Beyond symmetric self-assembly and effective molarity: unlocking functional enzyme mimics with robust organic cages

• Keith G. Andrews

Beilstein J. Org. Chem. 2025, 21, 421–443, doi:10.3762/bjoc.21.30

• typically not possible for imine [314] or metal-coordination cages [156][202][365]. Further, the robust amide cages could withstand harsh conditions such as ester hydrolysis, allowing access to the key acid-functionalized cages [38] that mimic aspartyl proteases and glycoside hydrolases. Otte has employed

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

• ; hydrolases; marine natural products; Introduction Microbial natural products represent an important reservoir for drug discovery and along with their (semi)synthetic derivatives, constitute a major component of the contemporary pharmaceutical arsenal. Their thusly validated utility is juxtaposed against the

• are glycoside hydrolases (GHs) that degrade agarose to smaller oligosaccharides [102]. Marine bacteria of diverse genera produce agarases [103][104][105]. Based on the reactions that they catalyze, bacterial agarases are grouped as α- and β-agarases wherein they hydrolyze α-1,3 linkages and β-1,4

• linkages in agarose, respectively (Figure 2). However, based on sequence similarity, agarases are alternatively classified into different families of glycoside hydrolases (GHs): GH-96 and GH-117 for α-agarases, and GH-16, GH-50, GH-86, and GH-118 for β-agarases [106]. All agarases characterized from

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

Synthesis and bioactivity of pyrrole-conjugated phosphopeptides

• Qiuxin Zhang,
• Weiyi Tan and
• Bing Xu

Beilstein J. Org. Chem. 2022, 18, 159–166, doi:10.3762/bjoc.18.17

• . Switching the ᴅ-phosphoserine in 4a and 4b by ʟ-phosphoserine (pS), creates 5a and 5b. ᴅ-Trialanine replaces triglycine in 2f–h to produce 6a–c, which should resist to proteases, such as polyglycine hydrolases [73], which are known to cleave at the glycine–glycine site. The addition of an arginine residue

Progress and challenges in the synthesis of sequence controlled polysaccharides

• Giulio Fittolani,
• Theodore Tyrikos-Ergas,
• Denisa Vargová,
• Manishkumar A. Chaube and
• Martina Delbianco

Beilstein J. Org. Chem. 2021, 17, 1981–2025, doi:10.3762/bjoc.17.129

• (LG, e.g., phosphate, fluoride, nucleotide) are polymerized by the enzyme to form the desired polysaccharide (Figure 1A). Several classes of enzymes are available, including hydrolases, phosphorylases, sucrases, glycosyltransferases, and glycosynthases [19][20][21][22]. An excellent overview of the

• activity, as demonstrated using partially acetylated COS obtained by enzymatic degradation of chitosan promoted by hydrolases [221]. Chemical degradation of chitin promoted by acid treatment [222][223][224][225][226][227][228] or using chitinases and chitosanases [229][230][231] generates mixtures of short

• hydrolases is an interesting option to produce long COS from shorter oligomers [241]. After cleaving the glycosidic linkage, the enzyme remains attached to the new reducing end of the oligomer, releasing the cleaved part. Subsequently, the oligomer is transferred to another COS acceptor, forming a new

A systems-based framework to computationally describe putative transcription factors and signaling pathways regulating glycan biosynthesis

• Theodore Groth,
• Rudiyanto Gunawan and
• Sriram Neelamegham

Beilstein J. Org. Chem. 2021, 17, 1712–1724, doi:10.3762/bjoc.17.119

• -linked precursor structure emerging from the dolichol pathway into complex structures. Enzymes involved include mannosidases, glucosidases, some enzymes facilitating protein folding, and also enzymes that direct acid hydrolases to the lysosome. 6) N-glycan branching: These glycogenes are responsible for

Nanangenines: drimane sesquiterpenoids as the dominant metabolite cohort of a novel Australian fungus, Aspergillus nanangensis

