Selective tert-Butyl Ester Deprotection in the Presence of Acid Labile Protecting Groups with Use of ZnBr2

Traceless Staudinger Ligation to Access Stable Aminoacyl- or Peptidyl-Dinucleotide

Aminoacyl- and peptidyl-tRNA are specific biomolecules involved in many biological processes, from ribosomal protein synthesis to the synthesis of peptidoglycan precursors. Here, we report a post-synthetic approach based on traceless Staudinger ligation for the synthesis of a stable amide bond to access aminoacyl- or peptidyl-di-nucleotide. A series of amino-acid and peptide ester phenyl phosphines were synthetized, and their reactivity was studied on a 2'-N₃ di-nucleotide. The corresponding 2'-amide di-nucleotides were obtained and characterized by LC-HRMS, and mechanistic interpretations of the influence of the amino acid phenyl ester phosphine were proposed. We also demonstrated that enzymatic 5'-OH phosphorylation is compatible with the acylated di-nucleotide, allowing the possibility to access stable aminoacylated-tRNA.

Synthesis of RNA-cofactor conjugates and structural exploration of RNA recognition by an m6A RNA methyltransferase

Chemical synthesis of RNA conjugates has opened new strategies to study enzymatic mechanisms in RNA biology. To gain insights into poorly understood RNA nucleotide methylation processes, we developed a new method to synthesize RNA-conjugates for the study of RNA recognition and methyl-transfer mechanisms of SAM-dependent m⁶A RNA methyltransferases. These RNA conjugates contain a SAM cofactor analogue connected at the N6-atom of an adenosine within dinucleotides, a trinucleotide or a 13mer RNA. Our chemical route is chemo- and regio-selective and allows flexible modification of the RNA length and sequence. These compounds were used in crystallization assays with RlmJ, a bacterial m⁶A rRNA methyltransferase. Two crystal structures of RlmJ in complex with RNA–SAM conjugates were solved and revealed the RNA-specific recognition elements used by RlmJ to clamp the RNA substrate in its active site. From these structures, a model of a trinucleotide bound in the RlmJ active site could be built and validated by methyltransferase assays on RlmJ mutants. The methyl transfer by RlmJ could also be deduced. This study therefore shows that RNA-cofactor conjugates are potent molecular tools to explore the active site of RNA modification enzymes.

Versatile synthesis of pathogen specific bacterial cell wall building blocks

Full details on the design, strategies and tactics for development of a novel synthetic sequence to farnesyl lipid I and II analogs is reported. The modular route was based on a three coupling strategy involving an efficient solid phase synthesis of the elaborate peptide fragment, which proceeded with excellent yield and stereoselectivity and was efficiently applied for the convergent synthesis of 3-lipid I and II. Furthermore, the generality of this route was demonstrated by synthesis of 3-lipid I congeners that are characteristic for S. aureus and E. faecalis. All 3-lipid I and II building blocks were obtained in high purity revealing high spectroscopic resolution.

A modular three coupling strategy involving a versatile solid phase peptide synthesis enables access to pathogen specific lipid analogs in high yield, revealing high spectroscopic resolution of these key bacterial cell wall building blocks.

A unified total synthesis of benzo[d][1,3]dioxole-type benzylisoquinoline alkaloids of aporphines, coptisines, and dibenzopyrrocolines

The first total synthesis of (S)-(+)-ovigerine, (S)-(+)-N-formylovigerine, and (6aS,6a'S)-(+)-ovigeridimerine of aporphine alkaloids with a benzo[d][1,3]dioxole structure feature was established. The strategy was based upon the well-known Pd-catalyzed arylation to set the aporphine framework, and Noyori asymmetric hydrogenation followed by diastereoselective resolution to achieve excellent enantioselectivity. By slightly modifying the total synthetic route and strategically combining it with a aza-Michael addition, Bischler-Napieralski reaction and N-arylation, this methodology was also applied to the total syntheses of benzo[d][1,3]dioxole-type benzylisoquinoline alkaloids of coptisines and dibenzopyrrocolines, including two impatiens, tetrahydrocoptisine, and quaternary coptisine bromide of coptisines and two dibenzopyrrocoline analogues, with the syntheses of all of these target compounds being efficient. Among the nine synthesized compounds, the total syntheses of the three aporphines and the two impatiens, all with ee values of greater than 99%, were reported for the first time. This work also represents the first unification of synthetic routes for the total synthesis of benzo[d][1,3]dioxole-type aporphines, coptisines, and dibenzopyrrocolines.

