Protecting Group Chemistry Research Articles

Sec-isoamyl Mercaptan (SIT), a Multi-faceted Disulfide Based Protecting Group for Cysteine Thiol

IntroductionThe successful synthesis of a peptide requires the synchronization of several processes, including the efficient execution of protecting group chemistry. For cysteine (Cys)-peptides, this is more crucial because the trifunctional Cys has a free thiol in its side chain. During synthesis, this free thiol function remains protected with suitable protecting groups and can be removed after synthesis using appropriate methods. Sec-isoamyl mercaptan (SIT) is a versatile disulfide-based protecting group for Cys side chain thiol. The removal of SIT from Cys thiol can be achieved using a mild reducing agent (e. g. DTT). This later promotes efficient disulfide bond formation by oxidation. SIT can also direct/activate the Cys thiol for the chemoselective formation of disulfide bonds by thiol-disulfide interchange.MethodsPeptides were synthesized using solid-phase peptide synthesis techniques. The removal of the SIT group was carried out either in the solid phase or in the solution.ResultsIn the present study, we have shown that SIT can be efficiently removed both in solution and on-resin to facilitate disulfide-bridged peptide synthesis. This was exemplified by two syntheses of an atosiban derivative, where the SIT was removed in solution or in solid-phase. Furthermore, a SIT-based facile one-pot synthesis pathway was devised for disulfide-rich peptides. The strategy was faster and greener as it did not involve using an oxidizer. Conotoxin (two S–S) and linaclotide amide (three S–S) were successfully synthesized by adopting the SIT-based strategy. Finally, a racemization study was carried out for SIT, Trt and StBu-protected Cys-peptides. In all cases, SIT-protected peptides showed lesser racemization than StBu-protected peptides. In some instances (synthesis using DMF), SIT-protected peptides showed less racemization compared to the Trt congeners.ConclusionOverall, the multifaceted use of SIT-protection during the synthesis of disulfide-rich peptides has illustrated its versatility as a Cys thiol protecting group.

Sandmeyer Chlorosulfonylation of (Hetero)Aromatic Amines Using DABSO as an SO2 Surrogate.

Sulfonyl chlorides not only play a crucial role in protecting group chemistry but also are important starting materials in the synthesis of sulfonamides, which are in-demand motifs in drug discovery chemistry. Despite their importance, the number of different synthetic approaches to sulfonyl chlorides is limited, and most of them rely on traditional oxidative chlorination chemistry from thiol precursors. In this report, we disclose a novel Sandmeyer-type sulfonyl chloride synthesis from feedstock anilines and DABSO, used as a stable SO2 surrogate, in the presence of HCl and a Cu catalyst. The method works on a wide range of anilines and allows for the isolation of the sulfonyl chloride after aqueous workup or its direct conversion into the sulfonamide by simple addition of an amine after the completion of the Sandmeyer reaction. The scalability of this method was demonstrated on a 20 g scale, and the corresponding heterocyclic sulfonyl chloride was isolated in 80% yield and excellent purity.

Arginine-Functional Methacrylic Block Copolymer Nanoparticles: Synthesis, Characterization, and Adsorption onto a Model Planar Substrate.

Recently, we reported the synthesis of a hydrophilic aldehyde-functional methacrylic polymer (Angew. Chem., 2021, 60, 12032-12037). Herein we demonstrate that such polymers can be reacted with arginine in aqueous solution to produce arginine-functional methacrylic polymers without recourse to protecting group chemistry. Careful control of the solution pH is essential to ensure regioselective imine bond formation; subsequent reductive amination leads to a hydrolytically stable amide linkage. This new protocol was used to prepare a series of arginine-functionalized diblock copolymer nanoparticles of varying size via polymerization-induced self-assembly in aqueous media. Adsorption of these cationic nanoparticles onto silica was monitored using a quartz crystal microbalance. Strong electrostatic adsorption occurred at pH 7 (Γ = 14.7 mg m-2), whereas much weaker adsorption occurred at pH 3 (Γ = 1.9 mg m-2). These findings were corroborated by electron microscopy, which indicated a surface coverage of 42% at pH 7 but only 5% at pH 3.

