Exploring chemoselective S-to-N acyl transfer reactions in synthesis and chemical biology

Novel enantiopure δ-thiolactones: synthesis, structural characterization, and reactivity studies

A new series of chiral δ-thiolactone derivatives have been prepared. These compounds exemplify the acetalic N-C-S reversibility of fused thiazolidines toward the thermodynamic product. The stereochemistry of the synthesized compounds was elucidated using X-ray crystallography, NOESY spectroscopy, and DFT calculations. The aminolysis reaction of the δ-thiolactone was studied with various alkyl amines, which can open the thioester to yield amido thiols in a single step. This reaction has the potential to be applied in the synthesis of bioactive compounds, polymer chemistry, and dynamic combinatorial chemistry, among others fields.

Recyclable Polythioesters and Poly(thioester-co-peptoid)s via Ring-Opening Cascade Polymerization of Amino Acid N-Carboxyanhydrides

Polythioesters (PTEs) are emerging sustainable polymers for their degradability and recyclability. However, low polymerizability of monomers and extensive side reactions often hampered the polymerization process. Moreover, copolymers containing both thioester and other types of functional groups in the backbone are highly desirable but rarely accomplished owing to several synthetic challenges. Here, we report the ring-opening cascade polymerization (ROCAP) of N-(2-(acetylthio)ethyl)-glycine N-carboxyanhydrides (TE-NCA) to afford recyclable PTEs and unprecedented poly(thioester-co-peptoid)s (P(TE-co-PP)s) in a controlled manner. By developing appropriated carboxylic acid-tertiary amine dual catalysts, intramolecular S-to-N acyl shift is coupled into the ROCAP process of TE-NCA to yield products with dispersity below 1.10, molecular weight (Mn) up to 84.5 kDa, and precisely controlled ratio of thioester to peptoids. Random copolymerization of sarcosine NCA (Sar-NCA) and TE-NCA gives thioester-embedded polysarcosine with facile backbone degradation while maintaining the water solubility. This work represents a paradigm shift for the ROP of NCAs, enriches the realm of cascade polymerizations, and provides a powerful synthetic approach to functional PTEs and P(TE-co-PP)s that are otherwise difficult or impossible to make.

Switching the Chemoselectivity in the Preparation of [18F]FNA-N-CooP, a Free Thiol-Containing Peptide for Targeted Positron Emission Tomography Imaging of Fatty Acid Binding Protein 3

Fatty acid binding protein 3 (FABP3) is expressed both in tumor cells and in the tumor vasculature, making it a potential target for medical imaging and therapy. In this study, we aimed to radiolabel a CooP peptide with a free amino and thiol group, and evaluate the radiolabeled product [18F]FNA-N-CooP for imaging FABP3 expression in breast cancer brain metastases by positron emission tomography. [18F]FNA-N-CooP was prepared by highly chemoselective N-acylation and characterized using different chemical approaches. We validated its binding to the target using in vitro tissue section autoradiography and performed stability tests in vitro and in vivo. [18F]FNA-N-CooP was successfully synthesized in 16.8% decay-corrected radiochemical yield with high radiochemical purity (98.5%). It exhibited heterogeneous binding on brain metastasis tissue sections from a patient with breast cancer, with foci of radioactivity binding corresponding to FABP3 positivity. Furthermore, the tracer binding was reduced by 55% in the presence of nonradioactive FNA-N-CooP a blocker, indicating specific tracer binding and that FABP3 is a viable target for [18F]FNA-N-CooP. Favorably, the tracer did not bind to necrotic tumor tissue. However, [18F]FNA-N-CooP displayed limited stability both in vitro in mouse plasma or human serum and in vivo in mouse, therefore further studies are needed to improve the stability [18F]FNA-N-CooP to be used for in vivo applications.

Azole reagents enabled ligation of peptide acyl pyrazoles for chemical protein synthesis

Native chemical ligation (NCL) has been playing an increasingly important role in chemical protein synthesis (CPS). More efficient ligation methods that circumvent the requirement of a peptidyl thioester and thiol additive-which allow the following desulfurization or refolding in one pot-are urgently needed for the synthesis of more complex protein targets and in large quantities. Herein, we discover that the weak acyl donor peptidyl N-acyl pyrazole can be activated by azole reagents like 3-methylpyrazole or imidazole to facilitate its ligation directly with an N-terminal cysteine peptide. As it requires no thioester or thiol additive, this ligation strategy can be conveniently combined with metal-free desulfurization (MFD) or oxidative protein folding to allow various one-pot protocols. The utility and generality of the strategy are showcased by the total synthesis of ubiquitin via an N-to-C sequential ligation-MFD strategy, the semi-synthesis of the copper protein azurin, and the efficient assembly of a sulfated hirudin variant and the cyclotide kalata B1, all in a one-pot fashion.

