Copper catalysis with redox-active ligands

• Agnideep Das,
• Yufeng Ren,
• Cheriehan Hessin and
• Marine Desage-El Murr

Beilstein J. Org. Chem. 2020, 16, 858–870, doi:10.3762/bjoc.16.77

• metalloenzymatic active site was not characterized in detail, it might bear some resemblance to the original biological active site. Building on their previously discussed phenol oxidation methodology (Scheme 5 and Scheme 6), Lumb and co-workers have targeted subsequent C–N bond formation to access oxindoles [34

Design and synthesis of diazine-based panobinostat analogues for HDAC8 inhibition

• Sivaraman Balasubramaniam,
• Sajith Vijayan,
• Liam V. Goldman,
• Xavier A. May,
• Kyra Dodson,
• Sweta Adhikari,
• Fatima Rivas,
• Davita L. Watkins and
• Shana V. Stoddard

Beilstein J. Org. Chem. 2020, 16, 628–637, doi:10.3762/bjoc.16.59

• that of panobinostat [12]. In developing such analogues, the hydroxamate tails and indole capping moiety were maintained as both are essential to binding at the active site of HDAC2 and HDAC8. Results suggested that TOI1, TOI2, and TOI4 [12] would be inhibitors exhibiting similar potency as that of

• the HDAC8 receptor. (a) Overlay of all compounds investigated in this study in the HDAC8 active site: panobinostat (green), TOI1 (purple), TOI2 (yellow) and TOI4 (grey); (b) TOI3-rev (pink) docking pose in active site; (c) TOI4 (grey) docking pose in the active site. General building blocks for the

Synthesis and herbicidal activities of aryloxyacetic acid derivatives as HPPD inhibitors

• Man-Man Wang,
• Hao Huang,
• Lei Shu,
• Jian-Min Liu,
• Jian-Qiu Zhang,
• Yi-Le Yan and
• Da-Yong Zhang

Beilstein J. Org. Chem. 2020, 16, 233–247, doi:10.3762/bjoc.16.25

• -dicarbonyl bidentate chelation with the active center metal, and 2) through favorable sandwich π–π stacking interactions between aromatic rings and the Phe360, Phe403 residues of the active site. Thus, 1,3-dicarbonyl and aromatic moieties are indispensable pharmacophores for potent HPPD-inhibiting compounds

• revealed the bioactive binding site positions of potential inhibitors within the targets active site. We modeled the interactions of I12 and II4 (C) with AtHPPD (PDB ID: 1TFZ). The structure of AtHPPD was taken from the PDB data bank. All molecular modeling studies were carried out as previously reported

• [10][19][32][33][34]. The results show that two main interactions exist between I12 and the AtHPPD active site (Figure 4), as was observed for mesotrione; the 1,3-dicarbonyl unit is chelated to the iron ion, and the aromatic ring moiety formed π–π interactions with Phe403 and Phe360. Electron

Understanding the role of active site residues in CotB2 catalysis using a cluster model

• Keren Raz,
• Ronja Driller,
• Thomas Brück,
• Bernhard Loll and
• Dan T. Major

Beilstein J. Org. Chem. 2020, 16, 50–59, doi:10.3762/bjoc.16.7

• active site cluster model. The results revealed the significant effect of the active site residues on the relative electronic energy of the intermediates and transition state structures with respect to gas phase data. A detailed understanding of the role of the enzyme environment on the CotB2 reaction

• cascade can provide important information towards a biosynthetic strategy for cyclooctatin and the biomanufacturing of related terpene structures. Keywords: active site; CotB2 cyclase; diterpene; mechanism; quantum mechanics; Introduction Enzymes catalyze numerous complex biochemical reactions in

• relevant, i.e., that have a ligand bound in a reactive configuration and have a fully closed active site. Recently, a crystal structure of the CotB2 enzyme that met these criteria was published [42]. In the current work, we describe the crucial role of the amino acids in the active site on the reaction

Synthesis of C-glycosyl phosphonate derivatives of 4-amino-4-deoxy-α-ʟ-arabinose

• Lukáš Kerner and
• Paul Kosma

Beilstein J. Org. Chem. 2020, 16, 9–14, doi:10.3762/bjoc.16.2

• have frequently been exploited as potential inhibitors for glycosyl transferases since the carbon–phosphorus bond is not hydrolyzed in the active site of glycosyl transferases [10][11][12][13]. Herein, we report on the synthesis of α-anomeric C-arabinosyl methylphosphonate ester derivatives as model

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

• . Indeed, besides the influence on kinetic properties by changing the conserved motifs, many bacterial TCs are able to produce novel skeletons through mutations of other active-site residues. This could result in either the arrest of catalytic intermediates or the creation of new trajectories to quench the

