Coenzyme A Analogues and Derivatives: Synthesis and Applications as Mechanistic Probes of Coenzyme A Ester-Utilizing Enzymes

Peptide Alkyl Thioester Synthesis from Advanced Thiols and Peptide Hydrazides

Peptide alkyl thioesters are versatile reagents in various synthetic applications, commonly generated from peptide hydrazides and thiols. However, a notable limitation is the need for a substantial excess of the thiol reagent, restricting the usage to simple thiols. Here, we introduce an adapted procedure that significantly enhances thioester production with just a minimal thiol excess, facilitating the use of advanced thiol nucleophiles.

Complete biosynthesis of the potent vaccine adjuvant QS-21

QS-21 is a potent vaccine adjuvant currently sourced by extraction from the Chilean soapbark tree. It is a key component of human vaccines for shingles, malaria, coronavirus disease 2019 and others under development. The structure of QS-21 consists of a glycosylated triterpene scaffold coupled to a complex glycosylated 18-carbon acyl chain that is critical for immunostimulant activity. We previously identified the early pathway steps needed to make the triterpene glycoside scaffold; however, the biosynthetic route to the acyl chain, which is needed for stimulation of T cell proliferation, was unknown. Here, we report the biogenic origin of the acyl chain, characterize the series of enzymes required for its synthesis and addition and reconstitute the entire 20-step pathway in tobacco, thereby demonstrating the production of QS-21 in a heterologous expression system. This advance opens up unprecedented opportunities for bioengineering of vaccine adjuvants, investigating structure-activity relationships and understanding the mechanisms by which these compounds promote the human immune response.

Activity of Fatty Acid Biosynthesis Initiating Ketosynthase FabH with Acetyl/Malonyl-oxa/aza(dethia)CoAs

Fatty acid and polyketide biosynthetic enzymes exploit the reactivity of acyl- and malonyl-thioesters for catalysis. A prime example is FabH, which initiates fatty acid biosynthesis in many bacteria and plants. FabH performs an acyltransferase reaction with acetyl-CoA to generate an acetyl-S-FabH acyl-enzyme intermediate and subsequent decarboxylative Claisen-condensation with a malonyl-thioester carried by an acyl carrier protein (ACP). We envision that crystal structures of FabH with substrate analogues can provide insight into the conformational changes and enzyme/substrate interactions underpinning the distinct reactions. Here, we synthesize acetyl/malonyl-CoA analogues with esters or amides in place of the thioester and characterize their stability and behavior as Escherichia coli FabH substrates or inhibitors to inform structural studies. We also characterize the analogues with mutant FabH C112Q that mimics the acyl-enzyme intermediate allowing dissection of the decarboxylation reaction. The acetyl- and malonyl-oxa(dethia)CoA analogues undergo extremely slow hydrolysis in the presence of FabH or the C112Q mutant. Decarboxylation of malonyl-oxa(dethia)CoA by FabH or C112Q mutant was not detected. The amide analogues were completely stable to enzyme activity. In enzyme assays with acetyl-CoA and malonyl-CoA (rather than malonyl-ACP) as substrates, acetyl-oxa(dethia)CoA is surprisingly slightly activating, while acetyl-aza(dethia)CoA is a moderate inhibitor. The malonyl-oxa/aza(dethia)CoAs are inhibitors with Ki's near the Km of malonyl-CoA. For comparison, we determine the FabH catalyzed decomposition rates for acetyl/malonyl-CoA, revealing some fundamental catalytic traits of FabH, including hysteresis for malonyl-CoA decarboxylation. The stability and inhibitory properties of the substrate analogues make them promising for structure-function studies to reveal fatty acid and polyketide enzyme/substrate interactions.

A Novel Coenzyme A Analogue in the Anaerobic, Sulfate-Reducing, Marine Bacterium Desulfobacula toluolica Tol2T

Coenzyme A (CoA) thioesters are formed during anabolic and catabolic reactions in every organism. Degradation pathways of growth-supporting substrates in bacteria can be predicted by differential proteogenomic studies. Direct detection of proposed metabolites such as CoA thioesters by high-performance liquid chromatography coupled with high-resolution mass spectrometry can confirm the reaction sequence and demonstrate the activity of these degradation pathways. In the metabolomes of the anaerobic sulfate-reducing bacterium Desulfobacula toluolica Tol2^T grown with different substrates various CoA thioesters, derived from amino acid, fatty acid or alcohol metabolism, have been detected. Additionally, the cell extracts of this bacterium revealed a number of CoA analogues with molecular masses increased by 1 dalton. By comparing the chromatographic and mass spectrometric properties of synthetic reference standards with those of compounds detected in cell extracts of D. toluolica Tol2^T and by performing co-injection experiments, these analogues were identified as inosino-CoAs. These CoA thioesters contain inosine instead of adenosine as the nucleoside. To the best of our knowledge, this finding represents the first detection of naturally occurring inosino-CoA analogues.