N-to-S Acyl Transfer as an Enabling Strategy in Asymmetric and Chemoenzymatic Synthesis

The observation of thioester-mediated acyl transfer processes in nature has inspired the development of novel protein synthesis and functionalization methodologies. The chemoselective transfer of an acyl group from S-to-N is the basis of several powerful ligation strategies. In this work, we sought to apply the reverse process, the transfer of an acyl group from N-to-S, as a method to convert stable chiral amides into more reactive thioesters. To this end, we developed a novel cysteine-derived oxazolidinone that serves as both a chiral imide auxiliary and an acyl transfer agent. This auxiliary combines the desirable features of rigid chiral imides as templates for asymmetric transformations with the synthetic applicability of thioesters. We demonstrate that the auxiliary can be applied in a range of highly selective asymmetric transformations. Subsequent intramolecular N-to-S acyl transfer of the chiral product and in situ trapping of the resulting thioester provides access to diverse carboxylic acid derivatives under mild conditions. The oxazolidinone thioester products can also be isolated and used in Pd-mediated transformations to furnish highly valuable chiral scaffolds, such as noncanonical amino acids, cyclic ketones, tetrahydropyrones, and dihydroquinolinones. Finally, we demonstrate that the oxazolidinone thioesters can also serve as a surrogate for SNAC-thioesters, enabling their seamless use as non-native substrates in biocatalytic transformations.

Engineered reactivity of a bacterial E1-like enzyme enables ATP-driven modification of protein C termini

In biological systems, ATP provides an energetic driving force for peptide bond formation, but protein chemists lack tools that emulate this strategy. Inspired by the eukaryotic ubiquitination cascade, we developed an ATP-driven platform for C-terminal activation and peptide ligation based on E. coli MccB, a bacterial ancestor of ubiquitin-activating (E1) enzymes that natively catalyzes C-terminal phosphoramidate bond formation. We show that MccB can act on non-native substrates to generate an O-AMPylated electrophile that can react with exogenous nucleophiles to form diverse C-terminal functional groups including thioesters, a versatile class of biological intermediates that have been exploited for protein semisynthesis. To direct this activity towards specific proteins of interest, we developed the Thioesterification C-terminal Handle (TeCH)-tag, a sequence that enables high-yield, ATP-driven protein bioconjugation via a thioester intermediate. By mining the natural diversity of the MccB family, we developed two additional MccB/TeCH-tag pairs that are mutually orthogonal to each other and to the E. coli system, facilitating the synthesis of more complex bioconjugates. Our method mimics the chemical logic of peptide bond synthesis that is widespread in biology for high-yield in vitro manipulation of protein structure with molecular precision.

Synthesis of Glycoconjugates through Chlorooxime-Thiol Conjugation

Introducing glycans represents an efficient chemical approach to improve the pharmacological properties of therapeutic biomolecules. Herein, we report an efficient synthesis of glycoconjugates through chlorooxime-thiol conjugation. The reactive glycosyl chlorooximes, derived from pyranoses or furanoses, readily couple to a wide range of thiol-containing substrates, including peptides, sugars, and thiophenols. This method features mild reaction conditions and fast kinetics. Capability for aqueous media and gram-scale synthesis demonstrates the potential of this method in the bioconjugation of saccharides with biologically active molecules.

Organocatalytic Asymmetric Cascade Michael-Acyl Transfer Reaction between 2-Fluoro-1,3-diketones and 2-Hydroxynitrostyrenes

An organocatalytic asymmetric cascade Michael-acyl transfer reaction of 2-hydroxynitrostyrenes and monofluorinated β-diketones has been developed employing a cooperative catalytic system. A combination of quinine-derived bifunctional squaramide catalyst and achiral hydrogen bond donor cocatalyst was found to be the most effective for this reaction and provided the fluorinated acyl transfer products in high yields with good diastereo- and excellent enantioselectivities. Synthetic transformations have been demonstrated, including the synthesis of functionalized 2,3-dihydrobenzofurans and 1-pyrroline.

Enzymatic Fluoromethylation as a Tool for ATP-Independent Ligation

S-adenosylmethionine-dependent methyltransferases are involved in countless biological processes, including signal transduction, epigenetics, natural product biosynthesis, and detoxification. Only a handful of carboxylate methyltransferases have evolved to participate in amide bond formation. In this report we show that enzyme-catalyzed F-methylation of carboxylate substrates produces F-methyl esters that readily react with N- or S-nucleophiles under physiological conditions. We demonstrate the applicability of this approach to the synthesis of small amides, hydroxamates, and thioesters, as well as to site-specific protein modification and native chemical ligation.

