Biomimetic Reaction Research Articles

Towards the semi-synthesis of phosphorylated mimics of glycosaminoglycans: Screening of methods for the regioselective phosphorylation of chondroitin

Glycosaminoglycan (GAG) mimics carrying phosphate rather than sulfate anionic groups have been poorly investigated, in spite of their interesting perspectives. While some GAG-mimicking phosphorylated polymers have been reported, to the best of our knowledge no phosphorylated polysaccharides having the same backbone of natural sulfated GAGs have been accessed yet. To fill this gap, in this work two standard phosphorylation protocols and two recently reported procedures have been screened on a set of polysaccharide species composed by microbial sourced chondroitin and three partially protected, semi-synthetic derivatives thereof. A detailed structural characterization by 1H, 13C and 31P NMR spectroscopy revealed the higher versatility of the innovative, biomimetic reaction employing monopotassium salt of phosphoenolpyruvate (PEPK) with respect to standard phosphorylating agents (phosphoric acid or phosphorus oxychloride). Indeed, PEP-K and H3PO4 gave similar results in the regioselective phosphorylation of the primary hydroxyls of unprotected chondroitin, while only the former reacted on partially protected chondroitin derivatives in a controlled, regioselective fashion, affording chondroitin phosphate (CP) polysaccharides with different derivatization patterns. The reported results represent the first, key steps towards the systematic semi-synthesis of phosphorylated GAGs as a new class of GAG mimics and to the evaluation of their biological activities in comparison with native sulfated GAGs.

DNA-Programmed Lipid Nanoreactors for Synthesis of Carbohydrate Mimetics by Fusion of Aqueous Sub-attoliter Compartments.

Lipid nanoreactors are biomimetic reaction vessels (nanoreactors) that can host aqueous or membrane-associated chemical and enzymatic reactions. Nanoreactors provide ultra-miniaturization from atto- to zeptoliter volumes per reaction vessel with the major challenge of encoding and spatio-temporal control over reactions at the individual nanoreactor or population level, thereby controlling volumes several orders of magnitude below advanced microfluidic devices. We present DNA-programmed lipid nanoreactors (PLNs) functionalized with lipidated oligonucleotides (LiNAs) that allow programming and encoding of nanoreactor interactions by controlled membrane fusion, exemplified for a set of carbohydrate mimetics with mono- to hexasaccharide azide building blocks connected by click-chemistry. Programmed reactions are initiated by fusion of distinct populations of nanoreactors with individually encapsulated building blocks. A focused library of triazole-linked carbohydrate-Cy5 conjugates formed by strain-promoted azide-alkyne cycloadditions demonstrated LiNA-programmed chemistry, including two-step reaction schemes. The PLN method is developed toward a robust platform for synthesis in confined space employing fully programmable nanoreactors, applicable to multistep synthesis for the generation of combinatorial libraries with subsequent analysis of the molecules formed, based on the addressability of the lipid nanoreactors.

Insights into Substrate Recognition by the Unusual Nitrating Enzyme RufO.

Nitration reactions are crucial for many industrial syntheses; however, current protocols lack site specificity and employ hazardous chemicals. The noncanonical cytochrome P450 enzymes RufO and TxtE catalyze the only known direct aromatic nitration reactions in nature, making them attractive model systems for the development of analogous biocatalytic and/or biomimetic reactions that proceed under mild conditions. While the associated mechanism has been well-characterized in TxtE, much less is known about RufO. Herein we present the first structure of RufO alongside a series of computational and biochemical studies investigating its unusual reactivity. We demonstrate that free l-tyrosine is not readily accepted as a substrate despite previous reports to the contrary. Instead, we propose that RufO natively modifies l-tyrosine tethered to the peptidyl carrier protein of a nonribosomal peptide synthetase encoded by the same biosynthetic gene cluster and present both docking and molecular dynamics simulations consistent with this hypothesis. Our results expand the scope of direct enzymatic nitration reactions and provide the first evidence for such a modification of a peptide synthetase-bound substrate. Both of these insights may aid in the downstream development of biocatalytic approaches to synthesize rufomycin analogues and related drug candidates.

