Pigmentosins from Gibellula sp. as antibiofilm agents and a new glycosylated asperfuran from Cordyceps javanica

• Soleiman E. Helaly,
• Wilawan Kuephadungphan,
• Patima Phainuphong,
• Mahmoud A. A. Ibrahim,
• Kanoksri Tasanathai,
• Suchada Mongkolsamrit,
• Janet Jennifer Luangsa-ard,
• Souwalak Phongpaichit,
• Vatcharin Rukachaisirikul and
• Marc Stadler

Beilstein J. Org. Chem. 2019, 15, 2968–2981, doi:10.3762/bjoc.15.293

• Northeastern Thailand. Their pure cultures were isolated and subsequently deposited at the BIOTEC Culture Collection (BCC), Pathum Thani, Thailand. Two nuclear DNA regions of all isolates including internal transcribed spacer regions of the ribosomal DNA (ITS) and translation elongation factor 1-alpha (EF1-α

Two new aromatic polyketides from a sponge-derived Fusarium

• Mada Triandala Sibero,
• Tao Zhou,
• Keisuke Fukaya,
• Daisuke Urabe,
• Ocky K. Karna Radjasa,
• Agus Sabdono,
• Agus Trianto and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2019, 15, 2941–2947, doi:10.3762/bjoc.15.289

• . Results and Discussion A fungal strain was isolated from a sponge Xestospongia sp. collected in Karimunjawa National Park, Central Java, and identified as a member of Fusarium on the basis of sequence similarity of the internal transcribed spacer (ITS) domain to Fusarium oxysporum strains in the DNA

Bacterial terpene biosynthesis: challenges and opportunities for pathway engineering

• Eric J. N. Helfrich,
• Geng-Min Lin,
• Christopher A. Voigt and
• Jon Clardy

Beilstein J. Org. Chem. 2019, 15, 2889–2906, doi:10.3762/bjoc.15.283

• fine control of terpene cyclases and tailoring enzymes. The reduced cost of DNA synthesis [153] and advanced cloning techniques [154], such as Gibson Assembly [155] and Golden Gate cloning [156], has made pathway construction more economically efficient, and the genetic parts can also be retrieved

Preparation of anthracene-based tetraperimidine hexafluorophosphate and selective recognition of chromium(III) ions

• Qing-Xiang Liu,
• Feng Yang,
• Zhi-Xiang Zhao,
• Shao-Cong Yu and
• Yue Ding

Beilstein J. Org. Chem. 2019, 15, 2847–2855, doi:10.3762/bjoc.15.278

• autoimmune and cardiovascular diseases [11]. On the other hand, the excessive incorporation of chromium(III) is toxic to humans, and can cause cancer through the oxidation of DNA and some proteins [12][13][14]. Therefore, the detection of chromium(III) has a vital practical significance for human health

Skeletocutins M–Q: biologically active compounds from the fruiting bodies of the basidiomycete Skeletocutis sp. collected in Africa

• Tian Cheng,
• Clara Chepkirui,
• Cony Decock,
• Josphat C. Matasyoh and
• Marc Stadler

Beilstein J. Org. Chem. 2019, 15, 2782–2789, doi:10.3762/bjoc.15.270

• that it belongs to a new species because neither DNA sequence data in the public domain nor morphological characteristics matched the previously reported species, as compared to the literature. The genus Skeletocutis (of the Polyporaceae) consists of approximately 40 species, which grow as a crust on

Diversity-oriented synthesis of spirothiazolidinediones and their biological evaluation

• Sambasivarao Kotha,
• Gaddamedi Sreevani,
• Lilya U. Dzhemileva,
• Milyausha M. Yunusbaeva,
• Usein M. Dzhemilev and
• Vladimir A. D’yakonov

Beilstein J. Org. Chem. 2019, 15, 2774–2781, doi:10.3762/bjoc.15.269

• hypodiploidal DNA peak appears 24 hours after the action of compounds 22, 20 and 17, which shows the inability to stop the fission cycle at the checkpoints, and ultimately, leads to cell death. Conclusion In summary, we have synthesized spirothiazolidinedione derivatives via a [2 + 2 + 2] cyclotrimerization

