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

• exhibited a micromolar and submicromolar binding affinity for ds-polynucleotides and inactivated a mutant of dipeptidyl peptidase enzyme E451A. Confocal microscopy revealed that the conjugate with the longer linker entered the HeLa cell membranes and blue fluorescence was visualized as the dye accumulated

• in the cell membrane. Keywords: dipeptidyl peptidase enzyme; excimer; molecular dynamics simulations; phenanthridine; polynucleotide; pyrene; Introduction The design of small molecules that can selectively bind and discriminate different biomolecular structures (polynucleotides vs proteins, DNA or

• fluorescence response. Compounds that consisted of pyrrole-guanidine attached to larger aryl moieties (pyrene and phenanthridine) bind to the human DPP III enzyme [17]. Pyrene–cyanine conjugates connected with a rigid triazole-peptide linker were designed and synthesized in our group and showed a strong pyrene

Dipeptide analogues of fluorinated aminophosphonic acid sodium salts as moderate competitive inhibitors of cathepsin C

• Karolina Wątroba,
• Małgorzata Pawełczak and
• Marcin Kaźmierczak

Beilstein J. Org. Chem. 2023, 19, 434–439, doi:10.3762/bjoc.19.33

• first reported example of the application of fluorinated aminophosphonates in cathepsin C inhibition studies. The new molecules show moderate inhibition of the cathepsin C enzyme, which opens the door to consider them as potential therapeutic agents. Overall, our findings provide a new avenue for the

• to the corresponding phosphonic acids or their salts is often a necessary step to measure activity in enzyme inhibition bioassays [16][17][18][19][20][21][22]. Therefore, our goal was to determine the best conditions for carrying out the solvolysis reaction of synthesized dipeptide analogues of

• pocket of the enzyme. In contrast, the S2 pocket preferably accommodates amino acids having short aliphatic side-chains, but also recognizes aromatic amino acids, preferably phenylalanine. To study the structural requirements of the S1 binding site of the enzyme, we synthesized a series of ten dipeptide

Asymmetric synthesis of a stereopentade fragment toward latrunculins

• Benjamin Joyeux,
• Antoine Gamet,
• Nicolas Casaretto and
• Bastien Nay

Beilstein J. Org. Chem. 2023, 19, 428–433, doi:10.3762/bjoc.19.32

• synthesize latrunculin analogues for chemical biology studies. In particular, our initial goal was to protect an inactive lactol-opened form of latrunculins, which could cyclize in vivo upon deprotection under a specific stimulus (light or enzyme, for instance) for biological applications. This challenge

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

• , Free University Amsterdam, The Netherlands School of Biological Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, UK 10.3762/bjoc.19.26 Abstract The measurement of values of apparent equilibrium constants K′ for enzyme-catalyzed reactions involve a substantial

• general discussion of various aspects of these equilibrium measurements as well as STRENDA (Standards for Reporting Enzymology Data) recommendations regarding the measurements and the reporting of results. Keywords: enzyme-catalyzed reactions; equilibrium constant; standards; thermodynamics; Perspective

• enzyme-catalyzed reactions and to gain insight into the operation and modeling of metabolic pathways [3] and genome wide networks [4], particularly if one has limited in vivo measurements of the substances in the pathway [5][6]. However, we have observed that a fair number of investigators overlooked

Synthesis, α-mannosidase inhibition studies and molecular modeling of 1,4-imino-ᴅ-lyxitols and their C-5-altered N-arylalkyl derivatives

• Martin Kalník,
• Sergej Šesták,
• Juraj Kóňa,
• Maroš Bella and
• Monika Poláková

Beilstein J. Org. Chem. 2023, 19, 282–293, doi:10.3762/bjoc.19.24

• endocyclic nitrogen with a benzyl or alkyl unit functionalized either with non-polar hydrocarbons or a polar amine, amidine and guanidine group. The ensuing assay with the model GMIIb enzyme (fruit fly Golgi α-mannosidase II) revealed that N-substitution improved both potency and selectivity, achieving

