Opportunities and challenges for the sustainable production of structurally complex diterpenoids in recombinant microbial systems

• Katarina Kemper,
• Max Hirte,
• Markus Reinbold,
• Monika Fuchs and
• Thomas Brück

Beilstein J. Org. Chem. 2017, 13, 845–854, doi:10.3762/bjoc.13.85

• committed step in synthesis of these Class I enzymes is the abstraction of the diphosphate group from the isoprenyl diphosphate substrate [50] at what the diphosphate group is postulated to remain inside the active site of the enzyme [51][52]. Class II terpene synthases harbor a distinct DXDD-motif [52] and

• , combinatorial enzyme design and microbial engineering. Mutational engineering of terpene synthases Site-directed mutagenesis of diterpene cyclases is conventionally applied to elucidate structure–function relationships and mostly targets the active site of the enzyme in order to change the polarity or dimension

• to phytotoxic fusicoccin A [60] and its derivative with presumably anticancer potential [61]. Exchange of two amino acid residues in the active site of the Class II peregrinol diphosphate synthase from the horehound Marrubium vulgare (MvCPS1) [58] resulted in an altered neutralization mechanism of a

Continuous-flow processes for the catalytic partial hydrogenation reaction of alkynes

• Carmen Moreno-Marrodan,
• Francesca Liguori and
• Pierluigi Barbaro

Beilstein J. Org. Chem. 2017, 13, 734–754, doi:10.3762/bjoc.13.73

• at full conversion) [119]. No justification for this evidence was proposed, however, a lower stability of the active site-adsorbed alkene intermediate with increasing steric hindrance may be hypothesized, which results in fewer interactions with hydrogen species, thus in enhanced the selectivity of

• from a diffusion-controlled to kinetic-limited regime [163][181]. The non-accumulation of co-products adsorbed on the catalyst surface may also significantly contribute to the minimization of active site inhibition under the conditions of continuous flow [27]. Flow reactor design. Performance

Polyketide stereocontrol: a study in chemical biology

• Kira J. Weissman

Beilstein J. Org. Chem. 2017, 13, 348–371, doi:10.3762/bjoc.13.39

• ][32][33][34][35][36][37], in combination with structure elucidation at high resolution of AT5 from the DEBS PKS, which was solved in the presence of acetate (Figure 7) [38]. For example, extender unit-specific ATs contain positively charged residues in the active site (R667 and H745, DEBS AT5

• numbering) capable of forming salt bridges with the carboxyl group of the building block, while these are non-polar amino acids in starter-unit specific ATs. The choice of methylmalonyl-CoA over malonyl-CoA is correlated with a YASH motif some 100 residues downstream of the active site serine, whereas

• malonyl-CoA specific ATs exhibit an alternative HAFH sequence (Figure 7a) [38]. In the AT5 crystal structure, the Tyr, Ser and His all lie within the active site (the His is the second member of the catalytic dyad). This leads to a model in which the C-2-methyl of methylmalonyl-CoA forms favorable

Biochemical and structural characterisation of the second oxidative crosslinking step during the biosynthesis of the glycopeptide antibiotic A47934

• Veronika Ulrich,
• Clara Brieke and
• Max J. Cryle

Beilstein J. Org. Chem. 2016, 12, 2849–2864, doi:10.3762/bjoc.12.284

• -domain likely hinders reorganisation of the P450/NRPS complex and hence can be trapped in states that display sub-optimal substrate orientation in the P450 active site [12]. In the case of StaF, it now seems clear that the natural X-domain is in fact the best system for peptide cyclisation, although

• reactions and provide further indication that its role appears to be more than just recruitment of the P450 to the substrate, but also ensuring proper substrate orientation via the PCP-domain in the P450 active site. Structure and active site architecture of StaF In order to gain insight into the structure

• feature of StaF is the long A’ helix at the N-terminus, which forms the ceiling of the active site. This helix seems to be specific for D-O-E ring catalysing P450s as it was only observed once before in OxyAtei, the D-O-E ring forming P450 from teicoplanin biosynthesis [14]. The centre of the active site

Chemical probes for competitive profiling of the quorum sensing signal synthase PqsD of Pseudomonas aeruginosa

• Michaela Prothiwa,
• Dávid Szamosvári,
• Sandra Glasmacher and
• Thomas Böttcher

Beilstein J. Org. Chem. 2016, 12, 2784–2792, doi:10.3762/bjoc.12.277

• developed a library of cysteine reactive chemical probes with an alkyne handle for fluorescence tagging and report the selective and highly sensitive in vitro labelling of the active site cysteine of this important enzyme. Interestingly, only one type of probe, with a reactive α-chloroacetamide was capable

• of covalently reacting with the active site. We demonstrated the potential of our probes in a competitive labelling platform where we screened a library of synthetic HHQ and PQS analogues with heteroatom replacements and found several inhibitors of probe binding that may represent promising scaffolds