Enzymatic Fluoromethylation as a Tool for ATP-Independent Ligation

S-adenosylmethionine-dependent methyltransferases are involved in countless biological processes, including signal transduction, epigenetics, natural product biosynthesis, and detoxification. Only a handful of carboxylate methyltransferases have evolved to participate in amide bond formation. In this report we show that enzyme-catalyzed F-methylation of carboxylate substrates produces F-methyl esters that readily react with N- or S-nucleophiles under physiological conditions. We demonstrate the applicability of this approach to the synthesis of small amides, hydroxamates, and thioesters, as well as to site-specific protein modification and native chemical ligation.

Site-selective chemical reactions by on-water surface sequential assembly

Controlling site-selectivity and reactivity in chemical reactions continues to be a key challenge in modern synthetic chemistry. Here, we demonstrate the discovery of site-selective chemical reactions on the water surface via a sequential assembly approach. A negatively charged surfactant monolayer on the water surface guides the electrostatically driven, epitaxial, and aligned assembly of reagent amino-substituted porphyrin molecules, resulting in a well-defined J-aggregated structure. This constrained geometry of the porphyrin molecules prompts the subsequent directional alignment of the perylenetetracarboxylic dianhydride reagent, enabling the selective formation of a one-sided imide bond between porphyrin and reagent. Surface-specific in-situ spectroscopies reveal the underlying mechanism of the dynamic interface that promotes multilayer growth of the site-selective imide product. The site-selective reaction on the water surface is further demonstrated by three reversible and irreversible chemical reactions, such as imide-, imine-, and 1, 3-diazole (imidazole)- bonds involving porphyrin molecules. This unique sequential assembly approach enables site-selective chemical reactions that can bring on-water surface synthesis to the forefront of modern organic chemistry.

Biomimetic construction of phospholipid membranes by direct aminolysis ligations

Construction of artificial cells requires the development of straightforward methods for mimicking natural phospholipid membrane formation. Here we describe the use of direct aminolysis ligations to spontaneously generate biomimetic phospholipid membranes from water-soluble starting materials. Additionally, we explore the suitability of such biomimetic approaches for driving the in situ formation of native phospholipid membranes. Our studies suggest that non-enzymatic ligation reactions could have been important for the synthesis of phospholipid-like membranes during the origin of life, and might be harnessed as simplified methods to enable the generation of lipid compartments in artificial cells.

Access to 2-pyridinones comprising enaminonitriles via AgOAc promoted cascade reactions of thioesters with aminomethylene malononitriles

The facile synthesis of 2-pyridinones containing enaminonitriles from thioesters with aminomethylene malononitriles is achieved through an AgOAc-promoted acylation/cyclization/tautomerization cascade reaction. Control experiments reveal that AgOAc acts as a versatile promoter, activating both thioester and cyano groups while also serving as a Brønsted base in the cascade sequence. Moreover, 2-pyridinones were transformed into biologically significant 2-pyridinone-fused 2-pyrimidones with intriguing fluorescence emission properties.

In vitro characterization of nonribosomal peptide synthetase-dependent O-(2-hydrazineylideneacetyl)serine synthesis indicates a stepwise oxidation strategy to generate the α-diazo ester moiety of azaserine

Azaserine, a natural product containing a diazo group, exhibits anticancer activity. In this study, we investigated the biosynthetic pathway to azaserine. The putative azaserine biosynthetic gene (azs) cluster, which contains 21 genes, including those responsible for hydrazinoacetic acid (HAA) synthesis, was discovered using bioinformatics analysis of the Streptomyces fragilis genome. Azaserine was produced by the heterologous expression of the azs cluster in Streptomyces albus. In vitro enzyme assays using recombinant Azs proteins revealed the azaserine biosynthetic pathway as follows. AzsSPTF and carrier protein (CP) AzsQ are used to synthesize the 2-hydrazineylideneacetyl (HDA) moiety attached to AzsQ from HAA. AzsD transfers the HDA moiety to the C-terminal CP domain of AzsN. The heterocyclization (Cy) domain of the nonribosomal peptide synthetase AzsO synthesizes O-(2-hydrazineylideneacetyl)serine (HDA-Ser) attached to its CP domain from l-serine and HDA moiety-attached AzsN. The thioesterase AzsB hydrolyzes it to yield HDA-Ser, which appears to be converted to azaserine by oxidation. Bioinformatics analysis of the Cy domain of AzsO showed that it has a conserved DxxxxD motif; however, two conserved amino acid residues (Thr and Asp) important for heterocyclization are substituted for Asn. Site-directed mutagenesis of two Asp residues in the DxxxxD motif (D193 and D198) and two substituted Asn residues (N414 and N447) indicated that these four residues are important for ester bond synthesis. These results showed that the diazo ester of azasrine is synthesized by the stepwise oxidation of the HAA moiety and provided another strategy to biosynthesize the diazo group.

