Methyltransferases from RiPP pathways: shaping the landscape of natural product chemistry

• Maria-Paula Schröder,
• Isabel P.-M. Pfeiffer and
• Silja Mordhorst

Beilstein J. Org. Chem. 2024, 20, 1652–1670, doi:10.3762/bjoc.20.147

• CsrA, which is a promising target for new anti-infective compounds. However, drug development is hampered by poor cellular uptake [86][87]. In the biosynthesis of cypemycin in Streptomyces sp. OH-4156, CypM adds two methyl groups to the N-terminal alanine residue. Cypemycin has a very narrow activity

Synthesis of new representatives of A₃B-type carboranylporphyrins based on meso-tetra(pentafluorophenyl)porphyrin transformations

• Victoria M. Alpatova,
• Evgeny G. Rys,
• Elena G. Kononova and
• Valentina A. Ol'shevskaya

Beilstein J. Org. Chem. 2024, 20, 767–776, doi:10.3762/bjoc.20.70

• biomacromolecule [10][11]. In this context, fluorinated porphyrins have attracted considerable interest due to their biological properties such as low toxicity, metabolic stability, and cellular uptake. The introduction of a fluorine atom into the molecule is the feasibility to change drastically its biological

Phenanthridine–pyrene conjugates as fluorescent probes for DNA/RNA and an inactive mutant of dipeptidyl peptidase enzyme

• Josipa Matić,
• Tana Tandarić,
• Marijana Radić Stojković,
• Filip Šupljika,
• Zrinka Karačić,
• Ana Tomašić Paić,
• Lucija Horvat,
• Robert Vianello and
• Lidija-Marija Tumir

Beilstein J. Org. Chem. 2023, 19, 550–565, doi:10.3762/bjoc.19.40

• cellular uptake and intracellular distribution of Phen-Py-1 in HeLa cells by TCS SP8 X confocal microscopy. The results showed that the dye entered the HeLa cell membranes fast, and after 1 hour of incubation at 1 µM concentration, blue fluorescence was visualized as the dye accumulated in the cell

Insight into oral amphiphilic cyclodextrin nanoparticles for colorectal cancer: comprehensive mathematical model of drug release kinetic studies and antitumoral efficacy in 3D spheroid colon tumors

• Sedat Ünal,
• Gamze Varan,
• Juan M. Benito,
• Yeşim Aktaş and
• Erem Bilensoy

Beilstein J. Org. Chem. 2023, 19, 139–157, doi:10.3762/bjoc.19.14

• (Figure 5a). Considering that the amount of drug and carrier is equal, it is thought that loading the drug into the nanoparticles may have increased cellular uptake and the amount of accumulated drug. When data from a 48-hour anticancer efficiency on HT29 cells was evaluated, it was observed that the drug

• concentration has been related to cell membrane fluidity and rigidity, treatment resistance in cancer cells, and drug uptake through the cell membrane. Excipients such as methyl-β-CD are widely used to extract cholesterol from cancer cells such as melanoma and MCF7 cells in order to promote cellular uptake of

Amamistatins isolated from Nocardia altamirensis

• Till Steinmetz,
• Wolf Hiller and
• Markus Nett

Beilstein J. Org. Chem. 2022, 18, 360–367, doi:10.3762/bjoc.18.40

• the presence of an oxazole or an oxazoline ring. Up to now, it is not clear whether these structural variations are biologically relevant in terms of iron sequestration and cellular uptake. Conclusion In summary, Nocardia altamirensis was found to synthesize various amamistatins under iron-deficient

Adjusting the length of supramolecular polymer bottlebrushes by top-down approaches

• Tobias Klein,
• Franka V. Gruschwitz,
• Maren T. Kuchenbrod,
• Ivo Nischang,
• Stephanie Hoeppener and
• Johannes C. Brendel

Beilstein J. Org. Chem. 2021, 17, 2621–2628, doi:10.3762/bjoc.17.175

• control of the assembly pathway and requires the use of organic solvents, such as THF and DMF, which limits the applicability in pharmaceutical formulations [21]. For an application in nanomedicine, a length in the range of 100–200 nm is particularly attractive to ensure cellular uptake and to access the

Post-functionalization of drug-loaded nanoparticles prepared by polymerization-induced self-assembly (PISA) with mitochondria targeting ligands

• Janina-Miriam Noy,
• Fan Chen and
• Martina Stenzel

Beilstein J. Org. Chem. 2021, 17, 2302–2314, doi:10.3762/bjoc.17.148

• evaluate the changes in cellular uptake or the toxicity of the conjugated arsenic drug. Attachment of TPP onto the PISA particles however was found not to enhance the mitochondrial accumulation, but it did influence overall the biological activity of pMPC-based particles in 2D and 3D cultured sarcoma SW982

