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

• nucleotides and amino acids, as well as energy molecules, salts, buffer, etc., are added. After successful protein synthesis, further substrates can be added for an enzyme activity assay. Although mimicking of cell-like conditions is an approach for optimization, the physical and chemical properties of CFPS

• biocatalysts [1][2]. The open environment allows easy manipulation of the protein synthesis [3] and coupling to subsequent enzyme activity assays, e.g., for substrate screening [4][5]. The CFPS system is advantageous for proteins that are difficult to express in a viable host cell, e.g., due to toxic effects

Natural resorcylic lactones derived from alternariol

• Joachim Podlech

Beilstein J. Org. Chem. 2024, 20, 2171–2207, doi:10.3762/bjoc.20.187

• ring was isolated from Ulocladium botrytis [219] and Microsphaeropsis olivacea [167]. Its structure was unambiguously confirmed by NMR spectroscopy and by total syntheses [44][220]. Ulocladol is a tyrosine kinase (p56lck) inhibitor leading to a reduction of enzyme activity to 7% at 0.02 µg/µL) [219

Polymer degrading marine Microbulbifer bacteria: an un(der)utilized source of chemical and biocatalytic novelty

• Weimao Zhong and
• Vinayak Agarwal

Beilstein J. Org. Chem. 2024, 20, 1635–1651, doi:10.3762/bjoc.20.146

• [48]. The three-dimensional structure of CEST revealed that it belongs to the α/β-class of proteins consisting of a central six-stranded β-sheet flanked by eight α-helices. Site-directed mutagenesis indicated that a Ser-His-Glu catalytic triad was essential for the enzyme activity [48]. Another cold

Synthesis of 1,4-azaphosphinine nucleosides and evaluation as inhibitors of human cytidine deaminase and APOBEC3A

• Maksim V. Kvach,
• Stefan Harjes,
• Harikrishnan M. Kurup,
• Geoffrey B. Jameson,
• Elena Harjes and
• Vyacheslav V. Filichev

Beilstein J. Org. Chem. 2024, 20, 1088–1098, doi:10.3762/bjoc.20.96

• development of more potent CDA and APOBEC3 inhibitors. Keywords: APOBEC3; cytidine deaminase; enzyme activity; inhibitor; nucleoside; nucleotide; zebularine; Introduction Spontaneous hydrolytic deamination of cytosine to uracil (Figure 1A) is very slow under ambient conditions [1], but it is greatly

Research progress on the pharmacological activity, biosynthetic pathways, and biosynthesis of crocins

• Zhongwei Hua,
• Nan Liu and
• Xiaohui Yan

Beilstein J. Org. Chem. 2024, 20, 741–752, doi:10.3762/bjoc.20.68

• enzyme activity was lower than CsCCD2 [2][92]. BoCCD4-3 from Bixa orellana was revealed to cleave various carotenoids, lycopene (5), β-carotene (6), and zeaxanthin (7), to form crocetin dialdehyde (8) by in vitro assay [93][94]. In contrast, CsCCD2, BdCCD4.1, and BdCCD4.3 could only cleave zeaxanthin (7

A myo-inositol dehydrogenase involved in aminocyclitol biosynthesis of hygromycin A

• Michael O. Akintubosun and
• Melanie A. Higgins

Beilstein J. Org. Chem. 2024, 20, 589–596, doi:10.3762/bjoc.20.51

• Hyg17 sequences with other members of the oxidoreductase family and inositol dehydrogenases and discuss specialized genome mining approaches using these sequences to identify new natural product biosynthetic clusters. Results and Discussion Hyg17 enzyme activity We found that Hyg17 formed inclusion

Functions of enzyme domains in 2-methylisoborneol biosynthesis and enzymatic synthesis of non-natural analogs

• Binbin Gu,
• Lin-Fu Liang and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2023, 19, 1452–1459, doi:10.3762/bjoc.19.104

• studied. Several 2-methylisoborneol synthases have a proline-rich N-terminal domain of unknown function. The results presented here demonstrate that this domain leads to a reduced enzyme activity, in addition to its ability to increase long-term solubility of the protein. Furthermore, the substrate scope

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

• is no interference from the enzyme or from the solution in which the enzyme may be situated. 3.9. Definition and establishment of chemical equilibrium Loss of enzyme activity due to product inhibition and thermal instability can lead to a failure to achieve equilibrium and consequently large

• approach to equilibrium are not performed. This is the most commonly used method for the measurement of K. But let us examine this method in detail and in regards to the matters of the possible loss of enzyme activity and the possibility of side reactions. Case I. The enzyme remains active. A. There are no

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

• is generally reached very quickly. This effect is experimentally observed – it is shown in the literature that kinetics should be expressed based on the thermodynamic activity of the enzyme [56]. The enzyme activity coefficients were not taken into account in the present work, which does not allow