Isoreticular chemistry guided enzymodynamic domino effect for biofilm microenvironment-responsive disinfection

Nanozyme therapy holds promise for overcoming daunting antimicrobial resistance, but skills to target the microbial microenvironment are lacking. Herein, an isoreticular principle was introduced in nanozyme discovery to directedly evolve a domino biomimetic reaction specific to drug-resistant bacterial biofilm. The isoreticular Ce-UiO-66-X (X = BDC, BDC-CH3, BDC-OH, BDC-NH2, BDC-NO2, ADC, Fum) MOFs exhibited linker-dependent mimicry of hydrolytic apyrase and redox oxidase, and the phosphorous reactants (ATP/ADP/AMP/Pi) produced by the ATP hydrolysis could spontaneously activate redox reaction in Ce-UiO-66-X. Evidenced by the representative Ce-BDC-X (X = –NO2, -H, and –NH2) nanozymes, the unique domino reaction of Ce-UiO-66-X could simultaneously deplete ATP molecules and trigger enhanced generation of superoxide radicals at the specific time window in the initial bacterial adhesion stage of methicillin-resistant Staphylococcus aureus (MRSA) biofilm formation. Due to the synergistic nanocatalytic mechanism, possible nanoscale penetration effect, and good biocompatibility, Ce-UiO-66-NO2 could effectively target and destroy the metabolic microenvironment of MRSA biofilm in vitro and in vivo, reducing the MRSA biofilm viability to as low as 3.64%. This work demonstrates a new prodrug-like enzymodynamic antibacterial therapeutics based on cooperative multienzyme reactivity.

β-cyclodextrin Mediated Green Synthesis of Bioactive Heterocycles

Abstract: In this review, we report β-cyclodextrin catalyzed green transformations of biologically active heterocycles. β-Cyclodextrin is a seminatural product, water-soluble, highly efficient, and biodegradable catalyst. β-Cyclodextrin is a versatile catalyst and promotes a variety of multicomponent transformations, biomimetic reactions, C-C bond formation, and synthesis of some biologically active natural products. It has been applicable to attain some name reactions, deprotection of THP/MOM/Ac/Ts ethers, oxidative cleavage of epoxides, oxidative dehydrogenation of alcohol, regioselective cyclization of chalcone epoxides and 2’-aminochalcones. The catalyst is useful to carry out diastereoselective reactions, and it also plays a very important role in phase transfer catalysts.

Designing a Light-Induced Glycosylation Reaction for Poststage Synthesis of ADP-2″-Deoxyribosyl Derivatives.

Modifications on the hydroxyl groups of ADP-ribosyl units can provide valuable tools for investigating ADP-ribosylation-related molecular interactions, but the chemical syntheses of these compounds are usually difficult due to their inherent complex structures. In this study, we report a poststage synthetic protocol for accessing novel ADP-2″-deoxyribosyl derivatives through designing a light-induced biomimetic reaction, and SPR assays revealed effective binding of ADP-2″-deoxyribosyl peptides to MacroH2A1.1 with a high affinity (KD = 3.75 × 10-6 M).

Oxidation Products from the Neolignan Licarin A by Biomimetic Reactions and Assessment of in vivo Acute Toxicity.

Licarin A, a dihydrobenzofuranic neolignan presents in several medicinal plants and seeds of nutmeg, exhibits strong activity against protozoans responsible for Chagas disease and leishmaniasis. From biomimetic reactions by metalloporphyrin and Jacobsen catalysts, seven products were determined: four isomeric products yielded by epoxidation from licarin A, besides a new product yielded by a vicinal diol, a benzylic aldehyde, and an unsaturated aldehyde in the structure of the licarin A. The incubation with rat and human liver microsomes partially reproduced the biomimetic reactions by the production of the same epoxidized product of m/z 343 [M + H]+. In vivo acute toxicity assays of licarin A suggested liver toxicity based on biomarker enzymatic changes. However, microscopic analysis of tissues sections did not show any tissue damage as indicative of toxicity after 14 days of exposure. New metabolic pathways of the licarin A were identified after in vitro biomimetic oxidation reaction and in vitro metabolism by rat or human liver microsomes.

Selectivity in Cationic Cyclizations Involving Alkynes: A Computational Study on the Biomimetic Synthesis of Steroids.