• cells. When TPP was conjugated to the pMPC PISA particles more cellular uptake as well as better spheroid penetration were observed, while TPP on PEG-based PISA had only little effect. It was hypothesized that TPP on the micelle surface may not be accessible enough to allow mitochondria targeting, but

• of hydrophobic groups in the surface can reduce the hydration and limit cellular uptake [51][52]. It is therefore evident that more studies such as in-depth scattering studies are needed to fully elucidate the structure of the micelle [53]. Although TPP is present, it may not be fully available on

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

• uptake assay was conducted between two 12-mer poly-T ASOs, one being an α-ASO with a fully modified guanidinobutyl phosphoramidate backbone and the other a PS-β-ASO control, both fluorescein-labelled at the 5’-end. The study found that the guanidinium modification increased the cellular uptake. However

• carrying the dimethylamino groups had a higher effect on the cellular uptake for 5’-FAM-labelled ASOs relative to the oligomers carrying BCNS being primary amines. However, both modifications demonstrated an improved cellular uptake relative to the unmodified 5’-end FAM-labelled 2’-OMe ASO [115]. Another

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

• notably lagged behind and is still limited by insufficient bioavailability and difficulties with tissue specific delivery. Relatively high doses are required to overcome poor cellular uptake and endosomal entrapment, which increases the risk of toxicity. These limitations remain unsolved problems waiting

• folding in compact structures and aggregation in concentrated solutions [13]. Other bottlenecks for in vivo applications of PNA have been poor cellular uptake and unfavorable pharmacokinetics [14][15][16]. Unmodified PNAs are not taken up by eukaryotic cells in vitro and are cleared rapidly (within 10–30

• duplexes with complementary DNA and RNA, without compromising the sequence selectivity, and improved the cellular uptake of PNA [71]. The same group later demonstrated that GPNA derived from ᴅ-arginine formed more stable duplexes with RNA and was readily taken up by both human somatic and embryonic stem

Synthesis of 1-indolyl-3,5,8-substituted γ-carbolines: one-pot solvent-free protocol and biological evaluation

• Premansh Dudhe,
• Mena Asha Krishnan,
• Kratika Yadav,
• Diptendu Roy,
• Krishnan Venkatasubbaiah,
• Biswarup Pathak and
• Venkatesh Chelvam

Beilstein J. Org. Chem. 2021, 17, 1453–1463, doi:10.3762/bjoc.17.101

• experiments were performed. In brief, HeLa cells were incubated with carboline 3ac (10 μM and 100 nM), and the cellular uptake was examined using confocal microscopy (λex = 405 nm; λem = 420–470 nm). Compound 3ac showed excellent cytosolic uptake in cancer cells when incubated at a 10 μM concentration (Figure

• derivative 3ac (10 nM, 100 nM, 1 μM, 10 μM, and 100 μM), the cellular uptake and distribution was monitored by using confocal microscopy (λex = 405 nm; λem range = 420–470 nm). Selected examples of compounds containing the γ-carboline core. Single-crystal XRD structure of 3ac (CCDC: 1897787). UV–vis

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

• improving metabolic stability, pairing properties (RNA affinity), protein binding and transport/cellular uptake are concerned, chemical modifications are a prerequisite for the discovery and development of oligonucleotide therapeutics [11][12][13][14][15]. Thus, the natural PS and 2'-OMe backbone

• oligonucleotides challenging. Thio-LNA (Figure 7F), which has sulfur incorporated at the C2' position, has similar binding properties as amino-LNA and β-ᴅ-LNA, but with varying biodistribution patterns and a higher cellular uptake in mice [145]. Work looking at carba-LNA, which lacks the O2' functionality, has

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

• % increase in cellular uptake through the BBB and into target cells and that these cells had higher LNP uptake (measured by a higher MFI) than the non-antigen-expressing counterparts, while the gp160 aptamer (A-1) had no apparent effect on target cell uptake. One could speculate that this may be the result

• ability of these to aid delivery of LNP–aptamer species across the BBB. We found that LNPs with either T7 or the Tat peptide did not significantly increase cellular uptake through the BBB above the LNPs-containing aptamers alone. T7 appeared to have an effect on cellular uptake when the LNPs were directly

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 major challenge in designing chemically modified ONs as antigene/antisense agents is to ensure an efficient cellular uptake and nuclease resistance while still maintaining, or ideally increasing, binding affinity and specificity of the ONs towards their DNA or RNA target. Many synthetic analogues

• only 54 ± 3% of 4Ts-ON13 was intact after 120 min of enzymatic digestion (Figure 2, see also Figure S17 in Supporting Information File 1). N+ONs possessing more than four modifications showed a full enzymatic resistance after 120 min [38]. Cell-uptake study The cellular uptake of three modified ONs

