Catalytic Regioselectivity Research Articles

Identify Regioselective Residues of Ginsenoside Hydrolases by Graph-Based Active Learning from Molecular Dynamics.

Identifying the catalytic regioselectivity of enzymes remains a challenge. Compared to experimental trial-and-error approaches, computational methods like molecular dynamics simulations provide valuable insights into enzyme characteristics. However, the massive data generated by these simulations hinder the extraction of knowledge about enzyme catalytic mechanisms without adequate modeling techniques. Here, we propose a computational framework utilizing graph-based active learning from molecular dynamics to identify the regioselectivity of ginsenoside hydrolases (GHs), which selectively catalyze C6 or C20 positions to obtain rare deglycosylated bioactive compounds from Panax plants. Experimental results reveal that the dynamic-aware graph model can excellently distinguish GH regioselectivity with accuracy as high as 96-98% even when different enzyme-substrate systems exhibit similar dynamic behaviors. The active learning strategy equips our model to work robustly while reducing the reliance on dynamic data, indicating its capacity to mine sufficient knowledge from short multi-replica simulations. Moreover, the model's interpretability identified crucial residues and features associated with regioselectivity. Our findings contribute to the understanding of GH catalytic mechanisms and provide direct assistance for rational design to improve regioselectivity. We presented a general computational framework for modeling enzyme catalytic specificity from simulation data, paving the way for further integration of experimental and computational approaches in enzyme optimization and design.

Regioselectivity and confinement effects for catalytic conversion of carbohydrates within zeolite H-BEA

Zeolites have established the importance during biomass conversion, and H-form zeolites, although extensively used, produce hydroxymethylfurfural (HMF) with low yields. Herein, dispersion-corrected density functional calculations are employed with aim to comprehensively understand glucose conversion to HMF within zeolite H-BEA and unravel the role of confinement effects. The low HMF yields originate from regioselectivity: The preferentially activated O3 and O6 sites are significantly driven to humin precursors, while less reactive O1 and O2 sites lead favorably to HMF. Glucose-to-fructose isomerization occurs only at O5 site, while seems unnecessary for HMF production. Owing to the peculiar confinement effects, HMF precursors are prone to emerge within H-BEA, both upon dehydration and during catalysis, while may turn to be acyclic within aqueous solutions. Direct conversion to levulinic acid without HMF as intermediate thus becomes difficult within acidic zeolites. Results facilitate catalyst design for biomass conversion, and further understanding of regioselective catalysis and confinement effects.

Bioinspired Non-Heme Mn Catalysts for Regio- and Stereoselective Oxyfunctionalizations with H2 O2.

In recent years, metalloenzymes-mediated highly selective oxidations of organic substrates under mild conditions have been inspiration for developing synthetic bioinspired catalyst systems, capable of conducting such processes in the laboratory (and, in the future, in industry), relying on easy-to-handle and environmentally benign oxidants such as H2 O2 . To date, non-heme manganese complexes with chiral bis-amino-bis-pyridylmethyl and structurally related ligands are considered as possessing the highest synthetic potential, having demonstrated the ability to mediate a variety of chemo- and stereoselective oxidative transformations, such as epoxidations, C(sp3 )-H hydroxylations and ketonizations, oxidative desymmetrizations, kinetic resolutions, etc. Furthermore, in the past few years non-heme Mn based catalysts have become the major platform for studies focused on getting insight into the molecular mechanisms of oxidant activation and (stereo)selective oxygen transfer, testing non-traditional hydroperoxide oxidants, engineering catalytic sites with enzyme-like substrate recognition-based selectivity, exploration of catalytic regioselectivity trends in the oxidation of biologically active substrates of natural origin. This contribution summarizes the progress in manganese catalyzed C-H oxygenative transformations of organic substrates, achieved essentially in the past 5 years (late 2018-2023).

Active Binding Modes of Caffeine with Cytochrome P450 1A2 Determine Its Metabolite Profiles.