• cationic species. For instance, remodeling the hydrophobic pocket of the active site by single-point mutation, epi-isozizaene (33) synthase was engineered to produce various linear, monocyclic, bicyclic, and tricyclic terpene skeletons (Figure 9b) [119][120][121]. Another prominent example is cyclooctat-9

• -en-7-ol (23, Figure 7a) synthase, for which the active-site residues responsible for cationic intermediate stabilization were identified through analysis of the crystal structure [122] and structural modeling [123]. Mutations of the identified residues were shown to alter product profiles and yielded

Synthetic terpenoids in the world of fragrances: Iso E Super^® is the showcase

• Alexey Stepanyuk and
• Andreas Kirschning

Beilstein J. Org. Chem. 2019, 15, 2590–2602, doi:10.3762/bjoc.15.252

• -protein receptors consisting of seven intermembrane domains [28]. The quaternary structure including the membrane set up the active site. Approximately 370 different G-type proteins are known, that are linked with the odour perception. Because molecules can bind to an array of olfactory receptors

Current understanding and biotechnological application of the bacterial diterpene synthase CotB2

• Ronja Driller,
• Daniel Garbe,
• Norbert Mehlmer,
• Monika Fuchs,
• Keren Raz,
• Dan Thomas Major,
• Thomas Brück and
• Bernhard Loll

Beilstein J. Org. Chem. 2019, 15, 2355–2368, doi:10.3762/bjoc.15.228

• segments and additional five short α-helices (α1 to α5; (Figure 2A and B)). CotB2 resembles the classical α-helical fold of TPSs [18] with significant differences in its primary sequence compared to other TPSs. The core α-helices surround a large, deep cleft, which forms the active site (Figure 2A and B

• active site. Moreover, the two missing Mg2+ ions prevent helix D, accommodating the Asp-rich motif, from shifting towards the active site (Figure 3). Consequently, the active site remains partially open and the C-terminus cannot fold over the active site, making a proper substrate positioning and

• , such as FGGDP, have been used for the crystallization of other TPSs and have been shown to stick to the active site without undergoing cyclization, trapping the enzyme in a closed state [52][53]. Comparing the overall structure of CotB2wt·Mg2+3·F-Dola to the open conformation of CotB2 reveals major

Harnessing enzyme plasticity for the synthesis of oxygenated sesquiterpenoids

• Melodi Demiray,
• David J. Miller and
• Rudolf K. Allemann

Beilstein J. Org. Chem. 2019, 15, 2184–2190, doi:10.3762/bjoc.15.215

• properties and are used to treat epilepsy [27][28]. This array of important compounds shows the potential of generating novel sesquiterpenoids with desirable bio-properties. ADS is a high fidelity sesquiterpene synthase that produces almost exclusively a single product. Its active site plasticity

• bisabolyl cation and the amorphane skeleton. Rather the active site conformations of 11 and cation 22 appear to enable a 1,11-cyclisation to 23. A subsequent [1,3]-hydride shift to cation 24 and deprotonation from C15 lead to 8-methoxy-γ-humulene (20, Scheme 3A). Alternatively, the nucleophilic 8-methoxy

Inherent atomic mobility changes in carbocation intermediates during the sesterterpene cyclization cascade

• Hajime Sato,
• Takaaki Mitsuhashi,
• Mami Yamazaki,
• Ikuro Abe and
• Masanobu Uchiyama

Beilstein J. Org. Chem. 2019, 15, 1890–1897, doi:10.3762/bjoc.15.184

• terpene cyclase active site [3][5][6]. Although many terpene cyclases are known [6][7][8][9][10], it is still challenging to identify the precise initial conformation of the oligoprenyl diphosphate substrate in the active site, even by X-ray crystal structure determination. This is because the substrate

• can sometimes bind to the active site in an unreactive conformation [11]. Recently, Siegel and Tantillo reported an innovative method for predicting the docking mode of carbocation intermediates in terpene cyclase [12][13], based on QM calculation and computational docking with the Rosetta protein

Molecular basis for the plasticity of aromatic prenyltransferases in hapalindole biosynthesis

• Takayoshi Awakawa and
• Ikuro Abe

Beilstein J. Org. Chem. 2019, 15, 1545–1551, doi:10.3762/bjoc.15.157

• distance from C-1 of GSPP to C-3 of 1 (Figure 4B, c: 4.6 Å) became closer than that to C-2 of 1 (Figure 4B, d: 5.4 Å). Importantly, an additional Mg2+ ion (Figure 3C, Mg-2) appeared in the active site close to the isonitrile of 1, stabilized by the hydrogen bonding with D172, T173, G208, and E209 (Figure

•  4B). The AmbP1 E209A and E209L mutants completely lost their activities, implying that E209 plays an important role in forming the catalytic cavity as well as binding the Mg2+ ion. The active site structure depicted by the surface mode indicated that E209 is important to form the wall of the cavity

