Ligation Tool Research Articles

Reactivity Profiling for High-Yielding Ynamine-Tagged Oligonucleotide Click Chemistry Bioconjugations.

The Cu-catalyzed azide-alkyne cycloaddition (CuAAC) reaction is a key ligation tool used to prepare bioconjugates. Despite the widespread utility of CuAAC to produce discrete 1,4-triazole products, the requirement of a Cu catalyst can result in oxidative damage to these products. Ynamines are superior reactive groups in CuAAC reactions and require lower Cu loadings to produce 1,4-triazole products. This study discloses a strategy to identify optimal reaction conditions for the formation of oligodeoxyribonucleotide (ODN) bioconjugates. First, the surveying of reaction conditions identified that the ratio of Cu to the choice of reductant (i.e., either sodium ascorbate or glutathione) influences the reaction kinetics and the rate of degradation of bioconjugate products. Second, optimized conditions were used to prepare a variety of ODN-tagged products and ODN-protein conjugates and compared to conventional CuAAC and Cu-free azide-alkyne (3 + 2)cycloadditions (SPAAC), with ynamine-based examples being faster in all cases. The reaction optimization platform established in this study provides the basis for its wider utility to prepare CuAAC-based bioconjugates with lower Cu loadings while maintaining fast reaction kinetics.

Mechanistic Basis of the Cu(OAc)2 Catalyzed Azide-Ynamine (3 + 2) Cycloaddition Reaction.

The Cu-catalyzed azide-alkyne cycloaddition (CuAAC) reaction is used as a ligation tool throughout chemical and biological sciences. Despite the pervasiveness of CuAAC, there is a need to develop more efficient methods to form 1,4-triazole ligated products with low loadings of Cu. In this paper, we disclose a mechanistic model for the ynamine-azide (3 + 2) cycloadditions catalyzed by copper(II) acetate. Using multinuclear nuclear magnetic resonance spectroscopy, electron paramagnetic resonance spectroscopy, and high-performance liquid chromatography analyses, a dual catalytic cycle is identified. First, the formation of a diyne species via Glaser-Hay coupling of a terminal ynamine forms a Cu(I) species competent to catalyze an ynamine-azide (3 + 2) cycloaddition. Second, the benzimidazole unit of the ynamine structure has multiple roles: assisting C-H activation, Cu coordination, and the formation of a postreaction resting state Cu complex after completion of the (3 + 2) cycloaddition. Finally, reactivation of the Cu resting state complex is shown by the addition of isotopically labeled ynamine and azide substrates to form a labeled 1,4-triazole product. This work provides a mechanistic basis for the use of mixed valency binuclear catalytic Cu species in conjunction with Cu-coordinating alkynes to afford superior reactivity in CuAAC reactions. Additionally, these data show how the CuAAC reaction kinetics can be modulated by changes to the alkyne substrate, which then has a predictable effect on the reaction mechanism.

Fluorescent Labeling of Outer Membrane Proteins Using the SpyCatcher-SpyTag System.

The SpyCatcher-SpyTag system has become a popular and versatile tool for protein ligation. It is based on a small globular protein (SpyCatcher) that binds to a 13-residue peptide (SpyTag), which subsequently leads to the formation of a covalent isopeptide bond. Thus, the reaction is essentially irreversible. Here, we describe how the SpyCatcher-SpyTag system can be used to label surface-exposed bacterial outer membrane proteins, e.g., for topology mapping or fluorescent time-course experiments. We cover using fluorescence measurements and microscopy to measure labeling efficiency using SpyCatcherfused with superfolderGFPin this chapter.

Methionine-enabled peptide modification through late-stage Pd-catalyzed β-C(sp3)-H olefination/cyclization.

We present a method for site-selective diversification of peptides via Pd-catalyzed β-C(sp3)-H olefination/cyclization. In this protocol, the native methionine residue acts as a directing group, enabling site-specific olefination/cyclization of peptides. This chemistry demonstrates broad substrate scope, offering a versatile tool for peptide 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.

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.

Synthesis and Reactions of Homoditopic Stable Nitrile N‐Oxide as a Powerful Tool for Catalyst‐Free Constructions of Macromolecular Architectures

AbstractNitrile N‐oxide is a highly reactive 1,3‐dipole that undergoes 1,3‐dipolar cycloaddition reactions to various dipolarophiles. However, the high reactivity of nitrile N‐oxide leads to side reactions with nucleophiles and self‐reactions, resulting in a decrease in the cycloadduct yield. The bulky substituent around nitrile N‐oxide kinetically suppresses such undesirable side reactions, stabilizing nitrile N‐oxide, and improving 1,3‐dipolar cycloaddition efficiency. Homoditopic stable nitrile N‐oxides as a ligation tool between unsaturated bonds are developed, although the challenge of the large‐scale synthesis remains. Herein, the practical synthesis of a homoditopic stable nitrile N‐oxide from bismaleimide is reported. Three simple steps, namely, Michael addition, oximation, and oxidation, produce the homoditopic nitrile N‐oxide in 87% overall yield without purification process using column chromatography. The ligation capacity of nitrile N‐oxide is discussed through polycycloadditions with several bisdipolarophiles and the cross‐linking reaction of polyacrylonitrile.