Thiomethyltetrazines Are Reversible Covalent Cysteine Warheads Whose Dynamic Behavior can be "Switched Off" via Bioorthogonal Chemistry Inside Live Cells

Electrophilic small molecules that can reversibly modify proteins are of growing interest in drug discovery. However, the ability to study reversible covalent probes in live cells can be limited by their reversible reactivity after cell lysis and in proteomic workflows, leading to scrambling and signal loss. We describe how thiomethyltetrazines function as reversible covalent warheads for cysteine modification, and this dynamic labeling behavior can be "switched off" via bioorthogonal chemistry inside live cells. Simultaneously, the tetrazine serves as a bioorthogonal reporter enabling the introduction of tags for fluorescent imaging or affinity purification. Thiomethyltetrazines can label isolated proteins, proteins in cellular lysates, and proteins in live cells with second-order rate constants spanning 2 orders of magnitude (k2, 1-100 M-1 s-1). Reversible modification by thiomethyltetrazines can be switched off upon the addition of trans-cyclooctene in live cells, converting the dynamic thiomethyltetrazine tag into a Diels-Alder adduct which is stable to lysis and proteomic workflows. Time-course quenching experiments were used to demonstrate temporal control over electrophilic modification. Moreover, it is shown that "locking in" the tag through Diels-Alder chemistry enables the identification of protein targets that are otherwise lost during sample processing. Three probes were further evaluated to identify unique pathways in a live-cell proteomic study. We anticipate that discovery efforts will be enabled by the trifold function of thiomethyltetrazines as electrophilic warheads, bioorthogonal reporters, and switches for "locking in" stability.

Zinc-Catalyzed Asymmetric Cascade Michael/Acyl Transfer Reaction between α-Hydroxy Aryl Ketones and Enynones

We described herein a neoteric enantioselective cascade Michael/acyl transfer reaction of enynones and α-hydroxy aryl ketones catalyzed by dinuclear zinc cooperative catalysis. A series of structurally diverse chiral 1,5-dicarbonyl compounds were synthesized in good yields with excellent stereoselectivities. This strategy features broad substrate scope, high atom economy, as well as enynones as efficient electrophilic acyl transfer reagents in asymmetric cascade reactions for the first time.

Design and Evaluation of Ambiphilic Aryl Thiol-Iminium-Based Molecules for Organocatalyzed Thioacyl Aminolysis

Progress toward the design and synthesis of ambiphilic aryl thiol-iminium-based small molecules for organocatalyzed thioacyl aminolysis is reported. Here we describe the synthesis of a novel tetrahydroisoquinoline-derived scaffold, bearing both thiol and iminium functionalities, capable of promoting the transthioesterification and subsequent amine capture reactions necessary to achieve organocatalyzed thioacyl aminolysis. Model studies demonstrate the ability of this designed organocatalyst to deliver critical intermediates capable of undergoing these individual reactions necessary for the proposed process. Future design improvements and directions toward cysteine-independent organocatalyzed native chemical ligation are discussed.

Base Dependent Rearrangement of Dithiane and Dithiolane under Visible-light Photoredox catalysis

The rearrangement of dithiolanes and dithianes to access disulfide-linked-dithioesters under visible-light photoredox catalysis via controlled C-S bond cleavage has been disclosed. Unlike, the usual deprotection of dithioacetals to corresponding aldehydes under the oxidative conditions, we observed unique regioselective oxidative reactivity of five and six membered cyclic dithioacetals to form disulfide-linked-dithioesters by exchanging DMAP and imidazole bases. The generality of the protocol has been demonstrated by exploring a wide range of substrates. As an application, in situ generated thiyl radical has been trapped with disulfides to prepare hetero-disulfides of potential utility. The protocol proved to be practical on gram scale quantity and relied on clean energy source for the transformation. Based on the series of control experiments, cyclic voltammetry and Stern-Volmer studies the plausible mechanism has been proposed.

Direct Access to Thiocyano-Thioesters from Cyclic Thioacetals via Photoredox Catalysis: An Introduction of Two Functional Groups in One Pot

The cyanation of organic compounds is an important synthetic transformation and mainly relies on a toxic CN source. Undeniably, thiocyanate salt has emerged as a very mild and environmentally benign CN source, yet its synthetic utility for cyanation is highly limited to very few types of organic compounds. Herein, we report the direct cyanation of cyclic thioacetals for accessing compounds with two different functional groups (thiocyano-thioesters) in one pot using sodium thiocyanate via photoredox catalysis. The protocol has been further extended for the direct cyanation of disulfides and diselenide to access aryl thiocyanates and aryl selenocyanate. A plausible mechanism has been proposed based on a series of control experiments, cyclic voltammetry and Stern-Volmer studies.