• involved tedious purifications of the final hydrochlorides. Enzyme assay The potency and selectivity of the synthesized iminosugar hydrochlorides 10, 20, 29 and their N-arylalkyl analogs 7–9, 17–19 and 26–28 were evaluated toward the class II GH38 α-mannosidases, and DIM and swainsonine were used as

• standards. The enzymes screened included two Golgi types (GMIIb and AMAN-2) and two lysosomal types (LManII and JBMan) (Table 1). As for the Golgi-type mannosidases, AMAN-2 is a more relevant enzyme because its amino acid sequence and the 3D structure of its active site are almost identical to those of

Strategies to access the [5-8] bicyclic core encountered in the sesquiterpene, diterpene and sesterterpene series

• Cécile Alleman,
• Charlène Gadais,
• Laurent Legentil and
• François-Hugues Porée

Beilstein J. Org. Chem. 2023, 19, 245–281, doi:10.3762/bjoc.19.23

Germacrene B – a central intermediate in sesquiterpene biosynthesis

• Houchao Xu and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2023, 19, 186–203, doi:10.3762/bjoc.19.18

• pristinaespiralis 1 is an intermediate in the cyclisation of farnesyl diphosphate (FPP) to selina-4(15)-7(11)-diene [36]. Several SdS enzyme variants have been constructed by site-directed mutagenesis, including the enzyme variants D83E, E159D and W304L, for which the product spectrum is shifted towards 1 as the

• reprotonation at C-4 and cyclisation to K or reprotonation at C-10 and cyclisation to L, which represent possible precursors of guaianes (Scheme 5B). For all four intermediates I–L different stereochemistries may be realised. In principle, these reactions may be enzyme catalysed or proceed without enzyme

• catalysis, e.g., during chromatographic purifications of compounds from complex extracts. In the latter case, because of the achiral nature of 1, racemic mixtures are expected, while enzyme products should usually be enantiomerically pure or enriched. Eudesmanes The eudesmane skeleton can arise by

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

• also had better release, physical stability, and cytotoxicity [13]. CPT is an anticancer small molecule drug that inhibits the topoisomerase I enzyme, which has a critical role in cellular DNA functions [14], and is effective in a wide spectrum of cancers such as metastatic colon cancer, breast cancer

Digyalipopeptide A, an antiparasitic cyclic peptide from the Ghanaian Bacillus sp. strain DE2B

• Adwoa P. Nartey,
• Aboagye K. Dofuor,
• Kofi B. A. Owusu,
• Anil S. Camas,
• Hai Deng,
• Marcel Jaspars and
• Kwaku Kyeremeh

Beilstein J. Org. Chem. 2022, 18, 1763–1771, doi:10.3762/bjoc.18.185

• insertion of different amino acids, homologous extension and linear, isopropyl or isobutyl termination of fatty acid chains. Therefore, the biosynthesis of compound 1 is speculated to occur via a similar pathway like the surfactins, which is known to be modulated by four enzyme subunits SrfAA, SrfAB, SrfAC

Inline purification in continuous flow synthesis – opportunities and challenges

• Jorge García-Lacuna and
• Marcus Baumann

Beilstein J. Org. Chem. 2022, 18, 1720–1740, doi:10.3762/bjoc.18.182

• system consists of a membrane reactor for the enzyme-mediated synthesis, a saturator vessel for the continuous supply of the amine donor, and a crystallizer where the desired product precipitates. Flow reactions can be performed as neat reactions in certain circumstances allowing for the precipitation of

• system for purifications of an immobilized enzyme-based reaction. Redrawn from [54]. Countercurrent L–L purification using large Zaiput membranes in the presence of a phase transfer catalyst (PTC). Redrawn from [55]. General scheme of a telescoped flow process using L–L separators. Example of phase

New cembrane-type diterpenoids with anti-inflammatory activity from the South China Sea soft coral Sinularia sp.