Caffeine is a very common kind of nervous stimulant, and it is primarily metabolized by Cytochrome P450 1A2 (CYP1A2) in the human body. Over the years, determining the interactions between caffeine and CYP1A2 has been a tough issue. The active binding modes and the catalytic regioselectivity of the metabolism between CYP1A2 and caffeine remain unclear. Here, to investigate the interactions between CYP1A2 and caffeine, we constructed the all-sequence CYP1A2-caffeine-membrane system using a multiple template approach. According to our simulation results, four active binding modes between CYP1A2 and caffeine that correspond to the four metabolic sites of caffeine are determined. What is more, a pre-reaction state for the CYP1A2-catalyzed reaction at caffeine's N3 site is identified. A more preponderant active binding mode might be the reason why the N3 site of caffeine becomes the primary metabolic site. Our findings could enhance our knowledge of the interactions between CYP1A2 and caffeine and help us better understand the regioselectivity of the metabolism between CYP1A2 and caffeine.

Diastereomer Resolution of M4L6 Coordination Cages by Ultra‐High‐Resolution Ion‐Mobility Mass Spectrometry

AbstractCoordination cages can be used for enantio‐ and regioselective catalysis and for the selective sensing and separation of isomeric guest molecules. Here, stereoisomers of a family of coordination cages are resolved using ultra‐high‐resolution cyclic ion‐mobility mass spectrometry (cIM‐MS). The observed ratio of diastereomers is dependent on both the metal ion and counter ion. Moreover, the point groups can be assigned through complementary NMR experiments. This method enables the identification and interrogation of the individual isomers in complex mixtures of cages which cannot be performed in solution. Furthermore, these techniques allow the stability of individual isomers within the mixture to be probed, with the T‐symmetric isomers in this case shown to be more robust than the C3 and S4 analogues.

Diastereomer Resolution of M₄L₆ Coordination Cages by Ultra-High-Resolution Ion Mobility-Mass Spectrometry.

Coordination cages can be used for enantio- and regioselective catalysis and for the selective sensing and separation of isomeric guest molecules. Here, stereoisomers of a family of coordination cages are resolved using high-resolution cyclic ion mobility-mass spectrometry (cIM-MS). The observed ratio of diastereomers is dependent on both the metal ion and counter ion. Moreover, the point groups can be assigned through complementary NMR experiments. This method enables the identification and interrogation of the individual isomers in complex mixtures of cages which cannot be performed in solution. Furthermore, these techniques allow the stability of individual isomers within the mixture to be probed, with the T-symmetric isomers in this case shown to be more robust than the C3 and S4 analogues.

Regioselective oxidation of heterocyclic aromatic hydrocarbons catalyzed by cytochrome P450: A case study of carbazole

Recently there are increasing interests in accurately evaluating the health effects of heterocyclic PAHs. However, the activation mechanism and possible metabolites of heterocyclic PAHs catalyzed by human CYP1A1 is still elusive to a great extent. Here, leveraged to high level QM/MM calculations, the corresponding activation pathways of a representative heterocyclic PAHs, carbazole, were systematically explored. The first stage is electrophilic addition or hydrogen abstraction from N-H group. Electrophilic addition was evidenced to be more feasible and regioselectivity at C3 and C4 sites were identified. Correlations between energy barriers and key structural/electrostatic parameters reveal that O-Cα distance and Fe-O-Cα angle are the main origin for the catalytic regioselectivity. Electrophilic addition was determined as the rate-determining step and the subsequent possible reactions include epoxidation, NIH shift (the hydrogen migration from the site of hydroxylation to the adjacent carbon) and proton shuttle. The corresponding products are epoxides, ketones and hydroxylated carbazoles, respectively. The main metabolites (hydroxylated carbazoles) are estimated to be more toxic than carbazole. The regioselectivity of carbazole activated by CYP1A1 is different from the environmental processes (gas and aqueous phase). Collectively, these results will inform the in-depth understanding the metabolic processes of heterocyclic PAHs and aid the accurate evaluation of their health effects.

