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

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

• 2.4.2.4) phosphorylases [36], and (ii) the role of structural features and electronic properties of the pyrimidine bases and nucleosides in the recognition by E. coli nucleoside phosphorylases. Results and Discussion Thioxo- and 6-aza-pyrimidines used in the transglycosylation reaction with recombinant E

• -deoxyribosides. Unexpectedly, 2-thiouridine (9) showed weak activity for PNP whereas 2-thiothymidine (11b) entirely was lacking such an activity. It is conceivable that in the case of such unusual substrates of PNP as pyrimidine nucleosides their structural features define the substrate properties, viz., 2

Synthesis, dynamic NMR characterization and XRD studies of novel N,N’-substituted piperazines for bioorthogonal labeling

• Constantin Mamat,
• Marc Pretze,
• Matthew Gott and
• Martin Köckerling

Beilstein J. Org. Chem. 2016, 12, 2478–2489, doi:10.3762/bjoc.12.242

• superimposed figure of the two conformers, where C1, the phenyl ring and F1 of both conformers are fitted on top of each other. The different structural arrangement of both conformers is clearly visible. Similar structural features are observed for 3a. The N1–C1 atom distance is again much shorter, 1.346(2) Å

Construction of bis-, tris- and tetrahydrazones by addition of azoalkenes to amines and ammonia

• Artem N. Semakin,
• Aleksandr O. Kokuev,
• Yulia V. Nelyubina,
• Alexey Yu. Sukhorukov,
• Petr A. Zhmurov,
• Sema L. Ioffe and
• Vladimir A. Tartakovsky

Beilstein J. Org. Chem. 2016, 12, 2471–2477, doi:10.3762/bjoc.12.241

• modulation of the molecular geometry, for example through coordination with metal cations, hydrogen bond formation or irradiation. These unique structural features of the hydrazone fragment have been successfully exploited in the design of various molecular switches, fluorophores and machines. Bis- and

New furoisocoumarins and isocoumarins from the mangrove endophytic fungus Aspergillus sp. 085242

• Ze’en Xiao,
• Senhua Chen,
• Runlin Cai,
• Shao’e Lin,
• Kui Hong and
• Zhigang She

Beilstein J. Org. Chem. 2016, 12, 2077–2085, doi:10.3762/bjoc.12.196

• , respectively. In addition, compounds 1 and 3 exhibited weak radical scavenging activity with EC50 values of 125 and 138 μM, respectively. Keywords: α-glucosidase; Aspergillus; DPPH·; furoisocoumarin; isocoumarin; Introduction Isocoumarins are an important group of natural products with diverse structural

• features and interesting biological activities. They have been widely isolated from fungi, lichens, bacteria, plants, and insects [1][2]. Furoisocoumarins combining a furan ring and an isocoumarin moiety are divided into two subclasses depending on their fusion type: linear furo[2,3-g]isocoumarins and

Synthesis of the C8’-epimeric thymine pyranosyl amino acid core of amipurimycin

• Pramod R. Markad,
• Navanath Kumbhar and
• Dilip D. Dhavale

Beilstein J. Org. Chem. 2016, 12, 1765–1771, doi:10.3762/bjoc.12.165

• ; carbohydrate; peptidyl nucleosides; Introduction Peptidyl nucleoside antibiotics are a class of complex molecules that encompass an extensive array of natural products [1]. The notable structural features of peptidyl nucleosides are responsible for their miscellaneous biological activities such as antitumor

Synthesis and characterization of benzodithiophene and benzotriazole-based polymers for photovoltaic applications

• Desta Gedefaw,
• Marta Tessarolo,
• Margherita Bolognesi,
• Mario Prosa,
• Renee Kroon,
• Wenliu Zhuang,
• Patrik Henriksson,
• Kim Bini,
• Ergang Wang,
• Michele Muccini,
• Mirko Seri and
• Mats R. Andersson

Beilstein J. Org. Chem. 2016, 12, 1629–1637, doi:10.3762/bjoc.12.160

• donor:acceptor intermixing combined with finely ordered and aggregated polymeric domains, in perfect agreement with the improved photovoltaic performance. This better self-organization of the PTzBDT-2:PC61BM blend seems in contrast with the intrinsic structural features of the polymer, where the double alkyl

Total synthesis of leopolic acid A, a natural 2,3-pyrrolidinedione with antimicrobial activity

• Atul A. Dhavan,
• Rahul D. Kaduskar,
• Loana Musso,
• Leonardo Scaglioni,
• Piera Anna Martino and
• Sabrina Dallavalle

Beilstein J. Org. Chem. 2016, 12, 1624–1628, doi:10.3762/bjoc.12.159

• ]. Chemical analysis of a terrestrial-derived Streptomyces sp. isolated from the rhizosphere of the plant Juniperus excelsa yielded a new metabolite, leopolic acid A (1, Figure 1) [2]. Leopolic acid has unprecedented structural features consisting of an aliphatic side chain attached to a 2,3-pyrrolidinedione

