Automated Synthesis for the Safe Production of Organic Azides from Primary Amines.

Described herein is the development of an automated and reproducible process for the conversion of primary amines to organic azides utilizing prepacked capsules containing all the required reagents, including imidazole-1-sulfonyl azide tetrafluoroborate. Apart from manually loading the primary amine into the reaction vessel, the entire reaction and product isolation process can be achieved automatically, with no further user involvement, and delivers the desired organic azide in high purity. This practical and simple automated capsule-based method offers a convenient and safe way of generating organic azides without handling or exposure of potentially explosive reagents.

Chemical Synthesis of Secretoglobin 3A2 Covalent Homodimer and Photocaged Monomeric Variants.

Secretoglobin (SCGB) 3A2 belongs to an intriguing family of small, secreted proteins present only in mammals. Although members of the SCGB protein family have distinct amino acid sequences, they share structural similarities. Of particularly interest is the not yet fully understood self-assembly ability of SCGBs, which arise from covalent disulfide dimerization and non-covalent oligomerization. Recently, SCGB3A2 has attracted attention for its singular expression profile in airways. However, the knowledge on SCGB3A2 (patho)physiology derives exclusively from in vivo and complex ex vivo mixtures, which hampers characterization of the mechanisms driving SCGB3A2 structural behavior. Herein, we document the chemical synthesis of SCGB3A2 in multi-milligram quantities. Key to access both monomeric and homodimeric SCGB3A2 analogues was the use of KAHA ligation and enabled masking of the cysteine residue. The synthetic proteins were used to investigate the SCGB3A2 self-assembly profile, confirming their high propensity to dimerization even in the absence of the key Cys residue.

Peptide-Directed Attachment of Hydroxylamines to Specific Lysines of IgG Antibodies for Bioconjugations with Acylboronates.

The role of monoclonal antibodies as vehicles to deliver payloads has evolved as a powerful tool in cancer therapy in recent years. The clinical development of therapeutic antibody conjugates with precise payloads holds great promise for targeted therapeutic interventions. The use of affinity-peptide mediated functionalization of native off-the-shelf antibodies offers an effective approach to selectively modify IgG antibodies with a drug-antibody ratio (DAR) of 2. Here, we report the traceless, peptide-directed attachment of two hydroxylamines to native IgGs followed by chemoselective potassium acyltrifluoroborate (KAT) ligation with quinolinium acyltrifluoroborates (QATs), which provide enhanced ligation rates with hydroxylamines under physiological conditions. By applying KAT ligation to the modified antibodies, conjugation of small molecules, proteins, and oligonucleotides to off-the-shelf IgGs proceeds efficiently, in good yields, and with simultaneous cleavage of the affinity peptide-directing moiety.

Time-Resolved Atomistic Imaging and Statistical Analysis of Daptomycin Oligomers with and without Calcium Ions.

Daptomycin (DP) is effective against multiple drug-resistant Gram-positive pathogens because of its distinct mechanism of action. An accepted mechanism includes Ca2+-triggered aggregation of the DP molecule to form oligomers. DP and its oligomers have so far defied structural analysis at a molecular level. We studied the ability of DP molecule to aggregate by itself in water, the effects of Ca2+ ions to promote the aggregation, and the connectivity of the DP molecules in the oligomers by the combined use of dynamic light scattering in water and atomic-resolution cinematographic imaging of DP molecules captured on a carbon nanotube on which the DP molecule is installed as a fishhook. We found that the DP molecule aggregates weakly into dimers, trimers, and tetramers in water, and strongly in the presence of calcium ions, and that the tetramer is the largest oligomer in homogeneous aqueous solution. The dimer remains as the major species, and we propose a face-to-face stacked structure based on dynamic imaging using millisecond and angstrom resolution transmission electron microscopy. The tetramer in its cyclic form is the largest oligomer observed, while the trimer forms in its linear form. The study has shown that the DP molecule has an intrinsic property of forming tetramers in water, which is enhanced by the presence of calcium ions. Such experimental structural information will serve as a platform for future drug design. The data also illustrate the utility of cinematographic recording for the study of self-organization processes.

Post-Assembly Modification of Protein Cages by Ubc9-Mediated Lysine Acylation.

Although viruses have been successfully repurposed as vaccines, antibiotics, and anticancer therapeutics, they also raise concerns regarding genome integration and immunogenicity. Virus-like particles and non-viral protein cages represent a potentially safer alternative but often lack desired functionality. Here, we investigated the utility of a new enzymatic bioconjugation method, called lysine acylation using conjugating enzymes (LACE), to chemoenzymatically modify protein cages. We equipped two structurally distinct protein capsules with a LACE-reactive peptide tag and demonstrated their modification with diverse ligands. This modular approach combines the advantages of chemical conjugation and genetic fusion and allows for site-specific modification with recombinant proteins as well as synthetic peptides with facile control of the extent of labeling. This strategy has the potential to fine-tune protein containers of different shape and size by providing them with new properties that go beyond their biologically native functions.