Steerable Engineering of Nickel Molybdenum Carbonitride Nanostructures for Catalytic Regioselectivity Cleavage of C–O and C–C Bonds in Deoxygenation of Methyl Palmitate

Steerable Engineering of Nickel Molybdenum Carbonitride Nanostructures for Catalytic Regioselectivity Cleavage of C–O and C–C Bonds in Deoxygenation of Methyl Palmitate

Role of Secondary Coordination Sphere Residues in Halogenation Catalysis of Non-heme Iron Enzymes

Chemo- and regio-selective catalysis of the C(sp3)-H halogenation reaction is a formidable goal in chemical synthesis. 2-Oxoglutarate (2OG)-dependent non-heme iron halogenases catalyze selective chlorination/bromination of C–H bonds and exhibit high sequence and structural similarities with non-heme iron hydroxylases. How the secondary coordination sphere (SCS) of these two enzyme systems differentiate and determine their reactivity is not well understood. In this work, we show that specific positioning of redox-active tyrosine residues in the SCS of non-heme iron halogenases has a huge impact on their structure, function, and reactivity. We discover that a tyrosine residue (F121Y) rationally incorporated to hydrogen bond to iron’s chloride ligand in SyrB2 halogenase undergoes post-translational oxidation to dihydroxyphenylalanine (DOPA) physiologically. A combination of spectroscopic, mass-spectrometric, and biochemical studies demonstrate that DOPA modification in SyrB2 renders the enzyme non-functional. Bioinformatic analysis suggests that SyrB2-like halogenases, unlike hydroxylases, have a conserved placement of phenylalanine at position 121 to preclude such unproductive oxidation. Furthermore, molecular dynamics simulations in tandem with experimental demonstration of DOPA incorporation exclusively at position 121 enables us to uniquely identify that an axial-chloro haloferryl isomer is operant in SyrB2. We also identify conserved redox-inactive residues in the SCS of other 2OG-dependent non-heme iron halogenases to avoid DOPA-like unproductive oxidations. Overall, this study demonstrates the importance of the SCS in controlling the structure and enzymatic activity of non-heme iron halogenases and will have significant implications toward the design of small-molecule and protein-based halogenation catalysts.

Efficient biodegradation of nitriles by a novel nitrile hydratase derived from Rhodococcus erythropolis CCM2595

In our previous study, we firstly cloned the gene of a novel ReNHase (NHase from Rhodococcus erythropolis CCM2595), and the strain was shown to degrade only phenol, hydroxybenzoate, p-chlorophenol, aniline and other aromatic compounds. Here in, we further purified the ReNHase from R. erythropolis CCM2595 and detected its properties of biodegradation. We constructed a plasmid with the gene of ReNHase with His-tag. The encoding ReNHase was cloned and overexpressed in recombinant Escherihia coli and confirmed by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE). The substrate scope of the new heterologous ReNHase was tested and the efficiency of degradation of nitriles by the ReNHase was also investigated by high efficiency liquid chromatography. We also studied the effect of temperature and pH on the catalysis of adiponitrile by the purified ReNHase. The recombinant E.coli showed high catalytic regioselectivity with high substrate affinity towards dinitriles (especially for adiponitrile) whereas lower affinity towards mononitriles. Compared to whole-cell catalysis, the catalytic time was shortened significantly with the purified ReNHase. The enzyme activity of crude recombinant E.coli was 635 U g −1 (DCW), while the specific activity of purified ReNHase was 63.107 U mg−1. The apparent Km value for the purified ReNHase is 6.6252 mmol L −1, which revealed the good affinity between the purified ReNHase and adiponitrile. The reaction Kcat is 82.77 s −1 and Kcat/Km is 1.249 × 104 (mol−1 L s −1), which showed high catalytic activity towards adiponitrile. We propose that this purified ReNHase may be applied for the industry and sewage treatment for environmental protection.