• Heather J. Lacey,
• Cameron L. M. Gilchrist,
• Andrew Crombie,
• John A. Kalaitzis,
• Daniel Vuong,
• Peter J. Rutledge,
• Peter Turner,
• John I. Pitt,
• Ernest Lacey,
• Yit-Heng Chooi and
• Andrew M. Piggott

Beilstein J. Org. Chem. 2019, 15, 2631–2643, doi:10.3762/bjoc.15.256

• terpene synthase family, showing similarity to haloacid dehalogenase (HAD)-like hydrolases [21]. Thus, we suspected that a related enzyme may be involved in the biosynthesis of the nanangenines, and used the amino acid sequence of AstC to probe the A. nanangensis genome. We also hypothesised that the acyl

• ionisation-activated cyclisation activity. Two other HAD-like hydrolases, AstI and AstK, with the class I (DDxxD/E) motif, are therefore required to catalyse other dephosphorylation steps. Despite overall low sequence homology, alignment with the amino acid sequences of AstC, AstI, AstK and related homologs

Towards the preparation of synthetic outer membrane vesicle models with micromolar affinity to wheat germ agglutinin using a dialkyl thioglycoside

• Dimitri Fayolle,
• Nathalie Berthet,
• Bastien Doumeche,
• Olivier Renaudet,
• Peter Strazewski and
• Michele Fiore

Beilstein J. Org. Chem. 2019, 15, 937–946, doi:10.3762/bjoc.15.90

• Fisher reaction between pyranoses and fatty alcohols of different lengths [8][9]. Alkyl thioglycosides are known for their properties as co-surfactants [10] and present interesting antimicrobial activities [11], acting as glycosidase inhibitors and being resistant towards glycoside hydrolases [12][13

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

• -ketosulfides [44]. Results and Discussion In a first set of experiments, a series of commercially available hydrolases were screened in aqueous buffer containing 5% v/v of an organic cosolvent towards a β-thioalkyl-substituted enolester as model substrate 1a (Table 1). As enol acetates, (e.g., vinyl acetate

• temperature one-pot two-step preparation of the phenacyl allyl sulfide 2h. cIsolated yield. Selective oxidation of the β-ketosulfide 2a. Screening of hydrolases and conditions towards a model substrate.a Lipase-catalysed hydrolysis–protonation sequence over a series of β-thioalkyl enol esters.a Supporting

Lectins of Mycobacterium tuberculosis – rarely studied proteins

• Katharina Kolbe,
• Sri Kumar Veleti,
• Norbert Reiling and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2019, 15, 1–15, doi:10.3762/bjoc.15.1

• have been found in glycosyltransferases as well as in bacterial hydrolases [95]. The Mtb gene product of Rv1419 shows 41% amino acid sequence similarity to R-type lectins and encodes the Mtb protein sMTL-13 (see Figure 5 for secondary structure prediction and alignment with the ricin B-like lectin from

Synthesis of 1,4-imino-L-lyxitols modified at C-5 and their evaluation as inhibitors of GH38 α-mannosidases

• Maroš Bella,
• Sergej Šesták,
• Ján Moncoľ,
• Miroslav Koóš and
• Monika Poláková

Beilstein J. Org. Chem. 2018, 14, 2156–2162, doi:10.3762/bjoc.14.189

• target GMIIb enzyme. In contrast, no inhibition effect of the pyrrolidines against LManII was observed. The modification of the imino-L-lyxitol core is therefore a suitable motif for the design of inhibitors with desired selectivity against the target GMIIb enzyme. Keywords: azasugars; hydrolases

• , indolizidines etc. which exhibited remarkable biological activities and are highly interesting as pharmaceutical agents [15][16][17][18][19]. In addition, iminosugars exhibited a powerful inhibitory activity against a wide range of glycoside hydrolases [20][21][22]. One naturally occurring iminosugar, alkaloid