Preparation of Potassium Acyltrifluoroborates (KATs) from Carboxylic Acids by Copper-Catalyzed Borylation of Mixed Anhydrides.

We report the preparation of potassium acyltrifluoroborates (KATs) from widely available carboxylic acids. Mixed anhydrides of carboxylic acids were prepared using isobutyl chloroformate and transformed to the corresponding KATs using a commercial copper catalyst, B2 (pin)2 , and aqueous KHF2 . This method allows for the facile preparation of aliphatic, aromatic, and amino acid-derived KATs and is compatible with a variety of functional groups including alkenes, esters, halides, nitriles, and protected amines.

Mechanism-Based Design of Quinoline Potassium Acyltrifluoroborates for Rapid Amide-Forming Ligations at Physiological pH.

Potassium acyltrifluoroborates (KATs) undergo chemoselective amide-forming ligations with hydroxylamines. Under aqueous, acidic conditions these ligations can proceed rapidly, with rate constants of ∼20 M-1 s-1. The requirement for lower pH to obtain the fastest rates, however, limits their use with certain biomolecules and precludes in vivo applications. By mechanistic investigations into the KAT ligation, including kinetic studies, X-ray crystallography, and DFT calculations, we have identified a key role for a proton in accelerating the ligation. We applied this knowledge to the design and synthesis of 8-quinolyl acyltrifluoroborates, a new class of KATs that ligates with hydroxylamines at pH 7.4 with rate constants >4 M-1 s-1. We trace the enhanced rate at physiological pH to unexpectedly high basicity of the 8-quinoline-KATs, which leads to their protonation even under neutral conditions. This proton assists the formation of the key tetrahedral intermediate and activates the leaving groups on the hydroxylamine toward a concerted 1,2-BF3 shift that leads to the amide product. We demonstrate that the fast ligations at pH 7.4 can be carried out with a protein substrate at micromolar concentrations.

Catalytic Synthesis of Potassium Acyltrifluoroborates (KATs) from Boronic Acids and the Thioimidate KAT Transfer Reagent.

We report the synthesis of potassium acyltrifluoroborates (KATs) by a palladium-catalyzed cross-coupling of boronic acids and the thioimidate KAT transfer reagent. The combination of widely available aryl- and vinylboronic acids with commercially available thioimidate 1 using catalytic PdII and a CuII additive enables the preparation of KATs in high yields and with good functional group tolerance. This formal insertion of CO into organoboronic acids can also be applied to boronic acid pinacol esters and potassium organotrifluoroborates using a slightly modified procedure. The cross-coupling can be telescoped into the one-pot synthesis of amides and α-aminotrifluoroborates by exploiting the unique chemistry of KATs and their trifluoroborate iminium (TIM) derivatives.

Aspartic Acid Forming α-Ketoacid-Hydroxylamine (KAHA) Ligations with (S)-4,4-Difluoro-5-oxaproline.

The α-ketoacid-hydroxylamine (KAHA) ligation allows the coupling of unprotected peptide segments. Currently, the most applied hydroxylamine is the 5-membered cyclic hydroxylamine (S)-5-oxaproline, which forms a homoserine ester as the primary ligation product. In order to access native aspartic acid residues at the ligation site, we synthesized a 4,4-difluoro version of this monomer. Upon KAHA ligation, the resulting difluoro alcohol hydrolyzes to an aspartic acid residue with little or no formation of aspartamide. We applied this monomer for the synthesis of the hormone peptides glucagon and an insulin variant, and as well for segment ligation of the peptides UbcH5a and SUMO3.

Synthesis of Acylboron Compounds.

Acylboron compounds are emerging as versatile functional groups with applications in multiple research fields. Their synthesis, however, is still challenging and requires innovative methods. This Minireview provides an overview on the obstacles of acylboron synthesis and highlights notable advances within the last three years on new strategies to overcome the challenges posed by the formation of acyl-boron bonds.

Chemical Synthesis of Interleukin-2 and Disulfide Stabilizing Analogues.

