Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

• Nikita Brodyagin,
• Martins Katkevics,
• Venubabu Kotikam,
• Christopher A. Ryan and
• Eriks Rozners

Beilstein J. Org. Chem. 2021, 17, 1641–1688, doi:10.3762/bjoc.17.116

• , Ganesh and co-workers [51][52][53][54] reported that either S,R- or R,S-modified chPNA had lower affinity for complementary DNA and RNA as well. The decreased binding affinity of chPNAs was most likely due to unfavorable dihedral angles for proper organization of PNA’s backbone. In contrast, Appella and

Icilio Guareschi and his amazing “1897 reaction”

• Gian Cesare Tron,
• Alberto Minassi,
• Giovanni Sorba,
• Mara Fausone and
• Giovanni Appendino

Beilstein J. Org. Chem. 2021, 17, 1335–1351, doi:10.3762/bjoc.17.93

• contributions to the area are in the realm of analytical chemistry and in the systematic organization of the topic. In the course of these studies, Guareschi also isolated succinic acid from meat, the first report of this Krebs cycle intermediate from muscle tissues. The monograph on ptomaines [31] that

Beyond ribose and phosphate: Selected nucleic acid modifications for structure–function investigations and therapeutic applications

• Christopher Liczner,
• Kieran Duke,
• Gabrielle Juneau,
• Martin Egli and
• Christopher J. Wilds

Beilstein J. Org. Chem. 2021, 17, 908–931, doi:10.3762/bjoc.17.76

• well accommodated in the minor groove and making a stabilizing interaction with a trapped water molecule and the adjacent phosphate (Figure 6). It’s this pre-organization of the MOE groups, making the duplex more rigid, which is hypothesized to cause the increase in RNA binding affinity. Furthermore

Simulating the enzymes of ganglioside biosynthesis with Glycologue

• Andrew G. McDonald and
• Gavin P. Davey

Beilstein J. Org. Chem. 2021, 17, 739–748, doi:10.3762/bjoc.17.64

• then to subsequent ceramide-linked glycoconjugate acceptors, before transport and eventual incorporation into the plasma membrane via vesicular fusion. Gangliosides, which function as antigenic determinants [4], may play a role in membrane organization [5], cell signaling [6], apoptosis [7], and in

Selective recognition of ATP by multivalent nano-assemblies of bisimidazolium amphiphiles through “turn-on” fluorescence response

• Rakesh Biswas,
• Surya Ghosh,
• Shubhra Kanti Bhaumik and
• Supratim Banerjee

Beilstein J. Org. Chem. 2020, 16, 2728–2738, doi:10.3762/bjoc.16.223

• vibronic bands at 343–345 nm and 327–329 nm, respectively) generally indicates a possible mode of organization of the pyrene chromophores upon self-assembly [63]. It was found that in the concentration range of 5–50 µM [65], although a decrease in this ratio was observed for PBIm4; much more pronounced

• that under these conditions, ATP binding was difficult for a receptor with two positive charges either in “molecular” form or as clusters and further signified the requirement of a multivalent organization of the charges as provided by the aggregates. Selectivity in the ATP detection One of the key

Optical detection of di- and triphosphate anions with mixed monolayer-protected gold nanoparticles containing zinc(II)–dipicolylamine complexes

• Lena Reinke,
• Julia Bartl,
• Marcus Koch and
• Stefan Kubik

Beilstein J. Org. Chem. 2020, 16, 2687–2700, doi:10.3762/bjoc.16.219

• reliably detect differences in the composition of the two nanoparticles because of the large uncertainties associated with our method (see Supporting Information File 1), and we therefore could not exclude that NP(R)-1 and NPrac-1 differed in the composition. Alternatively, the organization of the ligands

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

• conformational preference at Asp3 and Thr4 which correlates with the preferred states seen for the glycosylated antigen in solution. There is some evidence of a pre-structuring or pre-organization effect, where O-glycosylation shifts the conformational equilibrium of the peptide towards conformations that are

The B & B approach: Ball-milling conjugation of dextran with phenylboronic acid (PBA)-functionalized BODIPY

• Patrizia Andreozzi,
• Lorenza Tamberi,
• Elisamaria Tasca,
• Gina Elena Giacomazzo,
• Marta Martinez,
• Mirko Severi,
• Marco Marradi,
• Stefano Cicchi,
• Sergio Moya,
• Giacomo Biagiotti and
• Barbara Richichi

Beilstein J. Org. Chem. 2020, 16, 2272–2281, doi:10.3762/bjoc.16.188

• conjugate Dex-1b in aggregates or nanoparticles. Moreover, it is known that dye conjugation to a polymer even in small percentages can generate a large change in the environment of the chains affecting conformation and chain organization [36]. To assess the influence of hydrophobicity on the formation of

Models of necessity

• Timothy Clark and
• Martin G. Hicks

Beilstein J. Org. Chem. 2020, 16, 1649–1661, doi:10.3762/bjoc.16.137

• models and descriptions are poorly suited for the more varied interactions involved in, for instance, self-organization in technical systems. Requirement (2) results from the conformation problem. Any technique or model that requires a specific 3D molecular structure must deal with conformational

