Acid Thioesters Research Articles

An Enantioselective Decarboxylative Glycolate Aldol Reaction.

Herein, we report the application of a benzyloxy-functionalized malonic acid half thioester as an activated ester equivalent in a highly enantioselective decarboxylative glycolate aldol reaction. This robust method operates at ambient temperature, tolerates air and moisture, and generates CO2 as the only byproduct. The synthetic applicability of the method is demonstrated by the large-scale enantiodivergent synthesis of α-benzyloxy-β-hydroxybutyric acid thioester and its subsequent conversion to diverse polyoxygenated building blocks, deoxy-sugars, and (-)-angiopterlactone B.

Synthesis of Acyl Halides from Carboxylic Acid Thioesters for Synthesis of Ketones, Esters, Amides and Peptides

AbstractA synthesis of acyl halides from the corresponding carboxylic acid thioesters was achieved using commercially available Selectfluor or NCS, and the acyl fluoride or chloride intermediates were transformed to the corresponding esters, amides, and several carbon‐carbon bond formation products. This approach can be applied to the peptide synthesis from functionalized amino acid thioesters.

Direct α‐Hydroxy Acid Loading onto a Bacterial Thiotemplate Assembly Line via a Multienzyme Gateway

AbstractVarious nonribosomal peptide synthetases (NRPSs) create structural and functional diversity by incorporating α‐hydroxy acids into peptide backbones. Trigonic acid, an unusual cyclopropanol‐substituted hydroxy acid, is the source of the molecular warhead of malleicyprol, a critical virulence factor of human and animal pathogens of the Burkholderia pseudomallei (BP) group. The process of selecting and loading this building block remained enigmatic as the NRPS module designated for this task is incomplete. Using a combination of bioinformatics, mutational analyses, targeted metabolomics, and in vitro biochemical assays, we show that two trans‐acting enzymes are required to load this central building block onto the modular assembly line. An adenylation‐thiolation didomain enzyme (BurJ) activates trigonic acid, followed by the translocation of the enzyme‐bound α‐hydroxy acid thioester by an FkbH‐like protein with a mutated phosphatase domain (BurH). This specialized gateway is the first reported direct loading of an α‐hydroxy acid onto a bona fide NRPS module in bacteria and expands the synthetic biology toolbox for the site‐specific incorporation of non‐canonical building blocks. Moreover, insight into the biochemical basis of virulence factor biosynthesis can provide a foundation for developing enzyme inhibitors as anti‐virulence therapeutics against BP pathogen infections.

Direct α-Hydroxy Acid Loading onto a Bacterial Thiotemplate Assembly Line via a Multienzyme Gateway.

Various nonribosomal peptide synthetases (NRPSs) create structural and functional diversity by incorporating α-hydroxy acids into peptide backbones. Trigonic acid, an unusual cyclopropanol-substituted hydroxy acid, is the source of the molecular warhead of malleicyprol, a critical virulence factor of human and animal pathogens of the Burkholderia pseudomallei (BP) group. The process of selecting and loading this building block remained enigmatic as the NRPS module designated for this task is incomplete. Using a combination of bioinformatics, mutational analyses, targeted metabolomics, and in vitro biochemical assays, we show that two trans-acting enzymes are required to load this central building block onto the modular assembly line. An adenylation-thiolation didomain enzyme (BurJ) activates trigonic acid, followed by the translocation of the enzyme-bound α-hydroxy acid thioester by an FkbH-like protein with a mutated phosphatase domain (BurH). This specialized gateway is the first reported direct loading of an α-hydroxy acid onto a bona fide NRPS module in bacteria and expands the synthetic biology toolbox for the site-specific incorporation of non-canonical building blocks. Moreover, insight into the biochemical basis of virulence factor biosynthesis can provide a foundation for developing enzyme inhibitors as anti-virulence therapeutics against BP pathogen infections.

