Diels-Alder ribozyme catalysis: a computational approach

A computational comparison of the Diels-Alder reaction of a maleimide and an anthracene in water and the active site of the ribozyme Diels-Alderase is reported. During the course of the catalyzed reaction, the maleimide is held in the hydrophobic pocket while the anthracene approaches to the maleimide through the back passage of the active site. The active site is so narrow that the anthracene has to adopt a tilted approach angle toward maleimide. The conformation of the active site changes marginally at different states of the reaction. Active site dynamics contribution to catalysis has been ruled out. The active site stabilizes the product more than the transition state (TS). The reaction coordinates of the ribozyme reaction in TS, RC1-CD1 and RC4-CD2, are 2.35 and 2.33 A, respectively, compared to 2.37 and 2.36 A in water. The approach angle of anthracene toward maleimide is twisted by 18 degrees in the TS structure of ribozyme reaction while no twisted angle is found in TS of the reaction in water. The free energy barriers for reactions in both ribozyme and water were obtained by umbrella sampling combined with SCCDFTB/MM. The calculated free energy barriers for the ribozyme and water reactions are in good agreement with the experimental values. As expected, Mulliken charges of the atoms involved in the ribozyme reaction change in a similar manner as that of the reaction in water. The proficiency of the Diels-Alder ribozyme reaction originates from the active site holding the two reactants in reactive conformations, in which the reacting atoms are brought together in van der Waals distances and reactants approach to each other at an appropriate angle.     

Unravelling RNA–Substrate Interactions in a Ribozyme‐Catalysed Reaction Using Fluorescent Turn‐On Probes

The Diels–Alder reaction is one of the most important C?C bond‐forming reactions in organic chemistry, and much effort has been devoted to controlling its enantio‐ and diastereoselectivity. The Diels–Alderase ribozyme (DAse) catalyses the reaction between anthracene dienes and maleimide dienophiles with multiple‐turnover, stereoselectivity, and up to 1100‐fold rate acceleration. Here, a new generation of anthracene‐BODIPY‐based fluorescent probes was developed to monitor catalysis by the DAse. The brightness of these probes increases up to 93‐fold upon reaction with N‐pentylmaleimide (NPM), making these useful tools for investigating the stereochemistry of the ribozyme‐catalysed reaction. With these probes, we observed that the DAse catalyses the reaction with >91 % de and >99 % ee. The stereochemistry of the major product was determined unambiguously by rotating‐frame nuclear Overhauser NMR spectroscopy (ROESY‐NMR) and is in agreement with crystallographic structure information. The pronounced fluorescence change of the probes furthermore allowed a complete kinetic analysis, which revealed an ordered bi uni type reaction mechanism, with the dienophile binding first.     

Inverting External Asymmetric Induction via Selective Energy Transfer Catalysis: A Strategy to β‐Chiral Phosphonate Antipodes

Enantiodivergent, catalytic reduction of activated alkenes relays stereochemical information encoded in the antipodal chiral catalysts to the pro‐chiral substrate. Although powerful, the strategy remains vulnerable to costs and availability of sourcing both catalyst enantiomers. Herein, a stereodivergent hydrogenation of α,β‐unsaturated phosphonates is disclosed using a single enantiomer of the catalyst. This enables generation of the R‐ or S‐configured β‐chiral phosphonate with equal and opposite selectivity. Enantiodivergence is regulated at the substrate level through the development of a facile E → Z isomerisation. This has been enabled for the first time by selective energy transfer catalysis using anthracene as an inexpensive organic photosensitiser. Synthetically valuable in its own right, this process enables subsequent Rh^I‐mediated stereospecific hydrogenation to generate both enantiomers of the product using only the S‐catalyst (up to 99:1 and 3:97 e.r.). This strategy out‐competes the selectivities observed with the E‐substrate and the R‐catalyst.     