Acetoacetyl-CoA transferase ydiF regulates the biofilm formation of avian pathogenic Escherichia coli

Avian pathogenic Escherichia coli (APEC) causes persistent infection of poultry and multi-system diseases, which seriously endanger the development of the poultry industry. Biofilm allows bacteria to adapt to the natural environment and plays an important role in resistance to the external environment and the pathogenicity of APEC, but the mechanism of its formation and regulatory network have not been clarified. In this study, we used a Tn5 transposon random mutation library constructed with APEC and identified ydiF, a gene that has not previously been recognized in E. coli biofilm formation. To confirm that the ydiF gene really can regulate the formation of APEC biofilm, the ydiF gene deletion strain was constructed using APEC81. Protein association networks prediction results show that ydiF is mainly associated with genes related to the metabolism of sugars and fatty acids. Deletion of the ydiF gene significantly reduces the formation of APEC biofilm and scanning electron microscopy indicated that the degree of adhesion between the bacteria was also reduced. The deletion of the ydiF gene also significantly reduced the motility of APEC81 and through transmission electron microscopy APEC81 was observed to have significantly fewer flagella. However, the colony morphology of APEC81 on Congo red and Coomassie brilliant blue media was unaffected. The results of fluorescence quantification showed that the deletion of the ydiF gene caused a down-regulation in the transcription of genes related to the second messenger, sugar metabolism, and quorum sensing. These results indicate that ydiF plays an important role in biofilm formation and the movement of APEC. In addition, it may be possible to regulate the formation of APEC biofilms by different methods such as by regulating the second messenger and metabolic system.

Accurate Substrate-Like Probes for Trapping Late-Stage Intermediates in Nonribosomal Peptide Synthetase Condensation Domains

Nonribosomal peptide synthetases (NRPSs) are a family of multidomain enzymes dedicated to the production of peptide natural products. Central to NRPS function are condensation (C) domains, which catalyze peptide bond formation and a number of specialized transformations including dehydroamino acid and β-lactam synthesis. Structures of C domains in catalytically informative states are limited due to a lack of clear strategies for stabilizing C domain interactions with their substrates and client domains. Inspired by a β-lactam forming C domain, we report herein the synthesis and application of 1, which forms irreversible cross-links with engineered thiol nucleophiles in a C domain active site. Deployment of 1 demonstrates the synthetic tractability of trapping late-stage nascent peptides in C domains and provides a readily adaptable tactic for stabilizing C domain interactions in multidomain NRPS fragments.

Optical/electrochemical methods for detecting mitochondrial energy metabolism

This review highlights the biological importance of mitochondrial energy metabolism and the applications of multiple optical/electrochemical approaches to determine energy metabolites. Mitochondria, the main sites of oxidative phosphorylation and adenosine triphosphate (ATP) biosynthesis, provide the majority of energy required by aerobic cells for maintaining their physiological activity. They also participate in cell growth, differentiation, information transmission, and apoptosis. Multiple mitochondrial diseases, caused by internal or external factors, including oxidative stress, intense fluctuations of the ionic concentration, abnormal oxidative phosphorylation, changes in electron transport chain complex enzymes and mutations in mitochondrial DNA, can occur during mitochondrial energy metabolism. Therefore, developing accurate, sensitive, and specific methods for the in vivo and in vitro detection of mitochondrial energy metabolites is of great importance. In this review, we summarise the mitochondrial structure, functions, and crucial energy metabolic signalling pathways. The mechanism and applications of different optical/electrochemical methods are thoroughly reviewed. Finally, future research directions and challenges are proposed.

Screening of Acetyl Donors and the Robust Enzymatic Synthesis of Acetyl-CoA by 10-Deacetylbaccatin III-10-β-O-acetyltransferase

Acetyl-CoA is the precursor of many bio-manufacturing products and is also the hub of the cellular metabolism of energy and substances. However, acetyl-CoA is not a bulk commodity and its application is hindered due to its high cost and low yield. In this study, we screened acetyl donor candidates and utilized 10-deacetylbaccatin III-10-β-O-acetyltransferase (DBAT) in the synthesis of acetyl-CoA with CoASH as the acetyl acceptor. Among the tested candidates, acetylsalicylic acid methyl ester was identified to be the best acetyl donor, followed by acetyl-trans-resveratrol, acetylsalicylic acid ethyl ester, acetylsalicylsalicylic acid, and 4-acetoxyacetanilide. The enzymatic reaction conditions were optimized and the maximum yield of acetyl-CoA reached 14.82 mg/mL, which is the highest yield among all reported approaches to date. Meanwhile, 4.22 mg/mL of the by-product salicylic acid methyl ester, which is another industrial material, was produced. Additionally, a preliminary purification process for acetyl-CoA was established, in which 40 mg acetyl-CoA (HPLC purity > 98%) was acquired from the finished 20 mL reaction system (feeding 46 mg CoASH and 34 mg ASME) with a recovery rate of 86%. Our study lays the foundation for the large-scale production of acetyl-CoA by an enzymatic approach and will promote its application in different fields.

Diacerein as a Promising Acyl Donor in Biosynthetic Acetyl-CoA and Glycosyl Esters Mediated by a Multifunctional Maltose O-Acetyltransferase from Escherichia coli

Acetyl-coenzyme A (acetyl-CoA) is an important donor for acetylation modifications of nutritional supplements. The existing enzymatic methods for acetyl-CoA synthesis suffer from cofactor dependence, donor inaccessibility, and biocatalyst instability, leading to its high cost. Hence, a promising alternative is highly desired. Herein, a maltose O-acetyltransferase (MAT) with cofactor independence had been identified as a stable acetyl-CoA-synthesizing biocatalyst in a screen of the Escherichia coli genome. Under the action of MAT, an anthraquinone medicine containing two acetyl groups, diacerein, was screened as an acetyl donor. Saturation mutagenesis at Glu125 was performed to increase the acetyl-CoA-synthesizing capacity of MAT, while decreasing the accompanying hydrolase activities. A mutant MAT-E125F was thus generated and could convert diacerein and CoA into the highest yield of 3892.70 mg/L acetyl-CoA. Moreover, MAT could synthesize puerarin 6″-O-acetate and other glycosyl esters through acetyl-CoA-dependent acetylation or diacerein-based transesterification reaction. To most of the tested glycosides, the transesterification efficiency was higher than that of acetylation. The mutant MAT-E125V acquired the highest conversion of 94.0% to puerarin 6″-O-acetate through transesterification, while MAT-E125N yielded the highest conversion of 68.5% through acetylation. Taking together, the multifunctional MAT displayed a potent acetyl-CoA- and glycosyl ester-synthesizing capacity using diacerein as an acetyl donor.