Computational studies on the electrophilic cyclization between alkynes and transient carbocations or Lewis-acid-activated epoxides show that the regiochemistry of the reaction depends on the terminal or internal position of the triple bond. Reactants possessing terminal alkynyl groups lead to six-membered rings, whereas internal alkynes yield five-membered rings through 6-endo-dig and 5-exo-dig electrophilic cyclizations, respectively. The regiochemistry of the reaction is not determined by two-electron interactions, but by the minimization of Pauli repulsion. This scenario is preserved in related biomimetic reactions leading to steroid scaffolds. In this latter case, the stereochemistry of the cyclization reaction is oriented towards the formation of equatorial C-C bonds connecting the new six-six- and six-five-membered fused rings.

Effect of Binding Linkers on the Efficiency and Metabolite Profile of Biomimetic Reactions Catalyzed by Immobilized Metalloporphyrin.

The investigation of liver-related metabolic stability of a drug candidate is a widely used key strategy in early-stage drug discovery. Metalloporphyrin-based biomimetic catalysts are good and well-described models of the function of CyP450 in hepatocytes. In this research, the immobilization of an iron porphyrin was performed on nanoporous silica particles via ionic interactions. The effect of the metalloporphyrin binding linkers was investigated on the catalytic efficiency and the metabolic profile of chloroquine as a model drug. The length of the amino-substituted linkers affects the chloroquine conversion as well as the ratio of human major and minor metabolites. While testing the immobilized catalysts in the continuous-flow reactor, results showed that the presented biomimetic system could be a promising alternative for the early-stage investigation of drug metabolites regarding analytical or synthetic goals as well.

Architectural MCM 41 was anchored to the Schiff base Co(II) complex to enhance methylene blue dye degradation and mimic activity

A sequence of Schiff base Cobalt (II) Mobile Composite Matter 41 heterojunction (SBCo(II)-MCM 41) was prepared by post-synthetic protocols. Various characterization techniques were used to characterize the above samples and MCM 41: Morphology, functional groups, optical properties, crystalline nature, pore diameter, and binding energy by scanning electron microscope (SEM), High-resolution transition electron microscopy (HR-TEM), Fourier transform infrared spectroscopy (FTIR), Ultra Violet-Visible Spectroscopy (UV), X-ray powder diffraction (XRD), Brunauer-Emmett-Teller (BET) and X-ray Photoelectron Spectroscopy (XPS). After the encapsulation of SBCo(II) on the MCM 41, the intensity in the 100-plane in powder x-ray diffraction (XRD) decreased significantly; moreover, the light absorption behavior in UV analysis was improved. The change in the surface area and the decrease in the pore diameter of the sample were also demonstrated by the BET study. The XPS results confirmed the presence of Si, O, C, N, and Co in the SBCo(II)-MCM 41 complex. The photocatalytic performance of MCM 41 and SBCo(II)-MCM 41 materials tested by the degradation of methylene blue dye (MBD) shows that MCM 41 immobilization with SBCo(II)complex is rapidly degraded under natural sunlight irradiation. The optimized 10 mg SBCo(II)-MCM 41 catalyst concentrations showed effective enhancement with the highest efficiency of 98% achieved within 2 h compared to the other two SBCo(II)-MCM 41 concentrations. Moreover, the catalytic efficiency of SBCo(II)-MCM 41 showed a biomimetic reaction without using an oxidant, which exposed it as an effective catalyst for amine to imine conversion; it was useful in the medical field for enzymes with structural assembly.

Hydrophilic Antimicrobial Coatings for Medical Leathers from Silica-Dendritic Polymer-Silver Nanoparticle Composite Xerogels

Hybrid organic-inorganic (dendritic polymer-silica) xerogels containing silver nanoparticles (Ag Nps) were developed as antibacterial leather coatings. The preparation method is environmentally friendly and is based on two biomimetic reactions. Silica gelation and spontaneous Ag Nps formation were both mediated by hyperbranched poly (ethylene imine) (PEI) scaffolds of variable Mw (2000–750,000). The formation of precursor hydrogels was monitored by dynamic light scattering (DLS). The chemical composition of the xerogels was assessed by infrared spectroscopy (IR) and energy-dispersive X-ray spectroscopy (EDS), while the uniformity of the coatings was established by scanning electron microscopy (SEM). The release properties of coated leather samples and their overall behavior in water in comparison to untreated analogs were investigated by Ultraviolet-Visible (UV-Vis) spectroscopy. Antibacterial activity was tested against Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus, and antibiofilm properties against Staphylococcus aureus, Staphylococcus epidermidis, Escherichia coli, Acinetobacter baumannii, and Enterococcus faecalis, while the SARS-CoV-2 clinical isolate was employed for the first estimation of their antiviral potential. Toxicity was evaluated using the Jurkat E6.1 cell line. Finally, water-contact angle measurements were implemented to determine the enhancement of the leather surface hydrophilicity caused by these composite layers. The final advanced products are intended for use in medical applications.