Nickel-Catalyzed Decarbonylation of α-Oxyacetic Acid Thioesters: Hydroxymethylation of Mercaptans

AbstractA strategy for the Ni-catalyzed decarbonylation of α-oxyacetic acid thioesters is described, providing a new pathway for the synthesis of monosulfide acetals, and further proving that oxygen atoms can stabilize an α-carbocation and promote a decarbonylation reaction. This method has good functional-group compatibility and can tolerate a wide range of electron-withdrawing, electron-neutral, and electron-donating substituents. In addition, this method complements the conventional cross-coupling reactions.

Lithio Tris(methylthio)methane as Hydroxy/Thio/Aminocarbonyl Anion Equivalent: Asymmetric Synthesis of α-Amino Acid Esters, Thioesters, Amides, and Peptides.

The use of lithio tris(methylthio)methane as a hydroxy/thio/amino carbonyl anion equivalent in the synthesis of α-amino acids is reported. Addition of the reagent to nonracemic sulfinimines furnished the α-sulfinamido trithioformates in excellent diastereoselectivity. Unmasking the trithioformates to diverse functionalities, such as α-amino acid thioesters, esters, anilides, amides, and di/tri peptides, without epimerization of chiral centers was accomplished.

Structure-Based Analysis of Transient Interactions between Ketosynthase-like Decarboxylase and Acyl Carrier Protein in a Loading Module of Modular Polyketide Synthase.

Ketosynthase-like decarboxylase (KSQ) domains are widely distributed in the loading modules of modular type I polyketide synthases (PKSs) and catalyze the decarboxylation of the (alkyl-)malonyl unit bound to the acyl carrier protein (ACP) in the loading module for the construction of the PKS starter unit. Previously, we performed a structural and functional analysis of the GfsA KSQ domain involved in the biosynthesis of macrolide antibiotic FD-891. We furthermore revealed the recognition mechanism for the malonic acid thioester moiety of the malonyl-GfsA loading module ACP (ACPL) as a substrate. However, the exact recognition mechanism for the GfsA ACPL moiety remains unclear. Here, we present a structural basis for the interactions between the GfsA KSQ domain and GfsA ACPL. We determined the crystal structure of the GfsA KSQ-acyltransferase (AT) didomain in complex with ACPL (ACPL=KSQAT complex) by using a pantetheine crosslinking probe. We identified the key amino acid residues involved in the KSQ domain-ACPL interactions and confirmed the importance of these residues by mutational analysis. The binding mode of ACPL to the GfsA KSQ domain is similar to that of ACP to the ketosynthase domain in modular type I PKSs. Furthermore, comparing the ACPL=KSQAT complex structure with other full-length PKS module structures provides important insights into the overall architectures and conformational dynamics of the type I PKS modules.

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.

Evolution of Proliferative Model Protocells Highly Responsive to the Environment.

In this review, we discuss various methods of reproducing life dynamics using a constructive approach. An increase in the structural complexity of a model protocell is accompanied by an increase in the stage of reproduction of a compartment (giant vesicle; GV) from simple reproduction to linked reproduction with the replication of information molecules (DNA), and eventually to recursive proliferation of a model protocell. An encounter between a plural protic catalyst (C) and DNA within a GV membrane containing a plural cationic lipid (V) spontaneously forms a supramolecular catalyst (C@DNA) that catalyzes the production of cationic membrane lipid V. The local formation of V causes budding deformation of the GV and equivolume divisions. The length of the DNA strand influences the frequency of proliferation, associated with the emergence of a primitive information flow that induces phenotypic plasticity in response to environmental conditions. A predominant protocell appears from the competitive proliferation of protocells containing DNA with different strand lengths, leading to an evolvable model protocell. Recently, peptides of amino acid thioesters have been used to construct peptide droplets through liquid–liquid phase separation. These droplets grew, owing to the supply of nutrients, and were divided repeatedly under a physical stimulus. This proposed chemical system demonstrates a new perspective of the origins of membraneless protocells, i.e., the “droplet world” hypothesis. Proliferative model protocells can be regarded as autonomous supramolecular machines. This concept of this review may open new horizons of “evolution” for intelligent supramolecular machines and robotics.

Combinatorial Optimization of Activity-Based Probes for Acyl Protein Thioesterases 1 and 2.