Development of a Pantetheine Force Field Library for Molecular Modeling

Pantetheine is ubiquitous in nature in various forms of pantetheine-containing ligands (PCLs), including coenzyme A and phosphopantetheine. Lack of scalable force field libraries for PCLs has hampered the computational studies of biological macromolecules containing PCLs. We describe here the development of the first generation Pantetheine Force Field (PFF) library that is compatible with Amber force fields; parameterized using Gasteiger, AM1-BCC, or RESP charging methods combined with gaff2 and ff14SB parameter sets. In addition, a "plug-and-play" strategy was employed to enable the systematic charging of computationally expensive molecules sharing common substructural motifs. The validation studies performed on the PFF library showed promising performance where molecular dynamics (MD) simulations results were compared with experimental data of three representative systems. The PFF library represents the first force field library capable of modeling systems containing PCLs in silico and will aid in various applications including protein engineering and drug discovery.

Chemical Labeling of Protein 4'-Phosphopantetheinylation

Nature uses a diverse array of protein post-translational modifications (PTMs) to regulate protein structure, activity, localization, and function. Among them, protein 4'-phosphopantetheinylation derived from coenzyme A (CoA) is an essential PTM for the biosynthesis of fatty acids, polyketides, and nonribosomal peptides in prokaryotes and eukaryotes. To explore its functions, various chemical probes mimicking the natural structure of 4'-phosphopantetheinylation have been developed. In this minireview, we summarize these chemical probes and describe their applications in direct and metabolic labeling of proteins in bacterial and mammalian cells.

Polyketide β-branching: diversity, mechanism and selectivity

Covering: 2008 to August 2020 Polyketides are a family of natural products constructed from simple building blocks to generate a diverse range of often complex chemical structures with biological activities of both pharmaceutical and agrochemical importance. Their biosynthesis is controlled by polyketide synthases (PKSs) which catalyse the condensation of thioesters to assemble a functionalised linear carbon chain. Alkyl-branches may be installed at the nucleophilic α- or electrophilic β-carbon of the growing chain. Polyketide β-branching is a fascinating biosynthetic modification that allows for the conversion of a β-ketone into a β-alkyl group or functionalised side-chain. The overall transformation is catalysed by a multi-protein 3-hydroxy-3-methylglutaryl synthase (HMGS) cassette and is reminiscent of the mevalonate pathway in terpene biosynthesis. The first step most commonly involves the aldol addition of acetate to the electrophilic carbon of the β-ketothioester catalysed by a 3-hydroxy-3-methylglutaryl synthase (HMGS). Subsequent dehydration and decarboxylation selectively generates either α,β- or β,γ-unsaturated β-alkyl branches which may be further modified. This review covers 2008 to August 2020 and summarises the diversity of β-branch incorporation and the mechanistic details of each catalytic step. This is extended to discussion of polyketides containing multiple β-branches and the selectivity exerted by the PKS to ensure β-branching fidelity. Finally, the application of HMGS in data mining, additional β-branching mechanisms and current knowledge of the role of β-branches in this important class of biologically active natural products is discussed.

A Cu2+-assisted fluorescence switch biosensor for detecting of coenzyme A employing nitrogen-doped carbon dots

Herein, a simple and sensitive Cu²⁺-assisted fluorescence switch biosensor for the detection of coenzyme A (CoA) was proposed by employing nitrogen-doped carbon dots (N-CDs). N-CDs were successfully synthesized by sodium alginate and melatonin via pyrolysis. The as-prepared N-CDs were spherical with an average diameter of 2.8 nm and exhibited blue emission (λ_em = 480 nm, λ_ex = 360 nm) with a high fluorescence quantum yield of 50.2%. The intense blue emission of the N-CDs could be effectively quenched by copper ions through the formation of the N-CDs/Cu²⁺ complex. With the introduction of CoA, a more stable CoA/Cu²⁺ complex formed, leading to the fluorescence recovery of N-CDs. Based on this strategy, CoA could be sensitively and selectively detected with a good linear relationship in the range of 0.02-5.00 μM and with a detection limit of 12 nM. In addition, this sensor was applied for CoA detection in human serum samples with satisfactory recovery. The results showed great potential towards advancing applications in CoA-dependent bioresearch.

Round, round we go - strategies for enzymatic cofactor regeneration

Covering: up to the beginning of 2020Enzymes depending on cofactors are essential in many biosynthetic pathways of natural products. They are often involved in key steps: catalytic conversions that are difficult to achieve purely with synthetic organic chemistry. Hence, cofactor-dependent enzymes have great potential for biocatalysis, on the condition that a corresponding cofactor regeneration system is available. For some cofactors, these regeneration systems require multiple steps; such complex enzyme cascades/multi-enzyme systems are (still) challenging for in vitro biocatalysis. Further, artificial cofactor analogues have been synthesised that are more stable, show an altered reaction range, or act as inhibitors. The development of bio-orthogonal systems that can be used for the production of modified natural products in vivo is an ongoing challenge. In light of the recent progress in this field, this review aims to provide an overview of general strategies involving enzyme cofactors, cofactor analogues, and regeneration systems; highlighting the current possibilities for application of enzymes using some of the most common cofactors.