• for the development of customized PqsD inhibitors as well as a chemical toolbox to investigate the activity and active site specificity of the enzyme. Keywords: activity-based probes; PqsD; protein labelling; Pseudomonas aeruginosa; quinolones; Introduction The emergence of multi-drug resistant

Computational methods in drug discovery

• Sumudu P. Leelananda and
• Steffen Lindert

Beilstein J. Org. Chem. 2016, 12, 2694–2718, doi:10.3762/bjoc.12.267

• reported for HIV integrase. MD simulations that were performed with the holo-structure of HIV integrase bound to a known ligand showed signs of a novel binding pocket opening in close proximity to its active site [183]. RCS ligand docking showed that this binding site is a possible binding pocket for drug

Facile synthesis of a 3-deazaadenosine phosphoramidite for RNA solid-phase synthesis

• Elisabeth Mairhofer,
• Elisabeth Fuchs and
• Ronald Micura

Beilstein J. Org. Chem. 2016, 12, 2556–2562, doi:10.3762/bjoc.12.250

• plays a dominant role in catalysis [3][4][5]. Also for the pistol ribozyme, evidence exists that an adenine-N3 in the active site is significant for the cleavage activity, most likely by 5’-O-leaving group stabilization through proton shuttling [6][7]. Another example for a specific role of an adenine

Radical polymerization by a supramolecular catalyst: cyclodextrin with a RAFT reagent

• Kohei Koyanagi,
• Yoshinori Takashima,
• Takashi Nakamura,
• Hiroyasu Yamaguchi and
• Akira Harada

Beilstein J. Org. Chem. 2016, 12, 2495–2502, doi:10.3762/bjoc.12.244

• sites and catalytic active sites have been designed for polymerization reactions, relatively few reports have described a catalytic design in which the catalytic active site does not leave the CD monomer recognition site during the growing step. In a previous design of radical initiators with CDs, the

A detailed view on 1,8-cineol biosynthesis by Streptomyces clavuligerus

• Jan Rinkel,
• Patrick Rabe,
• Laura zur Horst and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2016, 12, 2317–2324, doi:10.3762/bjoc.12.225

• and achiral precursors such as geranyl diphosphate (GPP, monoterpenes), farnesyl diphosphate (FPP, sesquiterpenes) and geranylgeranyl diphosphate (GGPP, diterpenes). Terpene cyclases (type I) contain a trinuclear (Mg2+)3 cluster in their active site that is stabilised by binding to several highly

Three-component synthesis of highly functionalized aziridines containing a peptide side chain and their one-step transformation into β-functionalized α-ketoamides

• Lena Huck,
• Juan F. González,
• Elena de la Cuesta and
• J. Carlos Menéndez

Beilstein J. Org. Chem. 2016, 12, 1772–1777, doi:10.3762/bjoc.12.166

• for the preparation of peptides [2][3] and the synthesis of peptide-like compounds comprising the aziridine motif [4][5]. Furthermore, the incorporation of an electrophilic aziridine moiety in peptide or peptidomimetic frameworks is an interesting strategy for the design of active site-directed drugs

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

• to a histidine or an asparagine residue in their active site. This exchange avoids the dehydration reaction and might facilitate the activation of the hydroxy group for nucleophilic attack on the Michael system by proton abstraction. PS domains also form a distinct phylogenetic clade compared to DH

• proposed mechanism also proceeds via a dehydration–oxa-Michael addition cascade. A crystal structure revealed two crucial aspartic acid residues as candidates for the acid–base catalysis occurring in the active site [18]. 1.1.2 Processing of hemiacetals: Reduction or alkylation of hemiacetals in the

• and was verified by mutagenesis and kinetic studies. In the active site, Glu141 and His129 activate the C3 keto group by protonation. The pro-S hydride of the reduced nicotinamide adenine dinucleotide (phosphate) (NAD(P)H) is then transferred to the C3. The resulting hydroxy group participates in the

Beta-hydroxyphosphonate ribonucleoside analogues derived from 4-substituted-1,2,3-triazoles as IMP/GMP mimics: synthesis and biological evaluation

• Tai Nguyen Van,
• Audrey Hospital,
• Corinne Lionne,
• Lars P. Jordheim,
• Charles Dumontet,
• Christian Périgaud,
• Laurent Chaloin and
• Suzanne Peyrottes

Beilstein J. Org. Chem. 2016, 12, 1476–1486, doi:10.3762/bjoc.12.144

• -containing derivatives are biologically interesting (Figure 1) [7]. In addition, molecular docking studies have been performed and highlighted the importance of three binding areas within the active site of the protein: a hydrophobic clamp (Phe157, His209 and Tyr210) interacting with the nucleobase, a