Acyl protein thioesterases hydrolyze fatty acid thioesters on cysteine residues of proteins. The two protein depalmitoylases APT1 and APT2 have a very high degree of similarity and show substantial overlap in substrate utility. Potent, selective, and cell-permeable activity-based probes are needed to study the role of these enzymes. Here, we employ solid-phase synthesis to create a library of covalent probes based on a triazole urea-reactive electrophile, leading to several potent and cell-permeable probes of human APT1/2. We demonstrate that inhibition of APT1/2 in cells does not have an effect on steady-state levels of protein palmitoylation, implying that substrates hydrolyzed by APT1/2 can also be hydrolyzed by other protein depalmitoylases.

Palladium-Catalyzed Regiodivergent Decarboxylative Hydrothiocarbonylation of Vinylarenes Using Oxalic Acid Monothioesters

AbstractOxalic acid monothioester (OAM), an easily accessible and bench-stable reagent, is reported herein as a synthetic equivalent of thioester for palladium-catalyzed decarboxylative hydrothiocarbonylation of vinylarenes to achieve both branched and linear regioselectivity. The reactions provided user-friendly synthetic methods for preparation of α- or β-arylated propionic acid thioesters from vinylarenes without directly handling toxic carbon monoxide and odorous thiols.

Site-Selective Antibody-Drug Conjugation by a Proximity-Driven S to N Acyl Transfer Reaction on a Therapeutic Antibody.

Immunoglobulin Gs (IgGs) contain many Lys and Cys residues, which results in an unwanted complex product mixture with conventional drug conjugation methods. We selectively acylated the ε-NH2 of K248 on trastuzumab using an IgG Fc-binding peptide (FcBP) equipped with a 5-norbornene-2-carboxylic acid thioester (AbClick-1). AbClick-1 locates its thioester close to the ε-NH2 of K248 while binding to trastuzumab. Consequently, the thioester underwent proximity-driven selective acylation of ε-NH2 through an S to N acyl transfer reaction. Furthermore, N-tert-butyl maleimide accelerated the cross-linking reaction with an approximately 95% yield of the desired product by scavenging the byproduct (FcBP-SH). Only K248 was modified selectively with the 5-norbornene-2-carbonyl group, which was further modified by click reaction to afford an antibody-drug conjugate (ADC) with two drugs per antibody. The resulting ADCs showed remarkable in vitro and in vivo anticancer activity. Our results demonstrate that a thioester is a promising chemical entity for proximity-driven site-selective conjugation of antibodies.

Proliferating coacervate droplets as the missing link between chemistry and biology in the origins of life

The hypothesis that prebiotic molecules were transformed into polymers that evolved into proliferating molecular assemblages and eventually a primitive cell was first proposed about 100 years ago. To the best of our knowledge, however, no model of a proliferating prebiotic system has yet been realised because different conditions are required for polymer generation and self-assembly. In this study, we identify conditions suitable for concurrent peptide generation and self-assembly, and we show how a proliferating peptide-based droplet could be created by using synthesised amino acid thioesters as prebiotic monomers. Oligopeptides generated from the monomers spontaneously formed droplets through liquid–liquid phase separation in water. The droplets underwent a steady growth–division cycle by periodic addition of monomers through autocatalytic self-reproduction. Heterogeneous enrichment of RNA and lipids within droplets enabled RNA to protect the droplet from dissolution by lipids. These results provide experimental constructs for origins-of-life research and open up directions in the development of peptide-based materials.

Nickel-Catalyzed Selective Decarbonylation of α-Amino Acid Thioester: Aminomethylation of Mercaptans.

The nickel-catalyzed aminomethylation of mercaptans has been disclosed that offers efficient and expedient access to synthesize α-aminosulfides. The intramolecular fragment coupling shows excellent chemoselectivity. This transformation shows good functional-group compatibility, tolerates a wide range of electron-withdrawing, electron-neutral, and electron-donating substituents in this process, and can serve as a powerful synthetic tool for the synthesis of α-aminosulfides at a gram scale. Thus, the newly developed methodology enables a facile route for C-S bond formation in a straightforward fashion.

Structural Basis of Specificity for Carboxyl-Terminated Acyl Donors in a Bacterial Acyltransferase.