Research progress of Pictet-Spenglerases

Pictet-Spenglerases (P-Sases) catalyze the Pictet-Spengler (P-S) reactions and exhibit high stereoselectivity and regioselectivity under mild conditions. The typical P-S reaction refers to the condensation and recyclization of β-arylethylamine with aldehyde or ketone under acidic conditions to form tetrahydroisoquinoline and β-carboline alkaloid derivatives. The related enzymatic products of P-Sases are the backbones of various bioactive compounds, including clinical drugs: morphine, noscapine, quinine, berberine, ajmaline, morphine. Furthermore, the activity of P-Sases in stereoselective and regioselective catalysis is also valuable for chemoenzymatic synthesis. Therefore, this review summarizes the research progress in the discovery, functional identification, biological characteristics and catalytic applications of P-Sases, which provide the useful theoretical reference in future P-Sases research and development.

Switch in Selectivity for Formal Hydroalkylation of 1,3-Dienes and Enynes with Simple Hydrazones.

Controlling reaction selectivity is a permanent pursuit for chemists. Regioselective catalysis, which exploits and/or overcomes innate steric and electronic bias to deliver diverse regio-enriched products from the same starting materials, represents a powerful tool for divergent synthesis. Recently, the 1,2-Markovnikov hydroalkylation of 1,3-dienes with simple hydrazones was reported to generate branched allylic compounds when a nickel catalyst was used. As part of the effort, shown here is that a complete switch of Markovnikov to anti-Markovnikov addition is obtained by changing to a ruthenium catalyst, thus providing direct and efficient access to homoallylic products exclusively. Isotopic substitution experiments indicate that no reversible hydro-metallation across the metal-π-allyl system occurred under ruthenium catalysis. Moreover, this protocol is applicable to the regiospecific hydroalkylation of the distal C=C bond of 1,3-enynes.

Switch in Selectivity for Formal Hydroalkylation of 1,3‐Dienes and Enynes with Simple Hydrazones

AbstractControlling reaction selectivity is a permanent pursuit for chemists. Regioselective catalysis, which exploits and/or overcomes innate steric and electronic bias to deliver diverse regio‐enriched products from the same starting materials, represents a powerful tool for divergent synthesis. Recently, the 1,2‐Markovnikov hydroalkylation of 1,3‐dienes with simple hydrazones was reported to generate branched allylic compounds when a nickel catalyst was used. As part of the effort, shown here is that a complete switch of Markovnikov to anti‐Markovnikov addition is obtained by changing to a ruthenium catalyst, thus providing direct and efficient access to homoallylic products exclusively. Isotopic substitution experiments indicate that no reversible hydro‐metallation across the metal‐π‐allyl system occurred under ruthenium catalysis. Moreover, this protocol is applicable to the regiospecific hydroalkylation of the distal C=C bond of 1,3‐enynes.

Regioselective Catalysis by the {Mo132} Nanocapsule: A Computational Inspection

By means of density functional calculations, we perform a mechanistic analysis of the Huisgen cycloaddition reaction taking place with the chemical involvement of the {Mo132} nanocapsule, initially reported by Besson and others [Dalton Trans. 2012, 41, 9852–9854], whereby a 2:1 regioselectivity is obtained by chemically grafting the reactants onto the cavity walls of this metal‐oxide catalyst. We explore the mechanistic pathways quantitatively and explore the basis of this regioselectivity. When propiolate is coordinated to the nanocapsule, the selectivity of the catalytic system is both kinetically and thermodynamically in favour of the formation of 1,4‐triazole, whereas in the alternative pathway, which begins with the triazidoacetate coordination, the selectivity is kinetic alone. The former and latter pathways have activation barrier differences between each isomer of 29.9 kJ/mol and 39.2 kJ/mol, respectively.

