Förster Resonance Energy Transfer Assay for Investigating the Reactivity of Thioesters in Biochemistry and Native Chemical Ligation

Thioesters are considered to be "energy-rich" functional groups that are susceptible to attack by thiolate and amine nucleophiles while remaining hydrolytically stable at neutral pH, which enables thioester chemistry to take place in an aqueous medium. Thus, the inherent reactivity of thioesters enables their fundamental roles in biology and unique applications in chemical synthesis. Here, we investigate the reactivity of thioesters that mimic acyl-coenzyme A (CoA) species and S-acylcysteine modifications as well as aryl thioesters applied in chemical protein synthesis by native chemical ligation (NCL). We developed a fluorogenic assay format for the direct and continuous investigation of the rate of reaction between thioesters and nucleophiles (hydroxide, thiolate, and amines) under various conditions and were able to recapitulate previously reported reactivity of thioesters. Further, chromatography-based analyses of acetyl- and succinyl-CoA mimics revealed striking differences in their ability to acylate lysine side chains, providing insight into nonenzymatic protein acylation. Finally, we investigated key aspects of native chemical ligation reaction conditions. Our data revealed a profound effect of the tris-(2-carboxyethyl)phosphine (TCEP) commonly used in systems where thiol-thioester exchange occurs, including a potentially harmful hydrolysis side reaction. These data provide insight into the potential optimization of native chemical ligation chemistry.

Rapid Biocatalytic Synthesis of Aromatic Acid CoA Thioesters by Using Microbial Aromatic Acid CoA Ligases

Chemically labile ester linkages can be introduced into lignin by incorporation of monolignol conjugates, which are synthesized in planta by acyltransferases that use a coenzyme A (CoA) thioester donor and a nucleophilic monolignol alcohol acceptor. The presence of these esters facilitates processing and aids in the valorization of renewable biomass feedstocks. However, the effectiveness of this strategy is potentially limited by the low steady-state levels of aromatic acid thioester donors in plants. As part of an effort to overcome this, aromatic acid CoA ligases involved in microbial aromatic degradation were identified and screened against a broad panel of substituted cinnamic and benzoic acids involved in plant lignification. Functional fingerprinting of this ligase library identified four robust, highly active enzymes capable of facile, rapid, and high-yield synthesis of aromatic acid CoA thioesters under mild aqueous reaction conditions mimicking in planta activity.

Iron-Catalyzed Cross-Coupling of Thioesters and Organomanganese Reagents

We report a Fukuyama-type coupling of thioesters with aliphatic organomanganese reagents utilizing a cheap and easily available iron(III) precatalyst. The reactions exhibit a wide tolerance of solvents and functional groups, allowing for the conversion of thioesters derived from natural products and pharmaceutical compounds. A strong steric impact from each reaction component (carboxylic moiety, thiol substituent and manganese reagent) was displayed, which enabled regioselective transformation of dithioesters. Mechanistic investigations showed that the released thiolate does not act as a mere spectator ligand, but rather positively influences the stability of intermediate alkyl(II)ferrates.

4D Printing of Extrudable and Degradable Poly(Ethylene Glycol) Microgel Scaffolds for Multidimensional Cell Culture

Granular synthetic hydrogels are useful bioinks for their compatibility with a variety of chemistries, affording printable, stimuli-responsive scaffolds with programmable structure and function. Additive manufacturing of microscale hydrogels, or microgels, allows for the fabrication of large cellularized constructs with percolating interstitial space, providing a platform for tissue engineering at length scales that are inaccessible by bulk encapsulation where transport of media and other biological factors are limited by scaffold density. Herein, synthetic microgels with varying degrees of degradability are prepared with diameters on the order of hundreds of microns by submerged electrospray and UV photopolymerization. Porous microgel scaffolds are assembled by particle jamming and extrusion printing, and semi-orthogonal chemical cues are utilized to tune the void fraction in printed scaffolds in a logic-gated manner. Scaffolds with different void fractions are easily cellularized post printing and microgels can be directly annealed into cell-laden structures. Finally, high-throughput direct encapsulation of cells within printable microgels is demonstrated, enabling large-scale 3D culture in a macroporous biomaterial. This approach provides unprecedented spatiotemporal control over the properties of printed microporous annealed particle scaffolds for 2.5D and 3D tissue culture.

The Grayness of the Origin of Life

In the search for life beyond Earth, distinguishing the living from the non-living is paramount. However, this distinction is often elusive, as the origin of life is likely a stepwise evolutionary process, not a singular event. Regardless of the favored origin of life model, an inherent "grayness" blurs the theorized threshold defining life. Here, we explore the ambiguities between the biotic and the abiotic at the origin of life. The role of grayness extends into later transitions as well. By recognizing the limitations posed by grayness, life detection researchers will be better able to develop methods sensitive to prebiotic chemical systems and life with alternative biochemistries.

