Computational model predicts protein binding sites of a luminescent ligand equipped with guanidiniocarbonyl-pyrrole groups

• Neda Rafieiolhosseini,
• Matthias Killa,
• Thorben Neumann,
• Niklas Tötsch,
• Jean-Noël Grad,
• Alexander Höing,
• Thies Dirksmeyer,
• Jochen Niemeyer,
• Christian Ottmann,
• Shirley K. Knauer,
• Michael Giese,
• Jens Voskuhl and
• Daniel Hoffmann

Beilstein J. Org. Chem. 2022, 18, 1322–1331, doi:10.3762/bjoc.18.137

• distances are in 0.1 nm. Supporting Information Supporting Information File 254: General information and instrumentation, cluster analysis, electrostatic potential surface of 14-3-3ζ, total energy of a simulation. Supporting Information File 255: PDB2PQR output for lysine. Supporting Information File 256

Identification of the new prenyltransferase Ubi-297 from marine bacteria and elucidation of its substrate specificity

• Jamshid Amiri Moghaddam,
• Huijuan Guo,
• Karsten Willing,
• Thomas Wichard and
• Christine Beemelmanns

Beilstein J. Org. Chem. 2022, 18, 722–731, doi:10.3762/bjoc.18.72

• the PATRIC database (3.6.12) [34]. The sequence clustering was generated by the CLANS (CLuster ANalysis of Sequences) program [35]. In brief, the relationships between sequences were assessed based on an all-against-all BLAST search and the E-values better (lower) than 1.0E−6 were used to connect each

Comparative ligand structural analytics illustrated on variably glycosylated MUC1 antigen–antibody binding

• Christopher B. Barnett,
• Tharindu Senapathi and
• Kevin J. Naidoo

Beilstein J. Org. Chem. 2020, 16, 2540–2550, doi:10.3762/bjoc.16.206

• solution and bound to antibody) were also measured. A standard hydrogen-bonding analysis using MDAnalysis and VMD was carried out with the default angle cut-off and distance cut-off. A cluster analysis of the peptide portion of the antigen was carried out (Figure 5) using TTClust [42]. The clusters were

• , there is a preference for (70°, 100°) with limited sampling observed in the negative regions of the ψ distribution. On binding, this preference is limited and changes slightly to (70°, 120°) with no sampling observed in the negative regions of the φ distribution. Cluster analysis A cluster analysis of

• in Figure 5C) as noted in previous analysis. A cluster analysis of the bound antigens yields 5 clusters for the antigen and 4 clusters for the Tn-antigen (Figure 5D and E). The predominant conformer in both antigens is similar (Figure 5F), as noted in previous analysis. For the antigen, the first

Synthesis and conformational preferences of short analogues of antifreeze glycopeptides (AFGP)

• Małgorzata Urbańczyk,
• Michał Jewgiński,
• Joanna Krzciuk-Gula,
• Jerzy Góra,
• Rafał Latajka and
• Norbert Sewald

Beilstein J. Org. Chem. 2019, 15, 1581–1591, doi:10.3762/bjoc.15.162

• conformation [36][37]. In case of pentapeptide 4 the calculation resulted in 1 000 conformers. Cluster analysis based on all backbone dihedral angles allowed to identify multiclusters, containing approximately 1% of structures each. However, the clustering based only on the part of the main chain led to higher

New terpenoids from the fermentation broth of the edible mushroom Cyclocybe aegerita

• Frank Surup,
• Florian Hennicke,
• Nadine Sella,
• Maria Stroot,
• Steffen Bernecker,
• Sebastian Pfütze,
• Marc Stadler and
• Martin Rühl

Beilstein J. Org. Chem. 2019, 15, 1000–1007, doi:10.3762/bjoc.15.98

• clusters. Keywords: bioinformatics; gene cluster analysis; natural products; secondary metabolites; structure elucidation; terpenes; Introduction The basidiomycete Agrocybe aegerita (synonym: A. cylindracea) was traditionally accommodated in the genus Agrocybe (family Bolbitiaceae) until a recent