• swainsonine, interferes with the glycosylation pathway where it specifically inhibits GH38 glycoside hydrolases [23][24]. Up to date, swainsonine is the most potent Golgi mannosidase II (GMII) inhibitor. It is known that inhibition of the biosynthesis of complex N-glycans in the Golgi apparatus influences

Acid-catalyzed ring-opening reactions of a cyclopropanated 3-aza-2-oxabicyclo[2.2.1]hept-5-ene with alcohols

• Katrina Tait,
• Alysia Horvath,
• Nicolas Blanchard and
• William Tam

Beilstein J. Org. Chem. 2017, 13, 2888–2894, doi:10.3762/bjoc.13.281

• the structure against cleavage by nucleoside phosphorylases or hydrolases [18][19]. The addition of a cyclopropane unit could provide further rigidity that could better stabilize the compound, thereby enhancing its biological activity. Both of these reported ring-openings of cyclopropanated 3-aza-2

Enzymatic synthesis of glycosides: from natural O- and N-glycosides to rare C- and S-glycosides

• Jihen Ati,
• Pierre Lafite and
• Richard Daniellou

Beilstein J. Org. Chem. 2017, 13, 1857–1865, doi:10.3762/bjoc.13.180

• Jihen Ati Pierre Lafite Richard Daniellou ICOA UMR CNRS 7311, University of Orléans, rue de Chartres, BP 6759, 45067 Orléans cedex 2, France 10.3762/bjoc.13.180 Abstract Carbohydrate related enzymes, like glycosyltransferases and glycoside hydrolases, are nowadays more easily accessible and are

• . Glycoside hydrolases (GHs) or glycosyltransferases (GTs) have been focused on in the search for glycosylation tools, and have been extensively studied for genetic engineering [9][10]. The corresponding compounds have proven useful in many applications ranging from glycosylation of natural products to

• rearrangement [37]. A last family of C-GT are the enzymes involved in C-mannosylation of protein tryptophanes [37]. However, if the corresponding C-GTs were identified, no mechanistic evidence was reported to date [52]. Glycoside hydrolases GHs (E.C. 3.2.1.x) are ubiquitous enzymes responsible for the

Selective enzymatic esterification of lignin model compounds in the ball mill

• Ulla Weißbach,
• Saumya Dabral,
• Laure Konnert,
• Carsten Bolm and
• José G. Hernández

Beilstein J. Org. Chem. 2017, 13, 1788–1795, doi:10.3762/bjoc.13.173

• Immobead), immobilized lipase from Burkholderia cepacia (PS-IM) and lipase A from Aspergillus niger were tested. Firstly, hoping to find differences between the two hydrolases derived from Candida antarctica, an experiment using CALA was conducted. Despite CALB and CALA being produced by the same yeast

Glycoscience@Synchrotron: Synchrotron radiation applied to structural glycoscience

• Serge Pérez and
• Daniele de Sanctis

Beilstein J. Org. Chem. 2017, 13, 1145–1167, doi:10.3762/bjoc.13.114

• of the families of most glycan-interacting proteins (including glycosyl transferases and hydrolases, lectins, antibodies and GAG-binding proteins) are presented. Examples concerned with glycolipids and colloids are also covered as well as some dealing with the structures and multiscale architectures

• hydrolases; glycosyl transferases; kinetic crystallography; lectins; polysaccharides; powder diffraction; small-angle X-ray scattering; starch; synchrotron radiation; transporters; X-ray crystallography; Introduction Over the last decade, glycoscience has greatly benefited from the development of structural

• recognition with the elucidation of glycosyl hydrolases mechanism by X-ray crystallography, but the scope of applications in glycobiology is much broader: it encompasses the range of glycan containing (macro)-molecules and their conjugates. The present article reviews the application of synchrotron radiation