Artificial Diels–Alderase based on the transmembrane protein FhuA

• Hassan Osseili,
• Daniel F. Sauer,
• Klaus Beckerle,
• Marcus Arlt,
• Tomoki Himiyama,
• Tino Polen,
• Akira Onoda,
• Ulrich Schwaneberg,
• Takashi Hayashi and
• Jun Okuda

Beilstein J. Org. Chem. 2016, 12, 1314–1321, doi:10.3762/bjoc.12.124

• absence of any enantioselectivity suggests that no preferential orientation of the substrate at the active site within the barrel structure is possible. Notably, no protein precipitated during catalysis, showing the advantageous feature of membrane proteins in terms of robustness as compared to soluble

Cyclisation mechanisms in the biosynthesis of ribosomally synthesised and post-translationally modified peptides

• Andrew W. Truman

Beilstein J. Org. Chem. 2016, 12, 1250–1268, doi:10.3762/bjoc.12.120

• , given that the active site Zn2+ is proposed to activate the cysteine side chains for cyclisation. The identification of the labyrinthopeptins [59] (Figure 4C) led to the discovery of a subset of class III lanthipeptides that contain an additional carbocyclic ring, which features the labionin (Lab) amino

Muraymycin nucleoside-peptide antibiotics: uridine-derived natural products as lead structures for the development of novel antibacterial agents

• Daniel Wiegmann,
• Stefan Koppermann,
• Marius Wirth,
• Giuliana Niro,
• Kristin Leyerer and
• Christian Ducho

Beilstein J. Org. Chem. 2016, 12, 769–795, doi:10.3762/bjoc.12.77

• within the superfamily of polyisoprenyl-phosphate N-acetyl hexosamine 1-phosphate transferases (PNPT). Mutation of these three aspartate residues (D115, D116 and D267 in the E. coli protein) resulted in a complete loss of catalytic activity. This led to a proposed model for the active site of MraY in

• protein E from bacteriophage X174, Bugg et al. reported a different site of inhibition in pronounced distance to the proposed active site. It has been demonstrated before that mutation of phenylalanine 288 (F288L) in helix 9 of MraY caused resistance against lysis protein E [72][73]. An interaction

Is conformation a fundamental descriptor in QSAR? A case for halogenated anesthetics

• Maria C. Guimarães,
• Mariene H. Duarte,
• Josué M. Silla and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2016, 12, 760–768, doi:10.3762/bjoc.12.76

• option would be to obtain the ligand geometries inside an enzyme active site. Since conformational search inside a receptor normally gives the mode of interaction between substrate and enzyme, as well as the intermolecular interaction energy (related to the ligand–receptor affinity and, consequently, to

From steroids to aqueous supramolecular chemistry: an autobiographical career review

• Bruce C. Gibb

Beilstein J. Org. Chem. 2016, 12, 684–701, doi:10.3762/bjoc.12.69

• exquisitely shaped hydrophobic pocket/active site. Ronald Breslow was asking similar questions and addressing it with cyclodextrin derivatives as enzyme mimics, but as I neared the end of my Ph.D. degree I confess I knew nothing of this facet of supramolecular chemistry. In 1991, as lab work started to be

• project on the synthesis of deep-cavity cavitands. The first was inspired by Murray Goodman’s work [13] on the covalent templation of small, stable collagen-like triple-helices, and involved positioning a metal-ion coordinating template into a collagen structure such that the “active site” was situated in

• ‘dangles’ above the zinc-bound water in the crystal structure of the enzyme. In addition to synthesis, the project also involved a good deal of potentiometry, and this began to teach me that synthesizing enzyme mimics was a difficult challenge of balancing the need to create functionality for the active

Biosynthesis of α-pyrones

• Till F. Schäberle

Beilstein J. Org. Chem. 2016, 12, 571–588, doi:10.3762/bjoc.12.56

• mechanism for CorB and MxnB closely resembles each other, but certain differences have also been proposed, as will be discussed here. First, one chain is transferred and covalently linked to the active-site cysteine. This results in an activation of the cysteine-tethered chain. In the second step, the other

• -oxohexanoyl thioester and different thioesters of straight-chain and iso-branched chain fatty acids [14]. The mechanism proposal also includes the catalytic cysteine. The first chain, i.e., thioester-activated 9-methyldecanoic acid, gets covalently tethered to that important residue within the active site

• chains are positioned face to face. A) Transacylation of the eastern chain to C121 of CorB. The simplified mimic of the eastern chain (shown in bold) was placed into the active site on the basis of its unbiased (F0–Fc)-difference electron density. The remaining portion of the eastern chain was modeled

Effective in silico prediction of new oxazolidinone antibiotics: force field simulations of the antibiotic–ribosome complex supervised by experiment and electronic structure methods