Carbon quaternization of redox active esters and olefins by decarboxylative coupling.

The synthesis of quaternary carbons often requires numerous steps and complex conditions or harsh reagents that act on heavily engineered substrates. This is largely a consequence of conventional polar-bond retrosynthetic disconnections that in turn require multiple functional group interconversions, redox manipulations, and protecting group chemistry. Here, we report a simple catalyst and reductant combination that converts two types of feedstock chemicals, carboxylic acids and olefins, into tetrasubstituted carbons through quaternization of radical intermediates. An iron porphyrin catalyst activates each substrate by electron transfer or hydrogen atom transfer, and then combines the fragments using a bimolecular homolytic substitution (SH2) reaction. This cross-coupling reduces the synthetic burden to procure numerous quaternary carbon---containing products from simple chemical feedstocks.

Deprotective Functionalization: A Direct Conversion of Nms-Amides to Carboxamides Using Carboxylic Acids.

The nature of protecting group chemistry necessitates a deprotection step to restore the initially blocked functionality prior to further transformation. As this aspect of protecting group manipulation inevitably adds to the step count of any synthetic sequence, the development of methods enabling simultaneous deprotection and functionalization ("deprotective functionalization"-distinct from "deprotection followed by functionalization") is appealing, as it has the potential to improve efficiency and streamline synthetic routes. Herein, we report a deprotective functionalization of the newly introduced Nms-amides guided by density functional theory (DFT) analysis, which exploits the inherent Nms reactivity. Mechanistic studies further substantiate and help rationalize the exquisite reactivity of Nms-amides, as other commonly used protecting groups are shown not to exhibit the same reactivity patterns. The practicality of this approach was ultimately demonstrated in selected case studies.

Synthesis of portimines reveals the basis of their anti-cancer activity.

Marine-derived cyclic imine toxins, portimine A and portimine B, have attracted attention because of their chemical structure and notable anti-cancer therapeutic potential1-4. However, access to large quantities of these toxins is currently not feasible, and the molecular mechanism underlying their potent activity remains unknown until now. To address this, a scalable and concise synthesis of portimines is presented, which benefits from the logic used in the two-phase terpenoid synthesis5,6 along with other tactics such as exploiting ring-chain tautomerization and skeletal reorganization to minimize protecting group chemistry through self-protection. Notably, this total synthesis enabled a structural reassignment of portimine B and an in-depth functional evaluation of portimine A, revealing that it induces apoptosis selectively in human cancer cell lines with high potency and is efficacious in vivo in tumour-clearance models. Finally, practical access to the portimines and their analogues simplified the development of photoaffinity analogues, which were used in chemical proteomic experiments to identify a primary target of portimine A as the 60S ribosomal export protein NMD3.

Development of an Effective Functional Lipid Anchor for Membranes (FLAME) for the Bioorthogonal Modification of the Lipid Bilayer of Mesenchymal Stromal Cells.

The glycosylation of cellular membranes is crucial for the survival and communication of cells. As our target is the engineering of the glycocalyx, we designed a functionalized lipid anchor for the introduction into cellular membranes called Functional Lipid Anchor for MEmbranes (FLAME). Since cholesterol incorporates very effectively into membranes, we developed a twice cholesterol-substituted anchor in a total synthesis by applying protecting group chemistry. We labeled the compound with a fluorescent dye, which allows cell visualization. FLAME was successfully incorporated in the membranes of living human mesenchymal stromal cells (hMSC), acting as a temporary, nontoxic marker. The availability of an azido function─a bioorthogonal reacting group within the compound─enables the convenient coupling of alkyne-functionalized molecules, such as fluorophores or saccharides. After the incorporation of FLAME into the plasma membrane of living hMSC, we were able to successfully couple our molecule with an alkyne-tagged fluorophore via click reaction. This suggests that FLAME is useful for the modification of the membrane surface. Coupling FLAME with a galactosamine derivative yielded FLAME-GalNAc, which was incorporated into U2OS cells as well as in giant unilamellar vesicles (GUVs) and cell-derived giant plasma membrane vesicles (GPMVs). With this, we have shown that FLAME-GalNAc is a useful tool for studying the partitioning in the liquid-ordered (Lo) and the liquid-disordered (Ld) phases. The molecular tool can also be used to analyze the diffusion behavior in the model and the cell membranes by fluorescence correlation spectroscopy (FCS).