Chemical protein synthesis allows the construction of well-defined structural variations and facilitates the development of deeper understanding of protein structure-function relationships and new protein engineering strategies. Herein, we report the chemical synthesis of interleukin-2 (IL-2) variants on a multimilligram scale and the formation of non-natural disulfide mimetics that improve stability against reduction. The synthesis was accomplished by convergent KAHA ligations; the acidic conditions of KAHA ligation proved to be valuable for the solubilization of the hydrophobic segments of IL-2. The bioactivity of the synthetic IL-2 and its analogues were shown to be equipotent to recombinant IL-2 and exhibit improved stability against reducing agents.

Synthesis of Polymers Containing Potassium Acyltrifluoroborates (KATs) and Post-polymerization Ligation and Conjugation.

We report the synthesis of monomers for atom-transfer radical polymerization (ATRP) and a reversible addition-fragmentation chain transfer (RAFT) agent bearing trifluoroborate iminiums (TIMs), which are quantitatively converted into potassium acyltrifluoroborates (KATs) after polymerization. The resulting KAT-containing polymers are suitable for rapid amide-forming ligations for both post-polymerization modification and polymer conjugation. The polymer conjugation occurs rapidly, even under dilute (micromolar) aqueous conditions at ambient temperatures, thereby enabling the synthesis of a variety of linear and star-shaped block copolymers. In addition, we applied post-polymerization modification to the covalent linking of a photocaged cyclic antibiotic (gramicidin S) to the side chains of the KAT-containing copolymer. Cellular assays revealed that the polymer-antibiotic conjugate is biocompatible and provides efficient light-controlled release of the antibiotic on demand.

Iterative Assembly of Polycyclic Saturated Heterocycles from Monomeric Building Blocks.

Polycyclic saturated heterocycles with predictable shapes and structures are assembled by iterative couplings of bifunctional stannyl amine protocol (SnAP) reagents and a single morpholine-forming assembly reaction. Combinations of just a few monomers enable the programmable construction of rotationally restricted, nonplanar heterocyclic arrays with discrete sizes and molecular shapes. The three-dimensional structures of these constrained scaffolds can be quickly and reliably predicted by DFT calculations and the target structures immediately decompiled into the constituent building blocks and assembly sequences. As a demonstration, in silico combinations of the building blocks predict saturated heptacyclic structures with elementary shapes including helices, S-turns and U-turns, which are synthesized in 5-6 steps from the monomers using just three chemical reactions.

Traceless Templated Amide-Forming Ligations.

Template assistance allows organic reactions to occur under highly dilute conditions-where intermolecular reactions often fail to proceed-by bringing reactants into close spatial proximity. This strategy has been elegantly applied to numerous systems, but always with the retention of at least one of the templating groups in the product. In this report, we describe a traceless, templated amide-forming ligation that proceeds at low micromolar concentration under aqueous conditions in the presence of biomolecules. We utilized the unique features of an acylboronate-hydroxylamine ligation, in which covalent bonds are broken in each of the reactants as the new amide bond is formed. By using streptavidin as a template and acylboronates and O-acylhydroxylamines bearing desthiobiotins that are cleaved upon amide formation, we demonstrate that traceless, templated ligation occurs rapidly even at submicromolar concentrations. The requirement for a close spatial orientation of the functional groups-achieved upon binding to streptavidin-is critical for the observed enhancement in the rate and quantity of product formed.

Olefin Amine (OLA) Reagents for the Synthesis of Bridged Bicyclic and Spirocyclic Saturated N-Heterocycles by Catalytic Hydrogen Atom Transfer (HAT) Reactions.

Spiro- and bridged bicyclic structures are in demand for their sp3-rich frameworks that offer unique physiochemical properties and precisely positioned substituent groups. In order to rapidly access such molecules in a cross-coupling fashion we describe olefin amine (OLA) reagents for the transformation of aldehydes and ketones into all three topological types of bicyclic N-heterocycles: bridged, spiro-, and fused rings. The OLA reagents are easily prepared and allow the synthesis of complex molecular frameworks under operationally simple conditions that tolerate a wide array of functional groups. Investigations into the Mn or Fe promoted reaction pathway support a metal hydride hydrogen atom transfer (MH-HAT) to generate a C-centered radical that undergoes addition to an unactivated imine, leading to an N-centered radical. A catalytic cycle featuring regeneration of the metal catalyst by O2 and a second HAT to form the unprotected saturated N-heterocycle appears to be operative.

Chemical Synthesis of Atomically Tailored SUMO E2 Conjugating Enzymes for the Formation of Covalently Linked SUMO-E2-E3 Ligase Ternary Complexes.

