Recent Developments and Strategies for Mutually Orthogonal Bioorthogonal Reactions

Over the past decade, several different metal-free bioorthogonal reactions have been developed to enable simultaneous double-click labeling with minimal-to-no competing cross-reactivities; such transformations are termed ‘mutually orthogonal’. More recently, several examples of successful triple ligation strategies have also been described. In this minireview, we discuss selected aspects of the development of orthogonal bioorthogonal reactions over the past decade, including general strategies to drive future innovations to achieve simultaneous, mutually orthogonal click reactions in one pot.     

Labeling small RNAs through chemical ligation at the 5' terminus: enzyme-free or combined with enzymatic 3'-labeling

The discovery of small RNAs such as microRNAs (miRNAs), small interfering RNAs (siRNAs), or Piwi-associated RNAs (piRNAs) has led to new challenges in the selective detection of RNAs. Many noncoding RNAs act as post-translational regulators of gene expression and are involved in the regulation of cell proliferation or apoptosis, but are difficult to amplify, label, and detect. Standard microarray detection procedures involve pre-hybridization labeling or enzymatic 3'-labeling by polymerase-catalyzed extension. Dual labeling would improve the fidelity of detection, but no polymerases for 5'-extension are known. Here we report a novel labeling method for RNAs bearing natural 5'-phosphate groups, such as miRNAs, based on enzyme-free ligation of a biotin- or fluorophore-labeled oligonucleotide to the 5' termini. The method uses in situ activation of the natural 5'-phosphate groups in these RNAs and was optimized to give near-quantitative conversion in solution. With use of biotin- or fluorophore-bearing labeling strands, different miRNA sequences were detected on microarrays with little background fluorescence. In combination with an established method of enzymatic on-chip labeling at the 3' termini, highly selective detection of related miRNAs was achieved by dual recognition at both termini, even in the case of miRNAs differing in only one nucleotide.     

Chemical Synthesis and Structure of the Prokineticin Bv8

Bv8, a 77‐residue protein isolated from frogs, is the prototypic member of the prokineticin family of cytokines. Prokineticins (PKs) have only recently been identified in vertebrates (including humans), and they are believed to be involved in a number of key physiological processes, such as angiogenesis, neurogenesis, nociception, and tissue development. We used a combination of Boc solid‐phase peptide synthesis, native chemical ligation, and in vitro protein folding to establish robust chemical access to this molecule. Synthetic Bv8 was obtained in good yield and exhibited full activity in a human neuroblastoma cell line and rat dorsal root ganglion (DRG) neurons. The 3D structure of the synthetic protein was determined by using NMR spectroscopy and it was found to be homologous with that of mamba intestinal toxin 1, which is the only other known prokineticin structure. Analysis of a truncated mutant lacking five residues at the N terminus that are critical for receptor binding and activation showed no perturbation to the core protein structure. Together with the functional data, this suggests that receptor binding is likely to be a highly cooperative process possibly involving major allosterically driven structural rearrangements. The facile and efficient synthesis presented here will enable preparation of unique chemical analogues of prokineticins, which should be powerful tools for modulating the structure and function of prokineticins and their receptors, and studying the many physiological processes that have been linked to them.     

Chemical Activation in Blood Serum and Human Cell Culture: Improved Ruthenium Complex for Catalytic Uncaging of Alloc‐Protected Amines

Chemical (as opposed to light‐induced) activation of caged molecules is a rapidly advancing approach to trigger biological processes. We previously introduced the ruthenium‐catalyzed release of allyloxycarbonyl (alloc)‐protected amines in human cells. A restriction of this and all other methods is the limited lifetime of the catalyst, thus hampering meaningful applications. In this study, we addressed this problem with the development of a new generation of ruthenium complexes for the uncaging of alloc‐protected amines with superior catalytic activity. Under biologically relevant conditions, we achieved a turnover number >300, a reaction rate of 580 m ^?1 s^?1, and we observed high activity in blood serum. Furthermore, alloc‐protected doxorubicin, as an anticancer prodrug, could be activated in human cell culture and induced apoptosis with a single low dose (1 μm ) of the new catalyst.     

Chemical Synthesis of Peptides and Proteins Bearing Base-Labile Post-Translational Modifications: Evolution of the Methods in Four Decades

The S-palmitoylation on Cys residue and O-acetylation on Ser/Thr residues are two types of base-labile post-translational modifications (PTMs) in cells. The lability of these PTMs to bases and nucleophiles makes the peptides/proteins bearing S-palmitoyl or O-acetyl groups challenging synthetic targets, which cannot be prepared via the standard Fmoc-SPPS and native chemical ligation. In this review, we summarized the efforts towards their preparation in the past 40 years, with the focus on the evolution of synthetic methods.     