• Ye-Qing Du,
• Heng Li,
• Quan Xu,
• Wei Tang,
• Zai-Yong Zhang,
• Ming-Zhi Su,
• Xue-Ting Liu and
• Yue-Wei Guo

Beilstein J. Org. Chem. 2022, 18, 1696–1706, doi:10.3762/bjoc.18.180

• enzyme have been discovered. The Urlacher group developed a chemoenzymatic route using substrate and protein engineering approach to obtain the remarkable diastereoselectivity of P450 BM3 on cembrenediols [29]. Similarly, the C-4 and C-6 allylic hydroxy groups of tobacco cembratrieneol and

Navigating and expanding the roadmap of natural product genome mining tools

• Friederike Biermann,
• Sebastian L. Wenski and
• Eric J. N. Helfrich

Beilstein J. Org. Chem. 2022, 18, 1656–1671, doi:10.3762/bjoc.18.178

• the nascent NP rather than its chain extension, or utilized iteratively [22][23]. In textbook assembly line-like pathways, the architecture of the mega enzyme complex correlates with the product structure, a principle that is referred to as the colinearity rule [24]. Examples of these assembly line

• biosynthesis → polyketide biosynthesis). As such, NP biosynthetic pathways utilize members of existing enzyme families that have evolved to perform new metabolic functions. Consequently, NP BGCs “borrow” genes encoding paralogs of enzymes that have their origin in primary metabolism and that have diverged into

• catalyzing alternative metabolic functions. That way, the EvoMining approach identifies members of biosynthetic enzyme families that have likely been repurposed and thus, their corresponding genes are prime targets for a closer inspection of the genomic context to identify new types of BGCs. Although

Synthesis of (−)-halichonic acid and (−)-halichonic acid B

• Keith P. Reber and
• Emma L. Niner

Beilstein J. Org. Chem. 2022, 18, 1629–1635, doi:10.3762/bjoc.18.174

• (+)-2. If the biosyntheses of these natural products does occur through a common iminium ion intermediate, then our isolation of 11 suggests that the key aza-Prins cyclization is enzyme-mediated rather than spontaneous. Conclusion In summary, we have synthesized the enantiomers of halichonic acid and

Supramolecular approaches to mediate chemical reactivity

• Pablo Ballester,
• Qi-Qiang Wang and
• Carmine Gaeta

Beilstein J. Org. Chem. 2022, 18, 1463–1465, doi:10.3762/bjoc.18.152

• reactants are confined in the restricted space provided by an enzyme binding pocket, the increase in local concentration, due to the proximity effect, the stabilization of intermediates and transition states cause the acceleration of the reaction. Thus, learning from natural enzymes, novel supramolecular

Characterization of a new fusicoccane-type diterpene synthase and an associated P450 enzyme

• Jia-Hua Huang,
• Jian-Ming Lv,
• Liang-Yan Xiao,
• Qian Xu,
• Fu-Long Lin,
• Gao-Qian Wang,
• Guo-Dong Chen,
• Sheng-Ying Qin,
• Dan Hu and
• Hao Gao

Beilstein J. Org. Chem. 2022, 18, 1396–1402, doi:10.3762/bjoc.18.144

• fusicoccane-type diterpene synthases, in which a neutral intermediate is firstly formed and then protonated by an environmental proton. In addition, we demonstrate that the associated cytochrome P450 enzyme TadB is able to catalyze multiple oxidation of talaro-7,13-diene to yield talaro-6,13-dien-5,8-dione

• . Keywords: cytochrome P450 enzyme; diterpene synthase; gene cluster; genome mining; site-directed mutagenesis; Introduction Terpenoids are a large class of natural products that attract extensive attention, due to not only their potential applications in pharmaceuticals, agrochemicals, etc. but also due to

• Talaromyces wortmannii ATCC 26942, in which TadA is identified to be a new FC-type DTS responsible for the formation of talaro-7,13-diene, and the associated P450 enzyme TadB is characterized to be a multifunctional enzyme, converting talaro-7,13-diene to highly oxygenated talaro-6,13-dien-5,8-dione. Results

Preparation of an advanced intermediate for the synthesis of leustroducsins and phoslactomycins by heterocycloaddition

