Switchable molecular tweezers: design and applications

• Pablo Msellem,
• Maksym Dekthiarenko,
• Nihal Hadj Seyd and
• Guillaume Vives

Beilstein J. Org. Chem. 2024, 20, 504–539, doi:10.3762/bjoc.20.45

• frequently employed in biological systems for communication and actuation (e.g., ATP). They, however, generate waste which is very well managed in biological systems by using compartmentalization strategies. Nonetheless, the challenge of waste management in artificial systems remains significant. On the

Development of a chemical scaffold for inhibiting nonribosomal peptide synthetases in live bacterial cells

• Fumihiro Ishikawa,
• Sho Konno,
• Hideaki Kakeya and
• Genzoh Tanabe

Beilstein J. Org. Chem. 2024, 20, 445–451, doi:10.3762/bjoc.20.39

• (Figure 1) [3]. The adenylation (A) domain in NRPSs is responsible for the selection and activation of amino acids, hydroxy acids, and aryl acids upon ATP consumption (Figure 2a) [4]. The activated aminoacyladenosine monophosphate (AMP) is transferred to the thiol group of a phosphopantetheine prosthetic

Identification of the p-coumaric acid biosynthetic gene cluster in Kutzneria albida: insights into the diazotization-dependent deamination pathway

• Seiji Kawai,
• Akito Yamada,
• Yohei Katsuyama and
• Yasuo Ohnishi

Beilstein J. Org. Chem. 2024, 20, 1–11, doi:10.3762/bjoc.20.1

• biosynthesis by heterologous expression of the cma cluster and in vitro enzyme assays using recombinant Cma proteins. The ATP-dependent diazotase CmaA6 catalyzed the diazotization of both 3-aminocoumaric acid and 3-aminoavenalumic acid using nitrous acid in vitro. In addition, the high efficiency of the CmaA6

• recent studies [9][10][11][12][13][14]. Most of them belong to the adenylate-forming enzyme superfamily (ANL superfamily) and utilize ATP to activate nitrous acid by AMPylation, with the only exception being AzpL in alazopeptin biosynthesis, which is a membrane protein that catalyzes diazotization

• , presumably in an ATP-independent manner [9][10][11][12][13][14]. Moreover, the genome database analysis indicated that there are many orphan BGCs containing genes encoding the ANS pathway, which implies that the biosynthesis of many unknown natural products requires nitrous acid derived from the ANS pathway

Synthesis of 5-arylidenerhodanines in L-proline-based deep eutectic solvent

• Stéphanie Hesse

Beilstein J. Org. Chem. 2023, 19, 1537–1544, doi:10.3762/bjoc.19.110

• compounds and allow, for example, the formation of rhodanine-fused spiro[pyrrolidine-2,3′-oxindoles] D having antidiabetic activity [6]. Thiazolidinediones and thiazolidinones were found to be potent moieties of a series of furan-2-ylmethylenethiazolidinediones E that were studied as selective ATP

Enabling artificial photosynthesis systems with molecular recycling: A review of photo- and electrochemical methods for regenerating organic sacrificial electron donors

• Grace A. Lowe

Beilstein J. Org. Chem. 2023, 19, 1198–1215, doi:10.3762/bjoc.19.88

• been used in artificial photosynthesis research to model different key photosynthesis processes. In plants, photosynthesis is a complex process where light-harvesting reactions are carried out in two photosystems to split water and recycle NADH and ADP. NADPH and ATP are then consumed in the Calvin

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

• reaction is taking place in aqueous media and c denotes the respective concentrations (units of mol∙dm−3) of total amounts of ATP, ADP, and phosphate. Note that Q′ and K′ have the same form but they differ critically in that a measured value of K′ refers to Equation 1 having been established to be at

• equilibrium. The total ATP concentration is the sum of the concentrations of the individual ionic species formed by the protonation or metal ion binding reactions of the ATP species Additional metal ion complexes (e.g., involving Ca2+, K+, and Na+) can also be included in Equation 4. Similar expressions can

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

• Petri A. Turhanen University of Eastern Finland, School of Pharmacy, Biocenter Kuopio, P.O. Box 1627, FIN-70211, Kuopio, Finland 10.3762/bjoc.18.153 Abstract The chemical synthesis of the dideuterium-labelled ATP analogue 1-adenosin-5’-yl-3-(3-methylbut-3-en-1,1-d2-1-ol) triphosphoric acid