• , phosphatidylserine molecules appear on the cell surface but the membrane is still impermeable for DNA-binding dyes (such as propidium iodide). The membrane integrity is lost at later stages of the cell death. Thus, while detecting the apoptosis, one can distinguish four types of cells: living cells (annexin V−/PI

A combinatorial approach to improving the performance of azoarene photoswitches

• Joaquin Calbo,
• Aditya R. Thawani,
• Rosina S. L. Gibson,
• Andrew J. P. White and
• Matthew J. Fuchter

Beilstein J. Org. Chem. 2019, 15, 2753–2764, doi:10.3762/bjoc.15.266

• including imaging applications [20], photopharmacology [21], supramolecular chemistry [22][23], responsive foams [24], coordination chemistry [25] and DNA nanotechnology [26][27]. Whilst the azopyrazoles have excellent properties for use in a variety of photo-addressable applications, it remains frustrating

Nanangenines: drimane sesquiterpenoids as the dominant metabolite cohort of a novel Australian fungus, Aspergillus nanangensis

• Heather J. Lacey,
• Cameron L. M. Gilchrist,
• Andrew Crombie,
• John A. Kalaitzis,
• Daniel Vuong,
• Peter J. Rutledge,
• Peter Turner,
• John I. Pitt,
• Ernest Lacey,
• Yit-Heng Chooi and
• Andrew M. Piggott

Beilstein J. Org. Chem. 2019, 15, 2631–2643, doi:10.3762/bjoc.15.256

• and bioinformatic analysis Genomic DNA was extracted from A. nanangensis (see Supporting Information File 1) and sent to the Australian Genome Research Facilities for de novo genome sequencing using Illumina HiSeq 2000. A draft genome assembly of A. nanangensis was obtained using SPAdes v3.13.0 via

• nanangenines A–C and G. Acknowledgements We thank Dr Matthew McKay (MQ) and Dr Nick Proschogo (USyd) for acquisition of HRMS data, Dr Ian Luck (USyd) for acquisition of preliminary NMR data and Si Shu (UWA) for preparation of genomic DNA for genome sequencing. This work was funded, in part, by the Australian

AgNTf₂-catalyzed formal [3 + 2] cycloaddition of ynamides with unprotected isoxazol-5-amines: efficient access to functionalized 5-amino-1H-pyrrole-3-carboxamide derivatives

• Ziping Cao,
• Jiekun Zhu,
• Li Liu,
• Yuanling Pang,
• Laijin Tian,
• Xuejun Sun and
• Xin Meng

Beilstein J. Org. Chem. 2019, 15, 2623–2630, doi:10.3762/bjoc.15.255

• catalyst, mild reaction conditions, simple operation and product purification. Notably, the core skeleton of these products is the substructure of many biologically active molecules. For example (Figure 1), compound 1 has significant activities as DNA-cleaving agent [39] and sangivamycin 2 has been in

α,ß-Didehydrosuberoylanilide hydroxamic acid (DDSAHA) as precursor and possible analogue of the anticancer drug SAHA

• Shital K. Chattopadhyay,
• Subhankar Ghosh,
• Sarita Sarkar and
• Kakali Bhadra

Beilstein J. Org. Chem. 2019, 15, 2524–2533, doi:10.3762/bjoc.15.245

• Table 5. Thus, FITC–Annexin V/PI FCM and LDH assays (vide supra) both supported higher percentage of apoptosis in comparison to the negligible necrosis in HeLa cells treated with 11b. Fluorescence microscopic images of Hela cells using different staining techniques and DNA ladder formation Hela cells

• (Figure 6 middle panel). One of the later steps in apoptosis is ultimately the DNA fragmentation, a process which results from the endonuclease activation during apoptosis. Hence, we further characterized the apoptotic phenomena in HeLa cells by the formation of comet tails (Figure 6, lower panel) and DNA

• gel electrophoresis (Figure 7). Apoptotic hallmark of chromosomal DNA laddering was clearly evident in HeLa cells, treated with different doses of the compound as compared to untreated cells. Thus these two assays comet formation and DNA laddering indicated DNA damage during the apoptotic induction

In search of visible-light photoresponsive peptide nucleic acids (PNAs) for reversible control of DNA hybridization