Influences of the Hydrophobicity of the Heme－binding Pocket on the Properties and Functions of Cytochrome b5 Mutants

The mutation sites of the four mutants F35Y, P40V, V45E and V45Y of cytochrome b5 are located at the edge of the heme-binding pocket. The solvent accessible areas of the “pocket inte-rior“ of the four mutants and the wild-type cytochrome b5 have been calculated based on their crystal structures at high resolu-tion. The change in the hydrophobicity of the heme-binding pocket resulting from the mutation can be quantitatively de-scribed using the difference of the solvent accessible area of the “pocket interior“ of each mutant from that of the wild-type cy-tochrome b5. The influences of the hydrophobicity of the heme-binding pocket on the protein stability and redox potential are discussed.     

Substrate‐Dependent Stereospecificity of Tyl‐KR1: An Isolated Polyketide Synthase Ketoreductase Domain from Streptomyces fradiae

The stereospecificity of an enzymatic reaction depends on the way in which a substrate and its enantiomer bind to the active site. These binding modes cannot be easily predicted. We have studied the stereospecificity and stereoselectivity of the ketoreductase domain Tyl‐KR1 of the tylactone polyketide synthase from Streptomyces fradiae by analysing the stereochemical outcome of the reduction of five different keto ester substrates. The absolute configuration of the Tyl‐KR1 reduction products was determined by using vibrational circular dichroism (VCD) spectroscopy combined with quantum chemical calculations. The conversion of only one of the tested substrates, 2‐methyl‐3‐oxovaleric acid N‐acetylcysteamine thioester, afforded the expected anti‐(2R,3R) configuration of the α‐methyl‐β‐hydroxyl ester product, representing the stereochemistry observed for the physiological polyketide product tylactone. For all other substrates, which were modified with respect to the type of ester and/or the chain length (C₄ instead of C₅), the opposite configuration (anti‐(2S,3S)) was obtained with significant enantio‐ and diastereoselectivity. Inversion of both stereocentres suggests completely different binding modes invoked by only minor modifications of the substrate structure.     

Dendronized polystyrene via orthogonal double‐click reactions

Dendronized copolymers bearing two different dendrons as side chains have been synthesized using a modular orthogonal “double‐click” reaction based strategy. The orthogonality of the Huisgen‐type azide‐alkyne cycloaddition and the Diels–Alder reaction was utilized to attach different dendrons to the polymer backbone via the “graft‐to” strategy. First through third generations of polyaryl ether dendrons appended with an alkyne group and polyester dendrons possessing a furan‐protected maleimide group at their focal point were reacted with a styrene based copolymer containing azide and anthracene moieties as side chains. The efficiency and selectivity of the orthogonal dendronization of the copolymers were examined via various analytical methods such as ¹H NMR spectroscopy, FTIR and gel permeation chromatography. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013 , 51, 5029–5037     

Cover Picture

The cover picture shows the catalysis of a Diels-Alder reaction by an artificial ribozyme. A series of anthracene and maleimide derivatives are converted with high efficiency, and with suitable substituents enantioselectivites greater than 95 % ee can be achieved. Shown in the mirror is a picture of a synthetic ribozyme built from unnatural L-ribonucleotides, which, as expected, catalyzes the formation of the other enantiomer of the product. The threadlike molecules in the background symbolize the combinatorial RNA pool from which the ribozymes were originally isolated. More about the fascinating properties of these ribozymes is reported by J?schke and co-workers on page 4576 ff. (The 3D model of a folded RNA molecule was generated with the program MOLMOL from the data set 1EHT.pdb.)     

Elucidation of the absolute configuration of rhizopine by chiral supercritical fluid chromatography and vibrational circular dichroism

The absolute configuration of rhizopine, an opine‐like natural product present in nitrogen‐fixing nodules of alfalfa infected by rhizobia, is elucidated using a combination of state‐of‐the‐art analytical and semi‐preparative supercritical fluid chromatography and vibrational circular dichroism spectroscopy. A synthetic peracetylated racemate was fractionated into its enantiomers and subjected to absolute configuration analysis revealing that natural rhizopine exists as a single enantiomer. The stereochemistry of non‐derivatized natural rhizopine corresponds to (1R,2S,3R,4R,5S,6R)‐4‐amino‐6‐methoxycyclohexane‐1,2,3,5‐tetraol.     