A Streptomyces P450 enzyme dimerizes isoflavones from plants

• Run-Zhou Liu,
• Shanchong Chen and
• Lihan Zhang

Beilstein J. Org. Chem. 2022, 18, 1107–1115, doi:10.3762/bjoc.18.113

• also catalyze isoflavone dimerization, the above results indicated that CYP158C1 dimerizes isoflavones and several plant-derived aromatic polyketides, albeit with low catalytic efficiency. Future optimization of the reductase partner or reaction conditions may be required to improve the enzyme activity

Synthesis and HDAC inhibitory activity of pyrimidine-based hydroxamic acids

• Virginija Jakubkiene,
• Gabrielius Ernis Valiulis,
• Markus Schweipert,
• Asta Zubriene,
• Daumantas Matulis,
• Franz-Josef Meyer-Almes and
• Sigitas Tumkevicius

Beilstein J. Org. Chem. 2022, 18, 837–844, doi:10.3762/bjoc.18.84

• characterization and analytical data; HDAC enzyme activity assay; references; NMR spectra. Acknowledgements The authors thank Mr. M. Malikenas for recording the HRMS. Results of the investigation were presented as part of a report on the 16th international conference of the Lithuanian Chemical Society “Chemistry

Identification of the new prenyltransferase Ubi-297 from marine bacteria and elucidation of its substrate specificity

• Jamshid Amiri Moghaddam,
• Huijuan Guo,
• Karsten Willing,
• Thomas Wichard and
• Christine Beemelmanns

Beilstein J. Org. Chem. 2022, 18, 722–731, doi:10.3762/bjoc.18.72

• the most favored substrate amongst the tested panel. Thus, we shortly investigated different reaction parameters using 8-HQA and FPP as substrates. First, we compared the enzyme activity of crude protein fractions directly obtained from cell lysate and enriched UbiA-297 fractions (Figure 6). As

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

• methacrylate and aldolase: amino methacrylate). The microenvironment and material surrounding the enzyme have a significant influence on the enzyme activity [30]. For reusability studies, the three most appropriate carriers were selected and analyzed with respect to the activity of the immobilized enzymes

• moisture (immobilized enzyme after filtration under vacuum) at 6 °C. Storage in 20 mM sodium phosphate buffer, pH 7.5 at 6 °C and 40 °C, respectively and storage at 40 °C while shaking at 1000 rpm. Enzyme activity was measured at regular intervals over the storage period. For each measuring point, the

Targeting active site residues and structural anchoring positions in terpene synthases

• Anwei Hou and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2021, 17, 2441–2449, doi:10.3762/bjoc.17.161

• ratios as for the wildtype, which may again have steric reasons. Taken together, these results demonstrate that residues found to be highly conserved and known to be critical for enzyme function in type I TPSs can in some cases be naturally substituted by other residues without consequences on the enzyme

• activity. Similar observations were recently made for spiroalbatene synthase from Allokutzneria albata, in which the otherwise highly conserved Ser within the NSE triad is naturally substituted by Gly. In this case, the G229S enzyme variant did not yield any soluble protein, possibly because the

Volatile emission and biosynthesis in endophytic fungi colonizing black poplar leaves

• Christin Walther,
• Pamela Baumann,
• Katrin Luck,
• Beate Rothe,
• Peter H. W. Biedermann,
• Jonathan Gershenzon,
• Tobias G. Köllner and
• Sybille B. Unsicker

Beilstein J. Org. Chem. 2021, 17, 1698–1711, doi:10.3762/bjoc.17.118

• sesquiterpene product was formed by each TPS: CxTPS1 produced (E,E)-α-farnesene (12) and CxTPS2 produced (E)-β-caryophyllene (1). With GGPP, no enzyme activity was recorded for CxTPS2, while CxTPS1 converted this substrate to (E,E)-β-springene (13) as the minor compound and major amounts of (E,E,E)-α-springene

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

• includes cellular transport and recycling. A limitation of the model is that it considers only absolute changes to enzyme activity, in which an activity is either off or on, which a kinetic model based on differential-equation-based rate laws [44][45][46][47][48] or stochastic kinetics [49][50] would

Selected peptide-based fluorescent probes for biological applications

• Debabrata Maity

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

• heparin stabilizes the tetrameric structure, without its tryptase dissociates into inactive monomers. The reported cationic ligand binds at the rim of anionic residues around the entrance of the central pore, blocks the access to the active sites, and inhibits enzyme activity. Schmuck et al. reported a

Synthesis of new fluorescent molecules having an aggregation-induced emission property derived from 4-fluoroisoxazoles

• Kazuyuki Sato,
• Akira Kawasaki,
• Yukiko Karuo,
• Atsushi Tarui,
• Kentaro Kawai and
• Masaaki Omote