A Nickel(II)-Mediated Thiocarbonylation Strategy for Carbon Isotope Labeling of Aliphatic Carboxamides

A series of pharmaceutically relevant small molecules and biopharmaceuticals bearing aliphatic carboxamides have been successfully labeled with carbon-13. Key to the success of this novel carbon isotope labeling technique is the observation that ¹³ C-labeled Ni^II -acyl complexes, formed from a ¹³ CO insertion step with Ni^II -alkyl intermediates, rapidly react in less than one minute with 2,2'-dipyridyl disulfide to quantitatively form the corresponding 2-pyridyl thioesters. Either the use of ¹³ C-SilaCOgen or ¹³ C-COgen allows for the stoichiometric addition of isotopically labeled carbon monoxide. Subsequent one-pot acylation of a series of structurally diverse amines provides the desired ¹³ C-labeled carboxamides in good yields. A single electron transfer pathway is proposed between the Ni^II -acyl complexes and the disulfide providing a reactive Ni^III -acyl sulfide intermediate, which rapidly undergoes reductive elimination to the desired thioester. By further optimization of the reaction parameters, reaction times down to only 11 min were identified, opening up the possibility of exploring this chemistry for carbon-11 isotope labeling. Finally, this isotope labeling strategy could be adapted to the synthesis of ¹³ C-labeled liraglutide and insulin degludec, representing two antidiabetic drugs.

Synthesis of Spirocycles via Ni-Catalyzed Intramolecular Coupling of Thioesters and Olefins

A nickel-catalyzed intramolecular coupling of thioesters and olefins has been developed for the efficient synthesis of spirocycles, a privileged scaffold commonly found in natural products. This transformation is characterized by the simultaneous transfer of both acyl and thiol moieties to the alkene, with the suppression of decarbonylation and β-hydrogen elimination. Initial mechanistic investigations are consistent with an oxidative addition/olefin insertion/reductive elimination mechanism. The incorporated methylene sulfide substituent can undergo a variety of further reactions to increase molecular diversity and complexity. These results demonstrate that thioester derivatives can be used as powerful building blocks for the assembly of complex scaffolds.

Tartryl-CoA inhibits succinyl-CoA synthetase

Succinyl-CoA synthetase (SCS) catalyzes the only substrate-level phosphorylation step in the tricarboxylic acid cycle. Human GTP-specific SCS (GTPSCS), an αβ-heterodimer, was produced in Escherichia coli. The purified protein crystallized from a solution containing tartrate, CoA and magnesium chloride, and a crystal diffracted to 1.52 Å resolution. Tartryl-CoA was discovered to be bound to GTPSCS. The CoA portion lies in the amino-terminal domain of the α-subunit and the tartryl end extends towards the catalytic histidine residue. The terminal carboxylate binds to the phosphate-binding site of GTPSCS.

Bioactive Compounds, Nutritional Value, and Potential Health Benefits of Indigenous Durian (Durio Zibethinus Murr.): A Review

Durian (Durio zibethinus Murr.) is an energy-dense seasonal tropical fruit grown in Southeast Asia. It is one of the most expensive fruits in the region. It has a creamy texture and a sweet-bitter taste. The unique durian flavour is attributable to the presence of fat, sugar, and volatile compounds such as esters and sulphur-containing compounds such as thioacetals, thioesters, and thiolanes, as well as alcohols. This review shows that durian is also rich in flavonoids (i.e., flavanols, anthocyanins), ascorbic acid, and carotenoids. However, limited studies exist regarding the variation in bioactive and volatile components of different durian varieties from Malaysia, Thailand, and Indonesia. Experimental animal models have shown that durian beneficially reduces blood glucose and cholesterol levels. Durian extract possesses anti-proliferative and probiotics effects in in vitro models. These effects warrant further investigation in human interventional studies for the development of functional food.

Thioesters as Acyl Donors in Biocatalytic Friedel-Crafts-type Acylation Catalyzed by Acyltransferase from Pseudomonas Protegens

Functionalization of aromatic compounds by acylation has considerable significance in synthetic organic chemistry. As an alternative to chemical Friedel-Crafts acylation, the C-acyltransferase from Pseudomonas protegens has been found to catalyze C-C bond formation with non-natural resorcinol substrates. Extending the scope of acyl donors, it is now shown that the enzyme is also able to catalyze C-S bond cleavage prior to C-C bond formation, thus aliphatic and aromatic thioesters can be used as acyl donors. It is worth to mention that this reaction can be performed in aqueous buffer. Identifying ethyl thioacetate as the most suitable acetyl donor, the products were obtained with up to >99 % conversion and up to 88 % isolated yield without using additional base additives; this represents a significant advancement to prior protocols.

Palladium-Catalyzed Insertion of Isocyanides into the C-S Bonds of Heteroaryl Sulfides

Insertion of tert-butyl isocyanide into the C(sp² )-S bonds of heteroaryl sulfides is catalyzed by a palladium diphosphine complex. Thioimidates generated through this reaction could be readily hydrolyzed under acidic conditions to yield the corresponding thioesters, which are of synthetic use. This insertion is useful because starting heteroaryl sulfides were readily prepared by either conventional ways or through sulfur-specific extended Pummerer reactions.

