Aqueous olefin metathesis: recent developments and applications

• Valerio Sabatino and
• Thomas R. Ward

Beilstein J. Org. Chem. 2019, 15, 445–468, doi:10.3762/bjoc.15.39

• metathase based on the dative anchoring of a biotinylated HG-type catalyst to human carbonic anhydrase II (hCAII) in 2015 [67]. The active site of hCAII contains Zn2+ which is coordinated to three histidines. Catalyst 61 contains an arylsulfonamide moiety that coordinates the metal with high affinity (Kd

• , entries 2, 7 and 12). Gebbink and co-workers anchored the HG-type catalyst 79 to cutinase, a serine hydrolase [75]. The phosphonate ester moiety acts as a suicide inhibitor forming an irreversible covalent bond to a serine residue present in the active site of the enzyme. Assembly of ArM 8 occurs at pH 5

Computational characterization of enzyme-bound thiamin diphosphate reveals a surprisingly stable tricyclic state: implications for catalysis

• Ferran Planas,
• Michael J. McLeish and
• Fahmi Himo

Beilstein J. Org. Chem. 2019, 15, 145–159, doi:10.3762/bjoc.15.15

• , serves as the prototypical ThDP-dependent enzyme. A model of the active site was constructed on the basis of available crystal structures, and the cofactor states were characterized in the presence of three different ligands (crystallographic water, benzoylformate as substrate, and (R)-mandelate as

• whose crystals had been soaked with pyruvate [47]. In a very recent study, we used quantum chemical methodology to investigate the detailed reaction mechanism of benzoylformate decarboxylase (BFDC) [29]. A model of the active site was designed on the basis of the X-ray structure of BFDC in complex with

• cofactor in the BFDC active site in the absence and presence of bound ligands. The active site model is built on the basis of the crystal structure (PDB ID 1MCZ) and is identical to that used in the mechanistic study [29]. As shown in Figure 1, the model comprises all groups that make up the active site

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

• concentrations. The average standard deviation of the measurements is evident in the scatter of the data from the fitted curve and can be estimated from the χ2 valued derived in fitting the data. Active site concentration Interpretation of steady state turnover rates is dependent on an accurate estimate of the

• direct measurement of the rates of the conformational change and the chemical reaction at the active site of the enzyme was required. Steady state kinetic methods do not suffice. Transient state kinetic analysis are needed to measure events occurring during a single enzyme cycle, but in the end, we must

• concentration of active sites. There are significant systematic errors in measurements of protein concentrations using dye-binding assays or by absorbance measurements, and the fraction of protein that is active is not known without direct measurement. For these reasons, it is important to perform an active

Thermophilic phosphoribosyltransferases Thermus thermophilus HB27 in nucleotide synthesis

• Ilja V. Fateev,
• Ekaterina V. Sinitsina,
• Aiguzel U. Bikanasova,
• Maria A. Kostromina,
• Elena S. Tuzova,
• Larisa V. Esipova,
• Tatiana I. Muravyova,
• Alexei L. Kayushin,
• Irina D. Konstantinova and
• Roman S. Esipov

Beilstein J. Org. Chem. 2018, 14, 3098–3105, doi:10.3762/bjoc.14.289

• . After optimization of the reaction conditions, kinetic parameters for TthHPRT were determined (Table 2). Based on the Km values, the affinity of 5-phosphoribosyl-α-1-pyrophosphate for the active site is much lower than that of heterocyclic bases. The similar situation we observed for TthAPRT [1

• ]. Comparison of the synthesis rates of inosine-5'-monophosphate and guanosine-5`-monophosphate showed that the first is synthesized 4.6 times faster. The literature data for similar enzymes (see Table 2) confirm a poor affinity of PRPP to the active site: Km for hypoxanthine is 17 fold less then for PRPP

Olefin metathesis catalysts embedded in β-barrel proteins: creating artificial metalloproteins for olefin metathesis

• Daniel F. Sauer,
• Johannes Schiffels,
• Takashi Hayashi,
• Ulrich Schwaneberg and
• Jun Okuda