Characterisation of four hotdog-fold thioesterases for their implementation in a novel organic acid production system

With increasing interest in the diverse properties of organic acids and their application in synthetic pathways, developing biological tools for producing known and novel organic acids would be very valuable. In such a system, organic acids may be activated as coenzyme A (CoA) esters, then modified by CoA-dependent enzymes, followed by CoA liberation by a broad-acting thioesterase. This study has focused on the identification of suitable thioesterases (TE) for utilisation in such a pathway. Four recombinant hotdog-fold TEs were screened with a range of CoA esters in order to identify a highly active, broad spectrum TE. The TesB-like TE, RpaL, from Rhodopseudomonas palustris was found to be able to use aromatic, alicyclic and both long and short aliphatic CoA esters. Size exclusion chromatography, revealed RpaL to be a monomer of fused hotdog domains, in contrast to the complex quaternary structures found with similar TesB-like TEs. Nonetheless, sequence alignments showed a conserved catalytic triad despite the variation in quaternary arrangement. Kinetic analysis revealed a preference towards short-branched chain CoA esters with the highest specificity towards DL-β-hydroxybutyryl CoA (1.6 × 10⁴ M⁻¹ s⁻¹), which was found to decrease as the acyl chain became longer and more functionalised. Substrate inhibition was observed with the fatty acyl n-heptadecanoyl CoA at concentrations exceeding 0.3 mM; however, this was attributed to its micellar aggregation properties. As a result of the broad activity observed with RpaL, it is a strong candidate for implementation in CoA ester pathways to generate modified or novel organic acids.

Air-Tolerant Direct Thiol Esterification with Carboxylic Acids Using Hydrosilane via Simple Inorganic Base Catalysis

Direct thioesterification of carboxylic acids with thiols using nontoxic activation agents is highly desirable. Herein, an efficient and practical protocol using safe and inexpensive industrial waste polymethylhydrosiloxane as the activation agent and K₃PO₄ with 18-crown-6 as a catalyst is described. Various functional groups on carboxylic acid and thiol substituents can be tolerated by the present system to afford thioesters in yields of 19-100%.

Single-excitation, dual-emission biomass quantum dots: preparation and application for ratiometric fluorescence imaging of coenzyme A in living cells

Ratiometric fluorescence imaging can decrease or even eliminate the influences of the microenvironment, localized probe distribution, and instrumental parameters, thereby permitting more accurate monitoring of intracellular molecular events. Therefore, developing ratiometric fluorescent nanoprobes is highly important. In this study, we proposed a distinctive approach by combining solvent extraction with a solvothermal method to synthesize novel biomass-derived carbon-based quantum dots (termed as biomass quantum dots, BQDs) with single-excitation and dual-emission properties, using chlorophyll extracted from pakchoi and polyoxyethylene bisamine as raw materials. The obtained BQDs emit blue and red emissions centered at 488 nm and 678 nm respectively under single 413 nm excitation. Low cytotoxicity and unique optical features make the obtained BQDs potentially useful in bio-application as ratiometric fluorescent probes. Taking advantage of these merits, we employ the obtained BQDs for the near-infrared ratiometric fluorescence detection of coenzyme A (CoA) by the assistance of copper ions. This ratiometric approach shows a good sensitivity and selectivity, and the ratiometric fluorescence imaging of CoA in living cells is also achieved.

Silver coordination complex amplified electrochemiluminescence sensor for sensitive detection of coenzyme A and histone acetyltransferase activity

A kind of coenzyme A (CoA)-silver coordination complex (CoA-Ag) was in-situ developed and verified to accelerate the electron transferring and electrochemical catalysis of H₂O₂ decomposition to enhance the cathode ECL intensity of CdTe@CdS QDs. Afterward, a convenient label-free signal-on ECL approach was constructed for CoA detection with excellent specificity. In addition, the unique ECL enhancing phenomenon was also proposed to assay the enzymatic activity of histone acetyltransferases (HAT) and screen relevant inhibitors, exhibiting a promising potential in the practical application of biochemical research, disease diagnosis and drug discovery.

Chemoenzymatic Synthesis of Starting Materials and Characterization of Halogenases Requiring Acyl Carrier Protein-Tethered Substrates

Flavin-adenine dinucleotide (FAD)-dependent halogenases are widespread in natural product biosynthetic gene clusters and have been demonstrated to employ small organic molecules as substrates for halogenation, as well as substrates that are tethered to carrier proteins (CPs). Despite numerous reports of FAD-dependent halogenases utilizing CP-tethered substrates, only a few have been biochemically characterized due to limited accessibility to the physiological substrates. Here, we describe a method for the preparation of acyl-S-CP substrates and their use in biochemical assays to query the activity of FAD-dependent halogenases. Furthermore, we describe a mass spectrometry-based method for the characterization of acyl-S-CP substrates and the corresponding halogenated products generated by the halogenases. Finally, we test the substrate specificity of a physiological chlorinase and a physiological brominase from marine bacteria, and, for the first time, demonstrate the distinct halide specificity of halogenases. The methodology described here will enable characterization of new halogenases employing CP-tethered substrates.

Scalable thioarylation of unprotected peptides and biomolecules under Ni/photoredox catalysis

A mechanistically distinct, Ni/photoredox-catalyzed arylation of unprotected, native thiols (e.g., cysteine residues) is reported – a process initiated through a visible light-promoted, hydrogen atom transfer (HAT) event under ambient conditions.