• Lei Zhang,
• Greta Linden and
• Olalla Vázquez

Beilstein J. Org. Chem. 2019, 15, 2500–2508, doi:10.3762/bjoc.15.243

• targets without causing a permanent knockout. During the last years, the pioneering structural studies of reversible photoregulation of DNA/RNA duplex stability of Asanuma and Komiyama [16][17] have become functional ones, affecting DNA/RNA cleavage [18][19][20], transcription [21][22][23], and

• been employed. In vivo application demands the development of a new generation of artificial agents to target DNA/RNA-associated processes. These compounds must be able to maintain their specificity and effectivity while still being nuclease resistant, nontoxic and susceptible to light of tissue

• -penetrating wavelengths. Peptide nucleic acids (PNAs) [31] are synthetic nucleic acid analogues, in which nucleobases are linked to a repeating N-(2-aminoethyl)glycine polyamide backbone. The lack of phosphate groups provides them with both higher binding affinities to complementary DNA or RNA sequences and

Reversible switching of arylazopyrazole within a metal–organic cage

• Anton I. Hanopolskyi,
• Soumen De,
• Michał J. Białek,
• Yael Diskin-Posner,
• Liat Avram,
• Moran Feller and
• Rafal Klajn

Beilstein J. Org. Chem. 2019, 15, 2398–2407, doi:10.3762/bjoc.15.232

• interfaces [1][2][3], in self-assembled cages [4][5][6][7], on DNA chains [8], and on the surfaces of inorganic nanoparticles [9][10]. Additionally, nanosized cages can induce preorganization of the encapsulated species, thus inducing unusual regioselectivities in various chemical reactions [11][12][13]. The

• selectivity [35][36][37][38][39][40]. Consequently, arylazopyrazoles have been employed as photoresponsive gelators [41] and adhesives [42] and for controlling antimicrobial response [43][44], cell adhesion to surfaces [45], as well as DNA [46] and microtubule [47] self-assembly using light. Here, we focused

Isolation of fungi using the diffusion chamber device FIND technology

• Benjamin Libor,
• Henrik Harms,
• Stefan Kehraus,
• Ekaterina Egereva,
• Max Crüsemann and
• Gabriele M. König

Beilstein J. Org. Chem. 2019, 15, 2191–2203, doi:10.3762/bjoc.15.216

• additionally identified by DNA sequencing. In total, experiments 1–4 led to 76 fungal isolates (41 fungi in experiment 1, 1 fungus in experiment 2, 1 fungus in experiment 3 and 33 fungi in experiment 4). All fungal cultures were obtained in single isolation steps directly via the FIND procedure and found to be

• comparison (BLAST) of DNA sequences (ITS1, ITS2, 18S, 5.8S, 28S, RPBII, tef1α and β-tubulin) with reference sequences deposited in public databases (GenBank) and microscopical analysis of morphological characteristics, identified 12 ascomycetes from 12 different genera. Except for Scopulariopsis brevicaulis

• microorganisms (BCCM/IHEM, Brussels) by extracting DNA using their usual protocols and genomic DNA extraction kits and generation of partial sequences of DNA loci using standard primers of ITS1, ITS2, ITS4, 5.8S, RPBII, tef1α and β-tubulin. Digitalized and formatted DNA sequences were compared to reference

Genome mining in Trichoderma viride J1-030: discovery and identification of novel sesquiterpene synthase and its products

• Xiang Sun,
• You-Sheng Cai,
• Yujie Yuan,
• Guangkai Bian,
• Ziling Ye,
• Zixin Deng and
• Tiangang Liu

Beilstein J. Org. Chem. 2019, 15, 2052–2058, doi:10.3762/bjoc.15.202

• synthase well-identified with products characterised in T. viride. In vitro analysis of Tvi09626 function To confirm the function of the candidate enzyme, the DNA sequence of Tvi09626 was amplified by touchdown PCR from the T. viride genome. The gene fragment was cloned into a pET28a (+) vector to

Archangelolide: A sesquiterpene lactone with immunobiological potential from Laserpitium archangelica

• Silvie Rimpelová,
• Michal Jurášek,
• Lucie Peterková,
• Jiří Bejček,
• Vojtěch Spiwok,
• Miloš Majdl,
• Michal Jirásko,
• Miloš Buděšínský,
• Juraj Harmatha,
• Eva Kmoníčková,
• Pavel Drašar and
• Tomáš Ruml

