Cationic oligonucleotide derivatives and conjugates: A favorable approach for enhanced DNA and RNA targeting oligonucleotides

• Mathias B. Danielsen and
• Jesper Wengel

Beilstein J. Org. Chem. 2021, 17, 1828–1848, doi:10.3762/bjoc.17.125

• . The key features of ASOs further enable them to be transformed into personalized medicines, eventually even targeting patient-specific sequences and very rare diseases [1]. ASOs can mediate gene silencing via different mechanisms of action. ASOs that induce RNase H degradation of the endogenous RNA

• improved liver targeting [22][23] and ASO–glucagon-like peptide-1 (GLP1) conjugation for improved delivery to pancreatic β-cells [24]. Previously, Menzi et al. reviewed the impact of cationic modifications and conjugations for ONs and siRNAs biophysical and biological activities until 2015 [25]. In this

• to a Watson–Crick interacting ON, both targeting the same ssDNA) exhibited the ability to invade double-stranded DNA (dsDNA) targets in vitro [56]. The functionalization with aminoalkyl variants onto the nucleobase is not limited to the C-5 position on the pyrimidine base. Another important site is

Natural products in the predatory defence of the filamentous fungal pathogen Aspergillus fumigatus

• Jana M. Boysen,
• Nauman Saeed and
• Falk Hillmann

Beilstein J. Org. Chem. 2021, 17, 1814–1827, doi:10.3762/bjoc.17.124

• . fumigatus as an example because of its high medical importance and its diverse profile of secondary metabolites which seems to fulfil dual roles: targeting innate immune cells during virulence and protect from environmental predators in natural habitats. Review Natural products of Aspergillus fumigatus The

A systems-based framework to computationally describe putative transcription factors and signaling pathways regulating glycan biosynthesis

• Theodore Groth,
• Rudiyanto Gunawan and
• Sriram Neelamegham

Beilstein J. Org. Chem. 2021, 17, 1712–1724, doi:10.3762/bjoc.17.119

• , which drives the epithelial to mesenchymal transition [35]. Kruppel-like factor 5 (KLF5) is commonly upregulated in several cancer types and promotes pancreatic cancer proliferation by targeting the cell cycle [36]. MECOM (also known as PRDM3) is a nuclear TF known to ablate inflammatory responses and

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

• cells [72]. GPNA targeting the transcriptional start-site of the human E-cadherin gene had potent and sequence-specific antisense activity and was less toxic to the cells than the PNA–polyarginine conjugate [73]. Interestingly, the α-arginine modification in either ʟ- or ᴅ-configuration destabilized PNA

• oligonucleotides at neutral pH [100][101][102]. Rozners and co-workers were the first to introduce M in triplex-forming PNAs targeting dsRNA [28]. Having a pKa of ≈6.7, M is partially protonated at physiological pH 7.4, which facilitates fast binding and formation of strong triplex [28][30][31]. While all

• bonding options on the purine base as well. An extended nucleobase S (Figure 7) originally developed for triplex-forming oligonucleotides [114][115], was introduced in PNAs targeting U interruptions in polypurine tracts of dsRNA triplexes [111]. However, in PNA, S showed limited sequence specificity

Double-headed nucleosides: Synthesis and applications

• Vineet Verma,
• Jyotirmoy Maity,
• Vipin K. Maikhuri,
• Ritika Sharma,
• Himal K. Ganguly and
• Ashok K. Prasad

Beilstein J. Org. Chem. 2021, 17, 1392–1439, doi:10.3762/bjoc.17.98

• was hybridized with a DNA target. The double-headed nucleoside 41 has potential in DNA invader probes as well as in RNA targeting and detection [23]. 1,3-Furanosyl double-headed nucleosides In this section, all double-headed nucleosides with furanosyl ring structures are collected. The first

Stereoselective synthesis and transformation of pinane-based 2-amino-1,3-diols

• Ákos Bajtel,
• Mounir Raji,
• Matti Haukka,
• Ferenc Fülöp and
• Zsolt Szakonyi

Beilstein J. Org. Chem. 2021, 17, 983–990, doi:10.3762/bjoc.17.80

• apoptosis [1][2][3][4][5][6][7]. Due to its involvement in a wide range of cellular processes, significant efforts have been made in the last two decades targeting sphingosine analogues signalling as a therapeutic strategy. For instance, FTY720-P (3), the phosphate of FTY720 (2, fingolimod), proved to be a

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

• ]. In combination with the high selectivity for RNA sequences, this makes LNA-modified oligonucleotides well suited for use as antisense therapeutics. Recent publications have used LNA’s high affinity for RNA sequences in gapmer-designed antisense oligonucleotides for successful targeting of a key gene

