Cell-free protein synthesis with technical additives – expanding the parameter space of in vitro gene expression

• Tabea Bartsch,
• Stephan Lütz and
• Katrin Rosenthal

Beilstein J. Org. Chem. 2024, 20, 2242–2253, doi:10.3762/bjoc.20.192

• for cell harvesting and washing was performed for 20 min at 3220g and storage was at −70 °C. The extract contained 46–67 mg/mL protein. It was premixed with the buffer consisting of magnesium and potassium glutamate, 20 amino acids, HEPES, ATP, GTP, cytidine triphosphate (CTP), uridine triphosphate

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

• synthesise SAM from ʟ-methionine and adenosine 5’-triphosphate (ATP) using a methionine adenosyltransferase. The MT then utilises SAM for the methylation reaction and the resulting SAH is degraded to adenine and S-ribosylhomocysteine, or to adenosine and ʟ-homocysteine [4][21][25]. To achieve complete SAM

Challenge N- versus O-six-membered annulation: FeCl₃-catalyzed synthesis of heterocyclic N,O-aminals

• Giacomo Mari,
• Lucia De Crescentini,
• Gianfranco Favi,
• Fabio Mantellini,
• Diego Olivieri and
• Stefania Santeusanio

Beilstein J. Org. Chem. 2024, 20, 1412–1420, doi:10.3762/bjoc.20.123

• imidazole and pyrazine pharmacophores, are well represented in the area of medicinal chemistry since they possess pharmacological properties as mammalian target of rapamycin (mTOR) inhibitors [7], adenosine triphosphate (ATP) competitive inhibitors of the insuline-like growth factor 1 (IGF-1) receptor

Synthesis of ether lipids: natural compounds and analogues

• Marco Antônio G. B. Gomes,
• Alicia Bauduin,
• Chloé Le Roux,
• Romain Fouinneteau,
• Wilfried Berthe,
• Mathieu Berchel,
• Hélène Couthon and
• Paul-Alain Jaffrès

Beilstein J. Org. Chem. 2023, 19, 1299–1369, doi:10.3762/bjoc.19.96

Recommendations for performing measurements of apparent equilibrium constants of enzyme-catalyzed reactions and for reporting the results of these measurements

• Robert N. Goldberg,
• Robert T. Giessmann,
• Peter J. Halling,
• Carsten Kettner and
• Hans V. Westerhoff

Beilstein J. Org. Chem. 2023, 19, 303–316, doi:10.3762/bjoc.19.26

• biochemical reaction and the many chemical reactions that accompany it is the hydrolysis reaction of ATP (adenosine 5’-triphosphate) to {ADP (adenosine 5’-diphosphate) + phosphate}: The apparent reaction quotient for this reaction is And the apparent equilibrium constant is Here, (aq) denotes that the

• .). In addition to the total concentration of ATP in all of its bound or liganded forms, one should report the unambiguous identifier of the substance that was actually used in the study. The identifiers can be a CAS number, a PubChem CID, ChEBI ID, or any database entry (e.g., adenosine 5′-triphosphate

New triazole-substituted triterpene derivatives exhibiting anti-RSV activity: synthesis, biological evaluation, and molecular modeling

• Elenilson F. da Silva,
• Krist Helen Antunes Fernandes,
• Denise Diedrich,
• Jessica Gotardi,
• Marcia Silvana Freire Franco,
• Carlos Henrique Tomich de Paula da Silva,
• Ana Paula Duarte de Souza and
• Simone Cristina Baggio Gnoatto

Beilstein J. Org. Chem. 2022, 18, 1524–1531, doi:10.3762/bjoc.18.161

• synthesis of guanosine triphosphate, which leads to a GTP depletion, thus, it prevents the replication of many RNA and DNA viruses [10]. Despite this, its efficacy has been controversial, as its use can cause hemolytic anemia, which is the leading cause for treatment being discontinued in 36% of real-life

Synthesis of the biologically important dideuterium-labelled adenosine triphosphate analogue ApppI(d₂)

• Petri A. Turhanen

Beilstein J. Org. Chem. 2022, 18, 1466–1470, doi:10.3762/bjoc.18.153

Make or break: the thermodynamic equilibrium of polyphosphate kinase-catalysed reactions

• Michael Keppler,
• Sandra Moser,
• Henning J. Jessen,
• Christoph Held and
• Jennifer N. Andexer

Beilstein J. Org. Chem. 2022, 18, 1278–1288, doi:10.3762/bjoc.18.134

• Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Str. 70, 44227 Dortmund, Germany 10.3762/bjoc.18.134 Abstract Polyphosphate kinases (PPKs) have become popular biocatalysts for nucleotide 5'-triphosphate (NTP) synthesis and regeneration. Two unrelated families are described: PPK1 and