• the modified ONs to enzymatic digestion by snake venom phosphodiesterase I. The FAM-labelled ONs were shown to enter cells without the use of a transfection reagent. After a 12 hour incubation, the Ts-ON was present in both the cytoplasm and nucleus. In comparison, there was less cellular uptake of 4N

Automated high-content imaging for cellular uptake, from the Schmuck cation to the latest cyclic oligochalcogenides

• Rémi Martinent,
• Javier López-Andarias,
• Dimitri Moreau,
• Yangyang Cheng,
• Naomi Sakai and
• Stefan Matile

Beilstein J. Org. Chem. 2020, 16, 2007–2016, doi:10.3762/bjoc.16.167

• results can be obtained from dose–response curves of the targeted delivery to selected cells and the cytotoxicity in the same experiment, even with poorly optimized cellular systems. Keywords: automation; cell-penetrating peptides; cellular uptake; cytosolic delivery; cytotoxicity; high-content imaging

• ]. This binding model 10 can be applied to cell-surface GAGs to enhance the cellular uptake efficiency. The peptide 9, with rhodamine B attached, successfully enters into the living cells while the control peptide 11 with a simple guanidinium group shows a negligible uptake efficiency. In addition, the

• transfection results. In contrast to the linear Schmuck peptides, the inactivity of a bafilomycin treatment in gene transfection processes indicates the nonendocytic cellular uptake pathway. Among the central challenges with CPPs in general are the cytotoxicity and the endosomal capture, particularly with an

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

• ester ring opening, while compound 11 demonstrated to be stable. The two compounds showed no toxicity on human primary fibroblasts. Further studies will be conducted to determine the cellular uptake of compounds 8 and 11. Structure of boronic acid analogues (for clarity, sugar numbering has been

Stereo- and regioselective hydroboration of 1-exo-methylene pyranoses: discovery of aryltriazolylmethyl C-galactopyranosides as selective galectin-1 inhibitors

• Alexander Dahlqvist,
• Axel Furevi,
• Niklas Warlin,
• Hakon Leffler and
• Ulf J. Nilsson

Beilstein J. Org. Chem. 2019, 15, 1046–1060, doi:10.3762/bjoc.15.102

• -linked glycans on the cell surface. Surface proteins such as integrins [6][7], vascular endothelial growth factor receptor [8], and lysosome-associated membrane proteins [9] are known to be crosslinked by galectins, giving galectins a modulating role in cell adhesion, blood vessel growth and cellular

• uptake and breakdown, respectively. The association of galectins to cell signaling and adhesion gives them roles in several different pathological processes, such as pulmonary fibrosis [6][10], pathological lymphangiogenesis [11], inflammation [12] and cancer [13], with galectin inhibitors demonstrated

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

• of the commercially available rhodamine dye, TAMRA (555ex/580em), to the dendrimer would allow for standard immunofluorescence assays, to track the microparticle following cellular uptake and intracellular processing. TAMRA’s high photostability, low pH sensitivity and ease of incorporation through

Cyclopropene derivatives of aminosugars for metabolic glycoengineering

• Jessica Hassenrück and
• Valentin Wittmann

Beilstein J. Org. Chem. 2019, 15, 584–601, doi:10.3762/bjoc.15.54

• approach, cells are cultivated with an unnatural carbohydrate derivative carrying a chemical reporter group. After cellular uptake, the derivative is deacetylated, metabolized by the biosynthetic machinery and incorporated into glycoconjugates. The chemical reporter group can then be visualized using a

• membrane glycoconjugates. However, many processes are responsible for the staining intensity of either intracellular or cell-surface proteins including cellular uptake of the carbohydrate derivative used for MGE, its metabolization, transport, speed of the ligation reaction, and the occurrence of

Pathoblockers or antivirulence drugs as a new option for the treatment of bacterial infections

• Matthew B. Calvert,
• Varsha R. Jumde and
• Alexander Titz

Beilstein J. Org. Chem. 2018, 14, 2607–2617, doi:10.3762/bjoc.14.239

• antagonize bacterial virulence [51]. AB toxins are widespread among species and consist of a catalytically active A-domain and one or more units of a receptor-binding domain B. The B domain is responsible for binding to a cell-surface receptor, which engages in receptor-mediated cellular uptake. The AB toxin

Comparative cell biological study of in vitro antitumor and antimetastatic activity on melanoma cells of GnRH-III-containing conjugates modified with short-chain fatty acids

• Eszter Lajkó,
• Sarah Spring,
• Rózsa Hegedüs,
• Beáta Biri-Kovács,
• Sven Ingebrandt,
• Gábor Mező and
• László Kőhidai

Beilstein J. Org. Chem. 2018, 14, 2495–2509, doi:10.3762/bjoc.14.226

• by all the tested conjugates. The modification of the GnRH-III in position 4 was accompanied by an increased cellular uptake, higher cytotoxic and cell adhesion inducer activity. By studying the cell movement of A2058 cells with a holographic microscope, it was found that the migratory behavior of

