The application of perfluoroheteroaromatic reagents in the preparation of modified peptide systems

Halogenated Phenylpyridines Possessing Chemo-Selectivity for Diverse Molecular Architectures

Pentafluoropyridine was used as a molecular building block for the installation of aryl bromides, affording a series of multisubstituted halogenated arenes. This operationally simplistic methodology offers precise regioselectivity, ease of scalability, and high purity. 19F Nuclear magnetic resonance (NMR) served as a key diagnostic tool for structural characterization, given the sensitivity with various aryl bromine substitutions on the fluorinated pyridine ring. Furthermore, molecular modeling simulations offered insight into this new class of halogenated phenylpyridines and their unique electronic and reactive properties. This study also demonstrates examples of efficient chemo-selectivity upon either metal-catalyzed aryl-aryl coupling or nucleophilic aromatic substitution of the aryl bromide or fluorinated pyridine scaffold, respectively. A diverse pool of polyarylene structures with high degree of complexity, functionalized linear polymers, and controlled network architectures were achieved from this simple methodology.

Site-Selective Polyfluoroaryl Modification and Unsymmetric Stapling of Unprotected Peptides

Peptide stapling is recognized as an effective strategy for improving the proteolytic stability and cell permeability of peptides. In this study, we present a novel approach for the site-selective unsymmetric perfluoroaryl stapling of Ser and Cys residues in unprotected peptides. The stapling reaction proceeds smoothly under very mild conditions, exhibiting a remarkably rapid reaction rate. It can furnish stapled products in both liquid and solid phases, and the presence of nucleophilic groups other than Cys thiol within the peptide does not impede the reaction, resulting in uniformly high yields. Importantly, the chemoselective activation of Ser β-C(sp3)-H enables the unreacted -OH to serve as a reactive handle for subsequent divergent modification of the staple moiety with various therapeutic functionalities, including a clickable azido group, a polar moiety, a lipid tag, and a fluorescent dye. In our study, we have also developed a visible-light-induced chemoselective C(sp3)-H polyfluoroarylation of the Ser β-position. This reaction avoids interference with the competitive reaction of Ser -OH, enabling the precise late-stage polyfluoroarylative modification of Ser residues in various unprotected peptides containing other highly reactive amino acid residues. The biological assay suggested that our peptide stapling strategy would potentially enhance the proteolytic stability and cellular permeability of peptides.

Stereoretentive Post-Translational Protein Editing

Chemical post-translational methods allow convergent side-chain editing of proteins without needing to resort to genetic intervention. Current approaches that allow the creation of constitutionally native side chains via C-C bond formation, using off-protein carbon-centered C· radicals added to unnatural amino acid radical acceptor (SOMOphile, singly occupied molecular orbital (SOMO)) "tags" such as dehydroalanine, are benign and wide-ranging. However, they also typically create epimeric mixtures of d/l-residues. Here, we describe a light-mediated desulfurative method that, through the creation and reaction of stereoretained on-proteinl-alanyl C_β· radicals, allows C_β-H_γ, C_β-O_γ, C_β-Se_γ, C_β-B_γ, and C_β-C_γ bond formation to flexibly generate site-selectively edited proteins with full retention of native stereochemistry under mild conditions from a natural amino acid precursor. This methodology shows great potential to explore protein side-chain diversity and function and in the construction of useful bioconjugates.

One-pot ester and thioester formation mediated by pentafluoropyridine (PFP)

Acyl fluorides are valuable synthetic intermediates, but in some cases they can be challenging to handle and difficult to isolate given their susceptibility to degradation. In addition, many reagents utilised to prepare acyl fluorides are incompatible with in situ generation strategies and require the acyl fluoride to be isolated before any further reaction can take place. The combination of these factors has meant that acyl fluorides are currently under investigated in nucleophilic substitution processes, and often only a limited substrate scope is tolerated where they have been used. Herein, we report that pentafluoropyridine can be utilised to generate acyl fluorides in situ under mild conditions, and that they can subsequently be used to generate a range of esters and thioesters. This methodology offers a simple one-pot synthesis of esters and thioesters directly from parent carboxylic acids.