• PPK2. They are structurally unrelated and use different catalytic mechanisms. PPK1 enzymes prefer the usage of adenosine 5'-triphosphate (ATP) for polyphosphate (polyP) synthesis while PPK2 enzymes favour the reverse reaction. With the emerging use of PPK enzymes in biosynthesis, a deeper understanding

• living organism investigated [1][2][3]. In 1956, Kornberg described the first polyP kinase (PPK) in Escherichia coli catalysing adenosine 5’-triphosphate (ATP)-dependent synthesis of polyP (Figure 2a) [4]. The enzyme was reclassified as family-1 PPK (PPK1) when a structurally different PPK (family-2

Shift of the reaction equilibrium at high pressure in the continuous synthesis of neuraminic acid

• Jannis A. Reich,
• Miriam Aßmann,
• Kristin Hölting,
• Paul Bubenheim,
• Jürgen Kuballa and
• Andreas Liese

Beilstein J. Org. Chem. 2022, 18, 567–579, doi:10.3762/bjoc.18.59

• standard activity assay was used for the free and immobilized enzymes. For the epimerase, the reaction conditions were 100 mM Tris, pH 8, 40 °C, 100 mM N-acetyl-ᴅ-glucosamine, 1 mM adenosine triphosphate, 1 mM MgCl2, and 10 g/L immobilized enzyme or 2.5 mg/L free enzyme, respectively. For the aldolase, the

Synthetic strategies toward 1,3-oxathiolane nucleoside analogues

• Umesh P. Aher,
• Dhananjai Srivastava,
• Girij P. Singh and
• Jayashree B. S

Beilstein J. Org. Chem. 2021, 17, 2680–2715, doi:10.3762/bjoc.17.182

• triphosphate substrate to bind to cellular DNA polymerase and viral reverse transcriptase [9]. The effectiveness of nucleoside analogues depends on the ability to replicate naturally occurring nucleosides, interfering with viral as well as cellular enzymes and hampering essential metabolism processes of

• ), which may be responsible for such differences [24]. Initial results point at a conventional mechanism of action. Therein, the investigation of the cellular metabolism predicts triphosphate formation of the compounds by phosphorylation, and the resulting nucleotide is a selective inhibitor of the HIV-1

• inhibitors [26][27][28]. 3TC (1) has a β-ʟ-oxathiolane ring structure, instead of the ribose ring in the canonical nucleosides, and studies have shown that the triphosphate of 1 (i.e., 3TCTP) inhibits reverse transcriptase due to DNA chain termination [26][29][30]. In comparison to some of the other NRTIs

Biochemistry of fluoroprolines: the prospect of making fluorine a bioelement

• Vladimir Kubyshkin,
• Rebecca Davis and
• Nediljko Budisa

Beilstein J. Org. Chem. 2021, 17, 439–460, doi:10.3762/bjoc.17.40

• of the native substrate, proline [83]. After being released from ProRS, the charged Pro-tRNAPro binds to the elongation factor Tu, which also binds a molecule of guanosine triphosphate (GTP). The resulting complex (known as the ternary complex) docks to an empty A-site of a translating ribosome

Selected peptide-based fluorescent probes for biological applications

• Debabrata Maity

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

• serum albumin. Other biomolecules such as adenosine, adenosine monophosphate, adenosine triphosphate, phosphate, pyrophosphate, glucose, heparin, hyaluronic acid and chondroitin sulfate, and amino acids containing two carboxylates (glutamic acid and aspartic acid) have not increased the fluorescence

Incorporation of a metal-mediated base pair into an ATP aptamer – using silver(I) ions to modulate aptamer function

• Marius H. Heddinga and
• Jens Müller

Beilstein J. Org. Chem. 2020, 16, 2870–2879, doi:10.3762/bjoc.16.236

• modulate the affinity of an aptamer towards its target. In particular, two artificial imidazole 2’-deoxyribonucleosides (Im) were incorporated into various positions of an established ATP-binding aptamer (ATP, adenosine triphosphate), resulting in the formation of three aptamer derivatives bearing Im:Im

• triphosphate) [25]. The choice of this aptamer was expected to have various advantages. 1) Its three-dimensional structure has been reported [26], so the position for the incorporation of the metal-mediated base pair can be chosen in a meaningful way. 2) Its structure is based on a duplex rather than a

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

• /bjoc.16.219 Abstract Gold nanoparticles covered with a mixture of ligands of which one type contains solubilizing triethylene glycol residues and the other peripheral zinc(II)–dipicolylamine (DPA) complexes allowed the optical detection of hydrogenphosphate, diphosphate, and triphosphate anions in