A Zinc-Mediated Deprotective Annulation Approach to New Polycyclic Heterocycles

A straightforward approach to new polycyclic heterocycles, 1H-benzo[4,5]imidazo[1,2-c][1,3]oxazin-1-ones, is presented. It is based on the ZnCl₂-promoted deprotective 6-endo-dig heterocyclization of N-Boc-2-alkynylbenzimidazoles under mild conditions (CH₂Cl₂, 40 °C for 3 h). The zinc center plays a dual role, as it promotes Boc deprotection (with formation of the tert-butyl carbocation, which can be trapped by substrates bearing a nucleophilic group) and activates the triple bond toward intramolecular nucleophilic attack by the carbamate group. The structure of representative products has been confirmed by X-ray diffraction analysis.

SAR Studies of the Leupyrrins: Design and Total Synthesis of Highly Potent Simplified Leupylogs

Leupyrrins are highly potent antifungal agents. A structure-activity-relationship study of natural and synthetic derivatives is reported which reveals important insights into the biological relevance of several structural subunits leading to the discovery of highly potent but drastically simplified leupylogs that incorporate a stable and readily available aromatic side chain. For their synthesis a concise strategy is described that enables a short and versatile access.

Peptidomimetics prepared by tail-to-side chain one component peptide stapling inhibit Alzheimer's amyloid-β fibrillogenesis

Alzheimer's disease (AD) is the most common form of dementia affecting the elderly population worldwide. Despite enormous efforts and considerable advancement in research, no therapeutic agents have come to light to date. However, many peptide-based and small molecule inhibitors interact efficiently with the amyloid-β (Aβ) peptide and alter its aggregation pathway. On the other hand, stapled peptides have been developed mainly to stabilize α-helix conformations and study protein–protein interactions. β-Sheet stabilization or destabilization by stapled peptides has not been explored enough. Herein, we describe the generation of a library of “tail-to-side chain” stapled peptides via lactamization and their application for the first time as modulators of Aβ_1-40 self-association and fibrillogenesis. They also disrupt the preformed fibrillar aggregates into nontoxic species. Their stability in the presence of proteolytic enzymes is increased due to stapling. Therefore, the stapled peptides thus formed can be useful as potent amyloid aggregation inhibitors and pave a therapeutic pathway for combating amyloid-related diseases. Also, they may help in gaining insight into the process of aggregation.

Tail to side-chain stapled peptides inhibit fibrillogenesis of Alzheimer's amyloid β peptide by facilitating off-pathway aggregation.

Protecting Groups in Peptide Synthesis

The protection of amino acid reactive functionalities including the α-amino group, the side chain (amines, carboxylic acids, alcohols, and thiols), or the carboxylic acid terminus is an essential strategy in peptide chemistry. This is mandatory to prevent polymerization of the amino acids and to minimize undesirable side reactions during the synthetic process. Proper protecting group manipulation strategies can maximize the yield of the desired product or allow the construction of complex peptide-based structures. Thus, the compatibility and orthogonality of each protecting group are key to achieve the proper control of molecular structure. Herein, we describe some common protecting groups and their general unmasking methods, in order to mask and expose amine, carboxylic acid, alcohol, and thiol functionalities to achieve the synthesis of peptides and related molecules.

Synthesis and RNA-Binding Properties of Extended Nucleobases for Triplex-Forming Peptide Nucleic Acids

Triple-helix formation, using Hoogsteen hydrogen bonding of triplex-forming oligonucleotides, represents an attractive method for sequence-specific recognition of double-stranded nucleic acids. However, practical applications using triple-helix-forming oligonucleotides and their analogues are limited to long homopurine sequences. The key problem for recognition of pyrimidines is that they present only one hydrogen-bond acceptor or donor group in the major groove. Herein, we report our first attempt to overcome this problem by using peptide nucleic acids (PNAs) modified with extended nucleobases that form three hydrogen bonds along the entire Hoogsteen edge of the Watson-Crick base pair. New nucleobase triples (five) were designed, and their hydrogen bonding feasibility was confirmed by ab initio calculations. PNA monomers carrying the modified nucleobases were synthesized and incorporated in short model PNA sequences. Isothermal titration calorimetry showed that these nucleobases had a modest binding affinity for their double-stranded RNA (dsRNA) targets. Finally, molecular modeling of the modified triples in PNA-dsRNA helix suggested that the modest binding affinity was caused by subtle structural deviations from ideal hydrogen-bonding arrangements or disrupted π-stacking of the extended nucleobase scaffolds.