Nickel-Catalyzed Chemoselective Arylation of Amino Alcohols.

A systematic evaluation of competitive bisphosphine/Ni-catalyzed C-N versus C-O cross-couplings involving model compounds enabled development of hitherto unknown chemoselective O- and N-arylation of amino alcohols with (hetero)aryl chloride electrophiles, without recourse to protection group chemistry. Use of the CyPAd-DalPhos pre-catalyst C2 enabled particularly challenging O-arylation chemoselectivity in amino alcohols featuring branched primary and secondary alkylamine groups, while selective N-arylation was observed in substrates featuring less-hindered linear alkylamine and aniline reacting groups. Useful reaction scope in the (hetero)aryl chloride was achieved throughout, and the ability to conduct such transformations using benchtop handling of materials is demonstrated.

Nickel‐Catalyzed Chemoselective Arylation of Amino Alcohols

AbstractA systematic evaluation of competitive bisphosphine/Ni‐catalyzed C−N versus C−O cross‐couplings involving model compounds enabled development of hitherto unknown chemoselective O‐ and N‐arylation of amino alcohols with (hetero)aryl chloride electrophiles, without recourse to protection group chemistry. Use of the CyPAd‐DalPhos pre‐catalyst C2 enabled particularly challenging O‐arylation chemoselectivity in amino alcohols featuring branched primary and secondary alkylamine groups, while selective N‐arylation was observed in substrates featuring less‐hindered linear alkylamine and aniline reacting groups. Useful reaction scope in the (hetero)aryl chloride was achieved throughout, and the ability to conduct such transformations using benchtop handling of materials is demonstrated.

Protection of Boronic Acids Using a Tridentate Aminophenol ONO Ligand for Selective Suzuki–Miyaura Coupling

Boronic acid protecting group chemistry powerfully enhances the versatility of Suzuki-Miyaura cross-coupling. Prominent examples include trifluoroborate salts, N-methyliminodiacetic acid (MIDA) boronates, and 1,8-diaminonaphthalene boronamides. In this work, we present a bis(2-hydroxybenzyl)methylamine (BOMA) ligand that forms tridentate complexes with boronic acids much like the MIDA ligand but the deprotection is facilitated by organic acids. The BOMA boronates showed considerable stability in both aqueous base and acid, and a variety of chemoselective reactions were performed on these boronates, including selective Suzuki-Miyaura coupling, palladium-catalyzed borylation, ester hydrolysis, alkylation, lithiation-borylation, and oxidative hydroxydeboronation.

Substrate specific closed-loop optimization of carbohydrate protective group chemistry using Bayesian optimization and transfer learning.

A new way of performing reaction optimization within carbohydrate chemistry is presented. This is done by performing closed-loop optimization of regioselective benzoylation of unprotected glycosides using Bayesian optimization. Both 6-O-monobenzoylations and 3,6-O-dibenzoylations of three different monosaccharides are optimized. A novel transfer learning approach, where data from previous optimizations of different substrates is used to speed up the optimizations, has also been developed. The optimal conditions found by the Bayesian optimization algorithm provide new insight into substrate specificity, as the conditions found are significantly different. In most cases, the optimal conditions include Et3N and benzoic anhydride, a new reagent combination for these reactions, discovered by the algorithm, demonstrating the power of this concept to widen the chemical space. Further, the developed procedures include ambient conditions and short reaction times.

Biotechnological production of cyclic dinucleotides-Challenges and opportunities.