Polythioesters Prepared by Ring-Opening Polymerization of Cyclic Thioesters and Related Monomers

Polyhydroxyalkanoates (PHAs) are biodegradable and biocompatible polyesters with a wide range of applications; in particular, they currently stand as promising alternatives to conventional polyolefin-based "plastics". The introduction of sulfur atoms within the PHAs backbone can endow the resulting polythioesters (PTEs) with differentiated, sometimes enhanced thermal, optical and mechanical properties, thereby widening their versatility and use. Hence, PTEs have been gaining increasing attention over the past half-decade. This review highlights recent advances towards the synthesis of well-defined PTEs by ring-opening polymerization (ROP) of cyclic thioesters - namely thiolactones - as well as of S-carboxyanhydrides and thionolactones; it also covers the ring-opening copolymerization (ROCOP) of cyclic thioanhydrides or thiolactones with epoxides or episulfides. Most of the ROP reactions described are of anionic type, mediated by inorganic, organic or organometallic initiators/catalysts, along with a few enzymatic reactions as well. Emphasis is placed on the reactivity of the thio monomers, in relation to their ring-size ranging from 4- to 5-, 6- and 7-membered cycles, the nature of the catalyst/initiating systems implemented and their efficiency in terms of activity and control over the PTE molar mass, dispersity, topology, and microstructure.

Thioester deprotection using a biomimetic NCL approach

The reversibility of the thiol-thioester linkage has been broadly employed in many fields of biochemistry (lipid synthesis) and chemistry (dynamic combinatorial chemistry and material science). When the transthioesterification is followed by a S-to-N acyl transfer to give an amide bond, it is called Native Chemical Ligation (NCL), a high-yield chemoselective process used for peptide synthesis. Recently, we described thioglycolic acid (TGA) as a useful reagent for thioester deprotection both in solution and anchored to a solid-support under mild conditions. Inspired by NCL, in this work, we extended this approach and explored the use of 2-aminothiols for the deprotection of thiols bearing an acyl group. The best results were obtained using cysteamine or L-cysteine in an aqueous buffer pH 8 at room temperature for 30 min. The described approach was useful for S-acetyl, S-butyryl, and S-benzoyl heterocycles deprotection with yields up to 84%. Employing this methodology, we prepared six new analogs 2 of mercaptomethyl bisthiazolidine 1, a useful inhibitor of a wide-range of Metallo-β-Lactamases (MBLs). Compared with the previous methodologies (TGA polymer supported and TGA in solution), the biomimetic deprotection herein described presents better performance with higher yields, shorter reaction times, less time-consuming operations, easier setup, and lower costs.

Cleavage Off-Loading and Post-assembly-Line Conversions Yield Products with Unusual Termini during Biosynthesis

Piscibactins and photoxenobactins are metallophores and virulence factors, whose biosynthetic gene cluster, termed pxb, is the most prevalent polyketide synthase/non-ribosomal peptide synthetase hybrid cluster across entomopathogenic bacteria. They are structurally similar to yersiniabactin, which contributes to the virulence of the human pathogen Yersinia pestis. However, the pxb-derived products feature various chain lengths and unusual carboxamide, thiocarboxylic acid, and dithioperoxoate termini, which are rarely found in thiotemplated biosyntheses. Here, we characterize the pxb biosynthetic logic by gene deletions, site-directed mutagenesis, and isotope labeling experiments. Notably, we propose that it involves (1) heterocyclization domains with various catalytic efficiencies catalyzing thiazoline and amide/thioester bond formation and (2) putative C–N and C–S bond cleavage off-loading manners, which lead to products with different chain lengths and usual termini. Additionally, the post-assembly-line spontaneous conversions of the biosynthetic end product contribute to production titers of the other products in the culture medium. This study broadens our knowledge of thiotemplated biosynthesis and how bacterial host generate a chemical arsenal.

Rapid syntheses of N-fused heterocycles via acyl-transfer in heteroaryl ketones

The wide-ranging potencies of bioactive N-fused heterocycles inspire the development of synthetic transformations that simplify preparation of their complex, diverse structural motifs. Heteroaryl ketones are ubiquitous, readily available, and inexpensive molecular scaffolds, and are thus synthetically appealing as precursors in preparing N-fused heterocycles via intramolecular acyl-transfer. To best of our knowledge, acyl-transfer of unstrained heteroaryl ketones remains to be demonstrated. Here, we show an acyl transfer-annulation to convert heteroaryl ketones to N-fused heterocycles. Driven via aromatisation, the acyl of a heteroaryl ketone can be transferred from the carbon to the nitrogen of the corresponding heterocycle. The reaction commences with the spiroannulation of a heteroaryl ketone and an alkyl bromide, with the resulting spirocyclic intermediate undergoing aromatisation-driven intramolecular acyl transfer. The reaction conditions are optimised, with the reaction exhibiting a broad substrate scope in terms of the ketone and alkyl bromide. The utility of this protocol is further demonstrated via application to complex natural products and drug derivatives to yield heavily functionalised N-fused heterocycles.