Brain-derived neurotrophic factor involved epigenetic repression of UGT2B7 in colorectal carcinoma: A mechanism to alter morphine glucuronidation in tumor.

Uridine diphosphate-glucuronosyltransferase (UGT) 2B7, as one of significant drug enzymes, is responsible on the glucuronidation of abundant endobiotics or xenobiotics. We here report that it is markedly repressed in the tumor tissues of colorectal carcinoma (CRC) patients. Accordingly, morphine in CRC cells will stimulate the expression of its main metabolic enzyme, UGT2B7 during tolerance generation by activating the positive signals in histone 3, especially for trimethylated lysine 27 (H3K4Me3) and acetylated lysine 4 (H3K27Ac). Further study reveals that brain-derived neutrophilic factor (BDNF), a secretory neurotrophin, enriched in CRC can interact and inhibit UGT2B7 by primarily blocking the positive signals of H3K4Me3 as well as activating H3K27Ac on the promoter region of UGT2B7. Meanwhile, BDNF repression attributes to the sensitizations of main core factors in poly-comb repressive complex (PRC) 1 rather than PRC2 as the reason of the depression of SUZ12 in the later complex. Besides that, the productions of two main morphine glucuronides are both increased in the BDNF deficient or TSA and BIX-01294 treated morphine tolerance-like HCT-116 cells. On the same condition, active metabolite, morphine-6-glucuronide (M6G) was accumulated more than inactive M3G. Our findings imply that enzymatic activity enhancement and substrate regioselective catalysis alteration of UGT2B7 may release morphine tolerance under the cure of tumor-induced pain.

ChemInform Abstract: Mechanistic Basis for Regioselection and Regiodivergence in Nickel‐Catalyzed Reductive Couplings

AbstractReview: 43 refs.

Δ10(E)-Sphingolipid Desaturase Involved in Fusaruside Mycosynthesis and Stress Adaptation in Fusarium graminearum

Sphingolipids are biologically important and structurally distinct cell membrane components. Fusaruside (1) is a 10,11-unsaturated immunosuppressive fungal sphingolipid with medical potentials for treating liver injury and colitis, but its poor natural abundance bottlenecks its druggability. Here, fusaruside is clarified biosynthetically, and its efficacy-related 10,11-double bond can be generated under the regioselective catalysis of an unprecedented Δ10(E)-sphingolipid desaturase (Δ10(E)-SD). Δ10(E)-SD shares 17.7% amino acid sequence similarity with a C9-unmethylated Δ10-sphingolipid desaturase derived from a marine diatom, and 55.7% with Δ8(E)-SD from Fusarium graminearum. Heterologous expression of Δ10(E)-SD in Pichia pastoris has been established to facilitate a reliable generation of 1 through the Δ10(E)-SD catalyzed desaturation of cerebroside B (2), an abundant fungal sphingolipid. Site directed mutageneses show that the conserved histidines of Δ10(E)-SD are essential for the 10,11-desaturation catalysis, which is also preconditioned by the C9-methylation of the substrate. Moreover, Δ10(E)-SD confers improved survival and faster growth to fungal strains at low temperature and high salinity, in parallel with to higher contents of 1 in the mycelia. Collectively, the investigation describes a new Δ10(E)-sphingolipid desaturase with its heterologous expression fundamentalizing a biotechnological supply of 1, and eases the follow-up clarification of the immunosuppression and stress-tolerance mechanism.