Strain-promoted alkyne-azide cycloadditions (SPAAC) reveal new features of glycoconjugate biosynthesis

We have shown that 4-dibenzocyclooctynol (DIBO), which can easily be obtained by a streamlined synthesis approach, reacts exceptionally fast in the absence of a Cu(I) catalyst with azido-containing compounds to give stable triazoles. Chemical modifications of DIBO, such as oxidation of the alcohol to a ketone, increased the rate of strain promoted azide-alkyne cycloadditions (SPAAC). Installment of a ketone or oxime in the cyclooctyne ring resulted in fluorescent active compounds whereas this property was absent in the corresponding cycloaddition adducts; this provides the first example of a metal-free alkyne-azide fluoro-switch click reaction. The alcohol or ketone functions of the cyclooctynes offer a chemical handle to install a variety of different tags, and thereby facilitate biological studies. It was found that DIBO modified with biotin combined with metabolic labeling with an azido-containing monosaccharide can determine relative quantities of sialic acid of living cells that have defects in glycosylation (Lec CHO cells). A combined use of metabolic labeling/SPAAC and lectin staining of cells that have defects in the conserved oligomeric Golgi (COG) complex revealed that such defects have a greater impact on O-glycan sialylation than galactosylation, whereas sialylation and galactosylation of N-glycans was similarly impacted. These results highlight the fact that the fidelity of Golgi trafficking is a critical parameter for the types of oligosaccharides being biosynthesized by a cell. Furthermore, by modulating the quantity of biosynthesized sugar nucleotide, cells might have a means to selectively alter specific glycan structures of glycoproteins.     

Intein-mediated construction of a library of fluorescent Rab GTPase probes

Rab GTPases play a key role in the regulation of membrane trafficking. Post-translational geranylgeranylation is critical for their biological activity and is conferred by Rab geranylgeranyl transferease (RabGGTase), together with an accessory factor, Rab escort protein (REP). Mechanistic studies of Rab prenylation and identification of RabGGTase inhibitors require sensitive reporters of Rab prenylation. In the present work, a combination of protein engineering and expressed protein ligation was used to construct a library of semisynthetic Rab7 fluorescent conjugates. In order to avoid synthesis of a large number of fluorescently labeled peptides, we developed a strategy that combined thiol-reactive dye-labeling of cysteine with in vitro protein ligation. Application of this strategy required optimization of labeling and ligation conditions to promote thiol labeling and disfavor intramolecular cyclization. Using this approach, we constructed 46 fluorescent sensors with different spectral properties that reported on the interaction of Rab7 with RabGGTase, REP-1, and the overall prenylation reaction. Two constructs, Rab7Δ3CCK(NBD) and Rab7Δ2SCCC-dans, displayed 2.5- and 1.5-fold increase in fluorescence, respectively, upon prenylation. Moreover, dansyl-, NBD (4-nitro-benzofurazan)-, I-BA-, and I-SO-labeled Rab7 conjugates exhibited two- to tenfold change in fluorescence upon binding to REP or RabGGTase. These fluorescent sensors allowed us to monitor Rab prenylation in real time and to investigate the assembly of Rab-REP binary and Rab-REP-RabGGTase ternary complexes.     

A reversible protection strategy to improve Fmoc-SPPS of peptide thioesters by the N-Acylurea approach

C-terminal peptide thioesters are an essential component of the native chemical ligation approach for the preparation of fully or semisynthetic proteins. However, the efficient generation of C-terminal thioesters by Fmoc solid-phase peptide synthesis remains a challenge. The recent N-acylurea approach to thioester synthesis relies on the deactivation of one amine of 3,4-diaminobenzoic acid (Dbz) during Fmoc SPPS. Here, we demonstrate that this approach results in the formation of side products through the over-acylation of Dbz, particularly when applied to Gly-rich sequences. We find that orthogonal allyloxycarbonyl (Alloc) protection of a single Dbz amine eliminates these side products. We introduce a protected Fmoc-Dbz(Alloc) base resin that may be directly used for synthesis with most C-terminal amino acids. Following synthesis, quantitative removal of the Alloc group allows conversion to the active N-acyl-benzimidazolinone (Nbz) species, which can be purified and converted in situ to thioester under ligation conditions. This method is compatible with the automated preparation of peptide-Nbz conjugates. We demonstrate that Dbz protection improves the synthetic purity of Gly-rich peptide sequences derived from histone H4, as well as a 44-residue peptide from histone H3.     

Cover Picture: Semisynthesis and Characterization of the First Analogues of Pro‐Neuropeptide Y (ChemBioChem 5/2003)

The cover picture shows how a combination of recombinant synthesis and chemical synthesis has been used to obtain chemically modified proteins. N‐terminal protein segments of pro‐neuropeptide Y (proNPY) were produced as intein‐fusion proteins in Escherischia coli in order to obtain thioesters. C‐terminal segments were synthesized by parallel automated peptide synthesis and derivatized to obtain carboxyfluorescein‐ (CF) and biotin‐labeled peptides. Native chemical ligation yielded chemically modified full‐length analogues of proNPY that can be used to monitor the biosynthesis of neuropeptide Y. Futher information can be found in the article by Beck‐Sickinger and co‐workers on p. 425 ff.