare compounds by three-dimensional features or for fast similarity searches starting with pharmacophores. The underlying 9600 generated drug conformers are downloadable from the Super Drug Web site 1. All superpositions are visualised at the same source. Additional conformers (110,000) of 2400 classified WHO-drugs are also available.
Molecular flexibility in protein-DNA interactions. Günther S, Rother K, Frömmel C. Biosystems. 2006;85:126-136.
PMID: 16488073 Abstract

In living cells protein-DNA interactions are fundamental processes. Here, we compare the 3D structures of several DNA-binding proteins frequently determined with and without attached DNA. We studied the global structure (backbone-traces) as well as the local structure (binding sites) by comparing pair-wise the related atoms. The DNA-interaction sites of uncomplexed proteins show conspicuously high local structural flexibility. Binding to DNA results in specific local conformations, which are clearly distinct from the unbound states. The adaptation of the protein's binding site to DNA can never be described by the lock and key model but in all cases by the induced fit model. Conformational changes in the seven protein backbone traces take place in different ways. Two of them dock onto DNA without a significant change, while the other five proteins are characterized by a backbone conformation change caused by DNA docking. In the case of three proteins of the latter group the DNA-complexed conformation also occurs in a few uncomplexed structures. This behavior can be described by a conformational ensemble, which is narrowed down by DNA docking until only one single DNA-complexed conformation occurs. Different docking models are discussed and each of the seven proteins is assigned to one of them.
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