Density Functional Theory Investigation of the Biocatalytic Mechanisms of pH-Driven Biomimetic Behavior in CeO2.

There is considerable interest in the pH-dependent, switchable, biocatalytic properties of cerium oxide (CeO2) nanoparticles in biomedicine, where these materials exhibit beneficial antioxidant activity against reactive oxygen species (ROS) at a basic physiological pH but cytotoxic prooxidant activity in an acidic cancer cell pH microenvironment. While the general characteristics of the role of oxygen vacancies are known, the mechanism of their action at the atomic scale under different pH conditions has yet to be elucidated. The present work applies density functional theory (DFT) calculations to interpret, at the atomic scale, the pH-induced behavior of the stable {111} surface of CeO2 containing oxygen vacancies. Analysis of the surface-adsorbed media species reveals the critical role of pH on the interaction between ROS (•O2- and H2O2) and the defective CeO2 {111} surface. Under basic conditions, the superoxide dismutase (SOD) and catalase (CAT) biomimetic reactions can be performed cyclically, scavenging and decomposing ROS to harmless products, making CeO2 an excellent antioxidant. However, under acidic conditions, the CAT biomimetic reaction is hindered owing to the limited reversibility of Ce3+ ↔ Ce4+ and formation ↔ annihilation of oxygen vacancies. A Fenton biomimetic reaction (H2O2 + Ce3+ → Ce4+ + OH- + •OH) is predicted to occur simultaneously with the SOD and CAT biomimetic reactions, resulting in the formation of hydroxyl radicals, making CeO2 a cytotoxic prooxidant.

Biomimetic Total Synthesis of Enterocin

AbstractThe first chemical total synthesis of the highly oxygenated polyketide enterocin has been accomplished. The key step of the synthesis was a late‐stage biomimetic reaction cascade involving two intramolecular aldol reactions in which each step proceeded in 52 % yield (averaged) and which established four of the seven stereogenic centers. The pivotal precursor for the cascade reaction was assembled from three readily available building blocks. A chiral dithioacetal with two stereogenic centers originating from L‐arabinose represented the core fragment to both ends of which the other building blocks were attached by aldol reactions. The remaining stereogenic center was installed by Davis oxygenation immediately prior to the key step.

Biomimetic Total Synthesis of Enterocin.

The first chemical total synthesis of the highly oxygenated polyketide enterocin has been accomplished. The key step of the synthesis was a late‐stage biomimetic reaction cascade involving two intramolecular aldol reactions in which each step proceeded in 52 % yield (averaged) and which established four of the seven stereogenic centers. The pivotal precursor for the cascade reaction was assembled from three readily available building blocks. A chiral dithioacetal with two stereogenic centers originating from L‐arabinose represented the core fragment to both ends of which the other building blocks were attached by aldol reactions. The remaining stereogenic center was installed by Davis oxygenation immediately prior to the key step.

Heteroleptic Ligation by an endo-Functionalized Cage.

A conceptual approach for the synthesis of quasi‐heteroleptic complexes with properly endo‐functionalized cages as ligands is presented. The cage ligand reported here is of a covalent organic nature, it has been synthesized via a dynamic combinatorial chemistry approach, making use of a masked amine. Inspired by enzymatic active sites, the described system bears one carboxylate and two imidazole moieties as independent ligating units through which it is able to coordinate to transition metals. Analysis of the iron(II) complex in solution and the solid state validates the structure and shows that no undesired but commonly observed dimerization process takes place. The solid‐state structure shows a five‐coordinate metal center with the carboxylate bidentately bound to iron, which makes Fe@2 an unprecedentedly detailed structural model complex for this kind of non‐heme iron oxygenases. As, as confirmed by the crystal structure, sufficient space for other organic ligands is available, the biologically relevant ligand α‐ketoglutarate is implemented. We observe biomimetic reaction behavior towards dioxygen that opens studies investigating Fe@2 as a functional model complex.