E2 conjugating enzymes are the key catalytic actors in the transfer of ubiquitin, SUMO, and other ubiquitin-like modifiers to their substrate proteins. Their high rates of transfer and promiscuous binding complicate studies of their interactions and binding partners. To access specific, covalently linked conjugates of the SUMO E2 conjugating enzyme Ubc9, we prepared synthetic variants bearing site-specific non-native modifications including the following: (1) replacement of Cys93 to 2,3-diaminopropionic acid to form the amide-linked stable E2-SUMO conjugate, which is known to have high affinity for E3 ligases; (2) a photoreactive group (diazirine) to trap E3 ligases upon UV irradiation; and (3) an N-terminal biotin for purification and detection. To construct these Ubc9 variants in a flexible, convergent manner, we combined the three leading methods: native chemical ligation (NCL), α-ketoacid-hydroxylamine (KAHA) ligation, and serine/threonine ligation (STL). Using the synthetic proteins, we demonstrated the selective formation of Ubc9-SUMO conjugates and the trapping of an E3 ligase (RanBP2) to form the stable, covalently linked SUMO1-Ubc9-RanBP2 ternary complex. The powerful combination of ligation methods-which minimizes challenges of functional group manipulations-will enable chemical probes based on E2 conjugating enzymes to trap E3 ligases and facilitate the synthesis of other protein classes.

A Threonine-Forming Oxazetidine Amino Acid for the Chemical Synthesis of Proteins through KAHA Ligation.

α-Ketoacid-hydroxylamine (KAHA) ligation allows the coupling of unprotected peptide segments through the chemoselective formation of an amide bond. Currently, the most widely used variant employs a 5-membered cyclic hydroxylamine that forms a homoserine ester as the primary ligation product. In order to directly form amide-linked threonine residues at the ligation site, we prepared a new 4-membered cyclic hydroxylamine building block. This monomer was applied to the synthesis of wild-type ubiquitin-conjugating enzyme UbcH5a (146 residues) and Titin protein domain TI I27 (89 residues). Both the resulting UbcH5a and the variant with two homoserine residues showed identical activity to a recombinant variant in a ubiquitination assay.

Catalytic Synthesis of Potassium Acyltrifluoroborates (KATs) through Chemoselective Cross-Coupling with a Bifunctional Reagent.

Potassium acyltrifluoroborates (KATs) are increasingly important functional groups, and general methods for their preparation are of great current interest. We report a bifunctional iminium reagent bearing both a tin nucleophile and a trifluoroborate, which was applied in chemoselective Pd0 -catalyzed Migita-Kosugi-Stille cross-coupling reactions owith aryl and vinyl halides. This method gives access to previously inaccessible aromatic and α,ß-unsaturated acyltrifluoroborates, including precursors to amino-acid derived KATs.

Introduction of d-Amino Acids in Minimalistic Peptide Substrates by an S-Adenosyl-l-Methionine Radical Epimerase.

Post-translational modifying enzymes from the S-adenosyl-l-methionine (AdoMet) radical superfamily garner attention due to their ability to accomplish challenging biochemical reactions. Among them, a family of AdoMet radical epimerases catalyze irreversible l- to d-amino acid transformations of diverse residues, including 18 sites in the complex sponge-derived polytheonamide toxins. Herein, the in vitro activity of the model epimerase OspD is reported and its catalytic mechanism and substrate flexibility is investigated. The wild-type enzyme was capable of leader-independent epimerization of not only the stand-alone core peptide, but also truncated and cyclic core variants. Introduction of d-amino acids can drastically alter the stability, structure, and activity of peptides; thus, epimerases offer opportunities in peptide bioengineering.

Leaving Groups as Traceless Topological Modifiers for the Synthesis of Topologically Isomeric Polymer Networks.

The chemical and topological structure of polymer networks can seldom be orthogonally controlled. For example, novel network topologies are often accessed via the direct incorporation of supramolecular assemblies into the network structure, introducing potentially undesirable chemical components. Here, we address this deficiency by programming topology into network precursors through the incorporation of self-assembly motifs in leaving groups, which become "traceless topological modifiers." Our method enables us to control polymer network topology using self-assembled structures as templates that are not themselves incorporated into the network. We demonstrate this strategy using a model network formed through potassium acyltrifluoroborate (KAT) ligation. Two four-arm polyethylene glycol (PEG)-based star polymers prepared with either O-ethyl or O-octyl carbamoyl hydroxylamine chain ends serve as network precursors, where differences in chain end hydrophobicity produce different self-assembly states in solution. Addition of a bis-KAT reagent to these star polymers induces amide bond formation and concomitant expulsion of the ethyl or octyl traceless topological modifiers, producing topologically isomeric PEG gels with identical chemical compositions yet vastly different physical properties. This work highlights the impact of topology on polymer network properties and provides a new strategy, traceless topological modification, for polymer network design.