Revaluation of biomass-derived furfuryl alcohol derivatives for the synthesis of carbocyclic nucleoside phosphonate analogues

• Bemba Sidi Mohamed,
• Christian Périgaud and
• Christophe Mathé

Beilstein J. Org. Chem. 2017, 13, 251–256, doi:10.3762/bjoc.13.28

• (+/−)-16 and (+/−)-21 have structural similarity with carbonucleosides belonging to the neplanocin family, in particular, with neplanocin F [13]. Compounds (+/−)-26 and (+/−)-27 Based on the observation that carbocyclic methylphosphonates derived from the Mitsunobu coupling reaction are sensitive to

• transposition giving rise to carbocyclic nucleoside phosphonates having structural similarity with carbonucleosides belonging to the neplanocin family. All the newly synthesized compounds were evaluated for their antiviral properties against HIV-1, Zika virus, Dengue-2 virus, HSV-1, HSV-2 and Chikungunya virus

Dynamics and interactions of ibuprofen in cyclodextrin nanosponges by solid-state NMR spectroscopy

• Monica Ferro,
• Franca Castiglione,
• Nadia Pastori,
• Carlo Punta,
• Lucio Melone,
• Walter Panzeri,
• Barbara Rossi,
• Francesco Trotta and
• Andrea Mele

Beilstein J. Org. Chem. 2017, 13, 182–194, doi:10.3762/bjoc.13.21

• and line-width, may fail to provide an acceptable characterization due to high structural similarity at molecular level. Finally yet importantly, in the present work we also report on solid state 1H NMR spectra of the examined compounds acquired under fast magic angle spinning (Fast MAS) conditions

Biochemical and structural characterisation of the second oxidative crosslinking step during the biosynthesis of the glycopeptide antibiotic A47934

• Veronika Ulrich,
• Clara Brieke and
• Max J. Cryle

Beilstein J. Org. Chem. 2016, 12, 2849–2864, doi:10.3762/bjoc.12.284

• highest structural similarity to the natural substrate and the fact that StaF activity on Tei7-L-Hpg7 was obtained only with PCP-X constructs exhibiting the A47934 X-domain indicates that StaF is dependent on the corresponding X-domain from its own NRPS when using teicoplanin-like peptides. Comparison of

• of under 2.0 Å (Table 3). Other P450 enzymes with high structural similarity to StaF are those from secondary metabolism and involve oxidative functionalisation of large substrates, such as pravastatin (CYP105AS, PDB ID: 4OQS) [42], oleandomycin (OleP, PDB ID: 4XE3) [43], mycinamicin (MycG, PDB ID

• : 2YCA) [44] and filipin (CYP105P1, PDB ID: 3E5L) [45] (Table 3). StaF also shows moderate levels of structural similarity to other P450s that oxidise carrier protein-bound substrates, including the fattyacyl-ACP oxidase P450BioI (PDB ID: 3EJD) [46][47][48] and the aminoacyl-PCP hydroxylases OxyD (PDB ID

Characterization of the synthetic cannabinoid MDMB-CHMCZCA

• Carina Weber,
• Stefan Pusch,
• Dieter Schollmeyer,
• Sascha Münster-Müller,
• Michael Pütz and
• Till Opatz

Beilstein J. Org. Chem. 2016, 12, 2808–2815, doi:10.3762/bjoc.12.279

• TD-DFT; however, the experimental positive/negative sequence is inverted in the range from 200 to 230 nm. Overall, this yields an enantiomeric similarity index (ESI) [16] of only 34% in favor of the S-enantiomer, therefore not enabling a reliable assignment of the absolute configuration. The

Identification, synthesis and mass spectrometry of a macrolide from the African reed frog Hyperolius cinnamomeoventris

• Markus Menke,
• Pardha Saradhi Peram,
• Iris Starnberger,
• Walter Hödl,
• Gregory F.M. Jongsma,
• David C. Blackburn,
• Mark-Oliver Rödel,
• Miguel Vences and
• Stefan Schulz

Beilstein J. Org. Chem. 2016, 12, 2731–2738, doi:10.3762/bjoc.12.269

• respective pheromones [11][13]. Microhydrogenation of the frog extract furnished 13-tetradecanolide, thus confirming compound A to be a 13-tetradecenolide. The double bond position in this macrolide likely is at C-5, because of the similarity of the mass spectrum to that of the beetle macrolide. Nevertheless