Enhanced target cell specificity and uptake of lipid nanoparticles using RNA aptamers and peptides

• Roslyn M. Ray,
• Anders Højgaard Hansen,
• Maria Taskova,
• Bernhard Jandl,
• Jonas Hansen,
• Citra Soemardy,
• Kevin V. Morris and
• Kira Astakhova

Beilstein J. Org. Chem. 2021, 17, 891–907, doi:10.3762/bjoc.17.75

• Lipid nanoparticles (LNPs) constitute a facile and scalable approach for delivery of payloads to human cells. LNPs are relatively immunologically inert and can be produced in a cost effective and scalable manner. However, targeting and delivery of LNPs across the blood–brain barrier (BBB) has proven

• [9] and ligands [10], one can modulate the biodistribution of the LNP in the body. However, despite these advances, targeting of LNPs to the brain tissue remains a challenge [11]. In order to reach safer therapeutic options for treatment of brain diseases and disorders, a productive drug transport

• -1 aptamer incorporation into the LNP formulation does not appear to enhance specific targeting of gp160-expressing cells either through the hCMEC/D3 barrier or through direct addition, suggesting that it may not be an ideal candidate moving forward. LNPs do not stimulate an immune response In order

DNA with zwitterionic and negatively charged phosphate modifications: Formation of DNA triplexes, duplexes and cell uptake studies

• Yongdong Su,
• Maitsetseg Bayarjargal,
• Tracy K. Hale and
• Vyacheslav V. Filichev

Beilstein J. Org. Chem. 2021, 17, 749–761, doi:10.3762/bjoc.17.65

• The ability to detect and modify the genome of living organisms is important for the diagnosis, prevention, and treatment of many diseases [1]. The site-specific targeting and manipulation of genomic DNA or RNA using chemically modified short oligodeoxynucleotides (ONs) is considered to be a viable

Valorisation of plastic waste via metal-catalysed depolymerisation

• Francesca Liguori,
• Carmen Moreno-Marrodán and
• Pierluigi Barbaro

Beilstein J. Org. Chem. 2021, 17, 589–621, doi:10.3762/bjoc.17.53

• selective depolymerisation methods of plastics. Achievements are broken down according to the plastic material, namely polyolefins, polyesters, polycarbonates and polyamides. The focus is on recent advancements targeting sustainable and environmentally friendly processes. Biocatalytic or unselective

Synthesis and physicochemical evaluation of fluorinated lipopeptide precursors of ligands for microbubble targeting

• Masayori Hagimori,
• Estefanía E. Mendoza-Ortega and
• Marie Pierre Krafft

Beilstein J. Org. Chem. 2021, 17, 511–518, doi:10.3762/bjoc.17.45

• serine–glycine (SG)n segments rather than classical poly(oxyethylene) linkers between the lipid polar head and a targeting ligand were proposed for the liposome-mediated, selective delivery of anticancer drugs. Here, we report the synthesis of perfluoroalkylated lipopeptides (F-lipopeptides) bearing two

• hydrophobic chains (CnF2n+1, n = 6, 7, 8, 1–3) grafted through a lysine moiety on a hydrophilic chain composed of a lysine–serine–serine (KSS) sequence followed by 5 SG sequences. These F-lipopeptides are precursors of targeting lipopeptide conjugates. A hydrocarbon counterpart with a C10H21 chain (4) was

• . By contrast, the hydrocarbon lipopeptide led to microbubbles with a larger mean diameter and a significantly lower stability. Keywords: adsorption at fluid interfaces; drug delivery; microbubble targeting; molecular imaging; monolayer; perfluoroalkylated lipopeptide; solid-phase peptide synthesis

Synthetic strategies of phosphonodepsipeptides

• Jiaxi Xu

Beilstein J. Org. Chem. 2021, 17, 461–484, doi:10.3762/bjoc.17.41

• tetraacetate (Scheme 39) [60][61]. To develop novel bone-targeting prodrugs, a copper-catalyzed carbene insertion of tetraethyl diazomethyldiphosphonate (216) with N-Boc-protected amino acids 214 and 215 provided a simple method to synthesize phosphonodepsipeptides 217 and 218 containing a C-1

¹⁹F NMR as a tool in chemical biology

• Diana Gimenez,
• Aoife Phelan,
• Cormac D. Murphy and
• Steven L. Cobb

Beilstein J. Org. Chem. 2021, 17, 293–318, doi:10.3762/bjoc.17.28

• cell lines [44]. Here, the incorporation of CF3 and CF3O groups as NMR reporters into the tumour-targeting drug conjugates enabled the direct investigation of the mechanism of the pro-drug metabolic cleavage and the pharmacophore release by real-time 19F NMR analysis. 19F NMR was also employed as a