Beilstein J. Org. Chem. 2018, 14, 2861–2871, doi:10.3762/bjoc.14.265

• catalyst or redox catalyst. Various metalloenzymes have been applied in laboratory-scale reactions and a few metalloenzymes such as nitrile hydratase (cobalt(III) in the active site) for the production of acrylamide have found application in industry [25]. Notably, however, the reaction scope of natural

• active site from the protein easier as compared to supramolecular anchoring. However, the design of catalysts capable of undergoing dative anchoring is usually based on interactions of inhibitors with the active site of the protein. This makes the catalyst design challenging and the application is

• limited. Covalent anchoring of an organometallic complex offers the precise positioning of a catalyst within a protein scaffold. Formation of the covalent bond between cofactor and protein ensures an irreversible binding of the active site (i.e., the metal complex). This approach is highly versatile

Novel solid-phase strategy for the synthesis of ligand-targeted fluorescent-labelled chelating peptide conjugates as a theranostic tool for cancer

• Sagnik Sengupta,
• Mena Asha Krishnan,
• Premansh Dudhe,
• Ramesh B. Reddy,
• Bishnubasu Giri,
• Sudeshna Chattopadhyay and
• Venkatesh Chelvam

Beilstein J. Org. Chem. 2018, 14, 2665–2679, doi:10.3762/bjoc.14.244

• [42] of PSMA reveals that small molecule ligands such as DUPA would reach the PSMA active site through a gradually narrowing tunnel of amino acids of 20 Å length. Moreover, the inner surface of the PSMA tunnel possesses two hydrophobic pockets suitable for hydrophobic interactions with the amino acids

• present in the peptide spacer [38]. Therefore, it is pertinent to design a PSMA targeted conjugate that can pass through the tunnel smoothly and reach the active site as well as fit in hydrophobic pockets via hydrophobic interactions. Additionally, the carbonyl oxygen of the urea moiety of DUPA directly

• coordinates with two zinc atoms present in the active site of PSMA. The γ′-carboxylic acid of the DUPA ligand does not play a significant role in the interaction with the PSMA active site and hence exploited as a handle for the construction of peptidic spacer of bioconjugate 13. While designing the required

Targeting the Pseudomonas quinolone signal quorum sensing system for the discovery of novel anti-infective pathoblockers

• Christian Schütz and
• Martin Empting

Beilstein J. Org. Chem. 2018, 14, 2627–2645, doi:10.3762/bjoc.14.241

• -CoA) is then transferred to an active-site cysteine of the β-ketoacyl-ACP synthase III (FabH)-type enzyme PqsD [26][27]. Subsequently, another CoA-activated substrate comes into play. In analogy to fatty acid synthesis, malonyl-CoA is reacted with the enzyme-bound thioester to yield 2

• formed by action of the heterodimeric complex PqsBC. This time, CoA-activated octanoic acid is used to preload an active-site cysteine of PqsC with the fatty acid via a thioester linkage [30][31]. The previously produced 2-ABA is then consumed to from HHQ under decarboxylative condensation [30]. Finally

• concentration of 1.5 mM. Moreover, it was shown that 6-FABA had no impact on the bacterial growth. Lépine et al. suggested that 2 competitively occupies the active site of PqsA [45] and therefore serves as a substrate analogue of AA (1). It was stated that the introduction of electron-withdrawing substituents

Pathoblockers or antivirulence drugs as a new option for the treatment of bacterial infections

• Matthew B. Calvert,
• Varsha R. Jumde and
• Alexander Titz

Beilstein J. Org. Chem. 2018, 14, 2607–2617, doi:10.3762/bjoc.14.239

• infections [61]. While not typically classed as toxins, bacterial proteolytic enzymes, such as collagenases or elastases, often account for host cell damage and immune evasion. Janda and co-workers developed thiol-based small molecules targeting the active site zinc ion in P. aeruginosa elastase LasB showing

Microwave-assisted synthesis of biologically relevant steroidal 17-exo-pyrazol-5'-ones from a norpregnene precursor by a side-chain elongation/heterocyclization sequence

• Gergő Mótyán,
• László Mérai,
• Márton Attila Kiss,
• Zsuzsanna Schelz,
• Izabella Sinka,
• István Zupkó and
• Éva Frank