• depended on the nature of the anion, with diphosphate and triphosphate inducing visual changes at significantly lower concentrations than hydrogenphosphate. In addition, the sensing sensitivity was also affected by the ratio of the ligands on the nanoparticle surface, decreasing as the number of

• immobilized zinc(II)–dipicolylamine groups increased. A nanoparticle containing a 9:1 ratio of the solubilizing and the anion-binding ligand showed a color change at diphosphate and triphosphate concentrations as low as 10 μmol/L, for example, and precipitated at slightly higher concentrations

Reaction of indoles with aromatic fluoromethyl ketones: an efficient synthesis of trifluoromethyl(indolyl)phenylmethanols using K₂CO₃/n-Bu₄PBr in water

• Thanigaimalai Pillaiyar,
• Masoud Sedaghati and
• Gregor Schnakenburg

Beilstein J. Org. Chem. 2020, 16, 778–790, doi:10.3762/bjoc.16.71

• triphosphate (Table 1, entry 12; 76%) did not improve the yield. These results suggest that K2CO3 is the best catalyst for the reaction among the bases investigated. To find the best catalytic system, other quaternary salts were invested in the reaction. When tetrabutylammonium chloride (TBAC) or

An azobenzene container showing a definite folding – synthesis and structural investigation

• Abdulselam Adam,
• Saber Mehrparvar and
• Gebhard Haberhauer

Beilstein J. Org. Chem. 2019, 15, 1534–1544, doi:10.3762/bjoc.15.156

• far, a series of receptors based on these macrocycles were synthesized. They have been designed for the selective recognition of sulfate ions [4][5][6], di- and triphosphate ions [7], for sensing of pyrophosphate ions in aqueous solutions [8], as receptors for phenols [9], α-chiral primary

Complexation of a guanidinium-modified calixarene with diverse dyes and investigation of the corresponding photophysical response

• Yu-Ying Wang,
• Yong Kong,
• Zhe Zheng,
• Wen-Chao Geng,
• Zi-Yi Zhao,
• Hongwei Sun and
• Dong-Sheng Guo

Beilstein J. Org. Chem. 2019, 15, 1394–1406, doi:10.3762/bjoc.15.139

• photoactivity of photosensitizers (PSs) were annihilated by the complexation of guanidinium-modified calix[5]arene pentadodecyl ether while reactivated by adenosine triphosphate (a cancer biomarker) displacement. This novel supramolecular phototheranostics strategy realized both tumor-selective imaging and

New standards for collecting and fitting steady state kinetic data

• Kenneth A. Johnson

Beilstein J. Org. Chem. 2019, 15, 16–29, doi:10.3762/bjoc.15.2

• the alternate substrates are well known. Moreover, it is easy to perform single turnover kinetic measurements to examine steps leading up to the chemical reaction by mixing an enzyme DNA complex with only one nucleoside triphosphate. Recent work on DNA polymerase fidelity has shown that the rate of

Synthesis of new p-tert-butylcalix[4]arene-based polyammonium triazolyl amphiphiles and their binding with nucleoside phosphates

• Vladimir A. Burilov,
• Guzaliya A. Fatikhova,
• Mariya N. Dokuchaeva,
• Ramil I. Nugmanov,
• Diana A. Mironova,
• Pavel V. Dorovatovskii,
• Victor N. Khrustalev,
• Svetlana E. Solovieva and
• Igor S. Antipin

Beilstein J. Org. Chem. 2018, 14, 1980–1993, doi:10.3762/bjoc.14.173

• for nucleotides sensing through a dye replacement procedure. It is unusual that disubstituted macrocycles 10a,b bind more effectively a less charged adenosine 5'-diphosphate (ADP) than adenosine 5'-triphosphate (ATP). A simple colorimetric method based on polydiacetylene vesicles decorated with 10b

• are very important as a universal energy source and as intracellular mediators in many biological processes [6]. In the cellular metabolism, adenosine 5'-triphosphate (ATP) is hydrolyzed to adenosine 5'-monophosphate (AMP) or adenosine 5'-diphosphate (ADP) by enzymes [7]. Thus, the receptors for

• this reason the triphosphate fragment is rotated by ≈60° around the calixarene axis relative to the diphosphate position (Figure 4b and d). This leads to a weakening of the host–guest binding and to a decrease of ATP complex energy by 1.4 kcal/mol compared to ADP. So the ADP/ATP optical responses for

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

• kinases. Gemcitabine diphosphate (dFdCDP) and gemcitabine triphosphate (dFdCTP) are the active metabolites which inhibit processes required for DNA synthesis [91]. The incorporation of dFdCTP into DNA during polymerization, which causes DNA polymerases unable to proceed, is the major mechanism by which