Rhodium-Catalyzed Decarbonylative Borylation of Aromatic Thioesters for Facile Diversification of Aromatic Carboxylic Acids

Transformation of aromatic thioesters into arylboronic esters was achieved efficiently using a rhodium catalyst. The broad functional-group tolerance and mild conditions of the method have allowed for the two-step decarboxylative borylation of a wide range of aromatic carboxylic acids, including commercially available drugs.

Mass-Spectrometry-Based Quantification of Protein-Bound Fatty Acid Synthesis Intermediates from Escherichia coli

The production of fatty acids from simple nutrients occurs via a complex biosynthetic pathway with dozens of intermediate compounds and multiple branch points. Despite its importance for microbial physiology and biotechnology, critical aspects of fatty acid biosynthesis, especially dynamics of in vivo regulation, remain poorly characterized. We have developed a liquid chromatography/mass spectroscopy (LC-MS) method for relative quantification of fatty acid synthesis intermediates in Escherichia coli, a model organism for studies of fatty acid metabolism. The acyl carrier protein, a vehicle for the substrates and intermediates of fatty acid synthesis, is extracted from E. coli, proteolytically digested, resolved using reverse-phase LC, and detected using electrospray ionization coupled with a tandem MS. Our method reliably resolves 21 intermediates of fatty acid synthesis, with an average relative standard deviation in ratios of individual acyl-ACP species to total ACP concentrations of 20%. We demonstrate that fast sampling and quenching of cells is essential to accurately characterize intracellular concentrations of ACP species. We apply our method to examine the rapid response of fatty acid metabolism to the antibiotic cerulenin. We anticipate that our method will enable the characterization of in vivo regulation and kinetics of microbial fatty acid synthesis at unprecedented detail and will improve integration of fatty acid synthesis into models of microbial metabolism.

Imidazolinium and amidinium salts as Lewis acid organocatalysts

The application of imidazolinium and amidinium salts as soft Lewis acid organocatalysts is described. These salts were suitable catalysts for the activation of unsaturated thioesters in a Diels-Alder reaction and in the ring opening of thiiranes and epoxides. The products were isolated in good yields. The mild catalysts did not cause desulfurization of the products containing a thiol or thiocarbonyl group.

Use of empirical correlations to determine solvent effects in the solvolysis of S-methyl chlorothioformate

The specific rates of solvolysis of S-methyl chlorothioformate (MeSCOCl) are analyzed in 20 solvents of widely varying nucleophilicity and ionizing power at 25.0 degrees C using the extended Grunwald-Winstein Equation. A stepwise S(N)1 (D(N) + A(N)) mechanism is proposed in the more ionizing solvents including six aqueous fluoroalcohols. In these solvents, a large sensitivity value of 0.79 towards changes in solvent nucleophilicity (l) is indicative of profound rearside nucleophilic solvation of the developing carbocation. In twelve of the more nucleophilic pure alchohols and aqueous solutions, the sensitivities obtained for solvent nucleophilicity (l) and solvent ionizing power (m) are similar to those found in acyl chlorides where an association-dissociation (A(N) + D(N)) mechanism is believed to be operative.

Cloning, expression, purification, crystallization and preliminary X-ray analysis of Thermus aquaticus succinyl-CoA synthetase

Succinyl-CoA synthetase (SCS) is an enzyme of the citric acid cycle and is thus found in most species. To date, there are no structures available of SCS from a thermophilic organism. To investigate how the enzyme adapts to higher temperatures, SCS from Thermus aquaticus was cloned, overexpressed, purified and crystallized. Attempts to crystallize the enzyme were thwarted by proteolysis of the beta-subunit and preferential crystallization of the truncated form. Crystals of full-length SCS were grown after the purification protocol was modified to include frequent additions of protease inhibitors. The resulting crystals, which diffract to 2.35 A resolution, are of the protein in complex with Mn2+-GDP.

Pantetheine-linked peptide intermediates in gramicidin S and tyrocidine biosynthesis

To study the function of pantetheine in gramicidin S and tyrocidine biosynthesis, pepsin digests of the polymerizing enzymes, of which only the heavy ones contain pantetheine, were analyzed. The digests of gramicidin S enzymes charged with either [(14)C]proline or with D-phenylalanyl-[(14)C]proline, were analyzed by thin-layer chromatography; only the dipeptide showed a derivative associated with pantetheine. Similar results were obtained from the heavy tyrocidine enzyme charged with either [(14)C]asparagine alone or with the pentapeptide D-Phe-Pro-Phe-D-Phe-[(14)C]Asn. Several radioactive products appeared on the thin-layer chromatograms of both these digests; association with pantetheine was found only in the case of the pentapeptide. Exposure of the chromatogram from the pentapeptide-labeled digest to performic acid and development in a second direction separated the peptide from pantetheine, indicating that a nascent peptide was originally linked to the cofactor by a thioester bond. The connection of pantetheine only with peptide residues appears to confirm its role in transpeptidation during peptide chain growth.