Beilstein J. Org. Chem. 2020, 16, 1411–1417, doi:10.3762/bjoc.16.117

• ; Introduction Fluorescence bioprobes based on conventional organic dyes are used for enzyme activity measurements and in bioimaging systems with promising applications in the field of clinical diagnostics [1][2][3][4][5][6][7]. Most of the fluorescence bioprobes are mainly excited with near-ultraviolet or blue

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

• engineer more active pathway enzyme variants [136][137][138]. As the balanced pathway expression is often the key to high terpenoid titers, these pathway genes have been grouped into “modules”, using a multivariate-modular approach [80], in vitro enzyme activity assays [139], proteomics-based principal

Azologization and repurposing of a hetero-stilbene-based kinase inhibitor: towards the design of photoswitchable sirtuin inhibitors

• Christoph W. Grathwol,
• Nathalie Wössner,
• Sören Swyter,
• Adam C. Smith,
• Enrico Tapavicza,
• Robert K. Hofstetter,
• Anja Bodtke,
• Manfred Jung and
• Andreas Link

Beilstein J. Org. Chem. 2019, 15, 2170–2183, doi:10.3762/bjoc.15.214

• did not perturb the proper enzyme functioning as proved by an unaltered enzyme activity in the blank tests. Unfortunately, 365 nm radiation turned out to have only minor effects on the IC50 values of 11 (Table 3). Discussion In recent years, photopharmacology has become a reputable strategy to

A chemoenzymatic synthesis of ceramide trafficking inhibitor HPA-12

• Seema V. Kanojia,
• Sucheta Chatterjee,
• Subrata Chattopadhyay and
• Dibakar Goswami

Beilstein J. Org. Chem. 2019, 15, 490–496, doi:10.3762/bjoc.15.42

• least three times without any significant loss of enzyme activity. There are similar instances in literature [48] for a substantial slow-down of the transesterification reaction rate in organic solvents. This issue can be overcome by using room temperature ionic liquids, which not only substitute the

• reused the recovered lipase in ionic liquid at least three times without any significant loss of enzyme activity. The % ee of the (R)-5 and (S)-4 were determined from chiral HPLC analyses (150 mm × 4.6 mm, 5 μm, chiral AD-H column, 5% isopropanol/hexane @ 1.0 mL min−1, UV detection at 254 nm). The

Thiol-free chemoenzymatic synthesis of β-ketosulfides

• Adrián A. Heredia,
• Martín G. López-Vidal,
• Marcela Kurina-Sanz,
• Fabricio R. Bisogno and
• Alicia B. Peñéñory

Beilstein J. Org. Chem. 2019, 15, 378–387, doi:10.3762/bjoc.15.34

• both, substrate solubility and enzyme activity. Hence, two different buffer solutions (KPi 50 mM pH 7.5 and Tris·HCl 50 mM pH 7.5) containing 5% v/v of an (miscible or inmiscible) organic cosolvent, were tested towards a set of commercially available lipases. In this line, a remarkable hydrolytic

Protein–protein interactions in bacteria: a promising and challenging avenue towards the discovery of new antibiotics

• Laura Carro

Beilstein J. Org. Chem. 2018, 14, 2881–2896, doi:10.3762/bjoc.14.267

• antimicrobial molecules are presented below. β-Sliding clamp Sliding clamps are prokaryotic ring-shaped proteins that secure DNA polymerases to the DNA template and slide along the double helix, enabling enzyme activity at a specific region of the DNA and increasing the rapid and processive DNA synthesis [52

Mechanochemistry of nucleosides, nucleotides and related materials

• Olga Eguaogie,
• Joseph S. Vyle,
• Patrick F. Conlon,
• Manuela A. Gîlea and
• Yipei Liang

Beilstein J. Org. Chem. 2018, 14, 955–970, doi:10.3762/bjoc.14.81

• ]. Dubinskaya reviewed early investigations into the grinding and stretching of polypeptides and proteins which showed rapid loss of enzyme activity at 80 K [101]. In contrast, more recent reports, in which both native and immobilised enzymes were ground at higher temperatures, demonstrated efficient

Biocatalytic synthesis of the Green Note trans-2-hexenal in a continuous-flow microreactor

• Morten M. C. H. van Schie,
• Tiago Pedroso de Almeida,
• Gabriele Laudadio,
• Florian Tieves,
• Elena Fernández-Fueyo,
• Timothy Noël,
• Isabel W. C. E. Arends and
• Frank Hollmann

Beilstein J. Org. Chem. 2018, 14, 697–703, doi:10.3762/bjoc.14.58

• Michaelis–Menten dependency of the enzyme activity (Figure 1). Apparent KM and kcat values of approximately 1 mM and 22 s−1 were estimated, respectively. These values are in the same order of magnitude as those for benzyl alcohol substrates reported previously [29]. The slightly decreasing enzyme activity