• Jörg Grunenberg and
• Giuseppe Licari

Beilstein J. Org. Chem. 2016, 12, 415–428, doi:10.3762/bjoc.12.45

• analogues complexed inside the model ribosomal active site. Sampling the lowest energy wells in a 40 kJ/mol energy window the lowest enthalpy minimum was used to assess the relevant terms in Equation 1 below. Since the linezolid complex represents the zero point of our relative binding energy scale, a

• . In a second step, models of different size were cut out from this working shell in order to find the smallest model still including all relevant moieties affected by linezolid inside the active site (working shell I). The resulting ribosomal model still characterized by 1) the reproduction of

• , induced by subtle chemical differences (H vs CH3) favoring 5 over 6 by more than 13 kJ/mol. An inspection of our obtained minima reveals that, whereas the flexible terminal N-glycinyl chain is capable of making different water mediated H-bonds or with the residues from the active site entrance directly

Dynamic behavior of rearranging carbocations – implications for terpene biosynthesis

• Stephanie R. Hare and
• Dean J. Tantillo

Beilstein J. Org. Chem. 2016, 12, 377–390, doi:10.3762/bjoc.12.41

• indicated that the bornyl cation also has a short lifetime in the active site of the enzyme, but one – 185 fs on average – that is longer (by approximately a factor of 4) than in the absence of the enzyme and complexed diphosphate. Take home messages: • Secondary carbocations, which often correspond to

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

• ions in the solvent. Acting as the active site, the substitution of secondary hydroxy groups might impact the hydrolysis rate. This was investigated comparing the effect of β-CD, DIMEB and TRIMEB on the alkaline hydrolysis of parathion, methyl parathion, and fenitrothion [53][54]. In all host–guest

Biocatalysis for the application of CO₂ as a chemical feedstock

• Apostolos Alissandratos and
• Christopher J. Easton

Beilstein J. Org. Chem. 2015, 11, 2370–2387, doi:10.3762/bjoc.11.259

• , ranging from the use of carboxylated cofactors [28][32] to complex extended metabolic pathways in C4 and CAM plants [17][33][34] and substrate channelling. In addition, a number of enzymes accept HCO3− as a substrate, which is converted to CO2 close to the active site before the reductive step [26][28

Active site diversification of P450cam with indole generates catalysts for benzylic oxidation reactions

• Paul P. Kelly,
• Anja Eichler,
• Susanne Herter,
• David C. Kranz,
• Nicholas J. Turner and
• Sabine L. Flitsch

Beilstein J. Org. Chem. 2015, 11, 1713–1720, doi:10.3762/bjoc.11.186

• monooxygenases are useful biocatalysts for C–H activation, and there is a need to expand the range of these enzymes beyond what is naturally available. A panel of 93 variants of active self-sufficient P450cam[Tyr96Phe]-RhFRed fusion enzymes with a broad diversity in active site amino acids was developed by

• hydroxylations. Keywords: active site mutagenesis; biotransformation; C–H activation; cytochrome P450cam monooxygenase; hydroxylation; Introduction Selective C–H activation and oxyfunctionalisation of hydrocarbons offers a route to chiral alcohols and other industrially important synthetic building blocks from

• –alkyl compounds [3], olefins [4], polycyclic aromatic hydrocarbons [5], terpenes [6][7][8] and alkanes as small as ethane [9]. Over the years a number of active site mutants of P450cam have been generated by rational re-design, but the active site has not been explored in a comprehensive and systematic

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

• diacid derivative of oleic acid catalyzed by dibutyltin oxide and Novozyme 435 (Figure 10) [59]. Dibutyltin oxide catalysis resulted in cross-linking and gel formation. This was not observed by enzyme catalysis, presumably due to steric hindrance which may be imposed by the active site of the enzyme

A novel and widespread class of ketosynthase is responsible for the head-to-head condensation of two acyl moieties in bacterial pyrone biosynthesis

• Darko Kresovic,
• Florence Schempp,
• Zakaria Cheikh-Ali and
• Helge B. Bode

Beilstein J. Org. Chem. 2015, 11, 1412–1417, doi:10.3762/bjoc.11.152

• using stable isotope labeled precursors [7] suggested a two-chain biosynthesis mechanism for photopyrone biosynthesis (Scheme 1): First, thioester-activated 9-methyldecanoic acid 14 is covalently bound to an active site cysteine. Deprotonation of the α-carbon of 14 results in the formation of a

• covalent binding of the fatty acid precursor, as well as amino acids present at the dimer interface (Figure S3, Supporting Information File 1). Using this model we performed docking studies by covalently docking 14 and 16 (Figure 2) into the active site C129, revealing that the binding cavity of modeled

• , Supporting Information File 1) and docking experiments (Figure S9, Supporting Information File 1) with the proposed substrate 17 and intermediate 19 to the active site C124 also confirmed the glutamic acid inside the binding pocket as catalytically important suggesting a biosynthesis model (Scheme S1