Anthelmintic drug discovery: target identification, screening methods and the role of open science

• Frederick A. Partridge,
• Ruth Forman,
• Carole J. R. Bataille,
• Graham M. Wynne,
• Marina Nick,
• Angela J. Russell,
• Kathryn J. Else and
• David B. Sattelle

Beilstein J. Org. Chem. 2020, 16, 1203–1224, doi:10.3762/bjoc.16.105

• , diethylcarbamazine, ivermectin and praziquantel are insufficiently efficacious, contraindicated in some populations, or at risk of the development of resistance, thereby impeding progress towards World Health Organization goals to control or eliminate these neglected tropical diseases. However, there has been

• . Currently, the World Health Organization (WHO) recommends annual or biannual (where baseline prevalence is over 50%) intervention with the anthelmintics albendazole (ALB, 1) or mebendazole (MEB, 2), to treat STHs [25][26]. While achieving cure rates approaching 100% for Ascaris, these drugs, when used as

Opening up connectivity between documents, structures and bioactivity

• Christopher Southan

Beilstein J. Org. Chem. 2020, 16, 596–606, doi:10.3762/bjoc.16.54

• BindingDB. However, as a consequence of being free-to-mine a number of operations have carried out public large-scale automated D-C extractions. These include, SureChEMBL [31], IBM, World Intellectual Property Organization (WIPO) and most recently Google Patents. However, the problem arises in PubChem and

Visible-light-induced addition of carboxymethanide to styrene from monochloroacetic acid

• Kaj M. van Vliet,
• Nicole S. van Leeuwen,
• Albert M. Brouwer and
• Bas de Bruin

Beilstein J. Org. Chem. 2020, 16, 398–408, doi:10.3762/bjoc.16.38

• discussions regarding the IR spectroscopy measurements. Funding This research was supported by The Netherlands Organization for Scientific Research (NWO), the Holland Research School of Molecular Chemistry (HRSMC), the UvA Research Priority Area “Sustainable Chemistry” and the Advanced Research Center

The use of isoxazoline and isoxazole scaffolding in the design of novel thiourea and amide liquid-crystalline compounds

• Itamar L. Gonçalves,
• Rafaela R. da Rosa,
• Vera L. Eifler-Lima and
• Aloir A. Merlo

Beilstein J. Org. Chem. 2020, 16, 175–184, doi:10.3762/bjoc.16.20

• thioureas is the reaction of carbon disulfide with either one or two different amines [9]. Due to their self-assembly and self-organization through intermolecular hydrogen bonding, thioureas display interesting technological applications to this group of molecules, one of which explores its application in

• containing isoxazoline rings 17a–c and isoxazoles 18a–c, as well as LCs amides 19–22 and 24. All compounds listed in Table 1 are capable of self-organization by hydrogen bonds, either in their solid state or in solution. Solubility in protic or aprotic polar solvent is restricted at room temperature. However

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

• can be further modified by tailoring enzymes, but the core structure can be inferred from the organization of the biosynthetic genes and the modular architecture of the associated proteins [7][8]. Terpene biosynthesis has a very different logic. Five-carbon units called isoprenes are joined to create

Emission and biosynthesis of volatile terpenoids from the plasmodial slime mold Physarum polycephalum

• Xinlu Chen,
• Tobias G. Köllner,
• Wangdan Xiong,
• Guo Wei and
• Feng Chen

Beilstein J. Org. Chem. 2019, 15, 2872–2880, doi:10.3762/bjoc.15.281

• and similar residues, respectively. B) Intron/exon organization of the four PpolyTPS genes. Boxes and lines indicate exons and introns, respectively. PpolyTPS1 and PpolyTPS4 have terpene synthase activities. A) GC chromatogram of sesquiterpenes produced by recombinant PpolyTPS1 incubated with FPP. 2

A toolbox of molecular photoswitches to modulate the CXCR3 chemokine receptor with light

• Xavier Gómez-Santacana,
• Sabrina M. de Munnik,
• Tamara A. M. Mocking,
• Niels J. Hauwert,
• Shanliang Sun,
• Prashanna Vijayachandran,
• Iwan J. P. de Esch,
• Henry F. Vischer,
• Maikel Wijtmans and
• Rob Leurs

Beilstein J. Org. Chem. 2019, 15, 2509–2523, doi:10.3762/bjoc.15.244

• photochemical and binding characterization of compounds 3e, 4d, 6b and 6d–i. Structure and results of functional characterization of compounds 3e, 4d, 6b and 6d–h. Supporting Information Supporting Information File 618: Experimental part. Acknowledgements All authors acknowledge the Netherlands Organization

Perspective isomorphs – a new classification of molecular structures based on artistic and chemical concepts

• Jannis Neumann,
• Ansgar Schnurr and
• Hermann A. Wegner

Beilstein J. Org. Chem. 2019, 15, 2319–2326, doi:10.3762/bjoc.15.224

• group of molecules that are congruent in a hypothetical view with the human eye and from a defined perspective. Thus, the spatial organization of their incorporated atoms would not be distinguishable for the human mode of perception. Such molecules are called perspective isomorphs of a specific PI class