• spectrometry. Keywords: ApppI; ATP; deuterium labelling; HPCCC; mevalonate pathway; NMR; synthesis; Introduction It has become clear and evident that phosphonate chemistry plays a crucial role in drug research and development [1][2][3][4]. There are several phosphonate-containing compounds under research or

• the formation of ApppI, i.e., the isopentenyl ester of ATP (Figure 2), which may also isomerize to ApppD (Figure 2). The authors have also concluded that these compounds can act in two different ways: inhibition of the mevalonate pathway and blockade of mitochondrial ADP/ATP translocase, which is

On drug discovery against infectious diseases and academic medicinal chemistry contributions

• Yves L. Janin

Beilstein J. Org. Chem. 2022, 18, 1355–1378, doi:10.3762/bjoc.18.141

• consider the much less studied novobiocin (62) depicted in Figure 10. This compound is another naturally occurring antibiotic which was isolated in 1955 [311]. It turned out to be the first inhibitor of the bacterial ATP-ase function of gyrases found and it was actually instrumental in the discovery of

• these enzymes [312][313]. Since the ATP-ase function of these type IIA topoisomerases are not currently targeted by any prescribed antibiotics and since novobiocin (62) was banned in the past from humans use [314], it could be of interest to improve its very poor pharmacology. How about by removing its

• pharmacological data already available for this class of inhibitors such as compounds 63–65 [115][315]. Indeed, out of the structure–activity relationship of the many series of inhibitors of the ATP-ase function of type IIA topoisomerases discovered, it seems plausible to design and synthesize hybrids, combining

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

• 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

• concentrations of substrate, the different kinetic preferences of PPK1 and PPK2 can be observed. The implications of these results for the application of PPKs in chemical synthesis and as enzymes for ATP regeneration systems are discussed. Keywords: ATP regeneration; biocatalyst; ePC-SAFT; polyp; PPK

• 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

Isolation and biosynthesis of daturamycins from Streptomyces sp. KIB-H1544

• Yin Chen,
• Jinqiu Ren,
• Ruimin Yang,
• Jie Li,
• Sheng-Xiong Huang and
• Yijun Yan

Beilstein J. Org. Chem. 2022, 18, 1009–1016, doi:10.3762/bjoc.18.101

• , the DatA protein was expressed and purified (Figure 4B). Incubating DatA with substrate 7 and ATP resulted in a new product 8, which was confirmed by HRMS–ESI data (m/z 291.0663 [M − H]−, calcd for ([C18H12O4] − H)−, 291.0663) (Figure S22, Supporting Information File 1). The product was not present in

• enzymatic activity was tested in a 100 μL reaction mixture containing 100 mM Tris-HCl (pH 7.5), 10 mM MgCl2, 300 mM NaCl, 5 mM ATP, 0.5 mM phenylpyruvic acid and 5 μM DatA (or EchA), at 30 °C for 2 h. The reaction mixture was quenched by adding 200 μL methanal and then centrifuged at 12,000 rpm for 10 min

Heteroleptic metallosupramolecular aggregates/complexation for supramolecular catalysis

• Prodip Howlader and
• Michael Schmittel

Beilstein J. Org. Chem. 2022, 18, 597–630, doi:10.3762/bjoc.18.62

• allows, as demonstrated by Nature by the multicomponent ATP synthase motor, a more detailed and refined configuration of purposeful machinery. Furthermore, (metallo)supramolecular catalysis is shown to extend beyond the single "supramolecular unit" and to reach far into the field and concepts of systems

• multicomponent ATP synthase motor [23], a more detailed and refined configuration of purposeful machinery [24]. For the preparation of heteroleptic aggregates, one must differentiate between dynamic (rapidly exchanging) and kinetically inert heteroleptic metal–ligand interactions. While the inert heteroleptic

• stabilized within the catalytic cavity. Release from the active site then requires destruction of the stabilizing interactions. For instance, Nature has chosen in the ATP-synthase to use “fueled” nanomechanical motion to release ATP from the active site [23]. Switchable catalysis due to reversible assembly