Recent Advances in the Development of Tetrazine Ligation Tools for Pretargeted Nuclear Imaging.

Tetrazine ligation has gained interest as a bio-orthogonal chemistry tool within the last decade. In nuclear medicine, tetrazine ligation is currently being explored for pretargeted approaches, which have the potential to revolutionize state-of-the-art theranostic strategies. Pretargeting has been shown to increase target-to-background ratios for radiopharmaceuticals based on nanomedicines, especially within early timeframes. This allows the use of radionuclides with short half-lives which are more suited for clinical applications. Pretargeting bears the potential to increase the therapeutic dose delivered to the target as well as reduce the respective dose to healthy tissue. Combined with the possibility to be applied for diagnostic imaging, pretargeting could be optimal for theranostic approaches. In this review, we highlight efforts that have been made to radiolabel tetrazines with an emphasis on imaging.

A systematic approach to inserting split inteins for Boolean logic gate engineering and basal activity reduction

Split inteins are powerful tools for seamless ligation of synthetic split proteins. Yet, their use remains limited because the already intricate split site identification problem is often complicated by the requirement of extein junction sequences. To address this, we augment a mini-Mu transposon-based screening approach and devise the intein-assisted bisection mapping (IBM) method. IBM robustly reveals clusters of split sites on five proteins, converting them into AND or NAND logic gates. We further show that the use of inteins expands functional sequence space for splitting a protein. We also demonstrate the utility of our approach over rational inference of split sites from secondary structure alignment of homologous proteins, and that basal activities of highly active proteins can be mitigated by splitting them. Our work offers a generalizable and systematic route towards creating split protein-intein fusions for synthetic biology.

Evaluation of the outcomes of laparoscopic splenectomy in non-traumatic pathological splenic disorders

Background: currently,minimal invasive surgical techniques were used for several operations in general surgery. Less intra-operative blood loss,less post-operative pain and shorter hospital stay results are some of the benefits that make laparoscopy the best approach for many surgical procedures.Therefore, laparoscopic splenectomy since 1991 when was first described by Delaitre and Maignien. In general, indications for laparoscopic splenectomy are the same as those of open splenectomy, except for the trauma cases, where the role of laparoscopy is still debatable. The introduction of advanced laparoscopic tools for ligation, dissection and vessels sealing devices resulted in less operative time and less intra-operative complications. However, some contraindications still applied, more studies are needed to determine the real value of laparoscopy in massive splenomegaly. Objectives:The aim of the work is evaluation of the outcomes, safety and efficacy of laparoscopic splenectomy in non-traumatic splenic disorders. Patients and methods: This prospective study conducted on patients with hematological disorders indicated for splenectomy for one year. Results: We operated 20 patients of laparoscopic splenectomy, 70% were females, their mean of age by years were 18.9 ± 9.1. No post-operative complications the mean of operation time byhours was3.2 ± 0.7, while the mean of hospital stay was 2.3 ± 0.2 days. The total intra-operative blood loss was about 50–600 ml. Conclusion: Laparoscopic splenectomy for elective operations of the spleen is a safe method associated with a lower risk of peri-operative complications,less mortality and morbidity.

Biochemical and Structural Characterization of an Unusual and Naturally Split Class 3 Intein.

Split inteins are indispensable tools for protein engineering because their ligation and cleavage reactions enable unique modifications of the polypeptide backbone. Three different classes of inteins have been identified according to the nature of the covalent intermediates resulting from the acyl rearrangements in the multistep protein‐splicing pathway. Class 3 inteins employ a characteristic internal cysteine for a branched thioester intermediate. A bioinformatic database search of non‐redundant protein sequences revealed the absence of split variants in 1701 class 3 inteins. We have discovered the first reported split class 3 intein in a metagenomics data set and report its biochemical, mechanistic and structural analysis. The AceL NrdHF intein exhibits low sequence conservation with other inteins and marked deviations in residues at conserved key positions, including a variation of the typical class‐3 WCT triplet motif. Nevertheless, functional analysis confirmed the class 3 mechanism of the intein and revealed excellent splicing yields within a few minutes over a wide range of conditions and with barely detectable cleavage side reactions. A high‐resolution crystal structure of the AceL NrdHF precursor and a mutagenesis study explained the importance and roles of several residues at the key positions. Tolerated substitutions in the flanking extein residues and a high affinity between the split intein fragments further underline the intein's future potential as a ligation tool.