• unmodified GnRH-III-based one (GnRH-III(Dau=Aoa)) [17]. It is worth mentioning that the free Lys in this position also increased the in vitro cytostatic effect of the conjugate; however, its cellular uptake and enzyme stability were even lower than the parent conjugate had [17]. Therefore, it was not used in

• most potent one in all different assays (enzymatic stability, cellular uptake, and in vitro antitumor activity) on HT-29 colon carcinoma cell lines [19]. The different hydrophobicity of conjugates having a short, fatty acid side chain (2–6 carbon atoms) could be excluded as an explanation for their

Synthesis and photophysical studies of a multivalent photoreactive Ru^II-calix[4]arene complex bearing RGD-containing cyclopentapeptides

• Sofia Kajouj,
• Lionel Marcelis,
• Alice Mattiuzzi,
• Adrien Grassin,
• Damien Dufour,
• Pierre Van Antwerpen,
• Didier Boturyn,
• Eric Defrancq,
• Mathieu Surin,
• Julien De Winter,
• Pascal Gerbaux,
• Ivan Jabin and
• Cécile Moucheron

Beilstein J. Org. Chem. 2018, 14, 1758–1768, doi:10.3762/bjoc.14.150

• reactive-oxygen-species-dependent apoptosis. Another strategy for the design of cell penetrating photoreactive RuII complexes consists of tethering the complex to a vector that allows a cellular uptake. In this context, OsII, RhIII and RuII complexes were anchored to cell penetrating peptides (CPP) such as

Design and biological characterization of novel cell-penetrating peptides preferentially targeting cell nuclei and subnuclear regions

• Anja Gronewold,
• Mareike Horn and
• Ines Neundorf

Beilstein J. Org. Chem. 2018, 14, 1378–1388, doi:10.3762/bjoc.14.116

• ) with selective suborganelle-targeting properties. The nuclear localization sequence N50, as well as the nucleoli-targeting sequence NrTP, respectively, were fused to a shortened version of the cell-penetrating peptide sC18. We examined cellular uptake, subcellular fate and cytotoxicity of these novel

• peptides, N50-sC18* and NrTP-sC18*, and found that they are nontoxic up to a concentration of 50 or 100 µM depending on the cell lines used. Moreover, detailed cellular uptake studies revealed that both peptides enter cells via energy-independent uptake, although endocytotic processes cannot completely

• , all following uptake experiments were conducted at peptide concentrations between 1 and 10 μM, where no significant effect on cell viability was observed in both cell lines. Cellular uptake studies Next, we analyzed the intracellular fate of the new peptide variants using confocal fluorescence

Oligonucleotide analogues with cationic backbone linkages

• Melissa Meng and
• Christian Ducho

Beilstein J. Org. Chem. 2018, 14, 1293–1308, doi:10.3762/bjoc.14.111

• their oligoanionic phosphate diester backbone, severely hampers the penetration of biological barriers such as cellular membranes, thus leading to low cellular uptake. Second, unmodified ON structures are good substrates for nuclease-mediated degradation. Consequently, it is of vital importance to

• aspired improvement of cellular uptake, fully cationic oligonucleotide analogues might also be attractive candidate structures, as indicated by the advantageous properties of cationic cell-penetrating peptides (CPPs) [38]. However, the design of modifications of type 1–6 precludes the preparation of fully

• -functionalized analogues gave similar triplex stabilities. A fully cationic and fluorescently labelled guanidinylated oligonucleotide was subjected to comparative cellular uptake studies. Relative to its fluorescently labelled anionic phosphorothioate congener, it showed vastly enhanced cellular uptake

An overview of recent advances in duplex DNA recognition by small molecules

• Sayantan Bhaduri,
• Nihar Ranjan and
• Dev P. Arya

Beilstein J. Org. Chem. 2018, 14, 1051–1086, doi:10.3762/bjoc.14.93

• disrupting the NF-Y-ICB2 interaction. In addition, cellular uptake and nuclear localization of conjugate 22 could be easily monitored as a result of its inherent fluorescence property. Despite myriad important biological roles of hairpin and cyclic Py/Im polyamides in regulating natural gene expression via

• response element (ARE) and the estrogen response element (ERE) was synthesized in 12–17% overall yield. Selective modifications could also be done on the GABA turn units, which showed improved cellular uptake properties. Sugiyama et al. designed and synthesized a series of telomere-targeting synthetically

On the design principles of peptide–drug conjugates for targeted drug delivery to the malignant tumor site

• Eirinaios I. Vrettos,
• Gábor Mező and
• Andreas G. Tzakos

Beilstein J. Org. Chem. 2018, 14, 930–954, doi:10.3762/bjoc.14.80