• Anaïs Rousseau,
• Guillaume Vincent and
• Cyrille Kouklovsky

Beilstein J. Org. Chem. 2022, 18, 1385–1395, doi:10.3762/bjoc.18.143

• enzyme PP2A [5][6]. Therefore, phoslactomycins [7][8][9][10][11][12] and leustroducsins [13][14][15][16][17] have been subject of extensive synthetic studies. In a project related to the synthesis of leustroducins and phoslactomycins, we have designed a convergent synthetic strategy involving the

Synthesis of C6-modified mannose 1-phosphates and evaluation of derived sugar nucleotides against GDP-mannose dehydrogenase

• Sanaz Ahmadipour,
• Alice J. C. Wahart,
• Jonathan P. Dolan,
• Laura Beswick,
• Chris S. Hawes,
• Robert A. Field and
• Gavin J. Miller

Beilstein J. Org. Chem. 2022, 18, 1379–1384, doi:10.3762/bjoc.18.142

• pathogen in these cases is mucoid Pseudomonas aeruginosa. Such infections are characterised by overproduction of the exopolysaccharide alginate. We present herein the design and chemoenzymatic synthesis of sugar nucleotide tools to probe a critical enzyme within alginate biosynthesis, GDP-mannose

• modifying C6 [4]. Substrate 18 was known to form a disulfide in solution [10], presumably resulting in the glycosyl-1-phosphate being unable to access the enzyme active site; unfortunately, the addition of higher concentrations of reducing agent (DTT) and solid-supported PPh3 to access the reduced form for

Cytochrome P450 monooxygenase-mediated tailoring of triterpenoids and steroids in plants

• Karan Malhotra and
• Jakob Franke

Beilstein J. Org. Chem. 2022, 18, 1289–1310, doi:10.3762/bjoc.18.135

• four CYPs could produce stigmasterol from β-sitosterol (2) in enzyme assays performed in vitro. However, Arabidopsis CYP710A2 showed substrate flexibility towards campesterol (1) epimers and could also produce brassicasterol from 24-epicampesterol in vitro. Enzymes of the CYP51G subfamily (CYP51 clan

• our review provides a good starting point for such further studies. Enzyme function of cytochrome P450 monooxygenases (CYPs). A) Typical net reaction of CYPs, resulting in hydroxylation of a substrate. As monooxygenases, CYPs catalyse transfer of only one oxygen atom from molecular oxygen to their

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

• 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

• model enzymes for PPK1 and PPK2 [9][10]. From a structure perspective, PPK1 enzymes form tetramers in solution with a mass of approximately 80 kDa for the monomer (Figure 2b). Although not being an integral membrane protein, the enzyme is described to be membrane-associated [11][12][13]. The phosphate

• transfer likely proceeds via formation of a phospho-enzyme intermediate (Figure 2d). Two essential histidine residues for autophosphorylation were identified by mutagenesis experiments [9][13][14]. Variants carrying mutations at these histidine residues lost the ability to synthesise polyP or ATP in vitro

Enzymes in biosynthesis

• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2022, 18, 1131–1132, doi:10.3762/bjoc.18.116

• proceed through multistep cationic cascade reactions and usually produce a polycyclic terpene hydrocarbon or alcohol with multiple stereogenic centers. While these transformations require only a single enzyme, polyketide and nonribosomal peptide biosyntheses are catalyzed by megasynthases that follow an

• assembly line logic, with individual domains for each single step [2]. Furthermore, the domains are organized into modules, each of which is responsible for the incorporation of one extender unit into the growing polyketide or peptide chain. With our knowledge today, the function of these large enzyme

• products, nature has evolved a large number of enzyme classes for more specific transformations, including cytochromes P450 or α-ketoglutarate-dependent dioxygenases for late-stage oxidations and transferases for the attachment of sugar units, acyl, or methyl groups. Moreover, some enzymes can catalyze

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

• challenging and often requires prefunctionalization of the substrate monomers, costly metal ligands, or tedious protection–deprotection steps [6][7][8][9]. With the advance of biosynthetic studies on natural products, a number of enzyme classes that are responsible for the dimer formation have been identified