Domain selective labeling for NMR studies of multidomain proteins by domain ligation using highly active sortase A

Structural study of multidomain proteins using NMR is an emerging issue for understanding biological functions. To this end, domain-specific labeling is expected to be a key technology for facilitating the NMR-assignment process and for collecting distance information via spin labeling. To obtain domain-specific labeled samples, use of sortase A as a protein ligation tool is a viable approach. Sortase A enables ligation of separately expressed proteins (domains) through the Leu-Pro-X-Thr-Gly linker. However, the ligation reaction mediated by sortase A is not efficient. Poor yield and long reaction times hamper large-scale preparation using sortase A. Here we report the application of highly active sortases to NMR analyses. Optimal yields can be achieved within several hours when the ligation reaction are mediated by highly active sortases at 4 °C. We propose that this protocol can contribute to structural analyses of multidomain proteins by NMR.

Visible Light [2 + 2] Cycloadditions for Reversible Polymer Ligation

We introduce visible light induced dynamic covalent chemistry as a powerful reversible ligation tool based on a wavelength-dependent photon efficiency analysis (WPEA). We demonstrate by a monochromatic wavelength scan of the reversible dimerization of styrylpyrene at constant photon count that the system is most effective in its forward reaction at 435 nm, while the highest reverse reaction efficiency is observed at 330 nm. Critically, these optimum wavelengths are not accessible by inspection of the UV/vis spectra of the monomer and the dimer. Application of the identified reaction conditions enabled an entirely λ-orthogonal photoreversible polymer ligation using visible light, including with readily available light sources. The current study thus makes a [2 + 2] reaction system applicable in the critical visible light regime based on quantitative wavelength resolved data for applications in recodeable surface design in biological environments as well as reprogrammable materials systems.

Open vs Laparoscopic Splenectomy among Saudi Patients

The spleen is one of the most frequently injured intraperitoneal organs, and management of splenic injuries may require splenectomy. Traditionally, surgical removal of the spleen was done by an open approach using either an upper midline or left subcostal incision. Open splenectomy is performed in two major clinical scenarios: trauma and hematologic disease. With the advent of minimally invasive techniques, laparoscopic splenectomy has become a standard procedure for elective removal of the spleen for most indications. Nowadays laparoscopic splenectomy is the approach of choice for both benign and malignant diseases of the spleen. However, some contraindications still apply. The evolution of the technology has allowed though, cases which were considered to be absolute contraindications for performing a minimal invasive procedure to be treated with modified laparoscopic approaches. Moreover, the introduction of advanced laparoscopic tools for ligation resulted in less intraoperative complications. Today, laparoscopic splenectomy is considered safe, with better outcomes in comparison to open splenectomy, and the increased experience of surgeons allows operative times comparable to those of an open splenectomy. In this review we discussed the indications and the contraindications of laparoscopic splenectomy. Furthermore, we analyze the surgical techniques.

Segmental isotopic labeling of a single-domain globular protein without any refolding step by an asparaginyl endopeptidase.

Asparaginyl endopeptidases (AEPs) catalyze head-to-tail backbone cyclization of naturally occurring cyclic peptides such as cyclotides, and have become an important peptide-engineering tool for macrocyclization and peptide ligation. Here, we report efficient protein ligation in trans by mimicking efficient backbone cyclization by an AEP without any excess of reactants. We demonstrate a practical application of segmental isotopic labeling for NMR studies of a single-domain globular protein without any refolding step using the recombinant AEP prepared from Escherichia coli. This simple protein ligation approach using an AEP could be applied for incorporation of various biophysical probes into proteins as well as post-translational production of full-length proteins.

Laparoscopic splenectomy: Current concepts.

Since early 1990’s, when it was inaugurally introduced, laparoscopic splenectomy has been performed with excellent results in terms of intraoperative and postoperative complications. Nowadays laparoscopic splenectomy is the approach of choice for both benign and malignant diseases of the spleen. However some contraindications still apply. The evolution of the technology has allowed though, cases which were considered to be absolute contraindications for performing a minimal invasive procedure to be treated with modified laparoscopic approaches. Moreover, the introduction of advanced laparoscopic tools for ligation resulted in less intraoperative complications. Today, laparoscopic splenectomy is considered safe, with better outcomes in comparison to open splenectomy, and the increased experience of surgeons allows operative times comparable to those of an open splenectomy. In this review we discuss the indications and the contraindications of laparoscopic splenectomy. Moreover we analyze the standard and modified surgical approaches, and we evaluate the short-term and long-term outcomes.