Computational methods in drug discovery

• Sumudu P. Leelananda and
• Steffen Lindert

Beilstein J. Org. Chem. 2016, 12, 2694–2718, doi:10.3762/bjoc.12.267

• where the three-dimensional structures are known [35]. NCBI Basic Local Alignment Search Tool (BLAST) is one of the most popular bioinformatics sequence alignment tools used with sequence similarity searches [36]. Once a homologous protein structure for the sequence has been identified, building the

• % identity to a protein of a known three-dimensional structure. When the sequence similarity drops below 30%, homology modeling is not reliable enough for structure prediction [26]. Success of homology modeling is well documented and has been continuously shown in CASP (Critical Assessment of protein

• [147]. Measuring RMSD (root mean square deviation) is the most common way to compare the structural similarity between two superimposed structures. RMSD is given by: where n is the number of atom pairs and dx is the distance between the two atoms in the xth atom pair. However, it is important to note

Synthesis of polyhydroxylated decalins via two consecutive one-pot reactions: 1,4-addition/aldol reaction followed by RCM/syn-dihydroxylation

• Michał Malik and
• Sławomir Jarosz

Beilstein J. Org. Chem. 2016, 12, 2602–2608, doi:10.3762/bjoc.12.255

• to their similarity to carbohydrates, these compounds often possess interesting biological properties, e.g., they may act as glycosidase inhibitors [2][3][4]. One of such compounds, acarbose [5][6][7], found an application as a drug and is marketed worldwide. Five- and six-membered cyclitols are a

Enzymatic synthesis and phosphorolysis of 4(2)-thioxo- and 6(5)-azapyrimidine nucleosides by E. coli nucleoside phosphorylases

• Vladimir A. Stepchenko,
• Anatoly I. Miroshnikov,
• Frank Seela and
• Igor A. Mikhailopulo

Beilstein J. Org. Chem. 2016, 12, 2588–2601, doi:10.3762/bjoc.12.254

• and significantly slower than 4SUd, but comes to the similar ratio of the starting substrate and thymine formed after 10 h (Figure 1). On the contrary, (i) the close similarity of substrate activity of Ud and Td towards TP was observed, and (ii) the TP catalyzed phosphorolysis of 4-thiothymidine (11a

• E. coli UP. Under similar reaction conditions, 4-thiouracil revealed no substrate activity against E. coli TP suggesting the various types of the substrate binding and activation at E. coli UP and TP catalytic sites in spite of the some similarity of the interaction of the respective side-chains of

Effects of solvent additive on “s-shaped” curves in solution-processed small molecule solar cells

• John A. Love,
• Shu-Hua Chou,
• Ye Huang,
• Guilllermo C. Bazan and
• Thuc-Quyen Nguyen

Beilstein J. Org. Chem. 2016, 12, 2543–2555, doi:10.3762/bjoc.12.249

• voltage and spectral coverage. Despite the structural similarity to previously reported materials, however, blends of p-SIDT(FBTThCA8)2 and PC71BM did not have device performance akin to its predecessors when processed in the same manner. Specifically, when cast from chlorobenzene, the resulting J–V curve

Protonated paramagnetic redox forms of di-o-quinone bridged with p-phenylene-extended TTF: A EPR spectroscopy study

• Nikolay O. Chalkov,
• Vladimir K. Cherkasov,
• Gleb A. Abakumov,
• Andrey G. Starikov and
• Viacheslav A. Kuropatov

Beilstein J. Org. Chem. 2016, 12, 2450–2456, doi:10.3762/bjoc.12.238

• with a hydrogen atom localized at the semiquinone coordination site. The attribution of hyperfine coupling constants with specific protons was made according to data from DFT calculations. The similarity of characters of spin-density distribution in the corresponding mono- and trireduced species is an

A new paradigm for designing ring construction strategies for green organic synthesis: implications for the discovery of multicomponent reactions to build molecules containing a single ring

• John Andraos

Beilstein J. Org. Chem. 2016, 12, 2420–2442, doi:10.3762/bjoc.12.236

• greenness. In research practice, synthetic organic chemists rely on a combination of retrosynthetic analysis [91][92][93][94][95][96][97], similarity and analogy patterning to known reactions, bond dissociation energy and bond polarity analysis (forward and umpolung), chemical intuition, and random

• implementation relies entirely on knowledge of known transformations. Similarity and analogy patterning is limited to known reactions as starting points. Serendipity is purely based on accidental occurrences, which are rare, but can be capitalized to advantage by astute researchers. Reliance on all of these