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

• . Enzyme loading after immobilization of the epimerase and aldolase on different carriers. Evaluation of immobilized epimerase on different carriers with respect to specific activity. Reaction conditions: 40 °C, pH 8, 100 mM Tris, Ushaking = 1400 rpm, V = 1 mL, 100 mM GlcNAc, 1 mM ATP, 1 mM MgCl2, immo

• experiments of the immobilized epimerase on polymethacrylate DVB, epoxy methacrylate and epoxy butyl methacrylate. Reaction conditions: 40 °C, pH 8, 100 mM Tris, Ushaker = 1400 rpm, V = 1 mL, immo epimerase 1% (w/v), 100 mM N-acetyl-ᴅ-glucosamine, 1 mM ATP, 1 mM MgCl2. Relative activities in repetitive batch

• aldolase. Assay conditions: 100 mM Tris, pH 8, 40 °C, shaking with 1000 rpm, V = 1 mL. Between the batches the carrier was washed with 100 mM Tris pH 8 and stored until the next application at 4 °C. Reaction conditions: (i) immo epimerase: 100 mM N-acetyl-ᴅ-glucosamine, 1 mM ATP, 1 mM MgCl2, 10 gcarrier/L

(Phenylamino)pyrimidine-1,2,3-triazole derivatives as analogs of imatinib: searching for novel compounds against chronic myeloid leukemia

• Luiz Claudio Ferreira Pimentel,
• Lucas Villas Boas Hoelz,
• Henayle Fernandes Canzian,
• Frederico Silva Castelo Branco,
• Andressa Paula de Oliveira,
• Vinicius Rangel Campos,
• Floriano Paes Silva Júnior,
• Rafael Ferreira Dantas,
• Jackson Antônio Lamounier Camargos Resende,
• Anna Claudia Cunha,
• Nubia Boechat and
• Mônica Macedo Bastos

Beilstein J. Org. Chem. 2021, 17, 2260–2269, doi:10.3762/bjoc.17.144

• TKIs that are even more potent than IMT, such as nilotinib [6][7]. These drugs act as inhibitors at the ATP binding site in the inactive form of BCR-Abl-1, preventing the binding of the protein to ATP in a competitive manner and resulting in the interruption of the substrate phosphorylation process and

• compared to IMT (Table 2). The lacking of that interaction prevents the pyridine ring from mimicking the ATP adenine in the hinge region [39]. As previously mentioned, the absence of the hydrogen-bond interaction between the Glu305 residue and the amide group of 2c, 2d, and 2g (Figure 4b–d) also

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

• + 2H2 → CH2O + H2O [57]. The energy to fuel the process is associated with the vectorial chemistry of the electron transfer chain and the mitochondrial chemiosmotic generation of ATP, a suggestion by Mitchell long considered heretic in the biochemistry community, which searched for decades the highly

• reactive intermediate capable of transferring a phosphate group to ATP. The Guareschi “1897 reaction” shows a basically different strategy to generate reductive power, associated to aromatization of a prearomatic substrate. The chemiosmotic generation of energy is as universal as the genetic code, and the

Synthetic accesses to biguanide compounds

• Oleksandr Grytsai,
• Cyril Ronco and
• Rachid Benhida

Beilstein J. Org. Chem. 2021, 17, 1001–1040, doi:10.3762/bjoc.17.82

Synthetic strategies of phosphonodepsipeptides

• Jiaxi Xu

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

• , indicating that this strategy was not suitable for the synthesis of γ-phosphonodepsipeptides (Scheme 13) [28]. Folylpolyglutamate synthetase catalyzes an ATP-dependent ligation reaction. The reaction results in the synthesis of poly(γ-glutamate) metabolites of folates and some antifolates. Three γ

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

• proline as an external nutrient [65]. Another important transport system is the ATP-binding proline/betaine transporter. In E. coli, this permease activates in the course of osmotic shock response, represented by the transporter gene proP and the proU operon. The genes proV (encoding an ATP-binding

• biosynthesis occurs in an enzyme called aminoacyl-tRNA synthetase (AARS). An AARS usually performs several sequential steps (Figure 10A). First, an amino acid that fits into the binding pocket reacts with a molecule of ATP creating an aminoacyl adenylate. This step is called activation. An aminoacyl adenylate