Site-specific functionalization of unprotected native peptides and biomolecules remains a useful transformation in synthetic design and chemical biology, yet until recently, advancements in transition metal-catalyzed methods, which have prevailed in organic synthesis, have been relatively ineffective when applied to large and structurally complex biomolecules. Here, the mechanistically distinct, Ni/photoredox-catalyzed arylation of unprotected, native thiols (e.g., cysteine residues) is reported – a process initiated through a visible light-promoted, hydrogen atom transfer (HAT) event under ambient conditions. Sub-stoichiometric loadings of the dual-catalyst system (≤5 mol%) are employed, granting excellent site-specificity, broad substrate scope, and low chemical waste. Reaction scalability (from μg to grams) has been achieved through modest reagent adjustments, and high throughput experimentation (HTE) demonstrates the ease of reaction setup, enabling prompt screening of aryl halide coupling partners and conditions. Scores of thiol substrates and aryl entities were examined and effectively conjugated, suggesting further diverse, practical applications.

Efficient one-pot enzymatic synthesis of dephospho coenzyme A

Dephospho coenzyme A (depCoA) is the last intermediate for CoA biosynthesis, and it can be used as a transcription initiator to prepare CoA-linked RNA by in vitro transcription. However, commercially available depCoA is expensive. We hereby describe a simple and efficient enzymatic synthesis of depCoA in a single-step from commercially available and inexpensive oxidized pantethine (Ox-Pan) and ATP. A plasmid (pCoaDAa) was constructed to co-express and co-purify two enzymes pantothenate kinase (PanK/coaA) and phosphopantetheine adenylyltransferase (PPAT/coaD). Starting from Ox-Pan and ATP, two different synthetic routes of one-pot reaction catalyzed by PanK and PPAT, followed by a simple column purification step, afforded depCoA and its oxidized dimer (Ox-depCoA) with high yields and purity. The simplicity and low cost of our method should make depCoA easily accessible to a broad scientific community, and promote research on CoA-related areas in biology and biomedicine.

Postsynthetic Modification of Bacterial Peptidoglycan Using Bioorthogonal N-Acetylcysteamine Analogs and Peptidoglycan O-Acetyltransferase B

Bacteria have the natural ability to install protective postsynthetic modifications onto its bacterial peptidoglycan (PG), the coat woven into bacterial cell wall. Peptidoglycan O-acetyltransferase B (PatB) catalyzes the O-acetylation of PG in Gram (-) bacteria, which aids in bacterial survival, as it prevents autolysins such as lysozyme from cleaving the PG. We explored the mechanistic details of PatB's acetylation function and determined that PatB has substrate specificity for bioorthgonal short N-acetyl cysteamine (SNAc) donors. A variety of functionality including azides and alkynes were installed on tri-N-acetylglucosamine (NAG)3, a PG mimic, as well as PG isolated from various Gram (+) and Gram (-) bacterial species. The bioorthogonal modifications protect the isolated PG against lysozyme degradation in vitro. We further demonstrate that this postsynthetic modification of PG can be extended to use click chemistry to fluorescently label the mature PG in whole bacterial cells of Bacillus subtilis. Modifying PG postsynthetically can aid in the development of antibiotics and immune modulators by expanding the understanding of how PG is processed by lytic enzymes.

One-Step Transformation of Coenzyme A into Analogues by Transamidation

Several coenzyme A (CoA) analogues are made in a single step under mild conditions via transamidation reactions catalyzed by boric acid in water. This approach offers rapid access to compounds useful for the study of a wide spectrum of enzyme catalyzed reactions, especially processes involving acyl carrier proteins (ACP) of polyketide synthases (PKS), fatty acid synthases (FAS), and nonribosomal peptide synthetases (NRPS). The CoA analogues presented are readily elaborated or extended by precedented reactions for specific applications that may be required.

Biomimetic Thioesters as Probes for Enzymatic Assembly Lines: Synthesis, Applications, and Challenges

Thioesters play essential roles in many biosynthetic pathways to fatty acids, esters, polyketides, and non-ribosomal peptides. Coenzyme A (CoA) and related phosphopantetheine thioesters are typically employed as activated acyl units for diverse C-C, C-O, and C-N coupling reactions. To study and control these enzymatic assembly lines in vitro and in vivo structurally simplified analogs such as N-acetylcysteamine (NAC) thioesters have been developed. This review gives an overview on experimental strategies enabled by synthetic NAC thioesters, such as the elucidation of complex biosynthetic pathways and enzyme mechanisms as well as precursor-directed biosynthesis and mutasynthesis. The review also summarizes synthetic protocols and protection group strategies to access these versatile synthetic tools, which are reactive and often unstable compounds. In addition, alternative phosphopantetheine thioester mimics are presented that can be used as protein tags or suicide inhibitors for protein crosslinking and off-loading probes to elucidate polyketide intermediates.

Signal-on CoA-dependent electrochemical biosensor for highly sensitive and label-free detection of Citrate synthase activity

We report here a label-free and sensitive electrochemical method for probing Citrate synthase (CS) activity based on detailed investigations into the nucleic acid-mimicking coordination polymer (CP) formed from the coenzyme A (CoA)-Ag(I) repeat units. Our biosensing approach provides an especial and significant detection mechanism: CS can catalyze the essential condensation reaction between acetyl-coenzyme A (Ac-CoA) and oxaloacetate (OAA) to form citrate and CoA; then, in the presence of Ag(I), CoA-Ag(I) CP can be in situ formed because of the strong complexation ability of thiol groups of CoA toward Ag(I). The generated CoA-Ag(I) CP attaches to graphene-modified glassy carbon electrode surface by multiple adenine bases deriving from CoA and acting as the side groups along the polymeric backbone, which displays efficient H₂O₂-electrocatalyzing activity. More importantly, by using the formed polymer as signal output, the process is implemented to quantitatively analyze the activity of CS. Under the optimal conditions, CS with a detection limit as low as 0.00165U/µL could be sensitively probed with a wide linear range from 0.0033 to 0.264U/µL. Furthermore, with the character of label-free detection, high sensitivity and excellent selectivity, this strategy offers a convenient and specific method for CS activity detection and relevant inhibitors screening, which holds a promising potential in the practical application of CS-based biochemical research, disease diagnosis and drug discovery.