Biosynthesis of oxygen and nitrogen-containing heterocycles in polyketides

• Franziska Hemmerling and
• Frank Hahn

Beilstein J. Org. Chem. 2016, 12, 1512–1550, doi:10.3762/bjoc.12.148

• formation of up to two new stereocentres. Its appearance in several polyketide biosynthetic pathways was proposed for a decade based on gene cluster analysis. An in vitro characterisation of responsible catalytic units has however only recently been achieved. Two pyran-forming cyclase domains were

• salinosporamide A (199) (Scheme 27) [160][161]. Based on gene cluster analysis, it was proposed that both heterocycles of this PKS–NRPS hybrid product, an oxetan-2-one and a pyrrolidin-2-one, are formed by a bicyclisation mechanism. Aldol addition of the amino acid α-position on the carbonyl gives the pyrrolidin

• available from the gene cluster analysis of the O-methylated, highly substituted α-pyridinone piericidin A1 (221) from Streptomyces piomogeues var. Hangzhouwanensis (Scheme 30b) [165][166]. Apart from the genes that code for a modular type I PKS as well as O-methyltransferases and an oxygenase, the cluster

Natural products from microbes associated with insects

• Christine Beemelmanns,
• Huijuan Guo,
• Maja Rischer and
• Michael Poulsen

Beilstein J. Org. Chem. 2016, 12, 314–327, doi:10.3762/bjoc.12.34

• cluster analysis also revealed that pederin is formed by an enzyme belonging to a functionally and evolutionarily novel group termed trans-acyltransferase PKSs (trans-AT PKSs) [24][52]. The structurally related compound diaphorin (4) was later found in a study of the defensive symbiosis between the Asian

A small azide-modified thiazole-based reporter molecule for fluorescence and mass spectrometric detection

• Stefanie Wolfram,
• Hendryk Würfel,
• Stefanie H. Habenicht,
• Christine Lembke,
• Phillipp Richter,
• Eckhard Birckner,
• Rainer Beckert and
• Georg Pohnert

Beilstein J. Org. Chem. 2014, 10, 2470–2479, doi:10.3762/bjoc.10.258

• molecules. These specific isotopic patterns also enable data processing by cluster analysis [19] or other algorithms for an automated structure mining [24][25]. Here we introduce the rational design, synthesis and application of a small thiazole-based, azide-tagged reporter molecule that supports

• allows the application of cluster analysis [19] or other software [38] as computational tools to identify probe-reactive analytes out of complex mixtures even of unknown mass. Visualization of proteins by in-gel fluorescence detection In a model reaction we tested the suitability of BPT (1) and the other

Synthesis of complex intermediates for the study of a dehydratase from borrelidin biosynthesis

• Frank Hahn,
• Nadine Kandziora,
• Steffen Friedrich and
• Peter F. Leadlay

Beilstein J. Org. Chem. 2014, 10, 634–640, doi:10.3762/bjoc.10.55

• biosynthesis, we became interested in the formation of the (12Z,14E)-diene [7]. Z-configured double bonds are much rarer in polyketides than their E-configured counterparts, and their biosynthesis has not been thoroughly investigated yet [7][8][9]. Gene cluster analysis suggested that the double bond at

Similarity analysis, synthesis, and bioassay of antibacterial cyclic peptidomimetics

• Workalemahu M. Berhanu,
• Mohamed A. Ibrahim,
• Girinath G. Pillai,
• Alexander A. Oliferenko,
• Levan Khelashvili,
• Farukh Jabeen,
• Bushra Mirza,
• Farzana Latif Ansari,
• Ihsan ul-Haq,
• Said A. El-Feky and
• Alan R. Katritzky

Beilstein J. Org. Chem. 2012, 8, 1146–1160, doi:10.3762/bjoc.8.128

• studied in order to identify new promising cyclic scaffolds. A large descriptor space coupled with cluster analysis was employed to digitize known antibacterial structures and to gauge the potential of new peptidomimetic macrocycles, which were conveniently synthesized by acylbenzotriazole methodology

• . Some of the synthesized compounds were tested against an array of microorganisms and showed antibacterial activity against Bordetella bronchistepica, Micrococcus luteus, and Salmonella typhimurium. Keywords: antibacterial; cluster analysis; N-acylbenzotriazoles; peptidomimetics; similarity

• generated, which served as an input for the cluster-analysis module in STATISTICA software. The use of descriptors in this study can give differing clustering patterns [50]. The first step in the structure clustering is the generation of a matrix containing similarity values of descriptors for all pairs of