Biosynthesis of oxygen and nitrogen-containing heterocycles in polyketides

• Franziska Hemmerling and
• Frank Hahn

Beilstein J. Org. Chem. 2016, 12, 1512–1550, doi:10.3762/bjoc.12.148

• chapter, we will focus on two examples in which one pyran ring is formed. Both characteristically deviate from the typical polyether-specific interplay between one epoxidase and one or a few epoxide hydrolases that collaboratively set up multiple oxygen heterocycles. Pseudomonic acid A. Mupirocin is a

• groups are involved (shown for monensin in Scheme 17) [109][110][111]. While polyepoxidation is usually effected by only one epoxidase, one or more epoxide hydrolases mediate regioselective epoxide opening and following controlled cyclisation. As the topic polyether biosynthesis is highly complex and a

Interactions of cyclodextrins and their derivatives with toxic organophosphorus compounds

• Sophie Letort,
• Sébastien Balieu,
• William Erb,
• Géraldine Gouhier and
• François Estour

Beilstein J. Org. Chem. 2016, 12, 204–228, doi:10.3762/bjoc.12.23

• potential immunogenic risks associated to proteins such as hydrolases [37]. This review focuses on the various aspects of the detoxification process mediated by CD derivatives: (1) the ability of CDs and their derivatives to form inclusion complexes with organophosphorus pesticides and G nerve agents; (2

Dicarboxylic esters: Useful tools for the biocatalyzed synthesis of hybrid compounds and polymers

• Ivan Bassanini,
• Karl Hult and
• Sergio Riva

Beilstein J. Org. Chem. 2015, 11, 1583–1595, doi:10.3762/bjoc.11.174

• eighties of the last century, the vast majority of them dealing with the synthetic exploitation of hydrolases [5][6]. It was found that reactions that are thermodynamically unfavorable in water, like esterifications, transesterifications (transacylations) and amidations, can be efficiently catalyzed by

• panel of different acylating agents and hydrolases [10][11][12]. Among the great number of investigated acyl donors, activated esters of dicarboxylic acids have been found to be particularly versatile for the production of bifunctionalized compounds. As it will be discussed in the following paragraphs

Intermediates in monensin biosynthesis: A late step in biosynthesis of the polyether ionophore monensin is crucial for the integrity of cation binding

• Wolfgang Hüttel,
• Jonathan B. Spencer and
• Peter F. Leadlay

Beilstein J. Org. Chem. 2014, 10, 361–368, doi:10.3762/bjoc.10.34

• undergoes a cascade of ring opening/closing catalysed by the combined action of the unusual epoxide hydrolases MonBI and MonBII, to give the putative protein-bound intermediate dehydroxydemethylmonensin. The next steps, catalysed respectively by the cytochrome P450 hydroxylase MonD and the methyltransferase

Elucidation of the regio- and chemoselectivity of enzymatic allylic oxidations with Pleurotus sapidus – conversion of selected spirocyclic terpenoids and computational analysis

• Verena Weidmann,
• Mathias Schaffrath,
• Holger Zorn,
• Julia Rehbein and
• Wolfgang Maison

Beilstein J. Org. Chem. 2013, 9, 2233–2241, doi:10.3762/bjoc.9.262

• slightly acidic conditions [49]. However, participation of hydrolases from the PSA lyophilisate is also possible. A fraction of the resulting alcohols 26 would then finally be oxidized to give enone 24. Support for an epoxide intermediate comes from oxidations of substrates containing similarly hindered

Use of 3-[¹⁸F]fluoropropanesulfonyl chloride as a prosthetic agent for the radiolabelling of amines: Investigation of precursor molecules, labelling conditions and enzymatic stability of the corresponding sulfonamides

• Reik Löser,
• Steffen Fischer,
• Achim Hiller,
• Martin Köckerling,
• Uta Funke,
• Aurélie Maisonial,
• Peter Brust and
• Jörg Steinbach