• highlighting a particular 3- or other partition, rather than just inputting the structure itself. A similarity search would be conducted based on inputted target bond dissection maps already encoded in the database. Essentially each literature citation currently in any search engine, which reports syntheses of

Efficient mechanochemical synthesis of regioselective persubstituted cyclodextrins

• Laszlo Jicsinszky,
• Marina Caporaso,
• Katia Martina,
• Emanuela Calcio Gaudino and
• Giancarlo Cravotto

Beilstein J. Org. Chem. 2016, 12, 2364–2371, doi:10.3762/bjoc.12.230

• or biological preparations – its physicochemical properties are very similar to those of the perazido derivatives, making separation impossible. The similarity is even higher after the azide’s conversion to an amine. Solvent removal in the synthesis of per-6-azido-CDs is generally also challenging

Robust C–C bonded porous networks with chemically designed functionalities for improved CO₂ capture from flue gas

• Damien Thirion,
• Joo S. Lee,
• Ercan Özdemir and
• Cafer T. Yavuz

Beilstein J. Org. Chem. 2016, 12, 2274–2279, doi:10.3762/bjoc.12.220

• , explaining the leftover carbonyl units. COP-157 shows similar results due to the chemical similarity of the structures and the reaction conditions (Supporting Information File 1, Figure S1 and Table S2). After post-modification, the nitrile stretching becomes very weak in both COP-156-amine and COP-156

The direct oxidative diene cyclization and related reactions in natural product synthesis

• Juliane Adrian,
• Leona J. Gross and
• Christian B. W. Stark

Beilstein J. Org. Chem. 2016, 12, 2104–2123, doi:10.3762/bjoc.12.200

• structural similarity with teurilene and glabrescol, but other than the latter two, eurylene (87) is neither CS- nor C2-symmetric (Scheme 18). It has been isolated from the wood of Eurycoma longifolia by Itokawa et al. in 1991 [152] and was shown to exhibit cytotoxic properties against lymphocytic leukemia

Dinuclear thiazolylidene copper complex as highly active catalyst for azid–alkyne cycloadditions

• Anne L. Schöffler,
• Ata Makarem,
• Frank Rominger and
• Bernd F. Straub

Beilstein J. Org. Chem. 2016, 12, 1566–1572, doi:10.3762/bjoc.12.151

• characterized in our group [40]. The similarity of NMR-spectroscopic data of the 1,2,4-triazol-5-ylidene and the 1,3-thiazol-2-ylidene dicopper complex indicate that the complexes of both NHC ligand types consist of a bis-NHC ligand, two copper(I) ions and a labile acetate ligand that bridges the metal centers

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

• kijanimicin. All these genes are remarkably small in size (vstJ for example codes for only 142 amino acids) and have no significant sequence similarity to other characterised proteins [146][147]. The homologous qmnH from quartromicin D1 (151) biosynthesis contains two tandem-vstJ sequences in agreement with

• dehydrative aromatisation. ACSs show high similarity on the amino acid level to other type III PKS systems like chalcone synthases and benzalacetone synthases, but their strict substrate specificity for nitrogen-containing starter units avoids mispriming with precursors of the latter group of enzymes [172

Cyclisation mechanisms in the biosynthesis of ribosomally synthesised and post-translationally modified peptides

• Andrew W. Truman

Beilstein J. Org. Chem. 2016, 12, 1250–1268, doi:10.3762/bjoc.12.120

• the acid side chains are activated as carboxylate-phosphate mixed anhydrides, which are then attacked by serine or threonine to release phosphate. The sequence similarity between the ligases in the microviridin pathway points towards an equivalent mechanism for lactam formation, although this has not

• to show that one of its domains (PatGmac) possesses similarity to subtilisin-like peptidases [104][107]; accordingly, this catalyses macrocyclisation via a serine protease-like mechanism. PatG features a canonical serine protease-like catalytic triad (Asp548, His618 and Ser783), which cuts before an

• producing a cyclic octapeptide. A serine protease-like cyclase (PCY1) is also found in the biosynthesis of Caryophyllaceae-type cyclic peptides in Saponaria vaccaria [109]. This cyclase functions in an analogous way to PatG, although PCY1 has structural similarity to S9a family serine peptidases, whereas

Unusual traits of cis and trans-2,3-dibromo-1,1-dimethylindane on the way from 1,1-dimethylindene to 2-bromo-, 3-bromo-, and 2,3-dibromo-1,1-dimethylindene