Perfluoropyridine: Discovery, Chemistry, and Applications in Polymers and Material Science

Perfluoropyridine (PFPy) is an organofluorine compound that has been employed for a variety of applications, from straightforward chemical synthesis to more advanced functions, such as fluorinated networks and polymers. This can be directly attributed to the highly reactive nature of PFPy, especially towards nucleophilic aromatic substitution (SNAr). The aim of this review is to highlight the discovery and synthesis of PFPy, discuss its reactive nature towards SNAr, and to summarize known reports of the utilization and thermal analysis of PFPy containing fluoropolymers and fluorinated network materials.

Small, but powerful and attractive: 19F in biomolecular NMR

Nuclear magnetic resonance (NMR) spectroscopy is a versatile tool for probing structure, dynamics, folding, and interactions at atomic resolution. While naturally occurring magnetically active isotopes, such as ¹H, ¹³C, or ¹⁵N, are most commonly used in biomolecular NMR, with ¹⁵N and ¹³C isotopic labeling routinely employed at the present time, ¹⁹F is a very attractive and sensitive alternative nucleus, which offers rich information on biomolecules in solution and in the solid state. This perspective summarizes the unique benefits of solution and solid-state ¹⁹F NMR spectroscopy for the study of biological systems. Particular focus is on the most recent studies and on future unique and important potential applications of fluorine NMR methodology.

Theoretical Prediction and Explanation of Reaction Site Selectivity in the Addition of a Phenoxy Group to Perfluoropyrimidine, Perfluoropyridazine, and Perfluoropyrazine

Perfluoroaromatics, such as perfluoropyridine and perfluorobenzene, are privileged synthetic scaffolds in organofluorine methodology, undergoing a series of regioselective substitution reactions with a variety of nucleophiles. This unique chemical behavior allows for the synthesis of many perfluoroaromatic derived molecules with unique and diverse architectures. Recently, it has been demonstrated that perfluoropyridine and perfluorobenzene can be utilized as precursors for a variety of materials, ranging from high performance polyaryl ethers to promising drug scaffolds. In this work, using density functional theory, we investigate the possibility of perfluoropyrimidine, perfluoropyridazine, and perfluoropyrazine participating in similar substitution reactions. We have found that the first nucleophilic addition of a phenoxide group substitution on perfluoropyrimidine and on perfluoropyridazine would happen at a site para to one of the nitrogen atoms. While previous literature points to mesomeric effects as the primary cause of this phenomenon, our work demonstrates that this effect is enhanced by the fact that the transition states for these reactions result in bond angles that allow the phenoxide to π-complex with the electron-deficient diazine ring. The second substitution on perfluoropyrimidine and on perfluoropyridazine is most likely to happen at the site para to the other nitrogen. The second substitution on perfluoropyrazine is most likely to happen at the site para to the first substitution. The activation energies for these reactions are in line with those reported for perfluoropyridine and suggest that these platforms may also be worth investigation in the lab as possible monomers for high performance polymers.

Fluoromaticity: The Molecular Orbital Contributions of Fluorine Substituents to the π-Systems of Aromatic Rings

The addition of fluorine atoms to an aromatic ring brings about an additional set of π-bonding and antibonding orbitals culminating after the addition of the sixth fluorine with a new set of π-aromatic-like orbitals that affect the molecule in a way that we will refer to hereafter as "fluoromaticity". Depending on the number and position of the fluorine atoms, the contributed π-orbitals can even further stabilize the ring leading to smaller bond lengths within the ring and higher resistance to addition reactions. This added ring stability partially explains the high thermostability and chemical resistance found in polymers containing fluorinated aromatics in their architecture. A similar molecular orbital effect is seen with the addition of other halogen atoms to aromatic rings, though to a much smaller degree and not resulting in the additional ring stability.