Novel library synthesis of 3,4-disubstituted pyridin-2(1H)-ones via cleavage of pyridine-2-oxy-7-azabenzotriazole ethers under ionic hydrogenation conditions at room temperature

• Romain Pierre,
• Anne Brethon,
• Sylvain A. Jacques,
• Aurélie Blond,
• Sandrine Chambon,
• Sandrine Talano,
• Catherine Raffin,
• Branislav Musicki,
• Claire Bouix-Peter,
• Loic Tomas,
• Gilles Ouvry,
• Rémy Morgentin,
• Laurent F. Hennequin and
• Craig S. Harris

Beilstein J. Org. Chem. 2021, 17, 156–165, doi:10.3762/bjoc.17.16

• -azabenzotriazole; hinge-binder; ionic hydrogenation; library; pyridine-2(1H)-one; Introduction During a recent medicinal chemistry program targeting a kinase to treat skin disorders, we identified the 4-amino-3-carboxamide disubstituted pyridine-2(1H)-one motif (1) as an interesting starting point. Recently, both

Supramolecular polymerization of sulfated dendritic peptide amphiphiles into multivalent L-selectin binders

• David Straßburger,
• Svenja Herziger,
• Katharina Huth,
• Moritz Urschbach,
• Rainer Haag and
• Pol Besenius

Beilstein J. Org. Chem. 2021, 17, 97–104, doi:10.3762/bjoc.17.10

• recently reported the successful application of functional supramolecular polymers in a biological context [30]. By decoration of the discotic peptide amphiphile monomers with dendritic mannose moieties, a specific cell targeting of macrophages and internalization in those antigen presenting cells has been

• achieved. As specific biological interactions strongly rely on the receptor–ligand interplays, we are interested in investigating the targeting of isolated receptors by supramolecular polymers built from peptide amphiphiles decorated with suitable ligand structures. The well-known L-selectin described

Molecular basis for protein–protein interactions

• Brandon Charles Seychell and
• Tobias Beck

Beilstein J. Org. Chem. 2021, 17, 1–10, doi:10.3762/bjoc.17.1

• functionality and the corresponding pathways. Important roles of PPIs include hormone reception [2], protease inhibition [3], antibody–antigen complexes [4], gene regulation [5], and large biomolecular assemblies [6]. PPI identification and prediction are important for targeting anticancer strategies [7

Semiautomated glycoproteomics data analysis workflow for maximized glycopeptide identification and reliable quantification

• Steffen Lippold,
• Arnoud H. de Ru,
• Jan Nouta,
• Peter A. van Veelen,
• Magnus Palmblad,
• Manfred Wuhrer and
• Noortje de Haan

Beilstein J. Org. Chem. 2020, 16, 3038–3051, doi:10.3762/bjoc.16.253

• developed to facilitate and improve both the identification and quantification of glycopeptides. Here, a selection of these tools was combined and evaluated with the aim of establishing a robust glycopeptide detection and quantification workflow targeting enriched glycoproteins. For this purpose, a tryptic

• targeting only a select set of glycoproteins. However, to capture the full complexity of, e.g., the human glycoproteome, improvements should be made in the automated integration between the described tools. In line with previous reports on single glycoproteins, the number of identified glycoforms was

Secondary metabolites of Bacillus subtilis impact the assembly of soil-derived semisynthetic bacterial communities

• Heiko T. Kiesewalter,
• Carlos N. Lozano-Andrade,
• Mikael L. Strube and
• Ákos T. Kovács

Beilstein J. Org. Chem. 2020, 16, 2983–2998, doi:10.3762/bjoc.16.248

• primarily against various filamentous fungi [47][48][49][50][51]. The broad-spectrum antibiotic bacillaene, synthesised by the pksB-S gene cluster, is mainly targeting bacterial protein synthesis [52]. Still, it was also shown that it could protect cells and spores from predation [53]. We recently

Selected peptide-based fluorescent probes for biological applications

• Debabrata Maity

Beilstein J. Org. Chem. 2020, 16, 2971–2982, doi:10.3762/bjoc.16.247

• ]. Peptides are comparatively small and can be easily synthesized in the laboratory using standard synthetic protocols [14][15]. The peptide sequence can be manipulated with precise functional groups of amino acids for selective targeting biomolecules. Peptides are large enough to contain a significant number