Macrolactins (MLNs) are a class of important antimacular degeneration and antitumor agents. Malonylated/succinylated MLNs are even more important due to their efficacy in overcoming multi-drug-resistant bacteria. However, which enzyme catalyzes this reaction remains enigmatic. Herein, we deciphered a β-lactamase homologue BmmI to be responsible for this step. BmmI could specifically attach C3-C5 alkyl acid thioesters onto 7-OH of MLN A and also exhibits substrate promiscuity toward acyl acceptors with different scaffolds. The crystal structure of BmmI covalently linked to the succinyl group and systematic mutagenesis highlighted the role of oxyanion holelike geometry in the recognition of carboxyl-terminated acyl donors. The engineering of this geometry expanded its substrate scope, with the R166A/G/Q variants recognizing up to C12 alkyl acid thioester. The structure of BmmI with acyl acceptor MLN A revealed the importance of Arg292 in the recognition of macrolide substrates. Moreover, the mechanism of the BmmI-catalyzed acyltransfer reaction was established, unmasking the deft role of Lys76 in governing acyl donors as well as catalysis. Our studies uncover the delicate mechanism underlying the substrate selectivity of acyltransferases, which would guide rational enzyme engineering for drug development.

Synthesis of benzyl sulfidesviasubstitution reaction at the sulfur of phosphinic acid thioesters

An ambident electrophilicity of phosphinic acid thioesters is disclosed. Unexpected carbon-sulfur bond formation took place in the reaction between phosphinic acid thioesters and benzyl Grignard reagents. The developed method for benzyl sulfides has a wide substrate scope and was applicable for the synthesis of a drug analog.

Amino Acid Thioesters Exhibit Inhibitory Activity against B1-B3 Subclasses of Metallo-β-lactamases.

Superbug infection caused by metallo-β-lactamases (MβLs) is a global public health threat. Previous studies reported that the thioesters specifically inhibited the B3 subclass MβL L1. In this work, nine amino acid thioesters 1-9 were synthesized, the activity evaluation revealed that all of these molecules exhibited broad-spectrum inhibitory efficacy against ImiS, IMP-1, NDM-1, and L1, with IC50 values range of 0.02-54.9 µM (except 5 and 7 on NDM-1), and 1 was found to be the best inhibitor with IC50 range of 0.02-16.63 µM. Minimal inhibitory concentration (MIC) assays showed that thioesters 1, 5 and 9 restored 2-32-fold antibacterial activity of cefazolin and/or imipenem against both Escherichia coli BL21 and DH10B strain expressing ImiS, L1, IMP-1 and NDM-1 (except 5 on NDM-1), and also, thioester 1 increased 2-4-fold antimicrobial activity of cefazolin on two clinical strains Pseudomonas aeruginosa and Klebsiella pneumoniae producing NDM-1. Stability evaluation indicated that thioester 1 was partially hydrolysed by MβLs to be converted into the mercaptoacetic acid, revealing that the thioester and its hydrolysate mercaptoacetic acid jointly inhibit MβLs. Isothermal titration calorimetry (ITC) monitoring showed that thioester 1 exhibited dose-dependent inhibition on four MβLs tested, and the binding of 1/L1 showed mainly enthalpy driven, while 1/NDM-1 was found to be more entropy driven. Docking studies suggested that 1 bound to Zn(II) ion(s) preferentially via its carboxylate group, while other moieties interacted mostly with the conserved active site residues.

Metal-Binding Pharmacophore Library Yields the Discovery of a Glyoxalase 1 Inhibitor.

Anxiety and depression are common, highly comorbid psychiatric diseases that account for a large proportion of worldwide medical disability. Glyoxalase 1 (GLO1) has been identified as a possible target for the treatment of anxiety and depression. GLO1 is a Zn2+-dependent enzyme that isomerizes a hemithioacetal, formed from glutathione and methylglyoxal, to a lactic acid thioester. To develop active inhibitors of GLO1, fragment-based drug discovery was used to identify fragments that could serve as core scaffolds for lead development. After screening a focused library of metal-binding pharmacophores, 8-(methylsulfonylamino)quinoline (8-MSQ) was identified as a hit. Through computational modeling and synthetic elaboration, a potent GLO1 inhibitor was developed with a novel sulfonamide core pharmacophore. A lead compound was demonstrated to penetrate the blood-brain barrier, elevate levels of methylglyoxal in the brain, and reduce depression-like behavior in mice. These findings provide the basis for GLO1 inhibitors to treat depression and related psychiatric illnesses.