A Click Ligation Based on SuFEx for the Metal‐Free Synthesis of Sugar and Iminosugar Clusters

Although the preparation of anomeric glycosylsulfonyl fluoride was unsuccessful, a tetra‐O‐acetylated C‐glucosylpropanesulfonyl fluoride was synthesized starting from the corresponding thioacetate via sulfonate formation as the key intermediate. This sulfonyl fluoride was a bench‐stable product that reacted promptly with primary and secondary alkylamines at 80 °C to give the corresponding sulfonamides in good yield. On the other hand, the same fluoride was inert toward arylamines whereas its precursor, the sulfonyl chloride, showed good reactivity. Another limitation of the acetylated sugar sulfonyl fluoride was its lack of reactivity with a multivalent aminated calixarene, this being due to acetyl transfer from the carbohydrate moiety to the amino groups of the scaffold. Fortunately, the tetra‐O‐benzylated C‐glucosylpropanesulfonyl fluoride, prepared by the same reaction sequence employed for the synthesis of the acetylated analogue, reacted with the tetra‐aminopropyl‐calix[4]arene to afford the corresponding sulfonamide‐linked sugar cluster in high isolated yield. A similar approach to the synthesis of calixarene‐based iminosugar clusters was unsuccessful because 1‐deoxynojirimycin sulfonyl fluoride derivatives could not be generated. However, a tetra‐propylsulfonyl fluoride calixarene, obtained from the free‐OH calix[4]arene through a three‐step reaction sequence, underwent clean coupling with both C‐glucosylpropylamine and N‐aminopentyl‐1‐deoxy‐deoxynojirimycin derivatives to give the corresponding tetravalent sugar and iminosugar clusters. This metal‐free click reaction may constitute a valuable tool in the arsenal of ligation tools for the synthesis of multivalent carbohydrate architectures.

Reporter Immobilization Assay (REIA) for Bioconjugating Reactions.

Enzymes able to ligate biomolecules are emerging tools to generate site-specific bioconjugates. In this study we present a detection and screening method for bioconjugating enzymes which overcomes limitations of analytical methods such as HPLC or MS. These techniques are experimentally demanding and often limited in sensitivity and throughput compared to enzymatic assays. The principle of this Reporter Immobilization Assay (REIA) is the ligation of a reporter enzyme to a peptide carrying an affinity handle, which can be utilized for its isolation. The REIA system exhibits a high sensitivity with a linear range down to 1 μg/mL (55 nM), a variation coefficient of 6.5%, and can be performed cost-efficiently in 96-well microtiter plate format. The application of this assay allowed the characterization of a thiol transpeptidase sortase from S. aureus which is an important drug target and a biotechnological tool for ligation and modification of proteins. Thereby, yet-undetectable promiscuous activity of sortase could be detected, e.g., the acceptance of alanine as nucleophile. In addition, we were able to provide evidence that the REIA is suitable for high throughput screening of enzyme libraries using crude cellular extract with a throughput of 600 samples per hour.

Nature's recipe for splitting inteins.

Protein splicing in trans by split inteins has increasingly become a powerful protein-engineering tool for protein ligation, both in vivo and in vitro. Over 100 naturally occurring and artificially engineered split inteins have been reported for protein ligation using protein trans-splicing. Here, we review the current status of the reported split inteins in order to delineate an empirical or rational strategy for constructing new split inteins suitable for various applications in biotechnology and chemical biology.

Metal‐Catalyzed and Metal‐Free Alkyne Hydrothiolation: Synthetic Aspects and Application Trends

AbstractAlkyne hydrothiolation – that is, the addition of the SH bond of a thiol across the carbon‐carbon triple bond of an unactivated alkyne – belongs to the ample class of hydrofunctionalization reactions whose main feature is their occurrence with total atom economy. Hence this reaction is emerging as a valuable tool for the preparation of sulfur‐containing compounds such as vinyl thioethers, which are of interest for their own biological properties and for their use as intermediates in total synthesis. Thus, the first part of this review deals with the various efforts directed towards the preparation of vinyl thioethers in a regio‐ and diastereoselective manner by metal‐catalyzed approaches in recent years. The number of methods employed, with use of a variety of catalysts and reaction conditions, allow the synthesis of vinyl thioethers to be carried out with high efficiency and selectivity. The second part of the article is based on the use of the photoinduced free‐radical approach to hydrothiolation, which allows the introduction of two thiol fragments across the carbon‐carbon triple bond, thereby leading to the formation of dithioethers. This approach turned out to be especially useful as a ligation tool for the installation of densely functionalized arrays on various scaffolds and complex biomolecular systems. Concluding remarks emphasize the role of the photoinduced free‐radical strategy as a complementary tool to copper‐catalyzed azide‐alkyne cycloaddition.