• Rudolf Knorr,
• David S. Stephenson,
• Ernst Lattke,
• Petra Böhrer and
• Jakob Ruhdorfer

Beilstein J. Org. Chem. 2016, 12, 1178–1184, doi:10.3762/bjoc.12.113

• from cis-1 became evident through the similarity of the emerging 3/4 ratios as compared with the trans-1/cis-1 ratios in the employed mixtures [11]. This regiospecificity is readily understandable since trans-1 has no anti relationship of vicinal Br and H available (Scheme 1), whereas each cis-1

Chiral cyclopentadienylruthenium sulfoxide catalysts for asymmetric redox bicycloisomerization

• Barry M. Trost,
• Michael C. Ryan and
• Meera Rao

Beilstein J. Org. Chem. 2016, 12, 1136–1152, doi:10.3762/bjoc.12.110

• propargyl alcohol. With a convenient route towards these enyne substrates in hand, we set our sights on optimizing the asymmetric enyne bicycloisomerization reaction. Initial experiments and reaction optimization Due to the similarity of 14 to the triple-uptake inhibitor GSK1360707 (see Scheme 2), we

Antibacterial structure–activity relationship studies of several tricyclic sulfur-containing flavonoids

• Lucian G. Bahrin,
• Henning Hopf,
• Peter G. Jones,
• Laura G. Sarbu,
• Cornelia Babii,
• Alina C. Mihai,
• Marius Stefan and
• Lucian M. Birsa

Beilstein J. Org. Chem. 2016, 12, 1065–1071, doi:10.3762/bjoc.12.100

• the X-ray section below. X-ray analyses The crystal structures of flavanones 4d and 4f are presented in Figure 3. We found that compounds of general structure 4, despite their close chemical similarity, display conformational differences, especially regarding the ethyl groups. Relevant torsion angles

The synthesis of functionalized bridged polycycles via C–H bond insertion

• Jiun-Le Shih,
• Po-An Chen and
• Jeremy A. May

Beilstein J. Org. Chem. 2016, 12, 985–999, doi:10.3762/bjoc.12.97

• two non-equivalent methylenes available for insertion, suggesting that the barriers for insertion into the 3 position from conformation 76 was similar to that for the 4 position from conformation 77 (Scheme 19). This similarity in rates makes the substrate 73 suitable as a test case to find a catalyst

Muraymycin nucleoside-peptide antibiotics: uridine-derived natural products as lead structures for the development of novel antibacterial agents

• Daniel Wiegmann,
• Stefan Koppermann,
• Marius Wirth,
• Giuliana Niro,
• Kristin Leyerer and
• Christian Ducho

Beilstein J. Org. Chem. 2016, 12, 769–795, doi:10.3762/bjoc.12.77

Antibiotics from predatory bacteria

• Juliane Korp,
• María S. Vela Gurovic and
• Markus Nett

Beilstein J. Org. Chem. 2016, 12, 594–607, doi:10.3762/bjoc.12.58

• , the enzymatic products of which exhibited high sequence similarity to proteins that are responsible for the biosynthesis of tuberculosinol and isotuberculosinol in Mycobacterium tuberculosis [128]. Following in vitro studies of the two Herpetosiphon enzymes as well as a reconstitution of the entire

Biosynthesis of α-pyrones

• Till F. Schäberle

Beilstein J. Org. Chem. 2016, 12, 571–588, doi:10.3762/bjoc.12.56

• cysteine as a result of substrate incubation prior to crystallization. This was only possible with a very short substrate mimic which renders more similarity to the eastern chain. Using the longer western chain mimic no suitable crystals for structure determination could be produced (neither for CorB, nor

Interactions between 4-thiothymidine and water-soluble cyclodextrins: Evidence for supramolecular structures in aqueous solutions

• Vito Rizzi,
• Sergio Matera,
• Paola Semeraro,
• Paola Fini and
• Pinalysa Cosma

Beilstein J. Org. Chem. 2016, 12, 549–563, doi:10.3762/bjoc.12.54

• glance, regardless of the structural similarity with thymidine, S4TdR (Figure 1) shows a different ultraviolet absorption spectrum. The UV–vis absorption spectrum of 1 × 10−5 M aqueous solution of S4TdR, was acquired and is reported in Figure 2 (black lines). Subsequently, a comparison in presence of CDs