Total chemical synthesis of polypeptides and proteins: chemistry of ligation techniques and beyond

Thioacids – synthons for amide bond formation and ligation reactions: assembly of peptides and peptidomimetics

The synthesis of α-amino thioacids and peptide thioacids and their applications in chemoselective amide bond formation, ligation of peptides/proteins/glycopeptides and synthesis of peptidomimetics are reviewed.

Are Aminomethyl Thioesters Viable Intermediates in Native Chemical Ligation Type Amide Bond Forming Reactions?

The condensation of N-mercaptomethyl amines and thioesters is a potential route to amides, via aminomethyl thioester intermediates, in a native chemical ligation type process followed by self-cleavage of the ‘mercaptomethyl’ auxiliary. This paper describes investigations towards the preparation of aminomethyl thioesters, and subsequent conversion into amides, from a three-component coupling of formaldehyde, a thioacid, and an amine. Our studies suggest that while such intermediates may be formed en route to amides, no advantages are offered over the direct reaction of the amine and thioacid precursors.

ortho-Quinones and Analogues Thereof: Highly Reactive Intermediates for Fast and Selective Biofunctionalization

Fast, selective and facile functionalization of biologically relevant molecules is a pursuit of ever‐growing importance. A promising approach in this regard employs the high reactivity of quinone and quinone analogues for fast conjugation chemistry by nucleophilic addition or cycloadditions. Combined with in situ generation of these compounds, selective conjugation on proteins and surfaces can be uniquely induced in a time and spatially resolved manner: generation of a quinone can often be achieved by simple addition of an enzyme or stoichiometric amounts of chemoselective oxidant, or by exposure to light. In this Minireview, we discuss the generation and subsequent functionalization of quinones, iminoquinones, and quinone methides. We also discuss practical applications regarding these conjugation strategies.

Probing the Catalytic Charge-Relay System in Alanine Racemase with Genetically Encoded Histidine Mimetics

Histidine is a unique amino acid with an imidazole side chain in which both of the nitrogen atoms are capable of serving as a proton donor and proton acceptor in hydrogen bonding interactions. In order to probe the functional role of histidine involved in hydrogen bonding networks, fine-tuning the hydrogen bonding potential of the imidazole side chain is required but not feasible through traditional mutagenesis methods. Here, we show that two close mimetics of histidine, 3-methyl-histidine and thiazole alanine, can be genetically encoded using engineered pyrrolysine incorporation machinery. Replacement of the three histidine residues predicted to be involved in an extended charge-relay system in alanine racemase with 3-methyl-histidine or thiazole alanine shows a dramatic loss in the enzyme's catalytic efficiency, implying the role of this extended charge-relay system in activating the active site residue Y265, a general acid/base catalyst in the enzyme.

On-Demand Complex Peptide Synthesis: An Aspirational (and Elusive?) Goal for Peptide Synthesis

Peptide synthesis is a truly interdisciplinary tool, familiar to a broad group of scientists who do not otherwise overlap scientifically. For this reason, some may perceive even complex peptide synthesis to be a "solved problem", while others might argue that immense opportunity remains untapped or simply inaccessible. At the extreme of complexity, what might a concise assessment of the state-of-the-art in peptide synthesis look like? As one of the most practiced forms of synthetic chemistry by chemists and non-chemists alike, what restrictions remain that constrain access to chemical space? Using popular terminology, what forms of peptide synthesis are appropriately termed "on-demand"? The purpose of this Perspective is to appraise synthetic access to complex peptides, particularly those containing unnatural α-amino amides. Several case studies in complex peptide synthesis are summarized here, each selected to characterize the challenges attendant to unnatural α-amino amide synthesis. As peptidic molecules find increasing value in therapeutic development, especially in clinical applications, their impact will ultimately be determined by efficient preparative methods.

Nonclassical Routes for Amide Bond Formation

The present review offers an overview of nonclassical (e.g., with no pre- or in situ activation of a carboxylic acid partner) approaches for the construction of amide bonds. The review aims to comprehensively discuss relevant work, which was mainly done in the field in the last 20 years. Organization of the data follows a subdivision according to substrate classes: catalytic direct formation of amides from carboxylic and amines ( section 2 ); the use of carboxylic acid surrogates ( section 3 ); and the use of amine surrogates ( section 4 ). The ligation strategies (NCL, Staudinger, KAHA, KATs, etc.) that could involve both carboxylic acid and amine surrogates are treated separately in section 5 .