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

The preparation and properties of 1,1-difluorocyclopropane derivatives

• Kymbat S. Adekenova,
• Peter B. Wyatt and
• Sergazy M. Adekenov

Beilstein J. Org. Chem. 2021, 17, 245–272, doi:10.3762/bjoc.17.25

Synthesis, crystal structures and properties of carbazole-based [6]helicenes fused with an azine ring

• Daria I. Tonkoglazova,
• Anna V. Gulevskaya,
• Konstantin A. Chistyakov and
• Olga I. Askalepova

Beilstein J. Org. Chem. 2021, 17, 11–21, doi:10.3762/bjoc.17.2

• last, carbazole-based heterohelicenes were found in nature, for example, purpurone [55] isolated from the marine sponge Iotrochota sp. and having an inhibitory effect on the ATP-citrate lyase, and the marine alkaloid ningalin D produced by Didemnum sp., Dictyodendrins [56] isolated from Dictyodendrilla

Selected peptide-based fluorescent probes for biological applications

• Debabrata Maity

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

• 540 nm in presence of 10 µM ATP (Figure 2B). The ATP binding constant is calculated to be 2.2 × 105 M−1. A fluorescence job plot between 1 and ATP confirms an 1:1 binding stoichiometry between ATP and probe 1. The fluorescence response follows the following order ATP > GTP > UTP > CTP > TTP > PPi

• , UMP, TBAP, MMP or other anions (SO42−, NO3−, HCO3−, CH3COO−) does not show any enhancement of fluorescence enabling the probe as selective for nucleoside triphosphates. The probe 1 is not toxic and has been demonstrated by fluorescence imaging of ATP in HeLa cells (Figure 2A, inset). Nucleic acid

• biological analytes including such as adenosine, adenosine monophosphate (AMP), adenosine triphosphates (ATP), phosphate (Pi), pyrophosphate (PPi), ct-DNA, glucose, bovine serum albumin (BSA), glutamic acid and aspartic acid. They are also selective over the similar biological analytes hyaluronic acid or

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

• mispairs with a reduced ATP affinity. A fluorescence spectroscopy assay and a binding assay with immobilized ATP were used to evaluate the aptamer derivatives. Upon the addition of one Ag(I) ion per mispair, stabilizing Im–Ag(I)–Im base pairs were formed. As a result, the affinity of the aptamer derivative

• towards ATP is restored again. The silver(I)-mediated base-pair formation was particularly suitable to modulate the aptamer function when the Im:Im mispairs (and hence the resulting metal-mediated base pairs) were located close to the ATP-binding pocket of the aptamer. Being able to trigger the aptamer

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

• presence of positive surface charges on the multivalent aggregates led to ATP binding which was accompanied by a significant increase in the excimeric emission intensity. This provided a convenient way of monitoring ATP binding in a “turn-on” mode and an efficient detection of ATP was achieved in aqueous

• buffer and also in buffer containing 150 mM NaCl at physiological pH value. Furthermore, the multivalent aggregates demonstrated a significant selectivity in ATP detection over ADP, AMP and pyrophosphate. Keywords: amphiphile; ATP; excimer; multivalency; self-assembly; Introduction Supramolecular anion

• [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

• [122][123], extend the possibility to monitor binding events to very large protein assemblies by NMR. It has mostly been used to investigate protein–protein interactions within large multi-protein assemblies [120][121] and the effect of small natural ligands like ATP or ADP on the dynamics of

Palladium-catalyzed synthesis and nucleotide pyrophosphatase inhibition of benzo[4,5]furo[3,2-b]indoles

• Hoang Huy Do,
• Saif Ullah,
• Alexander Villinger,
• Joanna Lecka,
• Jean Sévigny,
• Peter Ehlers,
• Jamshed Iqbal and
• Peter Langer

Beilstein J. Org. Chem. 2019, 15, 2830–2839, doi:10.3762/bjoc.15.276

• aryl substituent located on the nitrogen atom. Nucleotide pyrophosphatase activity Nucleotide pyrophosphatases belong to the family of ecto-nucleotidases [34][35]. They can hydrolyze nucleotides, dinucleotides, and nucleotide sugars, e.g., ATP, ADP, NAD+, ADP-ribose and diadenosine polyphosphates [36