Beilstein J. Org. Chem. 2018, 14, 2589–2596, doi:10.3762/bjoc.14.236

• -bulky heterocycle containing O, N or S atoms attached to position C-17 of the sterane skeleton with the lone electron pairs capable of coordinating with the heme iron at the active site; (ii) a N atom at either position 3′ or 4′ relative to the atom through which the heterocyclic ring is connected to

Learning from B₁₂ enzymes: biomimetic and bioinspired catalysts for eco-friendly organic synthesis

• Keishiro Tahara,
• Ling Pan,
• Toshikazu Ono and
• Yoshio Hisaeda

Beilstein J. Org. Chem. 2018, 14, 2553–2567, doi:10.3762/bjoc.14.232

• the anaerobic bacteria, Sulfurospiririllum multivorans, uses 1,1,2,2-tetrarchloroethene as a terminal electron acceptor to be reduced to trichloroethene (Scheme 8a) [87]. In electron transport chains, reductases reduce the Co(II) species of the B12 cofactor to the Co(I) species in the active site of

Synthesis of 3-aminocoumarin-N-benzylpyridinium conjugates with nanomolar inhibitory activity against acetylcholinesterase

• Nisachon Khunnawutmanotham,
• Cherdchai Laongthipparos,
• Patchreenart Saparpakorn,
• Nitirat Chimnoi and
• Supanna Techasakul

Beilstein J. Org. Chem. 2018, 14, 2545–2552, doi:10.3762/bjoc.14.231

• simultaneously bind to amino acid residues present in both the catalytic anionic site (CAS) and the peripheral anionic site (PAS) of AChE. The CAS is located deeply inside the narrow gorge and is responsible for ACh hydrolysis. On the other hand the PAS is located around the entrance of the active site gorge and

• is responsible for transient substrate binding before reaching the active site. Especially PAS plays a crucial role in β-amyloid (Aβ) fibrillogenesis in AD patients by forming stable AChE–Aβ complexes [3][4]. Thus, these types of effects may render them potential therapeutic agents for AD treatment

• program [19] was used to investigate the orientation of the compounds in the rhAChE binding site. Compounds 4a, 9a, 9b, 9e, 9h, 9i, and 10a were selected as representatives for the docking study. The active site of human AChE, which is at the bottom of a deep and narrow gorge, consists of several major

The enzymes of microbial nicotine metabolism

• Paul F. Fitzpatrick

Beilstein J. Org. Chem. 2018, 14, 2295–2307, doi:10.3762/bjoc.14.204

• -hydroxynicotine in the active site is followed by hydrolysis of the oxidized amine in a second site to yield 6-hydroxypseudooxynicotine (Scheme 3) [15]. However, a recent analysis of the structure of the product of the LHNO reaction utilizing NMR and continuous-flow mass spectrometry established that the enzyme

Spectroelectrochemical studies on the effect of cations in the alkaline glycerol oxidation reaction over carbon nanotube-supported Pd nanoparticles

• Dennis Hiltrop,
• Steffen Cychy,
• Karina Elumeeva,
• Wolfgang Schuhmann and
• Martin Muhler

Beilstein J. Org. Chem. 2018, 14, 1428–1435, doi:10.3762/bjoc.14.120

• -donating effect of the embedded nitrogen species [35]. Pd0 is also considered the active site in glycerol electrooxidation, and the observed lower overpotential may originate from the same interaction with the nitrogen-doped support. Furthermore, the thermal treatment of the oxygen-functionalized CNTs in

Acyl-group specificity of AHL synthases involved in quorum-sensing in Roseobacter group bacteria

• Lisa Ziesche,
• Jan Rinkel,
• Jeroen S. Dickschat and
• Stefan Schulz

Beilstein J. Org. Chem. 2018, 14, 1309–1316, doi:10.3762/bjoc.14.112

• among AHL synthases is observed. The preference for unsubstituted, 3-oxo or 3-hydroxyacyl precursors is mediated by binding interactions inside the active site of AHL synthases [18][21]. Investigations on the chain-length selectivity of the AHL synthases are limited. BjaI can accept substrates ranging