Perfluoroaryl and Perfluoroheteroaryl Reagents as Emerging New Tools for Peptide Synthesis, Modification and Bioconjugation

Peptides and proteins are becoming increasingly valuable as medicines, diagnostic agents and as tools for biomedical sciences. Much of this has been underpinned by the emergence of new methods for the manipulation and augmentation of native biomolecules. Perfluoroaromatic reagents are perhaps one of the most diverse and exciting tools with which to modify peptides and proteins, due principally to their nucleophilic substitution chemistry, high electron deficiency and the ability for their reactivity to be tuned towards specific nucleophiles. As discussed in this minireview, in recent years, perfluoroaromatic reagents have found applications as protecting groups or activating groups in peptide synthesis and as orthogonal handles for peptide modification. Furthermore, they have applications in chemoselective ‘tagging’, stapling and bioconjugation of peptides and proteins, as well as tuning of ‘drug‐like’ properties. This review will also explore possible future applications of these reagents in biological chemistry.

Carboxylic Acid Deoxyfluorination and One-Pot Amide Bond Formation Using Pentafluoropyridine (PFP)

This work describes the application of pentafluoropyridine (PFP), a cheap commercially available reagent, in the deoxyfluorination of carboxylic acids to acyl fluorides. The acyl fluorides can be formed from a range of acids under mild conditions. We also demonstrate that PFP can be utilized in a one-pot amide bond formation via in situ generation of acyl fluorides. This one-pot deoxyfluorination amide bond-forming reaction gives ready access to amides in yields of ≤94%.

Site-Selective Acylations of α- and β-Hydroxyamides in Complex Molecules: Application of Template-Driven Acylation to Disaccharides and a Glycopeptide

Site-selective acylations of α-and β-hydroxyamides in complex polyols are described. The combination of a pyridine aldoxime ester and Zn(OTf)₂ facilitates the acylation of two types of N-glycolyl disaccharides, namely, Gal-GlcNGc and Neu5Gc-Gal, both of which are partial structures of polysaccharides responsible for biological actions, with highly site-selective modifications achieved. Furthermore, biotinylation, one of the most important techniques in chemical biology, is used to site-selectively acylate the β-hydroxyl group in a glycopeptide.

19F NMR as a tool in chemical biology

We previously reviewed the use of 19F NMR in the broad field of chemical biology [Cobb, S. L.; Murphy, C. D. J. Fluorine Chem. 2009, 130, 132-140] and present here a summary of the literature from the last decade that has the technique as the central method of analysis. The topics covered include the synthesis of new fluorinated probes and their incorporation into macromolecules, the application of 19F NMR to monitor protein-protein interactions, protein-ligand interactions, physiologically relevant ions and in the structural analysis of proteins and nucleic acids. The continued relevance of the technique to investigate biosynthesis and biodegradation of fluorinated organic compounds is also described.

Synthesis of complex unnatural fluorine-containing amino acids

The area of fluorinated amino acid synthesis has seen rapid growth over the past decade. As reports of singly fluorinated natural amino acid derivatives have grown, researchers have turned their attention to develop methodology to access complex proteinogenic examples. A variety of reaction conditions have been employed in this area, exploiting new advances in the wider synthetic community such as photocatalysis and palladium cross-coupling. In addition, novel fluorinated functional groups have also been incorporated into amino acids, with SFX and perfluoro moieties now appearing with more frequency in the literature. This review focuses on synthetic methodology for accessing complex non-proteinogenic amino acids, along with amino acids containing multiple fluorine atoms such as CF3, SF5 and perfluoroaromatic groups.

Syntheses of Atypically Fluorinated Peptidyl Macrocycles through Sequential Vinylic Substitutions

Small peptides containing combinations of cysteine, tyrosine, histidine, and serine residues react with octafluorocyclopentene (OFCP) to afford atypically structured macrocycles through successive vinylic substitutions. The reactions proceed rapidly in air at 0 °C and are tolerant of spectating tryptophan, asparagine, glutamine, and threonine residues. Hexapeptides of consensus sequence YXCXXC displace four fluorine atoms from OFCP to generate fluorinated macrobicyclic compounds that display dual-turn surfaces. The method provides facile access to a wide range of previously unknown heterocyclic structures.