Heteroaryl ketones are ubiquitous molecular scaffolds but seldom used as synthetic precusors. Here, the authors develop an acyl transfer-annulation to convert heteroaryl ketones to N-fused heterocycles, which are prevalent in bioactive molecules.

SufB intein splicing in Mycobacterium tuberculosis is influenced by two remote conserved N-extein histidines

Inteins are auto-processing domains that implement a multistep biochemical reaction termed protein splicing, marked by cleavage and formation of peptide bonds. They excise from a precursor protein, generating a functional protein via covalent bonding of flanking exteins. We report the kinetic study of splicing and cleavage reaction in [Fe–S] cluster assembly protein SufB from Mycobacterium tuberculosis (Mtu). Although it follows a canonical intein splicing pathway, distinct features are added by extein residues present in the active site. Sequence analysis identified two conserved histidines in the N-extein region; His-5 and His-38. Kinetic analyses of His-5Ala and His-38Ala SufB mutants exhibited significant reductions in splicing and cleavage rates relative to the SufB wildtype (WT) precursor protein. Structural analysis and molecular dynamics (MD) simulations suggested that Mtu SufB displays a unique mechanism where two remote histidines work concurrently to facilitate N-terminal cleavage reaction. His-38 is stabilized by the solvent-exposed His-5, and can impact N–S acyl shift by direct interaction with the catalytic Cys1. Development of inteins as biotechnological tools or as pathogen-specific novel antimicrobial targets requires a more complete understanding of such unexpected roles of conserved extein residues in protein splicing.

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.

Recent Advances in Macrocyclic Drugs and Microwave-Assisted and/or Solid-Supported Synthesis of Macrocycles

Macrocycles represent attractive candidates in organic synthesis and drug discovery. Since 2014, nineteen macrocyclic drugs, including three radiopharmaceuticals, have been approved by FDA for the treatment of bacterial and viral infections, cancer, obesity, immunosuppression, etc. As such, new synthetic methodologies and high throughput chemistry (e.g., microwave-assisted and/or solid-phase synthesis) to access various macrocycle entities have attracted great interest in this chemical space. This article serves as an update on our previous review related to macrocyclic drugs and new synthetic strategies toward macrocycles (Molecules, 2013, 18, 6230). In this work, I first reviewed recent FDA-approved macrocyclic drugs since 2014, followed by new advances in macrocycle synthesis using high throughput chemistry, including microwave-assisted and/or solid-supported macrocyclization strategies. Examples and highlights of macrocyclization include macrolactonization and macrolactamization, transition-metal catalyzed olefin ring-closure metathesis, intramolecular C-C and C-heteroatom cross-coupling, copper- or ruthenium-catalyzed azide-alkyne cycloaddition, intramolecular SNAr or SN2 nucleophilic substitution, condensation reaction, and multi-component reaction-mediated macrocyclization, and covering the literature since 2010.

Hydrogel Formation with Enzyme-Responsive Cyclic Peptides

Self-assembling peptides (SAPs), which form hydrogels through physical cross-linking of soluble structures, are an intriguing class of materials that have been applied as tissue engineering scaffolds and drug delivery vehicles. For feasible application of these tissue mimetics via minimally invasive delivery, their bulk mechanical properties must be compatible with current delivery strategies. However, injectable SAPs which possess shear-thinning capacity, as well as the ability to reassemble after cessation of shearing can be technically challenging to generate. Many SAPs either clog the high-gauge needle/catheter at high concentration during delivery or are incapable of reassembly following delivery. In this chapter, we provide a detailed protocol for topological control of enzyme-responsive peptide-based hydrogels that enable the user to access both advantages. These materials are formulated as sterically constrained cyclic peptide progelators to temporarily disrupt self-assembly during injection-based delivery, which avoids issues with clogging of needles and catheters as well as nearby vasculature. Proteolytic cleavage by enzymes produced at the target tissue induces progelator linearization and hydrogelation. The scope of this approach is demonstrated by their ability to flow through a catheter without clogging and activated gelation upon exposure to target enzymes.