• PTases that utilize a Mg2+ ion to reorganise the active site cavity to control the regiospecificity of the prenylation reaction. X-ray crystal structure analysis of AmbP3 The crystal structures of AmbP3 complexed with DMSPP/hapalindole U (HU structure) and A (HA structure) were each solved at 2.00 Å [14

Synthesis and biological evaluation of truncated derivatives of abyssomicin C as antibacterial agents

• Leticia Monjas,
• Peter Fodran,
• Johanna Kollback,
• Carlo Cassani,
• Thomas Olsson,
• Maja Genheden,
• D. G. Joakim Larsson and
• Carl-Johan Wallentin

Beilstein J. Org. Chem. 2019, 15, 1468–1474, doi:10.3762/bjoc.15.147

• cysteine residue in the immediate proximity to the active site and the enone moiety of AbC. The PABA pathway is essential in bacteria but absent in humans, making AbC a promising compound for further development towards an antibiotic drug candidate. Because of its intriguing structure and antibacterial

• docking of known and proposed ligands. The crystal structure contains a tryptophan molecule in the active site. Restrained molecular dynamics [20][21] was employed to position the active site cysteine (Cys-263) in a position that would allow covalent binding of the ligands in the active site. The

• , which suggests a suitable level of structural truncation of compound 2. Further docking studies, using covalent docking, also showed that both atrop-O-benzyl-desmethyl-abyssomicin C and 2 can bind to the active site cysteine via a Michael addition to the α,β-unsaturated ketone, still maintaining the

Mechanistic investigations on multiproduct β-himachalene synthase from Cryptosporangium arvum

• Jan Rinkel and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2019, 15, 1008–1019, doi:10.3762/bjoc.15.99

• enantiomerically pure form (ee values were varying between 64% and 88%, as judged by integration), which may point to different possible binding and folding modes within the TS’s active site for GPP involving both enantiomers of linalyl diphosphate (LPP, Scheme 1) and the terpinyl cation (A). Other TSs producing

• or multiple compounds, are terpene synthases (TSs). These enzymes are able to guide complex cascade reactions from structurally simple oligoprenyl diphosphates to often complex, polycyclic products [4][5][6] circumventing the low selectivity observed for carbocationic reactions by a defined active

• -site architecture. Although these enzymes are mostly highlighted for their great product selectivity, TSs producing only one compound are by far not the general case. Mostly, the main product is accompanied by several side products. Prominent examples are the TS identified from the plant Medicago

Stereochemical investigations on the biosynthesis of achiral (Z)-γ-bisabolene in Cryptosporangium arvum

• Jan Rinkel and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2019, 15, 789–794, doi:10.3762/bjoc.15.75

• of the C-2,C-3-double bond by the enzyme’s active site (e.g., on top of it, Figure 4A). This migration of OPP to C-3 results in a reorganisation of the resulting structure to a cisoid conformation for the follow up 1,6-ring closure. To explain the astonishing selectivity between the two NPP

• enantiomers by BbS, different NPP conformations inside the chiral environment of the active site in BbS have to be assumed (Figure 4B + 4C). The architecture of the active site may stay the same in both cases, so a fixed OPP moiety with binding by the trinuclear Mg2+ cluster and a comparable folding of the

• isoprenoid chain in both cases is reasonable. Therefore, the two smallest substituents at the stereocentre formally change their places for the two enantiomers of NPP, representing a minor structural change of the substrate that can be tolerated in the active site. While the binding of (R)-NPP leads to a

Synthesis of polydicyclopentadiene using the Cp₂TiCl₂/Et₂AlCl catalytic system and thin-layer oxidation of the polymer in air

• Zhargolma B. Bazarova,
• Ludmila S. Soroka,
• Alex A. Lyapkov,
• Мekhman S. Yusubov and
• Francis Verpoort

Beilstein J. Org. Chem. 2019, 15, 733–745, doi:10.3762/bjoc.15.69

• bond from the norbornene ring of dicyclopentadiene in the double bond reaction, as a result of the rearrangement of the active site, structures of both exo- and endo-polydicyclopentadiene (A and B, see Scheme 2) can be formed [1][10]. At the same time, with participation in the reaction of the

Synthesis and SAR of the antistaphylococcal natural product nematophin from Xenorhabdus nematophila

• Frank Wesche,
• Hélène Adihou,
• Thomas A. Wichelhaus and
• Helge B. Bode

Beilstein J. Org. Chem. 2019, 15, 535–541, doi:10.3762/bjoc.15.47

• described as a potent inhibitor of various proteases, in particular trypsin and thrombin [17][18][19]. Hereby, the α-keto amide covalently binds to the serine oxygen in the active site under formation of a stable tetrahedral hemiketal. Furthermore, substitution of the indole hydrogen by alkyl, aryl or

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