New Molecular Insights into the Inhibition of Dipeptidyl Peptidase-4 by Natural Cyclic Peptide Oxytocin

Protease inhibition has led to treating many diseases and has been successful in producing many commercial drugs by pharmaceutical companies. Among many proteases, serine protease has been attractive in treating metabolic disorder diabetes mellitus (DM). Gliptins have been proven to inhibit dipeptidyl peptidase-4 (DPP4), a serine protease, and are an emerging therapeutic drug target to reduce blood glucose levels, but until now there is no natural cyclic peptide proven to inhibit serine protease DPP4. This study demonstrates the potential mechanism of natural cyclic peptide oxytocin (OXT) as a DPP4 inhibitor. To achieve this, initially, activity atlas and field-based models of DPP4 inhibitors were utilized to predict the possible features of positive and negative electrostatic, hydrophobic, and activity shapes of DPP4 inhibition. Oxytocin binding mode, flexibility, and interacting residues were studied using molecular docking simulations studies. 3D-RISM calculations studies revealed that the stability of water molecules at the binding site are favorable. Finally, an experimental study using fluorescence assay revealed OXT inhibits DPP4 in a concentration-dependent manner in a significant way (p < 0.05) and possess IC50 of 110.7 nM. These new findings significantly expand the pharmaceutical application of cyclic peptides, and in specific OXT, and implicate further optimization of OXT inhibition capacity to understand the effect of DPP4 inhibition. This work highlights the development of natural cyclic peptides as future therapeutic peptides to reduce glucose levels and treat diabetes mellitus.

Theoretical Explanation of Reaction Site Selectivity in the Addition of a Phenoxy Group to Perfluoropyridine

Pentafluoropyridine, a potentially useful precursor in organofluorine methodology, undergoes selective substitution of a fluorine with a phenoxide at the site para to the nitrogen. Subsequent aryloxide substitutions can be accomplished at the ortho-positions with aryloxide groups containing various functional groups para to the phenoxide oxygen. During this phase of the reaction, "reverse reactions" involving substitutions of the original para substituent with a free fluoride or with another aryloxide moiety are observed with a frequency that depends on the functional group para to the oxygen on the aryloxide. Herein, we provide a theoretical explanation of these observations through use of density functional theory.

Site-Selective Esterifications of Polyol β-Hydroxyamides and Applications to Serine-Selective Glycopeptide Modifications

The site-selective acylations of β-hydroxyamides in the presence of other hydroxyl groups are described. Central to the success of this modification is the metal-template-driven acylation using pyridine ketoxime esters as acylating reagents in combination with CuOTf. This strategy enables β-hydroxyl groups to be site-selectively acylated in various derivatives, including sterically hindered secondary β-alcohol. The utility of this methodology is showcased by the serine-selective modification of a glycopeptide with unprotected sugar.

Crystal structures and Hirshfeld surface analysis of a series of 4-O-aryl-perfluoro-pyridines

In each crystal of the title compounds the packing is driven by C—H⋯F inter­tactions, along with a variety of C—F⋯π, C—H⋯π, C—Br⋯N, C—H⋯N, and C—Br⋯π contacts. Hirshfeld surface analysis was conducted to aid in the visualization of these various influences on the packing.