Cyclic dinucleotides (CDNs) are widely used secondary signaling molecules in prokaryotic and eukaryotic cells. As strong agonists of the stimulator of interferon genes, they are of great interest for pharmaceutical applications. In particular, cyclic-GMP-AMP and related synthetic CDNs are promising candidates in preclinical work and even some in clinical phase 1 and 2 studies. The comparison of chemical and biocatalytic synthesis routes elucidated that biological CDN synthesis offers some advantages, such as shorter synthesis time, avoiding complex protective group chemistry, and the access to a new spectrum of CDNs. However, the synthesis of CDNs in preparative quantities is still a challenge, since the chemical synthesis of CDNs suffers from low yields and complex synthetic routes and the enzymatically catalyzed synthesis is limited by low product titers and process stability. We aim to review the latest discoveries and recent trends in chemical and biocatalytic synthesis of CDNs with a focus on the synthesis of a huge variety of CDN derivatives. We furthermore consider the most promising biotechnological processes for CDN production by evaluating key figures of the currently known processes.

Acetal-Based Functional Epoxide Monomers: Polymerizations and Applications.

Protecting group chemistry is essential for various organic transformation and polymerization processes. In particular, conventional anionic ring-opening polymerization (AROP) often requires proper protecting group chemistry because it is typically incompatible with most functional groups due to the highly basic and nucleophilic conditions. In this context, many functional epoxide monomers with proper protecting groups are developed, including the acetal group as a representative example. Since the early introduction of ethoxyethyl glycidyl ether, there is significant development of acetal-based monomers in the polyethers. These monomers are now utilized not only as protecting groups for hydroxyl groups under AROP conditions but also as pH-responsive moieties for biomedical applications, further expanding their utility in the use of functionalized polyethers. Recent progress in this field is outlined from their synthesis, polymerization, and biomedical applications.

A New Scalable Synthesis of ELQ-300, ELQ-316, and other Antiparasitic Quinolones.

The Endochin-Like Quinolone (ELQ) compound class may yield effective, safe treatments for a range of important human and animal afflictions. However, to access the public health potential of this compound series, a synthetic route needed to be devised that lowers costs and is amenable to large scale production. In the new synthetic route described here, a substituted β-keto ester, formed by an Ullmann reaction and subsequent acylation, is reacted with an aniline via a Conrad-Limpach reaction to produce 3-substituted 4(1H)-quinolones such as ELQ-300 and ELQ-316. This synthetic route, the first described to be truly amenable to industrial scale production, is relatively short (5 reaction steps), does not require palladium, chromatographic separation or protecting group chemistry, and may be performed without high vacuum distillation.

Aryl groups, supplement of amino protecting group chemistry!

Amino group protective strategy has consequently emerged in multistep organic synthesis. Easy and selective deprotection procedures are crucial to facilitate the chemical transformation. Recently, Zhang’s group from Henan Normal University collaborating with Chen’s group of Nankai University developed a novel strategy for the regiospecific cleavage of inert aryl CN bonds in N-aryl amides by hypervalent iodine(V) reagents. These procedures allow removal of sort of aryl groups under mild conditions to give primary amides in high efficiency. It bestows these aryl groups with the characteristics of amino protecting groups that might be the supplement of amino protecting group chemistry.

Protecting-Group-Free Iterative Exponential Growth Method for Synthesizing Sequence-Defined Polymers.

As a main synthetic strategy for monodisperse sequence-defined polymers, the known iterative exponential growth (IEG) methods were all developed on protecting-group chemistry, where the additional deprotection reactions increased their synthetic steps and decreased their atom economy. In this study, we developed a protecting-group-free IEG method for the formation of sequence-defined polymers by combining three orthogonal click reactions of copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC), sulfur-fluoride exchange reaction (SuFEx), and Ugi four-component reaction (Ugi-4CR). In this approach, oligomer synthesis began with three parallel CuAAC, SuFEx, and Ugi-4CR couplings among three monomers each with two orthogonal clickable end groups. By iteratively applying parallel CuAAC, SuFEx, and Ugi-4CR to couple three resultant oligomers, each having two orthogonal clickable terminals, this approach could exponentially grow three different sequence-defined polymers simultaneously with high efficiency, requiring no protecting-group chemistry. Additionally, each Ugi-4CR coupling reaction could introduce two external side groups to provide the molecular variation and side-chain functionalization for the resultant sequence-defined polymers.