Unique electrocatalytic activity of a nucleic acid-mimicking coordination polymer for the sensitive detection of coenzyme A and histone acetyltransferase activity

A nucleic acid-mimicking CoA-Ag(I) coordination polymer (CP) was in situ prepared and its unique electrocatalytic activity to H2O2 reduction was discovered. Based on it, a novel, label-free electrochemical sensor has been developed for the sensitive detection of coenzyme A (CoA) and histone acetyltransferase (HAT) activity.

A Chemo-Enzymatic Road Map to the Synthesis of CoA Esters

Coenzyme A (CoA) is a ubiquitous cofactor present in every known organism. The thioesters of CoA are core intermediates in many metabolic processes, such as the citric acid cycle, fatty acid biosynthesis and secondary metabolism, including polyketide biosynthesis. Synthesis of CoA-thioesters is vital for the study of CoA-dependent enzymes and pathways, but also as standards for metabolomics studies. In this work we systematically tested five chemo-enzymatic methods for the synthesis of the three most abundant acyl-CoA thioester classes in biology; saturated acyl-CoAs, α,β-unsaturated acyl-CoAs (i.e., enoyl-CoA derivatives), and α-carboxylated acyl-CoAs (i.e., malonyl-CoA derivatives). Additionally we report on the substrate promiscuity of three newly described acyl-CoA dehydrogenases that allow the simple conversion of acyl-CoAs into enoyl-CoAs. With these five methods, we synthesized 26 different CoA-thioesters with a yield of 40% or higher. The CoA esters produced range from short- to long-chain, include branched and α,β-unsaturated representatives as well as other functional groups. Based on our results we provide a general guideline to the optimal synthesis method of a given CoA-thioester in respect to its functional group(s) and the commercial availability of the precursor molecule. The proposed synthetic routes can be performed in small scale and do not require special chemical equipment, making them convenient also for biological laboratories.

Systematic Mutational Analysis of Histidine Kinase Genes in the Nosocomial Pathogen Stenotrophomonas maltophilia Identifies BfmAK System Control of Biofilm Development

The Gram-negative bacterium Stenotrophomonas maltophilialives in diverse ecological niches. As a result of its formidable capabilities of forming biofilm and its resistance to multiple antibiotic agents, the bacterium is also a nosocomial pathogen of serious threat to the health of patients whose immune systems are suppressed or compromised. Besides the histidine kinase RpfC, the two-component signal transduction system (TCS), which is the canonical regulatory machinery used by most bacterial pathogens, has never been experimentally investigated inS. maltophilia Here, we annotated 62 putative histidine kinase genes in the S. maltophilia genome and successfully obtained 51 mutants by systematical insertional inactivation. Phenotypic characterization identified a series of mutants with deficiencies in bacterial growth, swimming motility, and biofilm development. A TCS, named here BfmA-BfmK (Smlt4209-Smlt4208), was genetically confirmed to regulate biofilm formation inS. maltophilia Together with interacting partner prediction and chromatin immunoprecipitation screens, six candidate promoter regions bound by BfmA in vivo were identified. We demonstrated that, among them, BfmA acts as a transcription factor that binds directly to the promoter regions of bfmA-bfmK and Smlt0800(acoT), a gene encoding an acyl coenzyme A thioesterase that is associated with biofilm development, and positively controls their transcription. Genome-scale mutational analyses of histidine kinase genes and functional dissection of BfmK-BfmA regulation in biofilm provide genetic information to support more in-depth studies on cellular signaling inS. maltophilia, in the context of developing novel approaches to fight this important bacterial pathogen.

Synthesis of coenzyme A thioesters using methyl acyl phosphates in an aqueous medium

Regioselective S-acylation of coenzyme A (CoA) is achieved under aqueous conditions using various aliphatic and aromatic carboxylic acids activated as their methyl acyl phosphate monoesters. Unlike many hydrophobic activating groups, the anionic methyl acyl phosphate mixed anhydride is more compatible with aqueous solvents, making it useful for conducting acylation reactions in an aqueous medium.

Inhibitors of polyhydroxyalkanoate (PHA) synthases: synthesis, molecular docking, and implications

Polyhydroxyalkanoate (PHA) synthases (PhaCs) catalyze the formation of biodegradable PHAs that are considered to be ideal alternatives to non-biodegradable synthetic plastics. However, study of PhaCs has been challenging because the rate of PHA chain elongation is much faster than that of initiation. This difficulty, along with lack of a crystal structure, has become the main hurdle to understanding and engineering PhaCs for economical PHA production. Here we report the synthesis of two carbadethia CoA analogues--sT-CH2-CoA (26 a) and sTet-CH2-CoA (26 b)--as well as sT-aldehyde (saturated trimer aldehyde, 29), as new PhaC inhibitors. Study of these analogues with PhaECAv revealed that 26 a/b and 29 are competitive and mixed inhibitors, respectively. Both the CoA moiety and extension of PHA chain will increase binding affinity; this is consistent with our docking study. Estimation of the Kic values of 26 a and 26 b predicts that a CoA analogue incorporating an octameric hydroxybutanoate (HB) chain might facilitate the formation of a kinetically well-behaved synthase.