3D-QSAR Studies of 1,2,4-Oxadiazole Derivatives as Sortase A Inhibitors

Sortase A (SrtA) is an enzyme that catalyzes the attachment of proteins to the cell wall of Gram-positive bacterial membrane, preventing the spread of pathogenic bacterial strains. Here, one class of oxadiazole compounds was distinguished as an efficient inhibitor of SrtA via the "S. aureus Sortase A" substrate-based virtual screening. The current study on 3D-QSAR was done by utilizing preparation of the structure in the Schrödinger software suite and an assessment of 120 derivatives with the crystal structure of 1,2,4-oxadiazole which was extracted from the PDB data bank. The docking operation of the best compound in terms of pMIC (pMIC = 2.77) was done to determine the drug likeliness and binding form of 1,2,4-oxadiazole derivatives as antibiotics in the active site. Using the kNN-MFA way, seven models of 3D-QSAR were created and amongst them, and one model was selected as the best. The chosen model based on q 2 (pred_r 2) and R 2 values related to the sixth factor of PLS illustrates better and more acceptable external and internal predictions. Values of crossvalidation (pred_r 2), validation (q 2), and F were observed 0.5479, 0.6319, and 179.0, respectively, for a test group including 24 molecules and the training group including 96 molecules. The external reliability outcomes showed that the acceptable and the selective 3D-QSAR model had a high predictive potential (R 2 = 0.9235) which was confirmed by the Y-randomization test. Besides, the model applicability domain was described successfully to validate the estimation of the model.

Mercapto-functionalized polyhedral oligomeric silsesquioxane as a soluble support for the synthesis of peptide thioesters

The revival of peptide-based drugs has led to the increasing demand for the development of large-scale synthesis of these complex molecules. To meet this demand, the use of mercapto-functionalized polyhedral oligomeric silsesquioxane (POSS-SH) as a soluble support for the synthesis of a model pentapeptide POSS-thioester is reported. The synthetic process provided a total yield of 62% for the pentapeptide POSS-thioester and the 1H NMR spectra validated the high purity of the products. The successful synthesis of the pentapeptide POSS-thioester with high yield and purity provides a promising way to the scale-up chemical synthesis of peptide thioesters, peptides, peptide amides, cyclic peptides, and even proteins.

Site-selective lysine conjugation methods and applications towards antibody-drug conjugates

Site-selective protein modification is of significant interest in chemical biology research, with lysine residues representing a particularly challenging target. Whilst lysines are popular for bioconjugation, due to their nucleophilicity, solvent accessibility and the stability of the resultant conjugates, their high abundance means site-selectivity is very difficult to achieve. Antibody-drug conjugates (ADCs) present a powerful therapeutic application of protein modification, and have often relied extensively upon lysine bioconjugation for their synthesis. Here we discuss advances in methodologies for achieving site-selective lysine modification, particularly within the context of antibody conjugate construction, including the cysteine-to-lysine transfer (CLT) protocol which we have recently reported.

Organocatalytic Asymmetric Cascade Michael-acyl Transfer Reaction between 2-Fluoro-1,3-diketones and Unsaturated Thiazolones: Access to Fluorinated 4-Acyloxy Thiazoles

Quinine derived bifunctional urea catalyzed cascade Michael-acyl transfer reaction of 5-alkenyl thiazolones and monofluorinated β-diketones has been developed. The fluorine containing 4-acyloxy thiazoles were synthesized in high yields and good diastereo-and excellent enantioselectivities. Synthetic transformations, including synthesis of 4-hydroxy thiazoles, have been demonstrated.

Unmasking latent thioesters under hydrophobic-compatible conditions

Hydrophobic latent C-terminal thioesters were converted into thioesters, and were also coupled with cysteine in one-pot reactions, using conditions generally compatible with hydrophobic materials. The reaction conditions (ethanethiol and triethylamine in a mixture of DMF and THF) are compatible with acid-labile protecting groups (Boc/t-Bu) that are standard in Fmoc peptide synthesis.

N-Alkylation/aldol reaction of α-aldimino thioesters: a facile three-component coupling reaction

Theoretical calculation of the reactivity of α-imino thioesters indicates that they are very reactive substrates for Umpolung N-alkylation. In fact, treatment of α-aldimino thioesters with dialkylzinc reagents in the presence of aldehydes or imines gives three-component coupling products in good yields.

Bifunctional Urea/Hg(OAc)2-Mediated Synthesis of 4-Aryl-6-oxycarbonyl-2-pyrones and 2-Pyridones from Dithiomalonate and β,γ-Unsaturated α-Keto Esters

Disubstituted 2-pyrones and 2-pyridones were obtained by bifunctional urea-catalyzed Michael addition/lactonization or lactamization followed by a Hg(OAc)₂- or Hg(OAc)₂/DBU-mediated hydrolysis/decarboxylation/dehydrogenation process. This one-pot two-stage protocol enabled the rapid synthesis of 4,6-disubstituted 2-pyrones and 2-pyridones from dithiomalonate and β,γ-unsaturated α-keto esters in practical yields under mild reaction conditions. Additionally, the obtained 2-pyridones were facilely transformed to 2,4,6-trisubstituted pyridines in excellent yields.