Generalized electronic diabatic approach to structural similarity in two‐dimensional potential energy surfaces of various topologies

Active site properties in some proteins can be affected by conformational fluctuations of neighbor residues, even when the latter are not involved directly in the binding process. A local environment thus appears to alter the relevant potential energy surface and its reaction paths. Here, some aspects of this phenomenon are simulated within a generalized electronic diabatic (GED) scheme to study the geometry and structural similarity for a class of two‐dimensional (2D) energy surfaces. The electronic quantum state is a linear superposition of diabatic basis functions, each of which is taken to represent a single (pure) electronic state for the isolated material system. Here, we describe a model reaction of isomerization by shifts in amplitudes for three diabatic species (reactant, product, and an open‐shell transition state) coupled in an external field. The “effective” 2D energy surface in the field is characterized in terms of critical points, and the amplitudes along the main reaction paths. A new feature is the introduction of a phase diagram where all possible potential‐energy‐surface topologies (consistent with three‐state systems in two linear coordinates) are matched with actual model parameters. By varying the coupling strengths between diabatic states, we classify regions of this phase diagram in terms of electronic and structural similarities; some regions comprise models whose reaction paths have geometries that belong to the catchment region of the reactant, yet are electronically akin to the diabatic transition state or product. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Minor Enantiomer Recycling: Metal Catalyst,Organocatalyst and Biocatalyst Working in Concert

A minor enantiomer recycling one‐pot procedure employing two reinforcing chiral catalysts has been developed. Continuous regeneration of the achiral starting material is effected via selective enzyme‐catalyzed hydrolysis of the minor product enantiomer from Lewis acid–Lewis base catalyzed addition of acyl cyanides to prochiral aldehydes in a two‐phase solvent system. The process provides O‐acylated cyanohydrins in close to perfect enantioselectivities, higher than those obtained in the direct process, and in high yields. A combination of a (S,S)‐salen Ti Lewis acid and Candida antarctica lipase B provides the products with R absolute configuration, whereas the opposite enantiomer is obtained from the (R,R)‐salen Ti complex and Candida rugosa lipase.     

Fate of the Oxygen Atoms in the Diol‐Dehydratase‐Catalyzed Dehydration of meso‐Butane‐2,3‐diol

¹⁸O‐Substituted propane‐1,2‐diols and meso‐butane‐1,2‐diols were synthesized and fed to growing cells of Lactobacillus brevis. Propan‐1‐ol and butan‐2‐ol, prepared from such diols through diol‐dehydratase‐catalyzed dehydration followed by intracellular reduction, were analyzed for their ¹⁸O‐content. For each propane‐1,2‐diol enantiomer, partial retention or complete loss of the isotope appeared to be related to the mode of substrate binding. Specific retention of the O‐atom linked to the (R)‐configured C‐atom of meso‐butane‐1,2‐diol indicates that the diol dehydratase handles this substrate like (R)‐propane‐1,2‐diol.     

Cyclic homo and block copolymers through sequential double click reactions

Well‐defined linear α‐anthracene‐ω‐maleimide functionalized polystyrene (l‐Anth‐PS‐MI) and linear α‐alkyne‐ω‐maleimide functionalized poly(tert‐butyl acrylate) (l‐alkyne‐PtBA‐MI) homopolymers, and linear α‐anthracene‐ω‐maleimide functionalized PS‐b‐PtBA (l‐Anth‐PS‐b‐PtBA‐MI) and linear α‐anthracene‐ω‐maleimide functionalized PS‐b‐poly(ε‐caprolactone) (PCL) (l‐Anth‐PS‐b‐PCL‐MI) block copolymers were obtained via combination of atom transfer radical polymerization (ATRP)/ring opening polymerization (ROP) and azide‐alkyne click reaction strategy. Subsequently, these linear homo and block copolymers were efficiently clicked via Diels‐Alder reaction to give their corresponding cyclic homo and block copolymers at reflux temperature of toluene for 48 h under 7–4 × 10^?5 M conditions. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2010     