• distribution of the saturated AHLs as for the first experiment was observed with none of the additional substrates showing a significantly higher conversion. These results point to a very flexible active site of the investigated AHL synthase PgaI2, which converts a variety of substrates. The highest conversion

An overview of recent advances in duplex DNA recognition by small molecules

• Sayantan Bhaduri,
• Nihar Ranjan and
• Dev P. Arya

Beilstein J. Org. Chem. 2018, 14, 1051–1086, doi:10.3762/bjoc.14.93

• observed that the conjugates with alkynyl side chains show excellent E. coli DNA topoisomerase I inhibition properties with IC50 values of <5.0 μM, which was attributed to critical interactions between the inhibitor side chain and amino acids of the active site of DNA topoisomerase I, as suggested by the

Crystal structure of the inclusion complex of cholesterol in β-cyclodextrin and molecular dynamics studies

• Elias Christoforides,
• Andreas Papaioannou and
• Kostas Bethanis

Beilstein J. Org. Chem. 2018, 14, 838–848, doi:10.3762/bjoc.14.69

• of the [FeFe]-H2ase active site, (μ-SCH2NH(C6H4SO3−)CH2S)[FeI(CO)3]2, within the cavity of a 1·2 β-CD sodium salt clathrate. 28 water molecules are also found in the asymmetric unit. The incorporation of charged functional groups into the guest molecule of cyclodextrin host/guest system provides a

Nanoreactors for green catalysis

• M. Teresa De Martino,
• Loai K. E. A. Abdelmohsen,
• Floris P. J. T. Rutjes and
• Jan C. M. van Hest

Beilstein J. Org. Chem. 2018, 14, 716–733, doi:10.3762/bjoc.14.61

• of catalysts in a nanoreactor facilitates one-pot tandem reactions that, in most cases, require two or more incompatible catalysts [22][57]. Catalyst confinement leads to a high local concentration of the substrate at the active site, which results in higher reaction rates and better conversion [9

Position-dependent impact of hexafluoroleucine and trifluoroisoleucine on protease digestion

• Susanne Huhmann,
• Anne-Katrin Stegemann,
• Kristin Folmert,
• Damian Klemczak,
• Johann Moschner,
• Michelle Kube and
• Beate Koksch

Beilstein J. Org. Chem. 2017, 13, 2869–2882, doi:10.3762/bjoc.13.279

• increased steric bulk of the fluorinated amino acid, meaning protection from protease degradation is a result of the steric occlusion of the peptide from the active site [23][28]. In contrast, the Marsh lab found that the introduction of HfLeu into the antimicrobial peptide MSI-78 only renders it more

• binds in an extended conformation to the enzyme’s active site [42]. The positions P2, P1’ and P2’ at or adjacent to the cleavage site [41] carry the key residues for the recognition of the substrate by the protease and serve as substitution sites. The alanines at P2, P1’ or P2’ positions were

• enzymes in humans. It exhibits specificity for hydrophobic, especially aromatic residues like Phe, Trp, and Tyr at the P1 and P1’ positions [50][51][52][53][54]. It has an extended active site that can bind at least seven residues [66][67], and peptide bond cleavage occurs N-terminal to the residue at

Sulfation and amidinohydrolysis in the biosynthesis of giant linear polyenes

• Hui Hong,
• Markiyan Samborskyy,
• Katsiaryna Usachova,
• Katharina Schnatz and
• Peter F. Leadlay

Beilstein J. Org. Chem. 2017, 13, 2408–2415, doi:10.3762/bjoc.13.238

• each of the characteristic active site sequence motifs for the ketosynthase (KS), acyltransferase (AT), ketoreductase (KR), dehydratase (DH), and enoylreductase (ER) domains of each of the 27 extension modules, including the newly-recognised YGP motif of active DH domains [8] between the three PKS

18-Hydroxydolabella-3,7-diene synthase – a diterpene synthase from Chitinophaga pinensis

• Jeroen S. Dickschat,
• Jan Rinkel,
• Patrick Rabe,
• Arman Beyraghdar Kashkooli and
• Harro J. Bouwmeester