Beilstein J. Org. Chem. 2019, 15, 1933–1944, doi:10.3762/bjoc.15.189

• , the endoplasmic reticulum was visualized by transfection with a plasmid DNA coding mCherry-ER (0.5 µg) using Fugene HD (Promega, USA; DNA/Fugene HD = 1:3). Fluorescence microscopy The intracellular localization of compound 5 was studied by real-time live-cell fluorescence microscopy using an inverse

Identification of optimal fluorescent probes for G-quadruplex nucleic acids through systematic exploration of mono- and distyryl dye libraries

• Xiao Xie,
• Michela Zuffo,
• Marie-Paule Teulade-Fichou and
• Anton Granzhan

Beilstein J. Org. Chem. 2019, 15, 1872–1889, doi:10.3762/bjoc.15.183

• cationic dyes was synthesized and investigated with respect to their optical properties, propensity to aggregation in aqueous medium, and capacity to serve as fluorescence “light-up” probes for G-quadruplex (G4) DNA and RNA structures. Among the 61 compounds, 57 dyes showed preferential enhancement of

• fluorescence intensity in the presence of one or another G4-DNA or RNA structure, while no dye displayed preferential response to double-stranded DNA or single-stranded RNA analytes employed at equivalent nucleotide concentration. Thus, preferential fluorimetric response towards G4 structures appears to be a

• ] or its 4-isomer, as optimal fluorescent light-up probes characterized by high fluorimetric response (I/I0 of up to 550-fold), excellent selectivity with respect to double-stranded DNA or single-stranded RNA controls, high quantum yield in the presence of G4 analytes (up to 0.32), large Stokes shift

A heteroditopic macrocycle as organocatalytic nanoreactor for pyrroloacridinone synthesis in water

• Piyali Sarkar,
• Sayan Sarkar and
• Pradyut Ghosh

Beilstein J. Org. Chem. 2019, 15, 1505–1514, doi:10.3762/bjoc.15.152

• apoptotic cells, the investigation of the morphology of nuclei, the direct counting of cultivable bacteria, DNA intercalators, etc. [1][2][3][4]. Pyrrole, another biologically active heterocyclic compound, when fused with acridines affords promising bioactive pyrroloacridinone moieties demonstrating

Reversible end-to-end assembly of selectively functionalized gold nanorods by light-responsive arylazopyrazole–cyclodextrin interaction

• Maximilian Niehues,
• Patricia Tegeder and
• Bart Jan Ravoo

Beilstein J. Org. Chem. 2019, 15, 1407–1415, doi:10.3762/bjoc.15.140

• aggregates can be realized more or less efficiently through various approaches based on supramolecular interactions like metal–metal and π–π interactions [11], DNA mediated [12] or by host–guest chemistry [13]. Most of these approaches require selective functionalization of the ends of the AuNR and take

Anomeric sugar boronic acid analogues as potential agents for boron neutron capture therapy

• Daniela Imperio,
• Erika Del Grosso,
• Silvia Fallarini,
• Grazia Lombardi and
• Luigi Panza

Beilstein J. Org. Chem. 2019, 15, 1355–1359, doi:10.3762/bjoc.15.135

• or DNA ligands [4][5]. In the frame of a more general research program, we have recently published the synthesis of boronic acids derivatives of monosaccharides in which one of the sugar hydroxy groups is substituted by a boronic acid moiety [6]. A related approach has been described [7] recently

Genomics-inspired discovery of massiliachelin, an agrochelin epimer from Massilia sp. NR 4-1

• Jan Diettrich,
• Hirokazu Kage and
• Markus Nett

Beilstein J. Org. Chem. 2019, 15, 1298–1303, doi:10.3762/bjoc.15.128

• , unveiled the genetic basis of its biosynthesis. Results and Discussion The micacocidin-type BGC from Massilia sp. NR 4-1 and its enzymatic assembly line are depicted in Figure 1A and 1B. The gene cluster covers 34.7 kbp of contiguous DNA and includes ten genes (RS02190-RS02235), of which seven have

Phylogenomic analyses and distribution of terpene synthases among Streptomyces

• Lara Martín-Sánchez,
• Kumar Saurabh Singh,
• Mariana Avalos,
• Gilles P. van Wezel,
• Jeroen S. Dickschat and
• Paolina Garbeva