Synthesis of Novel Nonpeptidic Thrombin Inhibitors

A novel class of nonpeptidic, active, and selective thrombin inhibitors has resulted from X‐ray‐structure‐based design and subsequent improvement of the initial lead molecules. These inhibitors possess a bi‐ or tricyclic central core structure with attached side chains to reach the three binding pockets (selectivity S1 pocket, distal D pocket, and proximal P pocket) present in the active site of the enzyme. The key step in the preparation of these compounds is the 1,3‐dipolar cycloaddition between an azomethine ylide, prepared in situ by the decarboxylative method from an aromatic aldehyde and an α‐amino acid, with an N‐substituted maleimide (e.g., see Schemes 1 and 2). All potent inhibitors contain an amidinium residue in the side chain for incorporation into the S1 pocket, which was introduced in the last step of the synthesis by a Pinner reaction. The compounds were tested in biological assays for activity against thrombin and the related serine protease trypsin. The first‐generation lead compounds (±)‐ 11 and (±)‐ 19 (Scheme 1) with a bicyclic central scaffold showed K_i values for thrombin inhibition of 18 μM and 0.67 μM , respectively. Conformationally more restricted second‐generation analogs (Scheme 2) were more active ((±)‐ 22i : K_i=90 nM (Table 1)); yet the selectivity for thrombin over trypsin remained weak. In the third‐generation compounds, a small lipophilic side chain for incorporation into the hydrophobic P pocket was introduced (Schemes 7 and 8). Since this pocket is present in thrombin but not in trypsin, an increase in binding affinity was accompanied by an increase in selectivity for thrombin over trypsin. The most selective inhibitor (K_i=13 nM , 760‐fold selectivity for thrombin over trypsin; Table 2) was (±)‐ 1 with an i‐Pr group for incorporation into the P pocket. Optical resolution of (±)‐ 1 (Scheme 9) provided (+)‐ 1 with a K_i value of 7 nM and a 740‐fold selectivity, whereas (−)‐ 1 was 800‐fold less active (K_i=5.6 μM , 21‐fold selectivity). The absolute configuration of the stronger‐binding enantiomer was assigned based on the X‐ray crystal structure of the complex formed between thrombin and this inhibitor. Compound (+)‐ 1 mimics the natural thrombin substrate, fibrinogen, which binds to the enzyme with the Ph group of a phenylalanine (piperonyl in (+)‐ 1 ) in the distal D pocket, with the i‐Pr group of a valine (i‐Pr in (+)‐ 1 ) in the proximal P pocket, and with a guanidinium side chain of an arginine residue (phenylamidinium group in (+)‐ 1 ) in the selectivity S1 pocket of thrombin. A series of analogs of (±)‐ 1 with the phenylamidinium group replaced by aromatic and aliphatic rings bearing OH or NH₂ groups (Schemes 10 – 14) were not effectively bound by thrombin. A number of X‐ray crystal‐structure analyses of free inhibitors confirmed the high degree of preorganization of these compounds in the unbound state. Since all inhibitors prefer similar modes of association with thrombin, detailed information on the strength of individual intermolecular bonding interactions and their incremental contribution to the overall free energy of complexation was generated in correlative binding and X‐ray studies. The present study demonstrates that defined mutations in highly preorganized inhibitors provide an attractive alternative to site‐directed mutagenesis in exploring molecular‐recognition phenomena at enzyme active sites.     