Recent advances in synthetic approaches for medicinal chemistry of C-nucleosides

• Kartik Temburnikar and
• Katherine L. Seley-Radtke

Beilstein J. Org. Chem. 2018, 14, 772–785, doi:10.3762/bjoc.14.65

• endothelial cells and RSV with low cytotoxicity towards Huh-7, HEp-2 and MT4 cells. Moreover, the triphosphate of 4 selectively inhibits, HCV RdRp and RSV RdRp over human RNA Pol II and DNA polymerases (α, β, γ) [65]. The 2'-Me compound 7 as its triphosphate (TP) shows anti-HCV activity in replicon assays [77

• it to the masked monophosphates (10 and 11, Figure 7C), which serves to facilitate transport into the infected cells, and conversion to the active triphosphate form, thereby leading to high and persistent levels [63][64][65]. The 2-ethylbutyl L-alanine phosphoramidate prodrug (Sp isomer, GS-5734, 11

• ) increases the loading of macrophages derived from human monocytes over its unmasked analogue [64]. It was also observed that intravenous administration of the prodrug leads to increased liver loading (as the triphosphate) in hamsters compared to oral dosing [63]. Draffan et al. synthesized a series of 2'-β

An uracil-linked hydroxyflavone probe for the recognition of ATP

• Márton Bojtár,
• Péter Zoltán Janzsó-Berend,
• Dávid Mester,
• Dóra Hessz,
• Mihály Kállay,
• Miklós Kubinyi and
• István Bitter

Beilstein J. Org. Chem. 2018, 14, 747–755, doi:10.3762/bjoc.14.63

• ; nucleotide recognition; Introduction Nucleotides play essential roles in various physiological processes, such as energy transportation [1], DNA synthesis [2] and cell signaling events [3]. Especially, adenosine-5’-triphosphate (ATP) is vital, since it is the main energy source in living systems [4]. The

• -5’-triphosphate, GTP) and the strong solvation of the chemosensor and the analyte in aqueous media, reducing the association constant of their complex, and through that the sensitivity of the sensor [31][32]. The molecular recognition of nucleotides in most chemosensors is achieved by charged

• optimized geometries are presented in Figure 2. The investigation of the DEHF∙ATP 1:1 complex revealed a sandwich structure, which is held together by a π–π stacking- and an H-bond interaction. The triphosphate group is positioned near ring C of the DEHF and the π-stacking occurs between the adenine group

Synthetic mRNA capping

• Fabian Muttach,
• Nils Muthmann and
• Andrea Rentmeister

Beilstein J. Org. Chem. 2017, 13, 2819–2832, doi:10.3762/bjoc.13.274

• ; enzymatic capping; methyltransferase; RNA; Introduction The 5′-cap is a hallmark of eukaryotic mRNA and involved in numerous interactions required for cellular functions. Chemically, the 5′-cap consists of an inverted 7-methylguanosine connected to the rest of the eukaryotic mRNA via a 5′–5′ triphosphate

• ′-triphosphate. The most commonly used cap analogue is m7GpppG but several modified or alternative cap analogues are also accepted by RNA polymerases. Therefore, this route can be used to install non-natural dinucleotides at the 5′-end that are accessible for a further chemical reaction [46]. One often

• diphosphate (GDP, 15) and guanosine monophosphate (GMP, 16, Figure 4B), which are both accessible by phosphorylation of guanosine [54]. Methylation of GDP gives m7GDP (17) with high yield and regioselectivity [55]. The key step in cap analogue synthesis is the formation of the triphosphate linkage. Multiple

Oxidative dehydrogenation of C–C and C–N bonds: A convenient approach to access diverse (dihydro)heteroaromatic compounds

• Santanu Hati,
• Ulrike Holzgrabe and
• Subhabrata Sen

Beilstein J. Org. Chem. 2017, 13, 1670–1692, doi:10.3762/bjoc.13.162

• Hantzch 1,4-DHPs. DABCO and TEMPO-catalyzed aerobic oxidative dehydrogenation of quinazolines and 4H-3,1-benzoxazines. Putative mechanism for Cu(I)–DABCO–TEMPO catalyzed aerobic oxidative dehydrogenation of tetrahydroquinazolines. Potassium triphosphate modified Pd/C catalysts for the oxidative

G-Protein coupled receptors: answers from simulations

• Timothy Clark

Beilstein J. Org. Chem. 2017, 13, 1071–1078, doi:10.3762/bjoc.13.106

• the G-protein. On activation, bound guanosine diphosphate (GDP) in the G-protein is replaced by the triphosphate (GTP) and the α-subunit separates from β/γ. The separated G-protein subunits migrate to effectors in the nearby membrane, where GTP is hydrolyzed to GDP and the signaling cascade initiated