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

• -stimulating, and anticancer activities [2]. Since the World Health Organization (WHO) declared antibiotic resistance a global threat and urged the search for new antibiotics, the interest in fungal metabolites increased recently. In order to find new structural types, novel source organisms have to be

Host–guest interactions between p-sulfonatocalix[4]arene and p-sulfonatothiacalix[4]arene and group IA, IIA and f-block metal cations: a DFT/SMD study

• Valya K. Nikolova,
• Cristina V. Kirkova,
• Silvia E. Angelova and
• Todor M. Dudev

Beilstein J. Org. Chem. 2019, 15, 1321–1330, doi:10.3762/bjoc.15.131

• is shown that the metal cations induce different pre-organization of the calixarene structure upon binding. The preferred binding site for the guest metal cations is the plane of the upper rim (with p-sulfonato groups), i.e., the sulfonate groups of hosts serve as anchoring points for the positively

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

• domain organization of the two corresponding biosynthetic assembly lines further indicated that Massilia sp. NR 4-1 does not produce micacocidin, but a derivative of this secondary metabolite. The isolation of siderophores from microorganisms is usually straightforward due to their iron-dependent

• array detector. In total, 12.0 mg of 1 were isolated. Massiliachelin (1) pale yellow solid; UV (MeOH) λmax (log ε): 356 (3.06), 280 (4.18), 228 (4.64) nm; 1H and 13C NMR, Table 1; HRESIMS m/z: [M + H]+, calcd for C23H35N2O4S2, 467.2033; found, 467.2033. A) Organization of the micacocidin-type gene

Mechanochemistry of supramolecules

• Anima Bose and
• Prasenjit Mal

Beilstein J. Org. Chem. 2019, 15, 881–900, doi:10.3762/bjoc.15.86

• (terpyridines; Figure 1c) ligands [49]. The model systems depicted in Figure 1 are constructed using metals like Pd(II) or Pt(II) ions for square planar geometry, Cu(I) or Ag(I) ions for tetrahedral geometry and Co(II)/Cu(II)/Fe(II)/Zn(II)/Hg(II) for octahedral organization [50]. In Figure 2, Busch’s first

Design and synthesis of multivalent α-1,2-trimannose-linked bioerodible microparticles for applications in immune response studies of Leishmania major infection

• Chelsea L. Rintelmann,
• Tara Grinnage-Pulley,
• Kathleen Ross,
• Daniel E. K. Kabotso,
• Angela Toepp,
• Anne Cowell,
• Christine Petersen,
• Balaji Narasimhan and
• Nicola Pohl

Beilstein J. Org. Chem. 2019, 15, 623–632, doi:10.3762/bjoc.15.58

• ). The World Health Organization estimates that this neglected tropical disease causes between 1–2 million new cases annually [4]. Leishmaniasis manifests into three different forms, cutaneous, mucosal, or visceral, depending on parasite species, host immune system and location of infection [5

Application of olefin metathesis in the synthesis of functionalized polyhedral oligomeric silsesquioxanes (POSS) and POSS-containing polymeric materials

• Patrycja Żak and
• Cezary Pietraszuk

Beilstein J. Org. Chem. 2019, 15, 310–332, doi:10.3762/bjoc.15.28

• mild conditions, hydrogenolysis of the benzyl ester group to the carboxylic acid and hydrogenation of the C=C double bonds at the silicon atoms (Scheme 7). The ability of the obtained derivatives, in particular the carboxylic acids, to generate nanostructured materials through self-organization

Chemical structure of cichorinotoxin, a cyclic lipodepsipeptide that is produced by Pseudomonas cichorii and causes varnish spots on lettuce

• Hidekazu Komatsu,
• Takashi Shirakawa,
• Takeo Uchiyama and
• Tsutomu Hoshino

Beilstein J. Org. Chem. 2019, 15, 299–309, doi:10.3762/bjoc.15.27

• Administration, Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization, 3-1-1 Kannondai, Tsukuba, Ibaraki 305-8519, Japan 10.3762/bjoc.15.27 Abstract Pseudomonas cichorii, which causes varnish spots on lettuce and seriously damages lettuce production during the

• samples were allowed to stand for 3 days to estimate the activities, as shown in Supporting Information File 1, Figure S19B. Isolation of cichorinotoxin Pseudomonas cichorii isolate YM8705 has been deposited in NARO Genebank as MAFF730229 (NARO: National Agricultural and Food Research Organization). P

Lectins of Mycobacterium tuberculosis – rarely studied proteins

• Katharina Kolbe,
• Sri Kumar Veleti,
• Norbert Reiling and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2019, 15, 1–15, doi:10.3762/bjoc.15.1

• ][4][5]. However, the World Health Organization (WHO) reported 1.6 million fatalities worldwide from tuberculosis in 2017, with more than 10 million annual new cases, and an overall estimated global burden of almost 1.7 billion latently infected people [2]. The fight against this primarily pulmonary