Synthesis and reactivities of monofluoro acylboronates in chemoselective amide bond forming ligation with hydroxylamines

Synthesis and reactivities of monofluoroacylboronates are described in the context of bioorganic chemistry and chemical ligation.

Mechanically selflocked chiral gemini-catenanes

Mechanically interlocked and entangled molecular architectures represent one of the elaborate topological superstructures engineered at a molecular resolution. Here we report a methodology for fabricating mechanically selflocked molecules (MSMs) through highly efficient one-step amidation of a pseudorotaxane derived from dual functionalized pillar[5]arene (P[5]A) threaded by α,ω-diaminoalkane (DA-n; n=3-12). The monomeric and dimeric pseudo[1]catenanes thus obtained, which are inherently chiral due to the topology of P[5]A used, were isolated and fully characterized by NMR and circular dichroism spectroscopy, X-ray crystallography and DFT calculations. Of particular interest, the dimeric pseudo[1]catenane, named 'gemini-catenane', contained stereoisomeric meso-erythro and dl-threo isomers, in which two P[5]A moieties are threaded by two DA-n chains in topologically different patterns. This access to chiral pseudo[1]catenanes and gemini-catenanes will greatly promote the practical use of such sophisticated chiral architectures in supramolecular and materials science and technology.

Realizing serine/threonine ligation: scope and limitations and mechanistic implication thereof

Serine/Threonine ligation (STL) has emerged as an alternative tool for protein chemical synthesis, bioconjugations as well as macrocyclization of peptides of various sizes. Owning to the high abundance of Ser/Thr residues in natural peptides and proteins, STL is expected to find a wide range of applications in chemical biology research. Herein, we have fully investigated the compatibility of the STL strategy for X-Ser/Thr ligation sites, where X is any of the 20 naturally occurring amino acids. Our studies have shown that 17 amino acids are suitable for ligation, while Asp, Glu, and Lys are not compatible. Among the working 17 C-terminal amino acids, the retarded reaction resulted from the bulky β-branched amino acid (Thr, Val, and Ile) is not seen under the current ligation condition. We have also investigated the chemoselectivity involving the amino group of the internal lysine which may compete with the N-terminal Ser/Thr for reaction with the C-terminal salicylaldehyde (SAL) ester aldehyde group. The result suggested that the free internal amino group does not adversely slow down the ligation rate.

Synthesis and chemoselective ligations of MIDA acylboronates with O-Me hydroxylamines

A chemoselective amide-bond forming ligation of N-methyliminodiacetyl (MIDA) acylboronates and O-Me hydroxylamines, including unprotected peptide substrates, is described.

Traceless Staudinger acetylation of azides in aqueous buffers

In this paper, we demonstrate the applicability of water-soluble p-dimethylaminoethyl substituted phosphinomethanethiol in acetyl transfer reactions by the traceless Staudinger ligation with unprotected ε-azido lysine containing peptides in aqueous buffer systems. Additionally, we present an improved synthesis pathway for the water-soluble phosphinothiol linkers requiring less steps in a comparable overall yield in comparison to previously published protocols.

Non-enzymatic synthesis of ubiquitin chains: where chemistry makes a difference

Ubiquitination is a highly important posttranslational modification in eukaryotic cells where a target protein is conjugated to ubiquitin or a chain of ubiquitins via an isopeptide bond to trigger various cellular events such as proteasomal degradation. Rigorous investigations of the ubiquitin signal at the molecular level require homogeneous samples of ubiquitin chains in their free form or as anchored to a protein substrate in adequate quantities. The complexity of ubiquitin chains in terms of linkage types (owing to presence of seven Lys in ubiquitin) makes them difficult to prepare via enzymatic methods. Even more challenging is the attachment of these chains to a protein target at a selected site. This dearth is being filled by the recent developments of novel chemical tools that offer atomic level control over the synthesis for structural and functional studies. These emerging chemical approaches are discussed in this mini-review with focus on the preparation of ubiquitin chains to aid the ongoing efforts in understanding their role in the ubiquitin signal.