Mechanistic Basis for Regioselection and Regiodivergence in Nickel-Catalyzed Reductive Couplings

The control of regiochemistry is a considerable challenge in the development of a wide array of catalytic processes. Simple π-components such as alkenes, alkynes, 1,3-dienes, and allenes are among the many classes of substrates that present complexities in regioselective catalysis. Considering an internal alkyne as a representative example, when steric and electronic differences between the two substituents are minimal, differentiating among the two termini of the alkyne presents a great challenge. In cases where the differences between the alkyne substituents are substantial, overcoming those biases to access the regioisomer opposite that favored by substrate biases often presents an even greater challenge. Nickel-catalyzed reductive couplings of unsymmetrical π-components make up a group of reactions where control of regiochemistry presents a challenging but important objective. In the course of our studies of aldehyde-alkyne reductive couplings, complementary solutions to challenges in regiocontrol have been developed. Through careful selection of the ligand and reductant, as well as the more subtle reaction variables such as temperature and concentration, effective protocols have been established that allow highly selective access to either regiosiomer of the allylic alcohol products using a wide range of unsymmetrical alkynes. Computational studies and an evaluation of reaction kinetics have provided an understanding of the origin of the regioselectivity control. Throughout the various procedures described, the development of ligand-substrate interactions plays an essential role, and the overall kinetic descriptions were found to differ between protocols. Rational alteration of the rate-determining step plays a key role in the regiochemistry reversal strategy, and in one instance, the two possible regioisomeric outcomes in a single reaction were found to operate by different kinetic descriptions. With this mechanistic information in hand, the empirical factors that influence regiochemistry can be readily understood, and more importantly, the insights suggest simple and predictable experimental variables to achieving a desired reaction outcome. These studies thus present a detailed picture of the influences that control regioselectivity in a specific catalytic reaction, but they also delineate strategies for regiocontrol that may extend to numerous classes of reactions. The work provides an illustration of how insights into the kinetics and mechanism of a catalytic process can rationalize subtle empirical findings and suggest simple and rational modifications in procedure to access a desirable reaction outcome. Furthermore, these studies present an illustration of how important challenges in organic synthesis can be met by novel reactivity afforded by base metal catalysis. The use of nickel catalysis in this instance not only provides an inexpensive and sustainable method for catalysis but also enables unique reactivity patterns not accessible to other metals.

ChemInform Abstract: Supramolecular Control of Transition Metal Complexes in Water by a Hydrophobic Cavity: A Bio‐Inspired Strategy

AbstractReview: [67 refs.

Supramolecular control of transition metal complexes in water by a hydrophobic cavity: a bio-inspired strategy.

Supramolecular chemistry in water is a very challenging research area. In biology, water is the universal solvent where transition metal ions play major roles in molecular recognition and catalysis. In enzymes, it participates in substrate binding and/or activation in the heart of a pocket defined by the folded protein. The association of a hydrophobic cavity with a transition metal ion is thus a very appealing strategy for controlling the metal ion properties in the very competitive water solvent. Various systems based on intrinsically water-soluble macrocyclic structures such as cyclodextrins, cucurbituryls, and metallo-cages have been reported. Others use calixarenes and resorcinarenes functionalized with hydrophilic substituents. One approach for connecting a metal complex to these cavities is to graft a ligand for metal ion binding at their edge. Early work with cyclodextrins has shown Michaelis-Menten like catalysis displaying enhanced kinetics and substrate-selectivity. Remarkable examples of regio- and stereo-selective transformation of substrates have been reported as well. Dynamic two-phase systems for transition metal catalysis have also been developed. They rely on either water-transfer of the metal complex through ligand embedment or synergistic coordination of a metal ion and substrate hosting. Another strategy consists in using metallo-cages, which provide a well-defined hydrophobic space, to stabilize metal complexes in water. When the cages can host simultaneously a substrate and a reactive metal complex, size- and regio-selective catalysis was obtained. Finally, construction of a polydentate coordination site closely interlocked with a calixarene or resorcinarene macrocycle has been shown to be a very fruitful strategy for obtaining metal complexes with remarkable hosting properties. For each of these systems, the synergism resulting from the biomimetic association of a hydrophobic cavity and a metal ion is discussed within the objective of developing new tools for either selective molecular recognition (with analytical perspectives) or performant catalysis, in water.