Total syntheses of the bilirubin oxidation end product Z-BOX C and its isomeric form Z-BOX D

Oxidative degradation products of bilirubin (BOXes) are biologically highly active and certain BOXes cause long-lasting narrowing of cerebral blood vessels presumably with a significant role in subarachnoid hemorrhage. Due to the fact that mode of action as well as fate of these BOXes is widely unknown, larger amounts of these bilirubin degradation end products are required. The total synthesis of colorless (Z)-3-(5-(2-amino-2-oxoethylidene)-4-methyl-2-oxo-2,5-dihydro-1H-pyrrol-3-yl)propanoic acid (BOX C) succeeds via a seven-step procedure with a total yield of 20%. Its isomeric form (Z)-3-(2-(2-amino-2-oxoethylidene)-4-methyl-5-oxo-2,5-dihydro-1H-pyrrol-3-yl)propanoic acid (BOX D) can be prepared via a five-step protocol with a yield of 30%. NMR and crystallographic studies reveal that charge delocalization within the conjugated π-systems of BOXes C and D is negligible. Exposure of solutions of Z-BOX C and Z-BOX D to bright sunlight leads to Z/E-isomerization and mixtures of the respective E/Z-BOXes C and D.

FeCl3-Mediated Side Chain Modification of Aspartic Acid- and Glutamic Acid-Containing Peptides on a Solid Support

An efficient, convenient, and selective Lewis acid-based strategy for on-resin deprotection of the side chain tert-butyl-protected aspartic acid and glutamic acid of a peptide is achieved. The method is mild, cost-effective, and Fmoc chemistry compatible and allows on-resin incorporation of amides, esters, and thioesters in good yield. This method will find wide applicability in peptide and protein modification because it enriches the toolbox of orthogonal protection/deprotection techniques.

Total Synthesis of the Post-translationally Modified Polyazole Peptide Antibiotic Goadsporin

The structurally unique polyazole antibiotic goadsporin contains six heteroaromatic oxazole and thiazole rings integrated into a linear array of amino acids that also contains two dehydroalanine residues. An efficient total synthesis of goadsporin is reported in which the key steps are the use of rhodium(II)-catalyzed reactions of diazocarbonyl compounds to generate the four oxazole rings, which demonstrates the power of rhodium carbene chemistry in organic chemical synthesis.

Synthesis of highly porous poly(tert-butyl acrylate)-b-polysulfone-b-poly(tert-butyl acrylate) asymmetric membranes

For the first time, self-assembly and non-solvent induced phase separation was applied to polysulfone-based linear block copolymers, reaching mechanical stability much higher than other block copolymer membranes used in this method, which were mainly based on polystyrene blocks.

Towards new strategies for the synthesis of functional vinylidene fluoride-based copolymers with tunable wettability

–COOH functionalized poly(vinylidene fluoride) prepared using water-based non-fluorinated solvents displays tunable wettability suitable for potential application in coating, oil recovery and water purification.

A protic ionic liquid catalyzed strategy for selective hydrolytic cleavage of tert-butyloxycarbonyl amine (N-Boc)

An efficient strategy for selective hydrolytic cleavage of N-tert-butyloxycarbonyl (Boc) group is devised using protic ionic liquid as catalyst. The cleavage reaction proceeded well in the presence of many other labile protecting groups.

Synthesis of a bifunctional cytidine derivative and its conjugation to RNA for in vitro selection of a cytidine deaminase ribozyme

Over the past 20 years, the generation of functional RNAs by in vitro selection has become a standard technique. Apart from aptamers for simple binding of defined ligands, also RNAs for catalysis of chemical reactions have been selected. In the latter case, a key step often is the conjugation of one of the two reactants to the library, requiring suitable strategies for terminal or internal RNA functionalization. With the aim of selecting a ribozyme for deamination of cytidine, we have set up a selection scheme involving the attachment of the cytidine acting as deamination substrate to the 3'-terminus of the RNAs in the library, and library immobilization. Here, we report the synthesis of a bifunctional cytidine derivative suitable for conjugation to RNA and linkage of the conjugated library to a streptavidine-coated surface. Successful conjugation of the cytidine derivative to the 3'-terminus of a model RNA is demonstrated.