• to perform FRET in vitro and in vivo, particularly in living cells [30]. FRET-based peptide probes are heavily used for ratiometric fluorescence detection of biomolecules. Pyrene-functionalized oligonucleotides and locked nucleic acids (LNAs) are considerably used for targeting nucleic acids [31

• use of pyrene as a fluorophore has two major disadvantages such as poor quantum yield and an emission in the blue region, which is unfavorable for potential applications in biological systems. The Schmuck group successfully developed several peptide-based probes using these approaches for targeting

Synthesis and investigation of quadruplex-DNA-binding, 9-O-substituted berberine derivatives

• Jonas Becher,
• Daria V. Berdnikova,
• Heiko Ihmels and
• Christopher Stremmel

Beilstein J. Org. Chem. 2020, 16, 2795–2806, doi:10.3762/bjoc.16.230

• , G4-DNA-targeting ligands are searched for that bind selectively and sufficiently strong to quadruplex DNA and thereby influence the biological function of G-rich DNA sequences [17][18][19][20][21][22]. Among the numerous classes of compounds, mostly related to traditional DNA binders, that have been

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

• [20][21]. A number of elegant examples of self-assembled multivalent systems targeting biological analytes such as DNA, heparin, proteins, carbohydrates, etc. have been reported in the literature [22][23][24][25][26][27]. ATP is an important bio-anion that is the energy currency in cells and is

NMR Spectroscopy of supramolecular chemistry on protein surfaces

• Peter Bayer,
• Anja Matena and
• Christine Beuck

Beilstein J. Org. Chem. 2020, 16, 2505–2522, doi:10.3762/bjoc.16.203

• interaction of proteins with their interaction partners, both biomolecules and synthetic ligands. In recent years, the focus in chemistry has kept expanding from targeting small binding pockets in proteins to recognizing patches on protein surfaces, mostly via supramolecular chemistry, with the goal to

• recent years, the focus of biochemical research and drug development has shifted from the inhibition of single enzymes to targeting protein-protein interactions [1][2], which play key roles in cellular function and dysfunction [3][4]. Enzymes usually bind their substrates in deep pockets with specific

• inhibition of potassium ion transport [39]. Another guanidinium-calixarene variant was designed to hold together the four tetramer subunits of a p53-R337H tumor suppressor mutant and thus restore tetramer stability [40]. Further examples for ligands targeting negatively charged patches on proteins include

Naphthalene diimide bis-guanidinio-carbonyl-pyrrole as a pH-switchable threading DNA intercalator

• Poulami Jana,
• Filip Šupljika,
• Carsten Schmuck and
• Ivo Piantanida

Beilstein J. Org. Chem. 2020, 16, 2201–2211, doi:10.3762/bjoc.16.185

• spectroscopy methods (FDCD, CPL), the sensitivity of response is approaching the classical fluorimetric probes [14]. Our systematic work on aryl-guanidiniocarbonyl-pyrrole (GCP) derivatives characterised the GCP moiety as very useful building block in the design of new small molecules targeting DNA/RNA. The

• with diameter of 2 μm, or c) 500 nm. Done at pH 5, Na cacodylate buffer, I = 0.05 M. DNA-targeting roles of the structural components incorporated in the design of the novel small molecule. The NDI chromophore (DNA threading intercalator or possible groove binder) bearing two positive charges at

Photosensitized direct C–H fluorination and trifluoromethylation in organic synthesis

• Shahboz Yakubov and
• Joshua P. Barham

Beilstein J. Org. Chem. 2020, 16, 2151–2192, doi:10.3762/bjoc.16.183

Naphthalene diimide–amino acid conjugates as novel fluorimetric and CD probes for differentiation between ds-DNA and ds-RNA

• Annike Weißenstein,
• Myroslav O. Vysotsky,
• Ivo Piantanida and
• Frank Würthner

Beilstein J. Org. Chem. 2020, 16, 2032–2045, doi:10.3762/bjoc.16.170

• peptide chain and DNA/RNA interacting aromatic moiety, for instance peptide-based DNA/RNA-intercalators [1][2], as well as many DNA/RNA groove binding small molecules [3][4]. Inspired by these natural examples, the development of novel DNA/RNA targeting synthetic molecules has been in scientific focus for

• therefore adaptable for the design of FRET pairs with other dyes along the peptide backbone. Such amino acid construct would bring a novel functional property into peptide–multichromophore systems targeting DNA/RNA. For the design of our new constructs we noticed that the majority of DNA/RNA targeting NDIs

• peptide-backbone constructed multichromophores targeting FRET-based sensing [14][26][58]. For the application of here presented results in bioanalytical sciences or biologically relevant studies it will be necessary to further modify the presented compounds and precisely collect information about their