• before, we decided to incorporate the structural features found in leopolic acid into this novel heterocyclic system. Accordingly, Wittig olefination of 14, followed by coupling with L-phenylalanine benzyl ester, and subsequent catalytic hydrogenation in EtOAc of 16 afforded the analogue of leopolic acid

Beta-hydroxyphosphonate ribonucleoside analogues derived from 4-substituted-1,2,3-triazoles as IMP/GMP mimics: synthesis and biological evaluation

• Tai Nguyen Van,
• Audrey Hospital,
• Corinne Lionne,
• Lars P. Jordheim,
• Charles Dumontet,
• Christian Périgaud,
• Laurent Chaloin and
• Suzanne Peyrottes

Beilstein J. Org. Chem. 2016, 12, 1476–1486, doi:10.3762/bjoc.12.144

• (cN-II), an enzyme involved in the regulation of purine nucleotide pools. NMR and molecular modelling studies showed that a few derivatives adopted similar structural features to IMP or GMP. Five derivatives were identified as modest inhibitors with 53 to 64% of cN-II inhibition at 1 mM. Keywords

Modular synthesis of the pyrimidine core of the manzacidins by divergent Tsuji–Trost coupling

• Sebastian Bretzke,
• Stephan Scheeff,
• Felicitas Vollmeyer,
• Friederike Eberhagen,
• Frank Rominger and
• Dirk Menche

Beilstein J. Org. Chem. 2016, 12, 1111–1121, doi:10.3762/bjoc.12.107

• -metathesis of a challenging homoallylic urea substrate, which proceeds in good yields in the presence of an organic phosphoric acid. Keywords: cross-metathesis; natural products; pyrimidines; Tsuji–Trost reaction; synthetic methods; Introduction Chiral pyrimidine motifs constitute prevalent structural

• features in a variety of potent natural products and bioactive agents [1][2][3][4][5]. As exemplified by the marine natural products manzazidins A and C [2][3][4][5], they may be characterized by diverse configurations, including synthetically challenging quaternary centers. Owing to their pronounced

Catalytic asymmetric synthesis of biologically important 3-hydroxyoxindoles: an update

• Bin Yu,
• Hui Xing,
• De-Quan Yu and
• Hong-Min Liu

Beilstein J. Org. Chem. 2016, 12, 1000–1039, doi:10.3762/bjoc.12.98

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

• [22]. The naturally occurring muraymycins isolated from Streptomyces guided first insights into the structural features essential for MraY inhibition. For the most active member of the family, i.e., muraymycin A1, antibiotic activity could be found against various bacteria ranging from Staphylococci

From steroids to aqueous supramolecular chemistry: an autobiographical career review

• Bruce C. Gibb

Beilstein J. Org. Chem. 2016, 12, 684–701, doi:10.3762/bjoc.12.69

• specific orientations [19][20][21]. Beyond these structural features, the biggest determinant in guest binding was the solvent. Solvents such as DMSO gave the strongest complexations, whilst halogenated solvents gave the weakest. Apparently the former does not solvate the cavity well. One of the remarkable

Biosynthesis of α-pyrones

• Till F. Schäberle

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

• be discussed. Review 1 Occurrence and activities In this chapter special sub-types of α-pyrones will be described. The compounds are grouped into three categories depending on their structural features: (i) dibenzo-α-pyrones, (ii) monocyclic α-pyrones, and (iii) monobenzo-α-pyrones. 1.1 Dibenzo-α

Art, auto-mechanics, and supramolecular chemistry. A merging of hobbies and career

• Eric V. Anslyn

Beilstein J. Org. Chem. 2016, 12, 362–376, doi:10.3762/bjoc.12.40

• trielaidin over trielroselaidin (differing only by double bond position in each fatty acid chain, Figure 11) and a second synthetic receptor that did the opposite. Thus, if successful, the demonstration of a differential sensing approach that could classify glycerides, determine their structural features

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

• pharmaceutical properties evaluated, and on compounds with unique structural features. We demonstrate that the exploration of specific microbial–host interactions, in combination with multidisciplinary dereplication processes, has emerged as a successful strategy to identify novel chemical entities and to shed

Spiro-fused carbohydrate oxazoline ligands: Synthesis and application as enantio-discrimination agents in asymmetric allylic alkylation

• Jochen Kraft,
• Martin Golkowski and
• Thomas Ziegler

Beilstein J. Org. Chem. 2016, 12, 166–171, doi:10.3762/bjoc.12.18

• with Pd(cod)Cl2 (Figure 1). Single crystal X-ray diffraction of these Pd complexes revealed some interesting structural features in terms of ligand–metal bite angles and shielding of the palladium center by the carbohydrate scaffold from one specific side [17]. For example, we concluded from the

Inclusion complexes of 2-methoxyestradiol with dimethylated and permethylated β-cyclodextrins: models for cyclodextrin–steroid interaction