Cysteine protecting groups: applications in peptide and protein science.

Protecting group chemistry for the cysteine thiol group has enabled a vast array of peptide and protein chemistry over the last several decades. Increasingly sophisticated strategies for the protection, and subsequent deprotection, of cysteine have been developed, facilitating synthesis of complex disulfide-rich peptides, semisynthesis of proteins, and peptide/protein labelling in vitro and in vivo. In this review, we analyse and discuss the 60+ individual protecting groups reported for cysteine, highlighting their applications in peptide synthesis and protein science.

In vitro Targetability Validation of Peptide-Functionalized Mesoporous Silica Nanoparticles in the Presence of Serum Proteins.

Demonstration of receptor-mediated targeting of nanoparticles to specific organs and/or cell types is an integral aim in many bionanomedicine development projects. However, engagement of targeted receptors with ligands on nanocarriers, which is the cornerstone of the active targeting concept, is challenging to study under biologically relevant conditions and thus often stays overlooked. In this work, we utilize an in-house established bioassay for in vitro targetability validation of mesoporous silica nanoparticles (MSNs), functionalized with high-affinity peptide ligands to somatostatin receptors via protective group chemistry, ensuring the correct orientation of the peptide's pharmacophore. We demonstrate that targeted nanoparticles, but not scrambled peptide-decorated counterparts, specifically engage the targeted receptors in living cells in culture media containing serum protein. The importance of being able to exclude false positives originating from the premature detachment of targeting peptides from the MSNs is highlighted.

Synthesis strategies towards amorphous porous carbons with selective oxygen functionalization for the application as reference material

Manipulation of carbon surface functionalization and especially of oxygen surface groups has been demonstrated to be key for obtaining high performance materials in a multitude of applications. Although control of carbon surface chemistry offers large potential in many technical relevant applications, qualitative and quantitative analysis of surface oxides for amorphous and porous carbons remains challenging. In this study, we attempt selective, organic chemistry-based functionalization of a polymer-derived porous model carbon featuring high oxygen loadings, with the aim to establish analytical standards for temperature programmed desorption (TPD) and diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS). In this context, quantitative chemical reduction of an oxidized carbon material with lithium aluminum hydride (LiAlH4) is utilized as the key for the synthesis of carbon materials with defined ensembles of oxygen surface groups (hydroxyl groups and ethers). Based on this reduction strategy, selective LiAlH4 reduction based on protection group chemistry leads to aldehydes, ketones and quinones as surface functional groups and chemical grafting is studied for the selective introduction of phenyl esters, methyl ethers and carboxylic acids. All materials are evaluated with respect to the applicability as analytical standard by DRIFT spectroscopy, TPD, X-ray photoelectron spectroscopy and titration methods.

Yb(OTf)3-Catalyzed and Di-tert-butyl Dicarbonate-Mediated Decarboxylative Etherification and Esterification Reactions.

Protecting group chemistry has invariably captured the fascination of chemists because of its extensive viability in chemical synthesis. The present report describes our pioneer work of applying ytterbium triflate as a catalyst, for the reaction of alcohols with di-tert-butyl dicarbonate (Boc2O) leading to the formation of tert-butyl ethers. There exists no recorded evidence for the use of Yb(OTf)3 as a catalyst for the protection of alcohols to tert-butyl ethers, despite its excellent utility in various reactions. Yb(OTf)3 has been used predominantly in the catalytic deprotection studies such as selective deprotection of tert-butyl esters to carboxylic acids as well as prenyl ethers to alcohols. This study involved the critical evaluation of solvent, time, and temperature that finally led to an efficient protocol for the formation of tert-butyl ethers. Yb(OTf)3 catalyzed the formation of tert-butyl ethers, notably reducing the reaction time, which is exemplified by the achievement of up to 92% conversion of alcohols to tert-butyl ethers within an hour. Additionally, the report demonstrates the utility of this synthetic protocol for the protection of carboxylic acids.