Isolation, characterization and semi-synthesis of natural products dimeric amide alkaloids

Isolation, characterization and semi-synthesis of natural products dimeric amide alkaloids

Bridgehead Hydroxylation in the Annulation of Cyclic Aldimines

Key words alkaloids - cyclopropenones - [3+2] annulation - biomimetic reaction - hydroxylation - aldimines

A robust and tunable halogen bond organocatalyzed 2-deoxyglycosylation involving quantum tunneling

The development of noncovalent halogen bonding (XB) catalysis is rapidly gaining traction, as isolated reports documented better performance than the well-established hydrogen bonding thiourea catalysis. However, convincing cases allowing XB activation to be competitive in challenging bond formations are lacking. Herein, we report a robust XB catalyzed 2-deoxyglycosylation, featuring a biomimetic reaction network indicative of dynamic XB activation. Benchmarking studies uncovered an improved substrate tolerance compared to thiourea-catalyzed protocols. Kinetic investigations reveal an autoinductive sigmoidal kinetic profile, supporting an in situ amplification of a XB dependent active catalytic species. Kinetic isotopic effect measurements further support quantum tunneling in the rate determining step. Furthermore, we demonstrate XB catalysis tunability via a halogen swapping strategy, facilitating 2-deoxyribosylations of D-ribals. This protocol showcases the clear emergence of XB catalysis as a versatile activation mode in noncovalent organocatalysis, and as an important addition to the catalytic toolbox of chemical glycosylations.

Computational Insight into the Mechanism of Mannich Reaction between Glycinate and Aryl N‐Diphenylphosphinyl Imine Catalyzed by N‐Quaternized Pyridoxal

AbstractRecently, Chen et al. reported an asymmetric biomimetic Mannich reaction of tert‐butyl glycinate (sub‐1) with aryl N‐diphenylphosphinyl imine (sub‐2) catalyzed by N‐quaternized pyridoxal analogue (cat) (Chen et al., Science, 2018, 360, 1438–1442). By utilizing Gaussian 09 program, we provide the detailed density functional theory (DFT, including B3LYP−D3 and M06‐2X) investigations on the mechanisms of each section of the reaction with CHCl3 as implicit solvent. These cat, sub‐1 and OH− if it exists can act as catalytic base and need to overcome relative free energy barrier of ∼12, 13.5 and 4.2 kcal/mol, respectively, to achieve α‐carbon deprotonation. During the addition reaction, the most favorable transition structure was calculated to overcome a relative free energy barrier of 6.3 kcal/mol, verifying the bifunctional activation mode of cat. The final hydrolysis reaction starts with hydration to achieve protonation at the N atom of sub‐2 portion and generates a carbinolamine. These computational results help one obtain deep understanding of the reaction mechanism and benefit future design of pyridoxal catalyst and similar biomimetic reaction.

Model Substrate/Inactivation Reactions for MoaA and Ribonucleotide Reductases: Loss of Bromo, Chloro, or Tosylate Groups from C2 of 1,5-Dideoxyhomoribofuranoses upon Generation of an α-Oxy Radical at C3.

We report studies on radical-initiated fragmentations of model 1,5-dideoxyhomoribofuranose derivatives with bromo, chloro, and tosyloxy substituents on C2. The effects of stereochemical inversion at C2 were probed with the corresponding arabino epimers. In all cases, the elimination of bromide, chloride, and tosylate anions occurred when the 3-hydroxyl group was unprotected. The isolation of deuterium-labeled furanone products established heterolytic cleavage followed by the transfer of deuterium from labeled tributylstannane. In contrast, 3-O-methyl derivatives underwent the elimination of bromine or chlorine radicals to give the 2,3-alkene with no incorporation of label in the methyl vinyl ether. More drastic fragmentation occurred with both of the 3-O-methyl-2-tosyloxy epimers to give an aromatized furan derivative with no deuterium label. Contrasting results observed with the present anhydroalditol models relative to our prior studies with analogously substituted nucleoside models have demonstrated that insights from biomimetic chemical reactions can provide illumination of mechanistic pathways employed by ribonucleotide reductases (RNRs) and the MoaA enzyme involved in the biosynthesis of molybdopterin.