• Mino R. Caira,
• Susan A. Bourne,
• Halima Samsodien and
• Vincent J. Smith

Beilstein J. Org. Chem. 2015, 11, 2616–2630, doi:10.3762/bjoc.11.281

• host and guest during complexation [1]. Complex units A and B of TRIMEB·2ME, related by a pseudo-translation of ≈b/2, have nearly identical structural features, namely common TRIMEB host conformations and lack of host disorder, apparent twofold disorder of the 2ME methylene group at C6 (site-occupancy

Organocatalytic and enantioselective Michael reaction between α-nitroesters and nitroalkenes. Syn/anti-selectivity control using catalysts with the same absolute backbone chirality

• Jose I. Martínez,
• Uxue Uria,
• Maria Muñiz,
• Efraím Reyes,
• Luisa Carrillo and
• Jose L. Vicario

Beilstein J. Org. Chem. 2015, 11, 2577–2583, doi:10.3762/bjoc.11.277

• incorporation of additives or co-catalysts [10][11][12][13], the modification of some structural features of the substrate [14][15], the use of two catalysts that are structurally different to each other and that can also operate independently through a single transition state with minimal matched/mismatched

Smart molecules for imaging, sensing and health (SMITH)

• Bradley D. Smith

Beilstein J. Org. Chem. 2015, 11, 2540–2548, doi:10.3762/bjoc.11.274

• ) Two views of the threaded complex highlighting the structural features controlling the threading kinetics and thermodynamics. Acknowledgements First and foremost, I am extremely grateful to all of the students who have worked in my lab over years, and the names of many are listed in the references

Synthesis of Xenia diterpenoids and related metabolites isolated from marine organisms

• Tatjana Huber,
• Lara Weisheit and
• Thomas Magauer

Beilstein J. Org. Chem. 2015, 11, 2521–2539, doi:10.3762/bjoc.11.273

• a large group of structurally diverse secondary metabolites. Among these natural products, Xenia diterpenoids or xenicanes represent a unique family with intriguing structural features and diverse biological activities. Many xenicanes display significant cytotoxic and antibacterial activity and are

• -related diterpenoids. Additionally, total syntheses of xeniolides and of a crenulatane natural product were illustrated. It has been shown that the rare structural features of Xenia diterpenoids represent an enduring challenge for the total synthesis of these fascinating metabolites. For these reasons

2-Hetaryl-1,3-tropolones based on five-membered nitrogen heterocycles: synthesis, structure and properties

• Yury A. Sayapin,
• Inna O. Tupaeva,
• Alexandra A. Kolodina,
• Eugeny A. Gusakov,
• Vitaly N. Komissarov,
• Igor V. Dorogan,
• Nadezhda I. Makarova,
• Anatoly V. Metelitsa,
• Valery V. Tkachev,
• Sergey M. Aldoshin and
• Vladimir I. Minkin

Beilstein J. Org. Chem. 2015, 11, 2179–2188, doi:10.3762/bjoc.11.236

• relative the OH counterpart. The calculations reproduce sufficiently well the experimentally determined geometries of compounds 5g and 6e as well as their main structural features such as the very short O···N distances and the folding of the seven-membered rings (see Supporting Information File 1). We have

Hexacoordinate Ru-based olefin metathesis catalysts with pH-responsive N-heterocyclic carbene (NHC) and N-donor ligands for ROMP reactions in non-aqueous, aqueous and emulsion conditions

• Shawna L. Balof,
• K. Owen Nix,
• Matthew S. Olliff,
• Sarah E. Roessler,
• Arpita Saha,
• Kevin B. Müller,
• Ulrich Behrens,
• Edward J. Valente and
• Hans-Jörg Schanz

Beilstein J. Org. Chem. 2015, 11, 1960–1972, doi:10.3762/bjoc.11.212

• hydrophilic phosphine ligands [22][23][24][25], NHC ligands [26][27][28][29], N-donor ligands [30], alkylidene moieties [31][32][33] or combinations of these structural features [34][35][36][37]. Another recent development in homogeneous catalysis, and olefin metathesis in particular, have become switchable

Profluorescent substrates for the screening of olefin metathesis catalysts

• Raphael Reuter and
• Thomas R. Ward

Beilstein J. Org. Chem. 2015, 11, 1886–1892, doi:10.3762/bjoc.11.203

• small volumes, high boiling solvents with different structural features were selected. From the screening, the following features were apparent: Grubbs–Hoveyda and Grela catalysts 1 and 2 perform better for substrate 8 in most solvents. For solvents that contain a carbonyl or carboxyl function (i.e., 2

Pyridinoacridine alkaloids of marine origin: NMR and MS spectral data, synthesis, biosynthesis and biological activity

• Louis P. Sandjo,
• Victor Kuete and
• Maique W. Biavatti

Beilstein J. Org. Chem. 2015, 11, 1667–1699, doi:10.3762/bjoc.11.183

• atoms. Fortunately, NMR techniques such as 1,n-ADEQUATE can be used to solve the problem of carbon assignment but the experimental time is long, the sensitivity is poor, and a substantial amount of sample is required. However, pyridoacridines present some structural features that can be used for