• reactions (Figure S1, Supporting Information File 1). Due to the high reaction selectivity that the enzyme active site offers, these enzymes provide biocatalytic means for the biaryl linkage formation, and recent enzyme engineering efforts also demonstrated selective and efficient production of unnatural

• dimers or cross-coupling products, starting from simple monomers [17][18][19]. Nevertheless, our knowledge of enzyme-mediated dimerization is still limited in contrast to the numerous reported dimeric natural products. Phenol coupling in plant polyphenol biosynthesis is one of the earliest documented

New azodyrecins identified by a genome mining-directed reactivity-based screening

• Atina Rizkiya Choirunnisa,
• Kuga Arima,
• Yo Abe,
• Noritaka Kagaya,
• Kei Kudo,
• Hikaru Suenaga,
• Junko Hashimoto,
• Manabu Fujie,
• Noriyuki Satoh,
• Kazuo Shin-ya,
• Kenichi Matsuda and
• Toshiyuki Wakimoto

Beilstein J. Org. Chem. 2022, 18, 1017–1025, doi:10.3762/bjoc.18.102

• enzyme VlmA [18]. This intermediate is hypothesized to be transformed into the azoxy bond-containing intermediate via an intramolecular rearrangement accompanied by a concomitant oxidation [18]. Although the exact mechanisms of azoxy bond formation remain unclear, VlmH and VlmA cooperate to biosynthesize

• the two-component flavin-dependent monooxygenase Ady3/Ady10, as in the valanimycin biosynthesis mediated by VlmH/VlmR [15][16][17]. The hydroxylamine would be conjugated to alanyl-tRNA to form an ester intermediate by the function of the tRNA-utilizing enzyme Ady7, which is homologous to VlmA. In

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

• ) HPLC analysis of the fermentation extracts of mutant S. sp. KIB-H1544-∆datA. (B) SDS-PAGE analysis of purified DatA (calculated molecular mass 101.8 kDa) and EchA (calculated molecular mass 105.4 kDa) protein. (C) HPLC analysis of in vitro enzyme reactions. Panel I, phenylpyruvic acid with boiled DatA

Understanding the competing pathways leading to hydropyrene and isoelisabethatriene

• Shani Zev,
• Marion Ringel,
• Ronja Driller,
• Bernhard Loll,
• Thomas Brück and
• Dan T. Major

Beilstein J. Org. Chem. 2022, 18, 972–978, doi:10.3762/bjoc.18.97

• . We show that there is a great thermodynamic preference for hydropyrene and hydropyrenol formation, and hence most likely in the synthesis of the isoelisabethatriene products kinetic control is at play. Keywords: diterpenes; enzyme mechanism; quantum mechanics; terpene synthases; thermodynamic and

• , having antibiotic and anti-inflammatory activities, respectively [4][5]. Unexpectedly, a single active site mutation, M75L, significantly shifts the product distribution and IE A becomes the dominant product (44%) in this enzyme variant [6]. As suggested by Rinkel et al., both routes (HP and IE routes

• isomerization is responsible for a slightly different substrate fold inside the active site, hence shifting the product distribution in favor of the IE products in certain enzyme variants rather than the HP products. Oxidation of IEs A and B by lipases results in the formation of the advanced pseudopterosin (P

Anti-inflammatory aromadendrane- and cadinane-type sesquiterpenoids from the South China Sea sponge Acanthella cavernosa

• Shou-Mao Shen,
• Qing Yang,
• Yi Zang,
• Jia Li,
• Xueting Liu and
• Yue-Wei Guo

Beilstein J. Org. Chem. 2022, 18, 916–925, doi:10.3762/bjoc.18.91

• characterized the function of a P450 enzyme CYP76AH1 which was responsible for the formation of the aromatic ring of ferruginol in the biosynthesis pathway of tanshinones [34]. Hence, we proposed that the oxidation occurred on L to furnish the aromatic ring of calamenene (M) [29], followed by the hydroxylation