Beilstein J. Org. Chem. 2013, 9, 1002–1011, doi:10.3762/bjoc.9.115

• involvement of carboxylesterase (EC 3.1.1.1) is probable even though the participation of other hydrolases cannot be excluded [42][43]. Carboxylesterase belongs to the large class of α/β serine hydrolases, is located in the lumen of the endoplasmic reticulum of cells in many tissues, and is highly expressed

• -first-order rate constant of 0.012 min−1 corresponding to a half-life of 58 min at an enzyme concentration of 1.4 mg/mL. This result demonstrates that the degradation of aromatic fluoroacetamides in vivo can be mediated by carboxylesterase. However, other hydrolases such as arylacetamide deacetylase

An improved synthesis of a fluorophosphonate–polyethylene glycol–biotin probe and its use against competitive substrates

• Hao Xu,
• Hairat Sabit,
• Gordon L. Amidon and
• H. D. Hollis Showalter

Beilstein J. Org. Chem. 2013, 9, 89–96, doi:10.3762/bjoc.9.12

• Michigan, Ann Arbor, MI 48109-1065, USA 10.3762/bjoc.9.12 Abstract The fluorophosphonate (FP) moiety attached to a biotin tag is a prototype chemical probe used to quantitatively analyze and enrich active serine hydrolases in complex proteomes in an approach called activity-based protein profiling (ABPP

• evaluated against isolated protein mixtures and different rat-tissue homogenates, showing its ability to specifically target serine hydrolases. We also assessed the ability of FP–PEG–biotin to compete with substrates that have high enzyme turnover rates. The reduced protein-band intensities resulting in

• biological processes. In this regard, fluorophosphonate (FP) probes have been extensively used in activity-based protein profiling (ABPP) in proteomic studies [1][2]. FP probes, specifically designed to target serine hydrolases, originate from diisopropyl fluorophosphonate (DFP) [3][4]. DFP is a serine

Chemical modification allows phallotoxins and amatoxins to be used as tools in cell biology

• Jan Anderl,
• Hartmut Echner and
• Heinz Faulstich

Beilstein J. Org. Chem. 2012, 8, 2072–2084, doi:10.3762/bjoc.8.233

• 2b possess comparable affinities to actin (Table 1), but differ in their IC50 values by a factor of ca. 300. The effect is presumably a consequence of the faster hydrolysis of esters over amides by intracellular hydrolases. Polycationic derivatives of phalloidin, such as the polylysine conjugates

The use of glycoinformatics in glycochemistry

• Thomas Lütteke

Beilstein J. Org. Chem. 2012, 8, 915–929, doi:10.3762/bjoc.8.104

• glycan chain, and by glycoside hydrolases (GH) that remove specific monosaccharides [3]. For this reason there is no technique available to amplify carbohydrates comparable to Polymerase Chain Reaction (PCR) or protein expression systems. Instead, carbohydrates have to be analyzed in physiological

• the enzymes that build or degrade the glycan chains in vivo, the glycosyltransferases or glycoside hydrolases, respectively [46][47][48][49]. To plan such experiments, however, detailed knowledge of the substrate-specificity of these enzymes is required. The same applies to glycan-binding proteins

• (glycosyltransferases, glycoside hydrolases, polysaccharide lyases and carbohydrate esterases) as well as proteins that feature carbohydrate-binding modules is CAZy (Carbohydrate Active Enzymes). This database classifies proteins by sequence comparison and clusters them into families by using well-established

Tertiary alcohol preferred: Hydroxylation of trans-3-methyl-L-proline with proline hydroxylases

• Christian Klein and
• Wolfgang Hüttel

Beilstein J. Org. Chem. 2011, 7, 1643–1647, doi:10.3762/bjoc.7.193

• numerous approaches for the synthesis of tertiary alcohols with classical organic chemistry [1][2][3][4][5], enzyme-catalyzed approaches have also been successfully established, and especially, hydrolases, i.e., lipases and esterases, are used for the kinetic resolution of tertiary alcohols [6][7][8][9