Beilstein J. Org. Chem. 2017, 13, 1770–1780, doi:10.3762/bjoc.13.171

• ) and the NSE triad NDXXSXX(R,K)(E,D), modified to a DTE triad in plants, for binding of the Mg2+ cofactor that forms a trinuclear (Mg2+)3 cluster to which the diphosphate portion of the substrate binds. Upon substrate binding the active site closes, resulting in hydrogen bonds between the substrate’s

2-Methyl-2,4-pentanediol (MPD) boosts as detergent-substitute the performance of ß-barrel hybrid catalyst for phenylacetylene polymerization

• Julia Kinzel,
• Daniel F. Sauer,
• Marco Bocola,
• Marcus Arlt,
• Tayebeh Mirzaei Garakani,
• Andreas Thiel,
• Klaus Beckerle,
• Tino Polen,
• Jun Okuda and
• Ulrich Schwaneberg

Beilstein J. Org. Chem. 2017, 13, 1498–1506, doi:10.3762/bjoc.13.148

• the choice of the stabilization reagent. In case of PE–PEG, FhuA ΔCVFtev precipitation is observed. Filtering of the solution shows similar results as the reaction with the precipitate present, indicating a deactivation of the catalyst or restricted access of the substrate to the active site. The

Strategies in megasynthase engineering – fatty acid synthases (FAS) as model proteins

• Manuel Fischer and
• Martin Grininger

Beilstein J. Org. Chem. 2017, 13, 1204–1211, doi:10.3762/bjoc.13.119

• consideration for animal FAS (again abstracted as spanning a cylindrical reaction space, two full sets of active sites) gives a virtual active site concentration of 1.2 mM. Accordingly, both scaffolds of FA type I synthesis facilitate reactions at high virtual concentration of enzymatic domains. PKS

• megasynthases share basic principles with the mammalian FAS fold (Figure 2c) [6][7], and it is valid to assume that active site concentrations lie in the similar range. Bacterial and mitochondrial FA synthesis comprises separate enzymes. To compensate for the lower organizational level, key enzymes occur at

• “preserve-and-adapt”. While the adaptation of active sites will remain as a challenging task in such an approach, the generally profound description of substrate/active site complexes, the conservation of active sites beyond protein families, and their susceptibility for biophysical assays makes the

Characterization of non-heme iron aliphatic halogenase WelO5* from Hapalosiphon welwitschii IC-52-3: Identification of a minimal protein sequence motif that confers enzymatic chlorination specificity in the biosynthesis of welwitindolelinones

• Qin Zhu and
• Xinyu Liu

Beilstein J. Org. Chem. 2017, 13, 1168–1173, doi:10.3762/bjoc.13.115

• expanded substrate scope [18]. Moreover, our recent structural characterizations of WelO5 in the absence and presence of 2 have shown residues 215-232 of WelO5 encode an α-helical motif that helps keeping the small molecular substrate in the active site by undergoing a dramatic conformational change upon

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

• variants of these folds), namely GT-A and GT-B (Figure 8). Different folds are nevertheless observed for GTs that use lipid phosphate donor substrates. The achievement of the enzyme-transition state complex requires a particular arrangement of the active site that is the result of concomitant protein

• crystalline glycosyl transferase. The four steps of the “freeze-trigger” process could be validated throughout by elucidation of the crystal structure of the glycosyl transferase, which has the active site occupied in a semi-closed conformation of the substrate with various levels of ordering of the internal

A strategic approach to [6,6]-bicyclic lactones: application towards the CD fragment of DHβE

• Tue Heesgaard Jepsen,
• Emil Glibstrup,
• François Crestey,
• Anders A. Jensen and
• Jesper Langgaard Kristensen

Beilstein J. Org. Chem. 2017, 13, 988–994, doi:10.3762/bjoc.13.98

• active site. This is further supported by Wildeboer’s study from 2005 who reported a much lower affinity of desmethoxy-βE compared to the parent DHβE [27]. Conclusion In summary, we have successfully developed a strategy to construct the CD ring system of DHβE and to efficiently access the synthetically