Total synthesis of Septocylindrin B and C-terminus modified analogues

The total synthesis is reported of the peptaibol Septocylindrin B which is related to the well documented channel forming peptaibol antibiotic Alamethicin. Several analogues were synthesized with a modified C-terminus, to investigate the SAR of the terminal residue Phaol. All these peptides were tested for their membrane perturbation properties by fluorescent dye leakage assay and for their antibacterial activity.

Combining the benefits of homogeneous and heterogeneous catalysis with tunable solvents and nearcritical water

The greatest advantage of heterogeneous catalysis is the ease of separation, while the disadvantages are often limited activity and selectivity. We report solvents that use tunable phase behavior to achieve homogeneous catalysis with ease of separation. Tunable solvents are homogeneous mixtures of water or polyethylene glycol with organics such as acetonitrile, dioxane, and THF that can be used for homogeneously catalyzed reactions. Modest pressures of a soluble gas, generally CO₂, achieve facile post-reaction heterogeneous separation of products from the catalyst. Examples shown here are rhodium-catalyzed hydroformylation of 1-octene and p-methylstyrene and palladium catalyzed C-O coupling to produce o-tolyl-3,5-xylyl ether and 3,5-di-tert-butylphenol. Both were successfully carried out in homogeneous tunable solvents followed by separation efficiencies of up to 99% with CO₂ pressures of 3 MPa. Further examples in tunable solvents are enzyme catalyzed reactions such as kinetic resolution of rac-1-phenylethyl acetate and hydrolysis of 2-phenylethyl acetate (2PEA) to 2-phenylethanol (2PE). Another tunable solvent is nearcritical water (NCW), whose unique properties offer advantages for developing sustainable alternatives to traditional processes. Some examples discussed are Friedel-Crafts alkylation and acylation, hydrolysis of benzoate esters, and water-catalyzed deprotection of N-Boc-protected amine compounds.

The 9-phenyl-9-fluorenyl group for nitrogen protection in enantiospecific synthesis

One of the biggest challenges in asymmetric synthesis is to prevent racemization of enantiopure starting materials. However, at least some of the enantiopurity is lost in most of the existing reactions used in synthetic organic chemistry. This translates into unnecessary material losses. Naturally enantiopure proteinogenic amino acids that can be transformed into many useful intermediates in drug syntheses, for example, are especially vulnerable to this. The phenylfluoren-9-yl (Pf) group, a relatively rarely used protecting group, has proven to be able to prevent racemization in α-amino compounds. This review article showcases the use of Pf-protected amino acid derivatives in enantiospecific synthesis.

Mild and efficient Lewis acid-promoted detritylation in the synthesis of N-hydroxy amides: a concise synthesis of (-)-Cobactin T

An efficient, high-yielding Lewis acid promoted deprotection of O-trityl hydroxylamine derivatives is described. A range of acid-labile protecting groups, such as N-Boc and O-TBS, were tolerated under these mild conditions. The present method is applicable to the synthesis of a broad range of hydroxylamine derivatives, including N-hydroxy amides (hydroxamic acids), N-hydroxy sulfonamides, and N-hydroxy ureas, which often exhibit significant biological activities. An application of this methodology for a concise synthesis of (-)-Cobactin T (18) is also demonstrated.

Enantioselective Synthesis of (−)-cis-Clavicipitic Acid

An enantioselective synthetic method for (-)-cis-clavicipitic acid (1) was reported. 1 was obtained in 10 steps (99% ee and 20% overall yield) from 1H-indole-3-carboxylic acid methyl ester (9) via asymmetric phase-transfer catalytic alkylation and diastereoselective Pd(II)-catalyzed intramolecular aminocyclization as key steps.

Aqueous Phosphoric Acid as a Mild Reagent for Deprotection of tert-Butyl Carbamates, Esters, and Ethers

Aqueous phosphoric acid (85 wt %) is an effective, environmentally benign reagent for the deprotection of tert-butyl carbamates, tert-butyl esters, and tert-butyl ethers. The reaction conditions are mild and offer good selectivity in the presence of other acid-sensitive groups, including CBZ carbamates, azetidine, benzyl and methyl esters, TBDMS, and methyl phenyl ethers. The mildness of the reaction is further demonstrated in the synthesis of clarithromycin derivative, in which a tert-butyl ester is removed in the presence of cyclic carbamate, lactone, ketal, acetate ester, and epimerizable methyl ketone functionalities. The reaction preserves the stereochemical integrity of the substrates. The reactions are high yielding, and the workup is convenient.