Dendronized polymers via Diels–Alder “click” reaction

A modular approach toward the synthesis of polymers containing dendron groups as side chains is developed using the Diels–Alder “click” reaction. For this purpose, a styrene‐based polymer appended with anthracene groups as reactive side chains was synthesized. First through third‐generation polyester dendrons containing furan‐protected maleimide groups at their focal point were synthesized. Facile, reagent‐free, thermal Diels–Alder cycloaddition between the anthracene‐containing polymer and latent‐reactive dendrons leads to quantitative functionalization of the polymer chains to afford dendronized polymers. The efficiency of this functionalization step was monitored using ¹H and ¹³C NMR spectroscopy and FTIR and UV–vis spectrometry. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 410–416, 2010     

Synthesis of tadpole polymers via triple click reactions: Copper‐catalyzed azide–alkyne cycloaddition,diels–alder,and nitroxide radical coupling reactions

We designed a trifunctional initiator ( 3 ) containing anthracene, bromide, and OH functionalities and subsequently used as an initiator in atom transfer radical Polymerization (ATRP) of styrene to yield linear polystyrene (PS) with α‐anthracene, OH, and ω‐bromide terminal groups, of which bromide is later transformed into azide to result in the linear anthracene‐, OH‐, and azide‐terminated PS (l‐α‐anthracene‐OH‐ω‐azide‐PS). The copper‐catalyzed azide–alkyne cycloaddition reaction between l‐α‐anthracene‐OH‐ω‐azide‐PS and α‐furan‐protected‐maleimide‐ω‐alkyne linkage, 4 afforded the linear anthracene‐, OH‐, and maleimide‐terminated PS. The cyclization via intramolecular Diels–Alder click reaction of this linear PS and the subsequent conversion of the hydroxyl into bromide resulted in the cyclic PS with one bromide located on the ring, (c‐PS)‐Br. Finally, the c‐PS‐Br was clicked with either well‐defined tetramethylpiperidine‐1‐oxyl‐terminated poly(ethylene glycol) (PEG) or poly(ε‐caprolactone) (PCL) yielding the tadpole polymer, (c‐PS)‐b‐PEG or (c‐PS)‐b‐PCL. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012     

Enantioselective transesterification catalysis by nanosized serine protease subtilisin Carlsberg particles in tetrahydrofuran

Enzyme catalysis in organic solvents is a powerful tool for stereo-selective synthesis but the enantioselectivity is still hard to predict. To overcome this obstacle, we employed a nanoparticulate formulation of subtilisin Carlsberg (SC) and designed a series of 14 structurally related racemic alcohols. They were employed in the model transesterification reaction with vinyl butyrate and the enantioselectivities were determined. In general, short alcohol side chains led to low enantioselectivties, while larger and bulky side chains caused better discrimination of the enantiomers by the enzyme. With several bulky substrates high enantioselectivities with E>100 were obtained. Computational modeling highlighted that key to high enantioselectivity is the discrimination of the R and S substrates by the sole hydrophobic binding pocket based on their size and bulkiness. While bulky S enantiomer side chains could be accommodated within the binding pocket, bulky R enantiomer side chains could not. However, when also the S enantiomer side chain becomes too large and does not fit into the binding pocket anymore, enantioselectivity accordingly drops.     

Multiarm star block copolymers via Diels‐Alder click reaction

Two types of multiarm star block copolymers: (polystyrene)_m‐poly(divinylbenzene)‐poly(methyl methacrylate)_n, (PS)_m‐polyDVB‐(PMMA)_n and (polystyrene)_m‐poly(divinylbenzene)‐poly(tert‐butyl acrylate)_k, (PS)_m‐polyDVB‐(PtBA)_k were successfully prepared via a combination of cross‐linking and Diels–Alder click reactions based on “arm‐first” methodology. For this purpose, multiarm star polymer with anthracene functionality as reactive periphery groups was prepared by a cross‐linking reaction of divinyl benzene using α‐anthracene end functionalized polystyrene (PS‐Anth) as a macroinitiator. Thus, obtained multiarm star polymer was then reacted with furan protected maleimide‐end functionalized polymers: PMMA‐MI or PtBA‐MI at reflux temperature of toluene for 48 h resulting in the corresponding multiarm star block copolymers via Diels–Alder click reaction. The multiarm star and multiarm star block copolymers were characterized by using ¹H NMR, SEC, Viscotek triple detection SEC (TD‐SEC) and UV. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 178–187, 2009     

Monitoring structural transformations in crystals. 7. 1‐Chloro­anthracene and its photodimer

Crystals of the 1‐chloro­anthracene photodimer, viz. trans‐bi(1‐chloro‐9,10‐di­hydro‐9,10‐anthracenediyl), C₂₈H₁₈Cl₂, were obtained from the solid‐state [4+4]‐photodimerization of the monomer, C₁₄H₉Cl, followed by recrystallization. The symmetry of the product mol­ecules is defined by the orientation of the reactant mol­ecules in the crystal. The mutual orientation parameters calculated for adjacent monomers explain the reactivity of the compound. The mol­ecules in the crystal of the monomer and the recrystallized photodimer pack differently and the photodimer has crystallographically imposed inversion symmetry.     