Beilstein J. Org. Chem. 2019, 15, 1181–1193, doi:10.3762/bjoc.15.115

• S5 in Supporting Information File 1. Molecular evolution analysis The coding DNA sequence (CDS) of the three terpene synthase genes (coding for geosmin synthases, 2-MIB synthases and epi-isozizaene synthases) in the 93 Streptomyces species were collected and aligned with Mafft version 7.313 using

Electrophilic oligodeoxynucleotide synthesis using dM-Dmoc for amino protection

• Shahien Shahsavari,
• Dhananjani N. A. M. Eriyagama,
• Bhaskar Halami,
• Vagarshak Begoyan,
• Marina Tanasova,
• Jinsen Chen and
• Shiyue Fang

Beilstein J. Org. Chem. 2019, 15, 1116–1128, doi:10.3762/bjoc.15.108

• instability of the adduct under acidic conditions during ODN synthesis [7]. In recent years, applications of ODNs have extended to emerging areas such as nanotechnology [8][9], antisense drug development [10][11][12], DNA damage and repair [13][14], DNA methylation and demethylation [15][16][17][18], DNA

• –protein interactions [19][20], CRISPR genome editing [21][22][23], DNA data storage [24][25], synthetic biology [26], bioconjugation [27] and others [28][29][30]. These applications frequently require modified ODNs that contain a wide variety of functional groups including those that cannot survive known

• MerMade 6 DNA/RNA synthesizer. The dT-Dmoc-CPG (4) was used as the solid support. Detritylation was carried out under standard conditions suggested by the synthesizer manufacturer for 1 µmol synthesis. The 0.1 M acetonitrile solutions of phosphoramidite monomers 3a–c and the commercially available 5'-DMTr

Photochemical generation of the 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) radical from caged nitroxides by near-infrared two-photon irradiation and its cytocidal effect on lung cancer cells

• Ayato Yamada,
• Manabu Abe,
• Yoshinobu Nishimura,
• Shoji Ishizaka,
• Masashi Namba,
• Taku Nakashima,
• Kiyofumi Shimoji and
• Noboru Hattori

Beilstein J. Org. Chem. 2019, 15, 863–873, doi:10.3762/bjoc.15.84

• strong DNA-damaging activity [65], they play important roles as anticancer therapeutic agents [66]. Among the free radicals, nitroxides including the TEMPO radical have unique properties, where they can act not only as radical scavengers, but also as anticancer agents [67]. Due to the unique properties

An improved synthesis of adefovir and related analogues

• David J. Jones,
• Eileen M. O’Leary and
• Timothy P. O’Sullivan

Beilstein J. Org. Chem. 2019, 15, 801–810, doi:10.3762/bjoc.15.77

• cause nephrotoxicity [7]. The mode of action of adefovir has been widely studied and involves the inhibition of viral replication by the termination of DNA synthesis [8][9][10]. Although adefovir was described in 1986 for the first time by Holý, De Clercq and co-workers, it is still actively employed in

Synthesis and fluorescent properties of N(9)-alkylated 2-amino-6-triazolylpurines and 7-deazapurines

• Andrejs Šišuļins,
• Jonas Bucevičius,
• Yu-Ting Tseng,
• Irina Novosjolova,
• Kaspars Traskovskis,
• Ērika Bizdēna,
• Huan-Tsung Chang,
• Sigitas Tumkevičius and
• Māris Turks

Beilstein J. Org. Chem. 2019, 15, 474–489, doi:10.3762/bjoc.15.41

• for this type of molecules. Traditionally, fluorescent purine nucleoside analogs were recognized as valuable fluorescent probes for DNA and RNA research [17]. This paved a way for development of various adenosine and guanosine analogs which in many cases contained an additional substituent at C(8

• ] have been actively studied for their fluorescent properties. Among others, also azole containing compounds of type E [28] and F [29] have been described. Similarly, to purine derivatives also 7-deazapurines are used in DNA labeling [30]. On the other hand, modified purines have found also applications

• in the cytoplasm. The representative fluorescent image of the labeled MCF-7 cells with compound 9 is shown in Figure 8 (for other examples see Figure S82 in Supporting Information File 1). Based on the recent investigation of metabolic labelling of DNA [30][56] by deaza-7-ethenyl-2'-deoxyguanosine