Variances in cellular sedimentation behavior as an effective enrichment method of hydrocarbon-overproducing Micrococcus luteus strains

BackgroundAliphatic hydrocarbons of microbial origin are highly interesting candidate biofuels because these molecules are identical or very similar to the main components of petroleum-based gasoline and diesel fuels. The high-GC Gram-positive bacterium Micrococcus luteus is capable of naturally synthesizing long-chain, iso- and anteiso-branched alkenes which are formed via the head-to-head condensation of fatty acid thioesters by a dedicated enzyme system. The present study describes the relation we observed between olefin production and cell buoyancy in Micrococcus luteus and the use of this phenotype to simply and efficiently separate cells from a mixture based on their hydrocarbon content.MethodsWe generated M. luteus mutants producing different amounts of olefins and used them in mixing and sedimentation experiments, olefin content analysis by GC-MS and in equilibrium centrifugation in Percoll gradients.ResultsWe found well-detectable differences in the buoyant densities of the examined strains, which correlated with the amounts of hydrocarbons produced by the cells. We also demonstrate how our observations can be used to simply and efficiently fractionate cells based on their hydrocarbon content.ConclusionsIn summary, we show that cultures of M. luteus cells sediment at distinct rates depending on the amounts of alkenes produced. Our results indicate that buoyant cell density is the primary cause for the observed differences in sedimentation behaviour. The simple separation strategy described here can be a valuable tool in various mutagenesis and enrichment protocols, aimed at generating and isolating strains with increased olefin productivity.

Acyl-group specificity of AHL synthases involved in quorum-sensing in Roseobacter group bacteria.

N-Acylhomoserine lactones (AHLs) are important bacterial messengers, mediating different bacterial traits by quorum sensing in a cell-density dependent manner. AHLs are also produced by many bacteria of the marine Roseobacter group, which constitutes a large group within the marine microbiome. Often, specific mixtures of AHLs differing in chain length and oxidation status are produced by bacteria, but how the biosynthetic enzymes, LuxI homologs, are selecting the correct acyl precursors is largely unknown. We have analyzed the AHL production in Dinoroseobacter shibae and three Phaeobacter inhibens strains, revealing strain-specific mixtures. Although large differences were present between the species, the fatty acid profiles, the pool for the acyl precursors for AHL biosynthesis, were very similar. To test the acyl-chain selectivity, the three enzymes LuxI1 and LuxI2 from D. shibae DFL-12 as well as PgaI2 from P. inhibens DSM 17395 were heterologously expressed in E. coli and the enzymes isolated for in vitro incubation experiments. The enzymes readily accepted shortened acyl coenzyme A analogs, N-pantothenoylcysteamine thioesters of fatty acids (PCEs). Fifteen PCEs were synthesized, varying in chain length from C4 to C20, the degree of unsaturation and also including unusual acid esters, e.g., 2E,11Z-C18:2-PCE. The latter served as a precursor of the major AHL of D. shibae DFL-12 LuxI1, 2E,11Z-C18:2-homoserine lactone (HSL). Incubation experiments revealed that PgaI2 accepts all substrates except C4 and C20-PCE. Competition experiments demonstrated a preference of this enzyme for C10 and C12 PCEs. In contrast, the LuxI enzymes of D. shibae are more selective. While 2E,11Z-C18:2-PCE is preferentially accepted by LuxI1, all other PCEs were not, except for the shorter, saturated C10–C14-PCEs. The AHL synthase LuxI2 accepted only C14 PCE and 3-hydroxydecanoyl-PCE. In summary, chain-length selectivity in AHLs can vary between different AHL enzymes. Both, a broad substrate acceptance and tuned specificity occur in the investigated enzymes.