Kinetics and Protein‐Inhibitor Docking Studies of Enantiomers of exo‐2‐Norbornyl‐N‐n‐butylcarbamates as Pseudomonas Lipase Inhibitors to Probe the Enantioselectivity of the Enzyme

The Pseudomonas species lipase inhibition shows enantioselectivity for R‐enantiomer over S‐enantiomer of exo‐2‐norbornyl‐N‐n‐butylcarbamates. R‐, S‐, and racemic‐exo‐2‐norbornyl‐N‐n‐butylcarbamates are all characterized as pseudo substrate inhibitors of the enzyme. Thus, the mechanism for Pseudomonas species lipase‐catalyzed hydrolysis of the inhibitor is formation of the first enzyme‐inhibitor Michaelis complex via nucleophilic attack of the active site serine to the inhibitor (K_i step) then formation of the butylcarbamyl enzyme intermediate from this complex (k₂ step). Comparison of bimolecular rate constants (k_i = k₂ / K_i) of the inhibitors indicates that R‐enantiomer is 1.8 times more potent than S‐enantiomer. Thus, Pseudomonas species lipase shows enantioselectivity of 1.8 for R‐exo‐2‐norbornyl‐N‐n‐butyl‐carbamate over S‐exo‐2‐norbornyl‐N‐n‐butylcarbamate. Protein‐ligand interaction studies on both enantiomers of exo‐2‐norbornyl‐N‐n‐butylcarbamate as inhibitors of Pseudomonas species lipase using AutoDock suggest that R‐enantiomer binds more tightly into the active site of the enzyme than S‐enantiomer. The norbornyl ring of S‐exo‐2‐norbornyl‐N‐n‐butylcarbamate is repulsive to Ser 82 and His 251 of the catalytic triad as well as to Met 16 of the oxyanion hole. These repulsions may create few unfavorable interactions between S‐exo‐2‐norbornyl‐N‐n‐butylcarbamate and the enzyme and make this inhibitor a less potent one.     

Total Synthesis,Stereochemical Assignment,and Field‐Testing of the Sex Pheromone of the Strepsipteran Xenos peckii

The sex pheromone of the endoparasitoid insect Xenos peckii (Strepsiptera: Xenidae) was recently identified as (7E,11E)‐3,5,9,11‐tetramethyl‐7,11‐tridecadienal. Herein we report the asymmetric synthesis of three candidate stereostructures for this pheromone using a synthetic strategy that relies on an sp³–sp² Suzuki–Miyaura coupling to construct the correctly configured C7‐alkene function. Comparison of ¹H NMR spectra derived from the candidate stereostructures to that of the natural sex pheromone indicated a relative configuration of (3R*,5S*,9R*). Chiral gas chromatographic (GC) analyses of these compounds supported an assignment of (3R,5S,9R) for the natural product. Furthermore, in a 16‐replicate field experiment, traps baited with the synthetic (3R,5S,9R)‐enantiomer alone or in combination with the (3S,5R,9S)‐enantiomer captured 23 and 18 X. peckii males, respectively (mean±SE: 1.4±0.33 and 1.1±0.39), whereas traps baited with the synthetic (3S,5R,9S)‐enantiomer or a solvent control yielded no captures of males. These strong field trapping data, in combination with spectroscopic and chiral GC data, unambiguously demonstrate that (3R,5S,9R,7E,11E)‐3,5,9,11‐tetramethyl‐7,11‐tridecadienal is the X. peckii sex pheromone.