Smart core-shell microgel support for acetyl coenzyme A synthetase: a step toward efficient synthesis of polyketide-based drugs

The flexibility in tuning the structure and charge properties of PNIPAm microgels during their synthesis makes them a suitable choice for various biological applications. Two-step free radical polymerization, a common method employed for synthesis of core-shell microgel has been well adopted to obtain cationic poly(N-isopropylacrylamide-aminoethyl methacrylate) (PNIPAm-AEMA) shell and PNIPAm core. Scanning electron microscopy (SEM), dynamic light scattering (DLS), zeta potential, and ninhydrin assay suggests nearly monodispersed particles of cationic nature. Amino groups on the microgel provides suitable attachment point for covalent immobilization of acetyl coenzyme A synthetase (Acs) via 1-ethyl-3-(3-N,N- dimethylaminopropyl) carbodiimide (EDC) chemistry. On immobilization, 61.55% of initial activity of Acs has been retained, while Michaelis-Menten kinetics of the immobilized Acs indicates identical K(m) (Michaelis constant) but decrease in the V(max) (maximum substrate conversion rate) compared to free enzyme. Immobilized Acs shows an improvement in activity at wide temperature and pH range and also demonstrates good thermal, storage, and operational stability. The Acs-microgel bioconjugate has been successfully reused for four consecutive operation cycles with more than 50% initial activity.

Synthesis of complex intermediates for the study of a dehydratase from borrelidin biosynthesis

Herein, we describe the syntheses of a complex biosynthesis-intermediate analogue of the potent antitumor polyketide borrelidin and of reference molecules to determine the stereoselectivity of the dehydratase of borrelidin polyketide synthase module 3. The target molecules were obtained from a common precursor aldehyde in the form of N-acetylcysteamine (SNAc) thioesters and methyl esters in 13 to 15 steps. Key steps for the assembly of the polyketide backbone of the dehydratase substrate analogue were a Yamamoto asymmetric carbocyclisation and a Sakurai allylation as well as an anti-selective aldol reaction. Reference compounds representing the E- and Z-configured double bond isomers as potential products of the dehydratase reaction were obtained from a common precursor aldehyde by Wittig olefination and Still–Gennari olefination. The final deprotection of TBS ethers and methyl esters was performed under mildly acidic conditions followed by pig liver esterase-mediated chemoselective hydrolysis. These conditions are compatible with the presence of a coenzyme A or a SNAc thioester, suggesting that they are generally applicable to the synthesis of complex polyketide-derived thioesters suited for biosynthesis studies.

Metabolic perturbation of an essential pathway: evaluation of a glycine precursor of coenzyme A

Pantetheine and its corresponding disulfide pantethine play a key role in metabolism as building blocks of coenzyme A (CoA), an essential cofactor utilized in ~4% of primary metabolism and central to fatty acid, polyketide, and nonribosomal peptide synthases. Using a combination of recombinant engineering and chemical synthesis, we show that the disulfide of N-pantoylglycyl-2-aminoethanethiol (GlyPan), with one fewer carbon than pantetheine, can rescue a mutant E. coli strain MG1655ΔpanC lacking a functional pantothenate synthetase. Using mass spectrometry, we show that the GlyPan variant is accepted by the downstream CoA biosynthetic machinery, ultimately being incorporated into essential acyl carrier proteins. These findings point to further flexibility in CoA-dependent pathways and offer the opportunity to incorporate orthogonal analogues.

Inhibitors of aminoglycoside resistance activated in cells

The most common mechanism of resistance to aminoglycoside antibiotics entails bacterial expression of drug-metabolizing enzymes, such as the clinically widespread aminoglycoside N-6'-acetyltransferase (AAC(6')). Aminoglycoside-CoA bisubstrates are highly potent AAC(6') inhibitors; however, their inability to penetrate cells precludes in vivo studies. Some truncated bisubstrates are known to cross cell membranes, yet their activities against AAC(6') are in the micromolar range at best. We report here the synthesis and biological activity of aminoglycoside-pantetheine derivatives that, although devoid of AAC(6') inhibitory activity, can potentiate the antibacterial activity of kanamycin A against an aminoglycoside-resistant strain of Enterococcus faecium. Biological studies demonstrate that these molecules are potentially extended to their corresponding full-length bisubstrates by enzymes of the coenzyme A biosynthetic pathway. This work provides a proof-of-concept for the utility of prodrug compounds activated by enzymes of the coenzyme A biosynthetic pathway, to resensitize resistant strains of bacteria to aminoglycoside antibiotics.

Mechanism of the intramolecular Claisen condensation reaction catalyzed by MenB, a crotonase superfamily member

MenB, the 1,4-dihydroxy-2-naphthoyl-CoA synthase from the bacterial menaquinone biosynthesis pathway, catalyzes an intramolecular Claisen condensation (Dieckmann reaction) in which the electrophile is an unactivated carboxylic acid. Mechanistic studies on this crotonase family member have been hindered by partial active site disorder in existing MenB X-ray structures. In the current work the 2.0 Å structure of O-succinylbenzoyl-aminoCoA (OSB-NCoA) bound to the MenB from Escherichia coli provides important insight into the catalytic mechanism by revealing the position of all active site residues. This has been accomplished by the use of a stable analogue of the O-succinylbenzoyl-CoA (OSB-CoA) substrate in which the CoA thiol has been replaced by an amine. The resulting OSB-NCoA is stable, and the X-ray structure of this molecule bound to MenB reveals the structure of the enzyme-substrate complex poised for carbon-carbon bond formation. The structural data support a mechanism in which two conserved active site Tyr residues, Y97 and Y258, participate directly in the intramolecular transfer of the substrate α-proton to the benzylic carboxylate of the substrate, leading to protonation of the electrophile and formation of the required carbanion. Y97 and Y258 are also ideally positioned to function as the second oxyanion hole required for stabilization of the tetrahedral intermediate formed during carbon-carbon bond formation. In contrast, D163, which is structurally homologous to the acid-base catalyst E144 in crotonase (enoyl-CoA hydratase), is not directly involved in carbanion formation and may instead play a structural role by stabilizing the loop that carries Y97. When similar studies were performed on the MenB from Mycobacterium tuberculosis, a twisted hexamer was unexpectedly observed, demonstrating the flexibility of the interfacial loops that are involved in the generation of the novel tertiary and quaternary structures found in the crotonase superfamily. This work reinforces the utility of using a stable substrate analogue as a mechanistic probe in which only one atom has been altered leading to a decrease in α-proton acidity.