Five new crystal structures of perfluoro­pyridine substituted in the 4-position with phen­oxy, 4-bromo­phen­oxy, naphthalen-2-yl­oxy, 6-bromo­naphthalen-2-yl­oxy, and 4,4′-biphen­oxy are reported, viz. 2,3,5,6-tetra­fluoro-4-phen­oxy­pyridine, C₁₁H₅F₄NO (I), 4-(4-bromo­phen­oxy)-2,3,5,6-tetra­fluoro­pyridine, C₁₁H₄BrF₄NO (II), 2,3,5,6-tetra­fluoro-4-[(naphthalen-2-yl)­oxy]pyridine, C₁₅H₇F₄NO (III), 4-[(6-bromo­naphthalen-2-yl)­oxy]-2,3,5,6-tetra­fluoropyridine, C₁₅H₆BrF₄NO (IV), and 2,2′-bis­[(perfluoro­pyridin-4-yl)­oxy]-1,1′-biphenyl, C₂₂H₈F₈N₂O₂ (V). The dihedral angles between the aromatic ring systems in I–IV are 78.74 (8), 56.35 (8), 74.30 (7), and 64.34 (19)°, respectively. The complete mol­ecule of V is generated by a crystallographic twofold axis: the dihedral angle between the pyridine ring and adjacent phenyl ring is 80.89 (5)° and the equivalent angle between the biphenyl rings is 27.30 (5)°. In each crystal, the packing is driven by C—H⋯F inter­actions, along with a variety of C—F⋯π, C—H⋯π, C—Br⋯N, C—H⋯N, and C—Br⋯π contacts. Hirshfeld surface analysis was conducted to aid in the visualization of these various influences on the packing.

Arylation Chemistry for Bioconjugation

Bioconjugation chemistry has been used to prepare modified biomolecules with functions beyond what nature intended. Central to these techniques is the development of highly efficient and selective bioconjugation reactions that operate under mild, biomolecule compatible conditions. Methods that form a nucleophile-sp2 carbon bond show promise for creating bioconjugates with new modifications, sometimes resulting in molecules with unparalleled functions. Here we outline and review sulfur, nitrogen, selenium, oxygen, and carbon arylative bioconjugation strategies and their applications to modify peptides, proteins, sugars, and nucleic acids.

Toolbox of Diverse Linkers for Navigating the Cellular Efficacy Landscape of Stapled Peptides

Stapled peptides have great potential as modulators of protein-protein interactions (PPIs). However, there is a vast landscape of chemical features that can be varied for any given peptide, and identifying a set of features that maximizes cellular uptake and subsequent target engagement remains a key challenge. Herein, we present a systematic analysis of staple functionality on the peptide bioactivity landscape in cellular assays. Through application of a "toolbox" of diversified dialkynyl linkers to the stapling of MDM2-binding peptides via a double-click approach, we conducted a study of cellular uptake and p53 activation as a function of the linker. Minor changes in the linker motif and the specific pairing of linker with peptide sequence can lead to substantial differences in bioactivity, a finding which may have important design implications for peptide-based inhibitors of other PPIs. Given the complexity of the structure-activity relationships involved, the toolbox approach represents a generalizable strategy for optimization when progressing from in vitro binding assays to cellular efficacy studies.

Tetrafluoropyridyl (TFP): a general phenol protecting group readily cleaved under mild conditions

Herein we introduce tetrafluoropyridyl (TFP) as a new general protecting group for phenols. The TFP protecting group is readily cleaved under mild conditions.

Phenols are extremely valuable building blocks in the areas of pharmaceuticals, natural products, materials and catalysts. In order to carry out modifications on phenols, the phenolic oxygen is routinely protected to prevent unwanted side reactions. Presently many of the protecting groups available can require harsh conditions, specialist equipment, expensive or air/moisture-sensitive reagents to install and remove. Here we introduce the use of the tetrafluoropyridyl (TFP) group as a general protecting group for phenols. TFP can be installed in one step with no sensitivity to water or air, and it is stable under a range of commonly employed reaction conditions including acid and base. The TFP protecting group is readily cleaved under mild conditions with quantitative conversion to the parent phenol, observed in many cases in less than 1 hour.

2,2,2-Trifluoroethanol as a solvent to control nucleophilic peptide arylation

Trifluoroethanol enables selective perfluoro-heteroaromatic peptide arylation of cysteine residues.