Enzyme-Primed Native Chemical Ligation Produces Autoinducing Cyclopeptides in Clostridia

Clostridia coordinate many important processes such as toxin production, infection, and survival by density‐dependent communication (quorum sensing) using autoinducing peptides (AIPs). Although clostridial AIPs have been proposed to be (thio)lactone‐containing peptides, their true structures remain elusive. Here, we report the genome‐guided discovery of an AIP that controls endospore formation in Ruminiclostridium cellulolyticum. Through a combination of chemical synthesis and chemical complementation assays with a mutant strain, we reveal that the genuine chemical mediator is a homodetic cyclopeptide (cAIP). Kinetic analyses indicate that the mature cAIP is produced via a cryptic thiolactone intermediate that undergoes a rapid S→N acyl shift, in a manner similar to intramolecular native chemical ligation (NCL). Finally, by implementing a chemical probe in a targeted screen, we show that this novel enzyme‐primed, intramolecular NCL is a widespread feature of clostridial AIP biosynthesis.

Chemical Synthesis and Biological Applications of O-GlcNAcylated Peptides and Proteins

All human cells use O-GlcNAc protein modifications (O-linked N-acetylglucosamine) to rapidly adapt to changing nutrient and stress conditions through signaling, epigenetic, and proteostasis mechanisms. A key challenge for biologists in defining precise roles for specific O-GlcNAc sites is synthetic access to homogenous isoforms of O-GlcNAc proteins, a result of the non-genetically templated, transient, and heterogeneous nature of O-GlcNAc modifications. Toward a solution, this review details the state of the art of two strategies for O-GlcNAc protein modification: advances in "bottom-up" O-GlcNAc peptide synthesis and direct "top-down" installation of O-GlcNAc on full proteins. We also describe key applications of synthetic O-GlcNAc peptide and protein tools as therapeutics, biophysical structure-function studies, biomarkers, and as disease mechanistic probes to advance translational O-GlcNAc biology.

Synthesis of Fucose Derivatives with Thiol Motifs towards Suicide Inhibition of Helicobacter pylori

The syntheses of six thiol-exhibiting monosaccharides towards suicide inhibition of Helicobacter pylori are reported. Blood group Antigen Binding Adhesin (BabA), a bacterial membrane-bound lectin, binds to human ABO and Lewis b blood group structures displayed on the surface of host epithelial cells. Crystal structures of the carbohydrate-recognition domain revealed a conserved disulfide bonded loop that anchors a critical fucose residue in these blood group structures. Disruption of this loop by N-acetylcysteine results in reduced BabA-mediated adherence to human gastric tissue sections and attenuated virulence in Lewis b-expressing transgenic mice. With a view of creating specific inhibitors of the lectin, we designed and successfully synthesised six fucose-derived compounds with thiol motifs to engage in a thiol-disulfide exchange with this disulfide bond of BabA and form a glycan-lectin disulfide linkage. Branching and extending the fucose backbone with 2- and 3-carbon thiol motifs delivered a range of candidates to be tested for biological activity against BabA.

Enhancing native chemical ligation for challenging chemical protein syntheses

Native chemical ligation has enabled the chemical synthesis of proteins for a wide variety of applications (e.g., mirror-image proteins). However, inefficiencies of this chemoselective ligation in the context of large or otherwise challenging protein targets can limit the practical scope of chemical protein synthesis. In this review, we focus on recent developments aimed at enhancing and expanding native chemical ligation for challenging protein syntheses. Chemical auxiliaries, use of selenium chemistry, and templating all enable ligations at otherwise suboptimal junctions. The continuing development of these tools is making the chemical synthesis of large proteins increasingly accessible.

Methodologies for Backbone Macrocyclic Peptide Synthesis Compatible With Screening Technologies

Backbone macrocyclic structures are often found in diverse bioactive peptides and contribute to greater conformational rigidity, peptidase resistance, and potential membrane permeability compared to their linear counterparts. Therefore, such peptide scaffolds are an attractive platform for drug-discovery endeavors. Recent advances in synthetic methods for backbone macrocyclic peptides have enabled the discovery of novel peptide drug candidates against diverse targets. Here, we overview recent technical advancements in the synthetic methods including 1) enzymatic synthesis, 2) chemical synthesis, 3) split-intein circular ligation of peptides and proteins (SICLOPPS), and 4) in vitro translation system combined with genetic code reprogramming. We also discuss screening methodologies compatible with those synthetic methodologies, such as one-beads one-compound (OBOC) screening compatible with the synthetic method 2, cell-based assay compatible with 3, limiting-dilution PCR and mRNA display compatible with 4.