Synthesis of 4'-aminopantetheine and derivatives to probe aminoglycoside N-6'-acetyltransferase

A convenient synthesis of 4'-aminopantetheine from commercial D-pantethine is reported. The amino group was introduced by reductive amination in order to avoid substitution at a sterically congested position. Derivatives of 4'-aminopantetheine were also prepared to evaluate the effect of O-to-N substitution on inhibitors of the resistance-causing enzyme aminoglycoside N-6'-acetyltransferase. The biological results combined with docking studies indicate that in spite of its reported unusual flexibility and ability to adopt different folds, this enzyme is highly specific for AcCoA.

A mechanism based protein crosslinker for acyl carrier protein dehydratases

Recent advances in the structural study of fatty acid synthase (FAS) and polyketide synthase (PKS) biosynthetic enzymes have illuminated our understanding of modular enzymes of the acetate pathway. However, one significant and persistent challenge in such analyses is resolution of the acyl carrier protein (ACP), a small (approximately 9 kDa) protein to which biosynthetic intermediates are tethered throughout the biosynthetic cycle. Here we report a chemoenzymatic crosslinking strategy in which the installation of a historical suicide substrate scaffold upon the 4'-phosphopantetheine (PPant) arm of the ACP is used to capture the active site of acyl carrier protein dehydratase (DH) domains in FAS. Through the synthesis of a small panel of related probes we identify structural features essential for ACP-DH crosslinking, and apply gel-based assays to demonstrate the stability as well as purification strategies for isolation of the chemoenzymatically modified ACP. Applying these carrier protein crosslinking techniques to the structural analysis of FAS and PKS complexes has the potential to provide snapshots of these biosynthetic assembly lines at work.

Malonyl carba(dethia)- and malonyl oxa(dethia)-coenzyme A as tools for trapping polyketide intermediates

In order to study intermediates in polyketide biosynthesis two nonhydrolyzable malonyl coenzyme A analogues were synthesised by a chemoenzymatic route. In these analogues the sulfur atom of CoA was replaced either by a methylene group (carbadethia analogue) or by an oxygen atom (oxadethia analogue). These malonyl-CoA analogues were found to compete with the natural extender unit malonyl-CoA and to trap intermediates from stilbene synthase, a type III polyketide synthase (PKS). From the reaction of stilbene synthase with its natural phenylpropanoid substrates, diketide, triketide and tetraketide species were successfully off-loaded and characterised by LC-MS. Moreover, the reactivity of the nonhydrolyzable analogues offers insights into the flexibility of substrate alignment in the PKS active site for efficient malonyl decarboxylation and condensation.

Phosphopantetheinyl transferase catalyzed site-specific protein labeling with ADP conjugated chemical probes

Phosphopantetheinyl transferase (PPTase) catalyzed protein modification has been demonstrated as an efficient method for site specific protein labeling with small molecules of diverse structures. Previously coenzyme A conjugated small molecule probes have been used as the substrates of PPTase for the covalent attachment of the probes to a specific Ser residue in the carrier proteins or short peptide tags through a phosphopantetheinyl linkage. Here we discovered that small molecules directly conjugated to the 5'-diphosphate moiety of ADP can serve as the substrates of a mutant Sfp PPTase, R4-4. Based on this, we used R4-4 to transfer small molecule labels to the carrier protein or peptide tags fused to the target protein through structurally simplified synthetic linkers. The synthesis of ADP conjugated small molecule probes can be easily accomplished by one-step coupling between phosphate derivatized probes and morpholidate-activated AMP. The use of ADP-small molecule conjugates for PPTase catalyzed protein labeling would further expand the structural and functional diversity of the chemical probes attached to the target protein to elucidate or engineer their biological activities.

Catalytic turnover-based phage selection for engineering the substrate specificity of Sfp phosphopantetheinyl transferase

We report a high-throughput phage selection method to identify mutants of Sfp phosphopantetheinyl transferase with altered substrate specificities from a large library of the Sfp enzyme. In this method, Sfp and its peptide substrates are co-displayed on the M13 phage surface as fusions to the phage capsid protein pIII. Phage-displayed Sfp mutants that are active with biotin-conjugated coenzyme A (CoA) analogues would covalently transfer biotin to the peptide substrates anchored on the same phage particle. Affinity selection for biotin-labeled phages would enrich Sfp mutants that recognize CoA analogues for carrier protein modification. We used this method to successfully change the substrate specificity of Sfp and identified mutant enzymes with more than 300-fold increase in catalytic efficiency with 3'-dephospho CoA as the substrate. The method we developed in this study provides a useful platform to display enzymes and their peptide substrates on the phage surface and directly couples phage selection with enzyme catalysis. We envision this method to be applied to engineering the catalytic activities of other protein posttranslational modification enzymes.